Version: 1.1.1
A B C D E F G H I J K L M N O P Q R S T U V W X Z

A

AbstractAnnotationListPane<T extends Annotation,K extends AbstractAnnotationListPane.AnnotationListListener> - Class in org.inb.biomoby.client.gui.auxiliary
 
AbstractAnnotationListPane(boolean) - Constructor for class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
AbstractAnnotationListPane(List<T>, boolean) - Constructor for class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
AbstractAnnotationListPane.AnnotationListListener - Interface in org.inb.biomoby.client.gui.auxiliary
 
AbstractAsyncMobyImpl - Class in org.inb.biomoby.service
 
AbstractAsyncMobyImpl() - Constructor for class org.inb.biomoby.service.AbstractAsyncMobyImpl
 
AbstractAsyncMobyService - Class in org.inb.biomoby.service
 
AbstractAsyncMobyService() - Constructor for class org.inb.biomoby.service.AbstractAsyncMobyService
 
AbstractCellRenderer - Class in org.inb.biomoby.central.gui.renderer
A simple JLable based abstract renderer.
AbstractCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.AbstractCellRenderer
 
AbstractDescriptionMobyComponent - Class in org.inb.biomoby.client.gui.auxiliary
 
AbstractDescriptionMobyComponent() - Constructor for class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
AbstractEntity<T extends AbstractEntity> - Class in org.inb.biomoby.shared.registry
An abstract class that represents any Moby Central entity that could be named
AbstractEntity() - Constructor for class org.inb.biomoby.shared.registry.AbstractEntity
 
AbstractEntity(String) - Constructor for class org.inb.biomoby.shared.registry.AbstractEntity
 
AbstractEntity(String, String) - Constructor for class org.inb.biomoby.shared.registry.AbstractEntity
 
AbstractEntityTreeNode - Class in org.inb.biomoby.central.gui.model
 
AbstractEntityTreeNode(AbstractEntity) - Constructor for class org.inb.biomoby.central.gui.model.AbstractEntityTreeNode
 
AbstractEntityTreePanel - Class in org.inb.biomoby.central.gui
Compound abstract layered tree component.
AbstractEntityTreePanel() - Constructor for class org.inb.biomoby.central.gui.AbstractEntityTreePanel
 
AbstractMobyComponent<T extends AbstractMobyObject> - Class in org.inb.biomoby.client.gui
An abstract visualization component that all components must extend.
AbstractMobyComponent() - Constructor for class org.inb.biomoby.client.gui.AbstractMobyComponent
 
AbstractMobyComponent(T) - Constructor for class org.inb.biomoby.client.gui.AbstractMobyComponent
 
AbstractMobyDatatypesTreePanel - Class in org.inb.biomoby.central.gui
Abstract implementation of BioMoby datatypes tree component
AbstractMobyDatatypesTreePanel() - Constructor for class org.inb.biomoby.central.gui.AbstractMobyDatatypesTreePanel
 
AbstractMobyElement - Class in org.inb.biomoby.shared.message
 
AbstractMobyHandler<T extends Comparable<T> & LSIDAccessible> - Class in org.biomoby.registry.sync.handler
Basic abstract implementation of the MobyHandler interface.
AbstractMobyHandler(String) - Constructor for class org.biomoby.registry.sync.handler.AbstractMobyHandler
 
AbstractMobyObject - Class in org.inb.biomoby.shared.message
 
AbstractMobyObject() - Constructor for class org.inb.biomoby.shared.message.AbstractMobyObject
 
AbstractMobyObject(String, String) - Constructor for class org.inb.biomoby.shared.message.AbstractMobyObject
 
AbstractMobyObjectPropertyTable - Class in org.inb.biomoby.central.gui
Abstract BioMoby properties table implementation based on a model with concrete BioMoby ObjectType.
AbstractMobyObjectPropertyTable() - Constructor for class org.inb.biomoby.central.gui.AbstractMobyObjectPropertyTable
 
AbstractMobyObjectPropertyTable.DefaultPropertyNameValidator - Class in org.inb.biomoby.central.gui
 
AbstractMobyObjectPropertyTable.DefaultPropertyNameValidator(PropertyNameTableCellEditor) - Constructor for class org.inb.biomoby.central.gui.AbstractMobyObjectPropertyTable.DefaultPropertyNameValidator
 
AbstractMobyPropertyTable - Class in org.inb.biomoby.central.gui
Abstract BioMoby properties table implementation.
AbstractMobyPropertyTable() - Constructor for class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
AbstractMobyRenderer - Class in org.biomoby.service.dashboard.renderers
A class containing common utilities for renderers that process Biomoby data types.
AbstractMobyRenderer(String) - Constructor for class org.biomoby.service.dashboard.renderers.AbstractMobyRenderer
 
AbstractMobyRenderer(String, String) - Constructor for class org.biomoby.service.dashboard.renderers.AbstractMobyRenderer
 
AbstractMobyServicesTreePanel - Class in org.inb.biomoby.central.gui
Abstract implementation of BioMoby services tree component
AbstractMobyServicesTreePanel() - Constructor for class org.inb.biomoby.central.gui.AbstractMobyServicesTreePanel
 
AbstractMobySynchronize - Class in org.biomoby.registry.sync
Basic abstract class for the synchronization of a local moby central with a master moby central.
AbstractMobySynchronize() - Constructor for class org.biomoby.registry.sync.AbstractMobySynchronize
 
AbstractModel - Class in org.biomoby.service.dashboard
A common super-class for all Dashboard models.
AbstractModel<T> - Class in org.inb.biomoby.central.model
An abstract class for all BioMoby Registry models.
AbstractModel() - Constructor for class org.inb.biomoby.central.model.AbstractModel
 
AbstractMultilineDescriptionMobyComponent - Class in org.inb.biomoby.client.gui.auxiliary
 
AbstractMultilineDescriptionMobyComponent() - Constructor for class org.inb.biomoby.client.gui.auxiliary.AbstractMultilineDescriptionMobyComponent
 
AbstractPanel - Class in org.biomoby.service.dashboard
Parent of all panels of a Dashboard.
AbstractPopupMobyComponent - Class in org.inb.biomoby.client.gui.auxiliary
 
AbstractPopupMobyComponent() - Constructor for class org.inb.biomoby.client.gui.auxiliary.AbstractPopupMobyComponent
 
AbstractRenderer - Class in org.biomoby.service.dashboard.renderers
Abstract rendering class.
AbstractRenderer(String) - Constructor for class org.biomoby.service.dashboard.renderers.AbstractRenderer
 
AbstractRenderer(String, Icon) - Constructor for class org.biomoby.service.dashboard.renderers.AbstractRenderer
 
AbstractRenderer(String, String) - Constructor for class org.biomoby.service.dashboard.renderers.AbstractRenderer
 
AbstractServiceModelPanel - Class in org.inb.biomoby.generator.gui
 
AbstractServiceModelPanel() - Constructor for class org.inb.biomoby.generator.gui.AbstractServiceModelPanel
 
AbstractTableCellRenderer - Class in org.inb.biomoby.central.gui.renderer
A simple abstract TableCellRenderer based on JLabel
AbstractTableCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.AbstractTableCellRenderer
 
AbstractTransformableMobyPanel<T extends IDynamicComponent.MobyComponentListener> - Class in org.inb.biomoby.client.gui.auxiliary
 
AbstractTransformableMobyPanel() - Constructor for class org.inb.biomoby.client.gui.auxiliary.AbstractTransformableMobyPanel
 
AbstractTreeCellRenderer - Class in org.inb.biomoby.central.gui.renderer
A simple abstract TreeCellRenderer based on JLabel
AbstractTreeCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.AbstractTreeCellRenderer
 
AbstractTreeTableModel - Class in org.biomoby.service.dashboard.treetable
An abstract implementation of the TreeTableModel interface, handling the list of listeners.
AbstractTreeTableModel(Object) - Constructor for class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
AbstractTypeEntity<T extends AbstractTypeEntity> - Class in org.inb.biomoby.shared.registry
Represents Moby Central entity type (either ObjectType or ServiceType)
AbstractTypeEntity() - Constructor for class org.inb.biomoby.shared.registry.AbstractTypeEntity
 
AbstractTypeEntity(String) - Constructor for class org.inb.biomoby.shared.registry.AbstractTypeEntity
 
AbstractTypeEntity(String, String) - Constructor for class org.inb.biomoby.shared.registry.AbstractTypeEntity
 
accept(File) - Method in class ca.ucalgary.seahawk.util.DescriptiveFileFilter
Returns true if f is a file with the correct extension, false otherwise.
ACCEPTABLE_IMAGE_DATATYPE - Static variable in class ca.ucalgary.seahawk.util.HTMLUtils
 
acceptAnExistingWrapper(URL, MobyContentPane, MobyServicesGUI) - Static method in class ca.ucalgary.seahawk.services.DaggooClient
 
acceptAnExistingWrapper(URL, MobyContentPane, MobyServicesGUI, boolean) - Static method in class ca.ucalgary.seahawk.services.DaggooClient
Presents the user with a dialog showing all Moby services (wrappers) that exist for the provided URL.
ACD_FILE_PARAM - Static variable in class ca.ucalgary.services.ACDService
 
ACDFile - Class in ca.ucalgary.services.util
A class representing the contents of an ACD file (EMBOSS program parameter specification).
ACDFile(File) - Constructor for class ca.ucalgary.services.util.ACDFile
Reads an EMBOSS ACD file and populates data structures representing the sections of the file (see the getXXXSection() methods).
ACDFile(URL) - Constructor for class ca.ucalgary.services.util.ACDFile
 
ACDFile(InputStream) - Constructor for class ca.ucalgary.services.util.ACDFile
 
ACDFileTestCase - Class in ca.ucalgary.services.util.test
 
ACDFileTestCase(String) - Constructor for class ca.ucalgary.services.util.test.ACDFileTestCase
 
ACDService - Class in ca.ucalgary.services
A servlet that will read in an EMBOSS ACD file (which describes the command-line usage of a program in the suite) and publishes it as a MOBY service.
ACDService() - Constructor for class ca.ucalgary.services.ACDService
 
ACDServiceTestCase - Class in ca.ucalgary.services.test
For the testMain cases to be actually successful, the WEB-INF/web.xml file must be one with all the ACD parameters...
ACDServiceTestCase(String) - Constructor for class ca.ucalgary.services.test.ACDServiceTestCase
 
aCOMPLETED_STEPS - Static variable in interface org.omg.lsae.sax.LsaeTags
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.DataImportChoiceDialog
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.FilterSearchWidget
Called when the user has changed the xpath
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Called when a tab option (close) is selected
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
actionPerformed(ActionEvent) - Method in class ca.ucalgary.seahawk.gui.WorkflowPreviewDialog
 
actionPerformed(ActionEvent) - Method in class org.inb.biomoby.central.gui.RegistryComboBox
 
actionPerformed(ActionEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
actionPerformed(ActionEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
actionPerformed(ActionEvent) - Method in class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
add(JMenuItem) - Method in class ca.ucalgary.seahawk.util.DynamicJPopupMenu
 
add(Node) - Method in class ca.ucalgary.seahawk.util.MutableNodeList
 
add(Node) - Method in class ca.ucalgary.services.WrappingServlet.MyNodeList
 
add(NodeList) - Method in class ca.ucalgary.services.WrappingServlet.MyNodeList
 
add(Number) - Method in class org.biomoby.shared.data.MobyDataFloat
Add a specified number to the data value.
add(Number) - Method in class org.biomoby.shared.data.MobyDataInt
Perform the addition operand on the data value.
add(MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Add a single MobyDataObject to the collection.
add(MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
add(MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Add an object to the list.
add(int, MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Inserts the specified element at the specified position in this list.
add(Node) - Method in class org.biomoby.shared.MobyPrefixResolver.MobyNodeList
 
add(MobySimple) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
add(int, MobySimple) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
add(MobyException) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
add(int, MobyException) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
add2Filter(String...) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds a list of service names to the filter.
add2Filter(Collection<String>) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds the services to the filter list.
addActionListener(ActionListener) - Method in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
Any object registering themselves here will receive a callback when the value of the data changes.
addActionListener(ActionListener) - Method in class org.biomoby.service.dashboard.JProgressBarWithCancel
 
addAll(NodeList) - Method in class ca.ucalgary.seahawk.util.MutableNodeList
 
addAll(Collection<? extends MobyDataObject>) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Convenient way to add the input collection of MobyDataObjects (usually a MobyDataObjectSet, or a Vector of MobyDataObjects) to this collection.
addAll(Collection<? extends MobyDataObject>) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
addAll(Collection<? extends MobyDataObject>) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator.
addAll(int, Collection<? extends MobyDataObject>) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Inserts all of the elements in the specified collection into this list at the specified position.
addAll(Collection<? extends MobySimple>) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
addAll(int, Collection<? extends MobySimple>) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
addAll(Collection<? extends MobyException>) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
addAll(int, Collection<? extends MobyException>) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
addAllelicvariants(Text__formatted) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
addAllowedValue(String) - Method in class org.biomoby.shared.MobySecondaryData
 
addAminoAcidSequence(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.WeightedAminoAcidSequences
 
addAnnotatedDomain(AnnotatedDomain) - Method in class org.inb.biomoby.shared.ontology.DomainAnnotatedSequence
 
addAnnotatedSequence(LutefiskAnnotatedAASequence) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.EquicktandemAnnotationListPane
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.FeatureAnnotationListPane
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.InterProMotifAnnotationListPane
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.LabeledAnnotationListPane
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.RestrictAnnotationListPane
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.ScoredMotifAnnotationListPane
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.SigcleaveAnnotationListPane
 
addAnnotation2Tooltip(StringBuilder, StructureFragment) - Method in class org.inb.biomoby.client.gui.auxiliary.StructureFragmentListPane
 
addAnnotation2Tooltip(StringBuilder, T) - Method in class org.inb.biomoby.client.gui.auxiliary.TransmembraneAnnotationListPane
 
addAnnotations(AntigenicAnnotation) - Method in class org.inb.biomoby.shared.ontology.AntigenicAnnotatedAASequence
 
addAnnotations(FamilyBLOCKAnnotation) - Method in class org.inb.biomoby.shared.ontology.BlocksAnnotatedAASequence
 
addAnnotations(CpGAnnotation) - Method in class org.inb.biomoby.shared.ontology.CpGAnnotatedNASequence
 
addAnnotations(EquicktandemAnnotation) - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotatedNASequence
 
addAnnotations(FeatureAnnotation) - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotatedAASequence
 
addAnnotations(InterProMotifAnnotation) - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotatedAASequence
 
addAnnotations(LutefiskAnnotation) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotatedAASequence
 
addAnnotations(MolWeightAnnotation) - Method in class org.inb.biomoby.shared.ontology.MolWeightsAnnotatedAASequence
 
addAnnotations(MotifAnnotation) - Method in class org.inb.biomoby.shared.ontology.MotifAnnotatedAASequence
 
addAnnotations(ProbMolWeightAnnotation) - Method in class org.inb.biomoby.shared.ontology.ProbMolWeightsAnnotatedAASequence
 
addAnnotations(RestrictAnnotation) - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotatedNASequence
 
addAnnotations(ScoredMotifAnnotation) - Method in class org.inb.biomoby.shared.ontology.ScoredMotifAnnotatedAASequence
 
addAnnotations(SigcleaveAnnotation) - Method in class org.inb.biomoby.shared.ontology.SigcleaveAnnotatedAASequence
 
addAnnotations(TransmembraneAnnotation) - Method in class org.inb.biomoby.shared.ontology.TransmembraneAnnotatedAASequence
 
addArgument(MobyString) - Method in class org.inb.biomoby.shared.ontology.ByoDynTarget
 
addArray(ArrayFloat) - Method in class org.inb.biomoby.shared.ontology.MatrixFloat
 
addArray(ArrayInteger) - Method in class org.inb.biomoby.shared.ontology.MatrixInteger
 
addArray(ArrayString) - Method in class org.inb.biomoby.shared.ontology.MatrixString
 
addArticleNameType(Element, String, Vector) - Method in class org.biomoby.shared.schema.Builder
Given a vector containing possible article names and type name, add an XML Schema element to describe the restriction.
addBasicAnnotation(BasicAnnotation) - Method in class org.inb.biomoby.shared.ontology.AnnotatedDomain
 
addBlocks(BLOCKAnnotation) - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
addBuildListener(BuildListener) - Method in class org.biomoby.service.dashboard.SimpleAnt
 
addChangeListener(ChangeListener) - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Adds a listener that is notified when a new date is selected.
addChild(MobyRelationship) - Method in class org.biomoby.shared.MobyDataType
 
addChild(String, String, int) - Method in class org.biomoby.shared.MobyDataType
Create a MobyRelationship object from given parameters and add it as a new child.
addClinicalSynopsis(Text__formatted) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
addClipboardItem(JMenu, MobyDataInstance) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addCollection(Collection) - Method in class org.inb.biomoby.shared.registry.Data
 
addCollectionData(MobyDataInstance) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
The main way to add data to the clipboard, data gets appended to the query with the name given in CLIPBOARD_COLLECTION_NAME
addCollectionData(MobyDataInstance, boolean) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
addCollectionData(MobyContentInstance) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
Objects in the content instance will be flattened into a list and appended to the current contents of the collection.
addCollectionData(URL) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
Attempts to add data from the given URL as MOBY objects (converting if necessary).
addColor(String, Color) - Static method in class org.biomoby.service.dashboard.GraphColours
Adds a color to the application color table.
addComment(String) - Method in class org.biomoby.registry.rdfagent.util.ServiceProvider
 
addConfigPropertyFile(String) - Static method in class org.biomoby.service.dashboard.DashboardConfig
Add new configuration properties from a property file.
addContent(Object) - Method in class org.inb.wsrf.rp2.QueryExpressionType
 
addContent(Object) - Method in class org.inb.wsrf.rp2.QueryResourcePropertiesResponse
 
addContributor(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
addCookie(Cookie) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
addCrossReference(MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataObject
 
addCrossReference(MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
addCrossReferences(Element) - Method in class org.biomoby.shared.data.MobyDataObject
 
addCrossReferences(Element, Registry) - Method in class org.biomoby.shared.data.MobyDataObject
 
addData(String, MobyDataInstance) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
Adds a query to the clipboard with the since MobyDataInstance attached to it.
addData(String, String) - Method in class org.biomoby.service.dashboard.DeploymentTable
Add data representing one row to this table.
addData(MobySimple) - Method in class org.biomoby.shared.parser.MobyCollection
Add one more element to this envelope.
addData(MobyObject) - Method in class org.biomoby.shared.parser.MobyJob
Create an un-named Simple object and add it as the last one in the current data elements.
addData(MobyObject, String) - Method in class org.biomoby.shared.parser.MobyJob
Create a named Simple object and add it as the last one in the current data elements.
addDataElement(MobyDataElement) - Method in class org.biomoby.shared.parser.MobyJob
Add 'dataElement' to this job.
addDataSet(MobyObject[]) - Method in class org.biomoby.shared.parser.MobyJob
Create an un-named Collection object and add it as the last one in the current data elements.
addDataSet(MobyObject[], String) - Method in class org.biomoby.shared.parser.MobyJob
Create a named Collection object and add it as the last one in the current data elements.
addDateHeader(String, long) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
addDescriptNote(String, Element) - Method in class org.biomoby.shared.schema.Builder
add description or comment element to the element parent.
addEditorhistory(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
addElement(MobyPrimaryDataSimple) - Method in class org.biomoby.shared.MobyPrimaryDataSet
 
addElement(T) - Method in class org.inb.biomoby.central.model.AbstractModel
Method to add a model element.
addElement(ObjectType) - Method in class org.inb.biomoby.central.model.DatatypesModel
Method to register a new datatype with a BioMoby Registry.
addElement(MobyCentral) - Method in class org.inb.biomoby.central.model.MobyCentralModel
Method is not implemented
addElement(Namespace) - Method in class org.inb.biomoby.central.model.NamespacesModel
Method not implemented and throws an exeption
addElement(Service) - Method in class org.inb.biomoby.central.model.ServicesModel
Method to register a service with a BioMoby Registry.
addElement(ElementFloat) - Method in class org.inb.biomoby.shared.ontology.ArrayFloat
 
addElement(ElementInteger) - Method in class org.inb.biomoby.shared.ontology.ArrayInteger
 
addElement(ElementString) - Method in class org.inb.biomoby.shared.ontology.ArrayString
 
addElements(ElementXYData) - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
addEmptyData() - Method in class org.biomoby.service.dashboard.CommonDataTable
 
addEntityType(T) - Method in class org.inb.biomoby.shared.registry.Relationship
 
addEnum(String) - Method in class org.inb.biomoby.shared.registry.Parameter
 
addEventHandler(MobyRequestEventHandler) - Method in class org.biomoby.client.MobyRequest
 
addException(ServiceException) - Method in class org.biomoby.shared.data.MobyContentInstance
Adds a new exception to the list of exceptions associated with the content
addException(ServiceException) - Method in class org.biomoby.shared.parser.MobyPackage
Add a new exception reported by this service execution.
addException(ServiceException, MobyJob) - Method in class org.biomoby.shared.parser.MobyPackage
Add a new exception reported by this service execution.
addException(MobyException) - Method in class org.inb.biomoby.shared.message.MobyContent
Method adds an exeption to the content It creates a serviceNotes if needed.
addException(MobyException) - Method in class org.inb.biomoby.shared.message.ServiceNotes
 
addFilterRule(FilterRuleKeys, String) - Method in class org.biomoby.registry.sync.filtering.ServiceFilter
Adds a new filtering rule.
addFormFile(String) - Method in class ca.ucalgary.services.util.XHTMLForm
 
addHasaMElement(MElement) - Method in class org.biomoby.shared.schema.MElement
 
addHasMElement(MElement) - Method in class org.biomoby.shared.schema.MElement
 
addHASXPtrs(List<String>, Element) - Static method in class ca.ucalgary.seahawk.util.DataUtils
If any moby object member is in a HAS relationship, add it to the list of filterable items
addHeader(String, String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
addHeader(String, String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
addIcon - Static variable in class org.biomoby.service.dashboard.data.DataTypeTreeTable
 
addIdentifiabilityCriteria(MobyString) - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
addInitParameter(String, String) - Method in class org.biomoby.service.test.TestServletConfig
 
addInput(MobyData) - Method in class org.biomoby.shared.MobyService
 
addIntHeader(String, int) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
addJarFile(byte[]) - Method in class org.inb.util.MemoryFileManager
 
addJob(MobyJob) - Method in class org.biomoby.shared.parser.MobyPackage
Add one job to the already stored here.
addJournal(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
addListener(ModelListener<T>) - Method in class org.inb.biomoby.central.model.AbstractModel
Method to add a listener to be notified about a model changes.
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.auxiliary.DynamicMobyPanel
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.DynamicMobyComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in interface org.inb.biomoby.client.gui.IDynamicComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.MobyMessageQueue
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
addListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
addMappingsFromURL(URL) - Method in class ca.ucalgary.seahawk.services.MobyClient
Parses the XML formatted rules from the input stream specified by the URL.
addMappingsFromURL(URL) - Method in class ca.ucalgary.seahawk.services.TextClient
 
addMember(String, int) - Method in class org.biomoby.service.dashboard.BuildDataTypeTree
 
addMember(MobyRelationship) - Method in class org.biomoby.service.dashboard.BuildDataTypeTree
 
addMobyData(MobyData) - Method in class org.inb.biomoby.shared.message.MobyContent
 
addMobyData(MobyData) - Method in class org.inb.biomoby.shared.message.MobyMessage
 
addMobyDataElement(MobyDataElement) - Method in class org.inb.biomoby.shared.message.MobyData
 
addMultipleCallInput(String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
 
addMultipleCallInput(FeatureClient.JobIdentifier, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
 
addMultipleCallInput(FeatureClient.JobIdentifier, String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
 
addMultipleCallInput(FeatureClient.JobIdentifier, String, String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
 
addMultipleCallInput(String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds a new simple input to the client.
addMultipleCallInput(String, String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds a new simple input to the client.
addMultipleCallInput(String, MobyObject...) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
 
addMultipleCallInput(FeatureClient.JobIdentifier, MobyObject...) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds one or more input(s) to the client which are used to call services once or more.
addNameDivSubMenu(JMenu, MobyService[]) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addNamespace(MobyNamespace) - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
addNamespace(MobyNamespace) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Add given namespace of all elements of this collection.
addNamespace(MobyNamespace) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
addNamespace(MobyNamespace) - Method in class org.biomoby.shared.data.MobyDataXref
Values passed here are essentially ignored when a namespace already exists, because an Xref can only have one.
addNamespace(MobyNamespace) - Method in class org.biomoby.shared.MobyPrimaryData
 
addNamespace(MobyNamespace) - Method in class org.biomoby.shared.MobyPrimaryDataSet
Add given namespace of all elements of this collection.
addNamespace(MobyNamespace) - Method in class org.biomoby.shared.MobyPrimaryDataSimple
Add one namespace to already existing ones (but only if a namespace of the same name does not exist yet).
addNamespace(Namespace) - Method in class org.inb.biomoby.shared.registry.Simple
 
addNamespaceContext(String, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addNotificationListener(NotificationListener) - Method in class org.biomoby.client.CentralDigestImpl
 
addNotificationListener(NotificationListener) - Method in class org.biomoby.service.dashboard.RegistryModel
 
addNotificationListener(NotificationListener) - Method in interface org.biomoby.shared.event.Notifier
Adds the specified notification listener to receive notification events from the class that implements this interface.
addNotificationListeners(NotificationListener[]) - Method in class org.biomoby.client.CentralDigestImpl
 
addNotificationListeners(NotificationListener[]) - Method in class org.biomoby.service.dashboard.RegistryModel
 
addNotificationListeners(NotificationListener[]) - Method in interface org.biomoby.shared.event.Notifier
Adds the specified notification listeners to receive notification events from the class that implements this interface.
addObjectType(RegisterObjectClassOperation.ObjectType) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.Relationship
 
addOption(JMenuItem, boolean) - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
addOutput(String, String...) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds an output definition.
addOutput(String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds an output definition.
addOutput(MobyData) - Method in class org.biomoby.shared.MobyService
Adds an output parameter to the service.
addOutputTypeSubMenu(JMenu, MobyDataType) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addParameter(FindServiceOperation.Services.Parameter) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.SecondaryArticles
 
addParameter(MobyParameter) - Method in class org.inb.biomoby.shared.message.MobyData
 
addParentName(String) - Method in class org.biomoby.shared.MobyDataType
Add one parent of this data type.
addParentName(String) - Method in class org.biomoby.shared.MobyServiceType
 
addParticipant(Interactor) - Method in class org.inb.biomoby.shared.ontology.Interaction
 
addPopupOptions(Node, JPopupMenu, boolean) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Uses default handler for response callback
addPopupOptions(Node, JPopupMenu, boolean, MobyRequestEventHandler) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Find the list of available services based on the XML->moby datatype mapping utility in mobyClient.
addPopupOptions(String, JPopupMenu, boolean) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addPopupOptions(String, JPopupMenu, boolean, MobyRequestEventHandler) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addPopupOptions(MobyDataInstance, JPopupMenu, boolean) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Same as three arg addPopupOptions, but uses default response handler
addPopupOptions(MobyDataInstance, JPopupMenu, boolean, MobyRequestEventHandler) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Find the list of available services querying MobyCentral directly with a piece of data.
addPopupOptions(Object, JPopupMenu, boolean, MobyRequestEventHandler, MobyPayloadRequestListener, String) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Find the list of available services querying MobyCentral directly with a piece of data.
addPopupOptions(MobyPrimaryData, JPopupMenu, boolean, MobyRequestEventHandler) - Method in class ca.ucalgary.seahawk.gui.MobyShimmer
 
addPrimitiveComplexType(Element, String, String) - Method in class org.biomoby.shared.schema.Builder
add a complexType for string to the root element; Element parent is the root Element.
addPrimitiveElement(PrimitiveVector, Element) - Method in class org.biomoby.shared.schema.Builder
add all primitive element to the sequnece element.
addPrimitiveSimpleType(Element, Vector, String) - Method in class org.biomoby.shared.schema.Builder
add simpleType for the primitive element; create a enumeration XML schema element for article names.
addProperties(ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
addProperties(ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
addProperty(ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
Method to add a property into the table model
addProperty(ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
addProperty(QName) - Method in class org.inb.wsrf.rp2.GetMultipleResourceProperties
 
addProperty(Object) - Method in class org.inb.wsrf.rp2.GetResourcePropertyResponse
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biomoby.service.dashboard.PropertyChannel
Register listeners.
addProvisionInfo(Element) - Method in class org.biomoby.shared.data.MobyDataObject
 
ADDR - Static variable in interface org.w3c.addressing.sax.EprTags
 
addRegexMapping(String, String[]) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addRegexMapping(String, String, String[]) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addRegexMapping(String, String[]) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addRegexMapping(String, String[], String, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addRegexMapping(String, Map<String, String>, String, Map<String, String[]>) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addRegexMapping(String, Map<String, String>, String, Map<String, String[]>, String, String, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addRelationship(RegisterObjectClassOperation.Relationship) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
addRelationship(RegisterServiceTypeOperation.Relationship) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
addRelationship(Relationship.RELATIONSHIP_TYPE) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
addRelationship(Relationship<ObjectType>) - Method in class org.inb.biomoby.shared.registry.ObjectType
 
addRelationship(Relationship<ServiceType>) - Method in class org.inb.biomoby.shared.registry.ServiceType
 
addRenderer(Renderer) - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
Add a renderer to this registry.
addResponse(Object) - Method in class org.inb.wsrf.rp2.GetMultipleResourcePropertiesResponse
 
addRules(MobyString) - Method in class org.inb.biomoby.shared.ontology.Rules
 
addSearchItem(JMenu, int) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addSecondary(String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds a secondary (parameter) to the request.
addSecondaryArticle(Parameter) - Method in class org.inb.biomoby.shared.registry.Service
 
addSeealso(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
addSegments(StructureBoundaries) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
addSegments(StructureBoundaries) - Method in class org.inb.biomoby.shared.ontology.StructureDomain
 
addSensitivityParameters(MobyString) - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
addService(String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds a service to the request.
addService(String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Adds a service name to the list of service which will be called.
addService(FindServiceOperation.Services.Service) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services
 
addServiceType(RegisterServiceTypeOperation.ServiceType) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.Relationship
 
addServiceTypeSubMenu(JMenu, MobyServiceType) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addSimple(Simple) - Method in class org.inb.biomoby.shared.registry.Data
 
addStructureDomains(StructureDomain) - Method in class org.inb.biomoby.shared.ontology.AnnotatedStructure
 
addStructureFragments(StructureFragment) - Method in class org.inb.biomoby.shared.ontology.AnnotatedStructure
 
addSynonym(MobyString) - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
addTarget(ByoDynTarget) - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
addTargetSpecies(MobyString) - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
addToClipboard(MobyDataInstance) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Adds the given data to the Seahawk clipboard object collection.
addToReport(String) - Method in class org.biomoby.registry.rdfagent.util.Report
 
addTreeModelListener(TreeModelListener) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
addUniqueElement(Element, String, Vector) - Method in class org.biomoby.shared.schema.Builder
add an unique element as a child of an element parent.
addUnitTest(MobyUnitTest) - Method in class org.biomoby.shared.MobyService
 
addURLRegexMapping(String, String[], String, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addURLRegexMapping(String, Map<String, String>, String, Map<String, String[]>, String, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addUserData(MobyDataInstance, URL, FilterSearch) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Record a condition for data acceptability, another service call with an output filter criteria. i.e. records if(f1(x) matches f1's output filter){...}
addUserDataToPayload(MobyContentInstance, Document) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Tacks the data provenance info saved as processing instructions during saveInputData() back into the MobyContentInstance loaded from file using the usual, customization-oblivious MobyDataUtils.fromXMLDocument().
addValues(MobyString) - Method in class org.inb.biomoby.shared.ontology.MultiParameter
 
addVector(Vector, Vector) - Static method in class org.biomoby.shared.schema.PrimitiveVector
add the content of the second vector to the first vector
addXPathMapping(String, String[]) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addXPathMapping(String, String, String[]) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
addXPathMapping(String, String[]) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addXPathMapping(String, Map<String, String>, String, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addXPathMapping(String, Map<String, String>, String, Map<String, String[]>, String, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
addXref(MobyXref) - Method in class org.biomoby.shared.datatypes.MobyObject
Add a cross reference to those already attached.
adjustForDetachement() - Method in class org.biomoby.service.dashboard.ResultsPanel
Make chnages needed for a standalone result panel.
ADMIN_EMAIL - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The email address of the registry's administrator.
ADMIN_MODE - Static variable in class org.biomoby.service.MobyServlet
 
ADMIN_NAME - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The name of the registry's administrator.
ALIVE - Static variable in class org.biomoby.shared.MobyService
 
ALL - Static variable in class org.biomoby.registry.rdfagent.util.Log
log all messages
ALLOWED_FORMATS - Static variable in class org.biomoby.shared.datatypes.MobyDateTime
An array defining all allowed formats for Biomoby DateTime objects.
allTabsVisible() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
AminoAcidSequence - Class in org.inb.biomoby.shared.ontology
 
AminoAcidSequence() - Constructor for class org.inb.biomoby.shared.ontology.AminoAcidSequence
 
AminoAcidSequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
AminoAcidSequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.AminoAcidSequenceComponent
 
AminoAcidSequenceComponent(AminoAcidSequence) - Constructor for class org.inb.biomoby.client.gui.ontology.AminoAcidSequenceComponent
 
AnalysisEvent - Class in org.inb.lsae
 
AnalysisEvent() - Constructor for class org.inb.lsae.AnalysisEvent
 
AnalysisEvent - Class in org.omg.lsae.notifications
This class represent the base LSAE Notification Event. ------------ TODO -> should this really be abstract?
AnalysisEvent() - Constructor for class org.omg.lsae.notifications.AnalysisEvent
Default Constructor
AnalysisEventTestCase - Class in org.omg.lsae.sax.test
 
AnalysisEventTestCase(String) - Constructor for class org.omg.lsae.sax.test.AnalysisEventTestCase
 
ancle - Variable in class org.inb.biomoby.client.gui.swing.border.RoundedBorder
 
aNEW_STATE - Static variable in interface org.omg.lsae.sax.LsaeTags
 
AnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
AnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.AnnotatedAASequence
 
AnnotatedAASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
AnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotatedAASequenceComponent
 
AnnotatedAASequenceComponent(AnnotatedAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotatedAASequenceComponent
 
AnnotatedDomain - Class in org.inb.biomoby.shared.ontology
 
AnnotatedDomain() - Constructor for class org.inb.biomoby.shared.ontology.AnnotatedDomain
 
AnnotatedNASequence - Class in org.inb.biomoby.shared.ontology
 
AnnotatedNASequence() - Constructor for class org.inb.biomoby.shared.ontology.AnnotatedNASequence
 
AnnotatedNASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
AnnotatedNASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotatedNASequenceComponent
 
AnnotatedNASequenceComponent(AnnotatedNASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotatedNASequenceComponent
 
AnnotatedStructure - Class in org.inb.biomoby.shared.ontology
 
AnnotatedStructure() - Constructor for class org.inb.biomoby.shared.ontology.AnnotatedStructure
 
AnnotatedStructureComponent<T extends AnnotatedStructure> - Class in org.inb.biomoby.client.gui.ontology
 
AnnotatedStructureComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotatedStructureComponent
 
Annotation - Class in org.inb.biomoby.shared.ontology
 
Annotation() - Constructor for class org.inb.biomoby.shared.ontology.Annotation
 
AnnotationComponent<T extends Annotation> - Class in org.inb.biomoby.client.gui.ontology
 
AnnotationComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotationComponent
 
AnnotationHits - Class in org.inb.biomoby.shared.ontology
 
AnnotationHits() - Constructor for class org.inb.biomoby.shared.ontology.AnnotationHits
 
AnnotationHitsComponent - Class in org.inb.biomoby.client.gui.ontology
 
AnnotationHitsComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotationHitsComponent
 
AnnotationHitsComponent(AnnotationHits) - Constructor for class org.inb.biomoby.client.gui.ontology.AnnotationHitsComponent
 
annotationsSelected(List<? extends Annotation>) - Method in interface org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane.AnnotationListListener
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
annotationsSelected(List<? extends Annotation>) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
ANON_ARTICLE - Static variable in class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
AntigenicAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
AntigenicAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.AntigenicAnnotatedAASequence
 
AntigenicAnnotatedAASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
AntigenicAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
AntigenicAnnotatedAASequenceComponent(AntigenicAnnotatedAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
AntigenicAnnotatedAASequenceComponent.AntigenicAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
AntigenicAnnotation - Class in org.inb.biomoby.shared.ontology
 
AntigenicAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.AntigenicAnnotation
 
AntigenicAnnotationListPane<T extends AntigenicAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
AntigenicAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.AntigenicAnnotationListPane
 
AntigenicAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.AntigenicAnnotationListPane
 
AntigenicReport - Class in org.inb.biomoby.shared.ontology
 
AntigenicReport() - Constructor for class org.inb.biomoby.shared.ontology.AntigenicReport
 
AntigenicReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
AntigenicReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
AntigenicReportComponent(AntigenicReport) - Constructor for class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
AntigenicReportComponent.AntigenicReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
AntModel - Class in org.biomoby.service.dashboard
A model using Ant to achieve its tasks.
AntModel() - Constructor for class org.biomoby.service.dashboard.AntModel
Default constructor.
AntModel(RegistryModel) - Constructor for class org.biomoby.service.dashboard.AntModel
A usual constructor.
AnyMobyObject - Class in org.inb.biomoby.shared.message
This class is a substitution to ontology classes.
AnyMobyObject(String) - Constructor for class org.inb.biomoby.shared.message.AnyMobyObject
 
AnyMobyObject(String, String, String) - Constructor for class org.inb.biomoby.shared.message.AnyMobyObject
 
aPERCENTAGE - Static variable in interface org.omg.lsae.sax.LsaeTags
 
application - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
application - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
apply(Matcher) - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
apply(Matcher, byte[]) - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
applyXPath(Object, NamespaceContext) - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
approvedBy - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
aPREV_STATE - Static variable in interface org.omg.lsae.sax.LsaeTags
 
areAnnotationsOverlapped() - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
areInputsOutputsForServiceValid(MobyService) - Method in class org.biomoby.registry.rdfagent.verifier.MobyServiceComparator
 
aREMAINING - Static variable in interface org.omg.lsae.sax.LsaeTags
 
areServicesDifferent(MobyService, MobyService) - Method in class org.biomoby.registry.rdfagent.verifier.MobyServiceComparator
 
ArgumentListener - Interface in ca.ucalgary.util
 
Array - Class in org.inb.biomoby.shared.ontology
 
Array() - Constructor for class org.inb.biomoby.shared.ontology.Array
 
ArrayFloat - Class in org.inb.biomoby.shared.ontology
 
ArrayFloat() - Constructor for class org.inb.biomoby.shared.ontology.ArrayFloat
 
ArrayFloatChartPane - Class in org.inb.biomoby.client.gui.auxiliary
 
ArrayFloatChartPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.ArrayFloatChartPane
 
ArrayFloatChartPane(ArrayFloat) - Constructor for class org.inb.biomoby.client.gui.auxiliary.ArrayFloatChartPane
 
ArrayFloatChartPane.ArrayFloatListener - Interface in org.inb.biomoby.client.gui.auxiliary
 
ArrayInteger - Class in org.inb.biomoby.shared.ontology
 
ArrayInteger() - Constructor for class org.inb.biomoby.shared.ontology.ArrayInteger
 
ArrayString - Class in org.inb.biomoby.shared.ontology
 
ArrayString() - Constructor for class org.inb.biomoby.shared.ontology.ArrayString
 
ArrayXYData - Class in org.inb.biomoby.shared.ontology
 
ArrayXYData() - Constructor for class org.inb.biomoby.shared.ontology.ArrayXYData
 
ArrayXYDataComponent - Class in org.inb.biomoby.client.gui.ontology
 
ArrayXYDataComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
ArrayXYDataComponent(ArrayXYData) - Constructor for class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
ArrayXYDataComponent.Point - Class in org.inb.biomoby.client.gui.ontology
 
ArrayXYDataComponent.Point(double, double) - Constructor for class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent.Point
 
article_name - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
ARTICLE_PEERS_MODE - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
articleName - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
ARTICLENAME - Static variable in interface org.biomoby.shared.parser.MobyTags
 
ARTICLENAME_RULE_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
asBoolean() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
ASCENDING - Static variable in class org.biomoby.service.dashboard.TableSorter
 
asDateTime() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
asFloat() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
asInteger() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
AssertedWrapperComponent - Class in org.inb.biomoby.client.gui.auxiliary
 
AssertedWrapperComponent(AbstractMobyComponent) - Constructor for class org.inb.biomoby.client.gui.auxiliary.AssertedWrapperComponent
 
AssertedWrapperComponent(AbstractMobyComponent, boolean) - Constructor for class org.inb.biomoby.client.gui.auxiliary.AssertedWrapperComponent
 
asString() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
AsyncClient - Class in org.biomoby.client
Implements the client side of the asynchonous SOAP-based MOBY service invocation specification.
AsyncClient() - Constructor for class org.biomoby.client.AsyncClient
 
AsyncClientTestCase - Class in org.biomoby.client.test
 
AsyncClientTestCase(String) - Constructor for class org.biomoby.client.test.AsyncClientTestCase
 
Asynchronous - Interface in org.biomoby.service
This interface is used by MobyServlet to determine if the processRequest() method should be spawned in a separate thread.
aTOTAL_STEPS - Static variable in interface org.omg.lsae.sax.LsaeTags
 
AUTHOR_HINT - Static variable in class ca.ucalgary.seahawk.gui.WorkflowPreviewDialog
 
authoritative - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
authoritative - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
authoritative - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
AUTHORITIES_CANCELLED - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITIES_COUNT - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITIES_END - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITIES_RESET - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITIES_START - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITIES_UPDATED - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITY - Static variable in interface org.biomoby.shared.parser.MobyTags
 
AUTHORITY_LOADED - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITY_LOADING - Static variable in interface org.biomoby.shared.event.Notifier
 
AUTHORITY_SERVICE_HTTP_BINDING - Static variable in class org.biomoby.shared.LSIDResolver
 
AUTHORITY_SERVICE_SOAP_BINDING - Static variable in class org.biomoby.shared.LSIDResolver
 
AUTHORITY_WSDL_LOCATION - Static variable in class org.biomoby.shared.LSIDResolver
 
AUTHURI - Static variable in interface org.biomoby.shared.parser.MobyTags
 
autocomplete(HttpServletRequest, String) - Method in class ca.ucalgary.services.util.PBERecorder
Called via AJAX when the user is filling something on the form that's supposed to be the Moby ontology The returned value is the list of possible ontology matches, with relevant description excerpts.
AUTOCOMPLETE_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 

B

BACK_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
Base64 - Class in org.inb.biomoby.client.gui.auxiliary
A very fast and memory efficient class to encode and decode to and from BASE64 in full accordance with RFC 2045.
Base64() - Constructor for class org.inb.biomoby.client.gui.auxiliary.Base64
 
BASE64_DATATYPE - Static variable in class org.biomoby.shared.data.MobyDataBytes
 
Base64Coder - Class in org.biomoby.client.util
A Base64 Encoder/Decoder.
Base64Image - Class in org.biomoby.service.dashboard.renderers
Decode a byte array from a Base64 encoded Biomoby data types, and convert the resulting byte array to an image.
Base64Image() - Constructor for class org.biomoby.service.dashboard.renderers.Base64Image
 
Base64Image(String, String) - Constructor for class org.biomoby.service.dashboard.renderers.Base64Image
 
BaseClient - Class in org.biomoby.client
This is a base class for Biomoby clients.
BaseClient() - Constructor for class org.biomoby.client.BaseClient
 
BaseCmdLineClient - Class in org.biomoby.client
This is a base class for the command-line driven clients.
BaseCmdLineClient() - Constructor for class org.biomoby.client.BaseCmdLineClient
 
BaseCmdLineClient(String[]) - Constructor for class org.biomoby.client.BaseCmdLineClient
 
BaseFaultType - Class in org.inb.wsrf.bf2
 
BaseFaultType() - Constructor for class org.inb.wsrf.bf2.BaseFaultType
 
BaseFaultType.Description - Class in org.inb.wsrf.bf2
 
BaseFaultType.Description() - Constructor for class org.inb.wsrf.bf2.BaseFaultType.Description
 
BaseFaultType.ErrorCode - Class in org.inb.wsrf.bf2
 
BaseFaultType.ErrorCode() - Constructor for class org.inb.wsrf.bf2.BaseFaultType.ErrorCode
 
BaseFaultType.FaultCause - Class in org.inb.wsrf.bf2
 
BaseFaultType.FaultCause() - Constructor for class org.inb.wsrf.bf2.BaseFaultType.FaultCause
 
BaseService - Class in org.biomoby.service
A base class for all Biomoby services (if their providers choose to write their services this way, of course).
BaseService() - Constructor for class org.biomoby.service.BaseService
Default constructor.
BasicAnnotation - Class in org.inb.biomoby.shared.ontology
 
BasicAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.BasicAnnotation
 
BINARY_DATA_LABEL - Static variable in class ca.ucalgary.seahawk.util.HTMLUtils
 
bindTemplate(MobyDataType) - Method in class org.biomoby.shared.MobyDataTypeTemplate
 
BIOMOBY_SERVICE_URI - Static variable in class org.biomoby.shared.MobyService
An immutable string representing URI (namespace) of all Biomoby services.
BL2GAnnotation - Class in org.inb.biomoby.shared.ontology
 
BL2GAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.BL2GAnnotation
 
BLAST__Text - Class in org.inb.biomoby.shared.ontology
 
BLAST__Text() - Constructor for class org.inb.biomoby.shared.ontology.BLAST__Text
 
BLAST_XML - Class in org.inb.biomoby.shared.ontology
 
BLAST_XML() - Constructor for class org.inb.biomoby.shared.ontology.BLAST_XML
 
BLOCK_NAME_KEY - Static variable in class ca.ucalgary.services.util.ACDFile
 
BLOCK_TYPE_KEY - Static variable in class ca.ucalgary.services.util.ACDFile
 
BLOCKAnnotation - Class in org.inb.biomoby.shared.ontology
 
BLOCKAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.BLOCKAnnotation
 
BlocksAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
BlocksAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.BlocksAnnotatedAASequence
 
BlocksAnnotatedAASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
BlocksAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
BlocksAnnotatedAASequenceComponent(BlocksAnnotatedAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
BlocksAnnotatedAASequenceComponent.BlocksAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
BOOLEAN_TYPE - Static variable in class org.biomoby.shared.MobySecondaryData
 
booleanValue() - Method in class org.biomoby.shared.data.MobyDataBoolean
A convenience method to get a Java primitive representing the underlying Boolean of this object
BOTH_COLLECTIONS_CONNECTION - Static variable in class org.biomoby.client.ServicesEdge
 
BoxCollectionRenderer - Class in org.biomoby.service.dashboard.renderers
This is not a normal renderer that is loaded and used through SPI.
BoxCollectionRenderer(Renderer) - Constructor for class org.biomoby.service.dashboard.renderers.BoxCollectionRenderer
 
BrowserLauncher - Class in ca.ucalgary.seahawk.util
BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
build(MobyDataType[], MobyService[]) - Static method in class org.biomoby.client.ServiceConnections
Creates all (allowed) connections between given 'services' based on the given 'dataTypes'.
BuildDataTypeTree - Class in org.biomoby.service.dashboard
A tree for building a new data type (usually followed by registering the new data type).
BuildDataTypeTree(PropertyChannel) - Constructor for class org.biomoby.service.dashboard.BuildDataTypeTree
Constructor
Builder - Class in org.biomoby.shared.schema
 
Builder() - Constructor for class org.biomoby.shared.schema.Builder
 
buildMElement(String) - Static method in class org.biomoby.shared.schema.RdfParser
 
buildMobyEncapsulatedSchema(String) - Method in class org.biomoby.shared.schema.Builder
 
buildSchema(String) - Method in class org.biomoby.shared.schema.Builder
Given a string, we will give a element represnting an xml schema which describe the object of the name.
buildWorkflow(ServicesEdge[], String, Properties) - Static method in class org.biomoby.client.Taverna
Creates a workflow definition (an XML string known as 'scufl' or 'xscufl') from the set of graph edges.
ByoDynInput - Class in org.inb.biomoby.shared.ontology
 
ByoDynInput() - Constructor for class org.inb.biomoby.shared.ontology.ByoDynInput
 
ByoDynOEDParameter - Class in org.inb.biomoby.shared.ontology
 
ByoDynOEDParameter() - Constructor for class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
ByoDynTarget - Class in org.inb.biomoby.shared.ontology
 
ByoDynTarget() - Constructor for class org.inb.biomoby.shared.ontology.ByoDynTarget
 
BYTE_READ_SIZE - Static variable in class org.biomoby.shared.data.MobyDataBytes
How much is read from a input stream (e.g. file) at once

C

ca.ucalgary.minnow - package ca.ucalgary.minnow
 
ca.ucalgary.seahawk.gui - package ca.ucalgary.seahawk.gui
Seahawk is a graphical MOBY client that can be used standalone, or easily embedded in another Java application.
ca.ucalgary.seahawk.gui.splash - package ca.ucalgary.seahawk.gui.splash
 
ca.ucalgary.seahawk.gui.test - package ca.ucalgary.seahawk.gui.test
 
ca.ucalgary.seahawk.services - package ca.ucalgary.seahawk.services
 
ca.ucalgary.seahawk.services.test - package ca.ucalgary.seahawk.services.test
 
ca.ucalgary.seahawk.util - package ca.ucalgary.seahawk.util
 
ca.ucalgary.seahawk.util.test - package ca.ucalgary.seahawk.util.test
 
ca.ucalgary.services - package ca.ucalgary.services
 
ca.ucalgary.services.test - package ca.ucalgary.services.test
 
ca.ucalgary.services.util - package ca.ucalgary.services.util
 
ca.ucalgary.services.util.test - package ca.ucalgary.services.util.test
 
ca.ucalgary.util - package ca.ucalgary.util
 
CACHE_PART_DATATYPES - Static variable in interface org.biomoby.shared.CentralCached
An ID indicating data types part of a cache.
CACHE_PART_NAMESPACES - Static variable in interface org.biomoby.shared.CentralCached
An ID indicating namespaces part of a cache.
CACHE_PART_SERVICES - Static variable in interface org.biomoby.shared.CentralCached
An ID indicating services part of a cache.
CACHE_PART_SERVICETYPES - Static variable in interface org.biomoby.shared.CentralCached
An indicating service types part of a cache.
CACHE_POLICY_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
CACHE_PROP_COUNT - Static variable in interface org.biomoby.shared.CentralCached
 
CACHE_PROP_LOCATION - Static variable in interface org.biomoby.shared.CentralCached
 
CACHE_PROP_NAME - Static variable in interface org.biomoby.shared.CentralCached
 
CACHE_PROP_OLDEST - Static variable in interface org.biomoby.shared.CentralCached
 
CACHE_PROP_REGISTRY_URL - Static variable in interface org.biomoby.shared.CentralCached
 
CACHE_PROP_SIZE - Static variable in interface org.biomoby.shared.CentralCached
 
CACHE_PROP_YOUNGEST - Static variable in interface org.biomoby.shared.CentralCached
 
CacheConfig - Class in org.inb.biomoby.central.cache
BioMoby Registry cache implementation.
cacheRegistryOntology(Registry, String) - Static method in class org.biomoby.registry.meta.RegistryCache
Stores the given resource to a file for retrieval later with getOntologyFile().
cacheRegistryOntology(Registry, String, long) - Static method in class org.biomoby.registry.meta.RegistryCache
Stores the given resource to a file for retrieval later with getOntologyFile().
calcCentralCallFile(String, String) - Static method in class org.biomoby.registry.meta.RegistryCache
Reports where the message returned by the call should be stored on disk.
calcDataTypeOntologyFile(Registry) - Static method in class org.biomoby.registry.meta.RegistryCache
 
calcNamespaceOntologyFile(Registry) - Static method in class org.biomoby.registry.meta.RegistryCache
 
calcServiceOntologyFile(Registry) - Static method in class org.biomoby.registry.meta.RegistryCache
 
calcServiceTypeOntologyFile(Registry) - Static method in class org.biomoby.registry.meta.RegistryCache
 
call(Collection<MobyService>) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Calls all given services and returns their result.
call() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Calls one or several services (which are found by the find-service-procedure) and returns their results.
call(MobyService) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Calls the moby service and returns its result.
call(String, String) - Method in class org.biomoby.client.CentralImpl
 
call(String, String) - Method in interface org.biomoby.shared.Central
Call Moby registry's method with given XML as input and return whatever you get back.
call(DeregisterNamespaceOperation.DeregisterNamespace) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterNamespaceOperation
 
call(DeregisterObjectClassOperation.DeregisterObjectClass) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterObjectClassOperation
 
call(DeregisterServiceTypeOperation.DeregisterServiceType) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceTypeOperation
 
call(FindServiceOperation.FindService) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation
 
call(RegisterNamespaceOperation.RegisterNamespace) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation
 
call(RegisterObjectClassOperation.RegisterObjectClass) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation
 
call(RegisterServiceOperation.RegisterService) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation
 
call(RegisterServiceTypeOperation.RegisterServiceType) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation
 
call(RelationshipsOperation.RelationshipsInput) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation
 
call() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation
 
call(RetrieveObjectDefinitionOperation.RetrieveObjectDefinition) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation
 
call() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation
 
call(RetrieveObjectOperation.RetrieveObjectSchema) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation
 
call() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation
 
call() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation
 
call(RetrieveServiceOperation.RetrieveService) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation
 
call() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation
 
call() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation
 
call(MobyMessage) - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
call(MobyMessage) - Method in interface org.inb.biomoby.service.IAsyncMobyImpl
 
call(MobyMessage) - Method in class org.inb.biomoby.service.MobyProvider
 
CALL_CACHE_FILE_PREFIX - Static variable in class org.biomoby.registry.meta.RegistryCache
 
callback(int) - Method in class org.biomoby.client.CentralDigestImpl
 
callback(int) - Method in class org.biomoby.service.dashboard.RegistryModel
 
callback(int) - Method in interface org.biomoby.shared.event.Notifier
Call the notifier and signal that it can stop loading data (or whatever it is doing).
callRegistry(String, File) - Method in class org.biomoby.service.dashboard.RegistryModel
Call the given method (on worker) with data given in 'inputXML'.
callRemoteService(String) - Method in class org.biomoby.client.BaseClient
Call a SOAP-based BioMoby service.
callRemoteService(String) - Method in class org.biomoby.client.BaseCmdLineClient
Call either a local class implementing a service, or pass it to the superclass that does a real (usual) SOAP call to a service (or first to a registry and then to a service).
callRemoteService(String) - Method in class org.biomoby.client.ExtendedProtocolClient
Call either a local class implementing a service, or pass it to the superclass that does a real (usual) SOAP call to a service (or first to a registry and then to a service).
callService(MobyService, MobyContentInstance) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
callService(HttpServletRequest, HttpServletResponse, URL, PrintStream) - Method in class ca.ucalgary.services.SoapServlet
Post is for service submission (if the wsdl URL is provided)
callServiceMultipleTimes() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Calls a service multiple times and returns it results.
callWithMultipleResult() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Calls a service and returns the results of the service.
callWithSingleResult() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Calls a service and returns the one result the service returns.
cancelCellEditing() - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor
 
cancelCellEditing() - Method in class org.inb.biomoby.central.gui.renderer.PropertyNameTableCellEditor
 
canFilter() - Method in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
filter/search is disabled for the help, not implemented as a text search function, for consistency
canFilter() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
canGoBack() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
history is disabled for the clipboard
canGoBack() - Method in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
history is disabled for the help
canGoBack() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
canGoForward() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
history is disabled for the clipboard
canGoForward() - Method in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
history is disabled for the help
canGoForward() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
canHandle(String, Object) - Method in class org.biomoby.service.dashboard.renderers.AbstractRenderer
 
canHandle(String, Object) - Method in class org.biomoby.service.dashboard.renderers.Base64Image
 
canHandle(String, Object) - Method in class org.biomoby.service.dashboard.renderers.CollectionRenderer
Never used...
canHandle(String, Object) - Method in class org.biomoby.service.dashboard.renderers.ICISPedigreeTree
 
canHandle(String, Object) - Method in class org.biomoby.service.dashboard.renderers.PlainMobyText
Takes any Moby object (even the 'envelope' objects, such as MobyPackage, MobyJob, MobySimple and MobyCollection).
canHandle(String, Object) - Method in class org.biomoby.service.dashboard.renderers.PlainText
It can handle Strings.
canHandle(String, Object) - Method in interface org.biomoby.service.dashboard.renderers.Renderer
Return true if this SPI can handle (render) data whose type complies with given value within given criterion.
canHandle(String, Object) - Method in class org.biomoby.service.dashboard.renderers.XMLTreeRenderer
It can handle XML strings.
canImport(JComponent, DataFlavor[]) - Method in class ca.ucalgary.seahawk.gui.FileAndTextTransferHandler
Overrides same method in parent class, tells the dropper if we'll accept the data before the drop is actually attempted.
canImport(TransferHandler.TransferSupport) - Method in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferHandler
 
canProduceDataTypeFromString(MobyDataType) - Method in class ca.ucalgary.seahawk.services.MobyClient
Indicates whether at least one production rule exists for the data type or one of its children.
canProduceTextTypeFromMoby(String, MobyPrimaryData) - Method in class ca.ucalgary.seahawk.services.TextClient
Report whether a rule exists in the provided XSLT that converts the given MOBY data to the given text type.
CardinalityTableCellEditor - Class in org.inb.biomoby.central.gui.renderer
 
CardinalityTableCellEditor() - Constructor for class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor
 
CardinalityTableCellEditor.CardinalityComponent - Class in org.inb.biomoby.central.gui.renderer
 
CardinalityTableCellEditor.CardinalityComponent() - Constructor for class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor.CardinalityComponent
 
CardinalityTableCellRenderer - Class in org.inb.biomoby.central.gui.renderer
 
CardinalityTableCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.CardinalityTableCellRenderer
 
caretUpdate(CaretEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
CASE_INSENSITIVE_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.FilterSearchWidget
 
CASE_SENSITIVE_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.FilterSearchWidget
 
category - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
CATEGORY_CGI - Static variable in class org.biomoby.shared.MobyService
Name of a category for CGI BioMoby services.
CATEGORY_CGI_ASYNC - Static variable in class org.biomoby.shared.MobyService
Name of an asynchronous CGI category for BioMoby services.
CATEGORY_MOBY - Static variable in class org.biomoby.shared.MobyService
Name of a default category for BioMoby services.
CATEGORY_MOBY_ASYNC - Static variable in class org.biomoby.shared.MobyService
Name of a category for asynchornous BioMoby services.
CATEGORY_MOBY_DOCLIT - Static variable in class org.biomoby.shared.MobyService
Name of a category for document/literal BioMoby services.
CATEGORY_MOBY_DOCLIT_ASYNC - Static variable in class org.biomoby.shared.MobyService
Name of a category for asynchronous document/literal BioMoby services.
CATHDomain - Class in org.inb.biomoby.shared.ontology
 
CATHDomain() - Constructor for class org.inb.biomoby.shared.ontology.CATHDomain
 
CathDomainDescription_XML - Class in org.inb.biomoby.shared.ontology
 
CathDomainDescription_XML() - Constructor for class org.inb.biomoby.shared.ontology.CathDomainDescription_XML
 
Central - Interface in org.biomoby.registry.Central
An interface that outlines the methods needed to query a Moby central registry.
Central - Interface in org.biomoby.shared
An interface to the Moby Registry.
CENTRAL_IMPL_RESOURCE_NAME - Static variable in class org.biomoby.client.CentralImpl
The META-INF resource file that will be checked to determine what default class should be instantiated in order to create a Central Implementation when getDefaultCentral() is called.
CENTRAL_XML_MODE - Static variable in interface org.biomoby.shared.data.MobyDataInstance
 
CentralAdmin - Class in org.biomoby.registry.rdfagent.util
 
CentralAdmin(String, String, String, String, String) - Constructor for class org.biomoby.registry.rdfagent.util.CentralAdmin
 
CentralAll - Interface in org.biomoby.shared
A common interface to the classical features of a MobyRegistry (as expressed in Central) and to the cumulated (digested) contents of the Moby Registry (as expressed in CentralDigest).
CentralCached - Interface in org.biomoby.shared
A convenient interface combining together all methods for accessing the BioMoby registry and the handling its local cache.
CentralCachedCallsImpl - Class in org.biomoby.client
Implements the functionality of caching by reusing identical calls to MOBY central (e.g. asking multiple times what services take a DNA sequence in the gi namespace).
CentralCachedCallsImpl() - Constructor for class org.biomoby.client.CentralCachedCallsImpl
Default constructor.
CentralCachedCallsImpl(String) - Constructor for class org.biomoby.client.CentralCachedCallsImpl
Constructor allowing to specify which Moby Registry to use.
CentralCachedCallsImpl(String, String) - Constructor for class org.biomoby.client.CentralCachedCallsImpl
Constructor allowing to specify which Moby Registry and what namespace to use.
CentralDataAccess - Interface in org.biomoby.registry.rdfagent.util
Interface for interacting with the mobycentral data store.
CentralDataAccessImpl - Class in org.biomoby.registry.rdfagent.util
This class implements the interface CentralDataAccess using mysql
CentralDataAccessImpl() - Constructor for class org.biomoby.registry.rdfagent.util.CentralDataAccessImpl
Default Constructor
CentralDigest - Interface in org.biomoby.shared
An interface to the cumulated (digested) contents of the Moby Registry.
CentralDigestCachedImpl - Class in org.biomoby.client
An implementation of CentralAll, allowing to cache locally results of the cumulative methods so it does not need to access Moby registry all the time.
CentralDigestCachedImpl() - Constructor for class org.biomoby.client.CentralDigestCachedImpl
The same as calling CentralDigestCachedImpl(null)
CentralDigestCachedImpl(String) - Constructor for class org.biomoby.client.CentralDigestCachedImpl
Create an instance that will access a default Moby registry and will cache results in the 'cacheDir' directory.
CentralDigestCachedImpl(String, String) - Constructor for class org.biomoby.client.CentralDigestCachedImpl
Create an instance that will access a specific Moby registry and will cache results in the default cache directory.
CentralDigestCachedImpl(String, String, String) - Constructor for class org.biomoby.client.CentralDigestCachedImpl
Create an instance that will access a Moby registry defined by its 'endpoint' and 'namespace', and will cache results in the 'cacheDir' directory.
CentralDigestCachedSimpleImpl - Class in org.biomoby.client
An implementation of CentralAll, allowing to cache locally results of the cumulative methods so it does not need to access Moby registry all the time.
CentralDigestCachedSimpleImpl(String) - Constructor for class org.biomoby.client.CentralDigestCachedSimpleImpl
Create an instance that will access a default Moby registry and will cache results in the 'cacheDir' directory.
CentralDigestCachedSimpleImpl(String, String, String) - Constructor for class org.biomoby.client.CentralDigestCachedSimpleImpl
Create an instance that will access a Moby registry defined by its 'endpoint' and 'namespace', and will cache results in the 'cacheDir' directory.
CentralDigestImpl - Class in org.biomoby.client
A default implementation of CentralDigest to get (also) cumulated data from a Moby registry.
CentralDigestImpl() - Constructor for class org.biomoby.client.CentralDigestImpl
Default constructor.
CentralDigestImpl(String) - Constructor for class org.biomoby.client.CentralDigestImpl
Constructor allowing to specify which Moby Registry to use.
CentralDigestImpl(String, String) - Constructor for class org.biomoby.client.CentralDigestImpl
Constructor allowing to specify which Moby Registry and what namespace to use.
CentralFactory - Class in org.biomoby.registry.sync
Factory class to enable the access to the Central implementation of Biomoby.
CentralImpl - Class in org.biomoby.client
A default implementation of the interface Central allowing access to a Moby registry.
CentralImpl() - Constructor for class org.biomoby.client.CentralImpl
Default constructor.
CentralImpl(String) - Constructor for class org.biomoby.client.CentralImpl
Constructor allowing to specify which Moby Registry to use.
CentralImpl(String, String) - Constructor for class org.biomoby.client.CentralImpl
Constructor allowing to specify which Moby Registry and what namespace to use.
CentralImpl - Class in org.biomoby.registry.Central
 
CentralImpl() - Constructor for class org.biomoby.registry.Central.CentralImpl
 
CGIService - Class in ca.ucalgary.services
In this class, we reshape an XHTML form into a Moby description of a service, which then uses the standard MobyServlet mechanism for service signature creation, meta-data publishing, etc.
CGIService() - Constructor for class ca.ucalgary.services.CGIService
 
CGISERVICE_USERAGENT_NAME - Static variable in class ca.ucalgary.services.CGIService
 
CGIServiceTestCase - Class in ca.ucalgary.services.test
For the testMain cases to be actually successful, the WEB-INF/web.xml file must be one with all the CGI parameters...
CGIServiceTestCase(String) - Constructor for class ca.ucalgary.services.test.CGIServiceTestCase
 
CGIServlet - Class in ca.ucalgary.services
Provides an HTML interface for invoking CGI.
CGIServlet() - Constructor for class ca.ucalgary.services.CGIServlet
 
CGIUtils - Class in ca.ucalgary.services.util
 
CGIUtils() - Constructor for class ca.ucalgary.services.util.CGIUtils
 
change(T) - Method in class org.biomoby.registry.sync.handler.AbstractMobyHandler
 
change(T) - Method in interface org.biomoby.registry.sync.handler.MobyHandler
Changes the given object in the local repository.
changedUpdate(DocumentEvent) - Method in class ca.ucalgary.seahawk.gui.FilterSearchWidget
Called when the regex has been changed by the user
changedUpdate(DocumentEvent) - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
Called when the regex has been changed by the user
changedUpdate(DocumentEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyObjectPropertyTable.DefaultPropertyNameValidator
 
changedUpdate(DocumentEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
characters(char[], int, int) - Method in class org.biomoby.shared.parser.MobyParser
Called for #PCDATA.
characters(char[], int, int) - Method in class org.omg.lsae.sax.EventParser
Called for #PCDATA.
characters(char[], int, int) - Method in class org.soap.sax.SOAPFaultParser
Called for #PCDATA.
characters(char[], int, int) - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Called for #PCDATA.
charAt(int) - Method in class org.inb.biomoby.client.gui.Subsequence
 
checkAndCallAgent() - Method in class org.biomoby.service.dashboard.RegistrationServiceSubPanel
 
checkAndRegister(boolean) - Method in class org.biomoby.service.dashboard.RegistrationDataTypeSubPanel
 
checkAndRegister(boolean) - Method in class org.biomoby.service.dashboard.RegistrationNamespaceSubPanel
 
checkAndRegister(boolean) - Method in class org.biomoby.service.dashboard.RegistrationPanel
Should be overwritten by sub-panels.
checkAndRegister(boolean) - Method in class org.biomoby.service.dashboard.RegistrationServiceSubPanel
 
checkAndRegister(boolean) - Method in class org.biomoby.service.dashboard.RegistrationServiceTypeSubPanel
 
checkExit(int) - Method in class org.biomoby.service.dashboard.ExitSecurityManager
 
checkForHyperlinkText(String) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
Extracts a URL string from a given piece of text iof that's all it contains.
checkForMobyXML(String) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
Given an HTML fragment (e.g. cut'n'pasted from a browser), see if we unescape the HTML we get a MOBY XML block (e.g. from the biomoby.org web site examples).
checkForURLShortcut(File) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
Turns a file into a URL if the file was URL shortcut (Windows & Gnome).
checkOrCreateArticleName(String, String) - Static method in class org.biomoby.shared.Utils
Check or create an article name.
checkPermission(Permission, Object) - Method in class org.biomoby.service.dashboard.ExitSecurityManager
 
checkPermission(Permission) - Method in class org.biomoby.service.dashboard.ExitSecurityManager
 
CLASS - Static variable in interface org.biomoby.service.dashboard.renderers.Renderer
 
CLASS_NAME - Static variable in interface org.biomoby.service.dashboard.renderers.Renderer
 
ClassNameTreeCellEditor - Class in org.inb.biomoby.central.gui.renderer
 
ClassNameTreeCellEditor() - Constructor for class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor
 
ClassNameTreeCellEditor.EditorContainer - Class in org.inb.biomoby.central.gui.renderer
 
ClassNameTreeCellEditor.EditorContainer() - Constructor for class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor.EditorContainer
 
clean() - Method in class org.biomoby.service.dashboard.CommonConsole
Clean the console (disregading of any current modes).
cleanup() - Method in interface org.biomoby.registry.rdfagent.util.CentralDataAccess
Use this method to perform any 'clean up', i.e. for JDBC, close connections, etc.
cleanup() - Method in class org.biomoby.registry.rdfagent.util.CentralDataAccessImpl
 
clear() - Method in class ca.ucalgary.seahawk.services.MobyClient
Removes all mapping rules.
clear() - Method in class ca.ucalgary.seahawk.util.MutableNodeList
 
clear() - Method in class ca.ucalgary.services.util.SourceMap
Effectively deletes the composite, leaving you with a blank base object
clear() - Method in class org.biomoby.shared.data.MobyContentInstance
Effectively deletes the contents, leaving you with a data-less container.
clear() - Method in class org.biomoby.shared.data.MobyDataComposite
Effectively deletes the composite, leaving you with a blank base object
clear() - Method in class org.biomoby.shared.data.MobyDataObjectSet
Removes all of the MobyDataObject elements from this collection.
clear() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
clear() - Method in class org.biomoby.shared.data.MobyDataObjectVector
Removes all of the elements from this list.
clear() - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
clear() - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
clear() - Method in class org.inb.biomoby.shared.message.MobyCollection
 
clear() - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
CLEAR_CLIPBOARD_OPTION - Static variable in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
clearClipboard() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Removes any existing data from the clipboard.
clearData() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
clearGUIs() - Static method in class ca.ucalgary.seahawk.util.MobyUtils
 
clearIcon - Static variable in class org.biomoby.service.dashboard.AbstractPanel
 
clearRegexs() - Method in class ca.ucalgary.seahawk.services.MobyClient
 
clearURLRegexs() - Method in class ca.ucalgary.seahawk.services.MobyClient
 
clearXPaths() - Method in class ca.ucalgary.seahawk.services.MobyClient
 
CLIPBOARD_CMD - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
CLIPBOARD_COLLECTION_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
CLIPBOARD_FILE_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
CLIPBOARD_LABEL - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
CLIPBOARD_QUERY_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
CLIPBOARD_TAB_COLOR - Static variable in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
CLIPBOARD_TAB_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
CLIPBOARD_TAB_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
CLIPBOARD_TAB_TOOLTIP - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
clone() - Method in class org.biomoby.shared.data.MobyDataBoolean
 
clone() - Method in class org.biomoby.shared.data.MobyDataComposite
 
clone() - Method in class org.biomoby.shared.data.MobyDataDateTime
 
clone() - Method in class org.biomoby.shared.data.MobyDataFloat
 
clone() - Method in class org.biomoby.shared.data.MobyDataInt
 
clone() - Method in class org.biomoby.shared.data.MobyDataObject
Simply calls new constructor with object's existing data type, name and value.
clone() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
clone() - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
clone() - Method in class org.biomoby.shared.data.MobyDataString
 
clone() - Method in class org.biomoby.shared.data.MobyDataXref
 
clone() - Method in class org.biomoby.shared.MobyData
Must be overwritten by a subclass.
clone() - Method in class org.biomoby.shared.MobyObjectDecompositionImpl
 
clone() - Method in class org.biomoby.shared.MobyPrimaryData
Must be overwritten by a subclass.
clone() - Method in class org.biomoby.shared.MobyPrimaryDataSet
 
clone() - Method in class org.biomoby.shared.MobyPrimaryDataSimple
 
clone() - Method in class org.biomoby.shared.MobySecondaryData
 
clone() - Method in class org.biomoby.shared.MobyService
Generally, you don't need to clone a service, unless you plan on modifying fields of the object, but do not want it to affect the service definition used by other threads within the JVM (i.e. getService(serviceName) always returns the same object within a single JVM instance).
clone() - Method in class org.biomoby.shared.PrimitiveTypes
 
clone() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
clone() - Method in class org.inb.biomoby.shared.registry.AbstractTypeEntity
 
clone() - Method in class org.inb.biomoby.shared.registry.Collection
 
clone() - Method in class org.inb.biomoby.shared.registry.Data
 
clone() - Method in class org.inb.biomoby.shared.registry.Input
 
clone() - Method in class org.inb.biomoby.shared.registry.Namespace
 
clone() - Method in class org.inb.biomoby.shared.registry.ObjectType
 
clone() - Method in class org.inb.biomoby.shared.registry.Output
 
clone() - Method in class org.inb.biomoby.shared.registry.Parameter
 
clone() - Method in class org.inb.biomoby.shared.registry.Registration
 
clone() - Method in class org.inb.biomoby.shared.registry.Relationship
 
clone() - Method in class org.inb.biomoby.shared.registry.Resource
 
clone() - Method in class org.inb.biomoby.shared.registry.Service
 
clone() - Method in class org.inb.biomoby.shared.registry.ServiceProvider
 
clone() - Method in class org.inb.biomoby.shared.registry.ServiceType
 
clone() - Method in class org.inb.biomoby.shared.registry.Simple
 
cloneIcon - Static variable in class org.biomoby.service.dashboard.data.DataTypeTreeTable
 
close() - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Closes the stream.
close() - Method in class org.inb.biomoby.generator.gui.StatusBarHandler
 
CLOSE_OTHERS_OPTION - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
CLOSE_TAB_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.util.CloseTabIcon
 
CLOSE_TAB_OPTION - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
closeConnection() - Method in class org.biomoby.registry.rdfagent.util.DBConnector
close the connection to the database
CloseTabIcon - Class in ca.ucalgary.seahawk.util
 
CloseTabIcon() - Constructor for class ca.ucalgary.seahawk.util.CloseTabIcon
 
CloseTabIcon(Icon) - Constructor for class ca.ucalgary.seahawk.util.CloseTabIcon
 
CloseTabIcon(Icon, int) - Constructor for class ca.ucalgary.seahawk.util.CloseTabIcon
 
CloseTabIcon(Icon, int, int) - Constructor for class ca.ucalgary.seahawk.util.CloseTabIcon
 
Clustalw_Evaluated_Text - Class in org.inb.biomoby.shared.ontology
 
Clustalw_Evaluated_Text() - Constructor for class org.inb.biomoby.shared.ontology.Clustalw_Evaluated_Text
 
Clustalw_Text - Class in org.inb.biomoby.shared.ontology
 
Clustalw_Text() - Constructor for class org.inb.biomoby.shared.ontology.Clustalw_Text
 
Clustering - Class in org.inb.biomoby.shared.ontology
 
Clustering() - Constructor for class org.inb.biomoby.shared.ontology.Clustering
 
ClusterProfile_Text - Class in org.inb.biomoby.shared.ontology
 
ClusterProfile_Text() - Constructor for class org.inb.biomoby.shared.ontology.ClusterProfile_Text
 
CmdLineHelper - Class in org.biomoby.client
An abstract parent of various command-line tools.
CmdLineHelper() - Constructor for class org.biomoby.client.CmdLineHelper
 
CodcmpReport_Text - Class in org.inb.biomoby.shared.ontology
 
CodcmpReport_Text() - Constructor for class org.inb.biomoby.shared.ontology.CodcmpReport_Text
 
codeStringToCodeInt(String) - Static method in exception org.biomoby.shared.data.MobyServiceException
Converts an error code string to an integer defined in ServiceException, or ERROR_CODE_UNKNOWN if the code is not a standard one (3 digits and part of RFC 1863).
CodonUsageTable_Text - Class in org.inb.biomoby.shared.ontology
 
CodonUsageTable_Text() - Constructor for class org.inb.biomoby.shared.ontology.CodonUsageTable_Text
 
COL_ARTICLE - Static variable in class org.biomoby.service.dashboard.PrimaryDataTable
 
COL_ARTICLE - Static variable in class org.biomoby.service.dashboard.SecondaryDataTable
 
COL_BUTTON - Static variable in class org.biomoby.service.dashboard.CommonDataTable
 
COL_CLASSNAME - Static variable in class org.biomoby.service.dashboard.DeploymentTable
 
COL_DATATYPE - Static variable in class org.biomoby.service.dashboard.PrimaryDataTable
 
COL_DATATYPE - Static variable in class org.biomoby.service.dashboard.SecondaryDataTable
 
COL_DEFAULT - Static variable in class org.biomoby.service.dashboard.SecondaryDataTable
 
COL_DESC - Static variable in class org.biomoby.service.dashboard.SecondaryDataTable
 
COL_ENUM - Static variable in class org.biomoby.service.dashboard.SecondaryDataTable
 
COL_IN_SET - Static variable in class org.biomoby.service.dashboard.PrimaryDataTable
 
COL_MAX - Static variable in class org.biomoby.service.dashboard.SecondaryDataTable
 
COL_MIN - Static variable in class org.biomoby.service.dashboard.SecondaryDataTable
 
COL_NAMESPACE - Static variable in class org.biomoby.service.dashboard.PrimaryDataTable
 
COL_SERVICE - Static variable in class org.biomoby.service.dashboard.DeploymentTable
 
CollapsablePanel<T extends JComponent> - Class in org.inb.biomoby.client.gui.swing
 
CollapsablePanel(T) - Constructor for class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
CollapsablePanel(T, String, boolean) - Constructor for class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
collection - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
Collection - Static variable in class org.biomoby.client.rdf.vocabulary.MobyResources
Deprecated. Replaced by Predicates.Collection. The reason is that this property should not be under a different RDF document URI
Collection - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
collection - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
COLLECTION - Static variable in interface org.biomoby.shared.parser.MobyTags
 
Collection - Class in org.inb.biomoby.shared.registry
Represents Moby Central "collection of simple objects" abstract
Collection() - Constructor for class org.inb.biomoby.shared.registry.Collection
 
CollectionArticle - Static variable in class org.biomoby.client.rdf.vocabulary.MobyResources
Deprecated. Replaced by Predicates.articleName. The reason is that this property is never utilized and is redundant.
collectionParameter - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
collectionParameter - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
CollectionRenderer - Class in org.biomoby.service.dashboard.renderers
This is not a normal renderer that is loaded and used through SPI.
collectionServiceName - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
COLUMN_ADD - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column allowing to add an empty HAS member.
COLUMN_CDATA - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column indicating that a value should be stored as CDATA.
COLUMN_CLONE - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column allowing to add a HAS member by duplicating an exiting one.
COLUMN_ID - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column with identifiers.
COLUMN_NS - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column with namespaces.
COLUMN_REMOVE - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column allowing to remove a HAS member.
COLUMN_TAREA - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column indicating that a value editor should allow more lines.
COLUMN_TREE - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column with a data type tree.
COLUMN_VALUE - Static variable in class org.biomoby.service.dashboard.data.DataTypeModel
Index of a column with values.
columnMarginChanged(ChangeEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
CombinedIcon - Class in ca.ucalgary.seahawk.util
 
CombinedIcon(Icon, Icon) - Constructor for class ca.ucalgary.seahawk.util.CombinedIcon
 
CombinedIcon(Icon, Icon, int) - Constructor for class ca.ucalgary.seahawk.util.CombinedIcon
 
CombinedIcon(Icon, Icon, int, int) - Constructor for class ca.ucalgary.seahawk.util.CombinedIcon
 
comment - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
COMMENT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
CommentedAASequence - Class in org.inb.biomoby.shared.ontology
 
CommentedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.CommentedAASequence
 
CommentedAASequenceComponent<T extends CommentedAASequence> - Class in org.inb.biomoby.client.gui.ontology
 
CommentedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
CommentedAASequenceComponent(CommentedAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
CommentedAASequenceComponent.CommentedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
CommentedAASubsequence - Class in org.inb.biomoby.shared.ontology
 
CommentedAASubsequence() - Constructor for class org.inb.biomoby.shared.ontology.CommentedAASubsequence
 
CommentedAASubsequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
CommentedAASubsequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
CommentedAASubsequenceComponent(CommentedAASubsequence) - Constructor for class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
CommentedAASubsequenceComponent.CommentedAASubsequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
CommentedDNASequence - Class in org.inb.biomoby.shared.ontology
 
CommentedDNASequence() - Constructor for class org.inb.biomoby.shared.ontology.CommentedDNASequence
 
CommentedNASequence - Class in org.inb.biomoby.shared.ontology
 
CommentedNASequence() - Constructor for class org.inb.biomoby.shared.ontology.CommentedNASequence
 
CommentedNASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
CommentedNASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
CommentedNASequenceComponent(CommentedNASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
CommentedNASequenceComponent.CommentedNASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
CommentedObject - Class in org.inb.biomoby.shared.ontology
 
CommentedObject() - Constructor for class org.inb.biomoby.shared.ontology.CommentedObject
 
CommentedRNASequence - Class in org.inb.biomoby.shared.ontology
 
CommentedRNASequence() - Constructor for class org.inb.biomoby.shared.ontology.CommentedRNASequence
 
CommentedWeightedObject - Class in org.inb.biomoby.shared.ontology
 
CommentedWeightedObject() - Constructor for class org.inb.biomoby.shared.ontology.CommentedWeightedObject
 
CommonBoard - Class in org.biomoby.service.dashboard
This is a simple graphical widget combining together a tree (a subclass of CommonTree) and a progress bar showing how the tree is being loaded.
CommonConsole - Class in org.biomoby.service.dashboard
A simple console component.
CommonConsole() - Constructor for class org.biomoby.service.dashboard.CommonConsole
Constructor.
CommonDataTable - Class in org.biomoby.service.dashboard
A common parent to various swing JTables used for collecting definitions of data (input or ouput) for a service.
CommonDataTable(CommonDataTable.CommonDataTableModel) - Constructor for class org.biomoby.service.dashboard.CommonDataTable
Another constructor.
CommonNode - Class in org.biomoby.service.dashboard
A common node for various tree used in the dashboard.
CommonNode(String) - Constructor for class org.biomoby.service.dashboard.CommonNode
Usual constructor that sets both, meaning and appearance, to the same value.
CommonNode(String, String) - Constructor for class org.biomoby.service.dashboard.CommonNode
Another constructor setting separately meaning ('value') and appearance ('name').
CommonNode(String, int) - Constructor for class org.biomoby.service.dashboard.CommonNode
A constructor that sets both, meaning and appearance, to the same value, and add a node type.
CommonNode(String, String, int) - Constructor for class org.biomoby.service.dashboard.CommonNode
Another constructor setting separately meaning ('value') and appearance ('name'), and a node type.
CommonTree - Class in org.biomoby.service.dashboard
A common JTree re-used (and always slightly modified) by all Biomoby registry trees.
CommonTree(String) - Constructor for class org.biomoby.service.dashboard.CommonTree
Constructor
COMMUNICATION_FAILURE - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: A generic network failure.
COMPARABLE_COMAPRATOR - Static variable in class org.biomoby.service.dashboard.TableSorter
 
compare(MobyService, MobyService) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
compare(T, T) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
compareOutputXML(String) - Method in class org.biomoby.shared.MobyUnitTest
XML is assumed to be wellformed and valid.
compareTo(Object) - Method in class org.biomoby.shared.data.MobyDataFloat
Override BigDecimal.compareTo() because it only compares to other BigInteger.
compareTo(Object) - Method in class org.biomoby.shared.data.MobyDataInt
Override BigInteger.compareTo() because it only compares to other BigInteger.
compareTo(Object) - Method in class org.biomoby.shared.data.MobyDataObject
This method lexically compares in the order of value, ID, name if passed in object is a MobyDataObject.
compareTo(Object) - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
This method lexically compares in the order of value, ID, name if passed in object is a MobyDataObject.
compareTo(MobyDataType) - Method in class org.biomoby.shared.MobyDataType
 
compareTo(MobyNamespace) - Method in class org.biomoby.shared.MobyNamespace
 
compareTo(MobyService) - Method in class org.biomoby.shared.MobyService
Implementing Comparable interface.
compareTo(MobyServiceType) - Method in class org.biomoby.shared.MobyServiceType
 
compareTo(FindServiceOperation.Services.Service) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
compareTo(MobyCentral) - Method in class org.inb.biomoby.central.MobyCentral
 
compareTo(ArrayXYDataComponent.Point) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent.Point
 
compareTo(AbstractEntity) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
compareXmlWithREGEX(String, boolean) - Method in class org.biomoby.shared.MobyUnitTest
 
compareXmlWithXpath(String) - Method in class org.biomoby.shared.MobyUnitTest
 
CompilerProvider - Class in org.inb.util
Applets works with a Java Runtime and thus have no Java compiler accessible.
COMPLETED - Static variable in class org.omg.lsae.notifications.StateEvent
 
componentHidden(ComponentEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
componentMoved(ComponentEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
componentName - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
componentResized(ComponentEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Makes the panels of the tabbed pane have a preferred size to fit within the frame
componentShown(ComponentEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
Config - Class in org.biomoby.registry.rdfagent.util
a class to handle configs for different things.
Config(String) - Constructor for class org.biomoby.registry.rdfagent.util.Config
Create a Config for the specified file
CONFIG_FILE - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The config_file name.
configureServiceFromACDFile(MobyService, File, boolean) - Method in class ca.ucalgary.services.ACDService
Parses the ACD file and sets the MOBY signature parameters appropriately.
confirm(Object) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Return true if confirmation dialog passed.
confirm(Component, Object) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Return true if confirmation dialog passed.
confirmIcon - Static variable in class org.biomoby.service.dashboard.AbstractPanel
 
