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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.