Index (Apache Taverna Engine and Platform 3.1.0-incubating API)

A B C D E F G H I J K L M N O P R S T U V W Y

A

AbstractActivity<ConfigType> - Class in org.apache.taverna.workflowmodel.processor.activity: Convenience abstract superclass for generic Activity instances.
AbstractActivity() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
AbstractActivityEdit<T> - Class in org.apache.taverna.workflowmodel.impl: Abstraction of an edit acting on a Activity instance.
AbstractActivityEdit(Activity<T>) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractActivityEdit
AbstractAnnotatedThing<T> - Class in org.apache.taverna.annotation: Convenient abstract superclass for annotated things, manages edits.
AbstractAnnotatedThing() - Constructor for class org.apache.taverna.annotation.AbstractAnnotatedThing
AbstractAsynchronousActivity<ConfigType> - Class in org.apache.taverna.workflowmodel.processor.activity: Abstract superclass for asynchronous activities.
AbstractAsynchronousActivity() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity
AbstractCrystalizer - Class in org.apache.taverna.workflowmodel.impl: Receives Job and Completion events and emits Jobs unaltered.
AbstractCrystalizer() - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer
AbstractCrystalizer.CompletionAwareTreeCache - Class in org.apache.taverna.workflowmodel.impl
AbstractDataflowEdit - Class in org.apache.taverna.workflowmodel.impl: Abstraction of an edit acting on a Dataflow instance.
AbstractDataflowEdit(Dataflow) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDataflowEdit
AbstractDataflowInputPortEdit - Class in org.apache.taverna.workflowmodel.impl: Abstraction of an edit acting on a DataflowInputPort instance.
AbstractDataflowInputPortEdit(DataflowInputPort) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDataflowInputPortEdit
AbstractDataflowOutputPortEdit - Class in org.apache.taverna.workflowmodel.impl: Abstraction of an edit acting on a DataflowOutputPort instance.
AbstractDataflowOutputPortEdit(DataflowOutputPort) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDataflowOutputPortEdit
AbstractDatalinkEdit - Class in org.apache.taverna.workflowmodel.impl: Abstraction of an edit acting on a Datalink instance.
AbstractDatalinkEdit(Datalink) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDatalinkEdit
AbstractDispatchEvent<EventType extends AbstractDispatchEvent<EventType>> - Class in org.apache.taverna.workflowmodel.processor.dispatch.events: Superclass of events within the dispatch stack
AbstractDispatchEvent(String, int[], InvocationContext) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.events.AbstractDispatchEvent
AbstractDispatchLayer<ConfigurationType> - Class in org.apache.taverna.workflowmodel.processor.dispatch: Convenience abstract implementation of DispatchLayer
AbstractDispatchLayer() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
AbstractDispatchLayerEdit - Class in org.apache.taverna.workflowmodel.processor.dispatch.impl: Abstraction of an edit acting on a DispatchLayer instance.
AbstractDispatchLayerEdit(DispatchStack) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit
AbstractEntityImpl - Class in org.apache.taverna.reference.impl: Abstract superclass of ReferenceSetImpl, IdentifiedArrayList and ErrorDocumentImpl, manages the T2Reference field for these types and their hibernate backing.
AbstractEntityImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractEntityImpl
AbstractErrorDocumentServiceImpl - Class in org.apache.taverna.reference.impl: Abstract implementation of ErrorDocumentService, inject with an appropriate ErrorDocumentDao and T2ReferenceGenerator to enable.
AbstractErrorDocumentServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
AbstractErrorHandlerLayer<ConfigurationType> - Class in org.apache.taverna.workflowmodel.processor.dispatch: Superclass of error handling dispatch layers (for example retry and failover).
AbstractErrorHandlerLayer() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
AbstractErrorHandlerLayer.JobState - Class in org.apache.taverna.workflowmodel.processor.dispatch: Abstract superclass of all state models for pending failure handlers.