Consensus_Sequence_Text - Class in org.inb.biomoby.shared.ontology
 
Consensus_Sequence_Text() - Constructor for class org.inb.biomoby.shared.ontology.Consensus_Sequence_Text
 
ConsoleStream - Class in org.biomoby.service.dashboard
A simple stream writing data into given CommonConsole component.
ConsoleStream(CommonConsole, boolean) - Constructor for class org.biomoby.service.dashboard.ConsoleStream
A usual constructor.
Constants - Class in org.biomoby.registry.rdfagent.util
A class that retrieves the constants located in RDFagent.home/RDFagent_config.txt
Constants() - Constructor for class org.biomoby.registry.rdfagent.util.Constants
 
construct() - Method in class org.biomoby.service.dashboard.SwingWorker
Compute the value to be returned by the get method.
consume() - Method in class org.biomoby.client.MobyRequestEvent
Especially useful in that case that there is more than one listener to MobyRequest, denotes that the request has been processed by a listener, and therefore other listeners should probably ignore.
consumeMobyObject(String, MobyDataInstance) - Method in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
Callback routine MobyObjectTransferHandler calls when suitable data has been dropped on this widget.
consumeMobyObject(String, MobyDataInstance) - Method in interface ca.ucalgary.seahawk.gui.MobyObjectReceiver
Callback routine used by MobyObjectTransferHandler once it has resolved the data to paste.
consumes - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
contains(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
contains(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
contains(Object) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns true if this list contains the specified element.
contains(Object) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
contains(Object) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
containsAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
containsAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
containsAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns true if this list contains all of the elements of the specified collection.
containsAll(Collection<?>) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
containsAll(Collection<?>) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
containsHeader(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
containsKey(Object) - Method in class ca.ucalgary.services.util.SourceMap
To check for the presence of a field with a given name
containsKey(Object) - Method in class org.biomoby.shared.data.MobyContentInstance
To check for the presence of a data group with a given name
containsKey(Object) - Method in class org.biomoby.shared.data.MobyDataComposite
To check for the presence of a field with a given name
containsValue(Object) - Method in class ca.ucalgary.services.util.SourceMap
To check for the presence of a value in one of the members (e.g Integer, Float, String, Calendar)
containsValue(Object) - Method in class org.biomoby.shared.data.MobyContentInstance
To check for the presence of a data group as one of the members
containsValue(Object) - Method in class org.biomoby.shared.data.MobyDataComposite
To check for the presence of a value in one of the members (e.g Integer, Float, String, Calendar)
CONTENT_TYPE - Static variable in class org.biomoby.client.AsyncClient
 
CONTEXT_XPTR_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 
convert(String) - Static method in class ca.ucalgary.seahawk.util.TEX2HTML
 
convert(Service) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(Simple) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(Collection) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(Input) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(Output) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.Service) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.ServiceType) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.Parameter) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.Output) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.Input) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.Collection) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.Simple) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(FindServiceOperation.Services.Namespace) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(RetrieveNamespacesOperation.Namespace) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(Relationship<ServiceType>) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(ServiceType) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(RetrieveServiceNamesOperation.ServiceName) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(RetrieveServiceTypesOperation.ServiceType) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
convert(ObjectType) - Static method in class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
ConvertAAtoFASTA_AA - Class in org.biomoby.service.test
Simple service used for exemplary and testing purposes.
ConvertAAtoFASTA_AA() - Constructor for class org.biomoby.service.test.ConvertAAtoFASTA_AA
 
CONVERTER_HOST_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
CONVERTER_PORT_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
convertHTMLToXHTML(byte[]) - Static method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
convertMOBYDataToMOBYRequest(MobyDataInstance) - Method in class org.biomoby.client.MobyRequest
 
convertMOBYDataToMOBYRequest(MobyContentInstance) - Method in class org.biomoby.client.MobyRequest
Creates an XML representation of the data, renamed to fit the needs of the service if necessary, and adding any secondary parameter default values if not already specified in the incoming data.
convertStringToObjects(String) - Static method in class ca.ucalgary.seahawk.util.MobyUtils
 
convertToDisplayable(URL) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
convertToDisplayable(URLConnection) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
A method for converting Microsoft Office documents (and perhaps other formats in the future) into text that Seahawk can load.
convertToString(Transferable, boolean) - Method in class ca.ucalgary.seahawk.gui.FileAndTextTransferHandler
 
convertURLtoMobyBinaryData(MobyClient, URL) - Static method in class ca.ucalgary.seahawk.util.MobyUtils
The purpose of this method is to create a MOBY document to encapsulate a binary data object stored at the given URL.
CpGAnnotatedNASequence - Class in org.inb.biomoby.shared.ontology
 
CpGAnnotatedNASequence() - Constructor for class org.inb.biomoby.shared.ontology.CpGAnnotatedNASequence
 
CpGAnnotation - Class in org.inb.biomoby.shared.ontology
 
CpGAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.CpGAnnotation
 
CpGReport - Class in org.inb.biomoby.shared.ontology
 
CpGReport() - Constructor for class org.inb.biomoby.shared.ontology.CpGReport
 
createAndInstall() - Static method in class org.biomoby.service.dashboard.ExitSecurityManager
Create and install an instance of this exit manager as a new security manager.
createAnnotationChain(String, String, Document) - Method in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
createBoundary() - Static method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Creates a multipart boundary string by concatenating 20 hyphens (-) and the hexadecimal (base-16) representation of the current time in milliseconds.
createConnection(URL) - Static method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Creates a new java.net.URLConnection object from the specified java.net.URL.
CREATED - Static variable in class org.omg.lsae.notifications.StateEvent
 
createDataTypesGraph(MobyDataType[], Properties) - Static method in class org.biomoby.client.Graphviz
Creates a graph connecting 'dataTypes' using their ISA relationship and showing also their HASA children.
createFile(File, String) - Static method in class org.biomoby.shared.Utils
Create a file and fill it with given contents.
createFile(File, StringBuffer) - Static method in class org.biomoby.shared.Utils
Create a file and fill it with given contents.
createFileName(String[]) - Static method in class org.biomoby.service.dashboard.AntModel
Utility to create a filename from pieces, independently on a platform-specific file separator.
createFromXML(Object) - Static method in class org.biomoby.shared.parser.MobyPackage
Constructing a MobyPackage object from XML.
createFromXML(Object, String) - Static method in class org.biomoby.shared.parser.MobyPackage
Constructing a MobyPackage object from XML.
createFromXML(Object, Map<String, String>) - Static method in class org.biomoby.shared.parser.MobyPackage
Constructing a MobyPackage object from XML.
createFromXML(Object) - Static method in class org.biomoby.w3c.addressing.EndpointReference
 
createFromXML(Object) - Static method in class org.omg.lsae.notifications.AnalysisEvent
 
createFromXML(Object) - Static method in class org.soap.SOAPFault
 
createId(String, String, String, long, Properties) - Method in class org.biomoby.client.CentralCachedCallsImpl
Creates an ID of the parameters simply by concatenating them.
createId(String, String, String, long, Properties) - Method in class org.biomoby.client.CentralImpl
 
createId(String, String, String, long, Properties) - Method in class org.biomoby.client.FileCache
It creates an 'id' in the form: rootName / semanticType / { prop1_prop2_... } (time).syntaxType The part between { and } (inclusive) will be replaced by a unique shorter string in order to create a reasonably long real file name.
createId(String, String, String, long, Properties) - Method in interface org.biomoby.client.SimpleCache
Create a unique ID from the given parameters.
createInputSpecString(XHTMLForm) - Method in class ca.ucalgary.services.CGIService
 
createInputSpecString(E) - Method in class ca.ucalgary.services.WrapperService
 
createInputSpecString(WSDLConfig) - Method in class ca.ucalgary.services.WSDLService
 
createInstanceFromDOM(Element) - Static method in class org.biomoby.shared.data.MobyDataObject
This method creates a MobyDataObject of the appropriate subclass for a given input XML tree (e.g. base objects like MobyDataObject and MobyDataInt, or complex objects like MobyDataDateTime or MobyDataComposite, or even a MobyDataSecondaryInstance).
createInstanceFromDOM(Element, Registry) - Static method in class org.biomoby.shared.data.MobyDataObject
 
createInstanceFromString(String, String) - Static method in class org.biomoby.shared.data.MobyDataObject
Construct a primitive data type instance from a string value.
createInstanceFromString(String, String, Registry) - Static method in class org.biomoby.shared.data.MobyDataObject
 
createInstanceFromXML(String) - Static method in class org.biomoby.shared.data.MobyDataObject
Similar to createObjectFromDOM(), but parses the XML for you using the JAXP parser discovery mechanism.
createLiftingRuleAndMakeAvailable(String, String, String, Map<String, String>, Map<String, String>) - Static method in class ca.ucalgary.services.util.RuleCreator
Creates a new MOB rule based on the input xpaths, then uploads that rule to an LSID server.
createMenu(String, int, Icon, Icon) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Create a submenu.
createMenuItem(AbstractAction, String) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Create a menu item.
createMenuItem(AbstractAction, String, int, Icon, Icon) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Create a menu item.
createMenuItem(AbstractAction, String) - Static method in class org.biomoby.service.dashboard.CommonTree
Create a menu item.
createMenuItem(AbstractAction, String, Icon, Icon) - Static method in class org.biomoby.service.dashboard.CommonTree
Create a menu item.
createMobySequence(String, String) - Static method in class ca.ucalgary.seahawk.util.MobyUtils
 
createNode(MobyDataType, String, int, DataTypeNode, HashMap, DataTypeModel) - Static method in class org.biomoby.service.dashboard.data.DataTypeNode
A factory for a node.
createObjectSubMenu(Object, String) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Template object may be one of MobyPrimaryData, or in case of deferred content loading a MobyNamespace, MobyDataType, or MobyPrimaryDataSet.
createOutputSpecString(XHTMLForm) - Method in class ca.ucalgary.services.CGIService
 
createOutputSpecString(E) - Method in class ca.ucalgary.services.WrapperService
 
createOutputSpecString(WSDLConfig) - Method in class ca.ucalgary.services.WSDLService
 
createPayload(String) - Method in class ca.ucalgary.seahawk.gui.MobyPayloadCreator
 
createPayload(String) - Method in interface ca.ucalgary.seahawk.util.MobyPayloadRequestListener
Assumes the listener knows what payload to create based on some internal context stored by the listener.
createPrimitiveType(String, String) - Method in class org.biomoby.shared.MobyObjectDecompositionImpl
 
createRDFModel(Model, MobyService[], boolean) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
 
createSecondaryParameterSchema(String, String, String, String, String, String[]) - Method in class org.biomoby.shared.schema.ServiceInstanceWSDL
 
createSecondarySpecString(XHTMLForm) - Method in class ca.ucalgary.services.CGIService
 
createSecondarySpecString(E) - Method in class ca.ucalgary.services.WrapperService
 
createSecondarySpecString(WSDLConfig) - Method in class ca.ucalgary.services.WSDLService
 
createServiceFromConfig(HttpServletRequest) - Method in class ca.ucalgary.services.ACDService
Determines the command-line program to execute when service requests come in, based on the values for the EMBOSS_ROOT_PARAM and ACD_FILE_PARAM parameters in the servlet configuration.
createServiceFromConfig(HttpServletRequest) - Method in class ca.ucalgary.services.CGIService
 
createServiceFromConfig(HttpServletRequest) - Method in class ca.ucalgary.services.LegacyService
 
createServiceFromConfig(HttpServletRequest, E) - Method in class ca.ucalgary.services.WrapperService
 
createServiceFromConfig(HttpServletRequest) - Method in class ca.ucalgary.services.WSDLService
 
createServiceFromConfig() - Method in class ca.ucalgary.services.WSDLService
 
createServiceFromConfig(HttpServletRequest) - Method in class org.biomoby.service.MobyServlet
 
createServiceInputFileForPeers(MobyContentInstance, MobyDataJob) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Create a temp file that populates the MobyContentInstance from the sample data for all missing fields in peerJobs.
createServicesGraph(ServicesEdge[], Properties) - Static method in class org.biomoby.client.Graphviz
Creates a graph connecting Moby services as defined in a set of the graph 'edges'.
createServicesGraph(ServicesEdge[][], int, int, String[], Properties) - Static method in class org.biomoby.client.Graphviz
Creates a graph connecting Moby services as defined in a set of the graph 'paths'.
createServicesGraph(ServicesEdge[], Properties) - Static method in class org.biomoby.client.RDF
Creates a graph connecting Moby services as defined in a set of the graph 'edges.
createServiceTypesGraph(MobyServiceType[], Properties) - Static method in class org.biomoby.client.Graphviz
Creates a graph connecting 'serviceTypes' using their ISA relationship.
createTempDir(String, File) - Static method in class ca.ucalgary.services.util.TempDir
Creates a temp directory with a generated name (given a certain prefix) in a given directory.
createTransferable(MobyContentInstance) - Static method in class ca.ucalgary.seahawk.util.MobyUtils
 
creator - Static variable in class org.biomoby.client.rdf.vocabulary.DC_PROTEGE
 
CRIB_XML_MODE_OFF - Static variable in class org.biomoby.shared.data.MobyDataXref
 
CRIB_XML_MODE_ON - Static variable in class org.biomoby.shared.data.MobyDataXref
 
CROSSREFERENCE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
CrossReference - Class in org.inb.biomoby.shared.message
 
CrossReference() - Constructor for class org.inb.biomoby.shared.message.CrossReference
 
CSV_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
CSV_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
CSV_MIME - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
CSV_MIME2 - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
CUSTOM_INPUT_PART_OPTION - Static variable in class ca.ucalgary.services.util.PBERecorder
 
CUSTOM_INPUT_PART_VALUES_SUFFIX - Static variable in class ca.ucalgary.services.util.PBERecorder
 
CUSTOM_REGISTRY_DESC - Static variable in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
CUSTOM_REGISTRY_SYNONYM - Static variable in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
CUSTOM_REGISTRY_SYNONYM - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
CUSTOM_VALUE_XPATH_OPTION - Static variable in class ca.ucalgary.services.util.PBERecorder
 

D

DaggooClient - Class in ca.ucalgary.seahawk.services
Simple interface methods to get information from the Daggoo service wrapper database, e.g. is this WSDL already available as Moby services?
DaggooClient() - Constructor for class ca.ucalgary.seahawk.services.DaggooClient
 
DaggooClient.Action - Enum in ca.ucalgary.seahawk.services
The three outcomes possible from asking the user about the URL dropped on Seahawk.
DASGFF - Class in org.inb.biomoby.shared.ontology
 
DASGFF() - Constructor for class org.inb.biomoby.shared.ontology.DASGFF
 
Dashboard - Class in org.biomoby.service.dashboard
Dasboard is a graphical user interface for Biomoby service providers.
Dashboard() - Constructor for class org.biomoby.service.dashboard.Dashboard
Default constructor.
DASHBOARD_CONFIG_FILENAME - Static variable in class org.biomoby.service.dashboard.DashboardConfig
A filename indicating a file containing Dasboard run-time properties.
DashboardConfig - Class in org.biomoby.service.dashboard
An abstract class giving access to the global Dashboard configuration.
DashboardConfig() - Constructor for class org.biomoby.service.dashboard.DashboardConfig
 
DashboardPanel - Interface in org.biomoby.service.dashboard
An interface that must be implemented by each panel that wants to sit on a dashboard.
DashboardProperties - Interface in org.biomoby.service.dashboard
A list of names of most/all recognized properties that can be fired by dashboard panels, and a list of names of Java properties that can be used to configure the dashboard.
DATA - Static variable in interface org.biomoby.service.dashboard.renderers.Renderer
 
Data - Class in org.inb.biomoby.shared.registry
Represents an abstract Moby Central data structure (that can be either "input" or "output")
Data() - Constructor for class org.inb.biomoby.shared.registry.Data
 
DATA_CONTAINER - Static variable in interface org.biomoby.service.dashboard.renderers.Renderer
 
DATA_CONTENTS_PARAM - Static variable in class ca.ucalgary.services.util.RuleCreator
 
DATA_MAPPING_XML_RESOURCE - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
DATA_MAPPING_XSLT_RESOURCE - Static variable in class ca.ucalgary.seahawk.services.TextClient
 
DATA_TIME - Static variable in class org.biomoby.shared.schema.MElement
A moby:DateTime primitive type
DATA_TYPE_LOADED - Static variable in interface org.biomoby.shared.event.Notifier
 
DATA_TYPE_LOADING - Static variable in interface org.biomoby.shared.event.Notifier
 
DATA_TYPES_CANCELLED - Static variable in interface org.biomoby.shared.event.Notifier
 
DATA_TYPES_COUNT - Static variable in interface org.biomoby.shared.event.Notifier
 
DATA_TYPES_END - Static variable in interface org.biomoby.shared.event.Notifier
 
DATA_TYPES_RESET - Static variable in interface org.biomoby.shared.event.Notifier
 
DATA_TYPES_RESOURCE_NAME - Static variable in interface org.biomoby.shared.Central
A name of an ontology describing registered data types.
DATA_TYPES_START - Static variable in interface org.biomoby.shared.event.Notifier
 
DATA_TYPES_UPDATED - Static variable in interface org.biomoby.shared.event.Notifier
 
DATABASECOMMENT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
DATABASENAME - Static variable in interface org.biomoby.shared.parser.MobyTags
 
DATABASEVERSION - Static variable in interface org.biomoby.shared.parser.MobyTags
 
DataComponent - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
DataContainer - Class in org.biomoby.service.dashboard.data
A container for input and output service data.
DataContainer() - Constructor for class org.biomoby.service.dashboard.data.DataContainer
An empty constructor.
DataContainer(Object) - Constructor for class org.biomoby.service.dashboard.data.DataContainer
A usual constructor, filling his container with the given data.
DataContainer(Object, Object) - Constructor for class org.biomoby.service.dashboard.data.DataContainer
A usual constructor, filling his container with the given data.
dataCopied(MobyDataInstance, String, String) - Method in class ca.ucalgary.services.util.PBERecorder
Called by source of data going into the browser, i.e.
DataFlowRecorder - Class in ca.ucalgary.seahawk.util
Takes a browsing history in Seahawk and turns it into a Taverna2 workflow (Programming-by-Example).
DataFlowRecorder(Central) - Constructor for class ca.ucalgary.seahawk.util.DataFlowRecorder
 
DataImportChoiceDialog - Class in ca.ucalgary.seahawk.gui
 
DataImportChoiceDialog(Frame, MobyDataObject[], MobyDataType, MobyNamespace, DataImportChoiceListener) - Constructor for class ca.ucalgary.seahawk.gui.DataImportChoiceDialog
 
DataImportChoiceListener - Interface in ca.ucalgary.seahawk.gui
Callback interface for DataImportChoiceDialog that tells us what data to actually import according to the user's desires.
dataPasted(HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
 
dataPaths(DataServiceEdge[], ServicesEdge[], DataServiceEdge[]) - Static method in class org.biomoby.client.FilterServices
Find all paths (using available 'edges') that start by any of the 'startingEdges' and finish by any of the 'endingEdges'.
DataRecorder - Interface in ca.ucalgary.services.util
This interface allows implementing classes to intercept data as it is proxied between the HTML interface user and the remote Web Service in ca.ucalgary.services.SoapServlet or the remote CGIs in ca.ucalgary.services.CGIServlet .* This interception allows the DataRecorder to save and/or modify the on-the-wire messages to the service.
DATARECORDER_CONTEXTPARAM - Static variable in class ca.ucalgary.services.WrappingServlet
 
DataRecorderTestCase - Class in ca.ucalgary.seahawk.util.test
 
DataRecorderTestCase(String) - Constructor for class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
DataServiceEdge - Class in org.biomoby.client
An instance of this class is a container for a pair of a data type and a Moby service definitions, and for an information how they can be connected.
DataServiceEdge(MobyDataType, MobyService, String) - Constructor for class org.biomoby.client.DataServiceEdge
Constructs an instance with data type as a source and a service as a target, and a connector.
DataServiceEdge(MobyService, MobyDataType, String) - Constructor for class org.biomoby.client.DataServiceEdge
Constructs an instance with data type as a target and a service as a source, and a connector.
datatype - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
datatype - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
datatype - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
DATATYPE_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
DATATYPE_PEERS_MODE - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
DATATYPE_RULE_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
DATATYPE_RULE_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
DataTypeConnector - Class in org.biomoby.client
A simple container for a connection between two data types.
DataTypeConnector() - Constructor for class org.biomoby.client.DataTypeConnector
 
DatatypeGenerator - Class in org.inb.biomoby.generator
 
DatatypeGenerator() - Constructor for class org.inb.biomoby.generator.DatatypeGenerator
 
DataTypeHandler - Class in org.biomoby.registry.sync.handler
Class to synchronize the datatypes in the biomoby centrals.
DataTypeHandler(String) - Constructor for class org.biomoby.registry.sync.handler.DataTypeHandler
 
DataTypeModel - Class in org.biomoby.service.dashboard.data
DataTypeModel is a TreeTableModel representing Biomoby data type with all their members expanded until primitive types found.
DataTypeModel(MobyDataType, MobyDataType[]) - Constructor for class org.biomoby.service.dashboard.data.DataTypeModel
Constructor.
DataTypeNode - Class in org.biomoby.service.dashboard.data
A node in a tree representing a Biomoby data type.
DataTypeParser - Class in org.biomoby.shared.extended
 
DataTypeParser() - Constructor for class org.biomoby.shared.extended.DataTypeParser
Default constructor - need to set the URL for the RDF document that describes the Data Type ontology using setURL(String url) or setURL(URL url)
DataTypeParser(String) - Constructor for class org.biomoby.shared.extended.DataTypeParser
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the Data Type ontology.
DataTypeParser(URL) - Constructor for class org.biomoby.shared.extended.DataTypeParser
Parameterized Constructor that takes in a url for the RDF document that describes the Data Type ontology.
DataTypesBoard - Class in org.biomoby.service.dashboard
This is a simple graphical widget combining together a tree (a subclass of CommonTree) and a progress bar showing how the tree is being loaded.
DataTypesBoard(RegistryModel, CommonConsole, PropertyChannel) - Constructor for class org.biomoby.service.dashboard.DataTypesBoard
Constructor.
DataTypesBoard(RegistryModel, CommonConsole, PropertyChannel, CommonTree) - Constructor for class org.biomoby.service.dashboard.DataTypesBoard
Constructor.
DatatypesGenerationWorker - Class in org.inb.biomoby.generator.gui.worker
 
DatatypesGenerationWorker(File) - Constructor for class org.inb.biomoby.generator.gui.worker.DatatypesGenerationWorker
 
DataTypesGenerator - Class in org.biomoby.service.generator
A generator generating classes representing Biomoby data types.
DataTypesGenerator() - Constructor for class org.biomoby.service.generator.DataTypesGenerator
 
DataTypesGenerator(String) - Constructor for class org.biomoby.service.generator.DataTypesGenerator
 
DataTypesGenerator(String, String, String) - Constructor for class org.biomoby.service.generator.DataTypesGenerator
 
DataTypesGenerator(CentralCached) - Constructor for class org.biomoby.service.generator.DataTypesGenerator
 
DatatypesGeneratorPanel - Class in org.inb.biomoby.generator.gui
 
DatatypesGeneratorPanel() - Constructor for class org.inb.biomoby.generator.gui.DatatypesGeneratorPanel
 
DatatypesModel - Class in org.inb.biomoby.central.model
BioMoby datatypes model implementation class.
DataTypesTree - Class in org.biomoby.service.dashboard
A component showing and manipulating a tree of data types registered by a Biomoby registry.
DataTypesTree(RegistryModel, CommonConsole) - Constructor for class org.biomoby.service.dashboard.DataTypesTree
Constructor.
DataTypesTreeModel - Class in org.inb.biomoby.central.gui.model
TreeModel that contains BioMoby datatype elements.
DataTypesTreeModel() - Constructor for class org.inb.biomoby.central.gui.model.DataTypesTreeModel
 
DataTypeTreeTable - Class in org.biomoby.service.dashboard.data
A tree-table representing one BioMoby data type (with all its children types, both of HAS and HASA relationships).
DataTypeTreeTable(MobyDataType, MobyDataType[]) - Constructor for class org.biomoby.service.dashboard.data.DataTypeTreeTable
Default constructor.
DataUtils - Class in ca.ucalgary.seahawk.util
Contains methods for the storage and retrieval of Seahawk-specific information from Moby XML payloads, specifically in the context of data provenance for programming-by-example.
DataUtils() - Constructor for class ca.ucalgary.seahawk.util.DataUtils
 
DATE_INPUT_PART_OPTION - Static variable in class ca.ucalgary.services.util.PBERecorder
 
DATETIME_TYPE - Static variable in class org.biomoby.shared.MobySecondaryData
 
DateTimeChooser - Class in org.biomoby.service.dashboard.chooser
A Swing component that lets choose date and time.
DateTimeChooser() - Constructor for class org.biomoby.service.dashboard.chooser.DateTimeChooser
Creates a date-time chooser with the curent date as an initial date.
DateTimeChooser(Date) - Constructor for class org.biomoby.service.dashboard.chooser.DateTimeChooser
Creates a date-time chooser with the given date as an initial date.
DateTimeChooserEditor - Class in org.biomoby.service.dashboard.chooser
A cell editor that invokes DateTimeChooser to get a calendar GUI.
DateTimeChooserEditor() - Constructor for class org.biomoby.service.dashboard.chooser.DateTimeChooserEditor
 
DBConnector - Class in org.biomoby.registry.rdfagent.util
 
DBConnector() - Constructor for class org.biomoby.registry.rdfagent.util.DBConnector
Constructor
DC_PROTEGE - Class in org.biomoby.client.rdf.vocabulary
 
DC_PROTEGE() - Constructor for class org.biomoby.client.rdf.vocabulary.DC_PROTEGE
 
DCCP_Text - Class in org.inb.biomoby.shared.ontology
 
DCCP_Text() - Constructor for class org.inb.biomoby.shared.ontology.DCCP_Text
 
de.mpg.mpiz_koeln.featureClient - package de.mpg.mpiz_koeln.featureClient
 
DEAD - Static variable in class org.biomoby.shared.MobyService
 
DebuggingPanel - Class in org.biomoby.service.dashboard
A debugging panel.
DebuggingPanel() - Constructor for class org.biomoby.service.dashboard.DebuggingPanel
Default constructor.
decode(String) - Static method in class org.biomoby.client.util.Base64Coder
Decodes a byte array from Base64 format.
decode(char[]) - Static method in class org.biomoby.client.util.Base64Coder
Decodes a byte array from Base64 format.
decode(char[]) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Decodes a BASE64 encoded char array.
decode(byte[]) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Decodes a BASE64 encoded byte array.
decode(String) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Decodes a BASE64 encoded String.
decodeFast(char[]) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Decodes a BASE64 encoded char array that is known to be resonably well formatted.
decodeFast(byte[]) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Decodes a BASE64 encoded byte array that is known to be resonably well formatted.
decodeFast(String) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Decodes a BASE64 encoded string that is known to be resonably well formatted.
decodeSOAPMessage(Element, StringBuffer, String) - Method in class org.biomoby.client.MobyRequest
 
decodeSOAPMessage(Element, StringBuffer, String, boolean) - Method in class org.biomoby.client.MobyRequest
Isolates the MOBY Data from the SOAP message returned by the remote service host.
decodeString(String) - Static method in class org.biomoby.client.util.Base64Coder
Decodes a string from Base64 format.
DecoratedJScrollPane - Class in org.inb.swing
This is an extended JScrollPane component that paints a background image
DecoratedJScrollPane() - Constructor for class org.inb.swing.DecoratedJScrollPane
 
DecoratedJScrollPane(Component) - Constructor for class org.inb.swing.DecoratedJScrollPane
 
DecoratedJScrollPane(Component, int, int) - Constructor for class org.inb.swing.DecoratedJScrollPane
 
DecoratedJScrollPane(int, int) - Constructor for class org.inb.swing.DecoratedJScrollPane
 
decrementErrorCountForURL(String) - Method in interface org.biomoby.registry.rdfagent.util.CentralDataAccess
 
decrementErrorCountForURL(String) - Method in class org.biomoby.registry.rdfagent.util.CentralDataAccessImpl
 
DEFAULT_AUTHORITY - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
DEFAULT_CENTRAL_IMPL_CLASSNAME - Static variable in class org.biomoby.client.CentralImpl
The class to use for getDefaultCentral if all else fails
DEFAULT_ENDPOINT - Static variable in class org.biomoby.client.CentralImpl
Default location (endpoint) of a Moby registry.
DEFAULT_NAMESPACE - Static variable in class org.biomoby.client.CentralImpl
Default namespace used by the contacted Moby registry.
DEFAULT_REGISTRY_SYNONYM - Static variable in interface org.biomoby.registry.meta.Registries
A synonym (abbreviation) used for a default BioMoby registry.
DEFAULT_STARTUP_PAGE_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
DEFAULT_STATUS_MSG - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
DEFAULT_TEXT_SIZE - Static variable in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
default_value - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
DEFAULT_XSLT_CONVERTER_URL - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
defaultBackground - Static variable in class org.biomoby.service.dashboard.GraphColours
The default background color (white).
defaultColor - Static variable in class org.biomoby.service.dashboard.GraphColours
The default color of last resort in all cases (black).
defaultFillIn(MobyDataSecondaryInstance[]) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
Attempts to fill in all default values for automated submissions
defaultFontcolor - Static variable in class org.biomoby.service.dashboard.GraphColours
The default font color (black).
defaultForeground - Static variable in class org.biomoby.service.dashboard.GraphColours
The default foreground color (black).
DefaultMobyComponent<T extends AbstractMobyObject> - Class in org.inb.biomoby.client.gui
 
DefaultMobyComponent(T) - Constructor for class org.inb.biomoby.client.gui.DefaultMobyComponent
 
DefaultOS - Class in org.biomoby.registry.properties
This class encapsulates the logic needed when a OS cannot be determined.
defaultXOR - Static variable in class org.biomoby.service.dashboard.GraphColours
The default XOR color (light gray).
delete(File) - Static method in class ca.ucalgary.services.util.TempDir
Recursively destroys a directory and its contents.
deleteAllCacheFiles() - Static method in class org.biomoby.registry.meta.RegistryCache
 
deleteErrorCountForURL(String) - Method in interface org.biomoby.registry.rdfagent.util.CentralDataAccess
 
deleteErrorCountForURL(String) - Method in class org.biomoby.registry.rdfagent.util.CentralDataAccessImpl
 
deleteExpiredCacheFiles(long) - Static method in class org.biomoby.registry.meta.RegistryCache
 
deleteService(String, String) - Method in class org.biomoby.registry.rdfagent.util.CentralAdmin
 
DeploymentTable - Class in org.biomoby.service.dashboard
A swing JTable that collects names of services that are going to be deployed, and names of their implementtaion classes.
DeploymentTable() - Constructor for class org.biomoby.service.dashboard.DeploymentTable
Default constructor.
deregisterNamespace(String) - Method in interface org.biomoby.registry.Central.Registry
Deregister a deprecated namespace term
deregisterNamespace(String) - Method in class org.biomoby.registry.Central.RegistryImpl
 
deregisterNamespace(Namespace) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
deregisterNamespace(Namespace) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
DeregisterNamespaceOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
DeregisterNamespaceOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterNamespaceOperation
 
DeregisterNamespaceOperation.DeregisterNamespace - Class in org.inb.biomoby.central.factory.jaxb.registry
 
DeregisterNamespaceOperation.DeregisterNamespace() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterNamespaceOperation.DeregisterNamespace
 
DeregisterNamespaceOperation.DeregisterNamespace(String) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterNamespaceOperation.DeregisterNamespace
 
deregisterObjectClass(String) - Method in interface org.biomoby.registry.Central.Registry
Deregister a deprecated object class.
deregisterObjectClass(String) - Method in class org.biomoby.registry.Central.RegistryImpl
 
deregisterObjectClass(ObjectType) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
deregisterObjectClass(ObjectType) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
DeregisterObjectClassOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
DeregisterObjectClassOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterObjectClassOperation
 
DeregisterObjectClassOperation.DeregisterObjectClass - Class in org.inb.biomoby.central.factory.jaxb.registry
 
DeregisterObjectClassOperation.DeregisterObjectClass() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterObjectClassOperation.DeregisterObjectClass
 
DeregisterObjectClassOperation.DeregisterObjectClass(String) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterObjectClassOperation.DeregisterObjectClass
 
deregisterService(String) - Method in interface org.biomoby.registry.Central.Registry
Deprecated.  
deregisterService(String) - Method in class org.biomoby.registry.Central.RegistryImpl
Deprecated.  
DeregisterServiceOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
DEPRECATED
DeregisterServiceOperation.DeregisterService - Class in org.inb.biomoby.central.factory.jaxb.registry
 
DeregisterServiceOperation.DeregisterService() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceOperation.DeregisterService
 
deregisterServiceType(String) - Method in interface org.biomoby.registry.Central.Registry
Deregister a deprecated service type.
deregisterServiceType(String) - Method in class org.biomoby.registry.Central.RegistryImpl
 
deregisterServiceType(ServiceType) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
deregisterServiceType(ServiceType) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
DeregisterServiceTypeOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
DeregisterServiceTypeOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceTypeOperation
 
DeregisterServiceTypeOperation.DeregisterServiceType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
DeregisterServiceTypeOperation.DeregisterServiceType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceTypeOperation.DeregisterServiceType
 
DeregisterServiceTypeOperation.DeregisterServiceType(String) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceTypeOperation.DeregisterServiceType
 
DESC_HINT - Static variable in class ca.ucalgary.seahawk.gui.WorkflowPreviewDialog
 
DESCENDING - Static variable in class org.biomoby.service.dashboard.TableSorter
 
description - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
description - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
DESCRIPTION - Static variable in interface org.soap.sax.FaultTags
 
DescriptiveFileFilter - Class in ca.ucalgary.seahawk.util
A FileFilter used to provide meaningful extensions and descriptions when using a file dialog.
DescriptiveFileFilter(String, String) - Constructor for class ca.ucalgary.seahawk.util.DescriptiveFileFilter
 
destroy() - Static method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Method to be called when an applet is being decommissioned.
destroy() - Method in class ca.ucalgary.seahawk.gui.splash.SeahawkSplasher
 
destroy(EndpointReference) - Static method in class org.biomoby.client.AsyncClient
Method to be called when all results have been retrieved from a service invocation, or if the client wishes the invocation to be prematurely terminated.
destroy() - Method in class org.biomoby.service.MobyServlet
By default, this method does nothing.
destroy() - Method in class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
destroy() - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
destroy() - Method in interface org.inb.biomoby.service.IAsyncMobyImpl
 
destroyMobyGUI() - Static method in class ca.ucalgary.seahawk.util.MobyUtils
 
DGPI_Report - Class in org.inb.biomoby.shared.ontology
 
DGPI_Report() - Constructor for class org.inb.biomoby.shared.ontology.DGPI_Report
 
DIALOG_MODAL - Static variable in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
DIALOG_TITLE - Static variable in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
DifferentialExpressionTest__Text - Class in org.inb.biomoby.shared.ontology
 
DifferentialExpressionTest__Text() - Constructor for class org.inb.biomoby.shared.ontology.DifferentialExpressionTest__Text
 
DifferentialExpressionTest_Text - Class in org.inb.biomoby.shared.ontology
 
DifferentialExpressionTest_Text() - Constructor for class org.inb.biomoby.shared.ontology.DifferentialExpressionTest_Text
 
DigestReport - Class in org.inb.biomoby.shared.ontology
 
DigestReport() - Constructor for class org.inb.biomoby.shared.ontology.DigestReport
 
DigestReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
DigestReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
DigestReportComponent(DigestReport) - Constructor for class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
DigestReportComponent.DigestReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
dispose() - Method in class org.inb.biomoby.client.gui.auxiliary.JmolPane
 
disposeSplash() - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Closes the splash window.
disposeSplash() - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Closes the splash window.
Distance_Matrix - Class in org.inb.biomoby.shared.ontology
 
Distance_Matrix() - Constructor for class org.inb.biomoby.shared.ontology.Distance_Matrix
 
divide(Number) - Method in class org.biomoby.shared.data.MobyDataFloat
Divide the data value by a number n, using the rounding off mode BigDecimal.ROUND_HALF_EVEN.
divide(Number, int) - Method in class org.biomoby.shared.data.MobyDataFloat
Divide the data value by a number n, using the rounding off mode of your choice from BigDecimal.
divide(Number) - Method in class org.biomoby.shared.data.MobyDataInt
Perform the division operand on the data value.
DNASequence - Class in org.inb.biomoby.shared.ontology
 
DNASequence() - Constructor for class org.inb.biomoby.shared.ontology.DNASequence
 
DOC_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
DOC_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
DOC_MIME - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
DOC_MIME2 - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
DOC_PARAM_SENTINEL - Static variable in class ca.ucalgary.services.SoapServlet
 
docBuilder - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
DOCUMENT_BUILDER_FACTORIES - Static variable in class org.biomoby.client.CentralImpl
Thread local that gives each thread its own DocumentBuilderFactory (since it is not thread-safe).
doEverything() - Method in class org.biomoby.client.BaseCmdLineClient
 
doGet(HttpServletRequest, HttpServletResponse) - Method in interface ca.ucalgary.services.util.DataRecorder
The WrappingServlet may delegate the whole request to the data recorder (if a parameter named after PASSTHROUGH_ACTION is in the GET request).
doGet(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.util.PBERecorder
Called when data in a field is being updated via a paste event.
doGet(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.WrappingServlet
GETs are for form creation
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.biomoby.client.GraphsServlet
An entry point...
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.biomoby.service.MobyServlet
 
doImports(Document, URL) - Static method in class ca.ucalgary.services.SoapServlet
Expand any import or include statements in-place.
doLayout() - Method in class org.inb.biomoby.central.gui.AbstractEntityTreePanel
 
doLayout() - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor.EditorContainer
 
doLayout() - Method in class org.inb.biomoby.client.gui.auxiliary.AssertedWrapperComponent
 
Domain - Class in org.inb.biomoby.shared.ontology
 
Domain() - Constructor for class org.inb.biomoby.shared.ontology.Domain
 
DomainAnnotatedSequence - Class in org.inb.biomoby.shared.ontology
 
DomainAnnotatedSequence() - Constructor for class org.inb.biomoby.shared.ontology.DomainAnnotatedSequence
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.util.PBERecorder
Called when data a form is being submitted, or when submitting the PBE form
doPost(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.WrappingServlet
Post is for service submission (if the wsdl URL is provided), or the PBERecorder (any other case)
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.biomoby.client.GraphsServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.biomoby.service.MobyServlet
 
doubleValue() - Method in class org.biomoby.shared.data.MobyDataFloat
A convenience method, which returns the underlying BigInteger's primitive int representation.
DP_ANT_MODEL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_AUTHENTICATION - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_AXIS_ADMIN - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_AXIS_IN_TOMCAT - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_BGCOLOR - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_CACHE_DIR - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CALL_SERVICE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CBS_DEPLOY - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CONSOLE_FILE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CONTACT - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_CS_CLASS - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CS_NEWURL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CS_NONE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CS_REGISTRY - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_CS_URL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_DATATYPE_NAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_DEFAULT_REGISTRY - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_DEPL_SERVICES - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_DEPLOY_IN_TOMCAT - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_DESCRIPTION - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_DESCRIPTION_FILE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_DETACH_VIEW - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_DOT_LOC - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_ENDPOINT - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_FL_BIOCASE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_FL_HIBERNATE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_FL_NONE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_FL_SOAPLAB - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_HOSTNAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_ICON - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_IMPL_CLASS - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_INP_ASBYTES - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_INP_PING - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_INP_SHOW - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_INP_SHOWXML - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_LOCAL_DEPLOY - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_MOSES_FLAVOUR - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_OUT_FILE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_OUT_SHOW - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_OUT_SHOWXML - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_OUT_VIEWER - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_P_DESCRIPTION - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_P_DESCRIPTION_FILE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_PASSWORD_AUTHENTICATION - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_PATTERN - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_PORT - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_DT_AUTH - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_DT_DESC - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_DT_EMAIL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_DT_NAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_DT_TREE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_INFO - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_NS_AUTH - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_NS_DESC - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_NS_EMAIL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_NS_NAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_AUTH - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_CATEGORY - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_EMAIL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_NAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_RDF_PATH - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_RDF_URL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_TYPE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_URL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_S_XML_PATH - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_ST_AUTH - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_ST_DESC - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_ST_EMAIL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_ST_ISA - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_ST_NAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REG_VERBOSE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REGISTRY_CACHE_DIR - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_REGISTRY_ENDPOINT - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REGISTRY_MODEL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REGISTRY_NAMESPACE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_REGISTRY_SYNONYM - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_RESULT_FILE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_S_SELECTED - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SC_IN_FILE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SC_INPUT_FILE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SC_SERVICE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SC_SERVICE_NAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SC_SERVICES - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SEL_AUTHORITIES - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SEL_SERVICES - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_SERVICE_NAME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_STATUS_MSG - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_TITLE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_TITLE_ICON - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_TOMCAT_HOME - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_AUTHORITATIVE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_CACHE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_DOT - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_DT_COMP - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_DT_DOC - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_DT_GEN - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_DT_JAR - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_S_COMP - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_S_DOC - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_S_GEN - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_S_JAR - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_SIGNATURE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USE_SIMULATE - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_USER_AUTHENTICATION - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_USER_JARS - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
DP_WANTED_REGISTRIES - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
A property name.
DP_WSDD_TEMPL - Static variable in interface org.biomoby.service.dashboard.DashboardProperties
 
dragEnter(DropTargetDragEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
dragExit(DropTargetEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
dragOver(DropTargetDragEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
drawString(Graphics2D, String, StringPainter.ALIGNMENT) - Static method in class org.inb.biomoby.client.gui.StringPainter
 
drop(DropTargetDropEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
dropActionChanged(DropTargetDragEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
DSSP_Text - Class in org.inb.biomoby.shared.ontology
 
DSSP_Text() - Constructor for class org.inb.biomoby.shared.ontology.DSSP_Text
 
DTA_Text - Class in org.inb.biomoby.shared.ontology
 
DTA_Text() - Constructor for class org.inb.biomoby.shared.ontology.DTA_Text
 
DUBLIN_CORE_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
DUBLIN_CORE_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
DUMMY_NAME - Static variable in class org.biomoby.shared.MobyDataType
A dummy name used for MobyDataType instances that do not have (yet) a real name.
DUMMY_NAME - Static variable in class org.biomoby.shared.MobyService
A dummy name used for MobyService instances that do not have (yet) a real name.
DummyMobyObjectFactory - Class in org.inb.biomoby.client.gui.auxiliary
 
DummyMobyObjectFactory() - Constructor for class org.inb.biomoby.client.gui.auxiliary.DummyMobyObjectFactory
 
DynamicJPopupMenu - Class in ca.ucalgary.seahawk.util
This class was created to overcome the basic issue that JPopupMenus do not like to be resized once they have been set visible.
DynamicJPopupMenu() - Constructor for class ca.ucalgary.seahawk.util.DynamicJPopupMenu
 
DynamicMobyComponent<K extends AbstractMobyObject,T extends IDynamicComponent.MobyComponentListener> - Class in org.inb.biomoby.client.gui
 
DynamicMobyComponent() - Constructor for class org.inb.biomoby.client.gui.DynamicMobyComponent
 
DynamicMobyPanel<T extends IDynamicComponent.MobyComponentListener> - Class in org.inb.biomoby.client.gui.auxiliary
 
DynamicMobyPanel() - Constructor for class org.inb.biomoby.client.gui.auxiliary.DynamicMobyPanel
 

E

editingCanceled(ChangeEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
editingStopped(ChangeEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyObjectPropertyTable
 
Element - Class in org.inb.biomoby.shared.ontology
 
Element() - Constructor for class org.inb.biomoby.shared.ontology.Element
 
ELEMENT_NAME - Static variable in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
ElementFloat - Class in org.inb.biomoby.shared.ontology
 
ElementFloat() - Constructor for class org.inb.biomoby.shared.ontology.ElementFloat
 
elementInContextToNameBasedXPath(Element) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Generalizes the element instance into an XPath retrieving it and all similarly nested elements (based on traversing the parent nodes and prepending their names)
ElementInteger - Class in org.inb.biomoby.shared.ontology
 
ElementInteger() - Constructor for class org.inb.biomoby.shared.ontology.ElementInteger
 
ElementString - Class in org.inb.biomoby.shared.ontology
 
ElementString() - Constructor for class org.inb.biomoby.shared.ontology.ElementString
 
ElementXYData - Class in org.inb.biomoby.shared.ontology
 
ElementXYData() - Constructor for class org.inb.biomoby.shared.ontology.ElementXYData
 
EMBL_Text - Class in org.inb.biomoby.shared.ontology
 
EMBL_Text() - Constructor for class org.inb.biomoby.shared.ontology.EMBL_Text
 
EMBOSS_ADV_PARAMS_PARAM - Static variable in class ca.ucalgary.services.ACDService
 
EMBOSS_OUTPUT_PARAM - Static variable in class ca.ucalgary.services.ACDService
 
EMBOSS_PARAMS_PARAM - Static variable in class ca.ucalgary.services.ACDService
 
EMBOSS_ROOT_PARAM - Static variable in class ca.ucalgary.services.ACDService
 
EmowseAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
EmowseAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
encapsulateBinaryData(URL, String) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
 
encapsulateBinaryData(URL, String, Registry) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
 
encode(byte[]) - Static method in class org.biomoby.client.util.Base64Coder
Encodes a byte array into Base64 format.
encode(byte[], int) - Static method in class org.biomoby.client.util.Base64Coder
Encodes a byte array into Base64 format.
ENCODED_MEMBER_NAME - Static variable in class org.biomoby.shared.data.MobyDataBytes
 
encodeRedirectUrl(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
encodeRedirectURL(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
encodeString(String) - Static method in class org.biomoby.client.util.Base64Coder
Encodes a string into Base64 format.
encodeToByte(byte[], boolean) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Encodes a raw byte array into a BASE64 byte[] representation i accordance with RFC 2045.
encodeToChar(byte[], boolean) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Encodes a raw byte array into a BASE64 char[] representation i accordance with RFC 2045.
encodeToString(byte[], boolean) - Static method in class org.inb.biomoby.client.gui.auxiliary.Base64
Encodes a raw byte array into a BASE64 String representation i accordance with RFC 2045.
encodeUrl(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
encodeURL(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
ENCODING_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
ENCODING_ATTR_BASE64_VAL - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
ENCODING_ATTR_NONE_VAL - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
end() - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
end(int) - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
end - Variable in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
endDocument() - Method in class org.biomoby.shared.parser.MobyParser
Called at the end of the parsed document.
endDocument() - Method in class org.omg.lsae.sax.EventParser
Called at the end of the parsed document.
endDocument() - Method in class org.soap.sax.SOAPFaultParser
Called at the end of the parsed document.
endDocument() - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Called at the end of the parsed document.
endElement(String, String, String) - Method in class org.biomoby.shared.parser.MobyParser
Called at the end of an element.
endElement(String, String, String) - Method in class org.omg.lsae.sax.EventParser
Called when an element ends.
endElement(String, String, String) - Method in class org.soap.sax.SOAPFaultParser
Called when an element ends.
endElement(String, String, String) - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Called when an element ends.
EndpointReference - Class in org.biomoby.w3c.addressing
This class models the EndpointReference object described in the WSRF addressing protocol.
EndpointReference() - Constructor for class org.biomoby.w3c.addressing.EndpointReference
Default Constructor
EndpointReferenceParser - Class in org.w3c.addressing.sax
 
EndpointReferenceParser() - Constructor for class org.w3c.addressing.sax.EndpointReferenceParser
 
ENSEMBLHomolog - Class in org.inb.biomoby.shared.ontology
 
ENSEMBLHomolog() - Constructor for class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
EntityTreeCellRenderer - Class in org.inb.biomoby.central.gui.renderer
BioMoby entity (DataType, Service, Namespace...) tree renderer class.
EntityTreeCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.EntityTreeCellRenderer
 
entrySet() - Method in class ca.ucalgary.services.util.SourceMap
Retrieves each field name/value pair for the members of the composite object
entrySet() - Method in class org.biomoby.shared.data.MobyContentInstance
Retrieves each name/data group pair for the members of content.
entrySet() - Method in class org.biomoby.shared.data.MobyDataComposite
Retrieves each field name/MobyDataObject pair for the members of the composite object
enumeration - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
enumeration - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
enumeration - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
Environment - Interface in org.biomoby.registry.properties
An interface for extracting environment variables.
Enzymatic_Text - Class in org.inb.biomoby.shared.ontology
 
Enzymatic_Text() - Constructor for class org.inb.biomoby.shared.ontology.Enzymatic_Text
 
EPR - Static variable in interface org.w3c.addressing.sax.EprTags
 
EprTags - Interface in org.w3c.addressing.sax
EPR specific tag names and attributes.
equals(Object) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
equals(Object) - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
equals(Object) - Method in class ca.ucalgary.services.util.SourceMap
Returns true if and only if both objects have the same fields with the same values, and the same object ID
equals(Object) - Method in class org.biomoby.shared.data.MobyContentInstance
Returns true if and only if both query sets have the same queries with the same values
equals(Object) - Method in class org.biomoby.shared.data.MobyDataComposite
Returns true if and only if both objects have the same fields with the same values, and the same object ID
equals(Object) - Method in class org.biomoby.shared.data.MobyDataFloat
Override BigDecimal.equals() because it only compares to other BigInteger.
equals(Object) - Method in class org.biomoby.shared.data.MobyDataObject
Used to see if two objects are equivalent.
equals(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Compare two MobyDataObject collections.
equals(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
equals(Object) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Compares the specified object with this list for equality.
equals(Object) - Method in class org.biomoby.shared.MobyDataType
 
equals(Object) - Method in class org.biomoby.shared.MobyNamespace
 
equals(Object) - Method in class org.biomoby.shared.MobyService
 
equals(MobyService) - Method in class org.biomoby.shared.MobyService
 
equals(Object) - Method in class org.biomoby.shared.MobyServiceType
 
equals(Object) - Method in class org.biomoby.shared.schema.MElement
 
equals(Object) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
equals(Object) - Method in class org.inb.biomoby.central.MobyCentral
 
equals(Object) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
EquicktandemAnnotatedNASequence - Class in org.inb.biomoby.shared.ontology
 
EquicktandemAnnotatedNASequence() - Constructor for class org.inb.biomoby.shared.ontology.EquicktandemAnnotatedNASequence
 
EquicktandemAnnotatedNASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
EquicktandemAnnotatedNASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
EquicktandemAnnotatedNASequenceComponent(EquicktandemAnnotatedNASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
EquicktandemAnnotatedNASequenceComponent.EquicktandemAnnotatedNASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
EquicktandemAnnotation - Class in org.inb.biomoby.shared.ontology
 
EquicktandemAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.EquicktandemAnnotation
 
EquicktandemAnnotationListPane<T extends EquicktandemAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
EquicktandemAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.EquicktandemAnnotationListPane
 
EquicktandemAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.EquicktandemAnnotationListPane
 
EquicktandemReport - Class in org.inb.biomoby.shared.ontology
 
EquicktandemReport() - Constructor for class org.inb.biomoby.shared.ontology.EquicktandemReport
 
EquicktandemReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
EquicktandemReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
EquicktandemReportComponent(EquicktandemReport) - Constructor for class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
EquicktandemReportComponent.EquicktandemReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
error(String, MobyPackage) - Method in class org.biomoby.service.BaseService
Error handling.
error(Object) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Display an error message.
error(String, Exception) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Display an error message.
ERROR - Static variable in exception org.biomoby.shared.parser.ServiceException
A severity code that corresponds to a fatal error.
error(int, String) - Static method in exception org.biomoby.shared.parser.ServiceException
Create an instance of ServiceException that represents an error.
error(String) - Static method in exception org.biomoby.shared.parser.ServiceException
Create an instance of ServiceException that represents an error.
ERROR_CODE_UNKNOWN - Static variable in exception org.biomoby.shared.data.MobyServiceException
This will be the error code assigned if none is available from the instatiating XML
errorsInResponse(String) - Method in class org.biomoby.client.BaseClient
Extracts errors from a raw service response.
escapeXML(String) - Method in class org.biomoby.client.CentralImpl
Convert non-suitable characters in a XML string into their entity references.
evaluateExceptions(Log, boolean) - Method in class org.biomoby.shared.parser.MobyPackage
Evaluate current exceptions.
evaluateIterativeRule(Matcher, String, String, String, byte[]) - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
Event - Interface in org.inb.lsae
 
eventDispatched(AWTEvent) - Method in class org.inb.swing.LabelButton
 
EventParser - Class in org.omg.lsae.sax
 
EventParser() - Constructor for class org.omg.lsae.sax.EventParser
 
evidenceAbbrevToCode(String) - Static method in class org.biomoby.shared.data.MobyDataXref
Given one of the static final evidence codes from this class, returns the 2 or 3 letter GO evidence abbreviations.
EVIDENCECODE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
evidenceCodeToAbbrev(String) - Static method in class org.biomoby.shared.data.MobyDataXref
Given one of the static final evidence codes from this class, returns the 2 or 3 letter GO evidence abbreviations.
exampleInput - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
ExampleList - Class in org.biomoby.registry.meta
An example how to write a class that adds your own registries to the default list of registries.
ExampleList() - Constructor for class org.biomoby.registry.meta.ExampleList
A default constructor that adds a new registry to the default list.
ExamplePanel - Class in org.biomoby.service.dashboard
A tutorial panel.
ExamplePanel() - Constructor for class org.biomoby.service.dashboard.ExamplePanel
Default constructor.
exception(String, String, Throwable) - Static method in class org.biomoby.registry.rdfagent.util.Log
 
EXCEPTIONCODE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
EXCEPTIONMESSAGE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
executeGet(String, Map<String, byte[]>) - Static method in class ca.ucalgary.services.util.CGIUtils
 
executePost(String, Map<String, byte[]>) - Static method in class ca.ucalgary.services.util.CGIUtils
 
executePostMultipart(String, Map<String, byte[]>, List<String>) - Static method in class ca.ucalgary.services.util.CGIUtils
 
exists(HttpServletRequest, String) - Static method in class org.biomoby.client.GraphsServlet
Return TRUE if the named parameter exists in given 'req' request.
existsInCache(String) - Method in class org.biomoby.client.CentralCachedCallsImpl
 
existsInCache(String) - Method in class org.biomoby.client.CentralImpl
 
existsInCache(String) - Method in class org.biomoby.client.FileCache
It expects the 'id' in the form as created by 'createId'.
existsInCache(String) - Method in interface org.biomoby.client.SimpleCache
Is the object identified by its 'id' already cached?
ExitSecurityManager - Class in org.biomoby.service.dashboard
A security manager allowing to enable and disable usage of System.exit() calls.
ExitSecurityManager() - Constructor for class org.biomoby.service.dashboard.ExitSecurityManager
Default constructor.
exportDocument(MobyContentPane) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
exportDone(JComponent, Transferable, int) - Method in class ca.ucalgary.seahawk.gui.FileAndTextTransferHandler
 
exportDone(String, String) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
Called after data copied from this pane is pasted.
exportDone() - Method in class ca.ucalgary.seahawk.gui.SeahawkTransferable
 
exportHTML(MobyContentPane, File) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
exportMobyContent() - Method in interface ca.ucalgary.seahawk.gui.MobyContentProducer
Callback routine used by MobyObjectTransferHandler once it has resolved the data to paste.
exportMobyContent() - Method in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
Used to send data out to the clipboard.
exportToClipboard(JComponent, Clipboard, int) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
Drag and copy functiunality.
exportWorkflow(MobyContentPane, File) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
exportWorkflow(Map<URL, FilterSearch>, OutputStream, String, String, String, String, int) - Method in class ca.ucalgary.seahawk.util.DataFlowRecorder
Given a MOBY document, traces back the workflow required to create it.
exportXML(MobyContentPane, File) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
expression - Variable in class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
ExpressionCore - Class in org.inb.biomoby.shared.ontology
 
ExpressionCore() - Constructor for class org.inb.biomoby.shared.ontology.ExpressionCore
 
ExpressionStatistics - Class in org.inb.biomoby.shared.ontology
 
ExpressionStatistics() - Constructor for class org.inb.biomoby.shared.ontology.ExpressionStatistics
 
ExtendedProtocolClient - Class in org.biomoby.client
A client that can (additionally to the normal features) communicate with an implementation of a Biomoby service using a non-biomoby protocol.
ExtendedProtocolClient() - Constructor for class org.biomoby.client.ExtendedProtocolClient
 
ExtendedServiceLocator - Class in org.biomoby.client
An extended container allowing to store information how to call a biomoby service using non-biomoby protocols.
ExtendedServiceLocator() - Constructor for class org.biomoby.client.ExtendedServiceLocator
Default constructor.
ExtendedServiceLocator(MobyService) - Constructor for class org.biomoby.client.ExtendedServiceLocator
Another constructor, seeting also a service.
extractExceptions(Element) - Static method in class org.biomoby.shared.parser.JDOMUtils
Extract all exceptions from a serviceNotes XML element.
extractExceptions(Element) - Static method in exception org.biomoby.shared.parser.ServiceException
Extract all exceptions from a serviceNotes XML element.
extractNamespace() - Method in class org.biomoby.client.ServicesEdge
 
extractServices(String) - Method in class org.biomoby.client.CentralImpl
Extract one or more MobyService objects from the given XML piece.
extractServicesFromURL(String) - Method in class org.biomoby.registry.rdfagent.util.SignatureURLConnection
 

F

failed(String) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
FAILED_TAB_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentPane
 
FamilyBLOCKAnnotation - Class in org.inb.biomoby.shared.ontology
 
FamilyBLOCKAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
FamilyBLOCKAnnotationPane<T extends BLOCKAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
FamilyBLOCKAnnotationPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.FamilyBLOCKAnnotationPane
 
FamilyBLOCKAnnotationPane(FamilyBLOCKAnnotation) - Constructor for class org.inb.biomoby.client.gui.auxiliary.FamilyBLOCKAnnotationPane
 
FASTA - Class in org.inb.biomoby.shared.ontology
 
FASTA() - Constructor for class org.inb.biomoby.shared.ontology.FASTA
 
FASTA_AA - Class in org.inb.biomoby.shared.ontology
 
FASTA_AA() - Constructor for class org.inb.biomoby.shared.ontology.FASTA_AA
 
FASTA_AA_multi - Class in org.inb.biomoby.shared.ontology
 
FASTA_AA_multi() - Constructor for class org.inb.biomoby.shared.ontology.FASTA_AA_multi
 
FASTA_NA - Class in org.inb.biomoby.shared.ontology
 
FASTA_NA() - Constructor for class org.inb.biomoby.shared.ontology.FASTA_NA
 
FASTA_NA_multi - Class in org.inb.biomoby.shared.ontology
 
FASTA_NA_multi() - Constructor for class org.inb.biomoby.shared.ontology.FASTA_NA_multi
 
FASTA_pep - Class in org.inb.biomoby.shared.ontology
 
FASTA_pep() - Constructor for class org.inb.biomoby.shared.ontology.FASTA_pep
 
FASTA_Text - Class in org.inb.biomoby.shared.ontology
 
FASTA_Text() - Constructor for class org.inb.biomoby.shared.ontology.FASTA_Text
 
FatiGO__XML - Class in org.inb.biomoby.shared.ontology
 
FatiGO__XML() - Constructor for class org.inb.biomoby.shared.ontology.FatiGO__XML
 
FatiGO_Text - Class in org.inb.biomoby.shared.ontology
 
FatiGO_Text() - Constructor for class org.inb.biomoby.shared.ontology.FatiGO_Text
 
FatiScan__XML - Class in org.inb.biomoby.shared.ontology
 
FatiScan__XML() - Constructor for class org.inb.biomoby.shared.ontology.FatiScan__XML
 
FatiScan_Text - Class in org.inb.biomoby.shared.ontology
 
FatiScan_Text() - Constructor for class org.inb.biomoby.shared.ontology.FatiScan_Text
 
FAULT - Static variable in interface org.soap.sax.FaultTags
 
FAULT_CODE - Static variable in interface org.soap.sax.FaultTags
 
FAULT_DETAIL - Static variable in interface org.soap.sax.FaultTags
 
FAULT_STRING - Static variable in interface org.soap.sax.FaultTags
 
FaultTags - Interface in org.soap.sax
 
FeatureAASequence - Class in org.inb.biomoby.shared.ontology
 
FeatureAASequence() - Constructor for class org.inb.biomoby.shared.ontology.FeatureAASequence
 
FeatureAASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
FeatureAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
FeatureAASequenceComponent(FeatureAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
FeatureAASequenceComponent.FeatureAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
FeatureAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
FeatureAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.FeatureAnnotatedAASequence
 
FeatureAnnotatedAASequenceComponent<T extends FeatureAnnotatedAASequence> - Class in org.inb.biomoby.client.gui.ontology
 
FeatureAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
FeatureAnnotatedAASequenceComponent(FeatureAnnotatedAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
FeatureAnnotatedAASequenceComponent.FeatureAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
FeatureAnnotation - Class in org.inb.biomoby.shared.ontology
 
FeatureAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
FeatureAnnotationComponent - Class in org.inb.biomoby.client.gui.ontology
 
FeatureAnnotationComponent(FeatureAnnotation) - Constructor for class org.inb.biomoby.client.gui.ontology.FeatureAnnotationComponent
 
FeatureAnnotationListPane<T extends FeatureAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
FeatureAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.FeatureAnnotationListPane
 
FeatureAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.FeatureAnnotationListPane
 
FeatureClient - Class in de.mpg.mpiz_koeln.featureClient
It features several things: Calling services with the concrete objects (like AminoAcidSequence) Service discovery based on service name or input/output definition (like return all services which consume an AGI locus code and return PMIDs) Parallelization for multiple service calls Using a timeout if the service does not return in that time Calling a service once with possible different inputs How to use the this client can be learned by looking a the examples found in the de.mpg.mpiz_koeln.featureClient.test.
FeatureClient(Central) - Constructor for class de.mpg.mpiz_koeln.featureClient.FeatureClient
Creates a new FeatureClient instance with the given moby central and the default timeout of 20s.
FeatureClient() - Constructor for class de.mpg.mpiz_koeln.featureClient.FeatureClient
Creates a new FeatureClient instance default the central in Canada.
FeatureClient(Central, long) - Constructor for class de.mpg.mpiz_koeln.featureClient.FeatureClient
Creates a new FeatureClient instance with the given moby central and a given timeout.
FeatureClient.JobIdentifier - Class in de.mpg.mpiz_koeln.featureClient
 
FeatureClient.JobIdentifier(String) - Constructor for class de.mpg.mpiz_koeln.featureClient.FeatureClient.JobIdentifier
 
FeatureClientException - Exception in de.mpg.mpiz_koeln.featureClient
Exception which is thrown in the featureClient project if exceptions occur.
FeatureClientException() - Constructor for exception de.mpg.mpiz_koeln.featureClient.FeatureClientException
 
FeatureClientException(String) - Constructor for exception de.mpg.mpiz_koeln.featureClient.FeatureClientException
 
FeatureClientException(Throwable) - Constructor for exception de.mpg.mpiz_koeln.featureClient.FeatureClientException
 
FeatureClientException(String, Throwable) - Constructor for exception de.mpg.mpiz_koeln.featureClient.FeatureClientException
 
FeatureClientResult - Class in de.mpg.mpiz_koeln.featureClient
The class FeatureClientResult stores the results of a service call from the FeatureClient.
FeatureClientUtility - Class in de.mpg.mpiz_koeln.featureClient
 
FetaVocabulary - Class in org.biomoby.client.rdf.vocabulary
 
FetaVocabulary() - Constructor for class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
FILE_CHOOSER_OPEN_TITLE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
FILE_CHOOSER_SAVE_TITLE - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
FILE_OPEN_OPTION - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
FILE_OPEN_OPTION_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
FileAndTextTransferHandler - Class in ca.ucalgary.seahawk.gui
 
FileAndTextTransferHandler(MobyContentGUI) - Constructor for class ca.ucalgary.seahawk.gui.FileAndTextTransferHandler
By default, opens pasted data in a new tab of the GUI
FileAndTextTransferHandler(MobyContentGUI, boolean) - Constructor for class ca.ucalgary.seahawk.gui.FileAndTextTransferHandler
 
FileCache - Class in org.biomoby.client
A simple cache implementation to save and later return (any) data, or to find that the given data are not available in the cache.
FileCache(String, String) - Constructor for class org.biomoby.client.FileCache
Constructor specifying where to create files with the cached objects.
fillIn(MobyDataSecondaryInstance[]) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
Calling this method makes a GUI pop up that corresponds to the required input parameters.
fillIn(MobyDataSecondaryInstance[], boolean) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
fillIn(MobyPrimaryData[], MobyDataSecondaryInstance[], boolean) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
fillInSecondariesAndExecute() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
fillRequest() - Method in class org.biomoby.client.BaseClient
Create raw XML input.
fillRequest(MobyPackage, int) - Method in class org.biomoby.client.BaseClient
Fill the whole 'mobyInput' - put there any number of jobs (queries) as you wish (you do not need to follow the 'jobCount' hint suggesting how many jobs should be put there).
fillRequest(MobyJob, MobyPackage) - Method in class org.biomoby.client.BaseClient
Crate data (fill them into 'request') for one Moby job (query).
fillRequest(MobyPackage, int) - Method in class org.biomoby.client.BaseCmdLineClient
 
fillRequest() - Method in class org.biomoby.client.BaseCmdLineClient
 
fillRequest(MobyJob, MobyPackage) - Method in class org.biomoby.client.BaseCmdLineClient
 
filter(ServicesEdge[], String[], String[], int) - Static method in class org.biomoby.client.FilterServices
Selects (from the given set of edges) only those edges that start in the nodes defined in 'authorities' or in 'serviceNames', and those that continue not farer then specified in 'depth'.
FILTER_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
FilterDataTypes - Class in org.biomoby.client
Utilities for dealing with a set of MobyDataTypes.
FilterDataTypes() - Constructor for class org.biomoby.client.FilterDataTypes
 
FilteredStream - Class in org.biomoby.client.rdf.builder
 
FilteredStream(OutputStream) - Constructor for class org.biomoby.client.rdf.builder.FilteredStream
 
filterNodes(Node, Map<String, String>) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Loads targetURL, minus the nodes specified by the xpath keys in filteredXPtrs (map values are not currently used).
FilterRuleKeys - Enum in org.biomoby.registry.sync.filtering
Enum class to determine which fields of a service are used to define filtering rules.
FilterSearch - Class in ca.ucalgary.seahawk.util
Holds info to limit the display of information from a document to some combination of a regex match and an XPath.
FilterSearch(String, XPathOption, boolean, boolean) - Constructor for class ca.ucalgary.seahawk.util.FilterSearch
A c-tor to manually populate the filter with a specific set of filter criteria.
FilterSearch(URL, DocumentBuilder) - Constructor for class ca.ucalgary.seahawk.util.FilterSearch
Autopopulates the possible search field values based on the incoming doc
FilterSearchWidget - Class in ca.ucalgary.seahawk.gui
Displays an editable SearchFilter within a MobyContentPane.
FilterSearchWidget(MobyContentPane) - Constructor for class ca.ucalgary.seahawk.gui.FilterSearchWidget
 
FilterServices - Class in org.biomoby.client
This class allows to filter a set of services using some criteria.
FilterServices() - Constructor for class org.biomoby.client.FilterServices
 
findAuthorityWSDL(String) - Method in class org.biomoby.shared.LSIDResolver
 
findClass(String) - Method in class ca.ucalgary.minnow.MinJarMaker
 
findEndingEdges(MobyPrimaryDataSimple, MobyDataType[], MobyService[]) - Static method in class org.biomoby.client.ServiceConnections
 
findFilteredNodes(URL, FilterSearch, Map<String, String>) - Static method in class ca.ucalgary.seahawk.util.DataUtils
For one-off filtering of a doc.
findFilteredNodes(Document, FilterSearch, List<String>, Map<String, String>, Map<String, Boolean>, MutableNodeList, StringBuffer, boolean) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Returns a list of xptrs to filterable nodes in the targetDoc, an populates the list of xptrs that should be filtered according to the provided filter.
findInDataTypes(String) - Method in class org.biomoby.service.dashboard.RegistryModel
Return a HashSet filled with names of data types that have somewhere given 'searchText'.
findInNamespaces(String) - Method in class org.biomoby.service.dashboard.RegistryModel
Return a HashSet filled with names of namespaces that have somewhere given 'searchText'.
findInServices(String) - Method in class org.biomoby.service.dashboard.RegistryModel
Return a Set filled with names of services that have somewhere given 'searchText'.
findInServiceTypes(String) - Method in class org.biomoby.service.dashboard.RegistryModel
Return a Set filled with names of service types that have somewhere given 'searchText'.
findMenuItem(JMenu, String) - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
findMenuItem(JMenu, String, Vector<JMenuItem>) - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
findMobyJobName(Node) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
findNode(ObjectType) - Method in class org.inb.biomoby.central.gui.model.DataTypesTreeModel
 
findResource(String) - Method in class ca.ucalgary.minnow.MinJarMaker
 
findResourceURL(Registry, String) - Static method in class org.biomoby.registry.meta.Registry
Learn the RDF location for resources of the registry.
findService(String, String) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
findService(String, String, String) - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
findService(String) - Method in class org.biomoby.client.CentralImpl
 
findService(String[]) - Method in class org.biomoby.client.CentralImpl
 
findService(MobyService) - Method in class org.biomoby.client.CentralImpl
 
findService(MobyService, String[]) - Method in class org.biomoby.client.CentralImpl
 
findService(MobyService, String[], boolean, boolean) - Method in class org.biomoby.client.CentralImpl
All 'findService' methods end up here.
findService(String, String, boolean) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
PRE: name is either a valid name or null POST: If authorURI is a valid authority, then a RDF containing all of the service instances will be returned.
findService(String, String) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
method that retrieves the RDF describing a specific service instance based on the parameters domain, serviceName.
findService(String, String, String, String, boolean) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
method that retrieves the RDF describing a specific service instance based on the parameters domain, serviceName, url and uri.
findService(String) - Method in interface org.biomoby.registry.Central.Central
Locate a service instance, matching various characteristics, such as the provider name, the kind of input expected by the service, the kind of output it provides, etc.
findService(String) - Method in class org.biomoby.registry.Central.CentralImpl
 
findService(String) - Method in interface org.biomoby.shared.Central
Find services of the given type and its sub-types.
findService(String[]) - Method in interface org.biomoby.shared.Central
Find services by given keywords.
findService(MobyService) - Method in interface org.biomoby.shared.Central
Find services matching whatever is non-empty in the given 'pattern'.
findService(MobyService, String[]) - Method in interface org.biomoby.shared.Central
Find service matching both all non-empty fields in the 'pattern' and the 'keywords'.
findService(MobyService, String[], boolean, boolean) - Method in interface org.biomoby.shared.Central
Find service matching both all non-empty fields in the 'pattern' and the 'keywords', and take into account also the whole ontology tree.
findService(Service, List<String>, boolean, boolean) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
findService(Service, List<String>, boolean, boolean) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
FindServiceOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation
 
FindServiceOperation.FindService - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.FindService() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
FindServiceOperation.FindService(String) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
FindServiceOperation.FindService(String, String) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
FindServiceOperation.FindService.Collection - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.FindService.Collection() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Collection
 
FindServiceOperation.FindService.Input - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.FindService.Input() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Input
 
FindServiceOperation.FindService.InputObjects - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.FindService.InputObjects() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.InputObjects
 
FindServiceOperation.FindService.InputObjects(FindServiceOperation.FindService.Input) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.InputObjects
 
FindServiceOperation.FindService.Output - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.FindService.Output() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Output
 
FindServiceOperation.FindService.OutputObjects - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.FindService.OutputObjects() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.OutputObjects
 
FindServiceOperation.FindService.OutputObjects(FindServiceOperation.FindService.Output) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.OutputObjects
 
FindServiceOperation.FindService.Simple - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.FindService.Simple() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Simple
 
FindServiceOperation.Services - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services
 
FindServiceOperation.Services.Collection - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Collection() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Collection
 
FindServiceOperation.Services.Data - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Data() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Data
 
FindServiceOperation.Services.Input - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Input() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Input
 
FindServiceOperation.Services.Namespace - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Namespace() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Namespace
 
FindServiceOperation.Services.ObjectType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.ObjectType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ObjectType
 
FindServiceOperation.Services.Output - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Output() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Output
 
FindServiceOperation.Services.Parameter - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Parameter() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
FindServiceOperation.Services.SecondaryArticles - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.SecondaryArticles() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.SecondaryArticles
 
FindServiceOperation.Services.Service - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Service() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
FindServiceOperation.Services.Service(String) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
FindServiceOperation.Services.ServiceType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.ServiceType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ServiceType
 
FindServiceOperation.Services.Simple - Class in org.inb.biomoby.central.factory.jaxb.registry
 
FindServiceOperation.Services.Simple() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Simple
 
findStartingEdges(MobyPrimaryDataSimple, MobyDataType[], MobyService[]) - Static method in class org.biomoby.client.ServiceConnections
 
finished() - Method in class org.biomoby.service.dashboard.SwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
fire(String, Object) - Method in class org.biomoby.service.dashboard.PropertyChannel
Fire an event to any registered listeners.
fire(Object, String, Object) - Method in class org.biomoby.service.dashboard.PropertyChannel
Fire an event to any registered listeners.
fireEvent(int, Object, Object) - Method in class org.biomoby.client.CentralDigestImpl
 
fireEvent(NotificationEvent) - Method in class org.biomoby.client.CentralDigestImpl
 
fireEvent(int, Object, Object) - Method in class org.biomoby.service.dashboard.RegistryModel
 
fireEvent(NotificationEvent) - Method in class org.biomoby.service.dashboard.RegistryModel
 
fireEvent(int, Object, Object) - Method in interface org.biomoby.shared.event.Notifier
 
fireEvent(NotificationEvent) - Method in interface org.biomoby.shared.event.Notifier
 
fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
Notify all listeners that underlying tree structure has been changed.
FIXED_PARAMS - Static variable in interface ca.ucalgary.services.Registration
 
fixValue(Object) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
If the given value does not correspond with the type of this node (which happens for empty values) change it to more appropriate value.
FLOAT - Static variable in class org.biomoby.shared.schema.MElement
A moby:Float primitive type
FLOAT_INPUT_PART_OPTION - Static variable in class ca.ucalgary.services.util.PBERecorder
 
FLOAT_TYPE - Static variable in class org.biomoby.shared.MobySecondaryData
 
flush() - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Flushes the stream.
flush() - Method in class org.inb.biomoby.generator.gui.StatusBarHandler
 
flushBuffer() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
focusGained(FocusEvent) - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
focusGained(FocusEvent) - Method in class org.inb.biomoby.central.gui.renderer.MobyNameCellEditor
 
focusLost(FocusEvent) - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
focusLost(FocusEvent) - Method in class org.inb.biomoby.central.gui.renderer.MobyNameCellEditor
 
format - Static variable in class org.biomoby.client.rdf.vocabulary.DC_PROTEGE
 
format(int) - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
format(int) - Method in class org.biomoby.shared.datatypes.MobyObject
Return the same contents as MobyObject.toString() method but indented by level expressed in the parameter 'indent'.
format(int) - Method in class org.biomoby.shared.datatypes.MobyXref
 
format(int) - Method in class org.biomoby.shared.MobyData
 
format(int) - Method in class org.biomoby.shared.MobyDataType
 
format(int) - Method in class org.biomoby.shared.MobyNamespace
 
format(int) - Method in class org.biomoby.shared.MobyPrimaryDataSet
 
format(int) - Method in class org.biomoby.shared.MobyPrimaryDataSimple
 
format(int) - Method in class org.biomoby.shared.MobySecondaryData
 
format(int) - Method in class org.biomoby.shared.MobyServiceType
 
format(int) - Method in class org.biomoby.shared.parser.MobyDataElement
Return the same contents as MobyDataElement.toString() method but indented by level expressed in the parameter 'indent'.
format(int) - Method in class org.biomoby.shared.parser.MobyJob
Return the same contents as MobyJob.toString() method but indented by level expressed in the parameter 'indent'.
format(int) - Method in class org.biomoby.shared.parser.MobyPackage
Return the same contents as MobyPackage.toString() method but indented by level expressed in the parameter 'indent'.
format(int) - Method in exception org.biomoby.shared.parser.ServiceException
Return the same contents as ServiceException.toString() method but indented by level expressed in the parameter 'indent'.
format(Object, int) - Static method in class org.biomoby.shared.Utils
 
formatAndLog(Throwable, Log) - Static method in exception org.biomoby.shared.MobyException
Format given exception 'e' depending on how serious it it.
formatFault(AxisFault, String, QName) - Static method in class org.biomoby.client.CentralImpl
Format an exception.
formatFault(AxisFault, PrintStream, String, QName) - Static method in class org.biomoby.client.CentralImpl
Format an exception.
FORWARD_BUTTON_MSG - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
FORWARD_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
Frame - Class in org.biomoby.shared.schema
 
Frame() - Constructor for class org.biomoby.shared.schema.Frame
 
FromFastaToDNASequence - Class in org.biomoby.service.test
 
FromFastaToDNASequence() - Constructor for class org.biomoby.service.test.FromFastaToDNASequence
 
fromXMLDocument(String) - Static method in class org.biomoby.shared.data.MobyDataUtils
Create a MOBY Java object representation from a MOBY XML payload stored in a String.
fromXMLDocument(String, Registry) - Static method in class org.biomoby.shared.data.MobyDataUtils
 
fromXMLDocument(InputStream) - Static method in class org.biomoby.shared.data.MobyDataUtils
Create a MOBY Java object representation from a MOBY XML payload coming from an InputStream (a byte stream that will becoverted by the parser into character data).
fromXMLDocument(InputStream, Registry) - Static method in class org.biomoby.shared.data.MobyDataUtils
 
fromXMLDocument(URL) - Static method in class org.biomoby.shared.data.MobyDataUtils
Create a MOBY Java object representation from a MOBY XML payload at the given URL.
fromXMLDocument(URL, Registry) - Static method in class org.biomoby.shared.data.MobyDataUtils
 
fromXMLDocument(Reader) - Static method in class org.biomoby.shared.data.MobyDataUtils
Create a MOBY Java object representation from a MOBY XML payload coming from a Reader (character data).
fromXMLDocument(Reader, Registry) - Static method in class org.biomoby.shared.data.MobyDataUtils
 
fromXMLDocument(Element) - Static method in class org.biomoby.shared.data.MobyDataUtils
Create a MOBY Java object representation from a MOBY XML payload represented in a DOM.
fromXMLDocument(Element, Registry) - Static method in class org.biomoby.shared.data.MobyDataUtils
Create a MOBY Java object representation from a MOBY XML payload represented in a DOM.
FSOLV_Text - Class in org.inb.biomoby.shared.ontology
 
FSOLV_Text() - Constructor for class org.inb.biomoby.shared.ontology.FSOLV_Text
 
FSSP_Text - Class in org.inb.biomoby.shared.ontology
 
FSSP_Text() - Constructor for class org.inb.biomoby.shared.ontology.FSSP_Text
 
FULL_FORMAT - Static variable in class org.biomoby.shared.datatypes.MobyDateTime
A string defining (in symbols used in Java's SimpleDateFormat) a full Biomoby DateTime format complying with ISO 8601.
FULL_RESOURCE_NAME - Static variable in interface org.biomoby.shared.Central
A name of an ontology describing all registered entities.
FunCUT_Annotation_XML - Class in org.inb.biomoby.shared.ontology
 
FunCUT_Annotation_XML() - Constructor for class org.inb.biomoby.shared.ontology.FunCUT_Annotation_XML
 

G

GenBank_Text - Class in org.inb.biomoby.shared.ontology
 
GenBank_Text() - Constructor for class org.inb.biomoby.shared.ontology.GenBank_Text
 
generate(Properties) - Method in class org.biomoby.service.generator.DataTypesGenerator
Generate classes for all data types from a given Biomoby registry.
generate(Properties) - Method in class org.biomoby.service.generator.Generator
Generate "things" from a given Biomoby registry.
generate(Properties) - Method in class org.biomoby.service.generator.ServicesGenerator
Generate classes for service(s) from a given Biomoby registry.
generateAccessorClass(List<Service>, ZipOutputStream) - Method in class org.inb.biomoby.generator.ServiceAccessorGenerator
 
generateAll() - Method in class org.inb.biomoby.generator.DatatypeGenerator
 
generateService(Service, ZipOutputStream) - Method in class org.inb.biomoby.generator.ServiceGenerator
 
Generator - Class in org.biomoby.service.generator
A common superclass to all Moses generators.
Generator() - Constructor for class org.biomoby.service.generator.Generator
Default constructor.
Generator(String) - Constructor for class org.biomoby.service.generator.Generator
Another constructor pointing to a cache directory where the retrieved data types are stored.
Generator(String, String, String) - Constructor for class org.biomoby.service.generator.Generator
Another constructor pointing to a cache directory and defining where is a Biomoby registry whoe data types will be generated.
Generator(CentralCached) - Constructor for class org.biomoby.service.generator.Generator
Another constructor getting a ready-to-use accessor (the 'worker') to a, hopefully locally cached, BioMoby registry.
GeneratorPanel - Class in org.biomoby.service.dashboard
A panel allowing to generate Java code for new services using the MoSeS generators.
GeneratorPanel() - Constructor for class org.biomoby.service.dashboard.GeneratorPanel
Default constructor.
GeneratorUtil - Class in org.inb.biomoby.generator
 
