Uses of Class
org.biomoby.shared.MobyService

Packages that use MobyService

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.util
ca.ucalgary.services
de.mpg.mpiz_koeln.featureClient
org.biomoby.client	The components used for developing Moby clients.
org.biomoby.client.rdf.builder	Provides the classes that are necessary for creating BioMoby RDF documents.
org.biomoby.registry.rdfagent.util
org.biomoby.registry.rdfagent.verifier
org.biomoby.registry.sync.filtering
org.biomoby.registry.sync.handler
org.biomoby.service	It contains general components that can be used by those writing code for Moby services.
org.biomoby.service.dashboard
org.biomoby.service.dashboard.data
org.biomoby.service.test
org.biomoby.shared	It contains components that are used from more than one (other) packages.
org.biomoby.shared.data	The package org.biomoby.shared.data allows you to easily build MOBY data instances for sending to services, or querying the registry.
org.biomoby.shared.datatypes	The package org.biomoby.shared.datatypes contains containers for basic Biomoby data types (a basic parent class MobyObject and all Biomoby primitive types).
org.biomoby.shared.extended

Uses of MobyService in ca.ucalgary.seahawk.gui

Methods in ca.ucalgary.seahawk.gui that return MobyService

MobyService

MobyContentGUI.findService(String providerURI, String serviceName)

Methods in ca.ucalgary.seahawk.gui with parameters of type MobyService

JMenu	MobyServicesGUI.addNameDivSubMenu(JMenu parentMenu, MobyService[] services)
MobyContentInstance	MobyContentGUI.callService(MobyService service, MobyContentInstance inEnvelope)
int	MobyServicesGUI.compare(MobyService o1, MobyService o2)
void	MobyServicesGUI.setupService(MobyService mobyService, MobyDataInstance mdi, MobyRequestEventHandler mreh) Call the service given, or first launch a GUI to get missing input data if not provided in the MobyDataInstance.
void	MobyServicesGUI.sortServicesByName(MobyService[] services)

Uses of MobyService in ca.ucalgary.seahawk.util

Methods in ca.ucalgary.seahawk.util that return MobyService

static MobyService	DataUtils.getService(Document responseDoc)
static MobyService	DataUtils.getService(URL responseURL) Find out what the service was that created the given URL.

Methods in ca.ucalgary.seahawk.util with parameters of type MobyService

static URL	DataUtils.saveOutputData(MobyContentInstance outputData, MobyService payloadSource, MobyContentInstance inputData, String registryEndpoint)
static URL	DataUtils.saveOutputData(String output, MobyService payloadSource, URL inputURL, String registryEndpoint)

Constructors in ca.ucalgary.seahawk.util with parameters of type MobyService

MobyDataObjectDeferredSAI(MobyDataObjectDeferred data, MobyService[] services)

MobyDataObjectSetDeferredSAI(MobyDataObjectSetDeferred data, MobyService[] services)

Uses of MobyService in ca.ucalgary.services

Methods in ca.ucalgary.services that return MobyService

MobyService	CGIService.createServiceFromConfig(javax.servlet.http.HttpServletRequest request)
MobyService	WSDLService.createServiceFromConfig(javax.servlet.http.HttpServletRequest request)
MobyService	LegacyService.createServiceFromConfig(javax.servlet.http.HttpServletRequest request)
MobyService	ACDService.createServiceFromConfig(javax.servlet.http.HttpServletRequest request) 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.
MobyService	WrapperService.createServiceFromConfig(javax.servlet.http.HttpServletRequest request, E wrapperSpec)

Methods in ca.ucalgary.services with parameters of type MobyService

void	ACDService.configureServiceFromACDFile(MobyService service, File acdFile, boolean useAdvancedParams) Parses the ACD file and sets the MOBY signature parameters appropriately.

Uses of MobyService in de.mpg.mpiz_koeln.featureClient

Methods in de.mpg.mpiz_koeln.featureClient that return MobyService

MobyService

FeatureClientResult.getMobyService() Returns the BioMOBY service which was called

Methods in de.mpg.mpiz_koeln.featureClient with parameters of type MobyService

Collection<FeatureClientResult>

FeatureClient.call(MobyService mobyService) Calls the moby service and returns its result.

Method parameters in de.mpg.mpiz_koeln.featureClient with type arguments of type MobyService

Collection<FeatureClientResult>

FeatureClient.call(Collection<MobyService> services) Calls all given services and returns their result.

Uses of MobyService in org.biomoby.client

Methods in org.biomoby.client that return MobyService

MobyService[]	CentralImpl.extractServices(String xml) Extract one or more MobyService objects from the given XML piece.
MobyService[]	CentralImpl.findService(MobyService pattern)
MobyService[]	CentralImpl.findService(MobyService pattern, String[] keywords)
MobyService[]	CentralImpl.findService(MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes, boolean includeParentDataTypes) All 'findService' methods end up here.
MobyService[]	CentralImpl.findService(String serviceType)
MobyService[]	CentralImpl.findService(String[] keywords)
MobyService	MobyRequest.getService()
MobyService	DataServiceEdge.getService() Retrieves the service from this edge.
MobyService	MobyRequestEvent.getService()
MobyService	MobyServiceLocator.getService()
MobyService[]	CentralDigestCachedImpl.getServices()
MobyService[]	CentralDigestImpl.getServices()
MobyService[]	CentralDigestCachedSimpleImpl.getServices()
MobyService	ServicesEdge.getSourceService() Retrieves the source service.
MobyService	ServicesEdge.getTargetService() Retrieves the target service.