GenericSequence - Class in org.inb.biomoby.shared.ontology
 
GenericSequence() - Constructor for class org.inb.biomoby.shared.ontology.GenericSequence
 
GenericSequenceComponent<T extends GenericSequence> - Class in org.inb.biomoby.client.gui.ontology
 
GenericSequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
GenericSequenceComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
GenericSequenceComponent.GenericSequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
GenericSubsequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
GenericSubsequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent
 
GenericSubsequenceComponent(CommentedAASubsequence) - Constructor for class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent
 
GenericSubsequenceComponent.GenericSubsequence - Class in org.inb.biomoby.client.gui.ontology
 
GenericSubsequenceComponent.GenericSubsequence() - Constructor for class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
GenericSubsequenceComponent.GenericSubsequence(CommentedAASubsequence) - Constructor for class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
GenericWindowListener - Class in org.biomoby.shared.schema
 
GenericWindowListener() - Constructor for class org.biomoby.shared.schema.GenericWindowListener
 
get(Object) - Method in class ca.ucalgary.services.util.SourceMap
Retrieves a member of the composite with a given field name.
get(String) - Method in interface org.biomoby.registry.meta.Registries
Return an object with properties of a given BioMoby registry.
get(String) - Method in class org.biomoby.registry.meta.RegistriesList
 
get() - Static method in class org.biomoby.service.dashboard.DashboardConfig
The main method returning a configuration object.
get() - Method in class org.biomoby.service.dashboard.JProgressBarWithCancel
Get the underlying progress bar component.
get(int) - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
Get index-th renderer.
get() - Method in class org.biomoby.service.dashboard.SwingWorker
Return the value created by the construct method.
get(Object) - Method in class org.biomoby.shared.data.MobyContentInstance
Retrieves a member (AbstractMap) of the composite with a given field name.
get(Object) - Method in class org.biomoby.shared.data.MobyDataComposite
Retrieves a member of the composite with a given field name.
get(int) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns the element at the specified position in this list.
get(int) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
get(String) - Method in class org.inb.biomoby.central.model.NamespacesModel
Method to find a BioMoby namespace object by its name
get(int) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
get(int) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
get_3prime() - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
get_3primerev() - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
get_5prime() - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
get_5primerev() - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
get_class() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
get_class() - Method in class org.inb.biomoby.shared.ontology.SCOPDomain
 
getAC() - Method in class org.inb.biomoby.shared.ontology.BLOCKAnnotation
 
getAC() - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
getAC() - Method in class org.inb.biomoby.shared.ontology.MotifAnnotation
 
getAC() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getAC() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getAcceptableData() - Method in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
List of data that we are willing to consume in consumeMobyObject() at the given moment.
getAcceptableData() - Method in interface ca.ucalgary.seahawk.gui.MobyObjectReceiver
List of data that the object is willing to consume in consumeMobyObject() at the given moment.
getAccession() - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
getAccuracy_ratio() - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
getActiveTab() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
getAdditionalParamsSection() - Method in class ca.ucalgary.services.util.ACDFile
 
getAddress() - Method in class org.biomoby.w3c.addressing.EndpointReference
 
getAdvancedParamsSection() - Method in class ca.ucalgary.services.util.ACDFile
 
getAlignment() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getAlignments() - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
getAlignments() - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
getAliphatic() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getAll() - Method in interface org.biomoby.registry.meta.Registries
Return properties of all known BioMoby registries.
getAll() - Method in class org.biomoby.registry.meta.RegistriesList
 
getAllChildren() - Method in class org.biomoby.shared.MobyDataType
Returns all HAS/HASA children for this object and all of its parent classes.
getAllContents(String) - Method in interface ca.ucalgary.seahawk.util.MobyContentCreator
 
getAllContents(String) - Method in class ca.ucalgary.seahawk.util.MobyDataObjectDeferred
 
getAllContents(String) - Method in class ca.ucalgary.seahawk.util.MobyDataObjectDeferredSAI
 
getAllContents(String) - Method in class ca.ucalgary.seahawk.util.MobyDataObjectSetDeferred
 
getAllContents(String) - Method in class ca.ucalgary.seahawk.util.MobyDataObjectSetDeferredSAI
 
getAllelicvariants() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getAllowedValues() - Method in class org.biomoby.shared.MobySecondaryData
 
getAminoAcidSequence() - Method in class org.inb.biomoby.shared.ontology.WeightedAminoAcidSequences
 
getAnnotatedDomain() - Method in class org.inb.biomoby.shared.ontology.DomainAnnotatedSequence
 
getAnnotatedSequence() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getAnnotationHits() - Static method in class org.inb.biomoby.client.gui.auxiliary.DummyMobyObjectFactory
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.AntigenicReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.CpGReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.DigestReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.EquicktandemReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.PatmatdbReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.PatmatmotifsReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.PepNovoReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.RestrictReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.SigcleaveReport
 
getAnnotationHits() - Method in class org.inb.biomoby.shared.ontology.TransmembraneReport
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.AntigenicAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.BlocksAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.CpGAnnotatedNASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotatedNASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.MolWeightsAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.MotifAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.ProbMolWeightsAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotatedNASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.ScoredMotifAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.SigcleaveAnnotatedAASequence
 
getAnnotations() - Method in class org.inb.biomoby.shared.ontology.TransmembraneAnnotatedAASequence
 
getAny() - Method in class org.inb.wsrf.bf2.BaseFaultType.FaultCause
 
getAny() - Method in class org.inb.wsrf.bf2.BaseFaultType
 
getApplicationSection() - Method in class ca.ucalgary.services.util.ACDFile
 
getArchitecture() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getArea() - Method in class org.biomoby.service.dashboard.CommonConsole
Direct access to the text area.
getArgument() - Method in class org.inb.biomoby.shared.ontology.ByoDynTarget
 
getAromatic() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getArray() - Method in class org.inb.biomoby.shared.ontology.MatrixFloat
 
getArray() - Method in class org.inb.biomoby.shared.ontology.MatrixInteger
 
getArray() - Method in class org.inb.biomoby.shared.ontology.MatrixString
 
getArticleName(String) - Method in class org.biomoby.shared.schema.Builder
create an xml schema element for article name attribute of a moby object
getArticleName() - Method in class org.biomoby.shared.schema.MElement
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Collection
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Simple
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Collection
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Simple
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.ObjectType
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Collection
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Simple
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.ObjectType
 
getArticleName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.ObjectType
 
getArticleName() - Method in class org.inb.biomoby.shared.message.AbstractMobyElement
 
getArticleName() - Method in class org.inb.biomoby.shared.registry.Collection
 
getArticleName() - Method in class org.inb.biomoby.shared.registry.ObjectType
 
getArticleName() - Method in class org.inb.biomoby.shared.registry.Parameter
 
getArticleName() - Method in class org.inb.biomoby.shared.registry.Simple
 
getArticleNames(String) - Method in class org.biomoby.shared.schema.MElementHashtable
given a name of Element, find a vector which includes all article names; we also are given a vector of MElement, and here it is called mVector.Normally mVector is hasVector or hasaVector in Builder.java
getAsyncMobyImpl() - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
getAtom() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getAttr(Element, String) - Static method in class org.biomoby.shared.MobyPrefixResolver
Convenience method that matches attributes in the MOBY namespace or, for now at least, with no declared namespace.
getAttribute(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getAttribute(String) - Method in class org.biomoby.service.test.TestServletContext
 
getAttribute(String) - Method in class org.inb.biomoby.shared.message.AnyMobyObject
Method makes public an access to internal properties
getAttributeNames() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getAttributeNames() - Method in class org.biomoby.service.test.TestServletContext
 
getAttributes(String) - Method in class org.inb.biomoby.shared.message.AnyMobyObject
 
getAttributes() - Method in class org.inb.biomoby.shared.message.MobyObject
The method returns all elements (has, hasa as well as inherited from parent elements) Usually there is no need to use this method because datatype generated classes suppose to have apropriate getters and setters for their data.
getAuthor() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getAuthoritativeService() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getAuthority() - Method in class org.biomoby.shared.MobyDataType
Return an authority for this data type.
getAuthority() - Method in class org.biomoby.shared.MobyNamespace
 
getAuthority() - Method in class org.biomoby.shared.MobyService
 
getAuthority() - Method in class org.biomoby.shared.MobyServiceType
 
getAuthority() - Method in class org.biomoby.shared.parser.MobyPackage
Get back the authority serving this package.
getAuthorityComparator() - Static method in class org.biomoby.shared.MobyDataType
Create a comparator for case-insensitive sorting of data types by their authorities.
getAuthorityComparator() - Static method in class org.biomoby.shared.MobyNamespace
 
getAuthorityComparator() - Static method in class org.biomoby.shared.MobyService
Create a comparator for case-insensitive sorting of services by their authorities.
getAuthorityComparator() - Static method in class org.biomoby.shared.MobyServiceType
Create a comparator for case-insensitive sorting of service types by their authorities.
getAuthType() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceOperation.DeregisterService
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
getAuthURI() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
getAuthURI() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
getBadUrlMap() - Method in class org.biomoby.registry.rdfagent.util.SignatureURLConnection
 
getBaseIdentifier() - Method in class org.biomoby.shared.MobyPrefixResolver
We don't really implement this as it can be extremely complicated.
getBasicAnnotation() - Method in class org.inb.biomoby.shared.ontology.AnnotatedDomain
 
getBLOCK_Evalue() - Method in class org.inb.biomoby.shared.ontology.BLOCKAnnotation
 
getBlocks() - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
getBody(HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to insert extra HTML elements into the body (at the start) of the WrappingServlet generates for the user-facing CGI form.
getBody(HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
 
getBodyAsDOM(HttpServletRequest, Document) - Method in interface ca.ucalgary.services.util.DataRecorder
 
getBodyAsDOM(HttpServletRequest, Document) - Method in class ca.ucalgary.services.util.PBERecorder
 
getBodyAttrs(HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to insert extra HTML element attributes into the body element the WrappingServlet generates for the Web Service's CGI form.
getBodyAttrs(HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
 
getBodyAttrsAsDOM(HttpServletRequest, Document) - Method in interface ca.ucalgary.services.util.DataRecorder
 
getBodyAttrsAsDOM(HttpServletRequest, Document) - Method in class ca.ucalgary.services.util.PBERecorder
 
getBoolean(HttpServletRequest, String) - Static method in class org.biomoby.client.GraphsServlet
Return value of a named parameter as boolean.
getBoolean(Object, boolean) - Method in class org.biomoby.service.dashboard.PropertyChannel
 
getBoolean() - Method in class org.inb.biomoby.shared.datatypes.MobyBoolean
 
getBooleanValue() - Method in class org.biomoby.shared.datatypes.MobyBoolean
Return the value of this object as a boolean.
getBorderInsets(Component) - Method in class org.inb.biomoby.client.gui.swing.border.HeaderBorder.EmptyBorder
 
getBorderInsets(Component) - Method in class org.inb.biomoby.client.gui.swing.border.HeaderBorder
 
getBorderInsets(Component) - Method in class org.inb.biomoby.client.gui.swing.border.HRBorder
 
getBorderInsets(Component) - Method in class org.inb.biomoby.client.gui.swing.border.RoundedBorder
 
getBoundary() - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Gets the multipart boundary string being used by this stream.
getBuffer() - Method in class org.biomoby.service.test.StringBufferServletOutputStream
 
getBufferSize() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
getBuilder(String) - Method in class ca.ucalgary.seahawk.services.MobyClient
If a rule was given this name, or url/lsid, the MOBY object builder for the rule is returned.
getButton() - Method in class org.biomoby.service.dashboard.JProgressBarWithCancel
Get the underlying cancel button component.
getButtonEditor(int) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a cell editor for given column, assuming that this column is one of those displaying buttons for adding, cloning and removing HAS siblings.
getButtonRenderer(int) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a cell renderer for given column, assuming that this column is one of those displaying buttons for adding, cloning and removing HAS siblings.
getBytes() - Method in class org.biomoby.shared.data.MobyDataBytes
The same as getObject, but doesn't require a cast of the result
getBytes() - Method in class org.inb.biomoby.shared.datatypes.MobyBinary
 
getCacheAge() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
Return age of the current (whole) cache in millis from the beginning of the Epoch; or -1 if cache is empty, or the age is unknown.
getCacheAge() - Method in interface org.biomoby.shared.CentralCached
Return an age of the current (whole) cache in millis from the beginning of the Epoch; or -1 if cache is empty, or the age is unknown.
getCacheDir() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
Return a directory name representing the current cache.
getCacheExpiry() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
getCacheInfo(String) - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
Return as many properties describing the given part of a cache as possible.
getCacheInfo(String) - Method in interface org.biomoby.shared.CentralCached
Return as many properties describing the given part of a cache as possible.
getCacheInfoFormatted(String) - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
 
getCacheInfoFormatted() - Method in class org.biomoby.service.dashboard.RegistryModel
 
getCacheInfoFormatted(String) - Method in interface org.biomoby.shared.CentralCached
Similar as CentralCached.getCacheInfo(java.lang.String) but formatted into a single string.
getCacheMode() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
It always (again, if it functions as a cache which is when 'cacheDir' is given) reports that caching is disabled (even though for the cumulative results is actually always enabled - but that is obvious from the name of this class, isn't it?).
getCacheMode() - Method in class org.biomoby.client.CentralImpl
Find if caching is currently enabled.
getCacheMode() - Method in interface org.biomoby.shared.Central
Reports whether server responses are being cached or not.
getCallerAddr() - Method in class org.biomoby.service.BaseService
Returns the Internet Protocol (IP) address of the client or last proxy that sent the request.
getCaptureGroupRange(Pattern, int) - Static method in class ca.ucalgary.seahawk.services.RegexParser
 
getCaptureGroupRange(Pattern, int, boolean) - Static method in class ca.ucalgary.seahawk.services.RegexParser
 
getCaptureGroupRegex(Pattern, int) - Static method in class ca.ucalgary.seahawk.services.RegexParser
Parses out the capture group corresponding to the given number in the pattern that produced the given matcher.
getCardinality() - Method in class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor.CardinalityComponent
 
getCaseSensitivity() - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
getCategory() - Method in class org.biomoby.shared.MobyService
 
getCategory() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getCategory() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getCategory() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getCategory() - Method in class org.inb.biomoby.shared.ontology.BasicAnnotation
 
getCategory() - Method in class org.inb.biomoby.shared.registry.Service
 
getCC() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getCDATAEditor(JTable) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a boolean cell editor for given table.
getCDATAFlag() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Get flag indicating whether to use a CDATA wrapper for values of String primitive types.
getCDATARenderer(JTable) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a boolean cell renderer for given table.
getCellCoordinate() - Method in class org.inb.biomoby.shared.ontology.TargetArgument
 
getCellCoordinate_1() - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
getCellCoordinate_2() - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
getCellEditorValue() - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooserEditor
 
getCellEditorValue() - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellEditor
 
getCellEditorValue() - Method in class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor
 
getCellEditorValue() - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor
 
getCellEditorValue() - Method in class org.inb.biomoby.central.gui.renderer.PropertyNameTableCellEditor
 
getCentralCallFile(String, String) - Static method in class org.biomoby.registry.meta.RegistryCache
Reports where the message returned by the call is stored on disk.
getCentralDigest(MobyCentral) - Method in class org.inb.biomoby.central.factory.jaxb.MobyCentralServiceImpl
 
getCentralDigest(MobyCentral) - Static method in class org.inb.biomoby.central.MobyCentralFactory
Factory method to obtain an implementation of MobyCentralOperations interface
getCentralDigest(MobyCentral) - Method in interface org.inb.biomoby.central.MobyCentralService
 
getCentralEndpoint() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getCentralImpl() - Method in class org.biomoby.client.MobyRequest
 
getCentralImpl() - Method in class org.biomoby.service.MobyServlet
Returns the Moby Central server that the service is associated with, based on the web.xml and the servlet annotation.
getChain() - Method in class org.inb.biomoby.shared.ontology.StructureBoundaries
 
getChangeListeners() - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Returns an array of all the ChangeListeners.
getCharacterEncoding() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getCharacterEncoding() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
getCharContent(boolean) - Method in class org.inb.util.MemoryFileManager.JavaSourceFromString
 
getCharged() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getChargeState() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getCharSequence() - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
getCharSequence() - Method in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
getCharSequence() - Method in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent
 
getCharSequence() - Method in class org.inb.biomoby.client.gui.Subsequence
 
getChild(Object, int) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
getChild(int) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return an i-th child of this node.
getChild(String) - Method in class org.biomoby.shared.MobyDataType
Returns the HAS/HASA child with the given name (if it exists) for this object or any of its parent classes.
getChild(Element, String) - Static method in class org.biomoby.shared.parser.JDOMUtils
Get a child by 'name' from 'parent'.
getChildCount(Object) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
getChildCount() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
How many children this node has.
getChildElement(Element, String) - Static method in class org.biomoby.shared.MobyPrefixResolver
Convenience method that matches attributes in the MOBY namespace or, for now at least, with no declared namespace.
getChildElements(Element, String) - Static method in class org.biomoby.shared.MobyPrefixResolver
Convenience method that matches child elements in the MOBY namespace or, for now at least, with no declared namespace. "*" acts as a wildcard.
getChildren() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return children nodes of this node (after loading them if not yet done).
getChildren(Element, Registry) - Static method in class org.biomoby.shared.data.MobyDataObjectSet
 
getChildren() - Method in class org.biomoby.shared.MobyDataType
Return children of this data type, and the way how they are ontologically related to this data type.
getChildText(Element, String) - Static method in class org.biomoby.shared.parser.JDOMUtils
Get text of a child 'name' from 'parent'.
getChoice(String, String[]) - Method in class ca.ucalgary.services.util.PBERecorder
Show the user a set of choices in the browser window, and waits until they pick one before returning.
getClass(String) - Method in interface org.biomoby.shared.datatypes.MapDataTypesIfc
 
getClass(String) - Method in class org.biomoby.shared.datatypes.MapPrimitiveDataTypes
Return a class that represents given data type.
getClassName(String) - Method in interface org.biomoby.shared.datatypes.MapDataTypesIfc
 
getClassName(String) - Method in class org.biomoby.shared.datatypes.MapPrimitiveDataTypes
Return a class name that represents given data type.
getClassNameForPrimitives(String) - Static method in class org.biomoby.shared.datatypes.MapPrimitiveDataTypes
Return a class name that represents given data type.
getClazz() - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
getClazz() - Method in class org.inb.biomoby.central.gui.renderer.PropertyTableCellRenderer
 
getClinicalSynopsis() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getCloseIconArea() - Method in class ca.ucalgary.seahawk.util.CloseTabIcon
 
getClosestSeq() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getCode() - Method in class org.soap.SOAPFault
 
getCollection() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
Get the Java representation of the data in the main clipboard collection.
getCollections() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Data
 
getCollections() - Method in class org.inb.biomoby.shared.registry.Data
 
getColor(char) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
getColorName(Color) - Static method in class org.biomoby.service.dashboard.GraphColours
Return the name of the supplied color.
getColour(String, Color) - Static method in class org.biomoby.service.dashboard.GraphColours
Return the color in the color table with the given name.
getColumnClass(int) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
getColumnClass(int) - Method in class org.biomoby.service.dashboard.TableSorter
 
getColumnClass(int) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
getColumnClass(int) - Method in interface org.biomoby.service.dashboard.treetable.TreeTableModel
Returns the type for column number column.
getColumnClass(int) - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
getColumnClass(int) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
getColumnCount() - Method in class org.biomoby.service.dashboard.data.DataTypeModel
TreeTableModel interface
getColumnCount() - Method in class org.biomoby.service.dashboard.TableSorter
 
getColumnCount() - Method in interface org.biomoby.service.dashboard.treetable.TreeTableModel
Returns the number of available columns.
getColumnCount() - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
getColumnCount() - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
getColumnName(int) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
getColumnName(int) - Method in class org.biomoby.service.dashboard.TableSorter
 
getColumnName(int) - Method in interface org.biomoby.service.dashboard.treetable.TreeTableModel
Returns the name for column number column.
getColumnName(int) - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
getColumnToolTip(int) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
Return a header tool tip for the given column.
getComb() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getCombined_Evalue() - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
getComentary() - Method in class org.inb.biomoby.shared.ontology.SCOPLayerNode
 
getComment() - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
getComment() - Method in class org.biomoby.shared.MobyDataType
Return a comment that is attached to this instance.
getComment() - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
getCommentedAASequence() - Static method in class org.inb.biomoby.client.gui.auxiliary.DummyMobyObjectFactory
 
getComments() - Method in class org.biomoby.registry.rdfagent.util.ServiceProvider
 
getCompiledClasses() - Method in class org.inb.util.MemoryFileManager
 
getCompletedSteps() - Method in class org.omg.lsae.notifications.StepEvent
 
getComplexType(MElement, String) - Method in class org.biomoby.shared.schema.Builder
create a complexType XML schema element for MElement which does not have has or hasa relation with other MElement
getComplexTypeRec(MElement, String, Vector) - Method in class org.biomoby.shared.schema.Builder
recursively get a complexType XML Shema element for MElement; when this MElement does not have has and hasa relation, we use another method called getComplexType;
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.Dashboard
 
getComponent(PropertyChannel) - Method in interface org.biomoby.service.dashboard.DashboardPanel
Return a graphical representation of this panel.
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.DebuggingPanel
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.ExamplePanel
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.GeneratorPanel
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.MobyUnitTestingPanel
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.PerlMoSeSPanel
 
getComponent(PropertyChannel, CommonConsole) - Method in class org.biomoby.service.dashboard.RegistrationDataTypeSubPanel
Panel to register a data type.
getComponent(PropertyChannel, CommonConsole) - Method in class org.biomoby.service.dashboard.RegistrationNamespaceSubPanel
Panel to register a namespace.
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.RegistrationPanel
 
getComponent(PropertyChannel, CommonConsole) - Method in class org.biomoby.service.dashboard.RegistrationServiceSubPanel
Panel to register a service.
getComponent(PropertyChannel, CommonConsole) - Method in class org.biomoby.service.dashboard.RegistrationServiceTypeSubPanel
Panel to register a service type.
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.RegistryPanel
 
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.AbstractRenderer
 
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.Base64Image
 
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.BoxCollectionRenderer
 
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.CollectionRenderer
 
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.ICISPedigreeTree
 
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.PlainText
 
getComponent(DataContainer) - Method in interface org.biomoby.service.dashboard.renderers.Renderer
Return a JComponent displaying (rendering) given data.
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.TabCollectionRenderer
 
getComponent(DataContainer) - Method in class org.biomoby.service.dashboard.renderers.XMLTreeRenderer
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.ResultsPanel
This creates an empty panel, without any data displayed.
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.SimpleClientPanel
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.StatisticsPanel
 
getComponent(PropertyChannel) - Method in class org.biomoby.service.dashboard.UnitTestingResultPanel
This creates an empty panel, without any data displayed.
getComponent() - Method in class org.inb.biomoby.central.gui.renderer.MobyNameCellEditor
 
getConnection() - Method in class org.biomoby.registry.rdfagent.util.DBConnector
 
getConnectionType() - Method in class org.biomoby.client.ServicesEdge
Retrieves connection type.
getConnector() - Method in class org.biomoby.client.ServicesEdge
Retrieves connector.
getConsensus() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getConsensus() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getContact() - Method in class org.biomoby.registry.meta.Registry
Get a contact person who is in charge of this BioMoby registry.
getContactEmail() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
getContactEmail() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
getContactEmail() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
getContent() - Method in class org.biomoby.client.MobyRequestEvent
 
getContent() - Method in class org.inb.biomoby.shared.ontology.Pattern
 
getContent() - Method in class org.inb.biomoby.shared.ontology.Text__plain
 
getContent() - Method in class org.inb.wsrf.bf2.BaseFaultType.ErrorCode
 
getContent() - Method in class org.inb.wsrf.rp2.QueryExpressionType
 
getContent() - Method in class org.inb.wsrf.rp2.QueryResourcePropertiesResponse
 
getContentGUI() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getContentLength() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getContents() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
Get the Java representation of the data on the clipboard (as a MOBY data envelope), including any possible non-standard contents.
getContents(String) - Method in class org.biomoby.client.CentralImpl
 
getContents(String) - Method in class org.biomoby.client.FileCache
This class does not implement this method.
getContents(String) - Method in interface org.biomoby.client.SimpleCache
Return 'data' identified by 'id'.
getContentSize() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Calculates the approximate space available for the content on a pane (i.e. frame size - tab size - status bar)
getContentsXML() - Method in class org.biomoby.client.MobyRequestEvent
 
getContentType(String) - Static method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Gets the content type string suitable for the java.net.URLConnection which includes the multipart boundary string.
getContentType() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getContentType() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
getContext(String) - Method in class org.biomoby.service.test.TestServletContext
 
getContext() - Static method in class org.inb.biomoby.MobyMessageContext
 
getContextPath() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getContextPath() - Method in class org.biomoby.service.test.TestServletContext
 
getContributor() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getCookies() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getCount() - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotation
 
getCpG() - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
getCreation_date() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getCrossReference() - Method in class org.inb.biomoby.shared.message.MobyObject
Return CrossReference block if present
getCrossReferences() - Method in class org.biomoby.shared.data.MobyDataObject
Call this method if you would like to modify the cross references, such as removing items, clearing the collection, etc.
getCrossReferences() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getCterminalMass() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getCterminalTagMass() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getCulprit() - Method in exception org.biomoby.shared.NoSuccessException
Retrieve the culprit.
getCurrentPane() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Returns the current tab's display component, mostly for testing purposes.
getCurrentURL() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
Overrides the default implementation in parent class because the clipboard does not have a standard history.
getCurrentURL() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Returns the URL of the document that is the source of the current tab's display
getCurrentURL() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getCysResMass() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getData() - Method in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
getData() - Method in class org.biomoby.service.dashboard.data.DataContainer
Get data from this container.
getData() - Method in class org.biomoby.service.dashboard.DeploymentTable
Return all data currently available in the table.
getData() - Method in class org.biomoby.service.dashboard.PrimaryDataTable
 
getData() - Method in class org.biomoby.service.dashboard.SecondaryDataTable
 
getData() - Method in class org.biomoby.shared.data.MobyDataJob
 
getData() - Method in class org.biomoby.shared.parser.MobyCollection
Get the contents of this envelope.
getData() - Method in class org.biomoby.shared.parser.MobyJob
Find and return the first data element of type Simple (which may not be the first data element in this job).
getData(String) - Method in class org.biomoby.shared.parser.MobyJob
Find and return a data element of a Simple type that is named by 'name'.
getData(String, String) - Method in class org.biomoby.shared.parser.MobyJob
Find and return a data element of a Simple type that is named by 'name' and has data type 'dataTypeName'.
getData() - Method in class org.biomoby.shared.parser.MobySimple
Return the contents of this envelope.
getData() - Method in class org.inb.biomoby.client.gui.AbstractMobyComponent
 
getData() - Method in class org.inb.biomoby.client.gui.auxiliary.AssertedWrapperComponent
 
getData() - Method in class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedAASequenceDescriptionPane
 
getData() - Method in class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedNASequenceDescriptionMobyComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.AnnotationComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.AnnotationHitsComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.HMMPfam_ReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.Image_EncodedComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.MobyObjectComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.PatternComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
getData() - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
getData(String) - Method in class org.inb.biomoby.shared.message.MobyData
 
getDataElements() - Method in class org.biomoby.shared.parser.MobyJob
Return all data elements stored in this job.
getDataFlowRecorder() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getDataFromFiles(Map<String, MobyPrimaryData>, Iterable<File>) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
getDataFromMobyContents(Map<String, MobyPrimaryData>, MobyContentInstance) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
getDataFromText(Map<String, MobyPrimaryData>, String) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
getDataFromURL(Map<String, MobyPrimaryData>, URL) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
getDataFromURLContents(Map<String, MobyPrimaryData>, URL) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
getDataInstance() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
Returns the underlying data instance we are shadowing
getDataName() - Method in exception org.biomoby.shared.parser.ServiceException
Return an article (data) name of an offending data input.
getDataSet(int) - Method in class org.biomoby.shared.parser.MobyJob
Find and return the 'index'-th data element, assuming that it is a Collection data element.
getDataSet() - Method in class org.biomoby.shared.parser.MobyJob
Find and return the first data element of type Collection (which may not be the first data element in this job).
getDataSet(String) - Method in class org.biomoby.shared.parser.MobyJob
Find and return a data element of a Collection type that is named by 'name'.
getDataSet(String, String) - Method in class org.biomoby.shared.parser.MobyJob
Find and return a data element coming from a Collection type that is named by 'name' and has data type 'dataTypeName'.
getDataThreshold() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getDataType() - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
Reports the data type of the objects returned by matched rules.
getDataType(String) - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getDataType() - Method in class org.biomoby.client.DataServiceEdge
Retrieves the data type (regardless if it is a source or a target data type, there is always only one data type in this class).
getDataType() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a Biomoby data type represented by this node.
getDataType(String) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getDataType(String) - Method in interface org.biomoby.shared.Central
Get definition of the given data type.
getDataType() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getDataType() - Method in class org.biomoby.shared.data.MobyDataObjectSet
Return the least upper bound parent class of all items in the collection.
getDataType() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getDataType(String) - Static method in class org.biomoby.shared.MobyDataType
 
getDataType(String, Registry) - Static method in class org.biomoby.shared.MobyDataType
Retrieves a datatype object from the registry's ontology.
getDataType() - Method in class org.biomoby.shared.MobyPrimaryData
 
getDataType() - Method in class org.biomoby.shared.MobyPrimaryDataSet
Return a data type of the first element of this collection (according the Biomoby API, however, all elements should have the same data type).
getDataType() - Method in class org.biomoby.shared.MobyPrimaryDataSimple
 
getDataType() - Method in class org.biomoby.shared.MobySecondaryData
 
getDatatype() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
getDatatype() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
getDatatype() - Method in class org.inb.biomoby.shared.registry.Parameter
 
getDataTypeName() - Method in class org.biomoby.shared.MobyRelationship
Return a name of a data type that is linked by this relationship.
getDataTypeNames() - Method in class org.biomoby.client.CentralDigestCachedImpl
 
getDataTypeNames() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
 
getDataTypeNames() - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getDataTypeNames() - Method in interface org.biomoby.shared.Central
Get the list of all registered data types.
getDataTypeRelationships(String) - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getDataTypeRelationships(String, String) - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getDataTypeRelationships(String) - Method in interface org.biomoby.shared.Central
Get all relationships of the given 'dataTypeName'.
getDataTypeRelationships(String, String) - Method in interface org.biomoby.shared.Central
Get all relationships of type 'relationshipType' for the given 'dataTypeName'.
getDataTypes() - Method in class org.biomoby.client.CentralDigestCachedImpl
 
getDataTypes() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
 
getDataTypes() - Method in class org.biomoby.client.CentralDigestImpl
 
getDataTypes() - Method in class org.biomoby.client.CentralImpl
 
getDataTypes(Object) - Method in class org.biomoby.service.dashboard.RegistryModel
Fetch data types (from a cache or from a registry).
getDataTypes() - Method in interface org.biomoby.shared.Central
 
getDataTypes() - Method in interface org.biomoby.shared.CentralDigest
Get definition of all known data types.
getDate() - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Gets the current value from the date-time chooser.
getDate() - Static method in class org.biomoby.shared.schema.Builder
get the date of current time
getDate() - Method in class org.inb.biomoby.shared.ontology.BasicAnnotation
 
getDate() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getDateHeader(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getDateTimeVector() - Method in class org.biomoby.shared.schema.PrimitiveVector
get the DateTimeVector field of this object.
getDB() - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotation
 
getDBComment() - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
getDBName() - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
getDBVersion() - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
getDefault() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
getDefault() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
getDefault() - Method in class org.inb.biomoby.shared.registry.Parameter
 
getDefaultCentral() - Static method in class org.biomoby.client.CentralImpl
Using this method to get a Central object will ensure that other parts of the org.biomoby.shared class hierarchy that implicitly check the registry will use the same cache.
getDefaultCentral(Registry) - Static method in class org.biomoby.client.CentralImpl
 
getDefaultRegistry() - Static method in class org.biomoby.registry.meta.RegistryCache
 
getDefaultRegistryEndpoint() - Method in class org.biomoby.service.dashboard.RegistryModel
Return an endpoint (a stringified URL) of a default Moby registry.
getDefaultRegistryNamespace() - Method in class org.biomoby.service.dashboard.RegistryModel
Return a namespace (a URI) used by a default Moby registry.
getDefaultsFile() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
getDefaultURI() - Static method in class org.biomoby.client.CentralImpl
 
getDefaultURL() - Static method in class org.biomoby.client.CentralImpl
 
getDefaultValue() - Method in class org.biomoby.shared.MobySecondaryData
 
getDefinition() - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
getDefinition() - Method in class org.inb.biomoby.shared.ontology.InteractionMethod
 
getDeNovoPeptide() - Method in class org.inb.biomoby.shared.ontology.ProbMolWeightAnnotation
 
getDesc() - Method in class ca.ucalgary.seahawk.util.XPathOption
 
getDescription() - Method in class ca.ucalgary.seahawk.util.DescriptiveFileFilter
Returns the file description
getDescription() - Method in class org.biomoby.registry.meta.Registry
Get a human-readable description of this BioMoby registry.
getDescription() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.Dashboard
 
getDescription() - Method in interface org.biomoby.service.dashboard.DashboardPanel
Return a short description (few lines only) of this panel.
getDescription() - Method in class org.biomoby.service.dashboard.DebuggingPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.ExamplePanel
 
getDescription() - Method in class org.biomoby.service.dashboard.GeneratorPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.MobyUnitTestingPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.PerlMoSeSPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.RegistrationPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.RegistryPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.SimpleClientPanel
 
getDescription() - Method in class org.biomoby.service.dashboard.StatisticsPanel
 
getDescription() - Method in class org.biomoby.shared.data.MobyDataXref
Provided by a called service A, describes in plain English(?)
getDescription() - Method in class org.biomoby.shared.datatypes.MobyXref
Get a human-readable description of this cross reference.
getDescription() - Method in class org.biomoby.shared.MobyDataType
Return a (usually) human readable description of this data type.
getDescription() - Method in class org.biomoby.shared.MobyNamespace
 
getDescription() - Method in class org.biomoby.shared.MobySecondaryData
Return a (usually) human readable description of this parameter.
getDescription() - Method in class org.biomoby.shared.MobyService
 
getDescription() - Method in class org.biomoby.shared.MobyServiceType
 
getDescription() - Method in class org.biomoby.shared.schema.MElement
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.Object
 
getDescription() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.CommentedAASequence
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.CommentedDNASequence
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.CommentedNASequence
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.CommentedObject
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.CommentedRNASequence
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.PDB_Enriched
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.PropertySequence
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getDescription() - Method in class org.inb.biomoby.shared.ontology.WeightedObject
 
getDescription() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
getDescription() - Method in class org.inb.biomoby.shared.registry.Parameter
 
getDescription() - Method in class org.inb.wsrf.bf2.BaseFaultType
 
getDescription() - Method in class org.soap.WSRFFault
 
getDetails() - Method in class org.biomoby.shared.event.NotificationEvent
Return an object with more details about this notification event.
getDevelopmentID() - Method in class org.inb.biomoby.shared.ontology.ExpressionStatistics
 
getDialect() - Method in class org.inb.wsrf.bf2.BaseFaultType.ErrorCode
 
getDialect() - Method in class org.inb.wsrf.rp2.QueryExpressionType
 
getDiameter() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getDifferences() - Method in class org.biomoby.registry.rdfagent.verifier.MobyServiceComparator
 
getDirection() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
getDisplay() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getDoc() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getDocConverterHost() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
May be null (in which case conversions will not be available)
getDocConverterPort() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
getDocumentBuilder() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
getDomain() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getDomain_acc() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getDomain_ID() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getDomains() - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
getDomains() - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
getDraggedData() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getEditingRow() - Method in class org.biomoby.service.dashboard.treetable.JTreeTable
 
getEditorhistory() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getElement(MElement) - Method in class org.biomoby.shared.schema.Builder
the input is a MElement object; we will find all its hasa and has relations with other object; then modify the root element of the output xml file; the root element is the root element of a xml schema xml file.
getElement(T) - Method in class org.inb.biomoby.central.model.AbstractModel
Method returns a model element referenced by a provided one (using equals() method).
getElement() - Method in class org.inb.biomoby.shared.ontology.ArrayFloat
 
getElement() - Method in class org.inb.biomoby.shared.ontology.ArrayInteger
 
getElement() - Method in class org.inb.biomoby.shared.ontology.ArrayString
 
getElementAt(int) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
getElementInstances() - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
getElementInstances() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getElements() - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
getElements() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getElements() - Method in class org.biomoby.shared.MobyPrimaryDataSet
 
getElements() - Method in class org.inb.biomoby.central.model.AbstractModel
 
getElements() - Method in class org.inb.biomoby.central.model.DatatypesModel
Method to get all datatypes from the model
getElements() - Method in class org.inb.biomoby.central.model.MobyCentralModel
Method returns all known (stored in "META-INF/MobyCentralList.xml") BioMoby Registries
getElements() - Method in class org.inb.biomoby.central.model.NamespacesModel
Method to get all namespaces from the model.
getElements() - Method in class org.inb.biomoby.central.model.ServicesModel
Method to get all services from the model
getElements() - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
getEmail() - Method in class org.biomoby.registry.rdfagent.util.ServiceProvider
 
getEmailContact() - Method in class org.biomoby.shared.MobyDataType
Return a contact email.
getEmailContact() - Method in class org.biomoby.shared.MobyNamespace
 
getEmailContact() - Method in class org.biomoby.shared.MobyService
 
getEmailContact() - Method in class org.biomoby.shared.MobyServiceType
 
getEnd() - Method in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
getEnd() - Method in class org.inb.biomoby.client.gui.Subsequence
 
getEnd() - Method in class org.inb.biomoby.shared.ontology.Annotation
 
getEnd() - Method in class org.inb.biomoby.shared.ontology.CommentedAASubsequence
 
getEnd() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getEnd() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getEndpoint() - Method in class org.biomoby.registry.meta.Registry
Get an endpoint (a stringified URL) of this BioMoby registry.
getEndpointReference() - Method in class org.inb.biomoby.shared.wsrf.SubmitResponseWrapper.Body
 
getEndpointReference() - Method in class org.inb.biomoby.shared.wsrf.SubmitResponseWrapper
 
getEndpointURL() - Method in class org.inb.biomoby.central.MobyCentral
 
getEntityTypeList() - Method in class org.inb.biomoby.shared.registry.Relationship
 
getEnum() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
getEnum() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
getEnum() - Method in class org.inb.biomoby.shared.registry.Parameter
 
getEnv() - Method in class org.biomoby.registry.properties.DefaultOS
 
getEnv() - Method in interface org.biomoby.registry.properties.Environment
 
getEnv() - Method in class org.biomoby.registry.properties.MacOS
 
getEnv() - Static method in class org.biomoby.registry.properties.RegistryOS
 
getEnv() - Method in class org.biomoby.registry.properties.UNIX
 
getEnv() - Method in class org.biomoby.registry.properties.Windows
 
getEnv() - Method in class org.biomoby.registry.properties.WindowsNT
 
getEnzyme_name() - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
getErrorCode() - Method in exception org.biomoby.shared.parser.ServiceException
Return an error code associated with this exception.
getErrorCode() - Method in class org.inb.wsrf.bf2.BaseFaultType
 
getErrorCodeAsString() - Method in exception org.biomoby.shared.parser.ServiceException
Return a stringified form of the error code associated with this exception.
getErrorCountForURL(String) - Method in interface org.biomoby.registry.rdfagent.util.CentralDataAccess
 
getErrorCountForURL(String) - Method in class org.biomoby.registry.rdfagent.util.CentralDataAccessImpl
 
getErrors() - Method in class org.biomoby.shared.extended.ServiceInstanceParser
 
getEvalue() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getEvent() - Method in class org.inb.lsae.AnalysisEvent
 
getEvidence() - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
getEvidence() - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotation
 
getEvidenceCode() - Method in class org.biomoby.shared.data.MobyDataXref
Provided by a called service A, indicates the source and strength of the relationship between the Xref (encapsulated in an Object returned by A) and the cross-referenced service B.
getEvidenceCode() - Method in class org.biomoby.shared.datatypes.MobyXref
Get an evidence code.
getExampleInput() - Method in class org.biomoby.shared.MobyUnitTest
Getter: get the example input that you can use to invoke this service
getException() - Method in class org.biomoby.client.MobyRequestEvent
If an invocation failed, the exception that caused the failure will be in here.
getExceptionCode() - Method in class org.inb.biomoby.shared.message.MobyException
 
getExceptionMessage() - Method in class org.inb.biomoby.shared.message.MobyException
 
getExceptions() - Method in class org.biomoby.shared.data.MobyContentInstance
 
getExceptions() - Method in class org.biomoby.shared.parser.MobyPackage
Return all so far set exceptions.
getExceptions() - Method in class org.inb.biomoby.shared.message.MobyContent
Method returns either a list of exceptions or null
getExceptions() - Method in class org.inb.biomoby.shared.message.MobyMessage
 
getExceptions() - Method in class org.inb.biomoby.shared.message.ServiceNotes
 
getExpandRelationship() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
getExportOption(String[]) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getExpressionLevel() - Method in class org.inb.biomoby.shared.ontology.ExpressionStatistics
 
getExpressionPattern() - Method in class org.inb.biomoby.shared.ontology.ExpressionStatistics
 
getExtNumber() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getExtThreshold() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getFaultCause() - Method in class org.inb.wsrf.bf2.BaseFaultType
 
getFaultInfo() - Method in exception org.inb.biomoby.shared.wsrf.fault.InvalidQueryExpressionFault
 
getFaultInfo() - Method in exception org.inb.biomoby.shared.wsrf.fault.InvalidResourcePropertyQNameFault
 
getFaultInfo() - Method in exception org.inb.biomoby.shared.wsrf.fault.QueryEvaluationErrorFault
 
getFaultInfo() - Method in exception org.inb.biomoby.shared.wsrf.fault.ResourceNotDestroyedFault
 
getFaultInfo() - Method in exception org.inb.biomoby.shared.wsrf.fault.ResourceUnavailableFault
 
getFaultInfo() - Method in exception org.inb.biomoby.shared.wsrf.fault.ResourceUnknownFault
 
getFaultInfo() - Method in exception org.inb.biomoby.shared.wsrf.fault.UnknownQueryExpressionDialectFault
 
getFeature() - Method in class org.inb.biomoby.shared.ontology.FeatureAASequence
 
getFilename(String) - Method in class org.biomoby.client.FileCache
 
getFilename(String) - Method in interface org.biomoby.client.SimpleFileCache
Return a fully qualified path to a file that represents the cached object identified by the 'id'.
getFilter() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
Gets the filter criteria currently being applied to the document being viewed.
getFilterRegex() - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
getFirstBlast() - Method in class org.inb.biomoby.shared.ontology.ISS_Report
 
getFirstFixedCharPosition() - Method in interface org.inb.biomoby.client.gui.ISequenceTransformer
 
getFirstFixedCharPosition() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getFirstIcon() - Method in class ca.ucalgary.seahawk.util.CombinedIcon
 
getFirstLevel(MElement, Element) - Method in class org.biomoby.shared.schema.Builder
create the top level of xml schema element for a moby object.
getFirstVisibleChar() - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
getFirstVisibleChar() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getFitness() - Method in class org.inb.biomoby.shared.ontology.MatchingPattern
 
getFixedParams() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getFlattenedPrims(String) - Method in interface org.biomoby.shared.MobyObjectDecomposition
PRE:None.
getFlattenedPrims(String) - Method in class org.biomoby.shared.MobyObjectDecompositionImpl
 
getFloat() - Method in class org.inb.biomoby.shared.datatypes.MobyFloat
 
getFloatValue() - Method in class org.biomoby.shared.datatypes.MobyFloat
Return the value of this object as a numeric object (double).
getFloatVector() - Method in class org.biomoby.shared.schema.PrimitiveVector
get the floatVector field of this object
getFormAction() - Method in class ca.ucalgary.services.util.XHTMLForm
 
getFormEncodingType() - Method in class ca.ucalgary.services.util.XHTMLForm
 
getFormFiles() - Method in class ca.ucalgary.services.util.XHTMLForm
 
getFormMethod() - Method in class ca.ucalgary.services.util.XHTMLForm
 
getFragIonTolerance() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getFrame() - Method in class org.inb.biomoby.shared.ontology.BLOCKAnnotation
 
getFrom() - Method in class org.inb.biomoby.shared.ontology.AnnotationHits
 
getFullNamespaces() - Method in class org.biomoby.client.CentralDigestCachedImpl
 
getFullNamespaces() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
 
getFullNamespaces() - Method in class org.biomoby.client.CentralDigestImpl
 
getFullNamespaces() - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getFullNamespaces() - Method in interface org.biomoby.shared.Central
Get the list of all registered namespaces, with all their attributes.
getFullNamespacesAsArray() - Method in class org.biomoby.registry.definitions.types.JNamespacesSqlImpl
Get all the data in the db regrading namespaces.
getFullObjectsAsArray() - Method in class org.biomoby.registry.definitions.types.JObjectsSqlImpl
method that returns the various object types, object relationship, object type that this relationship is with, the articlename (if it exists), description, the objects lsid, the authority of the creator of the object, the email address of the creator, and the LSID for the relationship this object has with the other object all tab-delimited.
getFullServicesAsArray() - Method in class org.biomoby.registry.definitions.types.JServicesSqlImpl
Get all the data in the db regrading service types.
getFullServiceTypes() - Method in class org.biomoby.client.CentralDigestImpl
 
getFullServiceTypes() - Method in interface org.biomoby.shared.CentralDigest
Get definition of all known service types.
getGaps() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getGeneID() - Method in class org.inb.biomoby.shared.ontology.ExpressionCore
 
getGenericSequence() - Static method in class org.inb.biomoby.client.gui.auxiliary.DummyMobyObjectFactory
 
getGenus() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getGlyphVector(CharSequence) - Method in interface org.inb.biomoby.client.gui.ISequenceTransformer
 
getGlyphVector(CharSequence) - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getHandler(MobyClient) - Static method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
This is how you get an instance of the handler.
getHasaMElements() - Method in class org.biomoby.shared.schema.MElement
 
getHashtable() - Method in class org.biomoby.shared.schema.MElementHashtable
get a hashtabe; the kyes are the names of MElement; the values are vectors containning article names.
getHasMElements() - Method in class org.biomoby.shared.schema.MElement
 
getHead(HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to insert extra HTML into the head element of the HTML the WrappingServlet generates for the Web Service's CGI form.
getHead(HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
 
getHeadAsDOM(HttpServletRequest, Document) - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to insert extra HTML into the head element of the HTML the WrappingServlet generates for the Web Service's CGI form.
getHeadAsDOM(HttpServletRequest, Document) - Method in class ca.ucalgary.services.util.PBERecorder
 
getHeader(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getHeader() - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
getHeader() - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
getHeaderNames() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getHeaders(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getHelp() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getHelp() - Method in class org.biomoby.service.dashboard.Dashboard
 
getHelp() - Method in interface org.biomoby.service.dashboard.DashboardPanel
The help system is centralized in Dashboard itself.
getHelpURL() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getHelpURL() - Method in class org.biomoby.service.dashboard.Dashboard
 
getHelpURL() - Method in interface org.biomoby.service.dashboard.DashboardPanel
Return a URL of this panel's help page.
getHigherRange() - Method in class org.inb.biomoby.shared.ontology.ParametersToVary
 
getHistogram() - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
getHistoryIndex() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getHistorySize() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getHit() - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
getHitcount() - Method in class org.inb.biomoby.shared.ontology.AnnotationHits
 
getHits() - Method in class org.inb.biomoby.shared.ontology.MatchingPattern
 
getHomologous_Superfamily() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getHTMLSource() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getHTTPHeaders() - Method in class org.biomoby.service.BaseService
Returns HTTP headers that were used when delivering a request to this services.
getHydropathy_KD() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getHydropathy_OHM() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getIcon() - Static method in class ca.ucalgary.seahawk.util.CloseTabIcon
 
getIcon() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getIcon() - Method in class org.biomoby.service.dashboard.Dashboard
 
getIcon() - Method in interface org.biomoby.service.dashboard.DashboardPanel
Return an icon decorating this panel.
getIcon() - Method in class org.biomoby.service.dashboard.renderers.AbstractRenderer
 
getIcon() - Method in interface org.biomoby.service.dashboard.renderers.Renderer
An icon for this SPI.
getIconHeight() - Method in class ca.ucalgary.seahawk.util.CombinedIcon
 
getIconHeight() - Method in class ca.ucalgary.seahawk.util.NullIcon
 
getIconURL() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getIconURL() - Method in class org.biomoby.service.dashboard.Dashboard
 
getIconURL() - Method in interface org.biomoby.service.dashboard.DashboardPanel
Return a URL of this panel's icon.
getIconWidth() - Method in class ca.ucalgary.seahawk.util.CombinedIcon
 
getIconWidth() - Method in class ca.ucalgary.seahawk.util.NullIcon
 
getID() - Method in class org.biomoby.client.MobyRequestEvent
 
getId() - Method in class org.biomoby.client.ServicesEdge
 
getId() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return an ID assigned to this node.
getID() - Method in class org.biomoby.shared.data.MobyDataJob
 
getId(Element) - Static method in class org.biomoby.shared.data.MobyDataObject
 
getId() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getId() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getId() - Method in class org.biomoby.shared.datatypes.MobyObject
Get an identifier of this object.
getId() - Method in class org.biomoby.shared.MobyData
 
getId() - Method in class org.biomoby.shared.MobyDataType
Return an ID that is given to this data type during its registration.
getId() - Method in class org.biomoby.shared.MobyNamespace
 
getId() - Method in class org.biomoby.shared.MobyService
Return an ID that is given to this service instance during its registration.
getId() - Method in class org.biomoby.shared.MobyServiceType
 
getId() - Method in class org.biomoby.shared.parser.MobyJob
 
getId() - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
getID() - Method in class org.inb.biomoby.service.resolver.MobyWSRFScopeFeature
 
getId() - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
getID() - Method in class org.inb.biomoby.shared.ontology.MotifAnnotation
 
getID() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getID() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getId() - Method in class org.inb.biomoby.shared.registry.Registration
 
getId() - Method in class org.inb.lsae.AnalysisEvent
 
getIDAttribute() - Method in class org.biomoby.shared.schema.Builder
create an xml schema element for ID attribute 0f a moby object.
getIdentifiabilityCriteria() - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
getImage_Encoded() - Static method in class org.inb.biomoby.client.gui.auxiliary.DummyMobyObjectFactory
 
getImageOptions() - Method in class ca.ucalgary.services.util.XHTMLForm
Lists the named submit buttons, and may contain a special key IMAGE_ANONYMOUS_NAME that denotes that an unnamed submit button can be used.
getIndexOfChild(Object, Object) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
getInitialDate() - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Returns a date that was used to initiate this date-time chooser instance.
getInitParameter(String) - Method in class org.biomoby.service.test.TestServletConfig
 
getInitParameter(String) - Method in class org.biomoby.service.test.TestServletContext
 
getInitParameterNames() - Method in class org.biomoby.service.test.TestServletConfig
 
getInitParameterNames() - Method in class org.biomoby.service.test.TestServletContext
 
getInnerModel() - Method in class org.biomoby.service.dashboard.treetable.JTreeTable
Returns the model that has been passed to this table in its constructor.
getInput() - Method in class org.biomoby.client.MobyRequest
 
getInput() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.InputObjects
 
getInput() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getInput() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getInput() - Method in class org.inb.biomoby.shared.registry.Service
 
getInputDoc(Document) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
getInputObjects() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getInputSample(Document, Registry) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Backtrack from a service result to the input doc sent to the service
getInputSample(Document, String, Registry) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Same as two-arg, but retrieves a specific job's input (or null if not a job name found in the doc).
getInputSection() - Method in class ca.ucalgary.services.util.ACDFile
Returns a list representing the blocks of the section.
getInputStream() - Method in class ca.ucalgary.services.util.SourceMap
Just before we give up the data, set the stream to be the contents of the Map set to date.
getInputStream() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getInputStream() - Method in class org.biomoby.shared.data.MobyDataBytes
Convenience method that returns an InputStream for use in image loaders, file savers, etc.
getInputStream() - Method in class org.biomoby.shared.extended.DataTypeParser
 
getInputStream() - Method in class org.biomoby.shared.extended.NamespaceParser
 
getInputStream(URL) - Static method in class org.biomoby.shared.Utils
Gets an InputStream on a URL
getInputStream() - Method in class org.inb.biomoby.shared.datatypes.MobyBinary
 
getInputStreamContents(InputStream) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
Convenience method to grab all data from a input stream into a String.
getInputURL(Document) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
getInputXPtrs(URL, URL) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Gets a list of XPointers of the style /1/1/1/4/3/1 from targetInputURL that were used as input to the service call that resulted in serviceResultURL.
getInputXSDTypes() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getInstance() - Static method in class org.biomoby.registry.meta.RegistriesList
Create a list of registries as dynamically found using the SPI mechanim.
getInt(String, int) - Static method in class org.biomoby.service.dashboard.DashboardConfig
Get an integer value associated with the given configuration key, or - if not found or not of integer value - get the given default value.
getInteger() - Method in class org.inb.biomoby.shared.datatypes.MobyInteger
 
getIntegerVector() - Method in class org.biomoby.shared.schema.PrimitiveVector
get the integerVector field of this object
getIntegrationMethod() - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
getIntHeader(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getIntScr() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
getIntValue() - Method in class org.biomoby.shared.datatypes.MobyInteger
Return the value of this object as a numeric object (long).
getInvalidServicesFoundInRDF() - Method in class org.biomoby.registry.rdfagent.util.SignatureURLConnection
 
getInvocationId() - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
getIonOffset() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getIonsResidue() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getIonsWindow() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getIssXML() - Method in class org.inb.biomoby.shared.ontology.ISS_Report
 
getIteration() - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
getJavaAttributeName(String) - Static method in class org.inb.biomoby.generator.GeneratorUtil
 
getJavaClassName(String) - Static method in class org.inb.biomoby.generator.GeneratorUtil
 
getJavaCompiler() - Static method in class org.inb.util.CompilerProvider
 
getJavaFileForInput(JavaFileManager.Location, String, JavaFileObject.Kind) - Method in class org.inb.util.MemoryFileManager
 
getJavaFileForOutput(JavaFileManager.Location, String, JavaFileObject.Kind, FileObject) - Method in class org.inb.util.MemoryFileManager
 
getJavaFileName(String) - Static method in class org.inb.biomoby.generator.GeneratorUtil
 
getJmolScript() - Method in class org.inb.biomoby.shared.ontology.PDB_Enriched
 
getJob(int) - Method in class org.biomoby.shared.parser.MobyPackage
Get back a job indicated by its order number.
getJobId() - Method in exception org.biomoby.shared.parser.ServiceException
Return an identifier of an offending job.
getJobs() - Method in class org.biomoby.shared.parser.MobyPackage
Get back all jobs stored here.
getJournal() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ArrayFloat
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ArrayInteger
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ArrayString
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ElementFloat
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ElementInteger
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ElementString
 
getKey() - Method in class org.inb.biomoby.shared.ontology.ElementXYData
 
getKey() - Method in class org.inb.biomoby.shared.ontology.MatrixFloat
 
getKey() - Method in class org.inb.biomoby.shared.ontology.MatrixInteger
 
getKey() - Method in class org.inb.biomoby.shared.ontology.MatrixString
 
getKeywords() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getKeywords() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getLabel(AntigenicAnnotation) - Method in class org.inb.biomoby.client.gui.auxiliary.AntigenicAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.EquicktandemAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.FamilyBLOCKAnnotationPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.FeatureAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.LabeledAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.MolWeightAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.MotifAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.RestrictAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.SigcleaveAnnotationListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.StructureBoundariesListPane
 
getLabel(T) - Method in class org.inb.biomoby.client.gui.auxiliary.TransmembraneAnnotationListPane
 
getLabel() - Method in class org.inb.biomoby.shared.ontology.Distance_Matrix
 
getLabelOfColumns() - Method in class org.inb.biomoby.shared.ontology.NCut_Matrix
 
getLabelOfRows() - Method in class org.inb.biomoby.shared.ontology.NCut_Matrix
 
getLang() - Method in class org.inb.wsrf.bf2.BaseFaultType.Description
 
getLastFixedCharPosition() - Method in interface org.inb.biomoby.client.gui.ISequenceTransformer
 
getLastFixedCharPosition() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getLastVisibleChar() - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
getLastVisibleChar() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getLatestLSID(String, String, String) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
 
getLegend() - Method in class org.inb.biomoby.shared.ontology.Typed_Image
 
getLength() - Method in class ca.ucalgary.seahawk.util.MutableNodeList
 
getLength() - Method in class ca.ucalgary.services.WrappingServlet.MyNodeList
 
getLength() - Method in class org.biomoby.shared.MobyPrefixResolver.MobyNodeList
 
getLength() - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
getLength() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getLength() - Method in class org.inb.biomoby.shared.ontology.VirtualSequence
 
getLineage() - Method in class org.biomoby.shared.MobyDataType
A convenience method for retrieving the entire inheritance tree for this MOBY object class.
getLineage() - Method in class org.biomoby.shared.MobyServiceType
 
getListAcc() - Method in class org.inb.biomoby.shared.ontology.NCut_Matrix
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class ca.ucalgary.seahawk.gui.DataImportChoiceDialog
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.inb.biomoby.central.gui.RegistryComboBox.RegistryComboBoxRenderer
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeListCellRenderer
 
getListeners() - Method in class org.inb.biomoby.client.gui.auxiliary.DynamicMobyPanel
 
getListeners() - Method in class org.inb.biomoby.client.gui.DynamicMobyComponent
 
getListeners() - Method in class org.inb.biomoby.client.gui.MobyMessageQueue
 
getLoadedClasses() - Method in class ca.ucalgary.minnow.MinJarMaker
 
getLocalAddr() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getLocalCentral() - Static method in class org.biomoby.registry.sync.CentralFactory
Returns the local central.
getLocalClass() - Method in class org.biomoby.client.ExtendedServiceLocator
Get a name of a local class that represents (implements) a service.
getLocale() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getLocale() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
getLocales() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getLocalName() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getLocalPort() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getLog() - Method in class org.inb.biomoby.shared.ontology.NAMD_Output
 
getLongName() - Method in class org.biomoby.registry.meta.Registry
Get a full name of this BioMoby registry.
getLookAndFeelMenu(String, Icon, JFrame) - Static method in class org.biomoby.service.dashboard.LookAndFeelUtils
Create a menu whose sub-menu items - when invoked - change Look and Feel of the whole application (represented by the given 'frame').
getLowerRange() - Method in class org.inb.biomoby.shared.ontology.ParametersToVary
 
getLSID() - Method in interface org.biomoby.shared.LSIDAccessible
 
getLSID() - Method in class org.biomoby.shared.MobyDataType
Return LSID representing this data type definition.
getLSID() - Method in class org.biomoby.shared.MobyNamespace
 
getLSID() - Method in class org.biomoby.shared.MobySecondaryData
 
getLSID() - Method in class org.biomoby.shared.MobyService
 
getLSID() - Method in class org.biomoby.shared.MobyServiceType
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Namespace
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ObjectType
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ServiceType
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.AbstractType
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.Relationship
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.ObjectType
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.Relationship
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.Object
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Object
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
getLsid() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
getLsid() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
getLsid() - Method in class org.inb.biomoby.shared.registry.Relationship
 
getLutefiskPeptide() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
getMajorVersion() - Method in class org.biomoby.service.test.TestServletContext
 
getMappingSize() - Method in interface org.biomoby.shared.datatypes.MapDataTypesIfc
 
getMappingSize() - Method in class org.biomoby.shared.datatypes.MapPrimitiveDataTypes
 
getMasterCentral() - Static method in class org.biomoby.registry.sync.CentralFactory
Returns the master central.
getMatrix() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getMaturePeptide() - Method in class org.inb.biomoby.shared.ontology.SigcleaveAnnotation
 
getMax() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
getMax() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
getMax() - Method in class org.inb.biomoby.shared.registry.Parameter
 
getMax_score_pos() - Method in class org.inb.biomoby.shared.ontology.AntigenicAnnotation
 
getMaximumSize() - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
getMaximumSize() - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
getMaximumSize() - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
getMaximumSize() - Method in class org.inb.biomoby.client.gui.ontology.RulesComponent
 
getMaximumSize() - Method in class org.inb.biomoby.client.gui.ontology.StructureDomainComponent
 
getMaximumSize() - Method in class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
getMaximumValue() - Method in class org.biomoby.shared.MobySecondaryData
 
getMaxValue() - Method in class org.biomoby.shared.MobySecondaryData
 
getMemberName() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a member name (article name) assigned to this node.
getMessage() - Method in class org.biomoby.shared.event.NotificationEvent
Return a message associated with this notification event.
getMessage() - Method in exception org.biomoby.shared.parser.ServiceException
Return an error message associated with this exception.
getMessage() - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
getMessage() - Method in class org.inb.biomoby.shared.registry.Registration
 
getMessage() - Method in class org.inb.lsae.AnalysisEvent
 
getMessage() - Method in class org.omg.lsae.notifications.AnalysisEvent
 
getMetadata() - Method in class org.biomoby.service.dashboard.data.DataContainer
Get metadata from this container.
getMethod() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getMethod() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getMethod() - Method in class org.inb.biomoby.shared.ontology.Interaction
 
getMicroarraydata() - Method in class org.inb.biomoby.shared.ontology.Clustering
 
getMicroarraydata() - Method in class org.inb.biomoby.shared.ontology.HierarchicalClustering
 
getMimeType(String) - Method in class org.biomoby.service.test.TestServletContext
 
getMimeType() - Method in class org.inb.biomoby.shared.ontology.Image_Encoded
 
getMimeTypte() - Method in class org.inb.biomoby.shared.ontology.Zip_Encoded
 
getMin() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
getMin() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
getMin() - Method in class org.inb.biomoby.shared.registry.Parameter
 
getMinimumSize() - Method in class org.inb.biomoby.client.gui.auxiliary.ScrollableTextPane
 
getMinimumValue() - Method in class org.biomoby.shared.MobySecondaryData
 
getMinorVersion() - Method in class org.biomoby.service.test.TestServletContext
 
getMinValue() - Method in class org.biomoby.shared.MobySecondaryData
 
getMobyCentral() - Static method in class org.biomoby.registry.properties.MobyCentralConfig
A method that retrieves the mySQL connection details for the database mobycentral.
getMobyCentralImpl() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
getMobyCentralImpl() - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
getMobyCentralImpl() - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getMobyClient() - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
getMobyComponent(AbstractMobyObject) - Static method in class org.inb.biomoby.client.gui.ontology.MobyComponentFactory
 
getMobyContent() - Method in class org.inb.biomoby.shared.message.MobyMessage
 
getMobyContentGUI(JLabel) - Static method in class ca.ucalgary.seahawk.util.MobyUtils
 
getMobyContents(HttpServletRequest) - Method in class org.biomoby.service.MobyServlet
 
getMobyData(String) - Method in class org.inb.biomoby.shared.message.MobyMessage
 
getMobyDataElements() - Method in class org.inb.biomoby.shared.message.MobyData
 
getMobyDataList() - Method in class org.inb.biomoby.shared.message.MobyContent
 
getMobyDataList() - Method in class org.inb.biomoby.shared.message.MobyMessage
 
getMobyDataTypesFromRDF() - Method in class org.biomoby.shared.extended.DataTypeParser
 
getMobyId() - Method in class org.inb.biomoby.shared.message.AbstractMobyObject
 
getMobyName(AbstractMobyObject) - Static method in class org.inb.biomoby.MobyMessageContext
 
getMobyNamespace() - Static method in class org.biomoby.registry.properties.MobyCentralConfig
A method that retrieves the mySQL connection details for the database mobynamespace.
getMobyNamespacesFromRDF() - Method in class org.biomoby.shared.extended.NamespaceParser
 
getMobyObject(Node, MobyPrimaryData) - Method in class ca.ucalgary.seahawk.services.MobyClient
Create a MOBY data instance from a DOM by applying the rules of the given MobyClient (xpaths).
getMobyObject(String, MobyPrimaryData) - Method in class ca.ucalgary.seahawk.services.MobyClient
Create a MOBY data instance from a string by applying the rules of the given MobyClient (regexes).
getMobyObject(Map<String, byte[]>, MobyPrimaryData) - Method in class ca.ucalgary.seahawk.services.MobyClient
Create a MOBY data instance from a map of name->bytes[] by applying the rules of the given MobyClient.
getMobyObject() - Static method in class org.biomoby.registry.properties.MobyCentralConfig
A method that retrieves the mySQL connection details for the database mobyobject.
getMobyObject() - Method in class org.inb.biomoby.shared.message.MobySimple
 
getMobyObjects(CharSequence, MobyDataType) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getMobyObjects(CharSequence, MobyDataType, MobyNamespace) - Method in class ca.ucalgary.seahawk.services.MobyClient
Using the regular expression mappings that have been set up, maps a string using rules producing moby objects of the given type.
getMobyObjects(byte[], MobyDataType) - Method in class ca.ucalgary.seahawk.services.MobyClient
Using the regular expression mappings that have been set up, maps a string using rules producing moby objects of the given type.
getMobyObjects(CharSequence) - Method in class ca.ucalgary.seahawk.services.MobyClient
Using the regular expression mappings that have been set up, maps a string to moby objects.
getMobyObjects(CharSequence, byte[]) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getMobyObjects(URL) - Method in class ca.ucalgary.seahawk.services.MobyClient
Using the URL regular expression mappings that have been set up, maps a string to moby objects.
getMobyObjects(URL, String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getMobyObjects(URL, MobyDataType) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getMobyObjects(URL, String, MobyDataType) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getMobyObjects(Node) - Method in class ca.ucalgary.seahawk.services.MobyClient
Using the XPath mappings that have been set up, maps a DOM node to moby objects.
getMobyObjectsURNMap(CharSequence) - Method in class ca.ucalgary.seahawk.services.MobyClient
Same as getMobyObjects(String), but returns only those generated Moby objects that are derived from URN-addressable rules (which are the keys), mostly for provenance and reproducibility purposes.
getMobyObjectsURNMap(CharSequence, byte[]) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getMobyObjectsURNMap(Node) - Method in class ca.ucalgary.seahawk.services.MobyClient
Same as getMobyObjects(Node), but applies only those rules that have a URN associated with them, mainly for provenance and reuse purposes.Map
getMobyParams2ServiceParams() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getMobyRelationship() - Static method in class org.biomoby.registry.properties.MobyCentralConfig
A method that retrieves the mySQL connection details for the database mobyrelationship.
getMobyService() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClientResult
Returns the BioMOBY service which was called
getMobyService() - Static method in class org.biomoby.registry.properties.MobyCentralConfig
A method that retrieves the mySQL connection details for the database mobyservice.
getMobyServicesFromRDF() - Method in class org.biomoby.shared.extended.ServiceInstanceParser
 
getMobyServicesFromRDF(Model) - Method in class org.biomoby.shared.extended.ServiceInstanceParser
 
getMobyServicesFromRDF(String) - Method in class org.biomoby.shared.extended.ServiceInstanceParser
 
getMobyServicesGUI(JLabel) - Static method in class ca.ucalgary.seahawk.util.MobyUtils
The first time this method is called within a JVM instance, the GUI is created.
getMobyServiceTypesFromRDF() - Method in class org.biomoby.shared.extended.ServiceTypeParser
 
getMobyServlet() - Method in class org.biomoby.service.test.MobyServletTestCase
 
getMobyTypeName() - Method in class org.biomoby.shared.datatypes.MobyObject
Return a Biomoby data type name represented by this object.
getModel() - Method in class org.inb.biomoby.central.gui.AbstractMobyObjectPropertyTable
 
getModel() - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
getModel() - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
getModelFormat() - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
getMolWeight() - Method in class org.inb.biomoby.shared.ontology.MolWeightAnnotation
 
getMsg() - Method in class org.soap.SOAPFault
 
getMulipleCallResult(String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClientResult
Returns the result from a multiple job call for a specific job id.
getMulitpliCallResultAsOne() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClientResult
 
getMultipartRequest(Map<String, byte[]>, HttpMethodParams, List<String>) - Static method in class ca.ucalgary.services.util.CGIUtils
 
getMultipleCallResult() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClientResult
Returns the result from a multiple job call.
getMultipleResourceProperties(GetMultipleResourceProperties) - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
GetMultipleResourceProperties - Class in org.inb.wsrf.rp2
 
GetMultipleResourceProperties() - Constructor for class org.inb.wsrf.rp2.GetMultipleResourceProperties
 
GetMultipleResourcePropertiesResponse - Class in org.inb.wsrf.rp2
 
GetMultipleResourcePropertiesResponse() - Constructor for class org.inb.wsrf.rp2.GetMultipleResourcePropertiesResponse
 
getMultipleResourcePropertiesResult(List<String>) - Method in class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
getMultipleResourcePropertiesStatus(List<String>) - Method in class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
getMVector() - Method in class org.biomoby.shared.schema.MElementHashtable
return the instance variable mVector
getMW() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getMWTolerance() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getName() - Method in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
getName() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getName() - Method in class org.biomoby.service.dashboard.CommonNode
Return back the appearance of this node.
getName() - Method in class org.biomoby.service.dashboard.Dashboard
 
getName() - Method in interface org.biomoby.service.dashboard.DashboardPanel
A name identifies a panel in the dashboard's tabs.
getName() - Method in class org.biomoby.service.dashboard.DebuggingPanel
 
getName() - Method in class org.biomoby.service.dashboard.ExamplePanel
 
getName() - Method in class org.biomoby.service.dashboard.GeneratorPanel
 
getName() - Method in class org.biomoby.service.dashboard.MobyUnitTestingPanel
 
getName() - Method in class org.biomoby.service.dashboard.PerlMoSeSPanel
 
getName() - Method in class org.biomoby.service.dashboard.RegistrationPanel
 
getName() - Method in class org.biomoby.service.dashboard.RegistryPanel
 
getName() - Method in class org.biomoby.service.dashboard.renderers.AbstractRenderer
 
getName() - Method in interface org.biomoby.service.dashboard.renderers.Renderer
A human-readable name for this SPI.
getName() - Method in class org.biomoby.service.dashboard.ResultsPanel
 
getName() - Method in class org.biomoby.service.dashboard.SimpleClientPanel
 
getName() - Method in class org.biomoby.service.dashboard.StatisticsPanel
 
getName() - Method in class org.biomoby.service.dashboard.UnitTestingResultPanel
 
getName() - Method in interface org.biomoby.shared.data.MobyDataInstance
 
getName(Element) - Static method in class org.biomoby.shared.data.MobyDataObject
Determine the name of the element if an enclosing tag (e.g.
getName() - Method in class org.biomoby.shared.datatypes.MobyObject
Get a name of this object.
getName() - Method in class org.biomoby.shared.MobyData
 
getName() - Method in class org.biomoby.shared.MobyDataType
 
getName() - Method in class org.biomoby.shared.MobyNamespace
 
getName() - Method in class org.biomoby.shared.MobyRelationship
Return name of this relationship (an "article name").
getName() - Method in class org.biomoby.shared.MobyService
 
getName() - Method in class org.biomoby.shared.MobyServiceType
 
getName() - Method in class org.biomoby.shared.parser.MobyDataElement
 
getName() - Method in class org.biomoby.shared.schema.MElement
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Namespace
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ObjectType
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ServiceType
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.ServiceType
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.AbstractType
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.ObjectType
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.Object
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Object
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation.Resource
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation.ServiceProvider
 
getName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
getName() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getName() - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
getName() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getName() - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
getName() - Method in class org.inb.biomoby.shared.ontology.MultiParameter
 
getName() - Method in class org.inb.biomoby.shared.ontology.Parameter
 
getName() - Method in class org.inb.biomoby.shared.ontology.StructureDomain
 
getName() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
getName() - Method in class org.inb.biomoby.shared.registry.Resource
 
getName() - Method in class org.inb.biomoby.shared.registry.ServiceProvider
 
getName() - Method in class org.soap.WSRFFault
 
getNamedDispatcher(String) - Method in class org.biomoby.service.test.TestServletContext
 
getNamespace() - Method in class org.biomoby.registry.meta.Registry
Get a namespace (a URI) of this BioMoby registry.
getNamespace() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a namespace assigned to this node.
getNamespace(String) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getNamespace() - Method in class org.biomoby.shared.data.MobyDataXref
Since an Xref can only have one namespace, this method returns the one that will be used in Xref-style XML output.
getNamespace() - Method in class org.biomoby.shared.datatypes.MobyObject
Get a namespace of the resource being represented by this object.
getNamespace(String) - Static method in class org.biomoby.shared.MobyNamespace
 
getNamespace(String, Registry) - Static method in class org.biomoby.shared.MobyNamespace
 
getNamespace() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Simple
 
getNamespace() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespaces
 
getNamespace() - Method in class org.inb.biomoby.central.MobyCentral
 
getNamespace() - Method in class org.inb.biomoby.shared.message.AbstractMobyObject
 
getNamespaceAttribute() - Method in class org.biomoby.shared.schema.Builder
create an xml schema element for namescape attribute of the moby element.
getNamespaceForPrefix(String) - Method in class org.biomoby.shared.MobyPrefixResolver
 
getNamespaceForPrefix(String, Node) - Method in class org.biomoby.shared.MobyPrefixResolver
Don't use this class if this method will be used.
getNamespaceOntologyFile(Registry) - Static method in class org.biomoby.registry.meta.RegistryCache
 
getNamespaces() - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
Reports the possible namespaces of the objects returned by matched rules.
getNamespaces() - Method in class org.biomoby.client.CentralImpl
Deprecated. Replaced by CentralImpl.getFullNamespaces() that gives more information for the same price.

getNamespaces() - Method in interface org.biomoby.registry.definitions.types.JNamespaceI
method that returns the various namespace types and descriptions all tab-delimited.
getNamespaces() - Method in class org.biomoby.registry.definitions.types.JNamespacesSqlImpl
 
getNamespaces(Object) - Method in class org.biomoby.service.dashboard.RegistryModel
Fetch namespaces (from a cache or from a registry).
getNamespaces() - Method in interface org.biomoby.shared.Central
Deprecated. Replaced by Central.getFullNamespaces() that gives more information for the same price.

getNamespaces() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getNamespaces() - Method in class org.biomoby.shared.data.MobyDataObjectSet
Return namespaces that occur in all items of the collection.
getNamespaces() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getNamespaces() - Method in class org.biomoby.shared.data.MobyDataXref
 
getNamespaces() - Method in class org.biomoby.shared.MobyPrimaryData
 
getNamespaces() - Method in class org.biomoby.shared.MobyPrimaryDataSet
Return namespaces of the first element of this collection.
getNamespaces() - Method in class org.biomoby.shared.MobyPrimaryDataSimple
Return all namespaces defined in this data container.
getNamespaces() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Simple
 
getNamespaces() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Simple
 
getNamespaces() - Method in class org.inb.biomoby.shared.registry.Simple
 
getNamespacesAsArray() - Method in interface org.biomoby.registry.definitions.types.JNamespaceI
method that returns the various namespace types and descriptions all tab-delimited.
getNamespacesAsArray() - Method in class org.biomoby.registry.definitions.types.JNamespacesSqlImpl
 
getNamespaceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterNamespaceOperation.DeregisterNamespace
 
getNamespaceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
getNamespaceURI(String) - Method in class org.biomoby.shared.NamespaceContextImpl
 
getNameValuePairs(Map<String, byte[]>) - Static method in class ca.ucalgary.services.util.CGIUtils
 
getNcutMatrix() - Method in class org.inb.biomoby.shared.ontology.ISS_Report
 
getNegative() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getNewState() - Method in class org.inb.lsae.StateChanged
 
getNewState() - Method in class org.omg.lsae.notifications.StateEvent
 
getNodeForLocation(Point) - Method in class org.inb.biomoby.central.gui.AbstractEntityTreePanel
Method to find a tree node by its location
getNodeFromXPointer(Node, String) - Static method in class ca.ucalgary.seahawk.util.XPointerResolver
Note, this currently only works for stuff like /1/1/2/3/1/67, not all XPointers, which includes functions, etc.
getNodeValue() - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
getNon__polar() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getNotes() - Method in class org.inb.biomoby.shared.message.ServiceNotes
 
getNotificationListeners() - Method in class org.biomoby.client.CentralDigestImpl
 
getNotificationListeners() - Method in class org.biomoby.service.dashboard.RegistryModel
 
getNotificationListeners() - Method in interface org.biomoby.shared.event.Notifier
Returns an array of all the NotificationListeners added to the class that implements this interface.
getNterminalMass() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getNterminalTagMass() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getNum_blocks() - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
getNumber() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getNumIterations() - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
getNumResidues() - Method in class org.inb.biomoby.shared.ontology.StructureFragment
 
getObject(String) - Method in class org.biomoby.registry.definitions.types.JObjectsSqlImpl
 
getObject() - Method in class org.biomoby.shared.data.MobyDataBoolean
Since the Boolean object is immutable, use the setValue(boolean) method instead to change the underlying value for this MOBYObject.
getObject() - Method in class org.biomoby.shared.data.MobyDataBytes
 
getObject() - Method in class org.biomoby.shared.data.MobyDataComposite
 
getObject() - Method in class org.biomoby.shared.data.MobyDataDateTime
 
getObject() - Method in class org.biomoby.shared.data.MobyDataFloat
 
getObject() - Method in interface org.biomoby.shared.data.MobyDataInstance
Each implementer will return the underlying Java object used to store the MOBY value.
getObject() - Method in class org.biomoby.shared.data.MobyDataInt
 
getObject() - Method in class org.biomoby.shared.data.MobyDataObject
Gives access to the Java object instance underlying the MobyData instance.
getObject() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getObject() - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
getObject() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getObject() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
For now, all secondary parameters are treated as strings.
getObject() - Method in class org.biomoby.shared.data.MobyDataString
 
getObject() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.ObjectNames
 
getObject() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Objects
 
getObject() - Method in class org.inb.biomoby.shared.message.MobySimple
 
getObjectComposition(String, String) - Method in interface org.biomoby.shared.MobyObjectDecomposition
PRE:None.
getObjectComposition(String, String) - Method in class org.biomoby.shared.MobyObjectDecompositionImpl
 
getObjectConsumed(URL, String, Registry) - Static method in class ca.ucalgary.seahawk.services.TextClient
Convenience method to backtrack from a mapping rule to the Moby datatype it consumes.
getObjectProduced(URL, String, Registry) - Static method in class ca.ucalgary.seahawk.services.MobyClient
Convenience method to backtrack from a mapping rule to the Moby datatype it produces.
getObjects() - Method in interface org.biomoby.registry.definitions.types.JObjectsI
method that returns the various object types, object relationship, object type that this relationship is with, the articlename (if it exists), and description, all tab-delimited.
getObjects() - Method in class org.biomoby.registry.definitions.types.JObjectsSqlImpl
 
getObjects() - Method in class org.inb.biomoby.shared.message.CrossReference
 
getObjectsAsArray() - Method in interface org.biomoby.registry.definitions.types.JObjectsI
method that returns the various object types, object relationship, object type that this relationship is with, the articlename (if it exists), and description, all tab-delimited.
getObjectsAsArray() - Method in class org.biomoby.registry.definitions.types.JObjectsSqlImpl
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterObjectClassOperation.DeregisterObjectClass
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Simple
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Simple
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.Relationship
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Simple
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.Relationship
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
getObjectType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.RetrieveObjectSchema
 
getObjectType() - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
getObjectType() - Method in class org.inb.biomoby.shared.registry.Simple
 
getOEDResolution() - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
getOnEventAsDOM(Document) - Method in interface ca.ucalgary.services.util.DataRecorder
 
getOnEventAsDOM(Document) - Method in class ca.ucalgary.services.util.PBERecorder
 
getOnEventText() - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to insert a javascript event handler into every form input element the WrappingServlet generates for the Web Service's CGI form.
getOnEventText() - Method in class ca.ucalgary.services.util.PBERecorder
 
getOnSubmitAsDOM(Document) - Method in interface ca.ucalgary.services.util.DataRecorder
 
getOnSubmitAsDOM(Document) - Method in class ca.ucalgary.services.util.PBERecorder
 
getOnSubmitText() - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to insert a javascript event handler into the form submission tags the WrappingServlet generates for the Web Service's CGI form.
getOnSubmitText() - Method in class ca.ucalgary.services.util.PBERecorder
 
getOntology() - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
getOntologyFile(Registry, String) - Static method in class org.biomoby.registry.meta.RegistryCache
Returns where a resource should be cached locally, whether it current exists or not.
getOperationEncoding() - Method in class ca.ucalgary.services.util.WSDLConfig
If style is not explicitly available, literal is the default
getOperationInputQName() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getOperationName() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getOperationOutputQName() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getOperationStyle() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getOriginalException() - Method in exception org.biomoby.shared.MobyException
Deprecated. Use instead getCause() directly.
getOriginator() - Method in class org.inb.wsrf.bf2.BaseFaultType
 
getOtherAttributes() - Method in class org.inb.wsrf.bf2.BaseFaultType.ErrorCode
 
getOtherAttributes() - Method in class org.inb.wsrf.bf2.BaseFaultType
 
getOutput() - Method in class org.biomoby.client.MobyRequest
 
getOutput() - Method in class org.biomoby.client.rdf.builder.FilteredStream
 
getOutput() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.OutputObjects
 
getOutput() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getOutput() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getOutput() - Method in class org.inb.biomoby.shared.registry.Service
 
getOutputObjects() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getOutputSection() - Method in class ca.ucalgary.services.util.ACDFile
 
getOutputStream() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
getOutputXSDTypes() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getParam(String) - Method in class org.biomoby.service.BaseService
Get value of a parameter 'name'.
getParameter(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getParameter(String) - Method in class org.biomoby.shared.parser.MobyJob
Find a Parameter object named by 'name', and return its value.
getParameter() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.SecondaryArticles
 
getParameterMap() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getParameterMap() - Method in class org.inb.biomoby.shared.message.MobyData
 
getParameterNames() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getParameters() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.SecondaryArticles
 
getParameters() - Method in class org.inb.biomoby.shared.message.MobyData
 
getParameterValues(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getParamNames() - Method in class org.biomoby.service.BaseService
Return a list containing the parameter names available within the context of the invoked web service together with the global context.
getParent() - Method in class org.biomoby.shared.MobyDataType
 
getParent() - Method in class org.biomoby.shared.MobyServiceType
 
getParentName() - Method in class org.biomoby.shared.MobyDataType
Return the first parent name (at the moment the only one set and used, anyway.
getParentName() - Method in class org.biomoby.shared.MobyServiceType
 
getParentNames() - Method in class org.biomoby.shared.MobyDataType
Return names of all parental data types (as stored in the BioMoby class ontology).
getParentNames() - Method in class org.biomoby.shared.MobyServiceType
 
getParentNode() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a parent node.
getParticipant() - Method in class org.inb.biomoby.shared.ontology.Interaction
 
getPassword() - Method in class org.biomoby.client.MobyServiceLocator
Returns the password for the authentication
getPathInfo() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getPathToRDF() - Method in class org.biomoby.shared.MobyService
 
getPathTranslated() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getPattern(String) - Method in class ca.ucalgary.seahawk.services.MobyClient
If a rule was given this name, the regex pattern for the rule is returned.
getPattern() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getPeakWidth() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getPeerElements(Document, MobyDataInstance, Map<String, String>, String) - Static method in class ca.ucalgary.seahawk.util.DataUtils
We need to enumerate the possible peer-sets for the selected data item.
getPercentage() - Method in class org.inb.lsae.PercentProgress
 
getPercentaje() - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
getPercentCompleted() - Method in class org.omg.lsae.notifications.PercentEvent
 
getPevzScr() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
getPlot_title() - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
getPolar() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getPortQName() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getPosition() - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
getPosition() - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
getPosition() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getPosition() - Method in class org.inb.biomoby.shared.ontology.TTS
 
getPositive() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getPossibleTextTypes(MobyPrimaryData, boolean) - Method in class ca.ucalgary.seahawk.services.TextClient
 
getPr__c__() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
getPreferredExtension(URLConnection) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
Given a file name to import, returns the file extension that Seahawk would prefer to convert the document to.
getPreferredSize() - Method in class org.biomoby.service.dashboard.Dashboard
 
getPreferredSize() - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor.EditorContainer
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractMultilineDescriptionMobyComponent
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.auxiliary.ArrayFloatChartPane
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.auxiliary.ImageComponent
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.auxiliary.ScrollableTextPane
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.ontology.AnnotationHitsComponent
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.ontology.Image_EncodedComponent
 
getPreferredSize() - Method in class org.inb.biomoby.client.gui.ontology.StructureDomainComponent
 
getPrefix() - Static method in class org.biomoby.client.rdf.vocabulary.XMLTypes
 
getPrefix(String) - Method in class org.biomoby.shared.NamespaceContextImpl
 
getPrefixes(String) - Method in class org.biomoby.shared.NamespaceContextImpl
 
getPreviewPanel() - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Returns the preview panel that shows a currently chosen date.
getPreviousState() - Method in class org.inb.lsae.StateChanged
 
getPreviousState() - Method in class org.omg.lsae.notifications.StateEvent
 
getPrimaryData() - Method in class org.biomoby.shared.data.MobyDataJob
 
getPrimaryDataObjects() - Method in class org.biomoby.shared.data.MobyDataJob
 
getPrimaryDataObjectSets() - Method in class org.biomoby.shared.data.MobyDataJob
 
getPrimaryInputFormats() - Method in class ca.ucalgary.services.util.MobySpecWrapper
Note that the string values for the formats are specialized for the various LegacyService child classes, as they will all have their own naming scheme for legacy formats.
getPrimaryInputs() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getPrimaryInputs() - Method in class org.biomoby.shared.MobyService
 
getPrimaryNamespace() - Method in class org.biomoby.shared.data.MobyDataObject
 
getPrimaryOutputFormats() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getPrimaryOutputs() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getPrimaryOutputs() - Method in class org.biomoby.shared.MobyService
 
getProbability() - Method in class org.inb.biomoby.shared.ontology.ProbMolWeightAnnotation
 
getProfiles() - Method in class org.inb.biomoby.shared.ontology.Clustering
 
getProfiles() - Method in class org.inb.biomoby.shared.ontology.HierarchicalClustering
 
getProperties(String) - Method in class org.biomoby.registry.rdfagent.util.Config
get the properties for a given section
getProperties() - Method in class org.inb.wsrf.rp2.GetResourcePropertyResponse
 
getProperty(String, String, String) - Method in class org.biomoby.registry.rdfagent.util.Config
get a property for given key in specified section
getProperty(String) - Static method in class org.biomoby.service.dashboard.Dashboard
Allow access to individual Dashboard properties that had been loaded when Dashboard started, and that may contain properties used also by individual panels.
getProtein_name() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getProtocol() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getProviders() - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getProviders() - Method in interface org.biomoby.shared.Central
Get the list of all providers (each provider is represented by an authority's URI.
getProviderURI() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getProvision() - Method in class org.biomoby.shared.datatypes.MobyObject
Get provision data attached to this object.
getProvisionInfo() - Method in class org.biomoby.shared.data.MobyDataObject
 
getProxyBaseUrl() - Static method in class ca.ucalgary.services.util.PBERecorder
 
getPsf() - Method in class org.inb.biomoby.shared.ontology.NAMD_Structure
 
getQuality() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
getQueryExpression() - Method in class org.inb.wsrf.rp2.QueryResourceProperties
 
getQueryID() - Method in class org.inb.biomoby.shared.message.MobyData
 
getQueryId() - Method in class org.omg.lsae.notifications.AnalysisEvent
 
getQueryString() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRadius() - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
getRank() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
getRatio() - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
getRawdata() - Method in class org.inb.biomoby.shared.ontology.Image_Encoded
 
getRawdata() - Method in class org.inb.biomoby.shared.ontology.Zip_Encoded
 
getRawXml(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.util.PBERecorder
 
getRDF() - Method in class org.biomoby.shared.MobyService
 
getRdf() - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
getRdf() - Method in class org.inb.biomoby.shared.registry.Registration
 
getRdfFromURL(String) - Method in class org.biomoby.registry.rdfagent.util.SignatureURLConnection
 
getReader() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getReader(URL) - Method in interface org.inb.biomoby.central.cache.IMobyCentralCache
 
getReader(URL) - Method in class org.inb.biomoby.central.cache.MobyCentralFileCache
 
getRealPath(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRealPath(String) - Method in class org.biomoby.service.test.TestServletContext
 
getRecorder() - Method in class ca.ucalgary.services.WrappingServlet
 
getRef() - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
getRefElement() - Method in class org.inb.biomoby.shared.message.MobyException
 
getRefQueryID() - Method in class org.inb.biomoby.shared.message.MobyException
 
getRegisterDataTypeXML(MobyDataType) - Method in class org.biomoby.client.CentralImpl
 
getRegisterDataTypeXML(MobyDataType) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getRegisterNamespaceXML(MobyNamespace) - Method in class org.biomoby.client.CentralImpl
 
getRegisterNamespaceXML(MobyNamespace) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getRegisterServiceTypeXML(MobyServiceType) - Method in class org.biomoby.client.CentralImpl
 
getRegisterServiceTypeXML(MobyServiceType) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getRegisterServiceXML(MobyService) - Method in class org.biomoby.client.CentralImpl
 
getRegisterServiceXML(MobyService) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getRegistry() - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getRegistry() - Method in class ca.ucalgary.seahawk.services.TextClient
 
getRegistry(Document) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Find out which registry the service that created the reponse is registered in.
getRegistry() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
getRegistry() - Method in class org.biomoby.shared.MobyDataType
 
getRegistry() - Method in class org.biomoby.shared.MobyNamespace
 
getRegistry() - Method in class org.biomoby.shared.MobyServiceType
 
getRegistryEndpoint() - Method in class org.biomoby.client.CentralImpl
 
getRegistryEndpoint() - Method in class org.biomoby.client.MobyServiceLocator
 
getRegistryEndpoint() - Method in interface org.biomoby.shared.Central
Return an endpoint (a stringified URL) representing a Moby registry that an instance of this implementation is connected to.
getRegistryNamespace() - Method in class org.biomoby.client.CentralImpl
 
getRegistryNamespace() - Method in class org.biomoby.client.MobyServiceLocator
 
getRegistryNamespace() - Method in interface org.biomoby.shared.Central
Return a namespace (a URI) used by a Moby registry that an instance of this implementation is connected to.
getRelationship(Relationship.RELATIONSHIP_TYPE) - Method in class org.inb.biomoby.shared.registry.ObjectType
Auxiliary method to find relationship by its type
getRelationships() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
getRelationships() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
getRelationships() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
getRelationships() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsOutput
 
getRelationships() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
getRelationships(DefaultMutableTreeNode, ObjectType) - Static method in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferHandler
 
getRelationships() - Method in class org.inb.biomoby.shared.registry.ObjectType
 
getRelationships() - Method in class org.inb.biomoby.shared.registry.ServiceType
 
getRelationshipType() - Method in class org.biomoby.shared.MobyRelationship
Return type of this relationship.
getRelationshipType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.Relationship
 
getRelationshipType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.Relationship
 
getRelationshipType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.Relationship
 
getRelationshipType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.Relationship
 
getRelationshipType() - Method in class org.inb.biomoby.shared.registry.Relationship
 
getRemaining() - Method in class org.inb.lsae.TimeProgress
 
getRemaining() - Method in class org.omg.lsae.notifications.TimeProgressEvent
 
getRemoteAddr() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRemoteHost() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRemotePort() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRemoteUser() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRenderer(String, Object) - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
Get a default renderer for given 'value' within given 'criterion'.
getRenderers(String, Object) - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
Get all renderers for given 'value' within given 'criterion'.
getRepetitions() - Method in class org.inb.biomoby.shared.ontology.WeightedObject
 
getReport() - Method in class org.biomoby.registry.rdfagent.util.Report
 
getReport() - Method in class org.inb.biomoby.shared.ontology.Structure_Alignment_Report
 
getRequestDispatcher(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRequestDispatcher(String) - Method in class org.biomoby.service.test.TestServletContext
 
getRequestedSessionId() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRequestLength() - Method in class org.biomoby.service.BaseService
Returns length (in bytes) of the request coming to this service.
getRequestURI() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRequestURL() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getRequiredParamsSection() - Method in class ca.ucalgary.services.util.ACDFile
 
getResolution() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getResource(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.util.PBERecorder
 
getResource(String) - Method in class org.biomoby.client.CentralImpl
 
getResource(String) - Method in class org.biomoby.service.test.TestServletContext
 
getResource(String) - Method in interface org.biomoby.shared.Central
First get (from a BioMoby registry) a URL for the given 'resourceName' and then retrieve a document from this URL.
getResource() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation.ResourceURLs
 
getResource(String) - Method in class org.inb.biomoby.MobyClassLoader
 
getResourceAsStream(String) - Method in class org.biomoby.service.test.TestServletContext
 
getResourceAsStream(String) - Method in class org.inb.biomoby.MobyClassLoader
 
getResourceContentType() - Method in class org.biomoby.shared.MobyResourceRef
Deprecated. Biomoby registry never gives the content type back. Therefore, this method does not have anything reasonable to return.
getResourceLocation() - Method in class org.biomoby.shared.MobyResourceRef
Return resource location.
getResourceName() - Method in class org.biomoby.shared.MobyResourceRef
Return resource name.
getResourcePaths(String) - Method in class org.biomoby.service.test.TestServletContext
 
getResourceProperties() - Method in class org.inb.wsrf.rp2.GetMultipleResourceProperties
 
getResourceProperty(QName) - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
GetResourcePropertyResponse - Class in org.inb.wsrf.rp2
 
GetResourcePropertyResponse() - Constructor for class org.inb.wsrf.rp2.GetResourcePropertyResponse
 
GetResourcePropertyResponse(Object) - Constructor for class org.inb.wsrf.rp2.GetResourcePropertyResponse
 
getResourcePropertyResult(String) - Method in class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
getResourcePropertyResult(String) - Method in class org.inb.biomoby.service.AbstractAsyncMobyImpl
 
getResourcePropertyResult() - Method in interface org.inb.biomoby.service.IAsyncMobyImpl
 
getResourcePropertyResult(String) - Method in interface org.inb.biomoby.service.IAsyncMobyImpl
 
getResourcePropertyStatus(String) - Method in class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
getResourcePropertyStatus(String) - Method in interface org.inb.biomoby.service.IAsyncMobyImpl
 
getResourceRefs() - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getResourceRefs() - Method in interface org.biomoby.shared.Central
Get URLs (and content types) of RDF documents describing various BioMoby ontologies.
getResourceURL(String, Class) - Static method in class org.biomoby.shared.Utils
Work in progress.
getResponseObject() - Method in class org.inb.biomoby.shared.wsrf.PropertyResponseWrapper
 
getResponses() - Method in class org.inb.wsrf.rp2.GetMultipleResourcePropertiesResponse
 
getResponseTransformer() - Method in class ca.ucalgary.services.WrappingServlet
 
getResponseXML() - Method in class org.biomoby.client.MobyRequest
 
getRestriction_site() - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
getRestrictionArticleName(Vector) - Method in class org.biomoby.shared.schema.Builder
create an xml schema element for articleName attribute if the values of the articleName can have multiple choices.
getResult() - Method in class org.inb.biomoby.shared.ontology.Interaction
 
getResultPackage(EndpointReference, String) - Static method in class org.biomoby.client.AsyncClient
 
getResultStream(EndpointReference, String) - Static method in class org.biomoby.client.AsyncClient
 
getResultStream(EndpointReference, Collection<String>) - Static method in class org.biomoby.client.AsyncClient
 
getResultStream(EndpointReference, String[]) - Static method in class org.biomoby.client.AsyncClient
Retrieves the result message for the given set of jobs in a service invocation.
getResultText(EndpointReference, String) - Static method in class org.biomoby.client.AsyncClient
Retrieves the result text for the given set of jobs in a service invocation.
getResultText(EndpointReference, Collection<String>) - Static method in class org.biomoby.client.AsyncClient
 
getResultText(EndpointReference, String[]) - Static method in class org.biomoby.client.AsyncClient
 
getResultUnits() - Method in class org.inb.biomoby.shared.ontology.Interaction
 
getRole() - Method in class org.inb.biomoby.shared.ontology.Interactor
 
getRoot() - Method in class org.biomoby.service.dashboard.data.DataTypeModel
TreeModel interface
getRoot() - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
getRoot(String) - Static method in class org.biomoby.shared.schema.Builder
create a root element for the schema to begin.
getRoot() - Method in class org.inb.biomoby.central.gui.model.DataTypesTreeModel
 
getRoot() - Method in class org.inb.biomoby.central.gui.model.ServicesTreeModel
 
getRowCount() - Method in class org.biomoby.service.dashboard.TableSorter
 
getRowCount() - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
getRowCount() - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
getRules() - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
getRules() - Method in class org.inb.biomoby.shared.ontology.Rules
 
getRunningType() - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
getS100() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getS35() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getS60() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getS95() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getScale() - Method in class org.inb.biomoby.shared.ontology.ParametersToVary
 
getSchema() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Object
 
getScheme() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getScore() - Method in class org.inb.biomoby.shared.ontology.AntigenicAnnotation
 
getScore() - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
getScore() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getScore() - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
getScore() - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotation
 
getScore() - Method in class org.inb.biomoby.shared.ontology.ScoredMotifAnnotation
 
getScore() - Method in class org.inb.biomoby.shared.ontology.SigcleaveAnnotation
 
getSeahawkAttrFromDoc(URL, String) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Retrieves processing instructions embedded in Moby XML docs if they have the for getSeahawkAttrFromDoc(Document, String) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
getSecondaryArticles() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getSecondaryArticles() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getSecondaryArticles() - Method in class org.inb.biomoby.shared.registry.Service
 
getSecondaryData() - Method in class org.biomoby.shared.data.MobyDataJob
 
getSecondaryInputFormats() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getSecondaryInputs() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getSecondaryInputs() - Method in class org.biomoby.shared.MobyService
 
getSecondaryParamRestrictions(Element) - Method in class ca.ucalgary.services.util.WSDLConfig
Checks out the Moby secondary parameter source attribute.
getSecondaryParamRestrictionsFromService(Element, String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
getSecondaryParamRestrictionsFromURL(URL) - Method in class ca.ucalgary.services.util.WSDLConfig
 
getSecondIcon() - Method in class ca.ucalgary.seahawk.util.CombinedIcon
 
getSections() - Method in class org.biomoby.registry.rdfagent.util.Config
get the available sections
getSeealso() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getSegments() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getSegments() - Method in class org.inb.biomoby.shared.ontology.StructureDomain
 
getSelectedCentral() - Method in class org.inb.biomoby.central.model.MobyCentralModel
Method returns a currently active BioMoby Registry
getSelectedItem() - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
getSelectedXPath() - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
getSelectionInversed() - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
getSendReferrerPolicy() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
getSensitivityParameters() - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
getSeqHits() - Method in class org.inb.biomoby.shared.ontology.MatchingPattern
 
getSequence() - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
getSequences() - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
getSequences() - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
getSequenceString() - Method in class org.inb.biomoby.shared.ontology.GenericSequence
 
getSequenceTag() - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
getServerInfo() - Method in class org.biomoby.service.test.TestServletContext
 
getServerName() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getServerPort() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getService(URL) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Find out what the service was that created the given URL.
getService(Document) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
getService() - Method in class org.biomoby.client.DataServiceEdge
Retrieves the service from this edge.
getService() - Method in class org.biomoby.client.MobyRequest
 
getService() - Method in class org.biomoby.client.MobyRequestEvent
 
getService() - Method in class org.biomoby.client.MobyServiceLocator
 
getService(String) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getService() - Method in class org.biomoby.shared.data.MobyDataXref
 
getService() - Method in class org.biomoby.shared.datatypes.MobyXref
Get an object representing a Biomoby service that can consume data this cross reference is included in.
getService(String) - Static method in class org.biomoby.shared.MobyService
 
getService(String, String) - Static method in class org.biomoby.shared.MobyService
 
getService() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.RetrieveService
 
getServiceAuthorityURI() - Method in class org.biomoby.shared.data.MobyContentInstance
 
getServiceDesc() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getServiceErrors(MobyService) - Method in class org.biomoby.registry.rdfagent.verifier.MobyServiceComparator
 
getServiceFilter() - Static method in class org.biomoby.registry.sync.filtering.ServiceFilter
The class is implemented as a singleton so this method returns the only instance
getServiceInvocationId() - Method in class org.biomoby.w3c.addressing.EndpointReference
 
getServiceInvocationId() - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
Proxy method to obtain a serviceInvocationId
getServiceInvocationId() - Method in interface org.inb.biomoby.service.IAsyncMobyService
 
getServiceLocator() - Method in class org.biomoby.client.BaseClient
Return characteristics of a BioMoby service that will be called, and that reveal where to find such service.
getServiceLocator() - Method in class org.biomoby.client.BaseCmdLineClient
 
getServiceName() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getServiceName() - Method in class org.biomoby.service.MobyServlet
Reads the service name from the mobyService annotation.
getServiceName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceOperation.DeregisterService
 
getServiceName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getServiceName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getServiceName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getServiceName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceNames
 
getServiceName() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
getServiceNames() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getServiceNames() - Method in class org.biomoby.client.CentralImpl
Deprecated. Replaced by CentralImpl.getServiceNamesByAuthority(). The reason is that this method returns a random result if there are more services with the same name but belonging to different authorities.

getServiceNames() - Method in interface org.biomoby.shared.Central
Deprecated. Replaced by Central.getServiceNamesByAuthority(). The reason is that this method returns a random result if there are more services with the same name but belonging to different authorities.

getServiceNamesByAuthority() - Method in class org.biomoby.client.CentralDigestCachedImpl
 
getServiceNamesByAuthority() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
 
getServiceNamesByAuthority() - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getServiceNamesByAuthority() - Method in interface org.biomoby.shared.Central
Get a list of all authorities - and for each of them a list of their registered service names.
getServiceNotes() - Method in class org.biomoby.shared.data.MobyContentInstance
 
getServiceNotes() - Method in class org.biomoby.shared.parser.MobyPackage
Get back service notes.
getServiceNotes() - Method in class org.inb.biomoby.shared.message.MobyContent
 
getServiceOntologyFile(Registry) - Static method in class org.biomoby.registry.meta.RegistryCache
 
getServiceProviders() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation.ServiceProviders
 
getServiceQName() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getServices(Node) - Method in class ca.ucalgary.seahawk.services.MobyClient
Performs the moby object creation and service association together (XPath rules).
getServices(String) - Method in class ca.ucalgary.seahawk.services.MobyClient
Performs the moby object creation and service association together (regex rules).
getServices(URL) - Method in class ca.ucalgary.seahawk.services.MobyClient
Performs the moby object creation and service association together (url_regex rules).
getServices(MobyDataObjectSet) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getServices(MobyDataObject) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getServices(MobyDataObjectSet[]) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getServices(MobyDataObject[]) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
getServices() - Method in class org.biomoby.client.CentralDigestCachedImpl
 
getServices() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
 
getServices() - Method in class org.biomoby.client.CentralDigestImpl
 
getServices() - Method in interface org.biomoby.registry.definitions.types.JServiceI
method that returns the various service types, service relationship, service type that this relationship is with, and description, all tab-delimited.
getServices() - Method in class org.biomoby.registry.definitions.types.JServicesSqlImpl
 
getServices(Object) - Method in class org.biomoby.service.dashboard.RegistryModel
Fetch services (from a cache or from a registry).
getServices() - Method in interface org.biomoby.shared.CentralDigest
Get definition of all registered service instances.
getServices() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getServices() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getServices() - Method in interface org.biomoby.shared.data.MobyDataServiceAssocInstance
 
getServices() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services
 
getServicesAsArray() - Method in interface org.biomoby.registry.definitions.types.JServiceI
method that returns the various service types, service relationship, service type that this relationship is with, and description, all tab-delimited.
getServicesAsArray() - Method in class org.biomoby.registry.definitions.types.JServicesSqlImpl
 
getServicesByAuthority() - Method in class org.biomoby.client.CentralImpl
Similar to CentralImpl.getServiceNamesByAuthority() but the resulting Map contains slightly more.
getServiceType() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getServiceType(String) - Method in class org.biomoby.service.dashboard.RegistryModel
 
getServiceType() - Method in class org.biomoby.shared.MobyService
 
getServiceType(String) - Static method in class org.biomoby.shared.MobyServiceType
 
getServiceType(String, Registry) - Static method in class org.biomoby.shared.MobyServiceType
 
getServiceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceTypeOperation.DeregisterServiceType
 
getServiceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getServiceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getServiceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getServiceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
getServiceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.Relationship
 
getServiceType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceTypes
 
getServiceType() - Method in class org.inb.biomoby.shared.registry.Service
 
getServiceTypeOntologyFile(Registry) - Static method in class org.biomoby.registry.meta.RegistryCache
 
getServiceTypeRelationships(String, boolean) - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getServiceTypeRelationships(String, boolean) - Method in interface org.biomoby.shared.Central
Get all ISA relationships of the given 'serviceTypeName'.
getServiceTypes() - Method in class org.biomoby.client.CentralImpl
Parses and imports the following XML.
getServiceTypes(Object) - Method in class org.biomoby.service.dashboard.RegistryModel
Fetch service types (from a cache or from a registry).
getServiceTypes() - Method in interface org.biomoby.shared.Central
Get the list of all registered service types.
getServiceWSDL(String) - Method in class org.biomoby.client.CentralImpl
 
getServiceWSDL(String, String) - Method in class org.biomoby.client.CentralImpl
 
getServiceWSDL(String, String) - Method in interface org.biomoby.shared.Central
Get WSDL defining a service given by its name and its authority.
getServiceWSDL(String) - Method in interface org.biomoby.shared.Central
Get WSDL defining a service given by its name.
getServlet(String) - Method in class org.biomoby.service.test.TestServletContext
 
getServletClassName() - Method in class org.biomoby.service.test.TestServletConfig
 
getServletContainer() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
getServletContext() - Method in class org.biomoby.service.test.TestServletConfig
 
getServletContextName() - Method in class org.biomoby.service.test.TestServletContext
 
getServletName() - Method in class org.biomoby.service.test.TestServletConfig
 
getServletNames() - Method in class org.biomoby.service.test.TestServletContext
 
getServletPath() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getServletRequest() - Method in class org.biomoby.service.BaseService
Returns a servlet request instance - the one that delivered a request to this service.
getServlets() - Method in class org.biomoby.service.test.TestServletContext
 
getSession(boolean) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getSession() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getSeverity() - Method in exception org.biomoby.shared.parser.ServiceException
Return the current severity level.
getSeverity() - Method in class org.inb.biomoby.shared.message.MobyException
 
getSeverityAsString() - Method in exception org.biomoby.shared.parser.ServiceException
Return the current severity level in a stringified form.
getShortlabel() - Method in class org.inb.biomoby.shared.ontology.InteractionMethod
 
getSignatureURL() - Method in class org.biomoby.shared.MobyService
Return a URL pointing to an RDF document that contains this service description (signature).
getSignatureURL() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
getSignatureURL() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getSignatureURL() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getSignatureURL() - Method in class org.inb.biomoby.shared.registry.Service
 
getSimple() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Collection
 
getSimple() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Collection
 
getSimple() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Collection
 
getSimple() - Method in class org.inb.biomoby.shared.registry.Collection
 
getSimples() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Data
 
getSimples() - Method in class org.inb.biomoby.shared.registry.Data
 
getSingleCallResult() - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClientResult
Returns the result for a simple, one-time call (so non multiple call).
getSize() - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
getSize() - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotation
 
getSmall() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getSoapAction() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getSoftwareComment() - Method in class org.biomoby.shared.data.MobyProvisionInfo
A human readable message about the software used to generate the object.
getSoftwareName() - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
getSoftwareVersion() - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
getSortingStatus(int) - Method in class org.biomoby.service.dashboard.TableSorter
 
getSource() - Method in class org.biomoby.client.MobyRequestEvent
 
getSource() - Method in class org.inb.biomoby.shared.ontology.AnnotatedStructure
 
getSource() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getSourceActions(JComponent) - Method in class ca.ucalgary.seahawk.gui.FileAndTextTransferHandler
Our components are copy-only
getSourceActions(JComponent) - Method in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferHandler
 
getSourceInput() - Method in class org.biomoby.client.MobyRequestEvent
This method should be used instead of getSource().getInput() because the MobyRequest object may have multiple concurrent threads using it, meaning that the inputXML is not necessarily what it was when the service was invoked.
getSourceService() - Method in class org.biomoby.client.ServicesEdge
Retrieves the source service.
getSpecies() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getSpecURL() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getSpecURL(String) - Method in class ca.ucalgary.services.WrapperService
 
getStart() - Method in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
getStart() - Method in class org.inb.biomoby.client.gui.Subsequence
 
getStart() - Method in class org.inb.biomoby.shared.ontology.Annotation
 
getStart() - Method in class org.inb.biomoby.shared.ontology.CommentedAASubsequence
 
getStart() - Method in class org.inb.biomoby.shared.ontology.Domain
 
getStart() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getState(String) - Method in class org.omg.lsae.notifications.StateEvent
 
getStatistics() - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
getStatus(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.util.PBERecorder
 
getStatus() - Static method in class org.biomoby.client.util.SplashScreenStatus
 
getStatus() - Method in class org.biomoby.shared.MobyService
 
getStatus() - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
getStatus() - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotation
 
getStatusComponent() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
getStepsCompleted() - Method in class org.inb.lsae.StepProgress
 
getStrand() - Method in class org.inb.biomoby.shared.ontology.BL2GAnnotation
 
getStrand() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getStrand() - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
getString(HttpServletRequest, String) - Static method in class org.biomoby.client.GraphsServlet
Return value of a named parameter as a string (trimmed etc.).
getString(String, String) - Static method in class org.biomoby.service.dashboard.DashboardConfig
Get a string associated with the given configuration key, or - if not found - get the given default value (which still may be null).
getString(Object) - Method in class org.biomoby.service.dashboard.PropertyChannel
 
getString(GregorianCalendar) - Static method in class org.biomoby.shared.data.MobyDataDateTime
A utility (static) method converting a GregorianCalendar object to an ISO 8601 string.
getString() - Method in class org.inb.biomoby.shared.datatypes.MobyString
 
getStrings(String, String) - Static method in class org.biomoby.service.dashboard.DashboardConfig
Almost the same functionality as getString method.
getStringVector() - Method in class org.biomoby.shared.schema.PrimitiveVector
get the stringVector field of this object
getStructureDomains() - Method in class org.inb.biomoby.shared.ontology.AnnotatedStructure
 
getStructureFragments() - Method in class org.inb.biomoby.shared.ontology.AnnotatedStructure
 
getStructureID() - Method in class org.inb.biomoby.shared.ontology.ExpressionCore
 
getSubmitOptions() - Method in class ca.ucalgary.services.util.XHTMLForm
Lists the named submit buttons, and may contain a special key SUBMIT_ANONYMOUS_NAME that denotes that an unnamed submit button can be used.
getSubTree(MobyDataType, MobyDataType[]) - Static method in class org.biomoby.client.FilterDataTypes
Return a subset of 'allDataTypes' that contains only a path from 'dataType' to the top-level object, including all HAS and HASA members along the way.
getSuccess() - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
getSuccess() - Method in class org.inb.biomoby.shared.registry.Registration
 
getSuggestedTimeout() - Method in class org.biomoby.client.MobyServiceLocator
 
getSynonym() - Method in class org.biomoby.registry.meta.Registry
Get a synonym (an abbreviation) of this BioMoby registry.
getSynonym() - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
getTabbedPaneParent() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooserEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.PropertyNameTableCellEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellRenderer
TreeCellRenderer method.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.AbstractTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.CardinalityTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.PropertyNameTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.inb.biomoby.central.gui.renderer.PropertyTableCellRenderer
 
getTableHeader() - Method in class org.biomoby.service.dashboard.TableSorter
 
getTableModel() - Method in class org.biomoby.service.dashboard.TableSorter
 
getTarget() - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
getTargetNamespaceURI() - Method in class ca.ucalgary.services.util.WSDLConfig
 
getTargetService() - Method in class org.biomoby.client.ServicesEdge
Retrieves the target service.
getTargetSpecies() - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
getTempDir() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
getTemplateNames() - Method in class org.biomoby.service.generator.DataTypesGenerator
 
getTemplateNames() - Method in class org.biomoby.service.generator.Generator
Getting names of templates is isolated here so a sub-class can override it (but any new teplate still needs to follow the same patterns as the original template - so it is not too flexible, anyway).
getTemplateNames() - Method in class org.biomoby.service.generator.ServicesGenerator
 
getTemplateURN(String) - Method in class ca.ucalgary.seahawk.services.TextClient
 
getTerm() - Method in class org.inb.biomoby.shared.ontology.BasicAnnotation
 
getTerm() - Method in class org.inb.biomoby.shared.ontology.InteractionMethod
 
getTestString(String) - Static method in class org.biomoby.registry.rdfagent.verifier.Main
 
getText(MobyDataInstance, String) - Method in class ca.ucalgary.seahawk.services.TextClient
Because XSLT works on XPath, and we don't know the MOBY tag name (it may be a subclass of the object type we have a rule for), we iteratively try representing the data in simpler top level objects until we get a rule that produces something.
getText() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getTextContent(Node) - Static method in class org.biomoby.shared.MobyObjectDecompositionImpl
Method to simulate DOM level 3 (Java 1.5 default) method for recursively getting text children from a Node.
getTextContent(Node, boolean) - Static method in class org.biomoby.shared.MobyObjectDecompositionImpl
Grabs the text and CDATA children of a Node (not necessairly contiguous) and returns them concatenated.
getTextContents(Element) - Static method in class org.biomoby.shared.data.MobyDataObject
Similar to DOM level 3 getTextContent, but only elements are excepted as input, and text inside children elements is not picked up.
getTheilerStage() - Method in class org.inb.biomoby.shared.ontology.ExpressionCore
 
getTime() - Method in class org.inb.biomoby.shared.datatypes.MobyDateTime
Method returns the "UNIX" time in milliseconds.
getTime() - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
getTime() - Method in class org.inb.biomoby.shared.ontology.ByoDynTarget
 
getTimestamp() - Method in class org.inb.lsae.AnalysisEvent
 
getTimestamp() - Method in class org.inb.wsrf.bf2.BaseFaultType
 
getTimestamp() - Method in class org.omg.lsae.notifications.AnalysisEvent
 
getTimestamp() - Method in class org.soap.WSRFFault
 
getTimestep() - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
getTiny() - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
getTitle() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
getTitle() - Method in class org.biomoby.service.dashboard.Dashboard
 
getTitle() - Method in interface org.biomoby.service.dashboard.DashboardPanel
A title is a more-detailed description of a panel, possibly including an image.
getTitle() - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
getTitle() - Method in class org.inb.biomoby.shared.ontology.OMIM
 
getTitle() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
getTm() - Method in class org.inb.biomoby.shared.ontology.TTS
 
getTo() - Method in class org.inb.biomoby.shared.ontology.AnnotationHits
 
getToolbar() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
getToolkit() - Method in class org.biomoby.service.BaseService
Return a toolkit that gives you broader access to the environment where this service is deployed in.
getTooltip(List<T>) - Method in class org.inb.biomoby.client.gui.auxiliary.LabeledAnnotationListPane
 
getTopology() - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
getTotalHits() - Method in class org.inb.biomoby.shared.ontology.PPSearchReport
 
getTotalSteps() - Method in class org.inb.lsae.StepProgress
 
getTotalSteps() - Method in class org.omg.lsae.notifications.StepEvent
 
getTransferData(DataFlavor) - Method in class ca.ucalgary.seahawk.gui.SeahawkTransferable
 
getTransferData(DataFlavor) - Method in class ca.ucalgary.seahawk.util.MobyDataTransferable
 
getTransferData(DataFlavor) - Method in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
getTransferDataFlavors() - Method in class ca.ucalgary.seahawk.gui.SeahawkTransferable
 
getTransferDataFlavors() - Method in class ca.ucalgary.seahawk.util.MobyDataTransferable
 
getTransferDataFlavors() - Method in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
getTransformer() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
getTransformer() - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractTransformableMobyPanel
 
getTransformer() - Method in interface org.inb.biomoby.client.gui.ITransformable
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
getTransformer() - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
getTransmembraneFragment() - Method in class org.inb.biomoby.shared.ontology.TransmembraneAnnotation
 
getTransmembraneNumber() - Method in class org.inb.biomoby.shared.ontology.TransmembraneAnnotation
 
getTree() - Method in class org.biomoby.service.dashboard.treetable.JTreeTable
Returns the tree that is being shared between the model.
getTree() - Method in class org.inb.biomoby.shared.ontology.Clustering
 
getTree() - Method in class org.inb.biomoby.shared.ontology.HierarchicalClustering
 
getTreeCellEditorComponent(JTree, Object, boolean, boolean, boolean, int) - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor.EditorContainer
 
getTreeCellEditorComponent(JTree, Object, boolean, boolean, boolean, int) - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor
 
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.inb.biomoby.central.gui.renderer.AbstractTreeCellRenderer
 
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.inb.biomoby.central.gui.renderer.EntityTreeCellRenderer
 
getTreedetHTML() - Method in class org.inb.biomoby.shared.ontology.TreeDet_Report
 
getTreedetXML() - Method in class org.inb.biomoby.shared.ontology.TreeDet_Report
 
getType() - Method in class org.biomoby.service.dashboard.CommonNode
Return back the type of this node.
getType() - Method in class org.biomoby.shared.event.NotificationEvent
Return a type of this notification event.
getType() - Method in class org.biomoby.shared.MobyService
 
getType() - Method in class org.biomoby.shared.schema.MElement
 
getType() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
getType() - Method in class org.inb.biomoby.shared.message.AnyMobyObject
 
getType() - Method in class org.inb.biomoby.shared.ontology.BL2GAnnotation
 
getType() - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
getType() - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
getType() - Method in class org.inb.biomoby.shared.ontology.MultiParameter
 
getType() - Method in class org.inb.biomoby.shared.ontology.Parameter
 
getTypes() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.Relationship
 
getUniqueName() - Method in class org.biomoby.shared.MobyService
 
getUnitTests() - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
getUnitTests() - Method in class org.biomoby.shared.MobyService
 
getURI() - Static method in class org.biomoby.client.rdf.vocabulary.DC_PROTEGE
 
getURI() - Static method in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
getURI() - Static method in class org.biomoby.client.rdf.vocabulary.MobyResources
Deprecated.  
getURI() - Static method in class org.biomoby.client.rdf.vocabulary.Predicates
 
getURI() - Static method in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
getURI() - Static method in class org.biomoby.client.rdf.vocabulary.XMLTypes
 
getURL(String) - Method in class org.biomoby.client.FileCache
Return a pointer to cached object identified by its 'id'.
getURL(String) - Method in class org.biomoby.client.ServletFileCache
Return a full URL of the cached object 'id'.
getURL(String) - Method in interface org.biomoby.client.SimpleFileCache
Return a full URL allowing to retrieve a cached object identified by its 'id'.
getUrl() - Method in class org.biomoby.shared.extended.DataTypeParser
 
getUrl() - Method in class org.biomoby.shared.extended.NamespaceParser
 
getUrl() - Method in class org.biomoby.shared.extended.ServiceInstanceParser
 
getUrl() - Method in class org.biomoby.shared.extended.ServiceTypeParser
 
getURL() - Method in class org.biomoby.shared.MobyService
Return a URL where this service is being served from.
getURL() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
getURL() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
getUrl() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation.Resource
 
getUrl() - Method in class org.inb.biomoby.shared.registry.Resource
 
getUrl() - Method in class org.inb.biomoby.shared.registry.Service
 
getURLContentBytes(URL) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
Convenience method to grab all data from a URL as a byte array (in case it's not text)
getURLContents(URL) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
Convenience method to grab all data from a URL into a String.
getURLQuery(Map<String, byte[]>) - Static method in class ca.ucalgary.services.util.CGIUtils
 
getURN() - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
Reports the URN identifying the rule, or null if it doesn't exist.
getUsage() - Method in class org.biomoby.client.BaseCmdLineClient
Return a help text about this this client.
getUsage(Class) - Static method in class org.biomoby.client.CmdLineHelper
Return a help text how to use a class 'helpOwner'.
getUser() - Method in class org.biomoby.client.MobyServiceLocator
Returns the user for the authentication
getUserData() - Method in interface org.biomoby.shared.data.MobyDataInstance
Retrieves any application-specific data that may have been stored in association with this Moby object.
getUserData() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getUserData() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getUserData() - Method in class org.biomoby.shared.MobyData
Retrieves any application-specific data that may have been stored in association with this Moby object.
getUserPrincipal() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
getValidOutputXML() - Method in class org.biomoby.shared.MobyUnitTest
Getter: get the expected XML output for this service (usually by sending it the input from getExampleInput()
getValidREGEX() - Method in class org.biomoby.shared.MobyUnitTest
Getter: get the Regular Expression for this unit test
getValidXPath() - Method in class org.biomoby.shared.MobyUnitTest
Getter: get the xpath expression for this unit test
getValue() - Method in class org.biomoby.service.dashboard.CommonNode
Return back the meaning of this node.
getValue() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a value stored in this node (makes sense only for Biomoby primitive types).
getValue() - Method in class org.biomoby.shared.data.MobyDataBoolean
 
getValue() - Method in class org.biomoby.shared.data.MobyDataDateTime
 
getValue() - Method in class org.biomoby.shared.data.MobyDataFloat
 
getValue() - Method in class org.biomoby.shared.data.MobyDataInt
 
getValue() - Method in class org.biomoby.shared.data.MobyDataObject
A lexical (prefereably human readable) representation of the underlying object value (not including the namespace and ID).
getValue() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getValue() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
getValue() - Method in class org.biomoby.shared.data.MobyDataString
 
getValue() - Method in class org.biomoby.shared.datatypes.MobyObject
Get the value of this object.
getValue() - Method in class org.biomoby.shared.parser.MobyParameter
 
getValue() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
getValue() - Method in class org.inb.biomoby.shared.message.MobyParameter
 
getValue() - Method in class org.inb.biomoby.shared.ontology.ElementFloat
 
getValue() - Method in class org.inb.biomoby.shared.ontology.ElementInteger
 
getValue() - Method in class org.inb.biomoby.shared.ontology.ElementString
 
getValue() - Method in class org.inb.biomoby.shared.ontology.ElementXYData
 
getValue() - Method in class org.inb.biomoby.shared.ontology.Parameter
 
getValue() - Method in class org.inb.wsrf.bf2.BaseFaultType.Description
 
getValueAt(Object, int) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
getValueAt(int, int) - Method in class org.biomoby.service.dashboard.TableSorter
 
getValueAt(Object, int) - Method in interface org.biomoby.service.dashboard.treetable.TreeTableModel
Returns the value to be displayed for node node, at column number column.
getValueAt(int, int) - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
getValueAt(int, int) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
getValueEditor(JTable) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a cell editor (of column containing the value) for given table.
getValueRenderer(JTable, Object) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return a cell renderer for given table and for given value.
getValues() - Method in class org.inb.biomoby.shared.ontology.MultiParameter
 
getVariance() - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
getVariance() - Method in class org.inb.biomoby.shared.ontology.TargetArgument
 
getWebServiceContext() - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
getWeight() - Method in class org.inb.biomoby.shared.ontology.CommentedWeightedObject
 
getWeightedObject() - Method in class org.inb.biomoby.shared.ontology.WeightedAminoAcidSequences
 
getWorker() - Method in class org.biomoby.service.generator.Generator
Return an underlying object (a worker) that does all data types retrieving and caching them.
getWrappingEnabled() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getWriter() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
getWriter(URL) - Method in interface org.inb.biomoby.central.cache.IMobyCentralCache
 
getWriter(URL) - Method in class org.inb.biomoby.central.cache.MobyCentralFileCache
 
getWSDL() - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
getWSDL() - Method in class org.inb.biomoby.shared.registry.ServiceType
 
getWsrfFault() - Method in class org.soap.SOAPFault
 
getX__corr() - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
getXCharPosition(int) - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
getXCharPosition(int) - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getXCharWidth(int) - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
getXCharWidth(int) - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getXFixedSegmentEnd() - Method in interface org.inb.biomoby.client.gui.ISequenceTransformer
 
getXFixedSegmentEnd() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getXFixedSegmentStart() - Method in interface org.inb.biomoby.client.gui.ISequenceTransformer
 
getXFixedSegmentStart() - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
getXMLDifferences(String) - Method in class org.biomoby.shared.MobyUnitTest
 
getXMLDocument() - Method in class org.biomoby.service.dashboard.data.DataTypeTreeTable
Return an XML document representing th Biomoby data type that was created in this tree table.
getXMLDocument() - Method in class org.biomoby.service.dashboard.data.ServiceInputPanel
Return an XML document representing complete input for a service given in the constructor of this class.
getXMLElement(String) - Static method in class org.biomoby.shared.parser.MobyPackage
Return a jDOM XML element equipped with the BioMoby namespace.
getXmlMode() - Method in class org.biomoby.shared.data.MobyContentInstance
Report whether toXML will produce Central template or service call instance XML.
getXmlMode() - Method in interface org.biomoby.shared.data.MobyDataInstance
Report whether toXML will produce Central template or service call instance XML.
getXmlMode() - Method in class org.biomoby.shared.data.MobyDataObject
Report whether toXML will produce Central template or service call instance XML.
getXmlMode() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
getXmlMode() - Method in class org.biomoby.shared.data.MobyDataObjectSet
Report whether toXML will produce Central template or service call instance XML.
getXmlMode() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
getXmlMode() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
Report whether toXML will produce Central template or service call instance XML.
getXMLSource() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
getXMLSource() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
getXPath() - Method in class ca.ucalgary.seahawk.util.XPathOption
 
getXPathOptions() - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
getXPtr(Node) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
getXrefs() - Method in class org.biomoby.shared.datatypes.MobyObject
Get cross references attached to this object.
getXrefType() - Method in class org.biomoby.shared.data.MobyDataXref
 
getXrefType() - Method in class org.biomoby.shared.datatypes.MobyXref
Get a semantic type of this cross reference.
getXtitle() - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
getYtitle() - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
GFF - Class in org.inb.biomoby.shared.ontology
 
GFF() - Constructor for class org.inb.biomoby.shared.ontology.GFF
 
GFF2 - Class in org.inb.biomoby.shared.ontology
 
GFF2() - Constructor for class org.inb.biomoby.shared.ontology.GFF2
 
GFF3 - Class in org.inb.biomoby.shared.ontology
 
GFF3() - Constructor for class org.inb.biomoby.shared.ontology.GFF3
 
goBackward() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
goBackward() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
goForward() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
goForward() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
GOGraph - Class in org.inb.biomoby.shared.ontology
 
GOGraph() - Constructor for class org.inb.biomoby.shared.ontology.GOGraph
 
GOTerm - Class in org.inb.biomoby.shared.ontology
 
GOTerm() - Constructor for class org.inb.biomoby.shared.ontology.GOTerm
 
gotoURL(URL, boolean) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
This is the URLLoader callback method the MOBY data fetcher will call when MOBY XML data is ready to be seen.
GPROP_AUTH - Static variable in class org.biomoby.service.generator.Generator
A regular expression that will be applied against service authority names.
GPROP_DOTLOCATION - Static variable in class org.biomoby.service.generator.Generator
A path to a Graphviz program dot.
GPROP_FILTER - Static variable in class org.biomoby.service.generator.Generator
A regular expression that will be applied to a data type name.
GPROP_NOGEN - Static variable in class org.biomoby.service.generator.Generator
A debugging property: do not generate anything, just print what you would generate.
GPROP_NOGRAPHS - Static variable in class org.biomoby.service.generator.Generator
Data type generator will not produce any graphs if this property is set to "true".
GPROP_OUTDIR - Static variable in class org.biomoby.service.generator.Generator
A name of a directory where a generator puts its generated results.
GPROP_SERVICE - Static variable in class org.biomoby.service.generator.Generator
A regular expression that will be applied against service names.
GPROP_VERBOSE - Static variable in class org.biomoby.service.generator.Generator
Generator will print some messages if this property is set to "true".
GraphColours - Class in org.biomoby.service.dashboard
This abstract class sets up and provides name-to-color and color-to-name mappings and some associated class methods.
GraphColours() - Constructor for class org.biomoby.service.dashboard.GraphColours
 
GraphsServlet - Class in org.biomoby.client
A servlet making graphs of Moby service instances, Moby data types, and Moby service types.
GraphsServlet() - Constructor for class org.biomoby.client.GraphsServlet
A default constructor, used usually by a servlet engine.
GraphsServlet(String, String) - Constructor for class org.biomoby.client.GraphsServlet
A real constructor that is called when it is known what Moby registry we are going to serve for.
Graphviz - Class in org.biomoby.client
A utility class that understands how to create graphviz graphs from a set of ServiceEdges, or from other data structures.
Graphviz() - Constructor for class org.biomoby.client.Graphviz
 
group() - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
group(int) - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
groupCount() - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
groupCount(Pattern) - Static method in class ca.ucalgary.seahawk.services.RegexParser
 

H

handlesNullPrefixes() - Method in class org.biomoby.shared.MobyPrefixResolver
 
has - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
HAS - Static variable in interface org.biomoby.shared.Central
A relationship type expressing a contaiment (as string).
HAS_LABEL - Static variable in class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor.CardinalityComponent
 
hasa - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
HASA - Static variable in interface org.biomoby.shared.Central
A relationship type expressing a contaiment (as string).
HASA_LABEL - Static variable in class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor.CardinalityComponent
 
hasAnError() - Method in class org.biomoby.shared.parser.MobyPackage
Return true if this package contains at least one exception of the severity ServiceException.ERROR).
hasAppendModeSwitcher() - Method in class org.biomoby.service.dashboard.CommonConsole
 
hasAuthentication() - Method in class org.biomoby.client.MobyServiceLocator
Returns true if the user AND the password is set
hasChanged(String, String) - Method in class org.biomoby.registry.sync.handler.AbstractMobyHandler
Checks whether the local object (represented by the lsid) is older than the central object (represented by the lsid)
hasCleanButton() - Method in class org.biomoby.service.dashboard.CommonConsole
 
hasCollectionType - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasCollectionType - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasCrossReferences() - Method in class org.biomoby.shared.data.MobyDataObject
 
hasCrossReferences() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
hasDefaultValue - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasDefaultValue - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasExceptions() - Method in class org.biomoby.shared.data.MobyContentInstance
Indicates whether the moby content has any exception (according to the style of MOBY-S RFC 1863)
hasExceptions(int) - Method in class org.biomoby.shared.data.MobyContentInstance
Indicates whether the moby content has any exception of the given severity or worse (according to the style of MOBY-S RFC 1863).
hasExceptions() - Method in class org.inb.biomoby.shared.message.MobyContent
Method returns wherever it the content has an exception
hasExceptions() - Method in class org.inb.biomoby.shared.message.MobyMessage
 
hasExceptions() - Method in class org.inb.biomoby.shared.message.ServiceNotes
 
hasFailure() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
hasFormat - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasFormat - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hashCode() - Method in class ca.ucalgary.services.util.SourceMap
 
hashCode() - Method in class org.biomoby.shared.data.MobyContentInstance
 
hashCode() - Method in class org.biomoby.shared.data.MobyDataComposite
 
hashCode() - Method in class org.biomoby.shared.data.MobyDataObjectSet
Implemented solely because of the general contract that c1.equals(c2) implies that c1.hashCode()==c2.hashCode()
hashCode() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
hashCode() - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns the hash code value for this list.
hashCode() - Method in class org.biomoby.shared.MobyService
 
hashCode() - Method in class org.biomoby.shared.schema.MElement
override the hashCode() and equals() method of Object; In MElementHashtable class, we will use a hashtable to /*store MElement and articleNames;
hashCode() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
hashCode() - Method in class org.inb.biomoby.central.MobyCentral
 
hashCode() - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
hasOperation - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasOperation - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasOperationDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasOperationDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasOperationNameText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasOperationNameText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasOrganisationDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasOrganisationDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasOrganisationNameText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasOrganisationNameText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasParameterDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasParameterDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasParameterNameText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasParameterNameText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasParameterType - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasParameterType - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasResourceContent - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasResourceContent - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasSaveButton() - Method in class org.biomoby.service.dashboard.CommonConsole
 
hasSchemaType - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasSchemaType - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasServiceDescriptionLocation - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasServiceDescriptionLocation - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasServiceDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasServiceDescriptionText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasServiceNameText - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasServiceNameText - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasServiceType - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasServiceType - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasTransportType - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasTransportType - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
hasUnitTest - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
hasVerboseModeSwitcher() - Method in class org.biomoby.service.dashboard.CommonConsole
 
hasXMLSource() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
hasXMLSource() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
HEAD_COLLECTION_CONNECTION - Static variable in class org.biomoby.client.ServicesEdge
 
HeaderBorder - Class in org.inb.biomoby.client.gui.swing.border
 
HeaderBorder(String) - Constructor for class org.inb.biomoby.client.gui.swing.border.HeaderBorder
 
HeaderBorder.EmptyBorder - Class in org.inb.biomoby.client.gui.swing.border
 
HeaderBorder.EmptyBorder() - Constructor for class org.inb.biomoby.client.gui.swing.border.HeaderBorder.EmptyBorder
 
HEARTBEAT - Static variable in interface org.omg.lsae.sax.LsaeTags
 
HeartBeatEvent - Class in org.omg.lsae.notifications
 
HeartBeatEvent() - Constructor for class org.omg.lsae.notifications.HeartBeatEvent
 
HeartbeatProgress - Class in org.inb.lsae
 
HeartbeatProgress() - Constructor for class org.inb.lsae.HeartbeatProgress
 
HELP_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
HELP_HTML_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
 
HELP_TAB_COLOR - Static variable in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
 
HELP_TAB_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
 
HELP_TAB_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
 
HIDDEN_PARAM - Static variable in class ca.ucalgary.services.CGIServlet
 
HIDDEN_SENTINEL - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
HierarchicalClustering - Class in org.inb.biomoby.shared.ontology
 
HierarchicalClustering() - Constructor for class org.inb.biomoby.shared.ontology.HierarchicalClustering
 
hierarchyChanged(HierarchyEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
HMM_Text - Class in org.inb.biomoby.shared.ontology
 
HMM_Text() - Constructor for class org.inb.biomoby.shared.ontology.HMM_Text
 
HMMPfam_Report - Class in org.inb.biomoby.shared.ontology
 
HMMPfam_Report() - Constructor for class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
HMMPfam_ReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
HMMPfam_ReportComponent(HMMPfam_Report) - Constructor for class org.inb.biomoby.client.gui.ontology.HMMPfam_ReportComponent
 
HMMSearch_Report - Class in org.inb.biomoby.shared.ontology
 
HMMSearch_Report() - Constructor for class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
HORIZONTAL - Static variable in class ca.ucalgary.seahawk.util.CombinedIcon
 
HRBorder - Class in org.inb.biomoby.client.gui.swing.border
 
HRBorder() - Constructor for class org.inb.biomoby.client.gui.swing.border.HRBorder
 
HRBorder(Color) - Constructor for class org.inb.biomoby.client.gui.swing.border.HRBorder
 
HSSP_Text - Class in org.inb.biomoby.shared.ontology
 
HSSP_Text() - Constructor for class org.inb.biomoby.shared.ontology.HSSP_Text
 
HTML_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
HTML_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
HTML_FORM_URL_PARAM - Static variable in class ca.ucalgary.services.CGIService
 
htmlifyToolTipText(String, int) - Static method in class ca.ucalgary.seahawk.util.HTMLUtils
By turning the tool tip text into HTML, we can make it multiline!
HTMLUtils - Class in ca.ucalgary.seahawk.util
 
HTMLUtils() - Constructor for class ca.ucalgary.seahawk.util.HTMLUtils
 
HTTP_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
HTTP_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
hyperlinkUpdate(HyperlinkEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
The editor pane calls back here when the user flies over or clicks on a hyperlink

I

IAsyncMobyImpl - Interface in org.inb.biomoby.service
 
IAsyncMobyService - Interface in org.inb.biomoby.service
 
IC - Static variable in class org.biomoby.shared.data.MobyDataXref
 
ICISPedigreeTree - Class in org.biomoby.service.dashboard.renderers
This is a very specific viewer (it understands just one specific Biomoby type - GCP_GermplasmPedigreeTree).
ICISPedigreeTree() - Constructor for class org.biomoby.service.dashboard.renderers.ICISPedigreeTree
 
ID - Static variable in class org.inb.biomoby.service.resolver.MobyWSRFScopeFeature
 
ID_PARAM - Static variable in class ca.ucalgary.services.WrappingServlet
 
IDA - Static variable in class org.biomoby.shared.data.MobyDataXref
 
identifier - Static variable in class org.biomoby.client.rdf.vocabulary.DC_PROTEGE
 
IDynamicComponent<T extends IDynamicComponent.MobyComponentListener> - Interface in org.inb.biomoby.client.gui
 
IDynamicComponent.MobyComponentListener - Interface in org.inb.biomoby.client.gui
 
IEA - Static variable in class org.biomoby.shared.data.MobyDataXref
 
IEP - Static variable in class org.biomoby.shared.data.MobyDataXref
 
IGI - Static variable in class org.biomoby.shared.data.MobyDataXref
 
iHAS - Static variable in interface org.biomoby.shared.Central
A relationship type expressing a contaiment (as integer).
iHASA - Static variable in interface org.biomoby.shared.Central
A relationship type expressing a contaiment (as integer).
iISA - Static variable in interface org.biomoby.shared.Central
A relationship type expressing a straight inheritance (as integer).
IMAGE_ANONYMOUS_NAME - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
IMAGE_DATATYPE - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
Image_Encoded - Class in org.inb.biomoby.shared.ontology
 
Image_Encoded() - Constructor for class org.inb.biomoby.shared.ontology.Image_Encoded
 
Image_EncodedComponent - Class in org.inb.biomoby.client.gui.ontology
 
Image_EncodedComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.Image_EncodedComponent
 
Image_EncodedComponent(Image_Encoded) - Constructor for class org.inb.biomoby.client.gui.ontology.Image_EncodedComponent
 
ImageComponent - Class in org.inb.biomoby.client.gui.auxiliary
 
ImageComponent(BufferedImage) - Constructor for class org.inb.biomoby.client.gui.auxiliary.ImageComponent
 
ImageLoader - Class in org.inb.swing
Auxiliary class for loading images with a simple soft reference based cache.
IMobyCentralCache - Interface in org.inb.biomoby.central.cache
An interface that defines where to store a cache
IMP - Static variable in class org.biomoby.shared.data.MobyDataXref
 
importCanceled(DataImportChoiceDialog) - Method in interface ca.ucalgary.seahawk.gui.DataImportChoiceListener
 
importCanceled(DataImportChoiceDialog) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
importConfirmed(DataImportChoiceDialog, MobyDataObject[]) - Method in interface ca.ucalgary.seahawk.gui.DataImportChoiceListener
 
importConfirmed(DataImportChoiceDialog, MobyDataObject[]) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
importData(JComponent, Transferable) - Method in class ca.ucalgary.seahawk.gui.FileAndTextTransferHandler
 
importData(JComponent, Transferable) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
incrementErrorCountForURL(String, int) - Method in interface org.biomoby.registry.rdfagent.util.CentralDataAccess
 
incrementErrorCountForURL(String, int) - Method in class org.biomoby.registry.rdfagent.util.CentralDataAccessImpl
 
INDENTATION_XSL_RESOURCE - Static variable in class ca.ucalgary.services.SoapServlet
 
indexOf(Object) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns the index in this list of the first occurrence of the specified element, or -1 if this list does not contain this element.
indexOf(Object) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
indexOf(Object) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
inferBinaryName(JavaFileManager.Location, JavaFileObject) - Method in class org.inb.util.MemoryFileManager
 
INFO - Static variable in class org.biomoby.registry.rdfagent.util.Log
log only info messages
info(String) - Static method in class org.biomoby.registry.rdfagent.util.Log
 
INFO - Static variable in exception org.biomoby.shared.parser.ServiceException
A severity code that corresponds to a message not related to any error.
info(String) - Static method in exception org.biomoby.shared.parser.ServiceException
Create an instance of ServiceException that represents an info.
INHERITED_MEMBERS_SENTINEL - Static variable in class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
inheritsFrom(String) - Method in class org.biomoby.shared.MobyDataType
Searches the ontology lineage of the current data type against the data type corresponding to the provided name.
inheritsFrom(MobyDataType) - Method in class org.biomoby.shared.MobyDataType
Searches the ontology lineage of the current data type against the provided type.
init() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
Sets up temporary files, icons, etc.
init() - Method in class ca.ucalgary.seahawk.gui.MobyContentHelpPane
Sets up icons, tab title, etc.
init() - Method in class ca.ucalgary.seahawk.gui.splash.SeahawkSplasher
Method invoked when running as an applet.
init() - Method in class ca.ucalgary.services.ACDService
 
init() - Method in class ca.ucalgary.services.CGIService
 
init() - Method in class ca.ucalgary.services.SoapServlet
 
init() - Method in class ca.ucalgary.services.WrappingServlet
 
init() - Method in class ca.ucalgary.services.WSDLService
 
init() - Method in class org.biomoby.client.GraphsServlet
Servlet initialization...
init(Properties) - Static method in class org.biomoby.registry.sync.CentralFactory
Initialise the master and the local centrals.
init() - Method in class org.biomoby.service.MobyServlet
If you override this method, be sure to call super.init()
INIT_OUTPUT_BUFFER_SIZE - Static variable in class org.biomoby.service.MobyServlet
 
initializeList() - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
initLogger(String, String) - Static method in class org.biomoby.registry.sync.logging.MobySecondaryLogging
Inits the logger.
inNamespaces - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
inNamespaces - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
inNamespaces - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
input - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
Input - Class in org.inb.biomoby.shared.registry
 
Input() - Constructor for class org.inb.biomoby.shared.registry.Input
 
INPUT_EMPTY_OBJECT - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Given an empty input data.
INPUT_INCORRECT_COLLECTION - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Given input of type Collection is incorrect.
INPUT_INCORRECT_NAMESPACE - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Incorrect Namespace in the input object.
INPUT_INCORRECT_PARAMETER - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Given parameter is incorrect.
INPUT_INCORRECT_SIMPLE - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Given input of type Simple is incorrect.
INPUT_NOT_ACCEPTED - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Used when a client tries to send input data to a job created in a previous call but the server does not any more accept input data.
INPUT_REQUIRED_PARAMETER - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Service requires a parameter but none was given.
INPUT_REQUIRED_PARAMETERS - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Service requires two or more data inputs.
INPUT_RULE_URIS_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
INPUT_XSD_TYPES_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
inputCollectionData - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
inputCollectionDataType - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
inputDataType - Variable in class org.biomoby.client.DataTypeConnector
 
inputParameter - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
inputParameter - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
INPUTS_INVALID - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Input data are invalid; they do not match with their definitions, or with their dependency conditions.
INPUTS_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
inputSimpleData - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
inputSimpleDataType - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
INPUTSRC_ATTR - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
insertErrorCountForURL(String, int) - Method in interface org.biomoby.registry.rdfagent.util.CentralDataAccess
 
insertErrorCountForURL(String, int) - Method in class org.biomoby.registry.rdfagent.util.CentralDataAccessImpl
 
insertString(int, String, AttributeSet) - Method in class org.biomoby.service.dashboard.PerlMoSeSSyntaxDocument
 
insertString(DocumentFilter.FilterBypass, int, String, AttributeSet) - Method in class org.inb.swing.RegExDocumentFilter
 
insertUpdate(DocumentEvent) - Method in class ca.ucalgary.seahawk.gui.FilterSearchWidget
 
insertUpdate(DocumentEvent) - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
insertUpdate(DocumentEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyObjectPropertyTable.DefaultPropertyNameValidator
 
insertUpdate(DocumentEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
instance() - Static method in class org.biomoby.service.dashboard.renderers.RendererRegistry
 
instance() - Static method in class org.inb.biomoby.central.cache.CacheConfig
A singleton instance creator.
instance() - Static method in class org.inb.biomoby.central.model.DatatypesModel
A singleton model creation method.
instance() - Static method in class org.inb.biomoby.central.model.MobyCentralModel
 
instance() - Static method in class org.inb.biomoby.central.model.NamespacesModel
A singleton model creation method.
instance() - Static method in class org.inb.biomoby.central.model.ServicesModel
 
INSTANTIATED_FG_COLOUR - Static variable in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
INSTANTIATED_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
INT_CHOICE_MAX - Static variable in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
INT_INPUT_PART_OPTION - Static variable in class ca.ucalgary.services.util.PBERecorder
 
IntAct_XML - Class in org.inb.biomoby.shared.ontology
 
IntAct_XML() - Constructor for class org.inb.biomoby.shared.ontology.IntAct_XML
 
INTEGER - Static variable in class org.biomoby.shared.schema.MElement
A moby:Integer primitive type
INTEGER_TYPE - Static variable in class org.biomoby.shared.MobySecondaryData
 
Interaction - Class in org.inb.biomoby.shared.ontology
 
Interaction() - Constructor for class org.inb.biomoby.shared.ontology.Interaction
 
InteractionMethod - Class in org.inb.biomoby.shared.ontology
 
InteractionMethod() - Constructor for class org.inb.biomoby.shared.ontology.InteractionMethod
 
Interactor - Class in org.inb.biomoby.shared.ontology
 
Interactor() - Constructor for class org.inb.biomoby.shared.ontology.Interactor
 
interceptRequest(HttpServletRequest, HttpServletResponse) - Method in interface ca.ucalgary.services.util.DataRecorder
 
interceptRequest(HttpServletRequest, HttpServletResponse) - Method in class ca.ucalgary.services.util.PBERecorder
 
interceptRequest(String) - Method in class org.biomoby.client.BaseClient
 
interceptRequest(String) - Method in class org.biomoby.client.BaseCmdLineClient
 
INTERNAL_PROCESSING_ERROR - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: A placeholder for all other errors not defined explicitly in the Biomoby API.
InterProMotifAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
InterProMotifAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.InterProMotifAnnotatedAASequence
 
InterProMotifAnnotatedAASequenceComponent<T extends InterProMotifAnnotatedAASequence> - Class in org.inb.biomoby.client.gui.ontology
 
InterProMotifAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
InterProMotifAnnotatedAASequenceComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
InterProMotifAnnotatedAASequenceComponent.InterProMotifAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
InterProMotifAnnotation - Class in org.inb.biomoby.shared.ontology
 
InterProMotifAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.InterProMotifAnnotation
 
InterProMotifAnnotationListPane<T extends InterProMotifAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
InterProMotifAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.InterProMotifAnnotationListPane
 
InterProMotifAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.InterProMotifAnnotationListPane
 
interrupt() - Method in class org.biomoby.service.dashboard.SwingWorker
A new method that interrupts the worker thread.
intValue() - Method in class org.biomoby.shared.data.MobyDataInt
A convenience method, which returns the underlying BigInteger's primitive int representation.
INVALID_PROP_QNAME - Static variable in interface org.soap.sax.FaultTags
 
InvalidQueryExpressionFault - Exception in org.inb.biomoby.shared.wsrf.fault
 
InvalidQueryExpressionFault(String, InvalidQueryExpressionFaultType) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.InvalidQueryExpressionFault
 
InvalidQueryExpressionFault(String, InvalidQueryExpressionFaultType, Throwable) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.InvalidQueryExpressionFault
 
InvalidQueryExpressionFaultType - Class in org.inb.wsrf.rp2
 
InvalidQueryExpressionFaultType() - Constructor for class org.inb.wsrf.rp2.InvalidQueryExpressionFaultType
 
InvalidResourcePropertyQNameFault - Exception in org.inb.biomoby.shared.wsrf.fault
 
InvalidResourcePropertyQNameFault(String, InvalidResourcePropertyQNameFaultType) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.InvalidResourcePropertyQNameFault
 
InvalidResourcePropertyQNameFault(String, InvalidResourcePropertyQNameFaultType, Throwable) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.InvalidResourcePropertyQNameFault
 
InvalidResourcePropertyQNameFaultType - Class in org.inb.wsrf.rp2
 
InvalidResourcePropertyQNameFaultType() - Constructor for class org.inb.wsrf.rp2.InvalidResourcePropertyQNameFaultType
 
invocationId - Variable in class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
invoke(MobyMessage) - Method in class org.inb.biomoby.client.MobyDispatch
Method to synchronously invoke BioMoby service (provided in constructor)
invoke(SOAPMessage) - Method in class org.inb.biomoby.service.MobyProvider
 
invokeAsync(MobyMessage) - Method in class org.inb.biomoby.client.MobyDispatch
 
invokeInit(String, JApplet) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Invokes the init method of the JApplet class provided by name.
invokeInit(String, JApplet) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Invokes the init method of the JApplet class provided by name.
invokeMain(String, String[]) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Invokes the main method of the provided class name.
invokeMain(String, String[]) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Invokes the main method of the provided class name.
invokeService() - Method in class org.biomoby.client.MobyRequest
The main method of the class.
invokeService(MobyRequestEventHandler) - Method in class org.biomoby.client.MobyRequest
Asynchronous call to invokeService.
invokeStaticMethod(String, String, int) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Invokes a method of the provided class name with an integer argument.
invokeStaticMethod(String, String, boolean) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Invokes a method of the provided class name with a boolean argument.
invokeStaticMethod(String, String, double) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Invokes a method of the provided class name with a double (real number) argument.
invokeStaticMethod(String, String) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Invokes a method of the provided class name with no arguments.
invokeStaticMethod(String, String, int) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Invokes a method of the provided class name with an integer argument.
invokeStaticMethod(String, String, boolean) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Invokes a method of the provided class name with a boolean argument.
invokeStaticMethod(String, String, double) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Invokes a method of the provided class name with a double (real number) argument.
invokeStaticMethod(String, String) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Invokes a method of the provided class name with no arguments.
IOUtils - Class in ca.ucalgary.services.util
 
IOUtils() - Constructor for class ca.ucalgary.services.util.IOUtils
 
IPI - Static variable in class org.biomoby.shared.data.MobyDataXref
 
IS_ALIVE_SERVICE_URL - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
isa - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
ISA - Static variable in interface org.biomoby.shared.Central
A relationship type expressing a straight inheritance (as string).
isAlive - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
isAppendMode() - Method in class org.biomoby.service.dashboard.CommonConsole
 
isArticleNameRule(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isAsBytes() - Method in class org.biomoby.client.MobyServiceLocator
Return the current setting - see MobyServiceLocator.setAsBytes(boolean).
isAsynchronous() - Method in class org.biomoby.shared.MobyService
 
isAuthoritative() - Method in class org.biomoby.shared.MobyService
 
isAuthoritative() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
isAuthoritative() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
isAuthoritative() - Method in class org.inb.biomoby.shared.registry.Service
 
isBorderOpaque() - Method in class org.inb.biomoby.client.gui.swing.border.HeaderBorder.EmptyBorder
 
isBorderOpaque() - Method in class org.inb.biomoby.client.gui.swing.border.HeaderBorder
 
isBorderOpaque() - Method in class org.inb.biomoby.client.gui.swing.border.HRBorder
 
isBorderOpaque() - Method in class org.inb.biomoby.client.gui.swing.border.RoundedBorder
 
isBound() - Method in class org.biomoby.shared.MobyDataTypeTemplate
 
isCached() - Method in class org.inb.biomoby.central.cache.CacheConfig
Method to check whether a cache must be used
isCellEditable(Object, int) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
isCellEditable(int, int) - Method in class org.biomoby.service.dashboard.TableSorter
 
isCellEditable(Object, int) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
By default, make the column with the Tree in it the only editable one.
isCellEditable(EventObject) - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellEditor
Overridden to return false, and if the event is a mouse event it is forwarded to the tree.
isCellEditable(Object, int) - Method in interface org.biomoby.service.dashboard.treetable.TreeTableModel
Indicates whether the the value for node node, at column number column is editable.
isCellEditable(int, int) - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
isCellEditable(int, int) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
Method allows to edit only those properties that belong to the editing object.
isCellEditable(int, int) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
isCommitted() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
isCompleted() - Method in class org.omg.lsae.notifications.AnalysisEvent
 
isCompleted() - Method in class org.omg.lsae.notifications.HeartBeatEvent
 
isCompleted() - Method in class org.omg.lsae.notifications.PercentEvent
 
isCompleted() - Method in class org.omg.lsae.notifications.StateEvent
 
isCompleted() - Method in class org.omg.lsae.notifications.StepEvent
 
isCompleted() - Method in class org.omg.lsae.notifications.TimeProgressEvent
 
isConfiguration - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
isConfiguration - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
isConsumed() - Method in class org.biomoby.client.MobyRequestEvent
 
isConvertible(URLConnection) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
isDataFlavorSupported(DataFlavor) - Method in class ca.ucalgary.seahawk.gui.SeahawkTransferable
 
isDataFlavorSupported(DataFlavor) - Method in class ca.ucalgary.seahawk.util.MobyDataTransferable
 
isDataFlavorSupported(DataFlavor) - Method in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
isDataTypeRule(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isDNA(String) - Static method in class ca.ucalgary.seahawk.util.Sequence
 
isEmpty() - Method in class ca.ucalgary.seahawk.util.MutableNodeList
 
isEmpty() - Method in class ca.ucalgary.services.util.SourceMap
Is this a blank, uninstantiated object?
isEmpty(String) - Static method in class org.biomoby.service.BaseService
A utility method returning true if 'value' is either null or a string consisting only from whitespaces.
isEmpty() - Method in class org.biomoby.shared.data.MobyContentInstance
Is this a blank, uninstantiated object?
isEmpty() - Method in class org.biomoby.shared.data.MobyDataComposite
Is this a blank, uninstantiated object?
isEmpty() - Method in class org.biomoby.shared.data.MobyDataObjectSet
Logically equivalent to size() == 0.
isEmpty() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
isEmpty() - Method in class org.biomoby.shared.data.MobyDataObjectVector
 
isEmpty() - Method in class org.inb.biomoby.shared.message.MobyCollection
 
isEmpty() - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
isEnabled(String, boolean, String, Object) - Static method in class org.biomoby.service.dashboard.DashboardConfig
Get a boolean value associated with the given configuration key, or - if not found - get the given default value.
isEndingEdge() - Method in class org.biomoby.client.DataServiceEdge
Indicate if this edge is a starting or ending edge of a graph.
ISequenceCoordinateTransformer - Interface in org.inb.biomoby.client.gui
 
ISequenceDependent - Interface in org.inb.biomoby.client.gui
 
ISequenceTransformer - Interface in org.inb.biomoby.client.gui
 
isExpandObjects() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
isExpandServices() - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
isFilterForwardConsistent() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
If the filter condition has changed since the next service was originally called, only allow navigation to that document (service results) again if the new filter allows the data used in the original call to pass (for logical dataflow consistency).
isFunctionOf - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
isFunctionOf - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
isHAS() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return true if this node has HAS relationship to its parents.
isLeaf(Object) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
isLeaf() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return true if this node represents a leaf in a data type tree.
isLeaf(Object) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
isLoggable() - Static method in class org.biomoby.registry.rdfagent.util.Log
 
isLoop() - Method in class org.biomoby.client.ExtendedServiceLocator
Get back what can be set by ExtendedServiceLocator.setLoop(boolean).
isLSID(String) - Static method in class org.biomoby.shared.LSIDResolver
 
isMandatory() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
isMandatory() - Method in class org.biomoby.service.dashboard.Dashboard
 
isMandatory() - Method in interface org.biomoby.service.dashboard.DashboardPanel
Some panels can be selected by users as not-needed - so they do not show at the start-up.
isMandatory() - Method in class org.biomoby.service.dashboard.RegistryPanel
 
isMapped(Node) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isMemberRule(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isMembersRule(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isMobyReserved(String) - Static method in class org.inb.biomoby.generator.GeneratorUtil
 
isMobyURL(URL) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
isNamespaceRule(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isNewShowing() - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
isNucleicAcid(String) - Static method in class ca.ucalgary.seahawk.util.Sequence
Case insensitve search for DNA or RNA like characters in the provid3ed string
isNucleicAcid(String) - Static method in class org.biomoby.service.test.FromFastaToDNASequence
 
isObjectValid() - Method in class org.biomoby.shared.data.MobyDataComposite
Report whether all required fields for the object's datatype have been instantiated (i.e. the object is ready to use as input to a service).
isPosixCharacterClass(String) - Static method in class ca.ucalgary.seahawk.services.RegexParser
 
isPrefixRule(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isPrimary() - Method in class org.biomoby.shared.MobyData
 
isPrimary() - Method in class org.biomoby.shared.MobyPrimaryData
Returns always true.
isPrimary() - Method in class org.biomoby.shared.MobySecondaryData
 
isPrimitive() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return true if this node represents a primitive data type.
isPrimitive(String) - Method in interface org.biomoby.shared.MobyObjectDecomposition
PRE:None.
isPrimitive(String) - Method in class org.biomoby.shared.MobyObjectDecompositionImpl
 
isPrimitive(String) - Static method in class org.biomoby.shared.PrimitiveTypes
 
isPrimitive(String) - Static method in class org.biomoby.shared.schema.MElement
 
isPrimitiveDataType(String) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isPrimitiveType(String) - Static method in class org.biomoby.service.generator.DataTypesGenerator
Return true if 'dataTypeName' is a Biomoby primitive type.
isPrimitiveType() - Method in class org.biomoby.shared.datatypes.MobyObject
Return true if this object represents a Biomoby primitive type.
isProtein(String) - Static method in class ca.ucalgary.seahawk.util.Sequence
 
isPublic() - Method in class org.biomoby.registry.meta.Registry
Return true if this BioMoby registry is open without any access restrictions.
isRDFValid() - Method in class org.biomoby.shared.extended.ServiceInstanceParser
Method to check whether an RDF document contained only valid services.
isRegex(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isRequestedSessionIdFromCookie() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
isRequestedSessionIdFromUrl() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
isRequestedSessionIdFromURL() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
isRequestedSessionIdValid() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
isRNA(String) - Static method in class ca.ucalgary.seahawk.util.Sequence
 
ISS - Static variable in class org.biomoby.shared.data.MobyDataXref
 
ISS_Annotation_XML - Class in org.inb.biomoby.shared.ontology
 
ISS_Annotation_XML() - Constructor for class org.inb.biomoby.shared.ontology.ISS_Annotation_XML
 
ISS_Report - Class in org.inb.biomoby.shared.ontology
 
ISS_Report() - Constructor for class org.inb.biomoby.shared.ontology.ISS_Report
 
isSecondaryParamDialogNew() - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
isSecure() - Method in class org.biomoby.service.test.TestHttpServletRequest
 
isServiceFiltered(MobyService) - Method in class org.biomoby.registry.sync.filtering.ServiceFilter
Returns whether a service was filtered and therefore is not processed any further in the update process.
isShowingFailure() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Reports whetehr the current tab (if any is showing) is displaying a failure, such as network or protocol failure while requesting a service.
isSimpleXref() - Method in class org.biomoby.shared.datatypes.MobyXref
Find what kind of cross reference this instance is.
isSorting() - Method in class org.biomoby.service.dashboard.TableSorter
 
isString() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Return true if this node represents a String Biomoby primitive type.
isURLRegex(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
isUserInRole(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
isUsingCache() - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
Indicate whether the implementtaion really is using a local cache.
isUsingCache() - Method in interface org.biomoby.shared.CentralCached
Indicate whether the implementtaion really is using a local cache.
isValid() - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
isVerboseMode() - Method in class org.biomoby.service.dashboard.CommonConsole
 
isWeakConnection() - Method in class org.biomoby.client.ServicesEdge
Returns quality of this connection.
isWrappingService() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
Tells whether the tab is in the middle of wrapping a Web Service at the moment.
isWsrf() - Method in class org.soap.SOAPFault
 
isXPath(Element) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
item(int) - Method in class ca.ucalgary.seahawk.util.MutableNodeList
 
item(int) - Method in class ca.ucalgary.services.WrappingServlet.MyNodeList
 
item(int) - Method in class org.biomoby.shared.MobyPrefixResolver.MobyNodeList
 
IterativeMatchResult - Class in ca.ucalgary.seahawk.services
A utility class used by MobyComplexBuilder to "trick" rule evaluation into seeing specific individual instances of quantified regex capture groups, e.g.
IterativeMatchResult(MatchResult, Map<Integer, String[]>) - Constructor for class ca.ucalgary.seahawk.services.IterativeMatchResult
 
iterator() - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
Return an iterator over all registered renderers.
iterator() - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
iterator() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
iterator() - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns an iterator over the elements in this list in proper sequence.
iterator() - Method in class org.inb.biomoby.central.ServiceLoader
 
iterator() - Method in class org.inb.biomoby.shared.message.MobyCollection
 
iterator() - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
ITransformable - Interface in org.inb.biomoby.client.gui
 

J

javaEscape(String) - Static method in class org.biomoby.shared.Utils
Make 'value' a valid Java identifier by trimming it and by replacing "unwanted" characters by underscores.
JAXBMobyCentralImpl - Class in org.inb.biomoby.central.factory.jaxb
 
JAXBMobyCentralImpl(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
JDOMUtils - Class in org.biomoby.shared.parser
 
JDOMUtils() - Constructor for class org.biomoby.shared.parser.JDOMUtils
 
JmolPane - Class in org.inb.biomoby.client.gui.auxiliary
 
JmolPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.JmolPane
 
JNamespaceI - Interface in org.biomoby.registry.definitions.types
 
JNamespacesSqlImpl - Class in org.biomoby.registry.definitions.types
 
JNamespacesSqlImpl() - Constructor for class org.biomoby.registry.definitions.types.JNamespacesSqlImpl
 
JObjectsI - Interface in org.biomoby.registry.definitions.types
 
JObjectsSqlImpl - Class in org.biomoby.registry.definitions.types
 
JObjectsSqlImpl() - Constructor for class org.biomoby.registry.definitions.types.JObjectsSqlImpl
 
join(Iterable, String) - Static method in class ca.ucalgary.services.util.WSDLConfig
 
join(String, String[]) - Static method in class ca.ucalgary.services.util.XHTMLForm
 
join(String, String[], StringBuffer) - Static method in class ca.ucalgary.services.util.XHTMLForm
 
joinPaths(ServicesEdge[][]) - Static method in class org.biomoby.client.FilterServices
Join together several paths.
JProgressBarWithCancel - Class in org.biomoby.service.dashboard
!!!
JProgressBarWithCancel() - Constructor for class org.biomoby.service.dashboard.JProgressBarWithCancel
Constructor with a horizontal progress bar.
JProgressBarWithCancel(int, int) - Constructor for class org.biomoby.service.dashboard.JProgressBarWithCancel
Creates a horizontal progress bar with the specified minimum and maximum.
JServiceI - Interface in org.biomoby.registry.definitions.types
 
JServicesSqlImpl - Class in org.biomoby.registry.definitions.types
 
JServicesSqlImpl() - Constructor for class org.biomoby.registry.definitions.types.JServicesSqlImpl
 
JTreeTable - Class in org.biomoby.service.dashboard.treetable
This example shows how to create a simple JTreeTable component, by using a JTree as a renderer (and editor) for the cells in a particular column in the JTable.
JTreeTable(TreeTableModel) - Constructor for class org.biomoby.service.dashboard.treetable.JTreeTable
A default constructor.
JTreeTable.TreeTableCellEditor - Class in org.biomoby.service.dashboard.treetable
TreeTableCellEditor implementation.
JTreeTable.TreeTableCellEditor() - Constructor for class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellEditor
 
JTreeTable.TreeTableCellRenderer - Class in org.biomoby.service.dashboard.treetable
A TreeCellRenderer that displays a JTree.
JTreeTable.TreeTableCellRenderer(TreeModel) - Constructor for class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellRenderer
 

K

keyPressed(KeyEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Implemented to provide paste functionality (control-v or the paste button on a Sun keyboard), since the editor panes are not editable and therefore by default do not respond to paste events.
keyPressed(KeyEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
Implemented to provide paste functionality (control-v or the paste button on a Sun keyboard), since the editor panes are not editable and therefore by default do not respond to paste events.
keyPressed(KeyEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent.ScriptTextField
 
keyReleased(KeyEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
keyReleased(KeyEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
keyReleased(KeyEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent.ScriptTextField
 
keySet() - Method in class ca.ucalgary.services.util.SourceMap
Retrieves a list of the field names in this object
keySet() - Method in class org.biomoby.shared.data.MobyContentInstance
Retrieves a list of the query names in this object.
keySet() - Method in class org.biomoby.shared.data.MobyDataComposite
Retrieves a list of the field names in this object
keyTyped(KeyEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
keyTyped(KeyEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
keyTyped(KeyEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent.ScriptTextField
 

L

label - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
LabelButton - Class in org.inb.swing
Light-weight JLabel based button.
LabelButton(Icon) - Constructor for class org.inb.swing.LabelButton
 
LabeledAnnotationListPane<T extends Annotation,K extends AbstractAnnotationListPane.AnnotationListListener> - Class in org.inb.biomoby.client.gui.auxiliary
 
LabeledAnnotationListPane(boolean) - Constructor for class org.inb.biomoby.client.gui.auxiliary.LabeledAnnotationListPane
 
LabeledAnnotationListPane(List<T>, boolean) - Constructor for class org.inb.biomoby.client.gui.auxiliary.LabeledAnnotationListPane
 
lastIndexOf(Object) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns the index in this list of the last occurrence of the specified element, or -1 if this list does not contain this element.
lastIndexOf(Object) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
lastIndexOf(Object) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
LegacyService - Class in ca.ucalgary.services
A base servlet for any servlet wanting to transform from Moby datatypers into legacy (semi-structured) data formats.
LegacyService() - Constructor for class ca.ucalgary.services.LegacyService
 
LegacyServiceTestCase - Class in ca.ucalgary.services.test
 
LegacyServiceTestCase(String) - Constructor for class ca.ucalgary.services.test.LegacyServiceTestCase
 
length() - Method in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
LEXICAL_COMPARATOR - Static variable in class org.biomoby.service.dashboard.TableSorter
 
LIFTING_SCHEMA_PATH - Static variable in class ca.ucalgary.services.util.RuleCreator
 
list() - Method in interface org.biomoby.registry.meta.Registries
Return a list of synonyms (abbreviations) of all known BioMoby registries.
list() - Method in class org.biomoby.registry.meta.RegistriesList
 
list(JavaFileManager.Location, String, Set<JavaFileObject.Kind>, boolean) - Method in class org.inb.util.MemoryFileManager
 
List__Text - Class in org.inb.biomoby.shared.ontology
 
List__Text() - Constructor for class org.inb.biomoby.shared.ontology.List__Text
 
LIST_CHOICE_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 
LIST_FILE - Static variable in interface org.biomoby.shared.CentralCached
A special file name, containing a list of cached entities.
List_Text - Class in org.inb.biomoby.shared.ontology
 