Methods in org.biomoby.client with parameters of type MobyService

static ServicesEdge[]	ServiceConnections.build(MobyDataType[] dataTypes, MobyService[] services) Creates all (allowed) connections between given 'services' based on the given 'dataTypes'.
static DataServiceEdge[]	ServiceConnections.findEndingEdges(MobyPrimaryDataSimple targetData, MobyDataType[] dataTypes, MobyService[] services)
MobyService[]	CentralImpl.findService(MobyService pattern)
MobyService[]	CentralImpl.findService(MobyService pattern, String[] keywords)
MobyService[]	CentralImpl.findService(MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes, boolean includeParentDataTypes) All 'findService' methods end up here.
static DataServiceEdge[]	ServiceConnections.findStartingEdges(MobyPrimaryDataSimple sourceData, MobyDataType[] dataTypes, MobyService[] services)
String	CentralImpl.getRegisterServiceXML(MobyService service)
void	CentralImpl.registerService(MobyService service)
static EndpointReference	AsyncClient.sendRequest(MobyService service, MobyContentInstance contents)
static EndpointReference	AsyncClient.sendRequest(MobyService service, String xml)
void	MobyRequest.setService(MobyService mobyservice)
void	MobyServiceLocator.setService(MobyService service)
void	CentralImpl.unregisterService(MobyService service)

Constructors in org.biomoby.client with parameters of type MobyService

DataServiceEdge(MobyDataType sourceDataType, MobyService targetService, String connector)
Constructs an instance with data type as a source and a service as a target, and a connector.

DataServiceEdge(MobyService sourceService, MobyDataType targetDataType, String connector)
Constructs an instance with data type as a target and a service as a source, and a connector.

ExtendedServiceLocator(MobyService service)
Another constructor, seeting also a service.

MobyRequestEvent(MobyContentInstance mci, MobyRequest requestSource, MobyService serv, MobyContentInstance serviceInput, Throwable e, int id)

MobyServiceLocator(MobyService service)
Another constructor, seeting also a service.

ServicesEdge(MobyService sourceService, int connectionType)
Constructs an instance with a source service and a connection type.

ServicesEdge(MobyService sourceService, MobyService targetService, String connector)
Constructs an instance with both source and target services, and a connector.

ServicesEdge(MobyService sourceService, String connector)
Constructs an instance with a source service and a connector.

Uses of MobyService in org.biomoby.client.rdf.builder

Methods in org.biomoby.client.rdf.builder with parameters of type MobyService

com.hp.hpl.jena.rdf.model.Model

ServiceInstanceRDF.createRDFModel(com.hp.hpl.jena.rdf.model.Model model, MobyService[] services, boolean useLSIDs)

Uses of MobyService in org.biomoby.registry.rdfagent.util

Methods in org.biomoby.registry.rdfagent.util that return MobyService

MobyService[]

SignatureURLConnection.extractServicesFromURL(String url)

Uses of MobyService in org.biomoby.registry.rdfagent.verifier

Methods in org.biomoby.registry.rdfagent.verifier with parameters of type MobyService

boolean	MobyServiceComparator.areInputsOutputsForServiceValid(MobyService service)
boolean	MobyServiceComparator.areServicesDifferent(MobyService service1, MobyService service2)
String	MobyServiceComparator.getServiceErrors(MobyService s)

Uses of MobyService in org.biomoby.registry.sync.filtering

Methods in org.biomoby.registry.sync.filtering with parameters of type MobyService

boolean

ServiceFilter.isServiceFiltered(MobyService service) Returns whether a service was filtered and therefore is not processed any further in the update process.

Uses of MobyService in org.biomoby.registry.sync.handler

Methods in org.biomoby.registry.sync.handler with parameters of type MobyService

boolean	ServiceHandler.register(MobyService service)
boolean	ServiceHandler.unregister(MobyService service)

Uses of MobyService in org.biomoby.service

Methods in org.biomoby.service that return MobyService

MobyService

MobyServlet.createServiceFromConfig(javax.servlet.http.HttpServletRequest request)

Methods in org.biomoby.service with parameters of type MobyService

static void

MobyServlet.validateArguments(MobyDataJob job, MobyService service, String errMessagePrefix) Throws an exception if the data in the job does not match the input spec of the service.

Uses of MobyService in org.biomoby.service.dashboard

Methods in org.biomoby.service.dashboard that return MobyService

MobyService	RegistryModel.getService(String combinedServiceName)
MobyService[]	RegistryModel.getServices(Object initiator) Fetch services (from a cache or from a registry).