List_Text() - Constructor for class org.inb.biomoby.shared.ontology.List_Text
 
listIterator() - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns a list iterator of the elements in this list (in proper sequence).
listIterator(int) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns a list iterator of the elements in this list (in proper sequence), starting at the specified position in this list.
listIterator() - Method in class org.inb.biomoby.shared.message.MobyCollection
 
listIterator(int) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
listIterator() - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
listIterator(int) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
load(MobyCentral, String) - Method in class org.inb.biomoby.central.cache.CacheConfig
Generic method to load BioMoby entities from a cache.
load(Reader) - Method in class org.inb.biomoby.central.cache.CacheConfig
Generic method to load BioMoby entities from a cache.
load(Class<T>) - Static method in class org.inb.biomoby.central.ServiceLoader
 
load(String) - Method in class org.inb.biomoby.client.gui.auxiliary.JmolPane
 
load(String) - Static method in class org.inb.swing.ImageLoader
 
loadB2JMapping() - Static method in class org.biomoby.shared.parser.MobyParser
Load mapping class between Biomoby data types names and their Java representations.
loadClass(String) - Method in class org.inb.biomoby.MobyClassLoader
 
loadDocument(InputStream) - Static method in class org.biomoby.client.CentralImpl
Loads a DOM Document from an InputStream.
LOADED_TAB_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentPane
 
loadIcon(String) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Load shared icon.
loadInstances(ClassLoader) - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
Load all Renderer implementations that are registered in the given ClassLoader.
loadMobyDataFromXPointer(URL, Map<String, String>, FilterSearch) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Get the data instance object associated with a given XPointer in a Moby XML doc.
loadMobyDataFromXPointer(URL, Document, String, Map<String, String>, FilterSearch) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.AbstractPanel
 
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.Dashboard
 
loadOnlyOnDemand() - Method in interface org.biomoby.service.dashboard.DashboardPanel
Some panels are less important for most users (e.g. debugging panels) so they are shown only when a user specifically selects them.
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.DebuggingPanel
 
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.ExamplePanel
 
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.GeneratorPanel
 
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.PerlMoSeSPanel
 
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.RegistrationPanel
 
loadOnlyOnDemand() - Method in class org.biomoby.service.dashboard.StatisticsPanel
 
loadPaneFromObject(MobyContentInstance, boolean) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Load a Seahawk browser tab with the data held in the given MobyContentInstance.
loadPaneFromURL(URL, boolean) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
loadPanels() - Method in class org.biomoby.service.dashboard.Dashboard
Load all available Dashboard panels...
loadServiceTypes(URL, Registry) - Static method in class org.biomoby.shared.MobyServiceType
Particularly useful for loading namespace definitions from cached file, or refreshing an in-memory cache.
locateBrowser() - Static method in class ca.ucalgary.seahawk.util.BrowserLauncher
Attempts to locate the default web browser on the local system.
locationToCaptureGroupNumber(String, int) - Static method in class ca.ucalgary.seahawk.services.RegexParser
 
locationURI - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
locationURI - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
log(String) - Method in class org.biomoby.client.GraphsServlet
 
Log - Class in org.biomoby.registry.rdfagent.util
A logging class for the agent.
Log() - Constructor for class org.biomoby.registry.rdfagent.util.Log
 
log(String) - Method in class org.biomoby.service.MobyServlet
 
log(String, Exception) - Method in class org.biomoby.service.MobyServlet
 
log(Exception, String) - Method in class org.biomoby.service.test.TestServletContext
 
log(String) - Method in class org.biomoby.service.test.TestServletContext
 
log(String, Throwable) - Method in class org.biomoby.service.test.TestServletContext
 
LOG_ENABLE - Static variable in class org.biomoby.registry.rdfagent.util.Constants
Should the agent log?
LOG_LEVEL - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The level of logging.
LOGFILE_PATH - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The directory in which to place logs.
LOGGER_NAME - Static variable in class org.biomoby.registry.sync.logging.MobySecondaryLogging
 
LogListener - Class in org.biomoby.shared.event
A simple implementation of a NotificationListener that prints all intercepted messages to a log.
LogListener() - Constructor for class org.biomoby.shared.event.LogListener
Default constructor.
logMessage(String) - Method in class org.inb.swing.StatusBar
Method sets a status bar message and logs it to the popup log panel.
logMessage(String, int) - Method in class org.inb.swing.StatusBar
Method sets a status bar message and logs it to the popup log panel.
longValue() - Method in class org.biomoby.shared.data.MobyDataInt
A convenience method, which returns the underlying BigInteger's primitive int representation.
LookAndFeelUtils - Class in org.biomoby.service.dashboard
A utility class helping to set different "Look and Feel"s.
LookAndFeelUtils() - Constructor for class org.biomoby.service.dashboard.LookAndFeelUtils
 
lostOwnership(Clipboard, Transferable) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
lostOwnership(Clipboard, Transferable) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
To satisfy the ClipboardOwner interface.
lostOwnership(Clipboard, Transferable) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
lostOwnership(Clipboard, Transferable) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
LOWERING_SCHEMA_PATH - Static variable in class ca.ucalgary.services.util.RuleCreator
 
LsaeTags - Interface in org.omg.lsae.sax
The tagnames for elements in AnalysisEvent XML
LSID_DATA_NAMESPACE - Static variable in class org.biomoby.shared.LSIDResolver
 
LSID_HTTP_NAMESPACE - Static variable in class org.biomoby.shared.LSIDResolver
 
LSID_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
LSID_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
LSID_SOAP_NAMESPACE - Static variable in class org.biomoby.shared.LSIDResolver
 
LSID_WSDL_NAMESPACE - Static variable in class org.biomoby.shared.LSIDResolver
 
LSIDAccessible - Interface in org.biomoby.shared
 
LSIDResolver - Class in org.biomoby.shared
Implementation of LSID resolution for data and metadata.
LSIDResolver() - Constructor for class org.biomoby.shared.LSIDResolver
 
LSIDResolverTestCase - Class in org.biomoby.shared.test
 
LSIDResolverTestCase(String) - Constructor for class org.biomoby.shared.test.LSIDResolverTestCase
 
LutefiskAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
LutefiskAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.LutefiskAnnotatedAASequence
 
LutefiskAnnotation - Class in org.inb.biomoby.shared.ontology
 
LutefiskAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
LutefiskReport - Class in org.inb.biomoby.shared.ontology
 
LutefiskReport() - Constructor for class org.inb.biomoby.shared.ontology.LutefiskReport
 

M

MacOS - Class in org.biomoby.registry.properties
This class incorporates the logic needed to obtain environment variables from the MacOS and Mac OS X.
Mailer - Class in org.biomoby.registry.rdfagent.util
This class is a mailer for the RDF agent.
Mailer() - Constructor for class org.biomoby.registry.rdfagent.util.Mailer
Constructor
main(String[]) - Static method in class ca.ucalgary.minnow.MinJarMaker
 
main(String[]) - Static method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
main(String[]) - Static method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
main(String[]) - Static method in class ca.ucalgary.seahawk.gui.splash.SeahawkSplasher
Shows the splash screen, launches the application and then disposes the splash screen.
main(String[]) - Static method in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
Runs the test suite when the class is invoked on the command line.
main(String[]) - Static method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
Runs the test suite when the class is invoked on the command line.
main(String[]) - Static method in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
main(String[]) - Static method in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
main(String[]) - Static method in class ca.ucalgary.seahawk.services.test.TextClientTestCase
 
main(String[]) - Static method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.test.ACDServiceTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.test.CGIServiceTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.test.LegacyServiceTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.test.SoapServletTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.test.WSDLServiceTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.util.test.ACDFileTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.util.test.WSDLConfigTestCase
 
main(String[]) - Static method in class ca.ucalgary.services.util.test.XHTMLFormTestCase
 
main(String[]) - Static method in class ca.ucalgary.util.SingletonApplication
 
main(String[]) - Static method in class org.biomoby.client.BaseCmdLineClient
 
main(String[]) - Static method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
 
main(String[]) - Static method in class org.biomoby.client.test.AsyncClientTestCase
Runs the test suite when the class is invoked on the command line.
main(String[]) - Static method in class org.biomoby.registry.definitions.types.JNamespacesSqlImpl
 
main(String[]) - Static method in class org.biomoby.registry.definitions.types.JObjectsSqlImpl
 
main(String[]) - Static method in class org.biomoby.registry.definitions.types.JServicesSqlImpl
 
main(String[]) - Static method in class org.biomoby.registry.properties.MobyCentralConfig
a brief test application that outputs the information obtained by calling each of the methods in this class.
main(String[]) - Static method in class org.biomoby.registry.properties.MobyProperties
 
Main - Class in org.biomoby.registry.rdfagent.verifier
The point of entry for the RDF agent.
Main() - Constructor for class org.biomoby.registry.rdfagent.verifier.Main
 
main(String[]) - Static method in class org.biomoby.registry.rdfagent.verifier.Main
 
main(String[]) - Static method in class org.biomoby.registry.sync.MobySyncExecuter
 
main(String[]) - Static method in class org.biomoby.service.dashboard.Dashboard
An entry point...
main(String[]) - Static method in class org.biomoby.service.MobyServlet
Expects one argument, an example MOBY XML input file or URL.
main(String[]) - Static method in class org.biomoby.service.test.MobyServletTestCase
Runs the test suite when the class is invoked on the command line.
main(String[]) - Static method in class org.biomoby.service.test.ServletTester
 
main(String[]) - Static method in class org.biomoby.shared.data.test.MobyDataDateTimeTestCase
Runs the test suite when the class is invoked on the command line.
main(String[]) - Static method in class org.biomoby.shared.extended.DataTypeParser
 
main(String[]) - Static method in class org.biomoby.shared.extended.NamespaceParser
 
main(String[]) - Static method in class org.biomoby.shared.extended.ServiceInstanceParser
 
main(String[]) - Static method in class org.biomoby.shared.extended.ServiceTypeParser
 
main(String[]) - Static method in class org.biomoby.shared.MobyObjectDecompositionImpl
 
main(String[]) - Static method in class org.biomoby.shared.schema.Builder
 
main(String[]) - Static method in class org.biomoby.shared.schema.MainGUI
 
main(String[]) - Static method in class org.biomoby.shared.schema.RdfParser
 
main(String[]) - Static method in class org.biomoby.shared.schema.ServiceInstanceWSDL
 
main(String[]) - Static method in class org.biomoby.shared.test.LSIDResolverTestCase
 
main(String[]) - Static method in class org.biomoby.shared.test.MobyNamespaceTestCase
 
main(String[]) - Static method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
Main - Class in org.inb.biomoby.generator.gui
 
Main() - Constructor for class org.inb.biomoby.generator.gui.Main
 
main(String[]) - Static method in class org.inb.biomoby.generator.gui.Main
 
main(String[]) - Static method in class org.omg.lsae.sax.test.AnalysisEventTestCase
Runs the test suite when the class is invoked on the command line.
main(String[]) - Static method in class org.soap.sax.test.SOAPFaultTestCase
Runs the test suite when the class is invoked on the command line.
MainGUI - Class in org.biomoby.shared.schema
 
MainGUI() - Constructor for class org.biomoby.shared.schema.MainGUI
 
MainPanel - Class in org.inb.biomoby.generator.gui
 
MainPanel() - Constructor for class org.inb.biomoby.generator.gui.MainPanel
 
makeBooleanWidget(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeDateTimeWidget(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeDirs(String, String) - Static method in class org.biomoby.service.generator.Generator
Create all needed sub-directories - as required by given Java package name.
makeEnumWidget(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeFloatWidget(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeIntWidget(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeJLabel(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeJLabel(MobyDataSecondaryInstance, String) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeStringWidget(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeSureItIsLoaded() - Method in interface org.biomoby.shared.datatypes.MapDataTypesIfc
 
makeWidget(MobyPrimaryData) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
makeWidget(MobyDataSecondaryInstance) - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
MANIFEST_MAIN_CLASS_PROPERTY - Static variable in class ca.ucalgary.minnow.MinJarMaker
 
MANIFEST_PATH - Static variable in class ca.ucalgary.minnow.MinJarMaker
 
MapDataTypesIfc - Interface in org.biomoby.shared.datatypes
 
MapPrimitiveDataTypes - Class in org.biomoby.shared.datatypes
Class containing static mapping between Biomoby primitive data types and names of classes they are represented by.
MapPrimitiveDataTypes() - Constructor for class org.biomoby.shared.datatypes.MapPrimitiveDataTypes
 
markupResponse(Source, HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to record or modify the Web Service response before WrappingServlet returns it to the HTTP client.
markupResponse(byte[], String, String, HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
Gives the data recorder an opportunity to record or modify the CGI response before WrappingServlet returns it to the HTTP client.
markupResponse(byte[], String, String, HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
 
markupResponse(Source, HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
Manipulates the Web Service response data so that it includes a bunch of links that can be used to create Moby services.
marshal(String, Object) - Static method in class org.inb.biomoby.client.MobyDispatch
 
marshal(String, Object, boolean) - Static method in class org.inb.biomoby.client.MobyDispatch
 
marshall(Object) - Static method in class org.inb.biomoby.MobyMessageContext
 
matchingNamespaceName - Variable in class org.biomoby.client.DataTypeConnector
 
MatchingPattern - Class in org.inb.biomoby.shared.ontology
 
MatchingPattern() - Constructor for class org.inb.biomoby.shared.ontology.MatchingPattern
 
Matrix - Class in org.inb.biomoby.shared.ontology
 
Matrix() - Constructor for class org.inb.biomoby.shared.ontology.Matrix
 
MatrixFloat - Class in org.inb.biomoby.shared.ontology
 
MatrixFloat() - Constructor for class org.inb.biomoby.shared.ontology.MatrixFloat
 
MatrixInteger - Class in org.inb.biomoby.shared.ontology
 
MatrixInteger() - Constructor for class org.inb.biomoby.shared.ontology.MatrixInteger
 
MatrixString - Class in org.inb.biomoby.shared.ontology
 
MatrixString() - Constructor for class org.inb.biomoby.shared.ontology.MatrixString
 
max - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
max - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
max - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
MAX_DATA_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
MAX_ID_LEN - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
MAX_ITEM_DESC_WIDTH - Static variable in class ca.ucalgary.seahawk.gui.DataImportChoiceDialog
 
MAX_ITEM_DESC_WIDTH - Static variable in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
MAX_OBJ_NAME_LEN - Static variable in class ca.ucalgary.seahawk.util.MobyUtils
 
MAX_SERVICE_DESC_LEN - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
MAX_SERVICES_PER_SUBMENU - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
MAX_TAB_NAME_LENGTH - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
MAX_TEXT_SIZE - Static variable in class org.biomoby.service.dashboard.renderers.XMLTree
 
MAX_TOOLTIP_WIDTH - Static variable in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
MElement - Class in org.biomoby.shared.schema
 
MElement() - Constructor for class org.biomoby.shared.schema.MElement
Default constructor.
MElement(String) - Constructor for class org.biomoby.shared.schema.MElement
 
MElement(String, String) - Constructor for class org.biomoby.shared.schema.MElement
 
MElement(String, String, String) - Constructor for class org.biomoby.shared.schema.MElement
 
MElementHashtable - Class in org.biomoby.shared.schema
 
MElementHashtable(Vector) - Constructor for class org.biomoby.shared.schema.MElementHashtable
 
MEMBER_RULE_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
MEMBER_RULE_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
MEMBERS_RULE_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
MEMBERS_RULE_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
MEME_Text - Class in org.inb.biomoby.shared.ontology
 
MEME_Text() - Constructor for class org.inb.biomoby.shared.ontology.MEME_Text
 
MemoryFileManager - Class in org.inb.util
In-memory file manager to dynamically compile generated java classes
MemoryFileManager(JavaFileManager) - Constructor for class org.inb.util.MemoryFileManager
 
MemoryFileManager.JavaSourceFromString - Class in org.inb.util
 
MemoryFileManager.JavaSourceFromString(String, String) - Constructor for class org.inb.util.MemoryFileManager.JavaSourceFromString
 
mergeDataMaps(Map<String, MobyDataInstance>, Map<String, MobyDataInstance>) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
Meta_Alignment_Text - Class in org.inb.biomoby.shared.ontology
 
Meta_Alignment_Text() - Constructor for class org.inb.biomoby.shared.ontology.Meta_Alignment_Text
 
METADATA_CONTENTS_PARAM - Static variable in class ca.ucalgary.services.util.RuleCreator
 
method - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
method - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
METHOD_GET - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
METHOD_POST - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
MicroArrayData__Text - Class in org.inb.biomoby.shared.ontology
 
MicroArrayData__Text() - Constructor for class org.inb.biomoby.shared.ontology.MicroArrayData__Text
 
MicroArrayData_Text - Class in org.inb.biomoby.shared.ontology
 
MicroArrayData_Text() - Constructor for class org.inb.biomoby.shared.ontology.MicroArrayData_Text
 
MIME_TYPE - Static variable in interface org.biomoby.service.dashboard.renderers.Renderer
 
min - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
min - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
min - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
MinJarMaker - Class in ca.ucalgary.minnow
This class should be called from the command line using a "clean" JVM (i.e. no extra libraries installed) to act as a recorder of what classes particular to a program are accessed during its running.
MinJarMaker(String, String, String[], boolean, String) - Constructor for class ca.ucalgary.minnow.MinJarMaker
 
MmCIF__Text - Class in org.inb.biomoby.shared.ontology
 
MmCIF__Text() - Constructor for class org.inb.biomoby.shared.ontology.MmCIF__Text
 
MmCIF_Text - Class in org.inb.biomoby.shared.ontology
 
MmCIF_Text() - Constructor for class org.inb.biomoby.shared.ontology.MmCIF_Text
 
MOBY - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MOBY_AUTHOR_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
MOBY_AUTHORITATIVE_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_AUTHORITY_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
MOBY_CENTRAL_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
MOBY_CENTRAL_URL_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_CONTACT_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_DESC_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
MOBY_INPUT_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_NAMESPACE - Static variable in interface org.inb.biomoby.service.IAsyncMobyService
 
MOBY_NOTES_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
MOBY_NS - Static variable in class org.biomoby.shared.parser.JDOMUtils
A Biomoby namespace.
MOBY_OUTPUT_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_PROVIDER_URI_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_RESERVED - Static variable in class org.inb.biomoby.generator.GeneratorUtil
 
MOBY_RESULT_PROPERTY_PREFIX - Static variable in class org.biomoby.client.AsyncClient
 
MOBY_RULES_DEFAULT_RESOURCE - Static variable in class ca.ucalgary.services.LegacyService
 
MOBY_RULES_LOCATION_PARAM - Static variable in class ca.ucalgary.services.LegacyService
 
MOBY_SECONDARY_SOURCE_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
MOBY_SECONDARYINPUT_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_SERVICE_DESC_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_SERVICE_INVOC_ID_TAG_NAME - Static variable in class org.biomoby.client.AsyncClient
 
MOBY_SERVICE_POPUP_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentPane
 
MOBY_SERVICENAME_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
MOBY_SERVICENAME_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_SERVICETYPE_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
MOBY_SERVICETYPE_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
MOBY_SHIM_SERVICE_TYPE - Static variable in class ca.ucalgary.seahawk.gui.MobyShimmer
 
MOBY_TRANSPORT_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
MOBY_TRANSPORT_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
MOBY_TYPE - Static variable in interface org.biomoby.service.dashboard.renderers.Renderer
 
MOBY_XML_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
MOBY_XML_NAMESPACE_INVALID - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
MOBY_XML_NS - Static variable in interface org.biomoby.shared.parser.MobyTags
BioMoby XML namespace.
MOBY_XML_NS_PREFIX - Static variable in interface org.biomoby.shared.parser.MobyTags
BioMoby XML prefix used when defining BioMoby namespace.
MOBY_XML_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
MobyBinary - Class in org.inb.biomoby.shared.datatypes
This class is a not standard Moby primitive type.
MobyBinary(byte[]) - Constructor for class org.inb.biomoby.shared.datatypes.MobyBinary
 
MobyBinary(InputStream) - Constructor for class org.inb.biomoby.shared.datatypes.MobyBinary
 
MobyBoolean - Class in org.biomoby.shared.datatypes
An object representing a Boolean, a Moby primitive data type.
MobyBoolean() - Constructor for class org.biomoby.shared.datatypes.MobyBoolean
Default constructor.
MobyBoolean(boolean) - Constructor for class org.biomoby.shared.datatypes.MobyBoolean
Another constructor.
MOBYBOOLEAN - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyBoolean - Class in org.inb.biomoby.shared.datatypes
 
MobyBoolean() - Constructor for class org.inb.biomoby.shared.datatypes.MobyBoolean
 
MobyBoolean(boolean) - Constructor for class org.inb.biomoby.shared.datatypes.MobyBoolean
 
MobyBoolean(String) - Constructor for class org.inb.biomoby.shared.datatypes.MobyBoolean
 
MobyCentral - Class in org.inb.biomoby.central
 
MobyCentral(String, String) - Constructor for class org.inb.biomoby.central.MobyCentral
 
MobyCentralConfig - Class in org.biomoby.registry.properties
 
MobyCentralConfig() - Constructor for class org.biomoby.registry.properties.MobyCentralConfig
 
MobyCentralFactory - Class in org.inb.biomoby.central
 
MobyCentralFileCache - Class in org.inb.biomoby.central.cache
Simple cache store definition based on file (located in a $HOME/.MobyCentralCache/ directory)
MobyCentralFileCache() - Constructor for class org.inb.biomoby.central.cache.MobyCentralFileCache
 
MobyCentralModel - Class in org.inb.biomoby.central.model
BioMoby registry model implementation class.
MobyCentralOperations - Interface in org.inb.biomoby.central
An interface that defines all standard BioMoby Registry operations.
MobyCentralService - Interface in org.inb.biomoby.central
 
MobyCentralServiceImpl - Class in org.inb.biomoby.central.factory.jaxb
 
MobyCentralServiceImpl() - Constructor for class org.inb.biomoby.central.factory.jaxb.MobyCentralServiceImpl
 
MobyClassLoader - Class in org.inb.biomoby
Custom classloader which is used to intercept JAXBContext loading.
MobyClassLoader(ClassLoader) - Constructor for class org.inb.biomoby.MobyClassLoader
 
MobyClient - Class in ca.ucalgary.seahawk.services
The engine that finds MOBY data in unstructured text or DOM of other XML languages according to a rules database.
MobyClient() - Constructor for class ca.ucalgary.seahawk.services.MobyClient
Nullary constructor that differs significantly in behaviour from the one-arg c-tor: it uses the registry from SeahawkOptions, or if not available, the RegistryCache default registry.
MobyClient(Registry) - Constructor for class ca.ucalgary.seahawk.services.MobyClient
Constructor specifying a particular registry to use.
MobyClientTestCase - Class in ca.ucalgary.seahawk.services.test
 
MobyClientTestCase(String) - Constructor for class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
MobyCollection - Class in org.biomoby.shared.parser
A specialized "envelope" that can carry a collection of other envelopes (represented by MobySimples objects), and giving them a name known as an article name for top-level object.
MobyCollection() - Constructor for class org.biomoby.shared.parser.MobyCollection
Default constructor.
MobyCollection<MobySimple> - Class in org.inb.biomoby.shared.message
 
MobyCollection() - Constructor for class org.inb.biomoby.shared.message.MobyCollection
 
MobyComplexBuilder - Class in ca.ucalgary.seahawk.services
Class used by MobyClient to build the MOBY rule database from a configuration file.
MobyComplexBuilder(String, Map<String, String[]>, Map<String, String>, MobyClient) - Constructor for class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
MobyComplexBuilder(String, Map<String, String[]>, Map<String, String>, MobyClient, String) - Constructor for class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
MobyComponentFactory - Class in org.inb.biomoby.client.gui.ontology
 
MobyComponentFactory() - Constructor for class org.inb.biomoby.client.gui.ontology.MobyComponentFactory
 
MOBYCONTENT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyContent - Class in org.inb.biomoby.shared.message
 
MobyContent() - Constructor for class org.inb.biomoby.shared.message.MobyContent
 
MobyContent(MobyData) - Constructor for class org.inb.biomoby.shared.message.MobyContent
 
MobyContent(ArrayList<MobyData>) - Constructor for class org.inb.biomoby.shared.message.MobyContent
 
MobyContentClipboard - Class in ca.ucalgary.seahawk.gui
The clipboard is a special tab that holds a query with a MOBY Collection that the user can add and subtract MobyDataInstances from.
MobyContentClipboard(MobyContentGUI, MobyServicesGUI, JTabbedPane, DataFlowRecorder, JLabel) - Constructor for class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
MobyContentCreator - Interface in ca.ucalgary.seahawk.util
Interface implemented by Seahawk moby data classes that are actually placeholders for lists of data.
MobyContentGUI - Class in ca.ucalgary.seahawk.gui
Main interface component: textually displays the data in a MOBY content XML document.
MobyContentGUI(MobyServicesGUI) - Constructor for class ca.ucalgary.seahawk.gui.MobyContentGUI
Constructor for a standalone visual interface.
MobyContentGUITestCase - Class in ca.ucalgary.seahawk.gui.test
 
MobyContentGUITestCase(String) - Constructor for class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
MobyContentHelpPane - Class in ca.ucalgary.seahawk.gui
Special text display tab in Seahawk for the Seahawk help file.
MobyContentHelpPane(MobyContentGUI, MobyServicesGUI, JTabbedPane, DataFlowRecorder, JLabel) - Constructor for class ca.ucalgary.seahawk.gui.MobyContentHelpPane
 
MobyContentInstance - Class in org.biomoby.shared.data
This class represents the data package sent back and forth between clients and servers.
MobyContentInstance() - Constructor for class org.biomoby.shared.data.MobyContentInstance
Creates a blank MOBY envelope, to be filled in programatically with data instances.
MobyContentInstance(MobyDataInstance, String) - Constructor for class org.biomoby.shared.data.MobyContentInstance
A convenience constructor when you want to create an envelope with just one object in it.
MobyContentInstance(Element) - Constructor for class org.biomoby.shared.data.MobyContentInstance
Builds a MobyContentInstance (i.e. one or more MOBY queries or responses) using a DOM-parsed XML MOBY envelope (i.e. the mobyContent tag).
MobyContentInstance(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyContentInstance
 
MobyContentPane - Class in ca.ucalgary.seahawk.gui
Text area contained in a Seahawk GUI tab.
MobyContentPane(MobyContentGUI, MobyServicesGUI, JTabbedPane, DataFlowRecorder, JLabel) - Constructor for class ca.ucalgary.seahawk.gui.MobyContentPane
 
MobyContentProducer - Interface in ca.ucalgary.seahawk.gui
This interface should be implemented by any application component that can produce data going to a MobyObjectTransferHandler for export.
MobyData - Class in org.biomoby.shared
A container keeping input or output data types together with few other attributes.
MobyData() - Constructor for class org.biomoby.shared.MobyData
Default constructor.
MobyData(String) - Constructor for class org.biomoby.shared.MobyData
Normal constructor.
MOBYDATA - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyData - Class in org.inb.biomoby.shared.message
 
MobyData() - Constructor for class org.inb.biomoby.shared.message.MobyData
 
MobyData(String) - Constructor for class org.inb.biomoby.shared.message.MobyData
 
MobyData(MobySimple, String) - Constructor for class org.inb.biomoby.shared.message.MobyData
 
MobyData(MobyCollection, String) - Constructor for class org.inb.biomoby.shared.message.MobyData
 
MobyDataBoolean - Class in org.biomoby.shared.data
A class representing a MOBY Boolean primitive.
MobyDataBoolean(Element) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
Construct the object using a DOM fragment.
MobyDataBoolean(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(String, Boolean) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
Constructor to build a MOBY base String object from a CharSequence (i.e.
MobyDataBoolean(String, Boolean, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
Every c-tor eventually winds up here
MobyDataBoolean(String, boolean) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(String, boolean, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(String, String) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
Uses Boolean.valueOf(String) to convert to a Boolean object.
MobyDataBoolean(String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(Boolean) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(Boolean, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(boolean) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(boolean, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(String) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBoolean(String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBoolean
 
MobyDataBytes - Class in org.biomoby.shared.data
A convenience class generally intended for the transmission of binary data that will be Base64 encoded to fit in the MOBY XML envelope.
MobyDataBytes(Element) - Constructor for class org.biomoby.shared.data.MobyDataBytes
Construct the object using a DOM fragment.
MobyDataBytes(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBytes
 
MobyDataBytes(String, byte[]) - Constructor for class org.biomoby.shared.data.MobyDataBytes
C-tor to use when you have binary data to encode
MobyDataBytes(String, byte[], Registry) - Constructor for class org.biomoby.shared.data.MobyDataBytes
 
MobyDataBytes(String, byte[], MobyDataType) - Constructor for class org.biomoby.shared.data.MobyDataBytes
C-tor to use when you have binary data to encode
MobyDataBytes(String, CharSequence) - Constructor for class org.biomoby.shared.data.MobyDataBytes
C-tor to use when you have received text-encoded binary.
MobyDataBytes(String, CharSequence, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBytes
 
MobyDataBytes(String, CharSequence, MobyDataType) - Constructor for class org.biomoby.shared.data.MobyDataBytes
C-tor to use when you have received text-encoded binary.
MobyDataBytes(String, URL) - Constructor for class org.biomoby.shared.data.MobyDataBytes
C-tor to use when you want to encode a resource, such as an image file.
MobyDataBytes(String, URL, Registry) - Constructor for class org.biomoby.shared.data.MobyDataBytes
 
MobyDataBytes(String, URL, MobyDataType) - Constructor for class org.biomoby.shared.data.MobyDataBytes
C-tor to use when you want to encode a resource, such as an image file.
MobyDataComposite - Class in org.biomoby.shared.data
This is the class that represents any non-primitive object instance (i.e. anything except object, boolean, integer, float, date-time, or string) from the MOBY data type ontology.
MobyDataComposite(Element) - Constructor for class org.biomoby.shared.data.MobyDataComposite
Construct the object using a DOM fragment.
MobyDataComposite(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(MobyDataType, String, MobyNamespace, String) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(MobyDataType, String, String, String) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(String, String, String, String) - Constructor for class org.biomoby.shared.data.MobyDataComposite
Only call this constructor if you are sure that the data type name is in the ontology, otherwise the datatype will be null.
MobyDataComposite(String, String, String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(MobyDataType, MobyNamespace, String, Object...) - Constructor for class org.biomoby.shared.data.MobyDataComposite
Instantiates a composite with a variable number of members using Java 1.5's varargs.
MobyDataComposite(MobyDataType, String) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(String, String) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(MobyDataType) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(String) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataComposite(String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataComposite
 
MobyDataDateTime - Class in org.biomoby.shared.data
A class representing a MOBY DateTime, which is a primitive in MOBY.
MobyDataDateTime(Element) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
Construct the object using a DOM fragment.
MobyDataDateTime(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
 
MobyDataDateTime(String, String) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
Constructor to build a MOBY DateTime object using the W3C profile of an ISO 8601 formatted input string.
MobyDataDateTime(String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
 
MobyDataDateTime(String) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
 
MobyDataDateTime(String, GregorianCalendar) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
 
MobyDataDateTime(String, GregorianCalendar, Registry) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
 
MobyDataDateTime(GregorianCalendar) - Constructor for class org.biomoby.shared.data.MobyDataDateTime
 
MobyDataDateTimeTestCase - Class in org.biomoby.shared.data.test
 
MobyDataDateTimeTestCase(String) - Constructor for class org.biomoby.shared.data.test.MobyDataDateTimeTestCase
 
MobyDataElement - Class in org.biomoby.shared.parser
A general "envelope" that can carry real Biomoby data objects.
MobyDataElement() - Constructor for class org.biomoby.shared.parser.MobyDataElement
Default constructor.
MobyDataElement - Class in org.inb.biomoby.shared.message
 
MobyDataElement() - Constructor for class org.inb.biomoby.shared.message.MobyDataElement
 
MobyDataFloat - Class in org.biomoby.shared.data
A class representing a MOBY Float primitive.
MobyDataFloat(Element) - Constructor for class org.biomoby.shared.data.MobyDataFloat
Construct the object using a DOM fragment.
MobyDataFloat(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(String, Number) - Constructor for class org.biomoby.shared.data.MobyDataFloat
Constructor to use if the incoming value is a number object such as Float, Double, Integer, BigDecimal, etc.
MobyDataFloat(String, Number, Registry) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(Number, Registry) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(Number) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(String, double) - Constructor for class org.biomoby.shared.data.MobyDataFloat
Constructor to use if the incoming value is a primitive.
MobyDataFloat(String, double, Registry) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(double, Registry) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(double) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(String, String) - Constructor for class org.biomoby.shared.data.MobyDataFloat
Constructor to use if the incoming value is a string representing a number (including mantissa/exponent format).
MobyDataFloat(String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(String) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataFloat(String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataFloat
 
MobyDataInstance - Interface in org.biomoby.shared.data
A convenience interface for passing arrays of instance data around without needing to type cast.
MobyDataInt - Class in org.biomoby.shared.data
A class representing a MOBY Integer primitive.
MobyDataInt(Element) - Constructor for class org.biomoby.shared.data.MobyDataInt
Construct the object using a DOM fragment.
MobyDataInt(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataInt
 
MobyDataInt(String, Number) - Constructor for class org.biomoby.shared.data.MobyDataInt
Constructor to use if the incoming value is a number object such as Float, Double, Integer, BigInteger, BigDecimal, etc.
MobyDataInt(String, Number, Registry) - Constructor for class org.biomoby.shared.data.MobyDataInt
 
MobyDataInt(Number) - Constructor for class org.biomoby.shared.data.MobyDataInt
 
MobyDataInt(Number, Registry) - Constructor for class org.biomoby.shared.data.MobyDataInt
 
MobyDataInt(String, int) - Constructor for class org.biomoby.shared.data.MobyDataInt
Constructor to use if the incoming value is a primitive.
MobyDataInt(String, int, Registry) - Constructor for class org.biomoby.shared.data.MobyDataInt
 
MobyDataInt(int) - Constructor for class org.biomoby.shared.data.MobyDataInt
 
MobyDataInt(String, String) - Constructor for class org.biomoby.shared.data.MobyDataInt
Constructor to use if the incoming value is a string representing an integer number.
MobyDataInt(String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataInt
 
MobyDataJob - Class in org.biomoby.shared.data
Groups together the primary and secondary data corresponding to a MOBY XML "mobyData" block, i.e.
MobyDataJob() - Constructor for class org.biomoby.shared.data.MobyDataJob
 
MobyDataObject - Class in org.biomoby.shared.data
A class representing a base MOBY object (i.e. just a namespace and id) that has been instantiated.
MobyDataObject(Element) - Constructor for class org.biomoby.shared.data.MobyDataObject
Construct the object using a DOM fragment.
MobyDataObject(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataObject
 
MobyDataObject(String) - Constructor for class org.biomoby.shared.data.MobyDataObject
Constructor with no instance information, just a name (which can be blank).
MobyDataObject(String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataObject
 
MobyDataObject(String, String) - Constructor for class org.biomoby.shared.data.MobyDataObject
Constructor convenient for a base object with a namespace and ID.
MobyDataObject(String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataObject
 
MobyDataObject(MobyDataObject) - Constructor for class org.biomoby.shared.data.MobyDataObject
Creates a base object with the same name, namespace and id as the input instance, as opposed to clone, which creates an exact copy of all the fields and the datatype.
MobyDataObjectDeferred - Class in ca.ucalgary.seahawk.util
A class that pretends it's a real moby data instance, but is actually a deferred list of data instances that should be submitted en-masse to services.
MobyDataObjectDeferred(MobyNamespace, MobyPayloadRequestListener) - Constructor for class ca.ucalgary.seahawk.util.MobyDataObjectDeferred
 
MobyDataObjectDeferred(MobyDataType, MobyPayloadRequestListener) - Constructor for class ca.ucalgary.seahawk.util.MobyDataObjectDeferred
 
MobyDataObjectDeferred(MobyDataType, MobyNamespace, MobyPayloadRequestListener) - Constructor for class ca.ucalgary.seahawk.util.MobyDataObjectDeferred
 
MobyDataObjectDeferredSAI - Class in ca.ucalgary.seahawk.util
 
MobyDataObjectDeferredSAI(MobyDataObjectDeferred, MobyService[]) - Constructor for class ca.ucalgary.seahawk.util.MobyDataObjectDeferredSAI
 
MobyDataObjectSAI - Class in org.biomoby.shared.data
A convenience class that just associates a set of possible services to run with a data instance.
MobyDataObjectSAI(String, String, MobyService[]) - Constructor for class org.biomoby.shared.data.MobyDataObjectSAI
Constructor for base Objects.
MobyDataObjectSAI(String, String, MobyService[], Registry) - Constructor for class org.biomoby.shared.data.MobyDataObjectSAI
 
MobyDataObjectSAI(MobyDataObject, MobyService[]) - Constructor for class org.biomoby.shared.data.MobyDataObjectSAI
Constructor that takes an existing object and associates services with it.
MobyDataObjectSet - Class in org.biomoby.shared.data
This class adds to MobyPrimaryDataSet the ability to get and set instantiated MOBY objects.
MobyDataObjectSet(Element) - Constructor for class org.biomoby.shared.data.MobyDataObjectSet
 
MobyDataObjectSet(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataObjectSet
 
MobyDataObjectSet(String) - Constructor for class org.biomoby.shared.data.MobyDataObjectSet
Creates an empty collection bag with a name.
MobyDataObjectSet(String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataObjectSet
 
MobyDataObjectSet(String, MobyDataObject[]) - Constructor for class org.biomoby.shared.data.MobyDataObjectSet
Creates a collection with a name, initializing the members with the given array.
MobyDataObjectSet(String, Collection<? extends MobyDataObject>) - Constructor for class org.biomoby.shared.data.MobyDataObjectSet
Creates a collection with a name, initializing the members with the members of the given collection.
MobyDataObjectSetDeferred - Class in ca.ucalgary.seahawk.util
A class that pretends it's a real moby data collection instance, but is actually a deferred list of data collection instances that should be submitted en-masse to services.
MobyDataObjectSetDeferred(MobyPrimaryDataSet, MobyPayloadRequestListener) - Constructor for class ca.ucalgary.seahawk.util.MobyDataObjectSetDeferred
 
MobyDataObjectSetDeferredSAI - Class in ca.ucalgary.seahawk.util
 
MobyDataObjectSetDeferredSAI(MobyDataObjectSetDeferred, MobyService[]) - Constructor for class ca.ucalgary.seahawk.util.MobyDataObjectSetDeferredSAI
 
MobyDataObjectSetSAI - Class in org.biomoby.shared.data
A convenience class that just associates a set of possible services to run with a data collection.
MobyDataObjectSetSAI(String, MobyService[]) - Constructor for class org.biomoby.shared.data.MobyDataObjectSetSAI
Constructor for base Objects.
MobyDataObjectSetSAI(String, MobyService[], Registry) - Constructor for class org.biomoby.shared.data.MobyDataObjectSetSAI
 
MobyDataObjectSetSAI(MobyDataObjectSet, MobyService[]) - Constructor for class org.biomoby.shared.data.MobyDataObjectSetSAI
Constructor that takes an existing object and associates services with it.
MobyDataObjectVector - Class in org.biomoby.shared.data
This class is primarily intended for use by MobyDataComposite to represent Object members in the HAS (1-to-many) relationship.
MobyDataObjectVector(String) - Constructor for class org.biomoby.shared.data.MobyDataObjectVector
Builds a vector with an initial capacity of 5.
MobyDataObjectVector(String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataObjectVector
 
MobyDataObjectVector(String, int) - Constructor for class org.biomoby.shared.data.MobyDataObjectVector
 
MobyDataObjectVector(String, int, Registry) - Constructor for class org.biomoby.shared.data.MobyDataObjectVector
 
MobyDataObjectWidget - Class in ca.ucalgary.seahawk.gui
A visual representation of a primary data object in Seahawk, intended for being a placeholder for data if it is not instantiated yet, allowing the user to drop data onto it via a MobyObjectTransferHandler (hence the implementation of MobyObjectReceiver).
MobyDataObjectWidget(String, MobyClient, MobyDataInstance, boolean) - Constructor for class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
C-tor for instantiated data.
MobyDataObjectWidget(String, MobyClient, MobyPrimaryData) - Constructor for class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
MobyDataObjectWidget(String, MobyClient, MobyDataType, MobyNamespace[], boolean) - Constructor for class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
C-tor for uninstantiated data.
MobyDataSecondaryInstance - Class in org.biomoby.shared.data
A class that holds and displays secondary input data to a service.
MobyDataSecondaryInstance(MobySecondaryData, String) - Constructor for class org.biomoby.shared.data.MobyDataSecondaryInstance
 
MobyDataSecondaryInstance(MobySecondaryData) - Constructor for class org.biomoby.shared.data.MobyDataSecondaryInstance
Basically clones the input parameter, and sets the value to the default value.
MobyDataSecondaryInstance(Element) - Constructor for class org.biomoby.shared.data.MobyDataSecondaryInstance
Create an instance from XML input.
MobyDataServiceAssocInstance - Interface in org.biomoby.shared.data
This interface defines a data instance that has already had remote MOBY services associated with it, probably through a call to MOBY central.
MobyDataString - Class in org.biomoby.shared.data
A class representing a MOBY String primitive.
MobyDataString(Element) - Constructor for class org.biomoby.shared.data.MobyDataString
Construct the object using a DOM fragment.
MobyDataString(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataString
 
MobyDataString(String, CharSequence) - Constructor for class org.biomoby.shared.data.MobyDataString
Constructor to build a MOBY base String object from a CharSequence (i.e.
MobyDataString(String, CharSequence, Registry) - Constructor for class org.biomoby.shared.data.MobyDataString
 
MobyDataString(CharSequence) - Constructor for class org.biomoby.shared.data.MobyDataString
 
MobyDataString(CharSequence, Registry) - Constructor for class org.biomoby.shared.data.MobyDataString
 
MobyDataTransferable - Class in ca.ucalgary.seahawk.util
Representation of Moby data from the org.biomoby.shared.data package when copied to a Clipboard.
MobyDataTransferable(MobyContentInstance) - Constructor for class ca.ucalgary.seahawk.util.MobyDataTransferable
C-tor to use when you have a whole MOBY payload to transfer (potentially many jobs, a.k.a. mobyData blocks).
MobyDataTransferable(MobyDataJob) - Constructor for class ca.ucalgary.seahawk.util.MobyDataTransferable
C-tor to use when you have a complete job to transfer (a.k.a. a mobyData block).
MobyDataTransferable(MobyDataInstance) - Constructor for class ca.ucalgary.seahawk.util.MobyDataTransferable
C-tor to use when you have just a single piece of data to transfer, such as a Simple, a secondary param, or a Collection.
MobyDataType - Class in org.biomoby.shared
A container representing a data type used in the Moby registry (in the BioMoby speak it is called "Object Class").
MobyDataType() - Constructor for class org.biomoby.shared.MobyDataType
Default constructor.
MobyDataType(String) - Constructor for class org.biomoby.shared.MobyDataType
Normal constructor.
MobyDataTypeTemplate - Class in org.biomoby.shared
You probably don't need to be looking at this class.
MobyDataTypeTemplate(MobyDataType) - Constructor for class org.biomoby.shared.MobyDataTypeTemplate
 
MobyDataUtils - Class in org.biomoby.shared.data
This class contains utilities that could be used on many of the data package classes, such as serialization and deserialization.
MobyDataUtils() - Constructor for class org.biomoby.shared.data.MobyDataUtils
 
MobyDataXref - Class in org.biomoby.shared.data
Note: This class has not been thoroughly tested.
MobyDataXref(MobyNamespace, String, MobyService) - Constructor for class org.biomoby.shared.data.MobyDataXref
 
MobyDataXref(String, String, MobyService) - Constructor for class org.biomoby.shared.data.MobyDataXref
Gets the registry implicitly from the service being passed in.
MobyDataXref(String, String, String, String) - Constructor for class org.biomoby.shared.data.MobyDataXref
 
MobyDataXref(String, String, String, String, Registry) - Constructor for class org.biomoby.shared.data.MobyDataXref
 
MobyDataXref(Element) - Constructor for class org.biomoby.shared.data.MobyDataXref
 
MobyDataXref(Element, Registry) - Constructor for class org.biomoby.shared.data.MobyDataXref
 
MobyDataXref(MobyDataObject, MobyService) - Constructor for class org.biomoby.shared.data.MobyDataXref
Build an Xref based on an existing object.
MobyDateTime - Class in org.biomoby.shared.datatypes
An object representing a date, or a date and time, a Moby primitive data type.
MobyDateTime() - Constructor for class org.biomoby.shared.datatypes.MobyDateTime
Default constructor.
MOBYDATETIME - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyDateTime - Class in org.inb.biomoby.shared.datatypes
 
MobyDateTime() - Constructor for class org.inb.biomoby.shared.datatypes.MobyDateTime
 
MobyDateTime(long) - Constructor for class org.inb.biomoby.shared.datatypes.MobyDateTime
 
MobyDateTime(String) - Constructor for class org.inb.biomoby.shared.datatypes.MobyDateTime
 
MobyDispatch - Class in org.inb.biomoby.client
 
MobyDispatch(Service) - Constructor for class org.inb.biomoby.client.MobyDispatch
 
MobyDispatch(Service, String, String) - Constructor for class org.inb.biomoby.client.MobyDispatch
 
MobyDispatch.MobyWSRFResource - Class in org.inb.biomoby.client
 
MobyDispatch.MobyWSRFResource(MobyEndpointReference) - Constructor for class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
MobyEndpointReference - Class in org.inb.biomoby.shared.wsrf
The class is used to extract "url" address and "ServiceInvocationId" parameter from W3CEndpointReference
MobyEndpointReference(String, String, String) - Constructor for class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
MobyEndpointReference(W3CEndpointReference) - Constructor for class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
mobyEscape(String) - Static method in class org.biomoby.shared.Utils
Make sure that an article name does not collide with the member names in the top-level MobyObject.
MobyException - Exception in org.biomoby.shared
A general exception which can be used as a wrapper around other exceptions.
MobyException() - Constructor for exception org.biomoby.shared.MobyException
 
MobyException(String) - Constructor for exception org.biomoby.shared.MobyException
A constructor specifying a reason for this exception.
MobyException(String, Throwable) - Constructor for exception org.biomoby.shared.MobyException
A constructor used for storing another exception in MobyException.
MOBYEXCEPTION - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyException - Class in org.inb.biomoby.shared.message
 
MobyException() - Constructor for class org.inb.biomoby.shared.message.MobyException
 
MobyException.SEVERITY - Enum in org.inb.biomoby.shared.message
 
MobyExceptions - Exception in org.inb.biomoby.shared.message
 
MobyExceptions() - Constructor for exception org.inb.biomoby.shared.message.MobyExceptions
 
MobyFloat - Class in org.biomoby.shared.datatypes
An object representing a Float, a Moby primitive data type.
MobyFloat() - Constructor for class org.biomoby.shared.datatypes.MobyFloat
Default constructor.
MobyFloat(double) - Constructor for class org.biomoby.shared.datatypes.MobyFloat
Another constructor.
MOBYFLOAT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyFloat - Class in org.inb.biomoby.shared.datatypes
 
MobyFloat() - Constructor for class org.inb.biomoby.shared.datatypes.MobyFloat
 
MobyFloat(double) - Constructor for class org.inb.biomoby.shared.datatypes.MobyFloat
 
MobyFloat(String) - Constructor for class org.inb.biomoby.shared.datatypes.MobyFloat
 
MobyHandler<T extends Comparable & LSIDAccessible> - Interface in org.biomoby.registry.sync.handler
Basic interface for classes to synchronize a specific entry of the mobycentrals (eg MobyServices, MobyDataType etc).
MobyInteger - Class in org.biomoby.shared.datatypes
An object representing an Integer, a Moby primitive data type.
MobyInteger() - Constructor for class org.biomoby.shared.datatypes.MobyInteger
Default constructor.
MobyInteger(long) - Constructor for class org.biomoby.shared.datatypes.MobyInteger
Another constructor.
MOBYINTEGER - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyInteger - Class in org.inb.biomoby.shared.datatypes
 
MobyInteger() - Constructor for class org.inb.biomoby.shared.datatypes.MobyInteger
 
MobyInteger(int) - Constructor for class org.inb.biomoby.shared.datatypes.MobyInteger
 
MobyInteger(String) - Constructor for class org.inb.biomoby.shared.datatypes.MobyInteger
 
MobyJob - Class in org.biomoby.shared.parser
This class represents one BioMoby query (in a client request), or a result of one query (in a service response).
MobyJob() - Constructor for class org.biomoby.shared.parser.MobyJob
Default constructor.
MobyJob(String) - Constructor for class org.biomoby.shared.parser.MobyJob
Another constructor, naming this job by an id.
MobyMessage - Class in org.inb.biomoby.shared.message
 
MobyMessage() - Constructor for class org.inb.biomoby.shared.message.MobyMessage
 
MobyMessage(MobyContent) - Constructor for class org.inb.biomoby.shared.message.MobyMessage
 
MobyMessage(MobyData) - Constructor for class org.inb.biomoby.shared.message.MobyMessage
 
MobyMessage(ArrayList<MobyData>) - Constructor for class org.inb.biomoby.shared.message.MobyMessage
 
MobyMessageComponent - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
MobyMessageContext - Class in org.inb.biomoby
Utility class with cached JAXBContext.
MobyMessageQueue<T extends IDynamicComponent.MobyComponentListener> - Class in org.inb.biomoby.client.gui
 
MobyMessageQueue() - Constructor for class org.inb.biomoby.client.gui.MobyMessageQueue
 
MobyNameCellEditor - Class in org.inb.biomoby.central.gui.renderer
 
MobyNameCellEditor() - Constructor for class org.inb.biomoby.central.gui.renderer.MobyNameCellEditor
 
MobyNamespace - Class in org.biomoby.shared
A container representing a namespace used in the Moby registry.
MobyNamespace(String) - Constructor for class org.biomoby.shared.MobyNamespace
Default constructor.
MobyNamespaceTestCase - Class in org.biomoby.shared.test
 
MobyNamespaceTestCase(String) - Constructor for class org.biomoby.shared.test.MobyNamespaceTestCase
 
MobyObject - Class in org.biomoby.shared.datatypes
An object representing a Biomoby Object, the main Biomoby data type, where all other data types are inherited from.
MobyObject() - Constructor for class org.biomoby.shared.datatypes.MobyObject
Default constructor.
MobyObject(String, String) - Constructor for class org.biomoby.shared.datatypes.MobyObject
Another constructor.
MOBYOBJECT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyObject - Class in org.inb.biomoby.shared.message
 
MobyObject() - Constructor for class org.inb.biomoby.shared.message.MobyObject
 
MobyObject(String, String) - Constructor for class org.inb.biomoby.shared.message.MobyObject
 
MobyObjectComponent - Class in org.inb.biomoby.client.gui.ontology
 
MobyObjectComponent(MobyObject) - Constructor for class org.inb.biomoby.client.gui.ontology.MobyObjectComponent
 
MobyObjectDecomposition - Interface in org.biomoby.shared
 
MobyObjectDecompositionImpl - Class in org.biomoby.shared
 
MobyObjectDecompositionImpl() - Constructor for class org.biomoby.shared.MobyObjectDecompositionImpl
 
MobyObjectPropertiesTableModel - Class in org.inb.biomoby.central.gui.model
 
MobyObjectPropertiesTableModel(AbstractModel<ObjectType>) - Constructor for class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
MobyObjectReceiver - Interface in ca.ucalgary.seahawk.gui
This interface should be implemented by any application component that desires to receive incoming data from MobyObjectTransferHandler.
MobyObjectTransferHandler - Class in ca.ucalgary.seahawk.gui
 
MobyPackage - Class in org.biomoby.shared.parser
This is the main container for Biomoby data once they are extracted from an XML format.
MobyPackage() - Constructor for class org.biomoby.shared.parser.MobyPackage
Default constructor.
MobyPackage(MobyObject, String) - Constructor for class org.biomoby.shared.parser.MobyPackage
Constructing a simplest MobyPackage - with one MobyObject.
MobyParameter - Class in org.biomoby.shared.parser
A mixture of an "envelope" (because it inherits from a general envelope MobyDataElement, and Biomoby data, representing a secondary input - a secondary means that it is not used in a service discovery process.
MobyParameter() - Constructor for class org.biomoby.shared.parser.MobyParameter
Default constructor.
MobyParameter - Class in org.inb.biomoby.shared.message
 
MobyParameter() - Constructor for class org.inb.biomoby.shared.message.MobyParameter
 
MobyParameter(String, String) - Constructor for class org.inb.biomoby.shared.message.MobyParameter
 
MobyParameter(MobyPrimitive, String) - Constructor for class org.inb.biomoby.shared.message.MobyParameter
 
MobyParser - Class in org.biomoby.shared.parser
The MobyParser is able to read a Biomoby service/client XML data, parse them and create from them an instance of MobyPackage.
MobyParser() - Constructor for class org.biomoby.shared.parser.MobyParser
Default constructor.
MobyParser(String) - Constructor for class org.biomoby.shared.parser.MobyParser
Another constructor, taking the "fallback" data type name.
MobyParser(Map<String, String>) - Constructor for class org.biomoby.shared.parser.MobyParser
Another constructor, taking more "fallback" data type names (indexed by their article names).
MobyPayloadCreator - Class in ca.ucalgary.seahawk.gui
Builds a MobyContentInstance based on the requested selection criteria.
MobyPayloadCreator(MobyContentPane, String) - Constructor for class ca.ucalgary.seahawk.gui.MobyPayloadCreator
 
MobyPayloadRequestListener - Interface in ca.ucalgary.seahawk.util
To be implemented by classes that can provide a Moby payload object (e.g. to submit to a service) upon request, with the auumption that the listener knows what to send in the context of the class to which it attached itself as a listener.
MobyPrefixResolver - Class in org.biomoby.shared
The main purpose of this class is to provide default mapping from prefices we will use in the XPath statements built in the various client classes to URI's of XML namespaces.
MobyPrefixResolver() - Constructor for class org.biomoby.shared.MobyPrefixResolver
 
MobyPrefixResolver.MobyNodeList - Class in org.biomoby.shared
 
MobyPrefixResolver.MobyNodeList() - Constructor for class org.biomoby.shared.MobyPrefixResolver.MobyNodeList
 
MobyPrimaryData - Class in org.biomoby.shared
A container representing primary (both input and output) data as they are registered by services.
MobyPrimaryData() - Constructor for class org.biomoby.shared.MobyPrimaryData
 
MobyPrimaryData(String) - Constructor for class org.biomoby.shared.MobyPrimaryData
 
MobyPrimaryDataSet - Class in org.biomoby.shared
A container representing a way how a named collection of various primary data types is used in a service.
MobyPrimaryDataSet(String) - Constructor for class org.biomoby.shared.MobyPrimaryDataSet
Default constructor.
MobyPrimaryDataSet(Element) - Constructor for class org.biomoby.shared.MobyPrimaryDataSet
Construct this instance from a piece of XML.
MobyPrimaryDataSimple - Class in org.biomoby.shared
A container representing a way how various primary data types are used in a service.
MobyPrimaryDataSimple() - Constructor for class org.biomoby.shared.MobyPrimaryDataSimple
Default constructor.
MobyPrimaryDataSimple(String) - Constructor for class org.biomoby.shared.MobyPrimaryDataSimple
Normal constructor.
MobyPrimaryDataSimple(Element) - Constructor for class org.biomoby.shared.MobyPrimaryDataSimple
Construct this instance from a piece of XML.
MobyPrimitive - Interface in org.inb.biomoby.shared.datatypes
 
MobyProperties - Class in org.biomoby.registry.properties
 
MobyProperties() - Constructor for class org.biomoby.registry.properties.MobyProperties
 
MobyPropertiesTableModel - Class in org.inb.biomoby.central.gui.model
 
MobyPropertiesTableModel() - Constructor for class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
MobyPropertyTable - Class in org.inb.biomoby.central.gui
 
MobyPropertyTable() - Constructor for class org.inb.biomoby.central.gui.MobyPropertyTable
 
MobyProvider - Class in org.inb.biomoby.service
 
MobyProvider() - Constructor for class org.inb.biomoby.service.MobyProvider
 
MobyProvisionInfo - Class in org.biomoby.shared.data
Class to hold data corresponginf to the MOBY PIB.
MobyProvisionInfo() - Constructor for class org.biomoby.shared.data.MobyProvisionInfo
Creates a blank provision information object.
MobyProvisionInfo(Element) - Constructor for class org.biomoby.shared.data.MobyProvisionInfo
Builds a provision information block from an XML fragment ("ProvisionInformation", as represented by a DOM node).
MobyRegistration - Class in org.inb.biomoby.central.factory.jaxb.registry
 
MobyRegistration() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
MobyRegistryEndpoint - Class in org.inb.biomoby.central.factory.jaxb
 
MobyRegistryEndpoint(String, MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.MobyRegistryEndpoint
 
MobyRelationship - Class in org.biomoby.shared
A container representing a name of a BioMoby data type and its relationship to another BioMoby data type.
MobyRelationship() - Constructor for class org.biomoby.shared.MobyRelationship
Default constructor.
MobyRelationship(String, String, int) - Constructor for class org.biomoby.shared.MobyRelationship
Normal constructor.
MobyRequest - Class in org.biomoby.client
This class handles the WSDL transaction to request a response from a remote SOAP Web service that handles the MOBY format.
MobyRequest(Central) - Constructor for class org.biomoby.client.MobyRequest
Default constructor.
MobyRequestEvent - Class in org.biomoby.client
This is the event passed to a MobyRequestEventHandler, representing either data for a request for service, or the data from a service response depending on whether the listener registered itself in a client or server.
MobyRequestEvent(MobyContentInstance, MobyRequest, MobyService, MobyContentInstance, Throwable, int) - Constructor for class org.biomoby.client.MobyRequestEvent
 
MobyRequestEventHandler - Interface in org.biomoby.client
This interface is used for callbacks when MobyRequest is acting as a server or client.
MobyResourceRef - Class in org.biomoby.shared
A container pointing to metadata available from a BioMoby registry.
MobyResourceRef(String, URL, String) - Constructor for class org.biomoby.shared.MobyResourceRef
Normal constructor.
MobyResources - Class in org.biomoby.client.rdf.vocabulary
Deprecated. Replaced by Predicates. The reason is that this class was redundant and ill conceived. From now on the BioMoby predicates, under the namespace moby, are located in Predicates.java.
MobyResources() - Constructor for class org.biomoby.client.rdf.vocabulary.MobyResources
Deprecated.  
MobySaveDialog - Class in ca.ucalgary.seahawk.gui
A utility to save the current document as XML or HTML, or the tab's history as a workflow.
MobySecondaryData - Class in org.biomoby.shared
A container representing a way how various secondary data types are used in a service.
MobySecondaryData(String) - Constructor for class org.biomoby.shared.MobySecondaryData
Default constructor.
MobySecondaryData(Element) - Constructor for class org.biomoby.shared.MobySecondaryData
Construct this instance from a piece of XML.
MobySecondaryInputGUI - Class in ca.ucalgary.seahawk.gui
A class that generates a GUI to fill in (instantiate or change) the values of Secondary Input to MOBY services.
MobySecondaryInputGUI(ActionListener, Frame, boolean, MobyClient) - Constructor for class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
MobySecondaryInputGUI(ActionListener, Frame, boolean, int, MobyClient) - Constructor for class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
MobySecondaryInputGUI(ActionListener, MobyClient) - Constructor for class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
MobySecondaryInputGUI(ActionListener, int, MobyClient) - Constructor for class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
MobySecondaryLogging - Class in org.biomoby.registry.sync.logging
Class to initialise the logger.
mobyService - Annotation Type in org.biomoby.service
Indicates that the annotated class is a MOBY Semantic Web Service, and provides the information that will populate the MOBY Central registry for this service instance.
MobyService - Class in org.biomoby.shared
A container representing a service.
MobyService() - Constructor for class org.biomoby.shared.MobyService
Default constructor.
MobyService(String) - Constructor for class org.biomoby.shared.MobyService
Normal constructor.
MobyService(String, String) - Constructor for class org.biomoby.shared.MobyService
Even more normal constructor - because a service is fully qualified only by its name and its authority.
MobyServiceComparator - Class in org.biomoby.registry.rdfagent.verifier
This class compares 2 services and determines what it is that is different between them.
MobyServiceComparator() - Constructor for class org.biomoby.registry.rdfagent.verifier.MobyServiceComparator
Constructor
MobyServiceException - Exception in org.biomoby.shared.data
 
MobyServiceException(Element) - Constructor for exception org.biomoby.shared.data.MobyServiceException
Builds an instance of an exception from a DOM element.
MobyServiceException(int, int, String) - Constructor for exception org.biomoby.shared.data.MobyServiceException
 
MobyServiceException(int, int, String, String) - Constructor for exception org.biomoby.shared.data.MobyServiceException
 
MobyServiceException(int, int, String, String, String) - Constructor for exception org.biomoby.shared.data.MobyServiceException
 
MobyServiceLocator - Class in org.biomoby.client
A container for information how to reach a Biomoby service.
MobyServiceLocator() - Constructor for class org.biomoby.client.MobyServiceLocator
Default constructor.
MobyServiceLocator(MobyService) - Constructor for class org.biomoby.client.MobyServiceLocator
Another constructor, seeting also a service.
MobyServicesGUI - Class in ca.ucalgary.seahawk.gui
Implementation of the actually popup menu that lists services available, and invokes them.
MobyServicesGUI() - Constructor for class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
MobyServiceType - Class in org.biomoby.shared
A container representing a service type used in the Moby registry.
MobyServiceType() - Constructor for class org.biomoby.shared.MobyServiceType
Default constructor.
MobyServiceType(String) - Constructor for class org.biomoby.shared.MobyServiceType
Normal constructor.
MobyServiceType(String, Registry) - Constructor for class org.biomoby.shared.MobyServiceType
 
MobyServlet - Class in org.biomoby.service
This the base implementation of a MOBY servlet that can be easily extended to provide a meaningful service (by overriding processRequest()).
MobyServlet() - Constructor for class org.biomoby.service.MobyServlet
 
MobyServletTestCase - Class in org.biomoby.service.test
 
MobyServletTestCase(String) - Constructor for class org.biomoby.service.test.MobyServletTestCase
 
MobyShimmer - Class in ca.ucalgary.seahawk.gui
The purpose of this class is to improve service interoperability "shims" by checking the MOBY service listings for services that do format conversion on the given data, then adds service options for the output types of those services, if they aren't in the menu already.
MobyShimmer(MobyServicesGUI) - Constructor for class ca.ucalgary.seahawk.gui.MobyShimmer
 
MobyShimmer(MobyServicesGUI, MobyServiceType) - Constructor for class ca.ucalgary.seahawk.gui.MobyShimmer
 
MobySimple - Class in org.biomoby.shared.parser
A specialized "envelope" that can carry one real Biomoby data object, and gives it (usually) a name, also known as an article name for top-level object.
MobySimple() - Constructor for class org.biomoby.shared.parser.MobySimple
Default constructor.
MobySimple - Class in org.inb.biomoby.shared.message
 
MobySimple() - Constructor for class org.inb.biomoby.shared.message.MobySimple
 
MobySimple(AbstractMobyObject) - Constructor for class org.inb.biomoby.shared.message.MobySimple
 
MobySimple(AbstractMobyObject, String) - Constructor for class org.inb.biomoby.shared.message.MobySimple
 
MobySpecWrapper - Class in ca.ucalgary.services.util
Base class for implementing classes that parse some existing service specification enhanced to wrap the operations with Moby Semantic information, such as CGIs and WSDL services.
MobySpecWrapper() - Constructor for class ca.ucalgary.services.util.MobySpecWrapper
 
MobyString - Class in org.biomoby.shared.datatypes
An object representing a String, a Moby primitive data type.
MobyString() - Constructor for class org.biomoby.shared.datatypes.MobyString
Default constructor.
MobyString(String) - Constructor for class org.biomoby.shared.datatypes.MobyString
Another constructor.
MOBYSTRING - Static variable in interface org.biomoby.shared.parser.MobyTags
 
MobyString - Class in org.inb.biomoby.shared.datatypes
 
MobyString() - Constructor for class org.inb.biomoby.shared.datatypes.MobyString
 
MobyString(String) - Constructor for class org.inb.biomoby.shared.datatypes.MobyString
 
MobySyncExecuter - Class in org.biomoby.registry.sync
The class MobySecondaryExecuter is the main class to start the synchronization process of a local Biomoby central and a master central.
MobySyncExecuter() - Constructor for class org.biomoby.registry.sync.MobySyncExecuter
 
MobySynchronize - Interface in org.biomoby.registry.sync
Basic interface to update a local Biomoby central.
MobySynchronizeImpl - Class in org.biomoby.registry.sync
Class to control the synchronization of the two moby centrals.
MobySynchronizeImpl() - Constructor for class org.biomoby.registry.sync.MobySynchronizeImpl
 
MobyTags - Interface in org.biomoby.shared.parser
An interface containing all Biomoby XML element and attribute names.
MobyThing - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
MobyUnitTest - Class in org.biomoby.shared
A class representing a moby unit test.
MobyUnitTest() - Constructor for class org.biomoby.shared.MobyUnitTest
Default Constructor - creates a blank MobyUnitTest object
MobyUnitTestingPanel - Class in org.biomoby.service.dashboard
This Panel uses the SimpleClient as a template panel and adds the functionality required to provide/perform unit tests on selected Moby services.
MobyUnitTestingPanel() - Constructor for class org.biomoby.service.dashboard.MobyUnitTestingPanel
Default constructor.
MobyUtils - Class in ca.ucalgary.seahawk.util
Contains utility methods for Moby Object creation from unstructured data, and for creating the Seahawk GUI.
MobyUtils() - Constructor for class ca.ucalgary.seahawk.util.MobyUtils
 
MobyWSRFScope - Annotation Type in org.inb.biomoby.service.resolver
 
MobyWSRFScopeFeature - Class in org.inb.biomoby.service.resolver
 
MobyWSRFScopeFeature() - Constructor for class org.inb.biomoby.service.resolver.MobyWSRFScopeFeature
 
MobyXref - Class in org.biomoby.shared.datatypes
An object representing a cross reference.
MobyXref() - Constructor for class org.biomoby.shared.datatypes.MobyXref
Default constructor.
mod(Number) - Method in class org.biomoby.shared.data.MobyDataInt
Perform the modulus operand on the data value.
MODE_HTTP_PARAM - Static variable in class org.biomoby.service.MobyServlet
 
modelCleared() - Method in class org.inb.biomoby.central.gui.AbstractEntityTreePanel
 
modelCleared() - Method in class org.inb.biomoby.central.gui.model.DataTypesTreeModel
 
modelCleared() - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
modelCleared() - Method in class org.inb.biomoby.central.gui.model.RegistryComboBoxModel
 
modelCleared() - Method in class org.inb.biomoby.central.gui.model.ServicesTreeModel
 
modelCleared() - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
modelCleared() - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
modelCleared() - Method in class org.inb.biomoby.central.model.DatatypesModel
An observer method that starts a model reloading once the default BioMoby Registry model has been changed
modelCleared() - Method in interface org.inb.biomoby.central.model.ModelListener
 
modelCleared() - Method in class org.inb.biomoby.central.model.NamespacesModel
An observer method that starts a model reloading once the default BioMoby Registry model has been changed
modelCleared() - Method in class org.inb.biomoby.central.model.ServicesModel
 
modelCleared() - Method in class org.inb.biomoby.generator.gui.AbstractServiceModelPanel
 
ModelConverter - Class in org.inb.biomoby.central.factory.jaxb
 
ModelConverter() - Constructor for class org.inb.biomoby.central.factory.jaxb.ModelConverter
 
modelIndex(int) - Method in class org.biomoby.service.dashboard.TableSorter
 
ModelListener<T> - Interface in org.inb.biomoby.central.model
A listener interface that must be implemented in order to be registered with BioMoby models
modelObjectChanged(MobyCentral, MobyCentral) - Method in class org.inb.biomoby.central.gui.AbstractEntityTreePanel
 
modelObjectChanged(ObjectType, ObjectType) - Method in class org.inb.biomoby.central.gui.model.DataTypesTreeModel
 
modelObjectChanged(ObjectType, ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
modelObjectChanged(MobyCentral, MobyCentral) - Method in class org.inb.biomoby.central.gui.model.RegistryComboBoxModel
 
modelObjectChanged(Service, Service) - Method in class org.inb.biomoby.central.gui.model.ServicesTreeModel
 
modelObjectChanged(ObjectType, ObjectType) - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
modelObjectChanged(ObjectType, ObjectType) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
modelObjectChanged(MobyCentral, MobyCentral) - Method in class org.inb.biomoby.central.model.DatatypesModel
 
modelObjectChanged(T, T) - Method in interface org.inb.biomoby.central.model.ModelListener
 
modelObjectChanged(MobyCentral, MobyCentral) - Method in class org.inb.biomoby.central.model.NamespacesModel
 
modelObjectChanged(MobyCentral, MobyCentral) - Method in class org.inb.biomoby.central.model.ServicesModel
 
modelObjectInserted(MobyCentral) - Method in class org.inb.biomoby.central.gui.AbstractEntityTreePanel
 
modelObjectInserted(ObjectType) - Method in class org.inb.biomoby.central.gui.model.DataTypesTreeModel
 
modelObjectInserted(ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
modelObjectInserted(MobyCentral) - Method in class org.inb.biomoby.central.gui.model.RegistryComboBoxModel
 
modelObjectInserted(Service) - Method in class org.inb.biomoby.central.gui.model.ServicesTreeModel
 
modelObjectInserted(ObjectType) - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
modelObjectInserted(ObjectType) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
modelObjectInserted(MobyCentral) - Method in class org.inb.biomoby.central.model.DatatypesModel
 
modelObjectInserted(T) - Method in interface org.inb.biomoby.central.model.ModelListener
 
modelObjectInserted(MobyCentral) - Method in class org.inb.biomoby.central.model.NamespacesModel
 
modelObjectInserted(MobyCentral) - Method in class org.inb.biomoby.central.model.ServicesModel
 
modelObjectRemoved(MobyCentral) - Method in class org.inb.biomoby.central.gui.AbstractEntityTreePanel
 
modelObjectRemoved(ObjectType) - Method in class org.inb.biomoby.central.gui.model.DataTypesTreeModel
 
modelObjectRemoved(ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
modelObjectRemoved(MobyCentral) - Method in class org.inb.biomoby.central.gui.model.RegistryComboBoxModel
 
modelObjectRemoved(Service) - Method in class org.inb.biomoby.central.gui.model.ServicesTreeModel
 
modelObjectRemoved(ObjectType) - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
modelObjectRemoved(ObjectType) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
modelObjectRemoved(MobyCentral) - Method in class org.inb.biomoby.central.model.DatatypesModel
 
modelObjectRemoved(T) - Method in interface org.inb.biomoby.central.model.ModelListener
 
modelObjectRemoved(MobyCentral) - Method in class org.inb.biomoby.central.model.NamespacesModel
 
modelObjectRemoved(MobyCentral) - Method in class org.inb.biomoby.central.model.ServicesModel
 
MolWeightAnnotation - Class in org.inb.biomoby.shared.ontology
 
MolWeightAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.MolWeightAnnotation
 
MolWeightAnnotationListPane<T extends MolWeightAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
MolWeightAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.MolWeightAnnotationListPane
 
MolWeightAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.MolWeightAnnotationListPane
 
MolWeightsAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
MolWeightsAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.MolWeightsAnnotatedAASequence
 
MolWeightsAnnotatedAASequenceComponent<T extends MolWeightsAnnotatedAASequence> - Class in org.inb.biomoby.client.gui.ontology
 
MolWeightsAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
MolWeightsAnnotatedAASequenceComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
MolWeightsAnnotatedAASequenceComponent.MolWeightsAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
MolWeightsArray - Class in org.inb.biomoby.shared.ontology
 
MolWeightsArray() - Constructor for class org.inb.biomoby.shared.ontology.MolWeightsArray
 
mosesAll() - Method in class org.biomoby.service.dashboard.AntModel
Deal both with Moses-generated datatypes and skeletons - in an appropriate order.
mosesCleanDatatypes() - Method in class org.biomoby.service.dashboard.AntModel
Remove generated datatypes.
mosesCleanSkeletons() - Method in class org.biomoby.service.dashboard.AntModel
Remove generated skeletons
mosesDatatypes() - Method in class org.biomoby.service.dashboard.AntModel
Deal with Moses-generated datatypes.
mosesDeploy() - Method in class org.biomoby.service.dashboard.AntModel
Deploy selected services to a server (Tomcat/Axis).
mosesSkeletons() - Method in class org.biomoby.service.dashboard.AntModel
Deal with Moses-generated skeletons.
mosesUndeploy() - Method in class org.biomoby.service.dashboard.AntModel
Undeploy selected services to a server (Tomcat/Axis).
MotifAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
MotifAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.MotifAnnotatedAASequence
 
MotifAnnotatedAASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
MotifAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
MotifAnnotatedAASequenceComponent(MotifAnnotatedAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
MotifAnnotatedAASequenceComponent.MotifAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
MotifAnnotation - Class in org.inb.biomoby.shared.ontology
 
MotifAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.MotifAnnotation
 
MotifAnnotationListPane<T extends MotifAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
MotifAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.MotifAnnotationListPane
 
MotifAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.MotifAnnotationListPane
 
MotifMatrix - Class in org.inb.biomoby.shared.ontology
 
MotifMatrix() - Constructor for class org.inb.biomoby.shared.ontology.MotifMatrix
 
MotifMatrixComponent - Class in org.inb.biomoby.client.gui.ontology
 
MotifMatrixComponent(MotifMatrix) - Constructor for class org.inb.biomoby.client.gui.ontology.MotifMatrixComponent
 
mouseClicked(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
mouseClicked(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
mouseClicked(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.RoundedButton
 
mouseClicked(MouseEvent) - Method in class org.inb.swing.LabelButton
 
mouseClicked(MouseEvent) - Method in class org.inb.swing.StatusBar
 
mouseClickedOverAnnotations(MouseEvent, List<T>) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
Default implementation notifies all listeners that it WANT to change a position
mouseDragged(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
mouseDragged(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mouseDragged(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
mouseDragged(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
mouseDragged(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
mouseDragged(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
mouseEntered(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
mouseEntered(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
Grabs the keyboard focus for the component if the mouse is over it, which eliminates the need for clicking before using keyboard shortcuts like Control-v to paste.
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.FamilyBLOCKAnnotationPane
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
mouseEntered(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.RoundedButton
 
mouseEntered(MouseEvent) - Method in class org.inb.swing.LabelButton
 
mouseEntered(MouseEvent) - Method in class org.inb.swing.StatusBar
 
mouseExited(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
mouseExited(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.FamilyBLOCKAnnotationPane
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
mouseExited(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.RoundedButton
 
mouseExited(MouseEvent) - Method in class org.inb.swing.LabelButton
 
mouseExited(MouseEvent) - Method in class org.inb.swing.StatusBar
 
mouseMoved(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
mouseMoved(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mouseMoved(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
mouseMoved(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
mouseMoved(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
mouseMoved(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
mouseMovedOverAnnotations(MouseEvent, List<T>) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mouseMovedOverAnnotations(MouseEvent, List<T>) - Method in class org.inb.biomoby.client.gui.auxiliary.LabeledAnnotationListPane
 
mousePressed(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
mousePressed(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
mousePressed(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.RoundedButton
 
mousePressed(MouseEvent) - Method in class org.inb.swing.LabelButton
 
mousePressed(MouseEvent) - Method in class org.inb.swing.StatusBar
 
mouseReleased(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
mouseReleased(MouseEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractDescriptionMobyComponent
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.CollapsablePanel
 
mouseReleased(MouseEvent) - Method in class org.inb.biomoby.client.gui.swing.RoundedButton
 
mouseReleased(MouseEvent) - Method in class org.inb.swing.LabelButton
 
mouseReleased(MouseEvent) - Method in class org.inb.swing.StatusBar
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
ms2Human(long) - Static method in class org.biomoby.shared.Utils
Give back an elapsed time (given in milllis) in a human readable form.
MSF - Class in org.inb.biomoby.shared.ontology
 
MSF() - Constructor for class org.inb.biomoby.shared.ontology.MSF
 
MSG - Static variable in interface org.omg.lsae.sax.LsaeTags
 
MSG_DEBUG - Static variable in class org.biomoby.service.dashboard.AntModel
 
MSG_INFO - Static variable in class org.biomoby.service.dashboard.AntModel
 
MSG_QUIET - Static variable in class org.biomoby.service.dashboard.AntModel
 
MSG_VERBOSE - Static variable in class org.biomoby.service.dashboard.AntModel
 
MultilineCommentedAASequenceDescriptionPane - Class in org.inb.biomoby.client.gui.auxiliary
 
MultilineCommentedAASequenceDescriptionPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedAASequenceDescriptionPane
 
MultilineCommentedAASequenceDescriptionPane(CommentedAASequence) - Constructor for class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedAASequenceDescriptionPane
 
MultilineCommentedNASequenceDescriptionMobyComponent - Class in org.inb.biomoby.client.gui.auxiliary
 
MultilineCommentedNASequenceDescriptionMobyComponent() - Constructor for class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedNASequenceDescriptionMobyComponent
 
MultilineCommentedNASequenceDescriptionMobyComponent(CommentedNASequence) - Constructor for class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedNASequenceDescriptionMobyComponent
 
MultiParameter - Class in org.inb.biomoby.shared.ontology
 
MultiParameter() - Constructor for class org.inb.biomoby.shared.ontology.MultiParameter
 
MULTIPART - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
MultiPartFormOutputStream - Class in ca.ucalgary.services.util
MultiPartFormOutputStream is used to write "multipart/form-data" to a java.net.URLConnection for POSTing.
MultiPartFormOutputStream(OutputStream, String) - Constructor for class ca.ucalgary.services.util.MultiPartFormOutputStream
Creates a new MultiPartFormOutputStream object using the specified output stream and boundary.
multiply(Number) - Method in class org.biomoby.shared.data.MobyDataFloat
Multiply the data value by a specified number.
multiply(Number) - Method in class org.biomoby.shared.data.MobyDataInt
Perform the multiplication operand on the data value.
MutableNodeList - Class in ca.ucalgary.seahawk.util
 
MutableNodeList() - Constructor for class ca.ucalgary.seahawk.util.MutableNodeList
 
mygInstance - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
mygInstance - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 

N

NAMD_Conf_Text - Class in org.inb.biomoby.shared.ontology
 
NAMD_Conf_Text() - Constructor for class org.inb.biomoby.shared.ontology.NAMD_Conf_Text
 
NAMD_Output - Class in org.inb.biomoby.shared.ontology
 
NAMD_Output() - Constructor for class org.inb.biomoby.shared.ontology.NAMD_Output
 
NAMD_Structure - Class in org.inb.biomoby.shared.ontology
 
NAMD_Structure() - Constructor for class org.inb.biomoby.shared.ontology.NAMD_Structure
 
name - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
name - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
NAMESPACE - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
namespace - Static variable in class org.biomoby.shared.schema.Builder
 
NAMESPACE - Static variable in class org.inb.biomoby.client.MobyDispatch
 
Namespace - Class in org.inb.biomoby.shared.registry
 
Namespace() - Constructor for class org.inb.biomoby.shared.registry.Namespace
 
Namespace(String) - Constructor for class org.inb.biomoby.shared.registry.Namespace
 
Namespace(String, String) - Constructor for class org.inb.biomoby.shared.registry.Namespace
 
NAMESPACE_LOADED - Static variable in interface org.biomoby.shared.event.Notifier
 
NAMESPACE_LOADING - Static variable in interface org.biomoby.shared.event.Notifier
 
NAMESPACE_MODEL_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
NAMESPACE_PROPERTIES() - Static method in class org.biomoby.registry.properties.MobyProperties
Retrieve the properties for [mobynamespace] in mobycentral.conf PRE: POST:The properties contained in mobycentral.conf for [mobynamespace] are returned in a Properties object.
NAMESPACE_RULE_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
namespace_type - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
namespace_type - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
NAMESPACE_VALUE_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
NAMESPACE_VALUE_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
NamespaceContextImpl - Class in org.biomoby.shared
This class is used to provide namespace context for XPath expression evaluation in the Seahawk data mapping rules file, and includes default mappings for prefixes such as moby:
NamespaceContextImpl(String, String) - Constructor for class org.biomoby.shared.NamespaceContextImpl
Sets just one prefix, the one provided, which also gets mapped to the blank prefix
NamespaceContextImpl(Node, String) - Constructor for class org.biomoby.shared.NamespaceContextImpl
Traverses up the DOM from the given element to enumerate all of the prefix <-> namespace mappings valid for this node.
NamespaceContextImpl() - Constructor for class org.biomoby.shared.NamespaceContextImpl
Populates the mapping table with an assortment of prefixes and namespaces used in Moby (see MobyPrefixResolver)
NamespaceHandler - Class in org.biomoby.registry.sync.handler
Class to synchronize the namespaces in the biomoby centrals.
NamespaceHandler(String) - Constructor for class org.biomoby.registry.sync.handler.NamespaceHandler
 
NamespaceParser - Class in org.biomoby.shared.extended
 
NamespaceParser() - Constructor for class org.biomoby.shared.extended.NamespaceParser
Default constructor - need to set the URL for the RDF document that describes the Namespace ontology using setURL(String url) or setURL(URL url)
NamespaceParser(String) - Constructor for class org.biomoby.shared.extended.NamespaceParser
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the Namespace ontology.
NamespaceParser(URL) - Constructor for class org.biomoby.shared.extended.NamespaceParser
Parameterized Constructor that takes in a url for the RDF document that describes the Namespace ontology.
NAMESPACES_CANCELLED - Static variable in interface org.biomoby.shared.event.Notifier
 
NAMESPACES_COUNT - Static variable in interface org.biomoby.shared.event.Notifier
 
NAMESPACES_END - Static variable in interface org.biomoby.shared.event.Notifier
 
NAMESPACES_RESET - Static variable in interface org.biomoby.shared.event.Notifier
 
NAMESPACES_RESOURCE_NAME - Static variable in interface org.biomoby.shared.Central
A name of an ontology describing registered service types.
NAMESPACES_START - Static variable in interface org.biomoby.shared.event.Notifier
 
NAMESPACES_UPDATED - Static variable in interface org.biomoby.shared.event.Notifier
 
NamespacesBoard - Class in org.biomoby.service.dashboard
This is a simple graphical widget combining together a tree (a subclass of CommonTree) and a progress bar showing how the tree is being loaded.
NamespacesBoard(RegistryModel, CommonConsole, PropertyChannel) - Constructor for class org.biomoby.service.dashboard.NamespacesBoard
Constructor.
NamespacesBoard(RegistryModel, CommonConsole, PropertyChannel, CommonTree) - Constructor for class org.biomoby.service.dashboard.NamespacesBoard
Constructor.
NamespacesModel - Class in org.inb.biomoby.central.model
BioMoby namespaces model implementation class.
NamespacesTree - Class in org.biomoby.service.dashboard
A component showing and manipulating a tree of namespaces registered by a Biomoby registry.
NamespacesTree(RegistryModel, CommonConsole) - Constructor for class org.biomoby.service.dashboard.NamespacesTree
Constructor.
NAS - Static variable in class org.biomoby.shared.data.MobyDataXref
 
NCBI_BLAST_Text - Class in org.inb.biomoby.shared.ontology
 
NCBI_BLAST_Text() - Constructor for class org.inb.biomoby.shared.ontology.NCBI_BLAST_Text
 
NCut_Clusters - Class in org.inb.biomoby.shared.ontology
 
NCut_Clusters() - Constructor for class org.inb.biomoby.shared.ontology.NCut_Clusters
 
NCut_Matrix - Class in org.inb.biomoby.shared.ontology
 
NCut_Matrix() - Constructor for class org.inb.biomoby.shared.ontology.NCut_Matrix
 
NCut_Text - Class in org.inb.biomoby.shared.ontology
 
NCut_Text() - Constructor for class org.inb.biomoby.shared.ontology.NCut_Text
 
ND - Static variable in class org.biomoby.shared.data.MobyDataXref
 
NDB__Text - Class in org.inb.biomoby.shared.ontology
 
NDB__Text() - Constructor for class org.inb.biomoby.shared.ontology.NDB__Text
 
Newick__Text - Class in org.inb.biomoby.shared.ontology
 
Newick__Text() - Constructor for class org.inb.biomoby.shared.ontology.Newick__Text
 
Newick_Text - Class in org.inb.biomoby.shared.ontology
 
Newick_Text() - Constructor for class org.inb.biomoby.shared.ontology.Newick_Text
 
NO_CONNECTION - Static variable in class org.biomoby.client.ServicesEdge
Indicates that there is no information how the services are connected.
NO_METADATA_AVAILABLE - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: There are no metadata available for the executed service/analysis.
NO_OUTPUT - Static variable in class org.biomoby.client.ServicesEdge
 
NODE_AUTHORITY - Static variable in class org.biomoby.service.dashboard.CommonNode
 
NODE_DATA_TYPE - Static variable in class org.biomoby.service.dashboard.CommonNode
 
NODE_NAMESPACE - Static variable in class org.biomoby.service.dashboard.CommonNode
 
NODE_SERVICE - Static variable in class org.biomoby.service.dashboard.CommonNode
 
NODE_SERVICE_TYPE - Static variable in class org.biomoby.service.dashboard.CommonNode
 
nodeForRow(int) - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
NON_PRIMITIVE - Static variable in class org.biomoby.shared.schema.MElement
A moby data type that is not a primitive.
NoSuccessException - Exception in org.biomoby.shared
A specific exception indicating that a request should not be fulfilled because something was not correctly specified, or was not found.
NoSuccessException() - Constructor for exception org.biomoby.shared.NoSuccessException
 
NoSuccessException(String, Object) - Constructor for exception org.biomoby.shared.NoSuccessException
A constructor specifying a reason and the potential culprit for this exception.
NOT_IMPLEMENTED - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: A requested method is not implemented.
NOT_RUNNABLE - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: The same job (analysis) has already been executed, or the data that had been set previously do not exist or are not accessible anymore.
NOT_RUNNING - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: A job (analysis) has not yet been started.
NOT_SORTED - Static variable in class org.biomoby.service.dashboard.TableSorter
 
NOT_TERMINATED - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: For some reasons, a job (analysis) is not interruptible, but an attempt to do so was done.
notEmpty(String) - Static method in class org.biomoby.service.BaseService
A utility method returning true if 'value' is neither null nor a string consisting only from whitespaces.
NOTES - Static variable in interface org.biomoby.shared.parser.MobyTags
 
NotificationEvent - Class in org.biomoby.shared.event
An event fired by various Moby components to inform that something has happened.
NotificationEvent(Object) - Constructor for class org.biomoby.shared.event.NotificationEvent
Constructor that does not do much.
NotificationEvent(Object, int, Object) - Constructor for class org.biomoby.shared.event.NotificationEvent
A usual constructor, setting notification type and a message.
NotificationEvent(Object, int, Object, Object) - Constructor for class org.biomoby.shared.event.NotificationEvent
A full constructor, setting notification type, message, and details.
NotificationListener - Interface in org.biomoby.shared.event
The listener interface for receiving notification events.
notified(NotificationEvent) - Method in class org.biomoby.service.dashboard.CommonBoard
An empty mplementation of a NotificationListener intereface.
notified(NotificationEvent) - Method in class org.biomoby.service.dashboard.DataTypesBoard
Implementation of a NotificationListener intereface
notified(NotificationEvent) - Method in class org.biomoby.service.dashboard.NamespacesBoard
Implementation of a NotificationListener intereface
notified(NotificationEvent) - Method in class org.biomoby.service.dashboard.ServicesBoard
Implementation of a NotificationListener intereface
notified(NotificationEvent) - Method in class org.biomoby.service.dashboard.ServiceTypesBoard
Implementation of a NotificationListener intereface
notified(NotificationEvent) - Method in class org.biomoby.service.dashboard.StatisticsPanel
Implementation of a NotificationListener intereface
notified(NotificationEvent) - Method in class org.biomoby.shared.event.LogListener
 
notified(NotificationEvent) - Method in interface org.biomoby.shared.event.NotificationListener
Invoked when a notification arrives.
notified(NotificationEvent) - Method in class org.biomoby.shared.event.SimpleListener
 
Notifier - Interface in org.biomoby.shared.event
 
NR - Static variable in class org.biomoby.shared.data.MobyDataXref
 
NS - Static variable in class org.biomoby.client.rdf.vocabulary.DC_PROTEGE
 
NS - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
NS_DIVIDER - Static variable in class org.biomoby.client.ServicesEdge
A divider used in connectors to separate namespace and data type name.
NucleotideSequence - Class in org.inb.biomoby.shared.ontology
 
NucleotideSequence() - Constructor for class org.inb.biomoby.shared.ontology.NucleotideSequence
 
NULL_NAME - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
NullIcon - Class in ca.ucalgary.seahawk.util
An empty icon that prints nothing (used for new tabs with no contents)
NullIcon() - Constructor for class ca.ucalgary.seahawk.util.NullIcon
 

O

OBJ_ID - Static variable in interface org.biomoby.shared.parser.MobyTags
 
OBJ_NAMESPACE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
OBJECT_PROPERTIES() - Static method in class org.biomoby.registry.properties.MobyProperties
Retrieve the properties for [mobyobject] in mobycentral.conf PRE: POST:The properties contained in mobycentral.conf for [mobyobject] are returned in a Properties object.
object_type - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
object_type - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
object_type - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
OBJECT_TYPE - Static variable in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
OBJECT_TYPES - Static variable in class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
OBJECT_URI - Static variable in class org.biomoby.shared.schema.RdfParser
 
ObjectType - Class in org.inb.biomoby.shared.registry
 
ObjectType() - Constructor for class org.inb.biomoby.shared.registry.ObjectType
 
ObjectType(String) - Constructor for class org.inb.biomoby.shared.registry.ObjectType
 
ObjectType(String, String) - Constructor for class org.inb.biomoby.shared.registry.ObjectType
 
ObjectTypeAnnotationPanel - Class in org.inb.biomoby.central.gui
A simple datatype annotations editor panel
ObjectTypeAnnotationPanel(AbstractModel<ObjectType>) - Constructor for class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
 
ObjectTypeListCellRenderer - Class in org.inb.biomoby.central.gui.renderer
 
ObjectTypeListCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.ObjectTypeListCellRenderer
 
ObjectTypeTableCellEditor - Class in org.inb.biomoby.central.gui.renderer
 
ObjectTypeTableCellEditor(AbstractModel<ObjectType>) - Constructor for class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor
 
ObjectTypeTableCellEditor.ObjectTypeComboBoxModel - Class in org.inb.biomoby.central.gui.renderer
 
ObjectTypeTableCellEditor.ObjectTypeComboBoxModel(AbstractModel<ObjectType>) - Constructor for class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
ObjectTypeTableCellRenderer - Class in org.inb.biomoby.central.gui.renderer
 
ObjectTypeTableCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellRenderer
 
ObjectTypeTransferable - Class in org.inb.biomoby.central.gui.dnd
BioMoby ObjectType[] transferable implementation
ObjectTypeTransferable(ObjectType) - Constructor for class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
ObjectTypeTransferable(ObjectType, DataFlavor) - Constructor for class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
ObjectTypeTransferable(Collection<ObjectType>) - Constructor for class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
ObjectTypeTransferable(Collection<ObjectType>, DataFlavor) - Constructor for class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferable
 
ObjectTypeTransferHandler - Class in org.inb.biomoby.central.gui.dnd
 
ObjectTypeTransferHandler(DataFlavor) - Constructor for class org.inb.biomoby.central.gui.dnd.ObjectTypeTransferHandler
 
ODP_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODP_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODP_MIME - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODS_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODS_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODS_MIME - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODT_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODT_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ODT_MIME - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
ofType - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
OK - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: No error.
OK_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
OMIM - Class in org.inb.biomoby.shared.ontology
 
OMIM() - Constructor for class org.inb.biomoby.shared.ontology.OMIM
 
OMIMComponent<T extends OMIM> - Class in org.inb.biomoby.client.gui.ontology
 
OMIMComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.OMIMComponent
 
ONCHANGE - Static variable in class org.biomoby.client.GraphsServlet
 
OP_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
OP_SPEC_DOC_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
OPEN_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
OPEN_OPTION_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
openDocument() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Displays the choice to the user to open a file or URL.
openURL(String) - Static method in class ca.ucalgary.seahawk.util.BrowserLauncher
Attempts to open the default web browser to the given URL.
operation - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
operation - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
operationTask - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
operationTask - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
operationType - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
operationType - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
optimizedDataTypes(MobyDataType[]) - Static method in class org.biomoby.client.ServiceConnections
Make the data types better searchable.
org.biomoby.client - package org.biomoby.client
The components used for developing Moby clients.
org.biomoby.client.rdf.builder - package org.biomoby.client.rdf.builder
Provides the classes that are necessary for creating BioMoby RDF documents.
org.biomoby.client.rdf.vocabulary - package org.biomoby.client.rdf.vocabulary
The components used for describing the vocabulary in MOBY related RDF documents.
org.biomoby.client.test - package org.biomoby.client.test
 
org.biomoby.client.util - package org.biomoby.client.util
 
org.biomoby.registry.Central - package org.biomoby.registry.Central
 
org.biomoby.registry.definitions.types - package org.biomoby.registry.definitions.types
 
org.biomoby.registry.meta - package org.biomoby.registry.meta
 
org.biomoby.registry.properties - package org.biomoby.registry.properties
Provides classes and interfaces that help utilize property and configuration files.
org.biomoby.registry.rdfagent.test - package org.biomoby.registry.rdfagent.test
 
org.biomoby.registry.rdfagent.util - package org.biomoby.registry.rdfagent.util
 
org.biomoby.registry.rdfagent.verifier - package org.biomoby.registry.rdfagent.verifier
 
org.biomoby.registry.sync - package org.biomoby.registry.sync
 
org.biomoby.registry.sync.filtering - package org.biomoby.registry.sync.filtering
 
org.biomoby.registry.sync.handler - package org.biomoby.registry.sync.handler
 
org.biomoby.registry.sync.logging - package org.biomoby.registry.sync.logging
 
org.biomoby.service - package org.biomoby.service
It contains general components that can be used by those writing code for Moby services.
org.biomoby.service.dashboard - package org.biomoby.service.dashboard
 
org.biomoby.service.dashboard.chooser - package org.biomoby.service.dashboard.chooser
 
org.biomoby.service.dashboard.data - package org.biomoby.service.dashboard.data
 
org.biomoby.service.dashboard.renderers - package org.biomoby.service.dashboard.renderers
 
org.biomoby.service.dashboard.treetable - package org.biomoby.service.dashboard.treetable
 
org.biomoby.service.generator - package org.biomoby.service.generator
 
org.biomoby.service.test - package org.biomoby.service.test
 
org.biomoby.shared - package org.biomoby.shared
It contains components that are used from more than one (other) packages.
org.biomoby.shared.data - package org.biomoby.shared.data
The package org.biomoby.shared.data allows you to easily build MOBY data instances for sending to services, or querying the registry.
org.biomoby.shared.data.test - package org.biomoby.shared.data.test
 
org.biomoby.shared.datatypes - package org.biomoby.shared.datatypes
The package org.biomoby.shared.datatypes contains containers for basic Biomoby data types (a basic parent class MobyObject and all Biomoby primitive types).
org.biomoby.shared.event - package org.biomoby.shared.event
 
org.biomoby.shared.extended - package org.biomoby.shared.extended
 
org.biomoby.shared.parser - package org.biomoby.shared.parser
The package org.biomoby.shared.parser contains classes for parsing Biomoby data from an XML format (a Biomoby XML envelope) into Java objects, and back to XML.
org.biomoby.shared.schema - package org.biomoby.shared.schema
 
org.biomoby.shared.test - package org.biomoby.shared.test
 
org.biomoby.w3c.addressing - package org.biomoby.w3c.addressing
 
org.inb.biomoby - package org.inb.biomoby
 
org.inb.biomoby.central - package org.inb.biomoby.central
 
org.inb.biomoby.central.cache - package org.inb.biomoby.central.cache
 
org.inb.biomoby.central.factory.jaxb - package org.inb.biomoby.central.factory.jaxb
 
org.inb.biomoby.central.factory.jaxb.registry - package org.inb.biomoby.central.factory.jaxb.registry
 
org.inb.biomoby.central.gui - package org.inb.biomoby.central.gui
 
org.inb.biomoby.central.gui.dnd - package org.inb.biomoby.central.gui.dnd
 
org.inb.biomoby.central.gui.model - package org.inb.biomoby.central.gui.model
 
org.inb.biomoby.central.gui.renderer - package org.inb.biomoby.central.gui.renderer
 
org.inb.biomoby.central.model - package org.inb.biomoby.central.model
 
org.inb.biomoby.client - package org.inb.biomoby.client
 
org.inb.biomoby.client.gui - package org.inb.biomoby.client.gui
 
org.inb.biomoby.client.gui.auxiliary - package org.inb.biomoby.client.gui.auxiliary
 
org.inb.biomoby.client.gui.ontology - package org.inb.biomoby.client.gui.ontology
 
org.inb.biomoby.client.gui.swing - package org.inb.biomoby.client.gui.swing
 
org.inb.biomoby.client.gui.swing.border - package org.inb.biomoby.client.gui.swing.border
 
org.inb.biomoby.generator - package org.inb.biomoby.generator
 
org.inb.biomoby.generator.gui - package org.inb.biomoby.generator.gui
 
org.inb.biomoby.generator.gui.worker - package org.inb.biomoby.generator.gui.worker
 
org.inb.biomoby.service - package org.inb.biomoby.service
 
org.inb.biomoby.service.resolver - package org.inb.biomoby.service.resolver
 
org.inb.biomoby.shared.datatypes - package org.inb.biomoby.shared.datatypes
 
org.inb.biomoby.shared.message - package org.inb.biomoby.shared.message
 
org.inb.biomoby.shared.ontology - package org.inb.biomoby.shared.ontology
 
org.inb.biomoby.shared.registry - package org.inb.biomoby.shared.registry
 
org.inb.biomoby.shared.wsrf - package org.inb.biomoby.shared.wsrf
 
org.inb.biomoby.shared.wsrf.fault - package org.inb.biomoby.shared.wsrf.fault
 
org.inb.lsae - package org.inb.lsae
 
org.inb.swing - package org.inb.swing
 
org.inb.util - package org.inb.util
 
org.inb.wsrf.bf2 - package org.inb.wsrf.bf2
 
org.inb.wsrf.r2 - package org.inb.wsrf.r2
 
org.inb.wsrf.rl2 - package org.inb.wsrf.rl2
 
org.inb.wsrf.rp2 - package org.inb.wsrf.rp2
 
org.omg.lsae.notifications - package org.omg.lsae.notifications
 
org.omg.lsae.sax - package org.omg.lsae.sax
 
org.omg.lsae.sax.test - package org.omg.lsae.sax.test
 
org.soap - package org.soap
 
org.soap.sax - package org.soap.sax
 
org.soap.sax.test - package org.soap.sax.test
 
org.w3c.addressing.sax - package org.w3c.addressing.sax
 
organisation - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
organisation - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
os - Static variable in class org.biomoby.registry.properties.DefaultOS
the singleton
os - Static variable in class org.biomoby.registry.properties.MacOS
the singleton
os - Static variable in class org.biomoby.registry.properties.UNIX
the singleton
os - Static variable in class org.biomoby.registry.properties.Windows
the singleton
os - Static variable in class org.biomoby.registry.properties.WindowsNT
the singleton
output - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
Output - Class in org.inb.biomoby.shared.registry
 
Output() - Constructor for class org.inb.biomoby.shared.registry.Output
 
OUTPUT_RULE_URI_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 
OUTPUT_RULE_URIS_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
OUTPUT_XSD_TYPES_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
outputDataType - Variable in class org.biomoby.client.DataTypeConnector
 
outputParameter - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
outputParameter - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
OUTPUTS_PARAM - Static variable in interface ca.ucalgary.services.Registration
 

P

paint(Graphics) - Method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Paints the image on the window.
paint(Graphics) - Method in class ca.ucalgary.seahawk.util.SplashWindow
Paints the image on the window.
paint(Graphics) - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellRenderer
Subclassed to translate the graphics such that the last visible row will be drawn at 0,0.
paint(Graphics) - Method in class org.inb.swing.DecoratedJScrollPane
 
paintAnnotations(Graphics2D, Rectangle, List<T>) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
paintAnnotations(Graphics2D, Rectangle, List<T>) - Method in class org.inb.biomoby.client.gui.auxiliary.LabeledAnnotationListPane
 
paintBorder(Component, Graphics, int, int, int, int) - Method in class org.inb.biomoby.client.gui.swing.border.HeaderBorder.EmptyBorder
 
paintBorder(Component, Graphics, int, int, int, int) - Method in class org.inb.biomoby.client.gui.swing.border.HRBorder
 
paintBorder(Component, Graphics, int, int, int, int) - Method in class org.inb.biomoby.client.gui.swing.border.RoundedBorder
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractMultilineDescriptionMobyComponent
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.auxiliary.ArrayFloatChartPane
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.auxiliary.FamilyBLOCKAnnotationPane
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.auxiliary.ImageComponent
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.auxiliary.JmolPane
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.ontology.AnnotationHitsComponent
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.ontology.Image_EncodedComponent
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent.ScriptTextField
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.ontology.StructureDomainComponent
 
paintComponent(Graphics) - Method in class org.inb.biomoby.client.gui.swing.RoundedMultilineLabel
 
paintComponent(Graphics) - Method in class org.inb.swing.DecoratedJScrollPane
 
paintIcon(Component, Graphics, int, int) - Method in class ca.ucalgary.seahawk.util.CloseTabIcon
 
paintIcon(Component, Graphics, int, int) - Method in class ca.ucalgary.seahawk.util.CombinedIcon
 
paintIcon(Component, Graphics, int, int) - Method in class ca.ucalgary.seahawk.util.NullIcon
 
PARAM_TOOLTIP_WIDTH - Static variable in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
parameter - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
parameter - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
PARAMETER - Static variable in interface org.biomoby.shared.parser.MobyTags
 
Parameter - Class in org.inb.biomoby.shared.ontology
 
Parameter() - Constructor for class org.inb.biomoby.shared.ontology.Parameter
 
Parameter - Class in org.inb.biomoby.shared.registry
 
Parameter() - Constructor for class org.inb.biomoby.shared.registry.Parameter
 
Parameter.PARAMETER_TYPE - Enum in org.inb.biomoby.shared.registry
 
parameterNamespace - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
parameterNamespace - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
Parameters4Values - Class in org.inb.biomoby.shared.ontology
 
Parameters4Values() - Constructor for class org.inb.biomoby.shared.ontology.Parameters4Values
 
ParametersTable - Class in org.biomoby.service.dashboard.data
A table for entering one or more BioMoby secondary inputs (parameters, in the Biomoby speak).
ParametersTable(MobySecondaryData[]) - Constructor for class org.biomoby.service.dashboard.data.ParametersTable
Default constructor.
ParametersToVary - Class in org.inb.biomoby.shared.ontology
 
ParametersToVary() - Constructor for class org.inb.biomoby.shared.ontology.ParametersToVary
 
parse(String) - Method in class org.biomoby.shared.parser.MobyParser
Parse the contents of the given file.
parse(InputStream) - Method in class org.biomoby.shared.parser.MobyParser
Parse the contents coming from the given input stream.
parse(Reader) - Method in class org.biomoby.shared.parser.MobyParser
Parse the contents coming from the given reader.
parse(String) - Method in class org.omg.lsae.sax.EventParser
Parse the contents of the given file.
parse(InputStream) - Method in class org.omg.lsae.sax.EventParser
Parse the contents coming from the given input stream.
parse(Reader) - Method in class org.omg.lsae.sax.EventParser
Parse the contents coming from the given reader.
parse(String) - Method in class org.soap.sax.SOAPFaultParser
Parse the contents of the given file.
parse(InputStream) - Method in class org.soap.sax.SOAPFaultParser
Parse the contents coming from the given input stream.
parse(Reader) - Method in class org.soap.sax.SOAPFaultParser
Parse the contents coming from the given reader.
parse(String) - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Parse the contents of the given file.
parse(InputStream) - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Parse the contents coming from the given input stream.
parse(Reader) - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Parse the contents coming from the given reader.
parseDataGroup(Element, Registry) - Method in class org.biomoby.shared.data.MobyContentInstance
 
parseISO8601(String) - Static method in class org.biomoby.shared.data.MobyDataDateTime
For a description of ISO 8601 as used on the Web, see http://www.w3.org/TR/NOTE-datetime This method is based on org.w3.util.DateParser v. 1.4 by Benoît Mahé (bmahe@w3.org)
parseMobyServiceSpecs() - Method in class ca.ucalgary.services.util.WSDLConfig
 
parseSelectField(Element, String) - Method in class ca.ucalgary.services.util.XHTMLForm
 
parseSOAPMessageSpecs() - Method in class ca.ucalgary.services.util.WSDLConfig
 
PART_DATA_TYPES - Static variable in class org.biomoby.service.dashboard.RegistryModel
 
PART_NAMESPACES - Static variable in class org.biomoby.service.dashboard.RegistryModel
 
PART_SERVICE_TYPES - Static variable in class org.biomoby.service.dashboard.RegistryModel
 
PART_SERVICES - Static variable in class org.biomoby.service.dashboard.RegistryModel
 
PASSTHROUGH_ACTION - Static variable in interface ca.ucalgary.services.util.DataRecorder
If this variable is passed in a GET request to WrappingServlet, WrappingServlet will forward the GET request as-is to the data recorder.
paste() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
pathes(ServicesEdge[], String, String) - Static method in class org.biomoby.client.FilterServices
Selects (from the given set of edges) only those edges that compose pathes from a service given by 'sourceServiceName' to a service given by 'targetServiceName', or vice-versa.
pathes2(ServicesEdge[], String, String) - Static method in class org.biomoby.client.FilterServices
 
PatmatdbReport - Class in org.inb.biomoby.shared.ontology
 
PatmatdbReport() - Constructor for class org.inb.biomoby.shared.ontology.PatmatdbReport
 
PatmatdbReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
PatmatdbReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
PatmatdbReportComponent(PatmatdbReport) - Constructor for class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
PatmatdbReportComponent.PatmatdbReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
PatmatmotifsReport - Class in org.inb.biomoby.shared.ontology
 
PatmatmotifsReport() - Constructor for class org.inb.biomoby.shared.ontology.PatmatmotifsReport
 
PatmatmotifsReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
PatmatmotifsReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
PatmatmotifsReportComponent(PatmatmotifsReport) - Constructor for class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
PatmatmotifsReportComponent.PatmatmotifsReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
Pattern - Class in org.inb.biomoby.shared.ontology
 
Pattern() - Constructor for class org.inb.biomoby.shared.ontology.Pattern
 
PatternComponent - Class in org.inb.biomoby.client.gui.ontology
 
PatternComponent(Pattern) - Constructor for class org.inb.biomoby.client.gui.ontology.PatternComponent
 
PBERecorder - Class in ca.ucalgary.services.util
This class controls the interaction between the web browser and Seahawk via the pasting actions.
PBERecorder() - Constructor for class ca.ucalgary.services.util.PBERecorder
 
PDB__Text - Class in org.inb.biomoby.shared.ontology
 
PDB__Text() - Constructor for class org.inb.biomoby.shared.ontology.PDB__Text
 
PDB__TextComponent<T extends PDB__Text> - Class in org.inb.biomoby.client.gui.ontology
 
PDB__TextComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
PDB__TextComponent.ScriptTextField - Class in org.inb.biomoby.client.gui.ontology
 
PDB__TextComponent.ScriptTextField() - Constructor for class org.inb.biomoby.client.gui.ontology.PDB__TextComponent.ScriptTextField
 
PDB_Enriched - Class in org.inb.biomoby.shared.ontology
 
PDB_Enriched() - Constructor for class org.inb.biomoby.shared.ontology.PDB_Enriched
 
PDF_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
PDF_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
PendingCurationException - Exception in org.biomoby.shared
A specific exception indicating that a request should not be fulfilled because registration or deregistration of an entity was not yet successful - but may be later.
PendingCurationException() - Constructor for exception org.biomoby.shared.PendingCurationException
 
Pepcoil_Text - Class in org.inb.biomoby.shared.ontology
 
Pepcoil_Text() - Constructor for class org.inb.biomoby.shared.ontology.Pepcoil_Text
 
Pepcoil_TextComponent - Class in org.inb.biomoby.client.gui.ontology
 
Pepcoil_TextComponent(Pepcoil_Text) - Constructor for class org.inb.biomoby.client.gui.ontology.Pepcoil_TextComponent
 
PepinfoReport - Class in org.inb.biomoby.shared.ontology
 
PepinfoReport() - Constructor for class org.inb.biomoby.shared.ontology.PepinfoReport
 
PepinfoReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
PepinfoReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
PepinfoReportComponent(PepinfoReport) - Constructor for class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
PepinfoReportComponent.PepinfoReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
PepNovoReport - Class in org.inb.biomoby.shared.ontology
 
PepNovoReport() - Constructor for class org.inb.biomoby.shared.ontology.PepNovoReport
 
Pepstats_Text - Class in org.inb.biomoby.shared.ontology
 
Pepstats_Text() - Constructor for class org.inb.biomoby.shared.ontology.Pepstats_Text
 
Pepstats_TextComponent - Class in org.inb.biomoby.client.gui.ontology
 
Pepstats_TextComponent(Pepstats_Text) - Constructor for class org.inb.biomoby.client.gui.ontology.Pepstats_TextComponent
 
PERCENT - Static variable in interface org.omg.lsae.sax.LsaeTags
 
PercentEvent - Class in org.omg.lsae.notifications
 
PercentEvent() - Constructor for class org.omg.lsae.notifications.PercentEvent
 
PercentProgress - Class in org.inb.lsae
 
PercentProgress() - Constructor for class org.inb.lsae.PercentProgress
 
performs_task - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
performsTask - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
performsTask - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
PerlMoSeSPanel - Class in org.biomoby.service.dashboard
 
PerlMoSeSPanel() - Constructor for class org.biomoby.service.dashboard.PerlMoSeSPanel
Default constructor: set the image, and determines whether or not we are using windows
PerlMoSeSSyntaxDocument - Class in org.biomoby.service.dashboard
This class implements the functionality needed to create a Stylized view of perl scripts in the Perl MoSeS editor sub panel that is part of the Perl-MoSeS panel.
PerlMoSeSSyntaxDocument() - Constructor for class org.biomoby.service.dashboard.PerlMoSeSSyntaxDocument
Default Constructor
PHD_Text - Class in org.inb.biomoby.shared.ontology
 
PHD_Text() - Constructor for class org.inb.biomoby.shared.ontology.PHD_Text
 
Phylip_Interleaved_Text - Class in org.inb.biomoby.shared.ontology
 
Phylip_Interleaved_Text() - Constructor for class org.inb.biomoby.shared.ontology.Phylip_Interleaved_Text
 
Phylip_Text - Class in org.inb.biomoby.shared.ontology
 
Phylip_Text() - Constructor for class org.inb.biomoby.shared.ontology.Phylip_Text
 
Phylip_tree_Text - Class in org.inb.biomoby.shared.ontology
 
Phylip_tree_Text() - Constructor for class org.inb.biomoby.shared.ontology.Phylip_tree_Text
 
Phylip_treefile_Text - Class in org.inb.biomoby.shared.ontology
 
Phylip_treefile_Text() - Constructor for class org.inb.biomoby.shared.ontology.Phylip_treefile_Text
 
PI_TARGET - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
PINGED - Static variable in class org.biomoby.shared.MobyService
 
PIR_Text - Class in org.inb.biomoby.shared.ontology
 
PIR_Text() - Constructor for class org.inb.biomoby.shared.ontology.PIR_Text
 
PlainMobyText - Class in org.biomoby.service.dashboard.renderers
Display a MobyObject in its internal simple string representation.
PlainMobyText() - Constructor for class org.biomoby.service.dashboard.renderers.PlainMobyText
 
PlainText - Class in org.biomoby.service.dashboard.renderers
Display any String as a plain text in a text area.
PlainText() - Constructor for class org.biomoby.service.dashboard.renderers.PlainText
 
PLAINVERSION - Static variable in interface org.biomoby.shared.parser.MobyTags
 
PMUT_Text - Class in org.inb.biomoby.shared.ontology
 
PMUT_Text() - Constructor for class org.inb.biomoby.shared.ontology.PMUT_Text
 
PNG_GENERATOR_PARAM - Static variable in class ca.ucalgary.seahawk.gui.WorkflowPreviewDialog
 
PNG_GENERATOR_URL - Static variable in class ca.ucalgary.seahawk.gui.WorkflowPreviewDialog
 
poll(EndpointReference, String) - Static method in class org.biomoby.client.AsyncClient
 
poll(EndpointReference, Collection<String>) - Static method in class org.biomoby.client.AsyncClient
 
poll(EndpointReference, String[]) - Static method in class org.biomoby.client.AsyncClient
Polls the status (e.g. running, completed) of queries associated with a service invocation.
populateData(MobyObject) - Method in class org.biomoby.service.dashboard.data.DataTypeTreeTable
 
popupMenuCanceled(PopupMenuEvent) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
If the popup is canceled, we want to remove any data we've stored, and kill any requests to MOBYCentral.
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
positionChanged(int) - Method in interface org.inb.biomoby.client.gui.ontology.GenericSequenceComponent.GenericSequenceListener
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
positionChanged(int) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
pow(Number) - Method in class org.biomoby.shared.data.MobyDataFloat
Raise the stored value to an exponent.
pow(Number) - Method in class org.biomoby.shared.data.MobyDataInt
Raise the stored value to an exponent.
PPSearchReport - Class in org.inb.biomoby.shared.ontology
 
PPSearchReport() - Constructor for class org.inb.biomoby.shared.ontology.PPSearchReport
 
PPSearchReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
PPSearchReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
PPSearchReportComponent(PPSearchReport) - Constructor for class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
PPSearchReportComponent.PPSearchReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
PPT_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
PPT_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
PPT_MIME - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
PPT_MIME2 - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
PREDICATE_HAS_INPUT - Static variable in class org.biomoby.client.RDF
 
PREDICATE_HAS_OUTPUT - Static variable in class org.biomoby.client.RDF
 
Predicates - Class in org.biomoby.client.rdf.vocabulary
 
Predicates() - Constructor for class org.biomoby.client.rdf.vocabulary.Predicates
 
Prediction__Text - Class in org.inb.biomoby.shared.ontology
 
Prediction__Text() - Constructor for class org.inb.biomoby.shared.ontology.Prediction__Text
 
PredictionModel__XML - Class in org.inb.biomoby.shared.ontology
 
PredictionModel__XML() - Constructor for class org.inb.biomoby.shared.ontology.PredictionModel__XML
 
PredictorTraining_Text - Class in org.inb.biomoby.shared.ontology
 
PredictorTraining_Text() - Constructor for class org.inb.biomoby.shared.ontology.PredictorTraining_Text
 
PREFIX_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
PREFIX_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
prepareOutput(MobyPackage) - Method in class org.biomoby.service.BaseService
Return a package that has the same number of jobs (and named the same) as the given input.
PrimaryDataTable - Class in org.biomoby.service.dashboard
A swing JTable that collects definitions of primary data (input or ouput) for a service.
PrimaryDataTable() - Constructor for class org.biomoby.service.dashboard.PrimaryDataTable
Default constructor.
PRIMITIVE_VALUE_SENTINEL - Static variable in class ca.ucalgary.seahawk.services.MobyComplexBuilder
 
PrimitiveTypes - Class in org.biomoby.shared
 
PrimitiveTypes() - Constructor for class org.biomoby.shared.PrimitiveTypes
 
PrimitiveVector - Class in org.biomoby.shared.schema
 
PrimitiveVector(Vector) - Constructor for class org.biomoby.shared.schema.PrimitiveVector
 
PrimitiveVector(Vector, Vector) - Constructor for class org.biomoby.shared.schema.PrimitiveVector
 
PRIMS - Static variable in class org.biomoby.shared.PrimitiveTypes
 
print(Graphics, PageFormat, int) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
print(Graphics, PageFormat, int) - Method in class ca.ucalgary.seahawk.util.PrintableJEditorPane
 
PRINT_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
PrintableJEditorPane - Class in ca.ucalgary.seahawk.util
A class used to make the rendered contents of a JEditorPane printable in Java.
PrintableJEditorPane() - Constructor for class ca.ucalgary.seahawk.util.PrintableJEditorPane
 
printCurrentPane() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
ProbMolWeightAnnotation - Class in org.inb.biomoby.shared.ontology
 
ProbMolWeightAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.ProbMolWeightAnnotation
 
ProbMolWeightsAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
ProbMolWeightsAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.ProbMolWeightsAnnotatedAASequence
 
process() - Method in class org.biomoby.client.BaseClient
The main method that packs input data, invokes a BioMoby service and uses its response.
process(int) - Method in class org.biomoby.client.BaseClient
The main method that packs input data, invokes a BioMoby service and uses its response.
processArgument(String) - Method in interface ca.ucalgary.util.ArgumentListener
 
processCGIResults(byte[], String) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
processChangedLines(int, int) - Method in class org.biomoby.service.dashboard.PerlMoSeSSyntaxDocument
 
processEvent(MobyRequestEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
processEvent(MobyRequestEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
processEvent(MobyRequestEvent) - Method in class ca.ucalgary.seahawk.gui.MobyShimmer
 
processEvent(MobyRequestEvent) - Method in interface org.biomoby.client.MobyRequestEventHandler
 
processIt(MobyPackage, MobyPackage) - Method in class org.biomoby.service.BaseService
A high-level processing.
processIt(MobyJob, MobyJob, MobyPackage) - Method in class org.biomoby.service.BaseService
A job-level processing: This is the main method to be overriden by a service provider!
Processor - Class in org.biomoby.registry.rdfagent.verifier
 
Processor() - Constructor for class org.biomoby.registry.rdfagent.verifier.Processor
 
processRegistryServices(Map, Central) - Method in class org.biomoby.registry.rdfagent.verifier.Processor
 
processRequest(MobyDataJob, MobyDataJob) - Method in class ca.ucalgary.services.ACDService
Runs the command-line program specified by the servlet config, reformatting along the way.
processRequest(MobyDataJob, MobyDataJob) - Method in class ca.ucalgary.services.CGIService
 
processRequest(MobyDataJob, MobyDataJob) - Method in class ca.ucalgary.services.WSDLService
 
processRequest(MobyDataJob, MobyDataJob) - Method in class org.biomoby.service.MobyServlet
The real worker method: implementing classes must override this method to do something useful.
processRequest(MobyDataJob, MobyDataJob) - Method in class org.biomoby.service.test.ConvertAAtoFASTA_AA
Builds a FastA record from a MOBY AminoAcidSequence object.
processRequest(MobyDataJob, MobyDataJob) - Method in class org.biomoby.service.test.FromFastaToDNASequence
Parses a FastA string into its header component and sequence, constructing a MOBY DNASequence object (or subclass thereof), which can be used in more services.
processRequests(MobyContentInstance, MobyContentInstance) - Method in class org.biomoby.service.MobyServlet
By default, this method will sequentially execute the individual jobs from the request payload (processRequest).
processServiceResults(Node) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
This method is called by the Programming-by-example (PBE) system when we have the response from a service that's being semantically wrapped.
processServicesFromURL(String, Central) - Method in class org.biomoby.registry.rdfagent.verifier.Processor
 
processServicesFromUrlTEST(String) - Method in class org.biomoby.registry.rdfagent.verifier.Processor
 
ProdomMotif - Class in org.inb.biomoby.shared.ontology
 
ProdomMotif() - Constructor for class org.inb.biomoby.shared.ontology.ProdomMotif
 
produces - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
PROP_DASHBOARD_CONFIGURATION - Static variable in class org.biomoby.service.dashboard.DashboardConfig
A property name.
PROP_HIGHLIGHT - Static variable in class org.biomoby.client.Graphviz
Property name.
PROP_HIGHLIGHT_COLOR - Static variable in class org.biomoby.client.Graphviz
Property name.
PROP_IMAGEMAP - Static variable in class org.biomoby.client.Graphviz
Property name.
PROP_RANKDIR - Static variable in class org.biomoby.client.Graphviz
Property name.
PROP_RAWINPUT - Static variable in class org.biomoby.client.Taverna
Property name.
PROP_RAWOUTPUT - Static variable in class org.biomoby.client.Taverna
Property name.
PROP_VERBOSE - Static variable in class org.biomoby.client.Taverna
Property name.
PROPERTIES() - Static method in class org.biomoby.registry.properties.MobyProperties
Constructs a Properties object with properties obtained from environment PRE:None.
propertyChange(PropertyChangeEvent) - Method in class org.biomoby.service.dashboard.BuildDataTypeTree
Here we get notified when a property change happens.
propertyChange(PropertyChangeEvent) - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Implementing PropertyChangeListener.
propertyChange(PropertyChangeEvent) - Method in class org.biomoby.service.dashboard.CommonConsole
Here this instance is notified when somebody fires a verbose message.
propertyChange(PropertyChangeEvent) - Method in class org.biomoby.service.dashboard.DebuggingPanel
I print to a console whatever is propagated througt the property channel (Hey, I am a debugging panel, am I not?)
propertyChange(PropertyChangeEvent) - Method in class org.biomoby.service.dashboard.RegistrationServiceSubPanel
Here we get notified when somebody somewhere select a service.
propertyChange(PropertyChangeEvent) - Method in class org.inb.biomoby.generator.gui.AbstractServiceModelPanel
 
propertyChange(PropertyChangeEvent) - Method in class org.inb.biomoby.generator.gui.DatatypesGeneratorPanel
 
PropertyChannel - Class in org.biomoby.service.dashboard
PropertyChannel is a shared storage for properties created by panels and their models.
PropertyChannel() - Constructor for class org.biomoby.service.dashboard.PropertyChannel
Default constructor.
PropertyNameTableCellEditor - Class in org.inb.biomoby.central.gui.renderer
 
PropertyNameTableCellEditor() - Constructor for class org.inb.biomoby.central.gui.renderer.PropertyNameTableCellEditor
 
PropertyNameTableCellRenderer - Class in org.inb.biomoby.central.gui.renderer
 
PropertyNameTableCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.PropertyNameTableCellRenderer
 
PropertyResponseWrapper - Class in org.inb.biomoby.shared.wsrf
The property response wrapper class.
PropertyResponseWrapper(MobyMessage) - Constructor for class org.inb.biomoby.shared.wsrf.PropertyResponseWrapper
 
PropertyResponseWrapper(AnalysisEvent) - Constructor for class org.inb.biomoby.shared.wsrf.PropertyResponseWrapper
 
PropertySequence - Class in org.inb.biomoby.shared.ontology
 
PropertySequence() - Constructor for class org.inb.biomoby.shared.ontology.PropertySequence
 
PropertyTableCellRenderer - Class in org.inb.biomoby.central.gui.renderer
Table cell renderer that changes a foreground brigthness if rendered property doesn't belong to an object provided in its constructor.
PropertyTableCellRenderer() - Constructor for class org.inb.biomoby.central.gui.renderer.PropertyTableCellRenderer
 
PROPS_FILE_COMMENT - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
PROPS_FILE_ENCODING - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
PROPS_FILE_NAME - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
PROPS_FILE_SYS_PROPERTY - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
PrositeDoc_Text - Class in org.inb.biomoby.shared.ontology
 
PrositeDoc_Text() - Constructor for class org.inb.biomoby.shared.ontology.PrositeDoc_Text
 
PrositeMotif - Class in org.inb.biomoby.shared.ontology
 
PrositeMotif() - Constructor for class org.inb.biomoby.shared.ontology.PrositeMotif
 
PrositeMotifComponent<T extends PrositeMotif> - Class in org.inb.biomoby.client.gui.ontology
 
PrositeMotifComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.PrositeMotifComponent
 
PROTOCOLS_UNACCEPTED - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Used when a service does not agree on using any of the proposed notification protocols.
providedBy - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
providedBy - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
PROVISIONINFORMATION - Static variable in interface org.biomoby.shared.parser.MobyTags
 
PSF_Text - Class in org.inb.biomoby.shared.ontology
 
PSF_Text() - Constructor for class org.inb.biomoby.shared.ontology.PSF_Text
 
publish(LogRecord) - Method in class org.inb.biomoby.generator.gui.StatusBarHandler
 
publisher - Static variable in class org.biomoby.client.rdf.vocabulary.DC_PROTEGE
 
pureName(String) - Static method in class org.biomoby.shared.Utils
Return just the last part of the LSID identifier.
put(String, String[]) - Method in class ca.ucalgary.services.util.SourceMap
To be used if a sequence is expected for a member.
put(String, String) - Method in class ca.ucalgary.services.util.SourceMap
 
put(Object, Object) - Method in class org.biomoby.service.dashboard.PropertyChannel
Maps the specified key to the specified value in this hashtable.
put(Object, Object, Object) - Method in class org.biomoby.service.dashboard.PropertyChannel
Maps the specified key to the specified value in this hashtable.
put(String, MobyDataJob) - Method in class org.biomoby.shared.data.MobyContentInstance
 
put(MobyDataJob) - Method in class org.biomoby.shared.data.MobyContentInstance
same as put(String, MobyDataJob), but the queryID will be automatically generated for this value
put(String, MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataComposite
Add a field to the composite.
putAll(Map<? extends String, ? extends String[]>) - Method in class ca.ucalgary.services.util.SourceMap
Sets a number of object fields at once.
putAll(Map<? extends String, ? extends MobyDataJob>) - Method in class org.biomoby.shared.data.MobyContentInstance
Sets a number of queries at once.
putAll(Map<? extends String, ? extends MobyDataObject>) - Method in class org.biomoby.shared.data.MobyDataComposite
Sets a number of object fields at once.
putAttribute(String, AbstractMobyObject) - Method in class org.inb.biomoby.shared.message.MobyObject
The method adds an attribute to the object
putIfAbsent(String, MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataComposite
 

Q

QueryEvaluationErrorFault - Exception in org.inb.biomoby.shared.wsrf.fault
 
QueryEvaluationErrorFault(String, QueryEvaluationErrorFaultType) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.QueryEvaluationErrorFault
 
QueryEvaluationErrorFault(String, QueryEvaluationErrorFaultType, Throwable) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.QueryEvaluationErrorFault
 
QueryEvaluationErrorFaultType - Class in org.inb.wsrf.rp2
 
QueryEvaluationErrorFaultType() - Constructor for class org.inb.wsrf.rp2.QueryEvaluationErrorFaultType
 
QueryExpressionType - Class in org.inb.wsrf.rp2
 
QueryExpressionType() - Constructor for class org.inb.wsrf.rp2.QueryExpressionType
 
QUERYID - Static variable in interface org.biomoby.shared.parser.MobyTags
 
queryResourceProperties(String) - Method in class org.inb.biomoby.service.AbstractAsyncMobyImpl
 
queryResourceProperties(QueryResourceProperties) - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
queryResourceProperties(String) - Method in interface org.inb.biomoby.service.IAsyncMobyImpl
 
QueryResourceProperties - Class in org.inb.wsrf.rp2
 
QueryResourceProperties() - Constructor for class org.inb.wsrf.rp2.QueryResourceProperties
 
QueryResourcePropertiesResponse - Class in org.inb.wsrf.rp2
 
QueryResourcePropertiesResponse() - Constructor for class org.inb.wsrf.rp2.QueryResourcePropertiesResponse
 
queryResourcePropertyResult(String) - Method in class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
quoteIt(String) - Static method in class org.biomoby.client.Graphviz
Surround given text by quotes.

R

RADIO_DEFAULT_SENTINEL - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
RADIO_SENTINEL - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
radioGroup(Html, String, String[], int) - Method in class org.biomoby.client.GraphsServlet
 
RAW_XPATH_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 
RCA - Static variable in class org.biomoby.shared.data.MobyDataXref
 
RDF - Class in org.biomoby.client
A utility class that understands how to create graphviz graphs from a set of ServiceEdges, or from other data structures.
RDF() - Constructor for class org.biomoby.client.RDF
 
RDF_FILE - Static variable in interface org.biomoby.shared.CentralCached
A special file name, containing an RDF document with the cached entities.
RDF_MODE - Static variable in class org.biomoby.service.MobyServlet
 
RDFagentHome - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The agents home directory.
RDFAgentTestSuite - Class in org.biomoby.registry.rdfagent.test
 
RDFAgentTestSuite() - Constructor for class org.biomoby.registry.rdfagent.test.RDFAgentTestSuite
 
RdfParser - Class in org.biomoby.shared.schema
 
RdfParser() - Constructor for class org.biomoby.shared.schema.RdfParser
 
read(String) - Static method in class org.inb.swing.ImageLoader
 
read() - Method in class org.inb.util.TemplateInputStream
 
read(byte[]) - Method in class org.inb.util.TemplateInputStream
 
read(byte[], int, int) - Method in class org.inb.util.TemplateInputStream
 
readFromConnection(HttpURLConnection) - Static method in class ca.ucalgary.services.util.IOUtils
Returns the response payload from a SOAP request
readResource(String, Object) - Static method in class org.biomoby.shared.Utils
Find the resource with the given 'filename', read it and return it.
readResource(String, Class) - Static method in class org.biomoby.shared.Utils
Work in progress.
ref - Variable in class org.inb.biomoby.client.MobyDispatch.MobyWSRFResource
 
ref - Variable in class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
REF_PARAM_NAME - Static variable in class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
REF_PARAMETERS - Static variable in interface org.w3c.addressing.sax.EprTags
 
REFELEMENT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
REFERRER_POLICY_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
REFQUERYID - Static variable in interface org.biomoby.shared.parser.MobyTags
 
RefSeq_Text - Class in org.inb.biomoby.shared.ontology
 
RefSeq_Text() - Constructor for class org.inb.biomoby.shared.ontology.RefSeq_Text
 
REG_CACHE_FILE_PREFIX - Static variable in class org.biomoby.registry.meta.RegistryCache
 
REGEX_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
RegExDocumentFilter - Class in org.inb.swing
Document Filter based on Regular Expressions
RegExDocumentFilter(String) - Constructor for class org.inb.swing.RegExDocumentFilter
 
RegexParser - Class in ca.ucalgary.seahawk.services
This class contains methods for extracting parts of regular expressions, mainly for use in MobyComplexBuilder in dealing with nested rules, etc.
RegexParser() - Constructor for class ca.ucalgary.seahawk.services.RegexParser
 
RegexParserTestCase - Class in ca.ucalgary.seahawk.services.test
 
RegexParserTestCase(String) - Constructor for class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
register() - Static method in class org.biomoby.registry.properties.MacOS
Register the terms that System.getProperty("os.name") returns with this os
register(String, Environment) - Static method in class org.biomoby.registry.properties.RegistryOS
 
register() - Static method in class org.biomoby.registry.properties.UNIX
Register the terms that System.getProperty("os.name") returns with this os
register() - Static method in class org.biomoby.registry.properties.Windows
Register the terms that System.getProperty("os.name") returns with this os
register() - Static method in class org.biomoby.registry.properties.WindowsNT
Register the terms that System.getProperty("os.name") returns with this os
register(MobyDataType) - Method in class org.biomoby.registry.sync.handler.DataTypeHandler
 
register(T) - Method in interface org.biomoby.registry.sync.handler.MobyHandler
Register a new object to the local moby central.
register(MobyNamespace) - Method in class org.biomoby.registry.sync.handler.NamespaceHandler
 
register(MobyService) - Method in class org.biomoby.registry.sync.handler.ServiceHandler
 
register(MobyServiceType) - Method in class org.biomoby.registry.sync.handler.ServiceTypeHandler
 
registerDataType(MobyDataType) - Method in class org.biomoby.client.CentralImpl
 
registerDataType(MobyDataType) - Method in class org.biomoby.service.dashboard.RegistryModel
 
registerDataType(MobyDataType) - Method in interface org.biomoby.shared.Central
Register new data type.
registerNamespace(MobyNamespace) - Method in class org.biomoby.client.CentralImpl
 
registerNamespace(String) - Method in interface org.biomoby.registry.Central.Registry
Register a new namespace.
registerNamespace(String) - Method in class org.biomoby.registry.Central.RegistryImpl
 
registerNamespace(MobyNamespace) - Method in class org.biomoby.service.dashboard.RegistryModel
 
registerNamespace(MobyNamespace) - Method in interface org.biomoby.shared.Central
Register new namespace.
registerNamespace(Namespace) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
registerNamespace(Namespace) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RegisterNamespaceOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterNamespaceOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation
 
RegisterNamespaceOperation.RegisterNamespace - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterNamespaceOperation.RegisterNamespace() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
registerObjectClass(String) - Method in interface org.biomoby.registry.Central.Registry
Register a new object class.
registerObjectClass(String) - Method in class org.biomoby.registry.Central.RegistryImpl
 
registerObjectClass(ObjectType) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
registerObjectClass(ObjectType) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RegisterObjectClassOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterObjectClassOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation
 
RegisterObjectClassOperation.ObjectType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterObjectClassOperation.ObjectType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.ObjectType
 
RegisterObjectClassOperation.RegisterObjectClass - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterObjectClassOperation.RegisterObjectClass() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
RegisterObjectClassOperation.Relationship - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterObjectClassOperation.Relationship() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.Relationship
 
registerService(MobyService) - Method in class org.biomoby.client.CentralImpl
 
registerService(String) - Method in interface org.biomoby.registry.Central.Registry
Register a new service instance.
registerService(String) - Method in class org.biomoby.registry.Central.RegistryImpl
 
registerService(MobyService) - Method in class org.biomoby.service.dashboard.RegistryModel
 
registerService(MobyService, Central) - Static method in class org.biomoby.service.test.ServletTester
 
registerService(MobyService) - Method in interface org.biomoby.shared.Central
Register a new service.
registerService(Service) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
registerService(Service) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RegisterServiceOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation
 
RegisterServiceOperation.Collection - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation.Collection() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Collection
 
RegisterServiceOperation.Input - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation.Input() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Input
 
RegisterServiceOperation.Output - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation.Output() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Output
 
RegisterServiceOperation.Parameter - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation.Parameter() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
RegisterServiceOperation.RegisterService - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation.RegisterService() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
RegisterServiceOperation.SecondaryArticles - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation.SecondaryArticles() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.SecondaryArticles
 
RegisterServiceOperation.Simple - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceOperation.Simple() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Simple
 
registerServiceType(MobyServiceType) - Method in class org.biomoby.client.CentralImpl
 
registerServiceType(String) - Method in interface org.biomoby.registry.Central.Registry
Register a new service type.
registerServiceType(String) - Method in class org.biomoby.registry.Central.RegistryImpl
 
registerServiceType(MobyServiceType) - Method in class org.biomoby.service.dashboard.RegistryModel
 
registerServiceType(MobyServiceType) - Method in interface org.biomoby.shared.Central
Register new service type.
registerServiceType(ServiceType) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
registerServiceType(ServiceType) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RegisterServiceTypeOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceTypeOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation
 
RegisterServiceTypeOperation.RegisterServiceType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceTypeOperation.RegisterServiceType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
RegisterServiceTypeOperation.Relationship - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceTypeOperation.Relationship() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.Relationship
 
RegisterServiceTypeOperation.ServiceType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RegisterServiceTypeOperation.ServiceType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.ServiceType
 
Registration - Interface in ca.ucalgary.services
Interface to hold constants shared between PBE system and server side proxy/registry
Registration - Class in org.inb.biomoby.shared.registry
 
Registration() - Constructor for class org.inb.biomoby.shared.registry.Registration
 
Registration.SUCCESS_CODE - Enum in org.inb.biomoby.shared.registry
 
RegistrationDataTypeSubPanel - Class in org.biomoby.service.dashboard
A panel allowing to register a data type in a Biomoby registry.
RegistrationDataTypeSubPanel() - Constructor for class org.biomoby.service.dashboard.RegistrationDataTypeSubPanel
Default constructor.
RegistrationNamespaceSubPanel - Class in org.biomoby.service.dashboard
A panel allowing to register a namespace in a Biomoby registry.
RegistrationNamespaceSubPanel() - Constructor for class org.biomoby.service.dashboard.RegistrationNamespaceSubPanel
Default constructor.
RegistrationPanel - Class in org.biomoby.service.dashboard
A panel allowing to register various entities in a Biomoby registry.
RegistrationPanel() - Constructor for class org.biomoby.service.dashboard.RegistrationPanel
Default constructor.
RegistrationServiceSubPanel - Class in org.biomoby.service.dashboard
A panel allowing to register a service in a Biomoby registry.
RegistrationServiceSubPanel() - Constructor for class org.biomoby.service.dashboard.RegistrationServiceSubPanel
Default constructor.
RegistrationServiceTypeSubPanel - Class in org.biomoby.service.dashboard
A panel allowing to register a service type in a Biomoby registry.
RegistrationServiceTypeSubPanel() - Constructor for class org.biomoby.service.dashboard.RegistrationServiceTypeSubPanel
Default constructor.
Registries - Interface in org.biomoby.registry.meta
An interface defining properties (such as endpoints) of all known BioMoby registries.
RegistriesList - Class in org.biomoby.registry.meta
A default implementation, providing a list of well-known BioMoby registries.
RegistriesList() - Constructor for class org.biomoby.registry.meta.RegistriesList
A default constructor.
RegistriesList(Registry[]) - Constructor for class org.biomoby.registry.meta.RegistriesList
A constructor that adds registries to the default list.
Registry - Interface in org.biomoby.registry.Central
An interface that outlines the methods needed to implement a Moby Registry.
Registry - Class in org.biomoby.registry.meta
A container for meta data about a BioMoby registry.
Registry(String, String, String) - Constructor for class org.biomoby.registry.meta.Registry
A minimal constructor
Registry(String, String, String, String, String, boolean, String) - Constructor for class org.biomoby.registry.meta.Registry
A full constructor
REGISTRY_ATTR - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
REGISTRY_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
REGISTRY_CONF_FILE - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The location of the mobycentral.conf file.
REGISTRY_DEREGISTER_COUNT - Static variable in class org.biomoby.registry.rdfagent.util.Constants
How many chances does a service get before deregistration?
REGISTRY_EMAIL - Static variable in class org.biomoby.registry.rdfagent.util.Constants
Should the agent email service providers with changes to their services?
REGISTRY_ENABLE_DEREGISTER - Static variable in class org.biomoby.registry.rdfagent.util.Constants
Should the agent deregister services?
REGISTRY_ENABLE_DEREGISTER_FROM_URL - Static variable in class org.biomoby.registry.rdfagent.util.Constants
Should the agent deregister services when invoked via registerService?
REGISTRY_ENABLE_SERVICE_UPDATES - Static variable in class org.biomoby.registry.rdfagent.util.Constants
Does the agent perform updates on modified services?
REGISTRY_ENDPOINT_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
REGISTRY_IGNORE_NULL - Static variable in class org.biomoby.registry.rdfagent.util.Constants
Should the agent ignore null signature urls?
REGISTRY_KEYPHRASE - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The passphrase that enables the agent to deregister from mobycentral.
REGISTRY_NAMESPACE_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
REGISTRY_REMOVAL_ENDPOINT - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The Central Admin endpoint for service removal
REGISTRY_REMOVAL_PASSWORD - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The password associated with the username
REGISTRY_REMOVAL_URI - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The Central Admin uri for service removal
REGISTRY_REMOVAL_USERNAME - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The username to access the password protected Central Admin dispatcher
REGISTRY_SYNONYM_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
REGISTRY_URI - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The registry's endpoint.
REGISTRY_URL - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The url for the registry.
RegistryCache - Class in org.biomoby.registry.meta
A class for storing MOBY RDFs and Central calls to disk for reuse in other JVMs.
RegistryCache() - Constructor for class org.biomoby.registry.meta.RegistryCache
 
RegistryComboBox - Class in org.inb.biomoby.central.gui
JComboBox based on BioMoby MobyCentralModel
RegistryComboBox() - Constructor for class org.inb.biomoby.central.gui.RegistryComboBox
 
RegistryComboBox.RegistryComboBoxRenderer - Class in org.inb.biomoby.central.gui
 
RegistryComboBox.RegistryComboBoxRenderer() - Constructor for class org.inb.biomoby.central.gui.RegistryComboBox.RegistryComboBoxRenderer
 
RegistryComboBoxModel - Class in org.inb.biomoby.central.gui.model
 
RegistryComboBoxModel() - Constructor for class org.inb.biomoby.central.gui.model.RegistryComboBoxModel
 
RegistryImpl - Class in org.biomoby.registry.Central
 
RegistryImpl() - Constructor for class org.biomoby.registry.Central.RegistryImpl
 
RegistryModel - Class in org.biomoby.service.dashboard
A real worker that supplies all data from a Biomoby registry (or from a local cache) to various panels, especially to the RegistryPanel and the RegistrationPanel.
RegistryModel() - Constructor for class org.biomoby.service.dashboard.RegistryModel
Default constructor.
RegistryOS - Class in org.biomoby.registry.properties
This class delegates the responisiblity for obtaining system environment variables to other classes.
RegistryOS() - Constructor for class org.biomoby.registry.properties.RegistryOS
 
RegistryPanel - Class in org.biomoby.service.dashboard
A panel displaying contents of a Biomoby registry.
RegistryPanel() - Constructor for class org.biomoby.service.dashboard.RegistryPanel
Default constructor.
Relationship<T extends AbstractTypeEntity> - Class in org.inb.biomoby.shared.registry
 
Relationship() - Constructor for class org.inb.biomoby.shared.registry.Relationship
 
Relationship.DIRECTION_TYPE - Enum in org.inb.biomoby.shared.registry
 
Relationship.RELATIONSHIP_TYPE - Enum in org.inb.biomoby.shared.registry
 
RELATIONSHIP_PROPERTIES() - Static method in class org.biomoby.registry.properties.MobyProperties
Retrieve the properties for [mobyrelationship] in mobycentral.conf PRE: POST:The properties contained in mobycentral.conf for [mobyrelationship] are returned in a Properties object.
Relationships(String) - Method in interface org.biomoby.registry.Central.Central
Retrieve a list of MOBY object classes having a specified relationship with the given class
Relationships(String) - Method in class org.biomoby.registry.Central.CentralImpl
 
relationships(ServiceType, List<Relationship.RELATIONSHIP_TYPE>, Relationship.DIRECTION_TYPE, boolean) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
relationships(ObjectType, List<Relationship.RELATIONSHIP_TYPE>, Relationship.DIRECTION_TYPE, boolean) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
relationships(ServiceType, List<Relationship.RELATIONSHIP_TYPE>, Relationship.DIRECTION_TYPE, boolean) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
relationships(ObjectType, List<Relationship.RELATIONSHIP_TYPE>, Relationship.DIRECTION_TYPE, boolean) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RelationshipsOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RelationshipsOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation
 
RelationshipsOperation.AbstractType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RelationshipsOperation.AbstractType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.AbstractType
 
RelationshipsOperation.ObjectType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RelationshipsOperation.ObjectType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.ObjectType
 
RelationshipsOperation.Relationship<T extends RelationshipsOperation.AbstractType> - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RelationshipsOperation.Relationship() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.Relationship
 
RelationshipsOperation.RelationshipsInput - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RelationshipsOperation.RelationshipsInput() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
RelationshipsOperation.RelationshipsOutput<T extends RelationshipsOperation.AbstractType> - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RelationshipsOperation.RelationshipsOutput() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsOutput
 
RelationshipsOperation.ServiceType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RelationshipsOperation.ServiceType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.ServiceType
 
reload() - Method in class org.inb.biomoby.central.model.DatatypesModel
Method to reload the model from a BioMoby Registry (also updating a cache)
reload() - Method in class org.inb.biomoby.central.model.NamespacesModel
Method to reload the model from a BioMoby Registry (also updating a cache)
reload() - Method in class org.inb.biomoby.central.model.ServicesModel
Method to reload the model from a BioMoby Registry (also updating a cache)
reloadDataTypesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
reloadNamespacesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
reloadServicesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
reloadServiceTypesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
remove(Component) - Method in class ca.ucalgary.seahawk.util.DynamicJPopupMenu
 
remove(Node) - Method in class ca.ucalgary.seahawk.util.MutableNodeList
 
remove(Object) - Method in class ca.ucalgary.services.util.SourceMap
Removes the field with the given name, if present
remove(int, int) - Method in class org.biomoby.service.dashboard.PerlMoSeSSyntaxDocument
 
remove(Object) - Method in class org.biomoby.shared.data.MobyContentInstance
Removes the query with the given name, if present
remove(Object) - Method in class org.biomoby.shared.data.MobyDataComposite
Removes the field with the given name, if present
remove(Object, Object) - Method in class org.biomoby.shared.data.MobyDataComposite
 
remove(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Removes a single instance of an element from this collection, if it satisfies mdsi.equals().
remove(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
remove(int) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Removes the element at the specified position in this list (optional operation).
remove(Object) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Removes the first occurrence in this list of the specified element.
remove(int) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
remove(int) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
remove(Object) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
remove(int) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
remove(Object) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
remove(int) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
remove(DocumentFilter.FilterBypass, int, int) - Method in class org.inb.swing.RegExDocumentFilter
 
removeActionListener(ActionListener) - Method in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
removeAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Set theory subtraction operator implementation.
removeAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
removeAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Removes from this list all the elements that are contained in the specified collection.
removeAll(Collection<?>) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
removeAll(Collection<?>) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
removeAllChildren() - Method in class org.biomoby.service.dashboard.BuildDataTypeTree
 
removeAttribute(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
removeAttribute(String) - Method in class org.biomoby.service.test.TestServletContext
 
removeAttribute(String) - Method in class org.inb.biomoby.shared.message.MobyObject
Remove attribute from a list of attributes
removeBuildListener(BuildListener) - Method in class org.biomoby.service.dashboard.SimpleAnt
 
removeChangeListener(ChangeListener) - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Remove a listener that has been previously added by DateTimeChooser.addChangeListener(javax.swing.event.ChangeListener).
removeCollectionData(MobyDataInstance) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
removeCrossReference() - Method in class org.inb.biomoby.shared.message.MobyObject
 
removeElement(T) - Method in class org.inb.biomoby.central.model.AbstractModel
Method to remove a model element
removeElement(ObjectType) - Method in class org.inb.biomoby.central.model.DatatypesModel
Method to unregister a datatype from a BioMoby Registry.
removeElement(MobyCentral) - Method in class org.inb.biomoby.central.model.MobyCentralModel
Method is not implemented
removeElement(Namespace) - Method in class org.inb.biomoby.central.model.NamespacesModel
Method to unregister a namespace from a BioMoby Registry.
removeElement(Service) - Method in class org.inb.biomoby.central.model.ServicesModel
Method to unregister a service from a BioMoby Registry.
removeEventHandler(MobyRequestEventHandler) - Method in class org.biomoby.client.MobyRequest
 
removeFormFile(String) - Method in class ca.ucalgary.services.util.XHTMLForm
 
removeFromCache(String) - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
Removes object groups from the cache.
removeFromCache(String) - Method in class org.biomoby.client.CentralImpl
 
removeFromCache(String) - Method in class org.biomoby.client.FileCache
 
removeFromCache(String) - Method in interface org.biomoby.client.SimpleCache
Remove cached object identified by its 'id' from the cache.
removeFromCache(String) - Method in interface org.biomoby.shared.CentralCached
Remove a group of objects from a cache.
removeFromClipboard(MobyDataInstance) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
removeIcon - Static variable in class org.biomoby.service.dashboard.data.DataTypeTreeTable
 
removeInput(MobyData) - Method in class org.biomoby.shared.MobyService
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.auxiliary.DynamicMobyPanel
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.DynamicMobyComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in interface org.inb.biomoby.client.gui.IDynamicComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.MobyMessageQueue
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
removeListener(IDynamicComponent.MobyComponentListener) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
removeNamespace(String) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Remove given namespace (defined by its name) from all elements of this collection.
removeNamespace(MobyNamespace) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Remove given namespace from all elements of this collection.
removeNamespace(String) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
removeNamespace(String) - Method in class org.biomoby.shared.MobyPrimaryData
 
removeNamespace(MobyNamespace) - Method in class org.biomoby.shared.MobyPrimaryData
 
removeNamespace(String) - Method in class org.biomoby.shared.MobyPrimaryDataSet
Remove given namespace (defined by its name) from all elements of this collection.
removeNamespace(MobyNamespace) - Method in class org.biomoby.shared.MobyPrimaryDataSet
Remove given namespace from all elements of this collection.
removeNamespace(String) - Method in class org.biomoby.shared.MobyPrimaryDataSimple
Remove namespace given by its name.
removeNamespace(MobyNamespace) - Method in class org.biomoby.shared.MobyPrimaryDataSimple
Remove given namespace.
removeNotificationListener(NotificationListener) - Method in class org.biomoby.client.CentralDigestImpl
 
removeNotificationListener(NotificationListener) - Method in class org.biomoby.service.dashboard.RegistryModel
 
removeNotificationListener(NotificationListener) - Method in interface org.biomoby.shared.event.Notifier
Removes the specified notification listener so that it no longer receives notification events from the class that implements this interface.
removeNotificationListeners(NotificationListener[]) - Method in class org.biomoby.client.CentralDigestImpl
 
removeNotificationListeners(NotificationListener[]) - Method in class org.biomoby.service.dashboard.RegistryModel
 
removeNotificationListeners(NotificationListener[]) - Method in interface org.biomoby.shared.event.Notifier
Removes the specified notification listeners so that they no longer receive notification events from the class that implements this interface.
removeOlderThen(long) - Method in class org.biomoby.client.FileCache
 
removeOlderThen(long) - Method in interface org.biomoby.client.SimpleFileCache
Remove all cached objects that are in cache longer that specifies by 'millis'.
removeOutput(MobyData) - Method in class org.biomoby.shared.MobyService
 
removePopupOptions(Object) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
removePopupOptions() - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biomoby.service.dashboard.PropertyChannel
Unregister listeners.
removeRenderer(Renderer) - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
Remove a renderer from this registry.
removeTreeModelListener(TreeModelListener) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
removeUnitTest(MobyUnitTest) - Method in class org.biomoby.shared.MobyService
 
removeUpdate(DocumentEvent) - Method in class ca.ucalgary.seahawk.gui.FilterSearchWidget
 
removeUpdate(DocumentEvent) - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
removeUpdate(DocumentEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyObjectPropertyTable.DefaultPropertyNameValidator
 
removeUpdate(DocumentEvent) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
renameSoapArrayElements(Element, String, Document) - Static method in class ca.ucalgary.services.util.WSDLConfig
 
Renderer - Interface in org.biomoby.service.dashboard.renderers
SPI for rendering a data container.
RendererRegistry - Class in org.biomoby.service.dashboard.renderers
A registry that maintains a list of all renderer service providers.
replace(String, MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataComposite
 
replace(String, MobyDataObject, MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataComposite
 
replace(DocumentFilter.FilterBypass, int, int, String, AttributeSet) - Method in class org.inb.swing.RegExDocumentFilter
 
replaceUserData(MobyDataInstance, String) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Replace the selection xpath info in the data instance
Report - Class in org.biomoby.registry.rdfagent.util
 
Report(String, String, String, boolean) - Constructor for class org.biomoby.registry.rdfagent.util.Report
Constructor
reportError(Throwable) - Method in class org.biomoby.client.BaseCmdLineClient
 
requiredXPathContext() - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
Call to find out if the result will be a String or NodeList, etc if there's an XPath.
reset() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
resetBuffer() - Method in class org.biomoby.service.test.TestHttpServletResponse
 
resolve(Packet) - Method in class org.inb.biomoby.service.resolver.WSRFResourceInstanceResolver
 
resolveDataURL(String) - Method in class org.biomoby.shared.LSIDResolver
 
resolveMetadataService(String) - Method in class org.biomoby.shared.LSIDResolver
 
resolveMetadataURL(String) - Method in class org.biomoby.shared.LSIDResolver
 
resource - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
resource - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
Resource - Class in org.inb.biomoby.shared.registry
 
Resource() - Constructor for class org.inb.biomoby.shared.registry.Resource
 
Resource(Resource.RESOURCE_NAME) - Constructor for class org.inb.biomoby.shared.registry.Resource
 
Resource.RESOURCE_NAME - Enum in org.inb.biomoby.shared.registry
 
RESOURCE_FILE_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 
RESOURCE_PREFIX - Static variable in class ca.ucalgary.services.util.PBERecorder
 
RESOURCE_SYSTEM_PROPERTY - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
RESOURCE_SYSTEM_PROPERTY - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
RESOURCE_SYSTEM_PROPERTY - Static variable in class ca.ucalgary.seahawk.services.TextClient
 
RESOURCE_UNAVAIL - Static variable in interface org.soap.sax.FaultTags
 
RESOURCE_UNKNOWN - Static variable in interface org.soap.sax.FaultTags
 
resourceContent - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
resourceContent - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
ResourceNotDestroyedFault - Exception in org.inb.biomoby.shared.wsrf.fault
 
ResourceNotDestroyedFault(String, ResourceNotDestroyedFaultType) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.ResourceNotDestroyedFault
 
ResourceNotDestroyedFault(String, ResourceNotDestroyedFaultType, Throwable) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.ResourceNotDestroyedFault
 
ResourceNotDestroyedFaultType - Class in org.inb.wsrf.rl2
 
ResourceNotDestroyedFaultType() - Constructor for class org.inb.wsrf.rl2.ResourceNotDestroyedFaultType
 
ResourceUnavailableFault - Exception in org.inb.biomoby.shared.wsrf.fault
 
ResourceUnavailableFault(String, ResourceUnavailableFaultType) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.ResourceUnavailableFault
 
ResourceUnavailableFault(String, ResourceUnavailableFaultType, Throwable) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.ResourceUnavailableFault
 
ResourceUnavailableFaultType - Class in org.inb.wsrf.r2
 
ResourceUnavailableFaultType() - Constructor for class org.inb.wsrf.r2.ResourceUnavailableFaultType
 
ResourceUnknownFault - Exception in org.inb.biomoby.shared.wsrf.fault
 
ResourceUnknownFault(String, ResourceUnknownFaultType) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.ResourceUnknownFault
 
ResourceUnknownFault(String, ResourceUnknownFaultType, Throwable) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.ResourceUnknownFault
 
ResourceUnknownFaultType - Class in org.inb.wsrf.r2
 
ResourceUnknownFaultType() - Constructor for class org.inb.wsrf.r2.ResourceUnknownFaultType
 
restoreSettings() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
Sets the options based on a shortcircuiting set of rules (PROPS_FILE_SYS_PROPERTY, java.io.tmpdir/PROPS_FILE_NAME), using a properties file saved in the location saveSettings() puts it.
restoreSettings(URL) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
Sets the options based on the contents of the file (created with saveSettings()).
RestrictAnnotatedNASequence - Class in org.inb.biomoby.shared.ontology
 
RestrictAnnotatedNASequence() - Constructor for class org.inb.biomoby.shared.ontology.RestrictAnnotatedNASequence
 
RestrictAnnotatedNASequenceComponent<T extends RestrictAnnotatedNASequence> - Class in org.inb.biomoby.client.gui.ontology
 
RestrictAnnotatedNASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
RestrictAnnotatedNASequenceComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
RestrictAnnotatedNASequenceComponent.RestrictAnnotatedNASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
RestrictAnnotation - Class in org.inb.biomoby.shared.ontology
 
RestrictAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
RestrictAnnotationListPane<T extends RestrictAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
RestrictAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.RestrictAnnotationListPane
 
RestrictAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.RestrictAnnotationListPane
 
RestrictReport - Class in org.inb.biomoby.shared.ontology
 
RestrictReport() - Constructor for class org.inb.biomoby.shared.ontology.RestrictReport
 
RestrictReportComponent<T extends RestrictReport> - Class in org.inb.biomoby.client.gui.ontology
 
RestrictReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
RestrictReportComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
RestrictReportComponent.RestrictReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
ResultsPanel - Class in org.biomoby.service.dashboard
A panel displaying service result data, using available renderers.
ResultsPanel() - Constructor for class org.biomoby.service.dashboard.ResultsPanel
 
retainAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Set theory intersection operator implementation.
retainAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
retainAll(Collection) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Retains only the elements in this list that are contained in the specified collection (optional operation).
retainAll(Collection<?>) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
retainAll(Collection<?>) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
retrieveNamespaces() - Method in interface org.biomoby.registry.Central.Central
Retrieve a list of all registered namespaces
retrieveNamespaces() - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveNamespaces() - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveNamespaces() - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RetrieveNamespacesOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveNamespacesOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation
 
RetrieveNamespacesOperation.Namespace - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveNamespacesOperation.Namespace() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
RetrieveNamespacesOperation.Namespaces - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveNamespacesOperation.Namespaces() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespaces
 
retrieveObjectDefinition(ObjectType) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveObjectDefinition(ObjectType) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RetrieveObjectDefinitionOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectDefinitionOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation
 
RetrieveObjectDefinitionOperation.ObjectType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectDefinitionOperation.ObjectType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.ObjectType
 
RetrieveObjectDefinitionOperation.Relationship - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectDefinitionOperation.Relationship() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.Relationship
 
RetrieveObjectDefinitionOperation.RetrieveObjectDefinition - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectDefinitionOperation.RetrieveObjectDefinition() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
retrieveObjectDefinitions(String) - Method in interface org.biomoby.registry.Central.Central
Retrieve the class definition, in the form of the full registration details for the class type specified by the input XML.
retrieveObjectDefinitions(String) - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveObjectNames() - Method in interface org.biomoby.registry.Central.Central
Retrieve the definitions and registration details of all registered object types.
retrieveObjectNames() - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveObjectNames() - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveObjectNames() - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RetrieveObjectNamesOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectNamesOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation
 
RetrieveObjectNamesOperation.Object - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectNamesOperation.Object() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.Object
 
RetrieveObjectNamesOperation.ObjectNames - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectNamesOperation.ObjectNames() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.ObjectNames
 
RetrieveObjectOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
NOT YET IMPLEMENTED BY CENTRAL
RetrieveObjectOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation
 
RetrieveObjectOperation.Object - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectOperation.Object() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Object
 
RetrieveObjectOperation.Objects - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectOperation.Objects() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Objects
 
RetrieveObjectOperation.RetrieveObjectSchema - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveObjectOperation.RetrieveObjectSchema() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.RetrieveObjectSchema
 
retrieveObjects() - Method in class org.biomoby.shared.data.MobyContentInstance
This is a convenience method that allows the user extract all Objects from all content job subgroups (simples and collections) into a single Collection, removing duplicates.
retrieveObjectSchema(String) - Method in interface org.biomoby.registry.Central.Central
Retrieve an XML schema representation of a particular object class.
retrieveObjectSchema(String) - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveResourceURLs() - Method in interface org.biomoby.registry.Central.Central
Retrieve the URLs of all registered services.
retrieveResourceURLs() - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveResourceURLs() - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveResourceURLs() - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RetrieveResourceURLsOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveResourceURLsOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation
 
RetrieveResourceURLsOperation.Resource - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveResourceURLsOperation.Resource() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation.Resource
 
RetrieveResourceURLsOperation.ResourceURLs - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveResourceURLsOperation.ResourceURLs() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation.ResourceURLs
 
retrieveService(String) - Method in interface org.biomoby.registry.Central.Central
Retrieve the definition for a service instance, as specified in WSDL format.
retrieveService(String) - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveService(ServiceType) - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveService(ServiceType) - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
retrieveServiceNames() - Method in interface org.biomoby.registry.Central.Central
Retrieve the names of all registered services.
retrieveServiceNames() - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveServiceNames() - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveServiceNames() - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RetrieveServiceNamesOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceNamesOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation
 
RetrieveServiceNamesOperation.ServiceName - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceNamesOperation.ServiceName() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
RetrieveServiceNamesOperation.ServiceNames - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceNamesOperation.ServiceNames() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceNames
 
RetrieveServiceOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation
 
RetrieveServiceOperation.RetrieveService - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceOperation.RetrieveService() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.RetrieveService
 
RetrieveServiceOperation.ServiceTemplate - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceOperation.ServiceTemplate() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
retrieveServiceProviders() - Method in interface org.biomoby.registry.Central.Central
Retrieve the names of all registered service providers.
retrieveServiceProviders() - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveServiceProviders() - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveServiceProviders() - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RetrieveServiceProvidersOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceProvidersOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation
 
RetrieveServiceProvidersOperation.ServiceProvider - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceProvidersOperation.ServiceProvider() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation.ServiceProvider
 
RetrieveServiceProvidersOperation.ServiceProviders - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceProvidersOperation.ServiceProviders() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation.ServiceProviders
 
retrieveServiceTypes() - Method in interface org.biomoby.registry.Central.Central
Retrieve the definitions and registration details of all registered service types.
retrieveServiceTypes() - Method in class org.biomoby.registry.Central.CentralImpl
 
retrieveServiceTypes() - Method in class org.inb.biomoby.central.factory.jaxb.JAXBMobyCentralImpl
 
retrieveServiceTypes() - Method in interface org.inb.biomoby.central.MobyCentralOperations
 
RetrieveServiceTypesOperation - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceTypesOperation(MobyCentral) - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation
 
RetrieveServiceTypesOperation.ServiceType - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceTypesOperation.ServiceType() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
RetrieveServiceTypesOperation.ServiceTypes - Class in org.inb.biomoby.central.factory.jaxb.registry
 
RetrieveServiceTypesOperation.ServiceTypes() - Constructor for class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceTypes
 
RETURN_XPATH_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 
reverseComplement(String) - Static method in class ca.ucalgary.seahawk.util.Sequence
 
RNASequence - Class in org.inb.biomoby.shared.ontology
 
RNASequence() - Constructor for class org.inb.biomoby.shared.ontology.RNASequence
 
RoundedBorder - Class in org.inb.biomoby.client.gui.swing.border
 
RoundedBorder(int) - Constructor for class org.inb.biomoby.client.gui.swing.border.RoundedBorder
 
RoundedBorder(int, Color) - Constructor for class org.inb.biomoby.client.gui.swing.border.RoundedBorder
 
RoundedButton - Class in org.inb.biomoby.client.gui.swing
 
RoundedButton() - Constructor for class org.inb.biomoby.client.gui.swing.RoundedButton
 
RoundedButton(ImageIcon) - Constructor for class org.inb.biomoby.client.gui.swing.RoundedButton
 
RoundedButton(String, ImageIcon) - Constructor for class org.inb.biomoby.client.gui.swing.RoundedButton
 
RoundedMultilineLabel - Class in org.inb.biomoby.client.gui.swing
 
RoundedMultilineLabel() - Constructor for class org.inb.biomoby.client.gui.swing.RoundedMultilineLabel
 
RoundedMultilineLabel(String) - Constructor for class org.inb.biomoby.client.gui.swing.RoundedMultilineLabel
 
ROWS - Static variable in class org.inb.biomoby.client.gui.ontology.PatternComponent
 
ROWS - Static variable in class org.inb.biomoby.client.gui.ontology.Text__plainComponent
 
RTF_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
RTF_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
RULE_CONTENTS_PARAM - Static variable in class ca.ucalgary.services.util.RuleCreator
 
RULE_NAME_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
RULE_SET_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
RuleCreator - Class in ca.ucalgary.services.util
Contains utility functions to create and store MOB and DEM rules (for Sehawk's MobyClient and TextClient)
RuleCreator() - Constructor for class ca.ucalgary.services.util.RuleCreator
 
Rules - Class in org.inb.biomoby.shared.ontology
 
Rules() - Constructor for class org.inb.biomoby.shared.ontology.Rules
 
RulesComponent<T extends Rules> - Class in org.inb.biomoby.client.gui.ontology
 
RulesComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.RulesComponent
 
RULESTORE_URL - Static variable in class ca.ucalgary.services.util.RuleCreator
 
run() - Method in class ca.ucalgary.minnow.MinJarMaker
 
run() - Method in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
run() - Method in class org.inb.biomoby.central.model.DatatypesModel
 
run() - Method in class org.inb.biomoby.central.model.NamespacesModel
 
run() - Method in class org.inb.biomoby.central.model.ServicesModel
 
run() - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent
 
run() - Method in class org.inb.biomoby.client.gui.ontology.PDB__TextComponent.ScriptTextField
 
run() - Method in class org.inb.swing.StatusBar
 
runIt(DataContainer) - Method in class org.biomoby.service.dashboard.ServiceCallerModel
Call a service.
runIt(DataContainer) - Method in class org.biomoby.service.dashboard.UnitTestingServiceCallermodel
Call a service.
RUNNING - Static variable in class org.omg.lsae.notifications.StateEvent
 
runService(String[]) - Method in class org.biomoby.service.test.ServletTester
 

S

sampleInputData - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
sampleOutputData - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
save(List<T>, MobyCentral, String) - Method in class org.inb.biomoby.central.cache.CacheConfig
Generic method that saves any BioMoby entities ("Namespace", "Service", "ServiceType" and "ObjectType") to a cache file.
save(List<T>, Writer) - Method in class org.inb.biomoby.central.cache.CacheConfig
Generic method to save BioMoby entities to the provided writer
save2File(DataContainer, File) - Method in class org.biomoby.service.dashboard.renderers.AbstractRenderer
Default implementation.
save2File(DataContainer, File) - Method in class org.biomoby.service.dashboard.renderers.Base64Image
 
save2File(DataContainer, File) - Method in class org.biomoby.service.dashboard.renderers.CollectionRenderer
It creates a separate file for each element of the collection in 'data' (it does nothing if 'data' is null, or if it does not contain a collection - an array).
save2File(DataContainer, File) - Method in class org.biomoby.service.dashboard.renderers.ICISPedigreeTree
Does not provide any file saving facility.
save2File(DataContainer, File) - Method in interface org.biomoby.service.dashboard.renderers.Renderer
Save given data in the given file.
SAVE_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
saveCurrentPane() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
saveOutputData(MobyRequestEvent) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
saveOutputData(MobyContentInstance, MobyService, MobyContentInstance, String) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
saveOutputData(String, MobyService, URL, String) - Static method in class ca.ucalgary.seahawk.util.DataUtils
 
saveReport(String, String) - Method in class org.biomoby.registry.rdfagent.util.Report
 
saveSettings(OutputStream) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
Store the settings in text form that can be understood by restoreSettings().
saveSettings() - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
Saves the current values of the preferences to a default location that restoreSettings() will use too.
saveUnitTest() - Method in class org.biomoby.service.dashboard.MobyUnitTestingPanel
Called when a user clicks on the save unit test button Obtains the selected services' signature url and parses it for the unit test information and fills out our ServiceInputPanel.
SAWSDL_INMAP_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
SAWSDL_MODEL_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
SAWSDL_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
SAWSDL_OUTMAP_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
SAWSDL_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
SCALAR_INPUT_PART_MAX_SUFFIX - Static variable in class ca.ucalgary.services.util.PBERecorder
 