Methods in org.biomoby.service.dashboard with parameters of type MobyService

String	RegistryModel.getRegisterServiceXML(MobyService service)
void	RegistryModel.registerService(MobyService service)
void	RegistryModel.unRegisterService(MobyService service)

Uses of MobyService in org.biomoby.service.dashboard.data

Constructors in org.biomoby.service.dashboard.data with parameters of type MobyService

ServiceInputPanel(MobyService service, MobyDataType[] dataTypes)
Create a GUI for all inputs for the given service.

Uses of MobyService in org.biomoby.service.test

Methods in org.biomoby.service.test with parameters of type MobyService

static void	ServletTester.registerService(MobyService service, Central central)
static void	ServletTester.unregisterService(MobyService service, Central central)

Uses of MobyService in org.biomoby.shared

Methods in org.biomoby.shared that return MobyService

MobyService	MobyService.clone() 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).
MobyService[]	Central.findService(MobyService pattern) Find services matching whatever is non-empty in the given 'pattern'.
MobyService[]	Central.findService(MobyService pattern, String[] keywords) Find service matching both all non-empty fields in the 'pattern' and the 'keywords'.
MobyService[]	Central.findService(MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes, boolean includeParentDataTypes) Find service matching both all non-empty fields in the 'pattern' and the 'keywords', and take into account also the whole ontology tree.
MobyService[]	Central.findService(String serviceType) Find services of the given type and its sub-types.
MobyService[]	Central.findService(String[] keywords) Find services by given keywords.
static MobyService	MobyService.getService(String lsid)
static MobyService	MobyService.getService(String name, String authority)
MobyService[]	CentralDigest.getServices() Get definition of all registered service instances.

Methods in org.biomoby.shared with parameters of type MobyService

int	MobyService.compareTo(MobyService obj) Implementing Comparable interface.
boolean	MobyService.equals(MobyService anotherOne)
MobyService[]	Central.findService(MobyService pattern) Find services matching whatever is non-empty in the given 'pattern'.
MobyService[]	Central.findService(MobyService pattern, String[] keywords) Find service matching both all non-empty fields in the 'pattern' and the 'keywords'.
MobyService[]	Central.findService(MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes, boolean includeParentDataTypes) Find service matching both all non-empty fields in the 'pattern' and the 'keywords', and take into account also the whole ontology tree.
void	Central.registerService(MobyService service) Register a new service.
void	Central.unregisterService(MobyService service) Unregister given Moby service.

Uses of MobyService in org.biomoby.shared.data

Methods in org.biomoby.shared.data that return MobyService

MobyService	MobyDataXref.getService()
MobyService[]	MobyDataObjectSetSAI.getServices()
MobyService[]	MobyDataServiceAssocInstance.getServices()
MobyService[]	MobyDataObjectSAI.getServices()

Methods in org.biomoby.shared.data with parameters of type MobyService

void	MobyDataXref.setServices(MobyService[] services) If more than one service is provided, only the first will be taken.
void	MobyDataObjectSetSAI.setServices(MobyService[] services)
void	MobyDataServiceAssocInstance.setServices(MobyService[] services)
void	MobyDataObjectSAI.setServices(MobyService[] services)

Constructors in org.biomoby.shared.data with parameters of type MobyService

MobyDataObjectSAI(MobyDataObject mdsi, MobyService[] services)
Constructor that takes an existing object and associates services with it.

MobyDataObjectSAI(String namespace, String id, MobyService[] services)
Constructor for base Objects.

MobyDataObjectSAI(String namespace, String id, MobyService[] services, Registry registry)

MobyDataObjectSetSAI(MobyDataObjectSet collection, MobyService[] services)
Constructor that takes an existing object and associates services with it.

MobyDataObjectSetSAI(String name, MobyService[] services)
Constructor for base Objects.

MobyDataObjectSetSAI(String name, MobyService[] services, Registry registry)

MobyDataXref(MobyDataObject mdsi, MobyService service)
Build an Xref based on an existing object.

MobyDataXref(MobyNamespace namespace, String id, MobyService service)

MobyDataXref(String namespace, String id, MobyService service)
Gets the registry implicitly from the service being passed in.

Uses of MobyService in org.biomoby.shared.datatypes

Methods in org.biomoby.shared.datatypes that return MobyService

MobyService

MobyXref.getService() Get an object representing a Biomoby service that can consume data this cross reference is included in.

Methods in org.biomoby.shared.datatypes with parameters of type MobyService

void	MobyXref.setService(MobyService service) Set a Biomoby service that can consume data this cross reference is included in.

Uses of MobyService in org.biomoby.shared.extended

Methods in org.biomoby.shared.extended that return MobyService

MobyService[]	ServiceInstanceParser.getMobyServicesFromRDF()
MobyService[]	ServiceInstanceParser.getMobyServicesFromRDF(com.hp.hpl.jena.rdf.model.Model model)
MobyService[]	ServiceInstanceParser.getMobyServicesFromRDF(String rdf)