SCALAR_INPUT_PART_MIN_SUFFIX - Static variable in class ca.ucalgary.services.util.PBERecorder
 
SCOPDomain - Class in org.inb.biomoby.shared.ontology
 
SCOPDomain() - Constructor for class org.inb.biomoby.shared.ontology.SCOPDomain
 
SCOPLayerNode - Class in org.inb.biomoby.shared.ontology
 
SCOPLayerNode() - Constructor for class org.inb.biomoby.shared.ontology.SCOPLayerNode
 
ScoredMotifAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
ScoredMotifAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.ScoredMotifAnnotatedAASequence
 
ScoredMotifAnnotatedAASequenceComponent - Class in org.inb.biomoby.client.gui.ontology
 
ScoredMotifAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
ScoredMotifAnnotatedAASequenceComponent(ScoredMotifAnnotatedAASequence) - Constructor for class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
ScoredMotifAnnotatedAASequenceComponent.ScoredMotifAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
ScoredMotifAnnotation - Class in org.inb.biomoby.shared.ontology
 
ScoredMotifAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.ScoredMotifAnnotation
 
ScoredMotifAnnotationListPane<T extends ScoredMotifAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
ScoredMotifAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.ScoredMotifAnnotationListPane
 
ScoredMotifAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.ScoredMotifAnnotationListPane
 
scriptEval(String) - Method in class org.inb.biomoby.client.gui.auxiliary.JmolPane
 
scriptWait(String) - Method in class org.inb.biomoby.client.gui.auxiliary.JmolPane
 
scrollable() - Method in class org.biomoby.service.dashboard.BuildDataTypeTree
Put this tree in a scrollable pane.
scrollable() - Method in class org.biomoby.service.dashboard.CommonDataTable
Put this table in a scrollable pane.
scrollable() - Method in class org.biomoby.service.dashboard.CommonTree
Put this tree in a scrollable pane.
scrollable() - Method in class org.biomoby.service.dashboard.data.ParametersTable
Put this table in a scrollable pane.
scrollable() - Method in class org.biomoby.service.dashboard.treetable.JTreeTable
Put this table in a scrollable pane.
ScrollableTextPane - Class in org.inb.biomoby.client.gui.auxiliary
 
ScrollableTextPane(String) - Constructor for class org.inb.biomoby.client.gui.auxiliary.ScrollableTextPane
 
SEAHAWK_NS_PREFIX - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
SEAHAWK_NS_URI - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
SEAHAWK_XPATH_ATTR - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
SeahawkOptions - Class in ca.ucalgary.seahawk.util
A class for storing user preferences affecting the behaviour of Seahawk.
SeahawkOptions() - Constructor for class ca.ucalgary.seahawk.util.SeahawkOptions
 
SeahawkOptionsGUI - Class in ca.ucalgary.seahawk.gui
A dialog box that allows the Seahawk user to configure options such as cache expiry and location, as well as the MOBY registry to use, and whether referrer headers should be sent to services.
SeahawkOptionsGUI(Frame) - Constructor for class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
SeahawkSplasher - Class in ca.ucalgary.seahawk.gui.splash
Modified to support both applet and application modes.
SeahawkSplasher() - Constructor for class ca.ucalgary.seahawk.gui.splash.SeahawkSplasher
 
SeahawkTestCase - Class in ca.ucalgary.seahawk.gui.test
Tests all of the major functionality of Seahawk, the standalone MOBY browser that can be embedded in other applications too.
SeahawkTestCase(String) - Constructor for class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
SeahawkTransferable - Class in ca.ucalgary.seahawk.gui
This class handles the export of data from the Seahawk interface into other applications, with special consideration for the use of drag 'n' drop in wrapping WSDL and CGI interfaces using Seahawk.
SeahawkTransferable(MobyContentPane) - Constructor for class ca.ucalgary.seahawk.gui.SeahawkTransferable
 
SEARCH_LABEL - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
SECONDARIES_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
Secondary - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
secondary_description - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
SECONDARY_RULE_URIS_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
SecondaryArticle - Static variable in class org.biomoby.client.rdf.vocabulary.MobyResources
Deprecated. Replaced by Predicates.Secondary. The reason is that this property should not be under a different RDF document URI
SecondaryDataTable - Class in org.biomoby.service.dashboard
A swing JTable that collects definitions of secondary data (parameters) for a service.
SecondaryDataTable() - Constructor for class org.biomoby.service.dashboard.SecondaryDataTable
Default constructor.
secondaryParameter - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
secondaryParameter - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
SELECT_ALL_XPATH - Static variable in class ca.ucalgary.seahawk.util.FilterSearch
 
selectionCanceled(ServiceSearchDialog) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
selectionCanceled(ServiceSearchDialog) - Method in interface ca.ucalgary.seahawk.gui.ServiceChoiceListener
 
sendDataToReceiver(MobyObjectReceiver, Map<String, MobyPrimaryData>, Map<String, MobyDataInstance>) - Method in class ca.ucalgary.seahawk.gui.MobyObjectTransferHandler
 
sendError(int) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
sendError(int, String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
sendMail(String, String, String) - Method in class org.biomoby.registry.rdfagent.util.Mailer
 
sendRedirect(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
sendRequest(MobyService, MobyContentInstance) - Static method in class org.biomoby.client.AsyncClient
 
sendRequest(MobyService, String) - Static method in class org.biomoby.client.AsyncClient
 
sendRequest(String, String, String) - Static method in class org.biomoby.client.AsyncClient
Initiates a request for service.
sendResponse(MobyRequestEvent) - Method in class org.biomoby.client.MobyRequest
 
sendSMTPMail(String, String, String, String, String, String, String) - Method in class org.biomoby.registry.rdfagent.util.Mailer
 
Sequence - Class in ca.ucalgary.seahawk.util
Utility methods to report properties of DNA and protein sequence.
Sequence() - Constructor for class ca.ucalgary.seahawk.util.Sequence
 
Sequence_alignment_report - Class in org.inb.biomoby.shared.ontology
 
Sequence_alignment_report() - Constructor for class org.inb.biomoby.shared.ontology.Sequence_alignment_report
 
Sequence_alignment_reportComponent - Class in org.inb.biomoby.client.gui.ontology
 
Sequence_alignment_reportComponent(Sequence_alignment_report) - Constructor for class org.inb.biomoby.client.gui.ontology.Sequence_alignment_reportComponent
 
SequenceDescription_Text - Class in org.inb.biomoby.shared.ontology
 
SequenceDescription_Text() - Constructor for class org.inb.biomoby.shared.ontology.SequenceDescription_Text
 
SequenceTransformerBean - Class in org.inb.biomoby.client.gui
 
SequenceTransformerBean() - Constructor for class org.inb.biomoby.client.gui.SequenceTransformerBean
 
serializeModel(Model) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
 
service - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
service - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
Service - Class in org.inb.biomoby.shared.registry
 
Service() - Constructor for class org.inb.biomoby.shared.registry.Service
 
Service(String, String) - Constructor for class org.inb.biomoby.shared.registry.Service
 
Service.CATEGORY - Enum in org.inb.biomoby.shared.registry
 
SERVICE_AUTH_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
SERVICE_CONTACT_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
SERVICE_CREATION_MSG - Static variable in class ca.ucalgary.seahawk.gui.MobyContentPane
 
SERVICE_DESC_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
SERVICE_INPUT_MAGIC - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
if URL starts with this, it's a service input payload spec of the form "url\tproviderURI\tserviceName"
SERVICE_INSTANCE_PROPERTIES() - Static method in class org.biomoby.registry.properties.MobyProperties
Retrieve the properties for [mobycentral] in mobycentral.conf PRE: POST:The properties contained in mobycentral.conf for [mobycentral] are returned in a Properties object.
SERVICE_INSTANCES_RESOURCE_NAME - Static variable in interface org.biomoby.shared.Central
A name of an ontology describing registered service types.
SERVICE_NAME_ATTR - Static variable in class ca.ucalgary.services.util.WSDLConfig
 
SERVICE_NAME_PROP - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
The Java property to set to specify what MOBY service should be tested
SERVICE_PROPERTIES() - Static method in class org.biomoby.registry.properties.MobyProperties
Retrieve the properties for [mobyservice] in mobycentral.conf PRE: POST:The properties contained in mobycentral.conf for [mobyservice] are returned in a Properties object.
SERVICE_SPEC_PARAM - Static variable in class ca.ucalgary.services.WrappingServlet
 
SERVICE_SUBMENU_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
SERVICE_TYPE_LOADED - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_TYPE_LOADING - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_TYPES_CANCELLED - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_TYPES_COUNT - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_TYPES_END - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_TYPES_RESET - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_TYPES_RESOURCE_NAME - Static variable in interface org.biomoby.shared.Central
A name of an ontology describing registered service types.
SERVICE_TYPES_START - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_TYPES_UPDATED - Static variable in interface org.biomoby.shared.event.Notifier
 
SERVICE_XML_MODE - Static variable in interface org.biomoby.shared.data.MobyDataInstance
 
ServiceAccessorGenerationWorker - Class in org.inb.biomoby.generator.gui.worker
 
ServiceAccessorGenerationWorker(File, List<Service>) - Constructor for class org.inb.biomoby.generator.gui.worker.ServiceAccessorGenerationWorker
 
ServiceAccessorGenerator - Class in org.inb.biomoby.generator
 
ServiceAccessorGenerator() - Constructor for class org.inb.biomoby.generator.ServiceAccessorGenerator
 
ServiceAccessorGeneratorPanel - Class in org.inb.biomoby.generator.gui
 
ServiceAccessorGeneratorPanel() - Constructor for class org.inb.biomoby.generator.gui.ServiceAccessorGeneratorPanel
 
ServiceCallerModel - Class in org.biomoby.service.dashboard
A model that achieves its task by calling (local, remote, or none) Biomoby service.
ServiceCallerModel() - Constructor for class org.biomoby.service.dashboard.ServiceCallerModel
 
ServiceChoiceListener - Interface in ca.ucalgary.seahawk.gui
Callback interface for ServiceSearchDialog that tells us what service to actually run according to the user's desires.
SERVICECOMMENT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
ServiceConnections - Class in org.biomoby.client
This class contains knowledge (an algorithm) how individual Moby services could be connected together based on their input and output data types.
ServiceConnections() - Constructor for class org.biomoby.client.ServiceConnections
 
SERVICEDATABASE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
serviceDescription - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
serviceDescription - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
ServiceDescriptionPredicates - Class in org.biomoby.client.rdf.vocabulary
 
ServiceDescriptionPredicates() - Constructor for class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
ServiceException - Exception in org.biomoby.shared.parser
A container for an exception raised by a service provider when something wrong has to be reported back to a client.
ServiceException() - Constructor for exception org.biomoby.shared.parser.ServiceException
An empty constructor.
ServiceException(int, int, String) - Constructor for exception org.biomoby.shared.parser.ServiceException
A usual constructor setting severity, code and message about an exception.
ServiceException(int, int, String, String) - Constructor for exception org.biomoby.shared.parser.ServiceException
A richer constructor setting more details about an exception.
ServiceException(int, int, String, String, String) - Constructor for exception org.biomoby.shared.parser.ServiceException
A full constructor setting more details about an exception.
ServiceFilter - Class in org.biomoby.registry.sync.filtering
Class which stores the filtering rules and checks whether a service matches with one of these rules.
ServiceGenerator - Class in org.inb.biomoby.generator
 
ServiceGenerator() - Constructor for class org.inb.biomoby.generator.ServiceGenerator
 
ServiceHandler - Class in org.biomoby.registry.sync.handler
Class to synchronize the services in the biomoby centrals.
ServiceHandler(String) - Constructor for class org.biomoby.registry.sync.handler.ServiceHandler
 
SERVICEID_ATTR - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
SERVICEINPUT_ATTR - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
ServiceInputPanel - Class in org.biomoby.service.dashboard.data
A swing panel that represents a user interface for entering input data for a Biomoby service.
ServiceInputPanel(MobyService, MobyDataType[]) - Constructor for class org.biomoby.service.dashboard.data.ServiceInputPanel
Create a GUI for all inputs for the given service.
serviceInstanceExists(String, String) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
PRE: None POST: If a service instance exists such that it has a name of name and an authoring URI of uri true is returned, otherwise false is returned.
serviceInstanceExists(String, String, String) - Method in class org.biomoby.client.rdf.builder.ServiceInstanceRDF
 
ServiceInstanceParser - Class in org.biomoby.shared.extended
 
ServiceInstanceParser() - Constructor for class org.biomoby.shared.extended.ServiceInstanceParser
Default constructor - need to set the URL for the RDF document that describes the service ontology using setURL(String url) or setURL(URL url)
ServiceInstanceParser(String) - Constructor for class org.biomoby.shared.extended.ServiceInstanceParser
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the service ontology.
ServiceInstanceParser(URL) - Constructor for class org.biomoby.shared.extended.ServiceInstanceParser
Parameterized Constructor that takes in a url for the RDF document that describes the service ontology.
ServiceInstanceRDF - Class in org.biomoby.client.rdf.builder
 
ServiceInstanceRDF() - Constructor for class org.biomoby.client.rdf.builder.ServiceInstanceRDF
Default Constructor: Uses the default mobycentral
ServiceInstanceRDF(Registry) - Constructor for class org.biomoby.client.rdf.builder.ServiceInstanceRDF
Constructor:
ServiceInstanceWSDL - Class in org.biomoby.shared.schema
 
ServiceInstanceWSDL() - Constructor for class org.biomoby.shared.schema.ServiceInstanceWSDL
 
ServiceLoader<T> - Class in org.inb.biomoby.central
 
SERVICENAME - Static variable in interface org.biomoby.shared.parser.MobyTags
 
SERVICENOTES - Static variable in interface org.biomoby.shared.parser.MobyTags
 
ServiceNotes - Class in org.inb.biomoby.shared.message
 
ServiceNotes() - Constructor for class org.inb.biomoby.shared.message.ServiceNotes
 
ServiceProvider - Class in org.biomoby.registry.rdfagent.util
 
ServiceProvider() - Constructor for class org.biomoby.registry.rdfagent.util.ServiceProvider
Constructor.
ServiceProvider - Class in org.inb.biomoby.shared.registry
 
ServiceProvider() - Constructor for class org.inb.biomoby.shared.registry.ServiceProvider
 
ServiceProvider(String) - Constructor for class org.inb.biomoby.shared.registry.ServiceProvider
 
ServicesBoard - Class in org.biomoby.service.dashboard
This is a simple graphical widget combining together a tree (a subclass of CommonTree) and a progress bar showing how the tree is being loaded.
ServicesBoard(RegistryModel, CommonConsole, PropertyChannel) - Constructor for class org.biomoby.service.dashboard.ServicesBoard
Constructor.
ServicesBoard(RegistryModel, CommonConsole, PropertyChannel, CommonTree) - Constructor for class org.biomoby.service.dashboard.ServicesBoard
Constructor.
SERVICESEARCH_CMD - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
ServiceSearchDialog - Class in ca.ucalgary.seahawk.gui
 
ServiceSearchDialog(Frame, String, ServiceChoiceListener) - Constructor for class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
ServicesEdge - Class in org.biomoby.client
An instance of this class is a container for a pair of Moby service definitions, and for an information how they can be connected.
ServicesEdge(MobyService, int) - Constructor for class org.biomoby.client.ServicesEdge
Constructs an instance with a source service and a connection type.
ServicesEdge(MobyService, String) - Constructor for class org.biomoby.client.ServicesEdge
Constructs an instance with a source service and a connector.
ServicesEdge(MobyService, MobyService, String) - Constructor for class org.biomoby.client.ServicesEdge
Constructs an instance with both source and target services, and a connector.
serviceSelected(ServiceSearchDialog, JMenuItem) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
serviceSelected(ServiceSearchDialog, JMenuItem) - Method in interface ca.ucalgary.seahawk.gui.ServiceChoiceListener
 
ServicesGenerationWorker - Class in org.inb.biomoby.generator.gui.worker
 
ServicesGenerationWorker(File, List<Service>) - Constructor for class org.inb.biomoby.generator.gui.worker.ServicesGenerationWorker
 
ServicesGenerator - Class in org.biomoby.service.generator
A generator generating skeleton classes for Biomoby services.
ServicesGenerator() - Constructor for class org.biomoby.service.generator.ServicesGenerator
 
ServicesGenerator(String) - Constructor for class org.biomoby.service.generator.ServicesGenerator
 
ServicesGenerator(String, String, String) - Constructor for class org.biomoby.service.generator.ServicesGenerator
 
ServicesGenerator(CentralCached) - Constructor for class org.biomoby.service.generator.ServicesGenerator
 
ServicesGeneratorPanel - Class in org.inb.biomoby.generator.gui
 
ServicesGeneratorPanel() - Constructor for class org.inb.biomoby.generator.gui.ServicesGeneratorPanel
 
ServicesModel - Class in org.inb.biomoby.central.model
BioMoby services model implementation class.
SERVICESOFTWARE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
ServicesTree - Class in org.biomoby.service.dashboard
A component showing and manipulating a tree of services registered by a Biomoby registry.
ServicesTree(RegistryModel, CommonConsole) - Constructor for class org.biomoby.service.dashboard.ServicesTree
Constructor.
ServicesTreeModel - Class in org.inb.biomoby.central.gui.model
TreeModel that contains Service elements.
ServicesTreeModel() - Constructor for class org.inb.biomoby.central.gui.model.ServicesTreeModel
 
ServiceType - Class in org.inb.biomoby.shared.registry
 
ServiceType() - Constructor for class org.inb.biomoby.shared.registry.ServiceType
 
ServiceType(String) - Constructor for class org.inb.biomoby.shared.registry.ServiceType
 
ServiceType(String, String) - Constructor for class org.inb.biomoby.shared.registry.ServiceType
 
ServiceTypeHandler - Class in org.biomoby.registry.sync.handler
Class to synchronize the servicetypes in the biomoby centrals.
ServiceTypeHandler(String) - Constructor for class org.biomoby.registry.sync.handler.ServiceTypeHandler
 
ServiceTypeParser - Class in org.biomoby.shared.extended
 
ServiceTypeParser() - Constructor for class org.biomoby.shared.extended.ServiceTypeParser
Default constructor - need to set the URL for the RDF document that describes the Service Type ontology using setURL(String url) or setURL(URL url)
ServiceTypeParser(String) - Constructor for class org.biomoby.shared.extended.ServiceTypeParser
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the Service Type ontology.
ServiceTypeParser(URL) - Constructor for class org.biomoby.shared.extended.ServiceTypeParser
Parameterized Constructor that takes in a url for the RDF document that describes the Service Type ontology.
ServiceTypesBoard - Class in org.biomoby.service.dashboard
This is a simple graphical widget combining together a tree (a subclass of CommonTree) and a progress bar showing how the tree is being loaded.
ServiceTypesBoard(RegistryModel, CommonConsole, PropertyChannel) - Constructor for class org.biomoby.service.dashboard.ServiceTypesBoard
Constructor.
ServiceTypesBoard(RegistryModel, CommonConsole, PropertyChannel, CommonTree) - Constructor for class org.biomoby.service.dashboard.ServiceTypesBoard
Constructor.
ServiceTypesTree - Class in org.biomoby.service.dashboard
A component showing and manipulating a tree of service types registered by a Biomoby registry.
ServiceTypesTree(RegistryModel, CommonConsole) - Constructor for class org.biomoby.service.dashboard.ServiceTypesTree
Constructor.
serviceWrapped(String, String, MobyDataJob) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Called after a service has been created by the wrapping system, with the intention that the new service should be called and included in the browsing session.
ServletFileCache - Class in org.biomoby.client
A simple cache implementation meant to be used in a servlet environment in order to save and later return (any) data, or to find that the given data are not available in the cache.
ServletFileCache(ServletContext, String) - Constructor for class org.biomoby.client.ServletFileCache
Constructor specifying a context of the calling servlet.
ServletTester - Class in org.biomoby.service.test
 
ServletTester() - Constructor for class org.biomoby.service.test.ServletTester
Runs a test on the service described in WEB-INF/web.xml
ServletTester(String) - Constructor for class org.biomoby.service.test.ServletTester
Mainly for JUnit tests, specify a web.xml file to be used for configuring the test run, rather than using the default WEB-INF/web.xml in the class path.
set(int, MobyDataObject) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Replaces the element at the specified position in this list with the specified element (optional operation).
set(int, MobySimple) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
set(int, MobyException) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
set3Attributes(MElement, Element, Vector) - Method in class org.biomoby.shared.schema.Builder
Add ID, namespace and article attributes elements into Element types; every moby object has these three attributes.
set_3prime(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
set_3primerev(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
set_5prime(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
set_5primerev(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
set_class(CommentedObject) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
set_class(SCOPLayerNode) - Method in class org.inb.biomoby.shared.ontology.SCOPDomain
 
setAC(MobyString) - Method in class org.inb.biomoby.shared.ontology.BLOCKAnnotation
 
setAC(MobyString) - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
setAC(MobyString) - Method in class org.inb.biomoby.shared.ontology.MotifAnnotation
 
setAC(MobyString) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setAC(MobyString) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setAccession(MobyString) - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
setAccuracy_ratio(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
setActiveTab(int) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
setAddress(String) - Method in class org.biomoby.w3c.addressing.EndpointReference
 
setAlignment(Sequence_alignment_report) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setAlignments(Stockholm_Text) - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
setAlignments(Stockholm_Text) - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
setAliphatic(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setAllNodesExpanded() - Method in class org.biomoby.service.dashboard.renderers.XMLTree
 
setAllowedValues(String[]) - Method in class org.biomoby.shared.MobySecondaryData
 
setAllowInput(boolean) - Method in class org.biomoby.service.dashboard.SimpleAnt
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.client.gui.ontology.AnnotationHitsComponent
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.AntigenicReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.CpGReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.DigestReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.EquicktandemReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.PatmatdbReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.PatmatmotifsReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.PepNovoReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.RestrictReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.SigcleaveReport
 
setAnnotationHits(AnnotationHits) - Method in class org.inb.biomoby.shared.ontology.TransmembraneReport
 
setAnnotationList(List<T>) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractAnnotationListPane
 
setAny(Object) - Method in class org.inb.wsrf.bf2.BaseFaultType.FaultCause
 
setAppendMode(boolean) - Method in class org.biomoby.service.dashboard.CommonConsole
 
setArchitecture(CommentedObject) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setArgumentListener(ArgumentListener) - Static method in class ca.ucalgary.util.SingletonApplication
This method should be called by the main() method of the target application.
setAromatic(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setArrayFloat(ArrayFloat) - Method in class org.inb.biomoby.client.gui.auxiliary.ArrayFloatChartPane
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Collection
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Simple
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Collection
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Simple
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.ObjectType
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Collection
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Simple
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.ObjectType
 
setArticleName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.ObjectType
 
setArticleName(String) - Method in class org.inb.biomoby.shared.message.AbstractMobyElement
 
setArticleName(String) - Method in class org.inb.biomoby.shared.registry.Collection
 
setArticleName(String) - Method in class org.inb.biomoby.shared.registry.ObjectType
 
setArticleName(String) - Method in class org.inb.biomoby.shared.registry.Parameter
 
setArticleName(String) - Method in class org.inb.biomoby.shared.registry.Simple
 
setAsBytes(boolean) - Method in class org.biomoby.client.MobyServiceLocator
Biomoby API requested that a service must accept input data either as a String, or as an byte array.
setAtom(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setAttribute(String, Object) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
setAttribute(String, Object) - Method in class org.biomoby.service.test.TestServletContext
 
setAuthentication(String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Sets the user and the password for a possible authentification of a service.
setAuthentication(String, String) - Method in class org.biomoby.client.MobyRequest
 
setAuthor(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
setAuthoritative(boolean) - Method in class org.biomoby.shared.MobyService
 
setAuthoritative(boolean) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setAuthoritative(boolean) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setAuthoritative(boolean) - Method in class org.inb.biomoby.shared.registry.Service
 
setAuthoritativeService(int) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setAuthority(String) - Method in class org.biomoby.shared.MobyDataType
 
setAuthority(String) - Method in class org.biomoby.shared.MobyNamespace
 
setAuthority(String) - Method in class org.biomoby.shared.MobyService
 
setAuthority(String) - Method in class org.biomoby.shared.MobyServiceType
 
setAuthority(String) - Method in class org.biomoby.shared.parser.MobyPackage
Fill in an authority of this whole package.
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceOperation.DeregisterService
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
setAuthURI(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
setAuthURI(String) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
setBackground(Color) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
setBackground(Color) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
setBackgroundImage(BufferedImage) - Method in class org.inb.swing.DecoratedJScrollPane
 
setBLOCK_Evalue(MobyString) - Method in class org.inb.biomoby.shared.ontology.BLOCKAnnotation
 
setBoolean(String) - Method in class org.inb.biomoby.shared.datatypes.MobyBoolean
 
setBorder(Border) - Method in class org.inb.biomoby.client.gui.swing.RoundedMultilineLabel
Prevent border changing...
setBounds(int, int, int, int) - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellRenderer
This is overridden to set the height to match that of the JTable.
setBufferSize(int) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setBytes(byte[]) - Method in class org.inb.biomoby.shared.datatypes.MobyBinary
 
setCache(IMobyCentralCache) - Method in class org.inb.biomoby.central.cache.CacheConfig
Method allows override a default cache location.
setCached(boolean) - Method in class org.inb.biomoby.central.cache.CacheConfig
Method to mark that a cache must be used.
setCacheExpiry(double) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
setCacheMode(boolean) - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
It always (if it functions as a cache which is when 'cacheDir' was given) disables caching in the parent (so no memory caching happens there).
setCacheMode(boolean) - Method in class org.biomoby.client.CentralDigestImpl
Methods re-writing the same methods from the superclass.
setCacheMode(boolean) - Method in class org.biomoby.client.CentralImpl
By default, caching is enabled to reduce network traffic.
setCacheMode(boolean) - Method in interface org.biomoby.shared.Central
Set whether the server responses should cached or not to speedup multiple calls for the same data.
setCardinality(Relationship.RELATIONSHIP_TYPE) - Method in class org.inb.biomoby.central.gui.renderer.CardinalityTableCellEditor.CardinalityComponent
 
setCaseSensitivity(boolean) - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
setCategory(String) - Method in class org.biomoby.shared.MobyService
 
setCategory(Service.CATEGORY) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setCategory(Service.CATEGORY) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setCategory(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setCategory(MobyString) - Method in class org.inb.biomoby.shared.ontology.BasicAnnotation
 
setCategory(Service.CATEGORY) - Method in class org.inb.biomoby.shared.registry.Service
 
setCC(MobyString) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setCDATAFlag(Object) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Set flag indicating whether to use a CDATA wrapper for values of String primitive types.
setCellCoordinate(MobyString) - Method in class org.inb.biomoby.shared.ontology.TargetArgument
 
setCellCoordinate_1(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
setCellCoordinate_2(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
setCentral(String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Sets the central to be used.
setCentral(MobyCentral) - Method in class org.inb.biomoby.central.model.DatatypesModel
Even the method declared public it is recommended to set BioMoby Registry globaly through a MobyCentralModel.
setCentral(MobyCentral) - Method in class org.inb.biomoby.central.model.NamespacesModel
Even the method declared public it is recommended to set BioMoby Registry globaly through a MobyCentralModel.
setCentral(MobyCentral) - Method in class org.inb.biomoby.central.model.ServicesModel
Even the method declared public it is recommended to set BioMoby Registry globaly through a MobyCentralModel.
setCentralEndpoint(String) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setChain(MobyString) - Method in class org.inb.biomoby.shared.ontology.StructureBoundaries
 
setCharacterEncoding(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
setCharacterEncoding(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setCharged(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setChargeState(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setChildren(MobyRelationship[]) - Method in class org.biomoby.shared.MobyDataType
 
setClazz(ObjectType) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
setClazz(ObjectType) - Method in class org.inb.biomoby.central.gui.renderer.PropertyTableCellRenderer
 
setClipboard(MobyContentClipboard) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
setClosestSeq(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setCoCInitParameter(String, String) - Method in class org.biomoby.service.MobyServlet
 
setCode(String) - Method in class org.soap.SOAPFault
 
setColor(Color) - Method in class org.inb.biomoby.client.gui.auxiliary.ArrayFloatChartPane
 
setColor(Color) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
setColor(Color) - Method in class org.inb.biomoby.client.gui.swing.border.RoundedBorder
 
setColumnComparator(Class, Comparator) - Method in class org.biomoby.service.dashboard.TableSorter
 
setComb(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setCombined_Evalue(MobyString) - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
setComentary(MobyString) - Method in class org.inb.biomoby.shared.ontology.SCOPLayerNode
 
setComment(String) - Method in class org.biomoby.shared.data.MobyProvisionInfo
This is a general comment about the provision of the object, some human readable message.
setComment(String) - Method in class org.biomoby.shared.MobyDataType
 
setComment(MobyString) - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
setCommentedAASequence(CommentedAASequence) - Method in class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedAASequenceDescriptionPane
 
setCommentedAASequence(CommentedNASequence) - Method in class org.inb.biomoby.client.gui.auxiliary.MultilineCommentedNASequenceDescriptionMobyComponent
 
setCompletedSteps(int) - Method in class org.omg.lsae.notifications.StepEvent
 
setConnectionType(int) - Method in class org.biomoby.client.ServicesEdge
Sets connection type.
setConnector(String) - Method in class org.biomoby.client.ServicesEdge
Sets connector.
setConsensus(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setConsensus(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setContact(String) - Method in class org.biomoby.registry.meta.Registry
 
setContactEmail(String) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
setContactEmail(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
setContactEmail(String) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
setContent(MobyContentInstance) - Method in class org.biomoby.client.MobyRequestEvent
If you are a service provider who got this event through a callback (client connection), this is where you would write the output, which also denotes that you are finished with client communication (anything done after calling this method will be ignore).
setContent(MobyString) - Method in class org.inb.biomoby.shared.ontology.Pattern
 
setContent(MobyString) - Method in class org.inb.biomoby.shared.ontology.Text__plain
 
setContentLength(int) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setContents(String, Object) - Method in class org.biomoby.client.CentralCachedCallsImpl
 
setContents(String, Object) - Method in class org.biomoby.client.CentralImpl
 
setContents(String, Object) - Method in class org.biomoby.client.FileCache
This class does not implement this method.
setContents(String, byte[]) - Method in class org.biomoby.client.FileCache
 
setContents(String, Object) - Method in interface org.biomoby.client.SimpleCache
Store/cache 'data' identified by 'id'.
setContents(String, byte[]) - Method in interface org.biomoby.client.SimpleFileCache
Store 'data' as an object identified by 'id'.
setContentsXML(String) - Method in class org.biomoby.client.MobyRequestEvent
 
setContentType(String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setCount(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotation
 
setCpG(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
setCreation_date(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
setCrossReference(CrossReference) - Method in class org.inb.biomoby.shared.message.MobyObject
 
setCterminalMass(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setCterminalTagMass(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setCurrentService(String) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setCurrentService(String) - Method in class ca.ucalgary.services.util.XHTMLForm
This method has extended functionality on this class, because the service can be set using the moby service name (as per XHTML markup), the index of the form (starting at 0) in the page, the form's HTML name, or the fully qualified action URL.
setCysResMass(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setData(MobyData[]) - Method in class org.biomoby.service.dashboard.CommonDataTable
 
setData(Object) - Method in class org.biomoby.service.dashboard.data.DataContainer
Fill this container with data.
setData(MobyData[]) - Method in class org.biomoby.service.dashboard.DeploymentTable
Ignored.
setData(MobySimple[]) - Method in class org.biomoby.shared.parser.MobyCollection
Fill this envelope with the objects carrying inside real data objects.
setData(MobyObject) - Method in class org.biomoby.shared.parser.MobyJob
Create an un-named Simple object as the first data element.
setData(MobyObject, String) - Method in class org.biomoby.shared.parser.MobyJob
Create a named Simple object as the first data element.
setData(MobyObject, String, int) - Method in class org.biomoby.shared.parser.MobyJob
Create a named Simple object and put it as the 'index'-th data element.
setData(MobyObject) - Method in class org.biomoby.shared.parser.MobySimple
Fill this envelope with a Biomoby object.
setData(ArrayXYData) - Method in class org.inb.biomoby.client.gui.ontology.ArrayXYDataComponent
 
setDataDescMax(int) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
setDataElements(MobyDataElement[]) - Method in class org.biomoby.shared.parser.MobyJob
Replace all current data elements (if any) by the new ones.
setDataFromFile(File) - Method in class org.biomoby.service.dashboard.data.DataContainer
Fill this container by data from the given file.
setDataName(String) - Method in exception org.biomoby.shared.parser.ServiceException
Set an article name of an offending data input.
setDataSet(MobyObject[]) - Method in class org.biomoby.shared.parser.MobyJob
Create an un-named Collection object as the first data element.
setDataSet(MobyObject[], String) - Method in class org.biomoby.shared.parser.MobyJob
Create a named Collection object as the first data element.
setDataSet(MobyObject[], String, int) - Method in class org.biomoby.shared.parser.MobyJob
Create a named Collection object and put it as the 'index'-th data element.
setDataThreshold(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setDataType(MobyDataType) - Method in class org.biomoby.shared.MobyPrimaryData
 
setDataType(MobyDataType) - Method in class org.biomoby.shared.MobyPrimaryDataSet
Set given data type to all elements of this collection (according the Biomoby API all elements should have the same data type).
setDataType(MobyDataType) - Method in class org.biomoby.shared.MobyPrimaryDataSimple
 
setDataType(String) - Method in class org.biomoby.shared.MobySecondaryData
 
setDatatype(Parameter.PARAMETER_TYPE) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
setDatatype(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
setDatatype(Parameter.PARAMETER_TYPE) - Method in class org.inb.biomoby.shared.registry.Parameter
 
setDataTypeName(String) - Method in class org.biomoby.shared.MobyRelationship
 
setDate(Date) - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Sets the given date as a new value for the date-time chooser.
setDate(MobyDateTime) - Method in class org.inb.biomoby.shared.ontology.BasicAnnotation
 
setDate(MobyString) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setDateHeader(String, long) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setDB(MobyString) - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotation
 
setDBComment(String) - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
setDBName(String) - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
setDBVersion(String) - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
setDebug(boolean) - Method in class org.biomoby.client.CentralImpl
 
setDebug(boolean) - Method in interface org.biomoby.shared.Central
Ask the implementation to create more verbose logs or messages about what is going on.
setDebugMode(boolean) - Method in class org.biomoby.client.MobyRequest
 
setDebugMode(boolean) - Static method in class org.biomoby.shared.data.MobyContentInstance
 
setDebugPrintStream(PrintStream) - Method in class org.biomoby.client.MobyRequest
Standard error is used unless this method is called.
setDebugPrintStream(PrintStream) - Static method in class org.biomoby.shared.data.MobyContentInstance
Standard error is used unless this method is called.
setDefault(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
setDefault(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
setDefault(String) - Method in class org.inb.biomoby.shared.registry.Parameter
 
setDefaultAppCloseOperation(int) - Static method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Value to be passed to application JFrame
setDefaultValue(String) - Method in class org.biomoby.shared.MobySecondaryData
 
setDefinition(MobyString) - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
setDefinition(MobyString) - Method in class org.inb.biomoby.shared.ontology.InteractionMethod
 
setDeNovoPeptide(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.ProbMolWeightAnnotation
 
setDescription(String) - Method in class org.biomoby.registry.meta.Registry
 
setDescription(String) - Method in class org.biomoby.shared.data.MobyDataXref
 
setDescription(String) - Method in class org.biomoby.shared.datatypes.MobyXref
Set a human-readable description of this cross reference.
setDescription(String) - Method in class org.biomoby.shared.MobyDataType
 
setDescription(String) - Method in class org.biomoby.shared.MobyNamespace
 
setDescription(String) - Method in class org.biomoby.shared.MobySecondaryData
 
setDescription(String) - Method in class org.biomoby.shared.MobyService
 
setDescription(String) - Method in class org.biomoby.shared.MobyServiceType
 
setDescription(String) - Method in class org.biomoby.shared.schema.MElement
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.Object
 
setDescription(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.CommentedAASequence
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.CommentedDNASequence
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.CommentedNASequence
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.CommentedObject
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.CommentedRNASequence
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.PDB_Enriched
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.PropertySequence
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setDescription(MobyString) - Method in class org.inb.biomoby.shared.ontology.WeightedObject
 
setDescription(String) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
setDescription(String) - Method in class org.inb.biomoby.shared.registry.Parameter
 
setDescription(String) - Method in class org.soap.WSRFFault
 
setDevelopmentID(MobyString) - Method in class org.inb.biomoby.shared.ontology.ExpressionStatistics
 
setDialect(String) - Method in class org.inb.wsrf.bf2.BaseFaultType.ErrorCode
 
setDialect(String) - Method in class org.inb.wsrf.rp2.QueryExpressionType
 
setDiameter(MobyString) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setDirection(Relationship.DIRECTION_TYPE) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
setDoc(MobyString) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setDocConverterHost(String) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
For more details on how to run your own file converter, see http://www.artofsolving.com/node/10
setDocConverterPort(int) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
setDocumentLocator(Locator) - Method in class org.biomoby.shared.parser.MobyParser
Set document locator.
setDocumentLocator(Locator) - Method in class org.omg.lsae.sax.EventParser
Set document locator.
setDocumentLocator(Locator) - Method in class org.soap.sax.SOAPFaultParser
Set document locator.
setDocumentLocator(Locator) - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Set document locator.
setDomain(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setDomain_acc(MobyString) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setDomain_ID(MobyString) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setDomains(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
setDomains(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
setEditor(Component) - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor.EditorContainer
 
setElements(MobyDataObject[]) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Replace whatever is in the collection right now with the values in the input array.
setElements(MobyDataObject[]) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
setElements(MobyPrimaryDataSimple[]) - Method in class org.biomoby.shared.MobyPrimaryDataSet
 
setEmail(String) - Method in class org.biomoby.registry.rdfagent.util.ServiceProvider
 
setEmailContact(String) - Method in class org.biomoby.shared.MobyDataType
 
setEmailContact(String) - Method in class org.biomoby.shared.MobyNamespace
 
setEmailContact(String) - Method in class org.biomoby.shared.MobyService
 
setEmailContact(String) - Method in class org.biomoby.shared.MobyServiceType
 
setEnabled(boolean) - Static method in class org.biomoby.registry.rdfagent.util.Log
 
setEnabledAppendMode(boolean) - Method in class org.biomoby.service.dashboard.CommonConsole
This allows to disable and enable append-mode check box - so user cannot change the append more.
setEnabledMenuItem(Container, String, boolean) - Static method in class org.biomoby.service.dashboard.AbstractPanel
Enable/disable a menu item (indicated by an 'actionCommand') in the given container.
setEnd(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.Annotation
 
setEnd(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.CommentedAASubsequence
 
setEnd(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setEnd(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setEndpoint(String) - Method in class org.biomoby.registry.meta.Registry
 
setEndpointReference(W3CEndpointReference) - Method in class org.inb.biomoby.shared.wsrf.SubmitResponseWrapper
 
setEnzyme_name(MobyString) - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
setErrorCode(int) - Method in exception org.biomoby.shared.parser.ServiceException
Assign an error code to this exception.
setErrorCode(BaseFaultType.ErrorCode) - Method in class org.inb.wsrf.bf2.BaseFaultType
 
setErrorStream(OutputStream) - Method in class org.biomoby.service.dashboard.AntModel
Set output stream where running Ant will be reporting errors.
setEvalue(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setEvent(Event) - Method in class org.inb.lsae.AnalysisEvent
 
setEvidence(MobyString) - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
setEvidence(MobyString) - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotation
 
setEvidenceCode(String) - Method in class org.biomoby.shared.data.MobyDataXref
 
setEvidenceCode(String) - Method in class org.biomoby.shared.datatypes.MobyXref
Set an evidence code.
setEvidenceCodeByAbbrev(String) - Method in class org.biomoby.shared.data.MobyDataXref
 
setExampleInput(String) - Method in class org.biomoby.shared.MobyUnitTest
Setter: set the example input that can be passed to the service to invoke it
setException(Throwable) - Method in class org.biomoby.client.MobyRequestEvent
If you are a service provider and cannot execute the service properly, setting an exception here will inform the client of the failure with a proper MOBY message, and terminate the communication.
setExceptionCode(String) - Method in class org.inb.biomoby.shared.message.MobyException
 
setExceptionMessage(String) - Method in class org.inb.biomoby.shared.message.MobyException
 
setExceptions(ServiceException[]) - Method in class org.biomoby.shared.data.MobyContentInstance
Sets the exception list for the content en masse, replacing any current values
setExceptions(ServiceException[]) - Method in class org.biomoby.shared.parser.MobyPackage
Set one or more exceptions reported by this service invocation.
setExitForbidden(boolean) - Method in class org.biomoby.service.dashboard.ExitSecurityManager
Enable od disable usage of System.exit().
setExpandObjects(boolean) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setExpandRelationship(int) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
setExpandServices(boolean) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setExpressionLevel(MobyString) - Method in class org.inb.biomoby.shared.ontology.ExpressionStatistics
 
setExpressionPattern(MobyString) - Method in class org.inb.biomoby.shared.ontology.ExpressionStatistics
 
setExtNumber(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setExtThreshold(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setFaultCause(BaseFaultType.FaultCause) - Method in class org.inb.wsrf.bf2.BaseFaultType
 
setFeature(ArrayFloat) - Method in class org.inb.biomoby.shared.ontology.FeatureAASequence
 
setFilter(FilterSearch) - Method in class ca.ucalgary.seahawk.gui.FilterSearchWidget
The filter to display as editable right now.
setFilterVisible(boolean) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
The search/filter widget is document specific (since you may want to have different view of different service responses), therefore setting the visibility is only valid for the time the current document is being shown.
setFirstBlast(NCBI_BLAST_Text) - Method in class org.inb.biomoby.shared.ontology.ISS_Report
 
setFitness(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.MatchingPattern
 
setFixedParams(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setFloat(double) - Method in class org.inb.biomoby.shared.datatypes.MobyFloat
 
setFontStyle(int) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractMultilineDescriptionMobyComponent
 
setFontStyle(int) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
setFontStyle(int) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
setFontStyle(int) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
setFormAction(String) - Method in class ca.ucalgary.services.util.XHTMLForm
 
setFormEncodingType(String) - Method in class ca.ucalgary.services.util.XHTMLForm
 
setFormMethod(String) - Method in class ca.ucalgary.services.util.XHTMLForm
 
setForwardButtonToolTip(String) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Allow others to set the forward navigation button message.
setFragIonTolerance(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setFrame(MobyString) - Method in class org.inb.biomoby.shared.ontology.BLOCKAnnotation
 
setFrom(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.AnnotationHits
 
setGaps(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setGeneID(MobyString) - Method in class org.inb.biomoby.shared.ontology.ExpressionCore
 
setGenus(MobyString) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setGUIMap(Map<String, MobyContentGUI>) - Method in class ca.ucalgary.services.util.PBERecorder
 
setHeader(String, String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setHeader(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
setHeader(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
setHeight(int) - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
setHeight(int) - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
setHigherRange(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ParametersToVary
 
setHistogram(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
setHit(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
setHitcount(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.AnnotationHits
 
setHits(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.MatchingPattern
 
setHomologous_Superfamily(CommentedObject) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setHtmlText(String) - Method in class org.inb.biomoby.central.gui.renderer.AbstractCellRenderer
 
setHydropathy_KD(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setHydropathy_OHM(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setId(String) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Assign an ID to this node.
setID(String) - Method in class org.biomoby.shared.data.MobyDataJob
 
setId(String) - Method in class org.biomoby.shared.data.MobyDataObject
Used to set the data instance value based on an ID string. i.e. just an Object.
setId(String) - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
setId(String) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
setId(String) - Method in class org.biomoby.shared.datatypes.MobyObject
Set an identifier (within the namespace) that specifies the precise resource represented by the object.
setId(String) - Method in class org.biomoby.shared.MobyData
 
setId(String) - Method in class org.biomoby.shared.MobyDataType
 
setId(String) - Method in class org.biomoby.shared.MobyNamespace
 
setId(String) - Method in class org.biomoby.shared.MobyService
Don't use it.
setId(String) - Method in class org.biomoby.shared.MobyServiceType
 
setId(String) - Method in class org.biomoby.shared.parser.MobyJob
Set a "query id" that identifies this job uniquely within a client request or a service response.
setId(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
setId(MobyString) - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
setID(MobyString) - Method in class org.inb.biomoby.shared.ontology.MotifAnnotation
 
setID(MobyString) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setID(MobyString) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setId(String) - Method in class org.inb.biomoby.shared.registry.Registration
 
setId(String) - Method in class org.inb.lsae.AnalysisEvent
 
setImage_Encoded(Image_Encoded) - Method in class org.inb.biomoby.client.gui.ontology.Image_EncodedComponent
 
setImageOptions(Map<String, String>) - Method in class ca.ucalgary.services.util.XHTMLForm
 
setInput(MobyContentInstance) - Method in class org.biomoby.client.MobyRequest
Sets the input data for the MOBY service request.
setInput(MobyDataInstance[]) - Method in class org.biomoby.client.MobyRequest
Takes the data in the array, with their current articleNames, as input for the service
setInput(MobyDataInstance) - Method in class org.biomoby.client.MobyRequest
Convenience method to run services that take one argument.
setInput(MobyDataInstance, String) - Method in class org.biomoby.client.MobyRequest
Convenience method to run services that take one named argument.
setInput(FindServiceOperation.FindService.Input) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.InputObjects
 
setInput(FindServiceOperation.Services.Input) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setInput(RegisterServiceOperation.Input) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setInput(Input) - Method in class org.inb.biomoby.shared.registry.Service
 
setInputObjects(FindServiceOperation.FindService.InputObjects) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setInputParams(HttpServletRequest, Map<String, byte[]>, List<String>) - Method in interface ca.ucalgary.services.util.DataRecorder
Lets the data recorder know what the input XML to the Web Service looked like.
setInputParams(HttpServletRequest, Map<String, byte[]>, List<String>) - Method in class ca.ucalgary.services.util.PBERecorder
This method is to be called just before submission of data to the CGI, so that the PBE system can record the input for data type analysis later in the wrapping process.
setInputs(MobyData[]) - Method in class org.biomoby.shared.MobyService
Adds an array of input parameter to the service.
setInputSource(HttpServletRequest, SourceMap) - Method in interface ca.ucalgary.services.util.DataRecorder
Lets the data recorder know what the input XML to the Web Service looked like.
setInputSource(HttpServletRequest, SourceMap) - Method in class ca.ucalgary.services.util.PBERecorder
This method is to be called just before submission of data to the Web Service, so that the PBE system can record the input for data type analysis later in the wrapping process.
setInputStream(InputStream) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
setInputStream(ServletInputStream) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
setInputStream(InputStream) - Method in class org.biomoby.shared.extended.DataTypeParser
If not null, overrides the URL when reading the definitions (e.g. if you have the RDF as a String, not a URL use this).
setInputStream(InputStream) - Method in class org.biomoby.shared.extended.NamespaceParser
If not null, overrides the URL when reading the definitions (e.g. if you have the RDF as a String, not a URL use this).
setInputStream(InputStream) - Method in class org.inb.biomoby.shared.datatypes.MobyBinary
 
setInputXSDTypes(Map<String, String>) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setInteger(int) - Method in class org.inb.biomoby.shared.datatypes.MobyInteger
 
setIntegrationMethod(MobyString) - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
setIntHeader(String, int) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setIntScr(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
setInvocationId(String) - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
setIonOffset(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setIonsResidue(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setIonsWindow(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setIssXML(ISS_Annotation_XML) - Method in class org.inb.biomoby.shared.ontology.ISS_Report
 
setIteration(int) - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
setJmolScript(MobyString) - Method in class org.inb.biomoby.shared.ontology.PDB_Enriched
 
setJobId(String) - Method in exception org.biomoby.shared.parser.ServiceException
Set an identifier of an offending job.
setJobId(MobyJob) - Method in exception org.biomoby.shared.parser.ServiceException
Set an identifier of an offending job.
setJobs(MobyJob[]) - Method in class org.biomoby.shared.parser.MobyPackage
Store here all jobs.
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ArrayFloat
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ArrayInteger
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ArrayString
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ElementFloat
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ElementInteger
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ElementString
 
setKey(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ElementXYData
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.MatrixFloat
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.MatrixInteger
 
setKey(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.MatrixString
 
setKeywords(List<String>) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setKeywords(MobyString) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setLabel(ArrayString) - Method in class org.inb.biomoby.shared.ontology.Distance_Matrix
 
setLabelOfColumns(ArrayString) - Method in class org.inb.biomoby.shared.ontology.NCut_Matrix
 
setLabelOfRows(ArrayString) - Method in class org.inb.biomoby.shared.ontology.NCut_Matrix
 
setLang(String) - Method in class org.inb.wsrf.bf2.BaseFaultType.Description
 
setLeafIcon(Icon) - Method in class org.biomoby.service.dashboard.CommonTree
 
setLegend(Text__html) - Method in class org.inb.biomoby.shared.ontology.Typed_Image
 
setLength(int) - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
setLength(int) - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
setLength(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.VirtualSequence
 
setListAcc(MobyString) - Method in class org.inb.biomoby.shared.ontology.NCut_Matrix
 
setLocalClass(String) - Method in class org.biomoby.client.ExtendedServiceLocator
Set name of a local class that represents (implements) a service.
setLocale(Locale) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setLog(MobyString) - Method in class org.inb.biomoby.shared.ontology.NAMD_Output
 
setLongName(String) - Method in class org.biomoby.registry.meta.Registry
 
setLoop(boolean) - Method in class org.biomoby.client.ExtendedServiceLocator
Setting 'enabled' to true indicates that no method should be call, at all.
setLowerRange(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ParametersToVary
 
setLSID(String) - Method in class org.biomoby.shared.MobyDataType
 
setLSID(String) - Method in class org.biomoby.shared.MobyNamespace
 
setLSID(String) - Method in class org.biomoby.shared.MobyService
 
setLSID(String) - Method in class org.biomoby.shared.MobyServiceType
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Namespace
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ObjectType
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ServiceType
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.AbstractType
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.Relationship
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.ObjectType
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.Relationship
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.Object
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Object
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
setLsid(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
setLsid(String) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
setLsid(String) - Method in class org.inb.biomoby.shared.registry.Relationship
 
setLutefiskPeptide(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
setMainName(String) - Method in class org.biomoby.service.dashboard.BuildDataTypeTree
 
setMainTerminationExit(boolean) - Static method in class org.biomoby.service.MobyServlet
Determines whether call to main() that terminate on error should call System.exit() or not.
setMatrix(MotifMatrix) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setMaturePeptide(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.SigcleaveAnnotation
 
setMax(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
setMax(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
setMax(String) - Method in class org.inb.biomoby.shared.registry.Parameter
 
setMax_score_pos(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.AntigenicAnnotation
 
setMaximumValue(int) - Method in class org.biomoby.shared.MobySecondaryData
Deprecated. Use MobySecondaryData.setMaxValue(java.lang.String) instead.
setMaxValue(String) - Method in class org.biomoby.shared.MobySecondaryData
 
setMessage(String) - Method in exception org.biomoby.shared.parser.ServiceException
Assign an error message to this exception.
setMessage(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
setMessage(String) - Method in class org.inb.biomoby.shared.registry.Registration
 
setMessage(String) - Method in class org.inb.lsae.AnalysisEvent
 
setMessage(String) - Method in class org.inb.swing.StatusBar
Method sets a status bar message (without logging).
setMessage(String, int) - Method in class org.inb.swing.StatusBar
Method sets a status bar message (without logging).
setMessage(String) - Method in class org.omg.lsae.notifications.AnalysisEvent
 
setMetadata(Object) - Method in class org.biomoby.service.dashboard.data.DataContainer
Fill this container with metadata.
setMethod(MobyString) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setMethod(MobyObject) - Method in class org.inb.biomoby.shared.ontology.Interaction
 
setMicroarraydata(MicroArrayData_Text) - Method in class org.inb.biomoby.shared.ontology.Clustering
 
setMicroarraydata(MicroArrayData_Text) - Method in class org.inb.biomoby.shared.ontology.HierarchicalClustering
 
setMimeType(MobyString) - Method in class org.inb.biomoby.shared.ontology.Image_Encoded
 
setMimeTypte(MobyString) - Method in class org.inb.biomoby.shared.ontology.Zip_Encoded
 
setMin(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Parameter
 
setMin(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Parameter
 
setMin(String) - Method in class org.inb.biomoby.shared.registry.Parameter
 
setMinimumValue(int) - Method in class org.biomoby.shared.MobySecondaryData
Deprecated. Use MobySecondaryData.setMinValue(java.lang.String) instead.
setMinValue(String) - Method in class org.biomoby.shared.MobySecondaryData
 
setMobyContent(MobyContent) - Method in class org.inb.biomoby.shared.message.MobyMessage
 
setMobyId(String) - Method in class org.inb.biomoby.shared.message.AbstractMobyObject
 
setMobyObject(AbstractMobyObject) - Method in class org.inb.biomoby.shared.message.MobySimple
 
setMobyParams2ServiceParams(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
Primarily for use by systems that allow renaming of params, since SAWSDL doesn't directly
setModelFormat(MobyString) - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
setMolWeight(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.MolWeightAnnotation
 
setMsg(String) - Method in class org.soap.SOAPFault
 
setMsgOutputLevel(int) - Method in class org.biomoby.service.dashboard.AntModel
 
setMsgOutputLevel(int) - Method in class org.biomoby.service.dashboard.SimpleAnt
 
setMW(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setMWTolerance(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setName(String) - Method in class org.biomoby.service.dashboard.CommonNode
Change the appearance of this node.
setName(String) - Method in interface org.biomoby.shared.data.MobyDataInstance
 
setName(String) - Method in class org.biomoby.shared.data.MobyDataObject
Please note that you almost never want to call this method in a client.
setName(String) - Method in class org.biomoby.shared.datatypes.MobyObject
Set a name (called also an article name) that identifies this objects within other Biomoby objects.
setName(String) - Method in class org.biomoby.shared.MobyData
 
setName(String) - Method in class org.biomoby.shared.MobyDataType
 
setName(String) - Method in class org.biomoby.shared.MobyRelationship
 
setName(String) - Method in class org.biomoby.shared.MobyService
 
setName(String) - Method in class org.biomoby.shared.MobyServiceType
 
setName(String) - Method in class org.biomoby.shared.parser.MobyDataElement
A name here means an article name of the top-level object.
setName(String) - Method in class org.biomoby.shared.schema.MElement
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Namespace
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ObjectType
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.ServiceType
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.ServiceType
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.AbstractType
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveNamespacesOperation.Namespace
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.ObjectType
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectNamesOperation.Object
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Object
 
setName(Resource.RESOURCE_NAME) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation.Resource
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation.ServiceProvider
 
setName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceType
 
setName(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setName(MobyString) - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
setName(MobyString) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setName(MobyString) - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
setName(MobyString) - Method in class org.inb.biomoby.shared.ontology.MultiParameter
 
setName(MobyString) - Method in class org.inb.biomoby.shared.ontology.Parameter
 
setName(MobyString) - Method in class org.inb.biomoby.shared.ontology.StructureDomain
 
setName(String) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
setName(Resource.RESOURCE_NAME) - Method in class org.inb.biomoby.shared.registry.Resource
 
setName(String) - Method in class org.inb.biomoby.shared.registry.ServiceProvider
 
setName(String) - Method in class org.soap.WSRFFault
 
setNamespace(String) - Method in class org.biomoby.registry.meta.Registry
 
setNamespace(String) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Assign a namespace to this node.
setNamespace(String) - Method in class org.biomoby.shared.datatypes.MobyObject
Set a namespace of the resource being represented by this object.
setNamespace(String) - Method in class org.inb.biomoby.shared.message.AbstractMobyObject
 
setNamespaces(MobyNamespace[]) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Set given namespaces of all elements of this collection.
setNamespaces(MobyNamespace[]) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
setNamespaces(MobyNamespace[]) - Method in class org.biomoby.shared.MobyPrimaryData
 
setNamespaces(MobyNamespace[]) - Method in class org.biomoby.shared.MobyPrimaryDataSet
Set given namespaces of all elements of this collection.
setNamespaces(MobyNamespace[]) - Method in class org.biomoby.shared.MobyPrimaryDataSimple
Replace all existing namespaces (if any) by a new array of namespaces.
setNamespaceType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterNamespaceOperation.DeregisterNamespace
 
setNamespaceType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterNamespaceOperation.RegisterNamespace
 
setNcutMatrix(NCut_Matrix) - Method in class org.inb.biomoby.shared.ontology.ISS_Report
 
setNegative(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setNewState(StateChanged.STATE) - Method in class org.inb.lsae.StateChanged
 
setNewState(int) - Method in class org.omg.lsae.notifications.StateEvent
 
setNodeValue(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
setNon__polar(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setNotes(String) - Method in class org.inb.biomoby.shared.message.ServiceNotes
 
setNterminalMass(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setNterminalTagMass(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setNum_blocks(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
setNumber(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
setNumResidues(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.StructureFragment
 
setObjectType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterObjectClassOperation.DeregisterObjectClass
 
setObjectType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Simple
 
setObjectType(FindServiceOperation.Services.ObjectType) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Simple
 
setObjectType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.RegisterObjectClass
 
setObjectType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Simple
 
setObjectType(List<RetrieveObjectDefinitionOperation.ObjectType>) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.Relationship
 
setObjectType(RetrieveObjectDefinitionOperation.ObjectType) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectDefinitionOperation.RetrieveObjectDefinition
 
setObjectType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.RetrieveObjectSchema
 
setObjectType(ObjectType) - Method in class org.inb.biomoby.central.gui.ObjectTypeAnnotationPanel
Set up a new BioMoby datatype to edit its annotations.
setObjectType(ObjectType) - Method in class org.inb.biomoby.shared.registry.Simple
 
setOEDResolution(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ByoDynOEDParameter
 
setOntology(MobyString) - Method in class org.inb.biomoby.shared.ontology.GOTerm
 
setOpaque(boolean) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
setOpaque(boolean) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
setOpaque(boolean) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
setOperationEncoding(String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setOperationInputQName(QName) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setOperationName(String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setOperationOutputQName(QName) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setOperationStyle(String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setOriginator(W3CEndpointReference) - Method in class org.inb.wsrf.bf2.BaseFaultType
 
setOutput(FindServiceOperation.FindService.Output) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.OutputObjects
 
setOutput(FindServiceOperation.Services.Output) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setOutput(RegisterServiceOperation.Output) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setOutput(Output) - Method in class org.inb.biomoby.shared.registry.Service
 
setOutputObjects(FindServiceOperation.FindService.OutputObjects) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setOutputs(MobyData[]) - Method in class org.biomoby.shared.MobyService
Adds an array of output parameter to the service.
setOutputStream(OutputStream) - Method in class org.biomoby.service.dashboard.AntModel
Set output stream where running Ant will be reporting.
setOutputStream(ServletOutputStream) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setOutputXSDTypes(Map<String, String>) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setParameter(HttpSession, String, String) - Method in interface ca.ucalgary.services.util.DataRecorder
Allows a WrappingServlet to set the equivalent of HTTP request parameters (which are normally immutable).
setParameter(HttpSession, String, String) - Method in class ca.ucalgary.services.util.PBERecorder
 
setParameter(String, String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
setParameter(String, String) - Method in class org.biomoby.shared.parser.MobyJob
Set secondary parameter 'name' to 'value'.
setParent(String) - Method in class org.biomoby.service.dashboard.BuildDataTypeTree
 
setParentNames(String[]) - Method in class org.biomoby.shared.MobyDataType
 
setParentNames(String[]) - Method in class org.biomoby.shared.MobyServiceType
 
setPassword(String) - Method in class org.biomoby.client.MobyServiceLocator
Sets the password for authentication
setPathToRDF(String) - Method in class org.biomoby.shared.MobyService
 
setPattern(Pattern) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setPeakWidth(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setPercentage(String) - Method in class org.inb.lsae.PercentProgress
 
setPercentaje(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
setPercentCompleted(int) - Method in class org.omg.lsae.notifications.PercentEvent
 
setPevzScr(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
setPlot_title(MobyString) - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
setPolar(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setPortQName(QName) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setPosition(int) - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
setPosition(int) - Method in interface org.inb.biomoby.client.gui.ISequenceDependent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
setPosition(int) - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
setPosition(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.TTS
 
setPositive(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setPr__c__(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
setPreferredSize(Dimension) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
setPrefix(String, String) - Method in class org.biomoby.shared.NamespaceContextImpl
 
setPreviewPanel(JPanel) - Method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Sets the current preview panel.
setPreviousState(StateChanged.STATE) - Method in class org.inb.lsae.StateChanged
 
setPreviousState(int) - Method in class org.omg.lsae.notifications.StateEvent
 
setPrimaryInputFormats(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setPrimaryInputs(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setPrimaryNamespace(MobyNamespace) - Method in class org.biomoby.shared.data.MobyDataObject
This sets the namespace that will be used in toXML(), since in the XML representation for service execution, you can only have one namespace.
setPrimaryOutputFormats(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setPrimaryOutputs(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setProbability(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ProbMolWeightAnnotation
 
setProfiles(ClusterProfile_Text) - Method in class org.inb.biomoby.shared.ontology.Clustering
 
setProfiles(ClusterProfile_Text) - Method in class org.inb.biomoby.shared.ontology.HierarchicalClustering
 
setPropertyChannel(PropertyChannel) - Method in class org.biomoby.service.dashboard.AbstractModel
Keep shared storage of properties updated in various panels.
setPropertyChannel(PropertyChannel) - Method in class org.biomoby.service.dashboard.CommonConsole
Remember the property channel.
setPropertyChannel(PropertyChannel) - Method in class org.biomoby.service.dashboard.CommonTree
Keep shared storage of properties updated in various panels.
setProtein_name(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setProviderURI(String) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setProvision(MobyProvisionInfo) - Method in class org.biomoby.shared.datatypes.MobyObject
Attach a service provision information to this object.
setProvisionInfo(MobyProvisionInfo) - Method in class org.biomoby.shared.data.MobyDataObject
 
setPsf(PSF_Text) - Method in class org.inb.biomoby.shared.ontology.NAMD_Structure
 
setPublic(boolean) - Method in class org.biomoby.registry.meta.Registry
 
setQuality(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
setQueryExpression(QueryExpressionType) - Method in class org.inb.wsrf.rp2.QueryResourceProperties
 
setQueryID(String) - Method in class org.inb.biomoby.shared.message.MobyData
 
setQueryId(String) - Method in class org.omg.lsae.notifications.AnalysisEvent
 
setRadius(MobyString) - Method in class org.inb.biomoby.shared.ontology.ProdomMotif
 
setRank(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
setRatio(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
setRawdata(MobyString) - Method in class org.inb.biomoby.shared.ontology.Image_Encoded
 
setRawdata(MobyString) - Method in class org.inb.biomoby.shared.ontology.Zip_Encoded
 
setRDF(String) - Method in class org.biomoby.shared.MobyService
 
setRdf(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
setRdf(String) - Method in class org.inb.biomoby.shared.registry.Registration
 
setRecorder(DataRecorder) - Method in class ca.ucalgary.services.WrappingServlet
Registers an object that hooks into various parts of the request and response in order to provide custom behaviours.
setRef(MobyString) - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
setRefElement(String) - Method in class org.inb.biomoby.shared.message.MobyException
 
setRefQueryID(String) - Method in class org.inb.biomoby.shared.message.MobyException
 
setRegistry(Registry) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
setRegistry(Registry) - Method in class org.biomoby.shared.MobyDataType
 
setRegistry(Registry) - Method in class org.biomoby.shared.MobyNamespace
 
setRegistry(Registry) - Method in class org.biomoby.shared.MobyServiceType
 
setRegistryEndpoint(String) - Method in class org.biomoby.client.MobyServiceLocator
 
setRegistryNamespace(String) - Method in class org.biomoby.client.MobyServiceLocator
 
setRelationshipType(int) - Method in class org.biomoby.shared.MobyRelationship
 
setRelationshipType(Relationship.RELATIONSHIP_TYPE) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterObjectClassOperation.Relationship
 
setRelationshipType(Relationship.RELATIONSHIP_TYPE) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.Relationship
 
setRelationshipType(Relationship.RELATIONSHIP_TYPE) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.Relationship
 
setRelationshipType(Relationship.RELATIONSHIP_TYPE) - Method in class org.inb.biomoby.shared.registry.Relationship
 
setRemaining(String) - Method in class org.inb.lsae.TimeProgress
 
setRemaining(long) - Method in class org.omg.lsae.notifications.TimeProgressEvent
 
setRepetitions(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.WeightedObject
 
setReport(Text__html) - Method in class org.inb.biomoby.shared.ontology.Structure_Alignment_Report
 
setRequestURL(String) - Method in class org.biomoby.service.test.TestHttpServletRequest
 
setRequiredServiceLevel(int) - Method in class ca.ucalgary.seahawk.services.MobyClient
 
setResolution(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setResponseHandler(MobyRequestEventHandler) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
If a service is invoked by this class, the event handler registered here will get a callback when the response is ready for display (MobyServicesGUI does not display service results, this is its way of delegating that responsibility).
setResponseTransformer(Transformer) - Method in class ca.ucalgary.services.WrappingServlet
Stylesheet to apply to service response if it's XML.
setRestriction_site(MobyString) - Method in class org.inb.biomoby.shared.ontology.RestrictAnnotation
 
setResult(MobyString) - Method in class org.inb.biomoby.shared.ontology.Interaction
 
setResultUnits(MobyString) - Method in class org.inb.biomoby.shared.ontology.Interaction
 
setRole(MobyString) - Method in class org.inb.biomoby.shared.ontology.Interactor
 
setRowHeight(int) - Method in class org.biomoby.service.dashboard.treetable.JTreeTable
Overridden to pass the new rowHeight to the tree.
setRowHeight(int) - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellRenderer
Sets the row height of the tree, and forwards the row height to the table.
setRules(Rules) - Method in class org.inb.biomoby.shared.ontology.PrositeMotif
 
setRunningType(MobyString) - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
setS100(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setS35(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setS60(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setS95(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setScale(MobyString) - Method in class org.inb.biomoby.shared.ontology.ParametersToVary
 
setSchema(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveObjectOperation.Object
 
setScore(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.AntigenicAnnotation
 
setScore(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
setScore(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setScore(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.EmowseAnnotatedAASequence
 
setScore(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotation
 
setScore(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ScoredMotifAnnotation
 
setScore(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.SigcleaveAnnotation
 
setSecondaryArticles(FindServiceOperation.Services.SecondaryArticles) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setSecondaryArticles(RegisterServiceOperation.SecondaryArticles) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setSecondaryInput(Collection<MobyDataSecondaryInstance>) - Method in class org.biomoby.client.MobyRequest
Same functionality as setSecondaryInput(MobyDataSecondaryInstance[])
setSecondaryInput(MobyDataSecondaryInstance[]) - Method in class org.biomoby.client.MobyRequest
This method will assign the provided secondary parameters to all primary input data currently in this object.
setSecondaryInputFormats(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setSecondaryInputs(Map<String, String>) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setSelectedCentral(MobyCentral) - Method in class org.inb.biomoby.central.model.MobyCentralModel
Method to setup a BioMoby Registry that entire application is working with.
setSelectedItem(Object) - Method in class org.inb.biomoby.central.gui.renderer.ObjectTypeTableCellEditor.ObjectTypeComboBoxModel
 
setSelectedXPath(int) - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
setSelectionInversed(boolean) - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
setSendReferrerPolicy(boolean) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
setSeqHits(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.MatchingPattern
 
setSequence(GenericSequence) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
setSequence(CommentedAASubsequence) - Method in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent
 
setSequence(MobyString) - Method in class org.inb.biomoby.shared.ontology.CpGAnnotation
 
setSequences(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMPfam_Report
 
setSequences(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
setSequenceString(MobyString) - Method in class org.inb.biomoby.shared.ontology.GenericSequence
 
setSequenceTag(MobyString) - Method in class org.inb.biomoby.shared.ontology.LutefiskReport
 
setSequenceVisible(boolean) - Method in interface org.inb.biomoby.client.gui.ISequenceDependent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
setSequenceVisible(boolean) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
setService(MobyService) - Method in class org.biomoby.client.MobyRequest
 
setService(MobyService) - Method in class org.biomoby.client.MobyServiceLocator
 
setService(MobyService) - Method in class org.biomoby.shared.datatypes.MobyXref
Set a Biomoby service that can consume data this cross reference is included in.
setService(RetrieveServiceOperation.ServiceTemplate) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.RetrieveService
 
setServiceAuthorityURI(String) - Method in class org.biomoby.shared.data.MobyContentInstance
 
setServiceDesc(String) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setServiceInvocationId(String) - Method in class org.biomoby.w3c.addressing.EndpointReference
 
setServiceName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceOperation.DeregisterService
 
setServiceName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setServiceName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setServiceName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setServiceName(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
setServiceNotes(String) - Method in class org.biomoby.shared.data.MobyContentInstance
Note this is only the human readable notes.
setServiceNotes(String) - Method in class org.biomoby.shared.parser.MobyPackage
Fill in any string representing service notes.
setServiceNotes(ServiceNotes) - Method in class org.inb.biomoby.shared.message.MobyContent
 
setServiceNotesXML(String) - Method in class org.biomoby.shared.parser.MobyPackage
Fill in any string representing service notes.
setServiceQName(QName) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setServices(MobyService[]) - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
setServices(MobyService[]) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
setServices(MobyService[]) - Method in interface org.biomoby.shared.data.MobyDataServiceAssocInstance
 
setServices(MobyService[]) - Method in class org.biomoby.shared.data.MobyDataXref
If more than one service is provided, only the first will be taken.
setServiceType(String) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setServiceType(MobyServiceType) - Method in class org.biomoby.shared.MobyService
 
setServiceType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.DeregisterServiceTypeOperation.DeregisterServiceType
 
setServiceType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setServiceType(FindServiceOperation.Services.ServiceType) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setServiceType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setServiceType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceTypeOperation.RegisterServiceType
 
setServiceType(ServiceType) - Method in class org.inb.biomoby.shared.registry.Service
 
setServletContainer(Serve) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
A shared resource for proxying requests such as WSDL PBE wrapping
setSeverity(int) - Method in exception org.biomoby.shared.parser.ServiceException
Set severity level.
setSeverity(String) - Method in exception org.biomoby.shared.parser.ServiceException
Set severity level.
setSeverity(MobyException.SEVERITY) - Method in class org.inb.biomoby.shared.message.MobyException
 
setShortlabel(MobyString) - Method in class org.inb.biomoby.shared.ontology.InteractionMethod
 
setSignatureURL(String) - Method in class org.biomoby.shared.MobyService
 
setSignatureURL(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService
 
setSignatureURL(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setSignatureURL(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setSignatureURL(String) - Method in class org.inb.biomoby.shared.registry.Service
 
setSimple(boolean) - Method in class org.biomoby.shared.datatypes.MobyXref
Set the kind of this cross reference.
setSimple(FindServiceOperation.FindService.Simple) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.FindService.Collection
 
setSimple(FindServiceOperation.Services.Simple) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Collection
 
setSimple(RegisterServiceOperation.Simple) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.Collection
 
setSimple(Simple) - Method in class org.inb.biomoby.shared.registry.Collection
 
setSingleCallInput(String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Sets the input for a single service call.
setSingleCallInput(String, String, String) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Sets the input for a single service call.
setSingleCallInput(MobyObject...) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Sets the inputs for a single service call.
setSize(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.EquicktandemAnnotation
 
setSmall(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setSoapAction(String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setSoftwareComment(String) - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
setSoftwareName(String) - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
setSoftwareVersion(String) - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
setSortingStatus(int, int) - Method in class org.biomoby.service.dashboard.TableSorter
 
setSource(MobyString) - Method in class org.inb.biomoby.shared.ontology.AnnotatedStructure
 
setSource(MobyString) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setSourceInput(MobyContentInstance) - Method in class org.biomoby.client.MobyRequestEvent
 
setSpecies(MobyString) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setSpecURL(URL) - Method in class ca.ucalgary.services.util.MobySpecWrapper
location of the WSDL, CGI form, etc., only one per class instance
setStart(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.Annotation
 
setStart(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.CommentedAASubsequence
 
setStart(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.Domain
 
setStart(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setStatistics(MobyString) - Method in class org.inb.biomoby.shared.ontology.HMMSearch_Report
 
setStatus(String) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
setStatus(String) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
setStatus(String) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
 
setStatus(String, boolean) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
 
setStatus(String) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
 
setStatus(String, boolean) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
 
setStatus(String) - Method in class ca.ucalgary.services.util.PBERecorder
 
setStatus(String) - Static method in class org.biomoby.client.util.SplashScreenStatus
 
setStatus(int) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setStatus(int, String) - Method in class org.biomoby.service.test.TestHttpServletResponse
 
setStatus(int, boolean) - Method in class org.biomoby.shared.MobyService
 
setStatus(MobyString) - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
setStatus(MobyString) - Method in class org.inb.biomoby.shared.ontology.InterProMotifAnnotation
 
setStatusPosition(int, int) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
 
setStatusPosition(int, int) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
 
setStepsCompleted(String) - Method in class org.inb.lsae.StepProgress
 
setStrand(MobyString) - Method in class org.inb.biomoby.shared.ontology.BL2GAnnotation
 
setStrand(MobyString) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setStrand(MobyString) - Method in class org.inb.biomoby.shared.ontology.FamilyBLOCKAnnotation
 
setString(String) - Method in class org.inb.biomoby.shared.datatypes.MobyString
 
setStructureID(MobyString) - Method in class org.inb.biomoby.shared.ontology.ExpressionCore
 
setSubmitOptions(Map<String, String>) - Method in class ca.ucalgary.services.util.XHTMLForm
 
setSuccess(Registration.SUCCESS_CODE) - Method in class org.inb.biomoby.central.factory.jaxb.registry.MobyRegistration
 
setSuccess(Registration.SUCCESS_CODE) - Method in class org.inb.biomoby.shared.registry.Registration
 
setSuggestedTimeout(int) - Method in class org.biomoby.client.MobyServiceLocator
Set a timeout that will be used when calling the service.
setSynonym(String) - Method in class org.biomoby.registry.meta.Registry
 
setTableHeader(JTableHeader) - Method in class org.biomoby.service.dashboard.TableSorter
 
setTableModel(TableModel) - Method in class org.biomoby.service.dashboard.TableSorter
 
setTargetNamespaceURI(String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
setTempDir(File) - Static method in class ca.ucalgary.seahawk.util.SeahawkOptions
 
setTempDir(File) - Static method in class org.biomoby.registry.meta.RegistryCache
 
setTerm(MobyString) - Method in class org.inb.biomoby.shared.ontology.BasicAnnotation
 
setTerm(MobyString) - Method in class org.inb.biomoby.shared.ontology.InteractionMethod
 
setText(String) - Method in class org.biomoby.service.dashboard.CommonConsole
 
setText(String) - Method in class org.inb.biomoby.client.gui.swing.RoundedMultilineLabel
 
setText(Text__formatted) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
setTheilerStage(MobyString) - Method in class org.inb.biomoby.shared.ontology.ExpressionCore
 
setTime(long) - Method in class org.inb.biomoby.shared.datatypes.MobyDateTime
 
setTime(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
setTime(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ByoDynTarget
 
setTimeout(long) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Sets the timeout in seconds how long the call shall be kept alive.
setTimestamp(String) - Method in class org.inb.lsae.AnalysisEvent
 
setTimestamp(XMLGregorianCalendar) - Method in class org.inb.wsrf.bf2.BaseFaultType
 
setTimestamp(String) - Method in class org.omg.lsae.notifications.AnalysisEvent
TODO - is there a specific format?
setTimestamp(String) - Method in class org.soap.WSRFFault
 
setTimestep(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ByoDynInput
 
SETTINGS_BUTTON_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
setTiny(FeatureAASequence) - Method in class org.inb.biomoby.shared.ontology.PepinfoReport
 
setTitle(MobyString) - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
setTitle(MobyString) - Method in class org.inb.biomoby.shared.ontology.OMIM
 
setTitle(String) - Method in class org.inb.biomoby.shared.registry.AbstractEntity
 
setTitlePosition(int, int) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
 
setTitlePosition(int, int) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
 
setTm(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.TTS
 
setTo(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.AnnotationHits
 
setTopology(CommentedObject) - Method in class org.inb.biomoby.shared.ontology.CATHDomain
 
setTotalHits(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.PPSearchReport
 
setTotalSteps(String) - Method in class org.inb.lsae.StepProgress
 
setTotalSteps(int) - Method in class org.omg.lsae.notifications.StepEvent
 
setTransformer(Transformer) - Method in interface ca.ucalgary.services.util.DataRecorder
Specify a XML transformation to be applied to the service results.
setTransformer(Transformer) - Method in class ca.ucalgary.services.util.PBERecorder
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.auxiliary.AbstractTransformableMobyPanel
 
setTransformer(ISequenceCoordinateTransformer) - Method in interface org.inb.biomoby.client.gui.ITransformable
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.AntigenicReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.BlocksAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.CommentedAASubsequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.CommentedNASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.DigestReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemAnnotatedNASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.EquicktandemReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.FeatureAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.GenericSequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.InterProMotifAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.MolWeightsAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.MotifAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.PatmatdbReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.PatmatmotifsReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.PepinfoReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.PPSearchReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.RestrictAnnotatedNASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.RestrictReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.ScoredMotifAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
setTransformer(ISequenceCoordinateTransformer) - Method in class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
setTransmembraneFragment(AminoAcidSequence) - Method in class org.inb.biomoby.shared.ontology.TransmembraneAnnotation
 
setTransmembraneNumber(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.TransmembraneAnnotation
 
setTree(Newick_Text) - Method in class org.inb.biomoby.shared.ontology.Clustering
 
setTree(Newick_Text) - Method in class org.inb.biomoby.shared.ontology.HierarchicalClustering
 
setTreedetHTML(TreeDet_Annotation_HTML) - Method in class org.inb.biomoby.shared.ontology.TreeDet_Report
 
setTreedetXML(TreeDet_Annotation_XML) - Method in class org.inb.biomoby.shared.ontology.TreeDet_Report
 
setType(int) - Method in class org.biomoby.service.dashboard.CommonNode
Change the type of this node.
setType(String) - Method in class org.biomoby.shared.MobyService
 
setType(String) - Method in class org.biomoby.shared.schema.MElement
 
setType(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RelationshipsOperation.RelationshipsInput
 
setType(MobyString) - Method in class org.inb.biomoby.shared.ontology.BL2GAnnotation
 
setType(MobyString) - Method in class org.inb.biomoby.shared.ontology.ENSEMBLHomolog
 
setType(MobyString) - Method in class org.inb.biomoby.shared.ontology.FeatureAnnotation
 
setType(MobyString) - Method in class org.inb.biomoby.shared.ontology.MultiParameter
 
setType(MobyString) - Method in class org.inb.biomoby.shared.ontology.Parameter
 
setUnitTests(MobyUnitTest[]) - Method in class ca.ucalgary.services.util.MobySpecWrapper
 
setUnitTests(MobyUnitTest[]) - Method in class org.biomoby.shared.MobyService
 
setUp() - Method in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
Sets up the test fixture.
setupService(MobyService, MobyDataInstance, MobyRequestEventHandler) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Call the service given, or first launch a GUI to get missing input data if not provided in the MobyDataInstance.
setupServiceSecondaryData(MobyRequestEventHandler) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Called when the 'Execute Service' button in the secondary input dialog in pushed.
setUrl(URL) - Method in class org.biomoby.shared.extended.DataTypeParser
 
setUrl(String) - Method in class org.biomoby.shared.extended.DataTypeParser
 
setUrl(URL) - Method in class org.biomoby.shared.extended.NamespaceParser
 
setUrl(String) - Method in class org.biomoby.shared.extended.NamespaceParser
 
setUrl(URL) - Method in class org.biomoby.shared.extended.ServiceInstanceParser
 
setUrl(String) - Method in class org.biomoby.shared.extended.ServiceInstanceParser
 
setUrl(URL) - Method in class org.biomoby.shared.extended.ServiceTypeParser
 
setUrl(String) - Method in class org.biomoby.shared.extended.ServiceTypeParser
 
setURL(String) - Method in class org.biomoby.shared.MobyService
 
setURL(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.FindServiceOperation.Services.Service
 
setURL(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RegisterServiceOperation.RegisterService
 
setUrl(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveResourceURLsOperation.Resource
 
setUrl(String) - Method in class org.inb.biomoby.shared.registry.Resource
 
setUrl(String) - Method in class org.inb.biomoby.shared.registry.Service
 
setURN(String) - Method in class ca.ucalgary.seahawk.services.MobyComplexBuilder
Call in order to provide a unique ID for the rule, for reuse purposes.
setUser(String) - Method in class org.biomoby.client.MobyServiceLocator
Sets the user for authentication
setUserData(MobyDataInstance, URL, String, String, FilterSearch) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Record the PbE pertinent info about the data to the Moby data object so it can be tracked through the rest of the app.
setUserData(Object) - Method in interface org.biomoby.shared.data.MobyDataInstance
Allows developers to track their application-specific information alongside the Moby functionality.
setUserData(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
setUserData(Object) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
setUserData(Object) - Method in class org.biomoby.shared.MobyData
Allows developers to track their application-specific information alongside the Moby functionality.
setValidateServices(boolean) - Method in class de.mpg.mpiz_koeln.featureClient.FeatureClient
Sets whether the services which will be called, shall be validated if they are working.
setValidOutputXML(String) - Method in class org.biomoby.shared.MobyUnitTest
Setter: set the expected XML output for this serivce
setValidREGEX(String) - Method in class org.biomoby.shared.MobyUnitTest
Setter: set the regular expression for this unit test
setValidXPath(String) - Method in class org.biomoby.shared.MobyUnitTest
Setter: set the xpath expression for this unit test
setValue(String) - Method in class org.biomoby.service.dashboard.CommonNode
Change the meaning of this node.
setValue(Object) - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Assign a new value to this node (makes sense only for Biomoby primitive types).
setValue(boolean) - Method in class org.biomoby.shared.data.MobyDataBoolean
 
setValue(Boolean) - Method in class org.biomoby.shared.data.MobyDataBoolean
 
setValue(String) - Method in class org.biomoby.shared.data.MobyDataBoolean
Uses Boolean.valueOf(String) to convert to a Boolean object.
setValue(String) - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
setValue(CharSequence) - Method in class org.biomoby.shared.data.MobyDataString
 
setValue(String) - Method in class org.biomoby.shared.datatypes.MobyBoolean
Additionally to the same method in the superclass, it checks for boolean value - but it takes always everything, so no exception thrown.
setValue(String) - Method in class org.biomoby.shared.datatypes.MobyDateTime
Additionally to the same method in the superclass, it checks for a correct format.
setValue(String) - Method in class org.biomoby.shared.datatypes.MobyFloat
Additionally to the same method in the superclass, it checks for numerical value (its length is not limited - internaly it uses BigDecimal object).
setValue(String) - Method in class org.biomoby.shared.datatypes.MobyInteger
Additionally to the same method in the superclass, it checks for numerical and integer value (its length is not limited - internaly it uses BigInteger object).
setValue(String) - Method in class org.biomoby.shared.datatypes.MobyObject
Set a value of this object.
setValue(String) - Method in class org.biomoby.shared.parser.MobyParameter
Fill in a value of this parameter.
setValue(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceNamesOperation.ServiceName
 
setValue(String) - Method in class org.inb.biomoby.shared.message.MobyParameter
 
setValue(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ElementFloat
 
setValue(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.ElementInteger
 
setValue(MobyString) - Method in class org.inb.biomoby.shared.ontology.ElementString
 
setValue(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.ElementXYData
 
setValue(MobyString) - Method in class org.inb.biomoby.shared.ontology.Parameter
 
setValue(String) - Method in class org.inb.wsrf.bf2.BaseFaultType.Description
 
setValueAt(Object, Object, int) - Method in class org.biomoby.service.dashboard.data.DataTypeModel
 
setValueAt(Object, int, int) - Method in class org.biomoby.service.dashboard.TableSorter
 
setValueAt(Object, Object, int) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
setValueAt(Object, Object, int) - Method in interface org.biomoby.service.dashboard.treetable.TreeTableModel
Sets the value for node node, at column number column.
setValueAt(Object, int, int) - Method in class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
setValueAt(Object, int, int) - Method in class org.inb.biomoby.central.gui.model.MobyObjectPropertiesTableModel
 
setValueAt(Object, int, int) - Method in class org.inb.biomoby.central.gui.model.MobyPropertiesTableModel
 
setValues(String) - Method in class org.biomoby.service.dashboard.data.ServiceInputPanel
 
setValueXML(String) - Method in class org.biomoby.shared.datatypes.MobyObject
Set a value of this object.
setVariance(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.Parameters4Values
 
setVariance(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.TargetArgument
 
setVerbose(boolean) - Method in class org.biomoby.service.dashboard.RegistryModel
 
setVerboseEventName(String) - Method in class org.biomoby.service.dashboard.CommonConsole
Remember what event name will be considered by this instance for its verbose messages.
setVerboseMode(boolean) - Method in class org.biomoby.service.dashboard.CommonConsole
 
setVisible(boolean) - Method in class ca.ucalgary.seahawk.gui.ServiceSearchDialog
 
setVisible(boolean) - Method in class ca.ucalgary.seahawk.util.DynamicJPopupMenu
 
setWaitScreen() - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
setWeakConnection(boolean) - Method in class org.biomoby.client.ServicesEdge
Sets quality of this connection.
setWeight(MobyInteger) - Method in class org.inb.biomoby.shared.ontology.CommentedWeightedObject
 
setWeightedObject(WeightedObject) - Method in class org.inb.biomoby.shared.ontology.WeightedAminoAcidSequences
 
setWidth(int) - Method in interface org.inb.biomoby.client.gui.ISequenceCoordinateTransformer
 
setWidth(int) - Method in class org.inb.biomoby.client.gui.SequenceTransformerBean
 
setWrappingEnabled(boolean) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
setWSDL(String) - Method in class org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceOperation.ServiceTemplate
 
setWSDL(String) - Method in class org.inb.biomoby.shared.registry.ServiceType
 
setWsrf(boolean) - Method in class org.soap.SOAPFault
 
setWsrfFault(WSRFFault) - Method in class org.soap.SOAPFault
 
setX__corr(MobyFloat) - Method in class org.inb.biomoby.shared.ontology.LutefiskAnnotation
 
setXMLAttribute(Element, String, String) - Static method in class org.biomoby.shared.parser.MobyPackage
Set attribute 'name' to 'value' in a jDOM XML element, equipped with the BioMoby namespace.
setXMLAttributeForced(Element, String, String) - Static method in class org.biomoby.shared.parser.MobyPackage
Set attribute 'name' to 'value' in a jDOM XML element, equipped with the BioMoby namespace.
setXmlMode(int) - Method in class org.biomoby.shared.data.MobyContentInstance
 
setXmlMode(int) - Method in interface org.biomoby.shared.data.MobyDataInstance
Determined whether toXML will return a Central template value or a service call instance value.
setXmlMode(int) - Method in class org.biomoby.shared.data.MobyDataObject
Determined whether toXML will return a Central template value or a service call instance value.
setXmlMode(int) - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
setXmlMode(int) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Determined whether toXML will return a Central template value or a service call instance value.
setXmlMode(int) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
setXmlMode(int) - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
setXmlMode(int) - Method in class org.biomoby.shared.data.MobyDataXref
If the XML mode is one of the constants defined by MobyDataInstance, this method calls its superclass equivalent (i.e. acts and prints like a Moby Object).
setXrefs(MobyXref[]) - Method in class org.biomoby.shared.datatypes.MobyObject
Attach cross references to this object.
setXrefType(String) - Method in class org.biomoby.shared.data.MobyDataXref
At the moment, no check is made for the validity of the type string in the cross reference ontology, mostly because I don't know how to access it properly.
setXrefType(String) - Method in class org.biomoby.shared.datatypes.MobyXref
Set a semantic type of this cross reference.
setXtitle(MobyString) - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
setYtitle(MobyString) - Method in class org.inb.biomoby.shared.ontology.ArrayXYData
 
SEVERE - Static variable in class org.biomoby.registry.rdfagent.util.Log
log severe messages
severe(String) - Static method in class org.biomoby.registry.rdfagent.util.Log
 
SEVERITY - Static variable in interface org.biomoby.shared.parser.MobyTags
 
SEVERITY_ERROR_STR - Static variable in exception org.biomoby.shared.data.MobyServiceException
 
SEVERITY_INFO_STR - Static variable in exception org.biomoby.shared.data.MobyServiceException
 
SEVERITY_UNKNOWN - Static variable in exception org.biomoby.shared.data.MobyServiceException
 
SEVERITY_WARNING_STR - Static variable in exception org.biomoby.shared.data.MobyServiceException
 
severityStringToSeverityInt(String) - Static method in exception org.biomoby.shared.data.MobyServiceException
Converts an error code string to an integer defined in ServiceException, or ERROR_CODE_UNKNOWN if the code is not a standard one (3 digits and part of RFC 1863).
shouldIntercept(HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
Lets the WrappingServlet know if the HTTP GET request should be handles by interceptRequest or not.
shouldIntercept(HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
 
show() - Method in class org.biomoby.service.dashboard.Dashboard
Show the main frame.
showDialog(Component, String, Date) - Static method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Shows a modal date-time chooser dialog and blocks until the dialog is hidden.
showDialog(Component, String, DateTimeChooser) - Static method in class org.biomoby.service.dashboard.chooser.DateTimeChooser
Shows a modal date-time chooser dialog and blocks until the dialog is hidden.
showFileOpenDialog(MobyContentGUI, boolean) - Static method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
showHelpTab() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
showMenuItem(JMenu, Vector<JMenuItem>, Robot) - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
showWebDialog(boolean) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
SIAM_Annotation_XML - Class in org.inb.biomoby.shared.ontology
 
SIAM_Annotation_XML() - Constructor for class org.inb.biomoby.shared.ontology.SIAM_Annotation_XML
 
SigcleaveAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
SigcleaveAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.SigcleaveAnnotatedAASequence
 
SigcleaveAnnotatedAASequenceComponent<T extends SigcleaveAnnotatedAASequence> - Class in org.inb.biomoby.client.gui.ontology
 
SigcleaveAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
SigcleaveAnnotatedAASequenceComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.SigcleaveAnnotatedAASequenceComponent
 
SigcleaveAnnotatedAASequenceComponent.SigcleaveAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
SigcleaveAnnotation - Class in org.inb.biomoby.shared.ontology
 
SigcleaveAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.SigcleaveAnnotation
 
SigcleaveAnnotationListPane<T extends SigcleaveAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
SigcleaveAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.SigcleaveAnnotationListPane
 
SigcleaveAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.SigcleaveAnnotationListPane
 
SigcleaveReport - Class in org.inb.biomoby.shared.ontology
 
SigcleaveReport() - Constructor for class org.inb.biomoby.shared.ontology.SigcleaveReport
 
SigcleaveReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
SigcleaveReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
SigcleaveReportComponent(SigcleaveReport) - Constructor for class org.inb.biomoby.client.gui.ontology.SigcleaveReportComponent
 
SigcleaveReportComponent.SigcleaveReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
SIGNAL_CANCEL_DATA_TYPES - Static variable in interface org.biomoby.shared.event.Notifier
 
SIGNAL_CANCEL_NAMESPACES - Static variable in interface org.biomoby.shared.event.Notifier
 
SIGNAL_CANCEL_SERVICE_TYPES - Static variable in interface org.biomoby.shared.event.Notifier
 
SIGNAL_CANCEL_SERVICES - Static variable in interface org.biomoby.shared.event.Notifier
 
SignatureURL - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
SignatureURLConnection - Class in org.biomoby.registry.rdfagent.util
This class retrieves the RDF from a url.
SignatureURLConnection() - Constructor for class org.biomoby.registry.rdfagent.util.SignatureURLConnection
Constructor
Simple - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
SIMPLE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
Simple - Class in org.inb.biomoby.shared.registry
 
Simple() - Constructor for class org.inb.biomoby.shared.registry.Simple
 
SIMPLE_CONNECTION - Static variable in class org.biomoby.client.ServicesEdge
 
SimpleAnt - Class in org.biomoby.service.dashboard
A wrapper that invokes Ant on a build.xml file in the current directory.
SimpleAnt() - Constructor for class org.biomoby.service.dashboard.SimpleAnt
Default constructor.
SimpleArticle - Static variable in class org.biomoby.client.rdf.vocabulary.MobyResources
Deprecated. Replaced by Predicates.Simple. The reason is that this property should not be under a different RDF document URI
SimpleCache - Interface in org.biomoby.client
An interface defining basic operation for caching data.
simpleClassName(String) - Static method in class org.biomoby.shared.Utils
Return just the last part of a Java class name (after the last dot).
SimpleClientPanel - Class in org.biomoby.service.dashboard
A panel allowing to formulate input data and to call an arbitrary Biomoby service.
SimpleClientPanel() - Constructor for class org.biomoby.service.dashboard.SimpleClientPanel
Default constructor.
SimpleFileCache - Interface in org.biomoby.client
An interface extending basic operations for caching data by pointing users directly to files with cached objects or for cached objects.
SimpleListener - Class in org.biomoby.shared.event
A simple implementation of a NotificationListener that prints all intercepted messages on standard output, or to the given output stream.
SimpleListener() - Constructor for class org.biomoby.shared.event.SimpleListener
Default constructor.
SimpleListener(PrintStream) - Constructor for class org.biomoby.shared.event.SimpleListener
A constructor directing messages to the given output stream.
simpleParameter - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
simpleParameter - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
simpleServiceName - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
simplifyParamName(String, Map<String, String>) - Static method in class ca.ucalgary.services.util.RuleCreator
Turns a complex xpath-based parameter name into something a moby user won't be afraid of Since the XPath is passd between the PBE system and the Daggoo registration engine, they should both cal this method to coordinate on Moby parameter names.
SINGLE_RETURNED_VALUE_KEY - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
SingletonApplication - Class in ca.ucalgary.util
Utility to launch a Java application if not running, or pass a new file for opening if the app is already open (per user).
SingletonApplication() - Constructor for class ca.ucalgary.util.SingletonApplication
 
size() - Method in class ca.ucalgary.services.util.SourceMap
Reports the number of data members in the composite object
size() - Method in class org.biomoby.service.dashboard.renderers.RendererRegistry
How many renderers are available.
size() - Method in class org.biomoby.shared.data.MobyContentInstance
Reports the number of queries
size() - Method in class org.biomoby.shared.data.MobyDataComposite
Reports the number of data members in the composite object
size() - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
size() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
size() - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns the number of elements in this list.
size() - Method in class org.biomoby.shared.parser.MobyJob
Return a number of data elements contained in this job.
size() - Method in class org.biomoby.shared.parser.MobyPackage
Return the number of jobs (queries) contained in this package.
size() - Method in class org.inb.biomoby.shared.message.MobyCollection
 
size() - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
SMTP_ENABLE - Static variable in class org.biomoby.registry.rdfagent.util.Constants
Should the agent try to email using smtp?
SMTP_LOGIN - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The smtp login.
SMTP_PSWD - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The smtp password.
SMTP_SERVER - Static variable in class org.biomoby.registry.rdfagent.util.Constants
The address of the smtp server.
SOAP_ENC_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
SOAP_ENC_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
SOAPException - Exception in org.biomoby.shared
This class is meant to be a implementation-independent wrapper around the exception classes provided by the underlying SOAP client used to run MOBY services.
SOAPException(String) - Constructor for exception org.biomoby.shared.SOAPException
 
SOAPFault - Class in org.soap
A class to represent a SOAP fault
SOAPFault() - Constructor for class org.soap.SOAPFault
 
SOAPFaultParser - Class in org.soap.sax
 
SOAPFaultParser() - Constructor for class org.soap.sax.SOAPFaultParser
 
SOAPFaultTestCase - Class in org.soap.sax.test
 
SOAPFaultTestCase(String) - Constructor for class org.soap.sax.test.SOAPFaultTestCase
 
SoapServlet - Class in ca.ucalgary.services
Provides an HTML interface for invoking SOAP-based Web Services.
SoapServlet() - Constructor for class ca.ucalgary.services.SoapServlet
 
SoapServletTestCase - Class in ca.ucalgary.services.test
 
SoapServletTestCase(String) - Constructor for class ca.ucalgary.services.test.SoapServletTestCase
 
SOFTWARECOMMENT - Static variable in interface org.biomoby.shared.parser.MobyTags
 
SOFTWARENAME - Static variable in interface org.biomoby.shared.parser.MobyTags
 
SOFTWAREVERSION - Static variable in interface org.biomoby.shared.parser.MobyTags
 
sortServicesByName(MobyService[]) - Method in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
SourceMap - Class in ca.ucalgary.services.util
Converts a Map of Strings into a Source for the Java SOAP libraries.
SourceMap(QName, String) - Constructor for class ca.ucalgary.services.util.SourceMap
 
SPEC_URL - Static variable in interface ca.ucalgary.services.Registration
 
splash(Image, String) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Open's a splash window using the specified image and title
splash(Image) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Open's a splash window using the specified image
splash(URL, String) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Open's a splash window using the specified image URL and title
splash(URL) - Static method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Open's a splash window using the specified image URL
splash(Image, String) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Open's a splash window using the specified image and title
splash(Image) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Open's a splash window using the specified image
splash(URL, String) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Open's a splash window using the specified image URL and title
splash(URL) - Static method in class ca.ucalgary.seahawk.util.SplashWindow
Open's a splash window using the specified image URL
SplashScreenStatus - Class in org.biomoby.client.util
Simple util other BioMoby classes can use to set the status of a splash screen, if one is present in an application and reads this status to keep the user imformed (e.g. ca.ucalgary.seahawk.gui.MobyContentGUI).
SplashScreenStatus() - Constructor for class org.biomoby.client.util.SplashScreenStatus
 
SplashWindow - Class in ca.ucalgary.seahawk.gui.splash
A Splash window.
SplashWindow - Class in ca.ucalgary.seahawk.util
A Splash window.
SRC_PARAM - Static variable in class ca.ucalgary.services.WrappingServlet
 
SRV_PREFIX - Static variable in class org.biomoby.shared.LSIDResolver
 
stackTraceIfSerious(Throwable) - Static method in class org.biomoby.shared.Utils
Return a stringified version of the given exception, containing - for more serious errors, such as NullPointerException - also a stack trace.
start(MobyRequestEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Called by MOBYRequest when the service request is being sent.
start(MobyRequestEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
Called by MOBYRequest when the service request is being sent.
start(MobyRequestEvent) - Method in class ca.ucalgary.seahawk.gui.MobyShimmer
 
start() - Method in class ca.ucalgary.seahawk.gui.splash.SeahawkSplasher
 
start() - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
start(int) - Method in class ca.ucalgary.seahawk.services.IterativeMatchResult
 
start(String) - Method in class org.biomoby.client.GraphsServlet
 
start(MobyRequestEvent) - Method in interface org.biomoby.client.MobyRequestEventHandler
If a client, denotes that a service request has been sent (and the contents is exactly what is being sent to the service).
start(String, Level, boolean, String) - Static method in class org.biomoby.registry.rdfagent.util.Log
 
start() - Method in class org.biomoby.service.dashboard.SwingWorker
Start the worker thread.
start - Variable in class org.inb.biomoby.client.gui.ontology.GenericSubsequenceComponent.GenericSubsequence
 
start(WSWebServiceContext, WSEndpoint) - Method in class org.inb.biomoby.service.resolver.WSRFResourceInstanceResolver
 
startAnt(String[], Properties) - Method in class org.biomoby.service.dashboard.SimpleAnt
Start Ant to execute given targets, possibly using additional properties.
startDocument() - Method in class org.biomoby.shared.parser.MobyParser
Called at the beginning of the parsed document.
startDocument() - Method in class org.omg.lsae.sax.EventParser
Called at the beginning of the parsed document.
startDocument() - Method in class org.soap.sax.SOAPFaultParser
Called at the beginning of the parsed document.
startDocument() - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Called at the beginning of the parsed document.
startElement(String, String, String, Attributes) - Method in class org.biomoby.shared.parser.MobyParser
Called when an element starts.
startElement(String, String, String, Attributes) - Method in class org.inb.biomoby.generator.TemplateFilter
 
startElement(String, String, String, Attributes) - Method in class org.omg.lsae.sax.EventParser
Called when an element starts.
startElement(String, String, String, Attributes) - Method in class org.soap.sax.SOAPFaultParser
Called when an element starts.
startElement(String, String, String, Attributes) - Method in class org.w3c.addressing.sax.EndpointReferenceParser
Called when an element starts.
startRecording(HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
Tells the data recorder that a new Web Service proxying has been requested.
startRecording(HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
 
STATE - Static variable in interface org.omg.lsae.sax.LsaeTags
 
stateChanged(ChangeEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
stateChanged(ChangeEvent) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
stateChanged(ChangeEvent) - Method in class org.biomoby.service.dashboard.Dashboard
Dashboard is listening to the changes of panels in order to repaint the header with a label of a currently selected panel.
stateChanged(ChangeEvent) - Method in class org.biomoby.service.dashboard.ResultsPanel
Called when a new tab was selected.
stateChanged(ChangeEvent) - Method in class org.biomoby.service.dashboard.UnitTestingResultPanel
Called when a new tab was selected.
stateChanged(ChangeEvent) - Method in class org.inb.biomoby.central.gui.AbstractEntityTreePanel
 
StateChanged - Class in org.inb.lsae
 
StateChanged() - Constructor for class org.inb.lsae.StateChanged
 
StateChanged.STATE - Enum in org.inb.lsae
 
StateEvent - Class in org.omg.lsae.notifications
 
StateEvent() - Constructor for class org.omg.lsae.notifications.StateEvent
 
StatisticsPanel - Class in org.biomoby.service.dashboard
A panel showing various statistics.
StatisticsPanel() - Constructor for class org.biomoby.service.dashboard.StatisticsPanel
Default constructor.
StatusBar - Class in org.inb.swing
StatusBar component implementation.
StatusBar() - Constructor for class org.inb.swing.StatusBar
 
StatusBarHandler - Class in org.inb.biomoby.generator.gui
 
StatusBarHandler(StatusBar) - Constructor for class org.inb.biomoby.generator.gui.StatusBarHandler
 
STEP - Static variable in interface org.omg.lsae.sax.LsaeTags
 
StepEvent - Class in org.omg.lsae.notifications
 
StepEvent() - Constructor for class org.omg.lsae.notifications.StepEvent
 
StepProgress - Class in org.inb.lsae
 
StepProgress() - Constructor for class org.inb.lsae.StepProgress
 
Stockholm_Text - Class in org.inb.biomoby.shared.ontology
 
Stockholm_Text() - Constructor for class org.inb.biomoby.shared.ontology.Stockholm_Text
 
Stockholm_TextComponent - Class in org.inb.biomoby.client.gui.ontology
 
Stockholm_TextComponent(Stockholm_Text) - Constructor for class org.inb.biomoby.client.gui.ontology.Stockholm_TextComponent
 
stop(MobyRequest, int) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
stop(MobyRequest, int) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
stop(MobyRequest, int) - Method in class ca.ucalgary.seahawk.gui.MobyShimmer
If a client, denotes the end of a service request.
stop() - Method in class ca.ucalgary.seahawk.gui.splash.SeahawkSplasher
 
stop(MobyRequest, int) - Method in interface org.biomoby.client.MobyRequestEventHandler
If a client, denotes the end of a service request.
stop(String) - Static method in class org.biomoby.registry.rdfagent.util.Log
A method to stop logging.
stopCellEditing() - Method in class org.inb.biomoby.central.gui.renderer.ClassNameTreeCellEditor
 
stopCellEditing() - Method in class org.inb.biomoby.central.gui.renderer.PropertyNameTableCellEditor
 
stopServletContainer() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
Explicitly stop the servlet container, if running, that is used for WSDL service wrapping.
straightDataPaths(DataServiceEdge[], ServicesEdge[], DataServiceEdge[]) - Static method in class org.biomoby.client.FilterServices
Find all paths (using available 'edges') that start by any of the 'startingEdges' and finish by any of the 'endingEdges'.
STRING - Static variable in class org.biomoby.shared.schema.MElement
A moby:String primitive type
STRING_TYPE - Static variable in class org.biomoby.shared.MobySecondaryData
 
StringBufferServletOutputStream - Class in org.biomoby.service.test
 
StringBufferServletOutputStream() - Constructor for class org.biomoby.service.test.StringBufferServletOutputStream
 
StringPainter - Class in org.inb.biomoby.client.gui
 
StringPainter.ALIGNMENT - Enum in org.inb.biomoby.client.gui
 
stringToPrimaryDataTemplate(String, Map<String, MobyDataTypeTemplate>) - Static method in class org.biomoby.service.MobyServlet
Strings have the form name:objectType:namespace, with ":namespace" optional If the input is expected to be a Collection, then the syntax is name:Collection(objectType):namespace
stringToSecondaryDataTemplate(String) - Static method in class org.biomoby.service.MobyServlet
Strings have the form name:paramType:default:spec where spec depends on the parameter type.
StructuralComponent - Static variable in class org.biomoby.client.rdf.vocabulary.Predicates
 
Structure_Alignment_Report - Class in org.inb.biomoby.shared.ontology
 
Structure_Alignment_Report() - Constructor for class org.inb.biomoby.shared.ontology.Structure_Alignment_Report
 
StructureBoundaries - Class in org.inb.biomoby.shared.ontology
 
StructureBoundaries() - Constructor for class org.inb.biomoby.shared.ontology.StructureBoundaries
 
StructureBoundariesComponent - Class in org.inb.biomoby.client.gui.ontology
 
StructureBoundariesComponent(StructureBoundaries) - Constructor for class org.inb.biomoby.client.gui.ontology.StructureBoundariesComponent
 
StructureBoundariesListPane<T extends StructureBoundaries> - Class in org.inb.biomoby.client.gui.auxiliary
 
StructureBoundariesListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.StructureBoundariesListPane
 
StructureBoundariesListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.StructureBoundariesListPane
 
StructureDomain - Class in org.inb.biomoby.shared.ontology
 
StructureDomain() - Constructor for class org.inb.biomoby.shared.ontology.StructureDomain
 
StructureDomainComponent<T extends StructureDomain> - Class in org.inb.biomoby.client.gui.ontology
 
StructureDomainComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.StructureDomainComponent
 
StructureFragment - Class in org.inb.biomoby.shared.ontology
 
StructureFragment() - Constructor for class org.inb.biomoby.shared.ontology.StructureFragment
 
StructureFragmentComponent - Class in org.inb.biomoby.client.gui.ontology
 
StructureFragmentComponent(StructureFragment) - Constructor for class org.inb.biomoby.client.gui.ontology.StructureFragmentComponent
 
StructureFragmentListPane - Class in org.inb.biomoby.client.gui.auxiliary
 
StructureFragmentListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.StructureFragmentListPane
 
StructureFragmentListPane(List<StructureFragment>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.StructureFragmentListPane
 
subList(int, int) - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns a view of the portion of this list between the specified fromIndex, inclusive, and toIndex, exclusive.
subList(int, int) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
subList(int, int) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
submit(MobyMessage) - Method in class org.inb.biomoby.service.AbstractAsyncMobyService
 
submit(MobyMessage) - Method in interface org.inb.biomoby.service.IAsyncMobyImpl
 
SUBMIT_ACTION_SUFFIX - Static variable in class org.biomoby.shared.MobyService
A suffix added to a service name in order to make a method name that submits input to an asynchronous service.
SUBMIT_ANONYMOUS_NAME - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
SUBMIT_DATATYPE - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
SUBMIT_DEFAULT_VALUE - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
SubmitResponseWrapper - Class in org.inb.biomoby.shared.wsrf
 
SubmitResponseWrapper() - Constructor for class org.inb.biomoby.shared.wsrf.SubmitResponseWrapper
 
SubmitResponseWrapper(W3CEndpointReference) - Constructor for class org.inb.biomoby.shared.wsrf.SubmitResponseWrapper
 
SubmitResponseWrapper.Body - Class in org.inb.biomoby.shared.wsrf
 
SubmitResponseWrapper.Body() - Constructor for class org.inb.biomoby.shared.wsrf.SubmitResponseWrapper.Body
 
Subsequence - Class in org.inb.biomoby.client.gui
 
Subsequence() - Constructor for class org.inb.biomoby.client.gui.Subsequence
 
subSequence(int, int) - Method in class org.inb.biomoby.client.gui.Subsequence
 
subtract(Number) - Method in class org.biomoby.shared.data.MobyDataFloat
Subtract a specified number from the data value.
subtract(Number) - Method in class org.biomoby.shared.data.MobyDataInt
Perform the subtraction operand on the data value.
succeeded(String) - Method in class ca.ucalgary.seahawk.gui.MobyContentPane
 
suggestValueXPathsFromSelectionXPath(String, Node) - Static method in class ca.ucalgary.services.util.RuleCreator
 
suite() - Static method in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
suite() - Static method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
suite() - Static method in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
suite() - Static method in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
suite() - Static method in class ca.ucalgary.seahawk.services.test.TextClientTestCase
 
suite() - Static method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
suite() - Static method in class ca.ucalgary.services.test.ACDServiceTestCase
 
suite() - Static method in class ca.ucalgary.services.test.CGIServiceTestCase
 
suite() - Static method in class ca.ucalgary.services.test.LegacyServiceTestCase
 
suite() - Static method in class ca.ucalgary.services.test.SoapServletTestCase
 
suite() - Static method in class ca.ucalgary.services.test.WSDLServiceTestCase
 
suite() - Static method in class ca.ucalgary.services.util.test.ACDFileTestCase
 
suite() - Static method in class ca.ucalgary.services.util.test.WSDLConfigTestCase
 
suite() - Static method in class ca.ucalgary.services.util.test.XHTMLFormTestCase
 
suite() - Static method in class org.biomoby.client.test.AsyncClientTestCase
 
suite() - Static method in class org.biomoby.service.test.MobyServletTestCase
 
suite() - Static method in class org.biomoby.shared.data.test.MobyDataDateTimeTestCase
 
suite() - Static method in class org.biomoby.shared.test.LSIDResolverTestCase
 
suite() - Static method in class org.biomoby.shared.test.MobyNamespaceTestCase
 
suite() - Static method in class org.omg.lsae.sax.test.AnalysisEventTestCase
 
suite() - Static method in class org.soap.sax.test.SOAPFaultTestCase
 
SVC_ID - Static variable in interface org.w3c.addressing.sax.EprTags
 
SwingWorker - Class in org.biomoby.service.dashboard
This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class org.biomoby.service.dashboard.SwingWorker
Start a thread that will call the construct method and then exit.
SwissProt_Text - Class in org.inb.biomoby.shared.ontology
 
SwissProt_Text() - Constructor for class org.inb.biomoby.shared.ontology.SwissProt_Text
 
synchronizeCentrals(T[], T[]) - Method in class org.biomoby.registry.sync.handler.AbstractMobyHandler
Synchronize the two centrals.

T

T2FLOW - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
T2FLOW_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
T2FLOW_DISPATCHXML - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
T2FLOW_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
T2FLOW_LISTFLATTEN_BEANSHELL - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
T2FLOW_NS - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
T2FLOW_PASSFILTER_BEANSHELL - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
T2FLOW_REGEXFILTER_BEANSHELL - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
T2FLOW_XPATHFILTER_BEANSHELL - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
TAB_TOOLTIP - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
TABBED_PANE_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
TabCollectionRenderer - Class in org.biomoby.service.dashboard.renderers
This is not a normal renderer that is loaded and used through SPI.
TabCollectionRenderer(Renderer) - Constructor for class org.biomoby.service.dashboard.renderers.TabCollectionRenderer
 
tableChanged(TableModelEvent) - Method in class org.inb.biomoby.central.gui.AbstractMobyPropertyTable
 
TableSorter - Class in org.biomoby.service.dashboard
TableSorter is a decorator for TableModels; adding sorting functionality to a supplied TableModel.
TableSorter() - Constructor for class org.biomoby.service.dashboard.TableSorter
 
TableSorter(TableModel) - Constructor for class org.biomoby.service.dashboard.TableSorter
 
TableSorter(TableModel, JTableHeader) - Constructor for class org.biomoby.service.dashboard.TableSorter
 
TAIL_COLLECTION_CONNECTION - Static variable in class org.biomoby.client.ServicesEdge
 
tAreaIcon - Static variable in class org.biomoby.service.dashboard.data.DataTypeTreeTable
 
Target - Class in org.inb.biomoby.shared.ontology
 
Target() - Constructor for class org.inb.biomoby.shared.ontology.Target
 
TARGET_NSURI_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
TargetArgument - Class in org.inb.biomoby.shared.ontology
 
TargetArgument() - Constructor for class org.inb.biomoby.shared.ontology.TargetArgument
 
TAS - Static variable in class org.biomoby.shared.data.MobyDataXref
 
task - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
task - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
Taverna - Class in org.biomoby.client
A utility class that understands how to create workflow definitions for Taverna.
Taverna() - Constructor for class org.biomoby.client.Taverna
 
TAVERNA15 - Static variable in class ca.ucalgary.seahawk.util.DataFlowRecorder
 
TEMP_DIR_PROP - Static variable in class ca.ucalgary.seahawk.util.SeahawkOptions
 
TEMP_FILE_PREFIX - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
TempDir - Class in ca.ucalgary.services.util
Provides a facility to generate a temporary directory that can be automaticallly deleted on program exit.
TempDir() - Constructor for class ca.ucalgary.services.util.TempDir
 
TemplateFilter - Class in org.inb.biomoby.generator
 
TemplateFilter(XMLReader) - Constructor for class org.inb.biomoby.generator.TemplateFilter
 
TemplateInputStream - Class in org.inb.util
 
TemplateInputStream(InputStream, Map) - Constructor for class org.inb.util.TemplateInputStream
 
TERMINATED_BY_ERROR - Static variable in class org.omg.lsae.notifications.StateEvent
 
TERMINATED_BY_REQUEST - Static variable in class org.omg.lsae.notifications.StateEvent
 
TEST_CAPGRP1 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP2 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP2_1 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP2_2 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP2_3 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP3_RANGE_END - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP3_RANGE_START - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP4_RANGE_END - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP4_RANGE_START - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP5_RANGE_END - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_CAPGRP5_RANGE_START - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_DATA1 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_DATA2 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_HASDATA - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_HASDATA_CLASSNAME - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_HASDATA_MEMBERNAME - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_HASDATA_MEMBERS1_CLASS - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_HASDATA_MEMBERS1_COUNT - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_HASDATA_MEMBERS2_COUNT - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_HASDATA_NUMOBJS - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_INHERIT_CLASSNAME - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_INHERIT_NUMOBJS - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_INHERITMEMBER_CLASSNAME - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_INHERITMEMBER_NUMOBJS - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_INHERITMEMBER_RESOURCE - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_INPUT_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
TEST_REGEX1 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_REGEX2 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_REGEX3 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_REGEX4 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_REGEX5 - Static variable in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
TEST_RULES_RESOURCE1 - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_RULES_RESOURCE2 - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_RULES_RESOURCE3 - Static variable in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
TEST_XPATH_PARAM - Static variable in interface ca.ucalgary.services.Registration
 
testAsync() - Method in class org.biomoby.service.test.MobyServletTestCase
 
testBinaryRegex() - Method in class ca.ucalgary.services.test.LegacyServiceTestCase
Loads a binary file, then tests it against a regex, creates a MOBY object, and then the new object is compared to the original file data (they should be identical byte arrays.
testCall() - Method in class org.biomoby.client.test.AsyncClientTestCase
 
testCaptureGroupExtraction() - Method in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
testCaptureGroupQuantifier() - Method in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
Ensure that extraction of capture groups, including their quantifier, works.
testCentralEuropeTimes() - Method in class org.biomoby.shared.data.test.MobyDataDateTimeTestCase
 
testClipboardTab() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testCloseOtherTabs() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testCloseTab() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testCorrectMobyClientBasedInvocation() - Method in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
Tries to use the Bluejay MobyClient to find services based on XPath mapping in a document's contents to MOBY types, then invoke the service on the XPath results.
testCorrectMobyServiceInvocationCollection() - Method in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
Tries to run a service that returns a Collection type.
testCorrectMobyServiceInvocationSimple() - Method in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
Tries to run a service that returns Simples.
testDaggoo() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testDataRecorderAutoLoad() - Method in class ca.ucalgary.services.test.SoapServletTestCase
 
testDataResolutionHTTP() - Method in class org.biomoby.shared.test.LSIDResolverTestCase
 
testDataVersionlessResolutionHTTP() - Method in class org.biomoby.shared.test.LSIDResolverTestCase
 
testDragnDrop() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
Checks that SeahawkTransferable works
TESTED - Static variable in class org.biomoby.shared.MobyService
 
testExcelFileConversion() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
TestException - Exception in org.biomoby.registry.rdfagent.test
I always wanted my own exception ;-)
TestException() - Constructor for exception org.biomoby.registry.rdfagent.test.TestException
 
TestException(String) - Constructor for exception org.biomoby.registry.rdfagent.test.TestException
 
testExternalBrowser() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testExternalLinks() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testHelpButton() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testHelpTab() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testHighlightOptions() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testHTML() - Method in class org.biomoby.service.test.MobyServletTestCase
 
TestHttpServletRequest - Class in org.biomoby.service.test
 
TestHttpServletRequest() - Constructor for class org.biomoby.service.test.TestHttpServletRequest
 
TestHttpServletResponse - Class in org.biomoby.service.test
 
TestHttpServletResponse() - Constructor for class org.biomoby.service.test.TestHttpServletResponse
 
testIdentity() - Method in class org.biomoby.shared.data.test.MobyDataDateTimeTestCase
 
testIOSpecsDocumentLiteral() - Method in class ca.ucalgary.services.util.test.WSDLConfigTestCase
 
testIOSpecsRPCEncoded() - Method in class ca.ucalgary.services.util.test.WSDLConfigTestCase
 
testLogic() - Method in class ca.ucalgary.services.util.test.XHTMLFormTestCase
See if the values for the parameters are correctly noted (i.e. rules of overriding and defaults are properly applied when combining the HTML spec and the Moby spec).
testLSAE() - Method in class org.omg.lsae.sax.test.AnalysisEventTestCase
 
testLSIDParsing() - Method in class org.biomoby.shared.test.LSIDResolverTestCase
 
testMain() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testMain() - Method in class org.biomoby.service.test.MobyServletTestCase
 
testMemberInheritance() - Method in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
testMetadata() - Method in class ca.ucalgary.services.util.test.WSDLConfigTestCase
 
testMetaData() - Method in class ca.ucalgary.services.util.test.XHTMLFormTestCase
See if the meta data for the service is parsed correctly
testMetadataInvalidResolutionHTTP() - Method in class org.biomoby.shared.test.LSIDResolverTestCase
 
testMetadataNonResolutionHTTP() - Method in class org.biomoby.shared.test.LSIDResolverTestCase
 
testMetadataResolutionHTTP() - Method in class org.biomoby.shared.test.LSIDResolverTestCase
 
testMetadataVersionlessResolutionHTTP() - Method in class org.biomoby.shared.test.LSIDResolverTestCase
 
testMobyTypes - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
testNamespaceRetrieval() - Method in class org.biomoby.shared.test.MobyNamespaceTestCase
Sees if a namspace that should exist is actually retrievable from Moby Central
testNavigationButtons() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testNewfoundlandTime() - Method in class org.biomoby.shared.data.test.MobyDataDateTimeTestCase
Interesting because offset is GMT-3.5 (a half-hour time zone).
testNode - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
testOpenButton() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testParsingBasic() - Method in class ca.ucalgary.services.util.test.ACDFileTestCase
 
testParsingBasic() - Method in class ca.ucalgary.services.util.test.WSDLConfigTestCase
See if the xhtml and moby spec class values are properly parsed
testParsingBasic() - Method in class ca.ucalgary.services.util.test.XHTMLFormTestCase
See if the xhtml and moby spec class values are properly parsed
testParsingSubsections() - Method in class ca.ucalgary.services.util.test.ACDFileTestCase
 
testParsingVariable() - Method in class ca.ucalgary.services.util.test.ACDFileTestCase
 
testPreviousOutputRecovery() - Method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
testPrint() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testRDF() - Method in class org.biomoby.service.test.MobyServletTestCase
 
testRegexAssumptions() - Method in class ca.ucalgary.seahawk.services.test.RegexParserTestCase
 
testRegexHASRelation() - Method in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
testRegexInheritance() - Method in class ca.ucalgary.seahawk.services.test.MobyClientTestCase
 
testRequestChain() - Method in class org.biomoby.service.test.MobyServletTestCase
 
testRunAsynchronousService() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testRunServiceSecondariesAndWorkflow() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testSave() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testSaveInput() - Method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
testSaveOutput() - Method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
testSecondariesRecovery() - Method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
testSecondaryParams() - Method in class org.biomoby.service.test.MobyServletTestCase
 
testServiceRecovery() - Method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
TestServletConfig - Class in org.biomoby.service.test
 
TestServletConfig(String, ServletContext) - Constructor for class org.biomoby.service.test.TestServletConfig
 
TestServletConfig(ServletContext, URL) - Constructor for class org.biomoby.service.test.TestServletConfig
 
TestServletContext - Class in org.biomoby.service.test
 
TestServletContext() - Constructor for class org.biomoby.service.test.TestServletContext
 
testServletTester() - Method in class org.biomoby.service.test.MobyServletTestCase
 
testSimpleToText() - Method in class ca.ucalgary.seahawk.services.test.TextClientTestCase
 
testSOAP() - Method in class org.omg.lsae.sax.test.AnalysisEventTestCase
 
testSOAP() - Method in class org.soap.sax.test.SOAPFaultTestCase
 
testSoapParsing() - Method in class org.biomoby.service.test.MobyServletTestCase
 
testTeXFileConversion() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testUserPreferences() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testWordFileConversion() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testWorkflowExport() - Method in class ca.ucalgary.seahawk.util.test.DataRecorderTestCase
 
testWSDL() - Method in class ca.ucalgary.seahawk.gui.test.SeahawkTestCase
 
testWSDLDocLitExecute() - Method in class ca.ucalgary.services.test.SoapServletTestCase
Checks against both NCBI and EBI services.
testWSDLRpcEncExecute() - Method in class ca.ucalgary.services.test.SoapServletTestCase
Checks against a KEGG service
testWSRF() - Method in class org.soap.sax.test.SOAPFaultTestCase
 
testXPath - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
TEX2HTML - Class in ca.ucalgary.seahawk.util
Converts a large subset of basic latex markup into equivalent HTML
TEX2HTML() - Constructor for class ca.ucalgary.seahawk.util.TEX2HTML
 
TEX_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
TEX_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
Text__formatted - Class in org.inb.biomoby.shared.ontology
 
Text__formatted() - Constructor for class org.inb.biomoby.shared.ontology.Text__formatted
 
Text__formattedComponent<T extends Text__formatted> - Class in org.inb.biomoby.client.gui.ontology
 
Text__formattedComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.Text__formattedComponent
 
Text__html - Class in org.inb.biomoby.shared.ontology
 
Text__html() - Constructor for class org.inb.biomoby.shared.ontology.Text__html
 
Text__plain - Class in org.inb.biomoby.shared.ontology
 
Text__plain() - Constructor for class org.inb.biomoby.shared.ontology.Text__plain
 
Text__plainComponent<T extends Text__plain> - Class in org.inb.biomoby.client.gui.ontology
 
Text__plainComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.Text__plainComponent
 
Text__xhtml - Class in org.inb.biomoby.shared.ontology
 
Text__xhtml() - Constructor for class org.inb.biomoby.shared.ontology.Text__xhtml
 
Text__xml - Class in org.inb.biomoby.shared.ontology
 
Text__xml() - Constructor for class org.inb.biomoby.shared.ontology.Text__xml
 
TEXT_RULES_DEFAULT_RESOURCE - Static variable in class ca.ucalgary.services.LegacyService
 
TEXT_RULES_LOCATION_PARAM - Static variable in class ca.ucalgary.services.LegacyService
 
TextClient - Class in ca.ucalgary.seahawk.services
This class uses XSLT rules to transform MOBY XML data representation (during service invocation) to plain text.
TextClient() - Constructor for class ca.ucalgary.seahawk.services.TextClient
 
TextClient(Registry) - Constructor for class ca.ucalgary.seahawk.services.TextClient
 
TextClientTestCase - Class in ca.ucalgary.seahawk.services.test
 
TextClientTestCase(String) - Constructor for class ca.ucalgary.seahawk.services.test.TextClientTestCase
 
TFscan_Text - Class in org.inb.biomoby.shared.ontology
 
TFscan_Text() - Constructor for class org.inb.biomoby.shared.ontology.TFscan_Text
 
TIME - Static variable in interface org.omg.lsae.sax.LsaeTags
 
TimeProgress - Class in org.inb.lsae
 
TimeProgress() - Constructor for class org.inb.lsae.TimeProgress
 
TimeProgressEvent - Class in org.omg.lsae.notifications
 
TimeProgressEvent() - Constructor for class org.omg.lsae.notifications.TimeProgressEvent
 
TIMESTAMP - Static variable in interface org.soap.sax.FaultTags
 
TITLE - Static variable in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
TITLE_HINT - Static variable in class ca.ucalgary.seahawk.gui.WorkflowPreviewDialog
 
toArray() - Method in class org.biomoby.shared.data.MobyDataObjectSet
 
toArray(T[]) - Method in class org.biomoby.shared.data.MobyDataObjectSet
Don't use this method if at all possible.
toArray() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
toArray(T[]) - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
toArray() - Method in class org.biomoby.shared.data.MobyDataObjectVector
Returns an array containing all of the elements in this list in proper sequence.
toArray(T[]) - Method in class org.biomoby.shared.data.MobyDataObjectVector
 
toArray() - Method in class org.inb.biomoby.shared.message.MobyCollection
 
toArray(T[]) - Method in class org.inb.biomoby.shared.message.MobyCollection
 
toArray() - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
toArray(T[]) - Method in exception org.inb.biomoby.shared.message.MobyExceptions
 
toShortString() - Method in class org.biomoby.shared.MobyService
It combines this service name and its authority name.
toString() - Method in class ca.ucalgary.seahawk.util.FilterSearch
 
toString() - Method in class ca.ucalgary.seahawk.util.XPathOption
 
toString() - Method in class ca.ucalgary.services.util.SourceMap
 
toString() - Method in class org.biomoby.client.DataServiceEdge
 
toString() - Method in class org.biomoby.client.DataTypeConnector
 
toString() - Method in class org.biomoby.client.ServicesEdge
 
toString() - Method in class org.biomoby.registry.meta.Registry
 
toString() - Method in class org.biomoby.registry.rdfagent.util.ServiceProvider
 
toString() - Method in class org.biomoby.service.dashboard.CommonNode
 
toString() - Method in class org.biomoby.service.dashboard.Dashboard
 
toString() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
 
toString() - Method in class org.biomoby.shared.data.MobyContentInstance
 
toString() - Method in class org.biomoby.shared.data.MobyDataBoolean
 
toString() - Method in class org.biomoby.shared.data.MobyDataDateTime
Return an ISO 8601 string representing the date/time represented by this Calendar.
toString() - Method in class org.biomoby.shared.data.MobyDataObject
Convenience method to get the basic XML representation
toString() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
toString() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
toString() - Method in class org.biomoby.shared.data.MobyDataString
 
toString() - Method in class org.biomoby.shared.data.MobyDataXref
 
toString() - Method in class org.biomoby.shared.data.MobyProvisionInfo
 
toString() - Method in class org.biomoby.shared.datatypes.MobyObject
Format all non-empty public members in a human-readable way.
toString() - Method in class org.biomoby.shared.datatypes.MobyXref
 
toString() - Method in class org.biomoby.shared.event.NotificationEvent
 
toString() - Method in class org.biomoby.shared.MobyDataType
 
toString() - Method in class org.biomoby.shared.MobyNamespace
 
toString() - Method in class org.biomoby.shared.MobyPrimaryDataSet
 
toString() - Method in class org.biomoby.shared.MobyPrimaryDataSimple
 
toString() - Method in class org.biomoby.shared.MobyRelationship
 
toString() - Method in class org.biomoby.shared.MobySecondaryData
 
toString() - Method in class org.biomoby.shared.MobyService
 
toString() - Method in class org.biomoby.shared.MobyServiceType
 
toString() - Method in class org.biomoby.shared.MobyUnitTest
 
toString() - Method in class org.biomoby.shared.parser.MobyCollection
 
toString() - Method in class org.biomoby.shared.parser.MobyDataElement
Format all non-empty public members in a human-readable way.
toString() - Method in class org.biomoby.shared.parser.MobyJob
Format all non-empty public members in a human-readable way.
toString() - Method in class org.biomoby.shared.parser.MobyPackage
Format all non-empty public members in a human-readable way.
toString() - Method in class org.biomoby.shared.parser.MobyParameter
 
toString() - Method in class org.biomoby.shared.parser.MobySimple
 
toString() - Method in exception org.biomoby.shared.parser.ServiceException
 
toString() - Method in class org.biomoby.shared.schema.MElement
 
toString() - Method in class org.biomoby.shared.schema.PrimitiveVector
get a string to represent this object.
toString() - Method in class org.biomoby.w3c.addressing.EndpointReference
 
toString() - Method in class org.inb.biomoby.central.gui.model.AbstractEntityTreeNode
 
toString() - Method in class org.inb.biomoby.shared.datatypes.MobyBoolean
 
toString() - Method in class org.inb.biomoby.shared.datatypes.MobyFloat
 
toString() - Method in class org.inb.biomoby.shared.datatypes.MobyInteger
 
toString() - Method in class org.inb.biomoby.shared.datatypes.MobyString
 
toString() - Method in class org.inb.biomoby.shared.message.AbstractMobyObject
 
toString() - Method in class org.inb.biomoby.shared.message.MobyObject
 
toString() - Method in class org.omg.lsae.notifications.AnalysisEvent
 
toString() - Method in class org.omg.lsae.notifications.HeartBeatEvent
 
toString() - Method in class org.omg.lsae.notifications.PercentEvent
 
toString() - Method in class org.omg.lsae.notifications.StateEvent
 
toString() - Method in class org.omg.lsae.notifications.StepEvent
 
toString() - Method in class org.omg.lsae.notifications.TimeProgressEvent
 
toString() - Method in class org.soap.SOAPFault
 
toString() - Method in class org.soap.WSRFFault
 
toXML() - Method in class org.biomoby.service.dashboard.data.DataTypeNode
Create an XML element representing this node.
toXML() - Method in class org.biomoby.service.dashboard.data.DataTypeTreeTable
Return an XML document representing th Biomoby data type that was created in this tree table.
toXML() - Method in class org.biomoby.service.dashboard.data.ParametersTable
Return each parameter (which corresponds to a row in this table) in its XML representation.
toXML() - Method in class org.biomoby.service.dashboard.data.ServiceInputPanel
Return an XML string representing complete input for a service given in the constructor of this class.
toXML() - Method in class org.biomoby.shared.data.MobyContentInstance
 
toXML() - Method in class org.biomoby.shared.data.MobyDataBoolean
 
toXML() - Method in class org.biomoby.shared.data.MobyDataComposite
 
toXML() - Method in class org.biomoby.shared.data.MobyDataDateTime
This class sanitizes strings of XML escape characters such as the ampersand (&) and the less-than sign (<).
toXML() - Method in class org.biomoby.shared.data.MobyDataFloat
 
toXML() - Method in interface org.biomoby.shared.data.MobyDataInstance
Returns the MOBY XML representation of the object.
toXML() - Method in class org.biomoby.shared.data.MobyDataInt
 
toXML() - Method in class org.biomoby.shared.data.MobyDataObject
Produces a full-blown XML fragment that depending on the value of getXmlMode() is either a template for use in MOBY Central services, or a Simple element for use in calling a service instance.
toXML() - Method in class org.biomoby.shared.data.MobyDataObjectSAI
 
toXML() - Method in class org.biomoby.shared.data.MobyDataObjectSet
Wraps the simple instances' XML in a MOBY Collection tag
toXML() - Method in class org.biomoby.shared.data.MobyDataObjectSetSAI
 
toXML() - Method in class org.biomoby.shared.data.MobyDataObjectVector
 
toXML() - Method in class org.biomoby.shared.data.MobyDataSecondaryInstance
This method sanitizes parameter data value strings of XML escape characters such as the ampersand (&) and the less-than sign (<).
toXML() - Method in class org.biomoby.shared.data.MobyDataString
This method sanitizes strings of XML escape characters such as the ampersand (&) and the less-than sign (<).
toXML() - Method in class org.biomoby.shared.data.MobyDataXref
 
toXML() - Method in class org.biomoby.shared.data.MobyProvisionInfo
This method formats the available information into an XML format suitable for inclusion in a MOBY Object.
toXML() - Method in class org.biomoby.shared.datatypes.MobyBoolean
 
toXML() - Method in class org.biomoby.shared.datatypes.MobyDateTime
 
toXML() - Method in class org.biomoby.shared.datatypes.MobyFloat
 
toXML() - Method in class org.biomoby.shared.datatypes.MobyInteger
 
toXML() - Method in class org.biomoby.shared.datatypes.MobyObject
Create an XML element representing this object.
toXML() - Method in class org.biomoby.shared.datatypes.MobyString
 
toXML() - Method in class org.biomoby.shared.datatypes.MobyXref
 
toXML() - Method in class org.biomoby.shared.MobyData
 
toXML() - Method in class org.biomoby.shared.MobyPrimaryDataSet
Convert this instance to the XML.
toXML() - Method in class org.biomoby.shared.MobyPrimaryDataSimple
Convert this instance into XML.
toXML() - Method in class org.biomoby.shared.MobySecondaryData
Convert this instance into XML.
toXML() - Method in class org.biomoby.shared.parser.MobyCollection
 
toXML(String, Element[]) - Static method in class org.biomoby.shared.parser.MobyCollection
 
toXML() - Method in class org.biomoby.shared.parser.MobyDataElement
Create an XML element representing this object.
toXML(String) - Static method in class org.biomoby.shared.parser.MobyDataElement
Create an XML element representing this object.
toXML() - Method in class org.biomoby.shared.parser.MobyJob
Create an XML element representing this object.
toXML(String, Element[]) - Static method in class org.biomoby.shared.parser.MobyJob
Create an XML element representing this object.
toXML() - Method in class org.biomoby.shared.parser.MobyPackage
Convert the whole contents and all its children to a Biomoby compliant XML string.
toXML() - Method in class org.biomoby.shared.parser.MobyParameter
 
toXML(String, String) - Static method in class org.biomoby.shared.parser.MobyParameter
 
toXML() - Method in class org.biomoby.shared.parser.MobySimple
 
toXML(String, Element) - Static method in class org.biomoby.shared.parser.MobySimple
 
toXML() - Method in exception org.biomoby.shared.parser.ServiceException
 
toXMLDocument(OutputStream, MobyContentInstance) - Static method in class org.biomoby.shared.data.MobyDataUtils
Writes the XML version of the contents, with an XML declaration.
toXMLDocument(OutputStream, MobyContentInstance, boolean) - Static method in class org.biomoby.shared.data.MobyDataUtils
Output the XML representation of the data to an OutputStream (i.e. an output that takes byte data, not character-encoded strings).
toXMLDocument(Writer, MobyContentInstance) - Static method in class org.biomoby.shared.data.MobyDataUtils
Writes the XML version of the contents, with an XML declaration.
toXMLDocument(Writer, MobyContentInstance, boolean) - Static method in class org.biomoby.shared.data.MobyDataUtils
Output the XML representation of the data to a Writer (i.e. an output that understands character-encoded strings).
toXMLDocument() - Method in class org.biomoby.shared.parser.MobyPackage
Convert the whole contents and all its children to a Biomoby compliant XML document.
toXMLDocument(Element[]) - Static method in class org.biomoby.shared.parser.MobyPackage
A static alternative returning much simpler XML document - without authority, without service notes, just with the given jobs.
toXMLElement(ServiceException) - Static method in class org.biomoby.shared.parser.JDOMUtils
 
toXMLElement(MobyProvisionInfo) - Static method in class org.biomoby.shared.parser.JDOMUtils
Turns a PIB Object into a JDOM representation.
toXMLString() - Method in exception org.biomoby.shared.parser.ServiceException
 
toXMLString() - Method in class org.omg.lsae.notifications.AnalysisEvent
 
toXMLString() - Method in class org.omg.lsae.notifications.HeartBeatEvent
 
toXMLString() - Method in class org.omg.lsae.notifications.PercentEvent
 
toXMLString() - Method in class org.omg.lsae.notifications.StateEvent
 
toXMLString() - Method in class org.omg.lsae.notifications.StepEvent
 
toXMLString() - Method in class org.omg.lsae.notifications.TimeProgressEvent
 
transform(String, T...) - Static method in class org.inb.biomoby.generator.GeneratorUtil
 
transform(String, Object) - Static method in class org.inb.biomoby.generator.GeneratorUtil
 
TransmembraneAnnotatedAASequence - Class in org.inb.biomoby.shared.ontology
 
TransmembraneAnnotatedAASequence() - Constructor for class org.inb.biomoby.shared.ontology.TransmembraneAnnotatedAASequence
 
TransmembraneAnnotatedAASequenceComponent<T extends TransmembraneAnnotatedAASequence> - Class in org.inb.biomoby.client.gui.ontology
 
TransmembraneAnnotatedAASequenceComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
TransmembraneAnnotatedAASequenceComponent(T) - Constructor for class org.inb.biomoby.client.gui.ontology.TransmembraneAnnotatedAASequenceComponent
 
TransmembraneAnnotatedAASequenceComponent.TransmembraneAnnotatedAASequenceListener - Interface in org.inb.biomoby.client.gui.ontology
 
TransmembraneAnnotation - Class in org.inb.biomoby.shared.ontology
 
TransmembraneAnnotation() - Constructor for class org.inb.biomoby.shared.ontology.TransmembraneAnnotation
 
TransmembraneAnnotationListPane<T extends TransmembraneAnnotation> - Class in org.inb.biomoby.client.gui.auxiliary
 
TransmembraneAnnotationListPane() - Constructor for class org.inb.biomoby.client.gui.auxiliary.TransmembraneAnnotationListPane
 
TransmembraneAnnotationListPane(List<T>) - Constructor for class org.inb.biomoby.client.gui.auxiliary.TransmembraneAnnotationListPane
 
TransmembraneReport - Class in org.inb.biomoby.shared.ontology
 
TransmembraneReport() - Constructor for class org.inb.biomoby.shared.ontology.TransmembraneReport
 
TransmembraneReportComponent - Class in org.inb.biomoby.client.gui.ontology
 
TransmembraneReportComponent() - Constructor for class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
TransmembraneReportComponent(TransmembraneReport) - Constructor for class org.inb.biomoby.client.gui.ontology.TransmembraneReportComponent
 
TransmembraneReportComponent.TransmembraneReportListener - Interface in org.inb.biomoby.client.gui.ontology
 
TreeDet_Annotation_HTML - Class in org.inb.biomoby.shared.ontology
 
TreeDet_Annotation_HTML() - Constructor for class org.inb.biomoby.shared.ontology.TreeDet_Annotation_HTML
 
TreeDet_Annotation_XML - Class in org.inb.biomoby.shared.ontology
 
TreeDet_Annotation_XML() - Constructor for class org.inb.biomoby.shared.ontology.TreeDet_Annotation_XML
 
TreeDet_Report - Class in org.inb.biomoby.shared.ontology
 
TreeDet_Report() - Constructor for class org.inb.biomoby.shared.ontology.TreeDet_Report
 
TreeTableModel - Interface in org.biomoby.service.dashboard.treetable
TreeTableModel is the model used by a JTreeTable.
TreeTableModelAdapter - Class in org.biomoby.service.dashboard.treetable
This is a wrapper class that takes a TreeTableModel and implements the table model interface.
TreeTableModelAdapter(TreeTableModel, JTree) - Constructor for class org.biomoby.service.dashboard.treetable.TreeTableModelAdapter
 
trName(String) - Static method in class org.biomoby.client.Graphviz
Replaces dashes by underscores in 'name'.
TSV_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
TSV_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
TTS - Class in org.inb.biomoby.shared.ontology
 
TTS() - Constructor for class org.inb.biomoby.shared.ontology.TTS
 
TXT_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
TXT_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
type - Variable in class org.inb.biomoby.shared.message.AnyMobyObject
 
type2str(int) - Static method in class org.biomoby.shared.MobyRelationship
A static method converting a relationship type to its string representation.
Typed_Image - Class in org.inb.biomoby.shared.ontology
 
Typed_Image() - Constructor for class org.inb.biomoby.shared.ontology.Typed_Image
 

U

unbindTemplate() - Method in class org.biomoby.shared.MobyDataTypeTemplate
 
UNBOUNDED_FLOAT_RANGE_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
UNBOUNDED_INT_RANGE_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySecondaryInputGUI
 
UNCATEGORIZED_LABEL - Static variable in class org.biomoby.shared.MobyServiceType
 
UNCHECKED - Static variable in class org.biomoby.shared.MobyService
 
UNINSTANTIATED_FG_COLOUR - Static variable in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
UNINSTANTIATED_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyDataObjectWidget
 
unitTest - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
UnitTestingResultPanel - Class in org.biomoby.service.dashboard
A panel displaying service result data, using available renderers.
UnitTestingResultPanel() - Constructor for class org.biomoby.service.dashboard.UnitTestingResultPanel
 
UnitTestingServiceCallermodel - Class in org.biomoby.service.dashboard
A model that achieves its task by calling Biomoby service.
UnitTestingServiceCallermodel() - Constructor for class org.biomoby.service.dashboard.UnitTestingServiceCallermodel
 
UNIX - Class in org.biomoby.registry.properties
This class incorporates the logic needed to obtain environment variables from UNIX and UNIX like machines.
UNKNOWN_NAME - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Setting input data under a non-existing name, or asking for a result using an unknown name.
UNKNOWN_STATE - Static variable in exception org.biomoby.shared.parser.ServiceException
Error code: Used when a service call expects to find an existing state but failed.
UnknownQueryExpressionDialectFault - Exception in org.inb.biomoby.shared.wsrf.fault
 
UnknownQueryExpressionDialectFault(String, UnknownQueryExpressionDialectFaultType) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.UnknownQueryExpressionDialectFault
 
UnknownQueryExpressionDialectFault(String, UnknownQueryExpressionDialectFaultType, Throwable) - Constructor for exception org.inb.biomoby.shared.wsrf.fault.UnknownQueryExpressionDialectFault
 
UnknownQueryExpressionDialectFaultType - Class in org.inb.wsrf.rp2
 
UnknownQueryExpressionDialectFaultType() - Constructor for class org.inb.wsrf.rp2.UnknownQueryExpressionDialectFaultType
 
unmarshal(SOAPMessage) - Static method in class org.inb.biomoby.client.MobyDispatch
 
unregister(MobyDataType) - Method in class org.biomoby.registry.sync.handler.DataTypeHandler
 
unregister(T) - Method in interface org.biomoby.registry.sync.handler.MobyHandler
Unregister an existing object from the local moby central.
unregister(MobyNamespace) - Method in class org.biomoby.registry.sync.handler.NamespaceHandler
 
unregister(MobyService) - Method in class org.biomoby.registry.sync.handler.ServiceHandler
 
unregister(MobyServiceType) - Method in class org.biomoby.registry.sync.handler.ServiceTypeHandler
 
unregisterDataType(MobyDataType) - Method in class org.biomoby.client.CentralImpl
B
unRegisterDataType(MobyDataType) - Method in class org.biomoby.service.dashboard.RegistryModel
 
unregisterDataType(MobyDataType) - Method in interface org.biomoby.shared.Central
Unregister given Moby data type.
unregisterNamespace(MobyNamespace) - Method in class org.biomoby.client.CentralImpl
 
unRegisterNamespace(MobyNamespace) - Method in class org.biomoby.service.dashboard.RegistryModel
 
unregisterNamespace(MobyNamespace) - Method in interface org.biomoby.shared.Central
Unregister given Moby namespace.
unregisterService(MobyService) - Method in class org.biomoby.client.CentralImpl
 
unRegisterService(MobyService) - Method in class org.biomoby.service.dashboard.RegistryModel
 
unregisterService(MobyService, Central) - Static method in class org.biomoby.service.test.ServletTester
 
unregisterService(MobyService) - Method in interface org.biomoby.shared.Central
Unregister given Moby service.
unregisterServiceType(MobyServiceType) - Method in class org.biomoby.client.CentralImpl
 
unRegisterServiceType(MobyServiceType) - Method in class org.biomoby.service.dashboard.RegistryModel
 
unregisterServiceType(MobyServiceType) - Method in interface org.biomoby.shared.Central
Unregister given Moby service type.
update(Graphics) - Method in class ca.ucalgary.seahawk.gui.splash.SplashWindow
Updates the display area of the window.
update(Graphics) - Method in class ca.ucalgary.seahawk.util.SplashWindow
Updates the display area of the window.
update(int, Object) - Method in class org.biomoby.service.dashboard.CommonTree
Get data from a registry model and update the tree.
update(int, Object) - Method in class org.biomoby.service.dashboard.DataTypesTree
Get data (usually from a registry model, but if not null, take them from 'newData') and update the tree.
update(int, Object) - Method in class org.biomoby.service.dashboard.NamespacesTree
Get data (usually from a registry model, but if not null, take them from 'newData') and update the tree.
update(int, Object) - Method in class org.biomoby.service.dashboard.ServicesTree
Get data (usually from a registry model, but if not null, take them from 'newData') and update the tree.
update(int, Object) - Method in class org.biomoby.service.dashboard.ServiceTypesTree
Get data (usually from a registry model, but if not null, take them from 'newData') and update the tree.
updateCache(String) - Method in class org.biomoby.client.CentralDigestCachedSimpleImpl
Update the indicated part of the cache.
updateCache(String) - Method in interface org.biomoby.shared.CentralCached
Update the indicated part of a cache.
updateComponent(DataContainer) - Method in class org.biomoby.service.dashboard.ResultsPanel
 
updateComponent(DataContainer) - Method in class org.biomoby.service.dashboard.UnitTestingResultPanel
 
updateDatatypes() - Method in interface org.biomoby.registry.sync.MobySynchronize
Synchronize the dataypes between the local and master central
updateDatatypes() - Method in class org.biomoby.registry.sync.MobySynchronizeImpl
 
updateDataTypesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
updateDisplay() - Method in class ca.ucalgary.seahawk.gui.MobyContentClipboard
 
updateElement(T, T) - Method in class org.inb.biomoby.central.model.AbstractModel
A method that updates an element referred by element1 with data provided by element2 Note that updated element is not necesary the same object as elemen1, but those located in an underlied collection.
updateElement(ObjectType, ObjectType) - Method in class org.inb.biomoby.central.model.DatatypesModel
A method that updates an element referred by element1 with data provided by element2.
updateElement(MobyCentral, MobyCentral) - Method in class org.inb.biomoby.central.model.MobyCentralModel
Method not implemented
updateElement(Namespace, Namespace) - Method in class org.inb.biomoby.central.model.NamespacesModel
A method that updates an element referred by element1 with data provided by element2.
updateElement(Service, Service) - Method in class org.inb.biomoby.central.model.ServicesModel
A method that updates a service description referred by element1 with data provided by element2.
updateHistory(MobyContentPane) - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
A pane whose history list has changed should call this method to ensure the forward and backward buttons are properly set to reflect the change.
updateHistoryButtons() - Method in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
updateInputFilter(URL, URL, FilterSearch) - Static method in class ca.ucalgary.seahawk.util.DataUtils
Edit a service input document's backtracking references to have a new filter criteria.
updateNamespaces() - Method in interface org.biomoby.registry.sync.MobySynchronize
Synchronize the namespaces between the local and master central
updateNamespaces() - Method in class org.biomoby.registry.sync.MobySynchronizeImpl
 
updateNamespacesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
updateRegistry(Properties) - Method in class org.biomoby.registry.sync.AbstractMobySynchronize
Updates the local registry.
updateServices() - Method in interface org.biomoby.registry.sync.MobySynchronize
Synchronize the services between the local and master central
updateServices() - Method in class org.biomoby.registry.sync.MobySynchronizeImpl
 
updateServicesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
updateServiceTypes() - Method in interface org.biomoby.registry.sync.MobySynchronize
Synchronize the servicetypes between the local and master central
updateServiceTypes() - Method in class org.biomoby.registry.sync.MobySynchronizeImpl
 
updateServiceTypesCache() - Method in class org.biomoby.service.dashboard.RegistryModel
 
updateTree(int) - Method in class org.biomoby.service.dashboard.CommonBoard
Update the underlying tree.
updateUI() - Method in class org.biomoby.service.dashboard.treetable.JTreeTable.TreeTableCellRenderer
updateUI is overridden to set the colors of the Tree's renderer to match that of the table.
updateUI() - Method in class org.biomoby.service.dashboard.treetable.JTreeTable
Overridden to message super and forward the method to the tree.
url - Variable in class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
URL__Text - Class in org.inb.biomoby.shared.ontology
 
URL__Text() - Constructor for class org.inb.biomoby.shared.ontology.URL__Text
 
URL_REGEX_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
URLENCODED - Static variable in class ca.ucalgary.services.util.XHTMLForm
 
USE_DEFAULT_HANDLER_MASK - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
Always spring MOBY response in a new window if this modifier is present for a click
USE_DEFAULT_SECONDARIES_MASK - Static variable in class ca.ucalgary.seahawk.gui.MobyServicesGUI
 
useLoadMonitor - Static variable in class org.biomoby.service.dashboard.Dashboard
 
USER_AGENT - Static variable in class org.biomoby.client.AsyncClient
 
useResponse(String) - Method in class org.biomoby.client.BaseClient
A raw-level processing.
useResponse(MobyPackage) - Method in class org.biomoby.client.BaseClient
A high-level processing.
useResponse(MobyJob, MobyPackage) - Method in class org.biomoby.client.BaseClient
Process a single job returned from a BioMoby service.
useResponse(String) - Method in class org.biomoby.client.BaseCmdLineClient
 
useResponse(MobyPackage) - Method in class org.biomoby.client.BaseCmdLineClient
 
useResponse(MobyJob, MobyPackage) - Method in class org.biomoby.client.BaseCmdLineClient
 
usesMethod - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
usesMethod - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
usesResource - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
usesResource - Static variable in class org.biomoby.client.rdf.vocabulary.ServiceDescriptionPredicates
 
Utils - Class in org.biomoby.shared
This is a set of several utility methods which may be useful for writing both registry and client code.
Utils() - Constructor for class org.biomoby.shared.Utils
 

V

validateArguments(MobyDataJob, MobyService, String) - Static method in class org.biomoby.service.MobyServlet
Throws an exception if the data in the job does not match the input spec of the service.
validOutputXML - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
validREGEX - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
validXPath - Static variable in class org.biomoby.client.rdf.vocabulary.FetaVocabulary
 
VALUE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
VALUE_NAME - Static variable in class org.biomoby.shared.data.MobyDataSecondaryInstance
 
VALUE_XPATH_PARAM - Static variable in class ca.ucalgary.services.util.PBERecorder
 
valueChanged(TreeSelectionEvent) - Method in class org.inb.biomoby.generator.gui.AbstractServiceModelPanel
 
valueForPathChanged(TreePath, Object) - Method in class org.biomoby.service.dashboard.treetable.AbstractTreeTableModel
 
valueOf(String) - Static method in enum ca.ucalgary.seahawk.services.DaggooClient.Action
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biomoby.registry.sync.filtering.FilterRuleKeys
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.client.gui.StringPainter.ALIGNMENT
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.service.resolver.WSRFOperation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.shared.message.MobyException.SEVERITY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.shared.registry.Parameter.PARAMETER_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.shared.registry.Registration.SUCCESS_CODE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.shared.registry.Relationship.DIRECTION_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.shared.registry.Relationship.RELATIONSHIP_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.shared.registry.Resource.RESOURCE_NAME
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.biomoby.shared.registry.Service.CATEGORY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.inb.lsae.StateChanged.STATE
Returns the enum constant of this type with the specified name.
values() - Static method in enum ca.ucalgary.seahawk.services.DaggooClient.Action
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class ca.ucalgary.services.util.SourceMap
 
values() - Static method in enum org.biomoby.registry.sync.filtering.FilterRuleKeys
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.biomoby.shared.data.MobyContentInstance
Returns all of the queries
values() - Method in class org.biomoby.shared.data.MobyDataComposite
For the user's convenience, the returned Collection is a MobyDataSetInstance, allowing for MOBY-savvy equivalency testing with another Collection of data instances.
values() - Static method in enum org.inb.biomoby.client.gui.StringPainter.ALIGNMENT
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.service.resolver.WSRFOperation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.shared.message.MobyException.SEVERITY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.shared.registry.Parameter.PARAMETER_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.shared.registry.Registration.SUCCESS_CODE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.shared.registry.Relationship.DIRECTION_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.shared.registry.Relationship.RELATIONSHIP_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.shared.registry.Resource.RESOURCE_NAME
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.biomoby.shared.registry.Service.CATEGORY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.inb.lsae.StateChanged.STATE
Returns an array containing the constants of this enum type, in the order they are declared.
VERBOSE - Static variable in class ca.ucalgary.minnow.MinJarMaker
 
VERBOSE_EVENT - Static variable in class org.biomoby.service.dashboard.CommonConsole
A default name of property change event that is considered to carry verbose messages.
VERTICAL - Static variable in class ca.ucalgary.seahawk.util.CombinedIcon
 
VirtualSequence - Class in org.inb.biomoby.shared.ontology
 
VirtualSequence() - Constructor for class org.inb.biomoby.shared.ontology.VirtualSequence
 

W

WAITING_TAB_ICON_RESOURCE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentPane
 
WARN - Static variable in class org.biomoby.registry.rdfagent.util.Log
log warning messages
warning(String) - Static method in class org.biomoby.registry.rdfagent.util.Log
 
WARNING - Static variable in exception org.biomoby.shared.parser.ServiceException
A severity code that corresponds to an informative diagnostic message.
warning(String) - Static method in exception org.biomoby.shared.parser.ServiceException
Create an instance of ServiceException that represents a warning.
warningIcon - Static variable in class org.biomoby.service.dashboard.AbstractPanel
 
WEB_ADDR_DIALOG_TITLE - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
WEB_OPEN_OPTION - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
WEB_OPEN_OPTION_NAME - Static variable in class ca.ucalgary.seahawk.gui.MobyContentGUI
 
WeightedAminoAcidSequences - Class in org.inb.biomoby.shared.ontology
 
WeightedAminoAcidSequences() - Constructor for class org.inb.biomoby.shared.ontology.WeightedAminoAcidSequences
 
WeightedList__Text - Class in org.inb.biomoby.shared.ontology
 
WeightedList__Text() - Constructor for class org.inb.biomoby.shared.ontology.WeightedList__Text
 
WeightedList_Text - Class in org.inb.biomoby.shared.ontology
 
WeightedList_Text() - Constructor for class org.inb.biomoby.shared.ontology.WeightedList_Text
 
WeightedObject - Class in org.inb.biomoby.shared.ontology
 
WeightedObject() - Constructor for class org.inb.biomoby.shared.ontology.WeightedObject
 
WHITESPACE_ATTR - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
WHITESPACE_ATTR_KEEP_VAL - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
WHITESPACE_ATTR_NORMALIZE_VAL - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
WHITESPACE_ATTR_STRIP_FLANKING_VAL - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
WHITESPACE_ATTR_STRIP_VAL - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
windowActivated(WindowEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
windowClosed(WindowEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
windowClosing(WindowEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
Invoked when the user attempts to close the window from the window's system menu.
windowClosing(WindowEvent) - Method in class org.biomoby.shared.schema.GenericWindowListener
 
windowDeactivated(WindowEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
windowDeiconified(WindowEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
windowIconified(WindowEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
windowOpened(WindowEvent) - Method in class ca.ucalgary.seahawk.gui.SeahawkOptionsGUI
 
Windows - Class in org.biomoby.registry.properties
This class incorporates the logic needed to obtain environment variables from Windows 95, Windows 98 and Windows Me.
WindowsNT - Class in org.biomoby.registry.properties
This class incorporates the logic needed to obtain environment variables from Windows NT like machines (XP, 2000, etc).
workflowCanceled(WorkflowPreviewDialog) - Method in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
workflowCanceled(WorkflowPreviewDialog) - Method in interface ca.ucalgary.seahawk.gui.WorkflowPreviewListener
 
workflowConfirmed(WorkflowPreviewDialog, byte[]) - Method in class ca.ucalgary.seahawk.gui.MobySaveDialog
Callback for when the user has approved the workflow preview and entered metadata.
workflowConfirmed(WorkflowPreviewDialog, byte[]) - Method in interface ca.ucalgary.seahawk.gui.WorkflowPreviewListener
 
WorkflowPreviewDialog - Class in ca.ucalgary.seahawk.gui
 
WorkflowPreviewDialog(Frame, Map<URL, FilterSearch>, DataFlowRecorder, String, WorkflowPreviewListener) - Constructor for class ca.ucalgary.seahawk.gui.WorkflowPreviewDialog
 
WorkflowPreviewListener - Interface in ca.ucalgary.seahawk.gui
Callback interface for saving a workflow after its preview is confirmed (and potentially metadata for the workflow entered by the user).
WPD_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
WPD_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
WrapperService<E extends MobySpecWrapper> - Class in ca.ucalgary.services
Based class for servlets implementing a Moby wrapper around existing Web-based interface specifications enhanced with semantic info (represented in a MobySpecWrapper), such as WSDL and CGI services.
WrapperService() - Constructor for class ca.ucalgary.services.WrapperService
 
WRAPPING_RESULTFILE_PREFIX - Static variable in class ca.ucalgary.seahawk.gui.MobyContentPane
 
WrappingServlet - Class in ca.ucalgary.services
 
WrappingServlet() - Constructor for class ca.ucalgary.services.WrappingServlet
 
WrappingServlet.MyNodeList - Class in ca.ucalgary.services
A mutable NodeList implementation for convenience.
WrappingServlet.MyNodeList() - Constructor for class ca.ucalgary.services.WrappingServlet.MyNodeList
 
write(byte[]) - Method in class org.biomoby.client.rdf.builder.FilteredStream
 
write(byte[], int, int) - Method in class org.biomoby.client.rdf.builder.FilteredStream
 
write(int) - Method in class org.biomoby.service.dashboard.ConsoleStream
TBD: I am still not sure - my code does not seem to be optimalized.
write(int) - Method in class org.biomoby.service.test.StringBufferServletOutputStream
 
write(File) - Method in class org.inb.biomoby.generator.DatatypeGenerator
 
writeField(String, boolean) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an boolean field value.
writeField(String, double) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an double field value.
writeField(String, float) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an float field value.
writeField(String, long) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an long field value.
writeField(String, int) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an int field value.
writeField(String, short) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an short field value.
writeField(String, char) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an char field value.
writeField(String, String) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes an string field value.
writeFile(String, String, File) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes a file's contents.
writeFile(String, String, String, InputStream) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes a input stream's contents.
writeFile(String, String, String, byte[]) - Method in class ca.ucalgary.services.util.MultiPartFormOutputStream
Writes the given bytes.
writeToConnection(URLConnection, byte[], String) - Static method in class ca.ucalgary.services.util.IOUtils
Creates a SOAP envelope around the request payload
writeWrapperForm(HttpServletRequest) - Method in interface ca.ucalgary.services.util.DataRecorder
 
writeWrapperForm(HttpServletRequest) - Method in class ca.ucalgary.services.util.PBERecorder
Uses the retained copy of the WSDL service response, matching it up with the xPath given by the user, to create an interface confirming the definition of a new Moby service.
WS_ADDRESSING_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WS_ADDRESSING_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WS_ADDRESSING_TO_TAG_NAME - Static variable in class org.biomoby.client.AsyncClient
 
WSDL20_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WSDL20_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WSDL_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WSDL_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WSDL_URL_PARAM - Static variable in class ca.ucalgary.services.WSDLService
 
WSDLConfig - Class in ca.ucalgary.services.util
Used to expose a WSDL file enhanced with SAWSDL and Moby markup as a Moby service.
WSDLConfig() - Constructor for class ca.ucalgary.services.util.WSDLConfig
C-tor to use when you'll programmatically set the values rarther than getting them from a SAWSDL file.
WSDLConfig(URL) - Constructor for class ca.ucalgary.services.util.WSDLConfig
 
WSDLConfigTestCase - Class in ca.ucalgary.services.util.test
 
WSDLConfigTestCase(String) - Constructor for class ca.ucalgary.services.util.test.WSDLConfigTestCase
 
wsdlParam2MobyParam(Element, String, String, String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
wsdlParam2MobySecondaryParam(Element, String, String, String) - Method in class ca.ucalgary.services.util.WSDLConfig
 
WSDLService - Class in ca.ucalgary.services
A servlet to wrap a Semantically Annotated WSDL file into a Moby Service using LSIDs to identify the models (Moby ontology terms) and lowering/lifting schema mappings (MOB and DEM rules) to bridge the semantic contents of Moby messages <-> the syntactic WSDL I/O.
WSDLService(WSDLConfig, boolean) - Constructor for class ca.ucalgary.services.WSDLService
C-tor for when you want to configure not from a SAWSDL file, but a configuration object.
WSDLService() - Constructor for class ca.ucalgary.services.WSDLService
 
WSDLServiceTestCase - Class in ca.ucalgary.services.test
For the testMain cases to be actually successful, the WEB-INF/web.xml file must be one with all the SOAP parameters...
WSDLServiceTestCase(String) - Constructor for class ca.ucalgary.services.test.WSDLServiceTestCase
 
WSRFFault - Class in org.soap
A class to represent a WSRF fault.
WSRFFault() - Constructor for class org.soap.WSRFFault
 
WSRFOperation - Enum in org.inb.biomoby.service.resolver
 
WSRFResourceInstanceResolver<T> - Class in org.inb.biomoby.service.resolver
 
WSRFResourceInstanceResolver(Class<T>) - Constructor for class org.inb.biomoby.service.resolver.WSRFResourceInstanceResolver
 
WSRP_MULTI_PROPERTY_TAG_NAME - Static variable in class org.biomoby.client.AsyncClient
 
WSRP_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WSRP_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
WSRP_PROPERTY_TAG_NAME - Static variable in class org.biomoby.client.AsyncClient
 

X

XHTML_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XHTML_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XHTMLForm - Class in ca.ucalgary.services.util
This class presents HTML forms as if they were ACD file descriptions of a command.
XHTMLForm(URL) - Constructor for class ca.ucalgary.services.util.XHTMLForm
 
XHTMLForm() - Constructor for class ca.ucalgary.services.util.XHTMLForm
C-tor to use when you want to set a bunch of parameters manually.
XHTMLFormTestCase - Class in ca.ucalgary.services.util.test
 
XHTMLFormTestCase(String) - Constructor for class ca.ucalgary.services.util.test.XHTMLFormTestCase
 
XLINK_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XLINK_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XLS_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
XLS_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
XLS_MIME - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
XLS_MIME2 - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
XML_DESC - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
XML_EXT - Static variable in class ca.ucalgary.seahawk.gui.MobySaveDialog
 
xmlDocumentFileName - Static variable in class ca.ucalgary.seahawk.gui.test.MobyContentGUITestCase
 
xmlIcon - Static variable in class org.biomoby.service.dashboard.data.DataTypeTreeTable
 
XMLTree - Class in org.biomoby.service.dashboard.renderers
Dislaying XML data in a JTree structure.
XMLTree(String) - Constructor for class org.biomoby.service.dashboard.renderers.XMLTree
Build a new XMLTree from the supplied String containing XML.
XMLTree(String, int) - Constructor for class org.biomoby.service.dashboard.renderers.XMLTree
Build a new XMLTree from the supplied String containing XML.
XMLTree(Document) - Constructor for class org.biomoby.service.dashboard.renderers.XMLTree
Build a new XMLTree from the supplied XML document.
XMLTree(Document, int) - Constructor for class org.biomoby.service.dashboard.renderers.XMLTree
Build a new XMLTree from the supplied XML document.
XMLTreeRenderer - Class in org.biomoby.service.dashboard.renderers
Render XML data using XMLTree.
XMLTreeRenderer() - Constructor for class org.biomoby.service.dashboard.renderers.XMLTreeRenderer
 
XMLTypes - Class in org.biomoby.client.rdf.vocabulary
 
XMLTypes() - Constructor for class org.biomoby.client.rdf.vocabulary.XMLTypes
 
XPATH_DEFAULT_NS_PREFIX - Static variable in class ca.ucalgary.services.util.PBERecorder
 
XPATH_PARAM_NAME - Static variable in class org.inb.biomoby.shared.wsrf.MobyEndpointReference
 
XPATH_TAG - Static variable in class ca.ucalgary.seahawk.services.MobyClient
 
xPathFactory - Static variable in class ca.ucalgary.seahawk.util.DataUtils
 
XPathOption - Class in ca.ucalgary.seahawk.util
Simple class to hold an XPath and a textual description of the XPath, generally for use in a JComboBox, etc. where the toString() is important.
XPathOption(String, String) - Constructor for class ca.ucalgary.seahawk.util.XPathOption
 
XPointerResolver - Class in ca.ucalgary.seahawk.util
Retrieves XML DOM Nodes form a document using XPointer locators such as /1/1/2/3/1/67.
XPointerResolver() - Constructor for class ca.ucalgary.seahawk.util.XPointerResolver
 
XREF - Static variable in interface org.biomoby.shared.parser.MobyTags
 
XREFTYPE - Static variable in interface org.biomoby.shared.parser.MobyTags
 
XSD_DATE_TIME - Static variable in class org.biomoby.client.rdf.vocabulary.XMLTypes
 
XSD_FLOAT - Static variable in class org.biomoby.client.rdf.vocabulary.XMLTypes
 
XSD_INTEGER - Static variable in class org.biomoby.client.rdf.vocabulary.XMLTypes
 
XSD_NAMESPACE - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XSD_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XSD_STRING - Static variable in class org.biomoby.client.rdf.vocabulary.XMLTypes
 
XSI1999_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XSI2001_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XSI_NAMESPACE1999 - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XSI_NAMESPACE2001 - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XSI_PREFIX - Static variable in class org.biomoby.shared.MobyPrefixResolver
 
XSL_DOC_SOURCE_PARAM - Static variable in class ca.ucalgary.seahawk.gui.MobyContentPane
The name of the param in the stylesheet that will hold the Moby doc URL for XPointer usage
XSLT_MODE_VAR - Static variable in class ca.ucalgary.seahawk.services.TextClient
 
XSLT_NS - Static variable in class ca.ucalgary.seahawk.services.TextClient
 

Z

Zip_Encoded - Class in org.inb.biomoby.shared.ontology
 
Zip_Encoded() - Constructor for class org.inb.biomoby.shared.ontology.Zip_Encoded
 

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