AbstractEventHandlingInputPort - Class in org.apache.taverna.workflowmodel.impl: Extends AbstractPort with the getIncomingLink method and an additional implementation method to set the incoming data link
AbstractEventHandlingInputPort(String, int) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
AbstractExecution - Class in org.apache.taverna.platform.execution.api: Abstract implementation of an Execution.
AbstractExecution(WorkflowBundle, Workflow, Profile, Bundle) - Constructor for class org.apache.taverna.platform.execution.api.AbstractExecution: Constructs an abstract implementation of an Execution.
AbstractExecutionEnvironment - Class in org.apache.taverna.platform.execution.api: A common super type for concrete implementations of ExecutionEnvironments.
AbstractExecutionEnvironment(String, String, String, ExecutionService) - Constructor for class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
AbstractExecutionService - Class in org.apache.taverna.platform.execution.api: A common super type for concrete implementations of ExecutionServices.
AbstractExecutionService(String, String, String) - Constructor for class org.apache.taverna.platform.execution.api.AbstractExecutionService
AbstractExternalReference - Class in org.apache.taverna.reference: A trivial implementation of ExternalReference.
AbstractExternalReference() - Constructor for class org.apache.taverna.reference.AbstractExternalReference
AbstractFilteringInputPort - Class in org.apache.taverna.workflowmodel.impl: Abstract superclass for filtering input ports, extend and implement the pushXXX methods to configure behaviour
AbstractFilteringInputPort(String, int) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
AbstractIterationStrategyNode - Class in org.apache.taverna.workflowmodel.processor.iteration: Abstract superclass for implementations of IterationStrategyNode, adds logic to connect nodes together and convenience methods to push jobs and completion events up to the parent node.
AbstractIterationStrategyNode() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
AbstractListServiceImpl - Class in org.apache.taverna.reference.impl: Abstract implementation of ListService, inject with an appropriate ListDao and T2ReferenceGenerator to enable.
AbstractListServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractListServiceImpl
AbstractMergeEdit - Class in org.apache.taverna.workflowmodel.impl
AbstractMergeEdit(Merge) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractMergeEdit
AbstractNumericRangeAssertion<NumericType extends Number> - Class in org.apache.taverna.annotation.annotationbeans: Generic annotation containing a pair of numeric values with precision determined by the type parameter which form a bound.
AbstractNumericRangeAssertion() - Constructor for class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion: Default constructor as mandated by java bean specification
AbstractNumericValueAssertion<NumericType extends Number> - Class in org.apache.taverna.annotation.annotationbeans: Generic annotation containing a single number of precision specified by the type variable
AbstractNumericValueAssertion() - Constructor for class org.apache.taverna.annotation.annotationbeans.AbstractNumericValueAssertion: Default constructor as mandated by java bean specification
AbstractOutputPort - Class in org.apache.taverna.workflowmodel: Simple implementation of OutputPort, extends AbstractPort and adds the granular depth bean getter.
AbstractOutputPort(String, int, int) - Constructor for class org.apache.taverna.workflowmodel.AbstractOutputPort
AbstractPort - Class in org.apache.taverna.workflowmodel: Port definition with depth and name
AbstractPort(String, int) - Constructor for class org.apache.taverna.workflowmodel.AbstractPort
AbstractProcessorEdit - Class in org.apache.taverna.workflowmodel.impl: Abstraction of an edit acting on a Processor instance.
AbstractProcessorEdit(Processor) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractProcessorEdit
AbstractProvenanceItem - Class in org.apache.taverna.provenance.item
AbstractProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.AbstractProvenanceItem
AbstractReferenceServiceImpl - Class in org.apache.taverna.reference.impl: Implementation of ReferenceService, inject with ReferenceSetService, ErrorDocumentService and ListService to enable.
AbstractReferenceServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
AbstractReferenceSetServiceImpl - Class in org.apache.taverna.reference.impl: Abstract implementation of ReferenceSetService, inject with an appropriate ReferenceSetDao to enable.
AbstractReferenceSetServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
AbstractServiceImpl - Class in org.apache.taverna.reference.impl: Abstract superclass for all service implementation objects, will be used to allow injection of thread pooling logic as and when we implement it.
AbstractServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractServiceImpl
AbstractT2ReferenceGenerator - Class in org.apache.taverna.reference.impl: An abstract class for implementing simple T2ReferenceGenerators.
AbstractT2ReferenceGenerator() - Constructor for class org.apache.taverna.reference.impl.AbstractT2ReferenceGenerator
AbstractTextualValueAssertion - Class in org.apache.taverna.annotation.annotationbeans: Generic bit of free text that can be stuck to anything, subclass for more specific uses
AbstractTextualValueAssertion() - Constructor for class org.apache.taverna.annotation.annotationbeans.AbstractTextualValueAssertion: Default constructor as mandated by java bean specification
Activity<ConfigurationType> - Interface in org.apache.taverna.workflowmodel.processor.activity: Defines a single abstract or concrete invokable activity.
activity - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
ActivityAndBeanWrapper - Class in org.apache.taverna.workflowmodel.processor.activity: Used when dragging activities from the palette onto "something".
ActivityAndBeanWrapper() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
ActivityConfigurationException - Exception in org.apache.taverna.platform.capability.api: Thrown when an activity's configuration is incorrect.
ActivityConfigurationException() - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
ActivityConfigurationException(String) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
ActivityConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
ActivityConfigurationException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
ActivityConfigurationException - Exception in org.apache.taverna.workflowmodel.processor.activity: Thrown when attempting to configure an Activity instance with an invalid configuration.
ActivityConfigurationException(String) - Constructor for exception org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException
ActivityConfigurationException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException
ActivityConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException
activityExists(URI) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
activityExists(URI) - Method in interface org.apache.taverna.platform.capability.api.ActivityService: Returns true if and only if the activity type exists.
activityExists(URI) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns true iff an activity exists for the specified URI in this ExecutionEnvironment.
activityExists(URI) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
ActivityFactory - Interface in org.apache.taverna.workflowmodel.processor.activity: Factory for creating Activity instances.
ActivityInputPort - Interface in org.apache.taverna.workflowmodel.processor.activity: Specialisation of InputPort to capture the extra information required by Activity instances.
ActivityInputPortDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config: A bean that describes properties of an Input port.
ActivityInputPortDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
ActivityInputPortImpl - Class in org.apache.taverna.workflowmodel.processor.activity.impl: An input port on an Activity instance.
ActivityInputPortImpl(String, int) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl: Constructs an Activity input port instance with the provided name and depth.
ActivityInputPortImpl(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl: Constructs an Activity input port with the provided name and depth, together with a list of predetermined annotations.
ActivityInvoker - Class in org.apache.taverna.activities.testutils: Helper class to facilitate in executing Activities in isolation.
ActivityInvoker() - Constructor for class org.apache.taverna.activities.testutils.ActivityInvoker
activityList - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
ActivityNotFoundException - Exception in org.apache.taverna.platform.capability.api: Thrown when an activity is not found.
ActivityNotFoundException() - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
ActivityNotFoundException(String) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
ActivityNotFoundException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
ActivityNotFoundException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
ActivityOutputPort - Interface in org.apache.taverna.workflowmodel.processor.activity: The output port of an Activity.
ActivityOutputPortDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config: A bean that describes properties of an Output port.
ActivityOutputPortDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean
ActivityOutputPortImpl - Class in org.apache.taverna.workflowmodel.processor.activity.impl: An output port on an Activity instance, used as a bean to hold port name, depth and granular depth properties.
ActivityOutputPortImpl(String, int, int) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityOutputPortImpl: Constructs an Activity output port instance with the provided name,depth and granular depth.
ActivityOutputPortImpl(String, int, int, Set<AnnotationChain>) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityOutputPortImpl: Constructs an Activity input port with the provided name, depth and granularDepth together with a list of predetermined annotations.
ActivityPort - Interface in org.apache.taverna.workflowmodel.processor.activity: The input or output port of an Activity.
ActivityPortDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config: A generic bean that describes the shared properties of input and output ports.
ActivityPortDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
ActivityPortsDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config: Defines a configuration type that relates directly to an Activity and in particular defines details its input and output ports.
An Activity that has its ports implicitly defined may define a ConfigType that extends this class, but this is not enforced.
ActivityPortsDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
ActivityProvenanceItem - Class in org.apache.taverna.provenance.item: Contains details for an enacted Activity.
ActivityProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.ActivityProvenanceItem
ActivityReport - Class in org.apache.taverna.platform.report: Report about the State of an Activity invocation.
ActivityReport(Activity) - Constructor for class org.apache.taverna.platform.report.ActivityReport: Constructs a new ActivityReport.
ActivityService - Interface in org.apache.taverna.platform.capability.api: Service for discovering available activities and the properties required to configure the activities.
ActivityServiceImpl - Class in org.apache.taverna.platform.capability.activity.impl
ActivityServiceImpl() - Constructor for class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
ActivityTypeNotFoundException - Exception in org.apache.taverna.services: Thrown when an activity type is not found.
ActivityTypeNotFoundException() - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
ActivityTypeNotFoundException(String) - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
ActivityTypeNotFoundException(String, Throwable) - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
ActivityTypeNotFoundException(Throwable) - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
add(T) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
add(int, T) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
addActivityReport(ActivityReport) - Method in class org.apache.taverna.platform.report.ProcessorReport
addAll(Collection<? extends T>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
addAll(int, Collection<? extends T>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
addAnnotation(Annotated<?>, AnnotationBeanSPI, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
addAnnotationAssertion(AnnotationAssertion<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationChainImpl: Add an annotation to the chain Added because without the edits stuff how else can we do it?
addCreator(Person) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
addCurationEvent(CurationEvent<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
addDataflowIdentification(Dataflow, String, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Add the identification of a Dataflow into its identification annotation chain (if necessary)
addEntity(Object) - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
addEntity(Object) - Method in class org.apache.taverna.reference.impl.EmptyReferenceContext
addEntity(Object) - Method in interface org.apache.taverna.reference.ReferenceContext: Add an entity to the context.
addFacadeListener(FacadeListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
addFacadeListener(FacadeListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: A failure listener reports on overall workflow failure.
addFragmentedURI(LinkedHashSet<URI>, URI, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
addInput(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity: Creates and adds a new input port with the provided properties.
addInput(NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
addInputPort(DataflowInputPortImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Adds an input port to the DataFlow.
addInputPortDirectory(Path) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
addInvocation(Invocation) - Method in class org.apache.taverna.platform.report.StatusReport
addIterable(Iterable<E>) - Method in class org.pingel.util.CrossProduct
addJobToStateList(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
addKeyPair(Key, Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Insert a new key entry containing private key and the corresponding public key certificate chain in the Keystore.
addKeyPair(Key, Certificate[]) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Insert a new key entry containing private key and the corresponding public key certificate chain in the Keystore.
addLayer(DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
addLayer(DispatchLayer<?>, int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
addMerge(MergeImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Adds a processor on the DataFlow.
addMonitorableProperty(MonitorableProperty<?>) - Method in interface org.apache.taverna.monitor.MonitorNode: Properties can be added to the monitor node after creation if required, although this should be used only when necessary to avoid race conditions
addObserver(Observer<Message>) - Method in class org.apache.taverna.lang.observer.MultiCaster: Register an observer ie.
addObserver(Observer<Message>) - Method in interface org.apache.taverna.lang.observer.Observable: Register an Observer
addObserver(Observer<MonitorManager.MonitorMessage>) - Method in class org.apache.taverna.monitor.MonitorManager: Register an Observer
addObserver(Observer<KeystoreChangedEvent>) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Add an observer of the changes to the Keystore or Truststore.
addObserver(Observer<KeystoreChangedEvent>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Add an observer of the changes to the Keystore or Truststore.
addObserver(Observer<ProcessorFinishedEvent>) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
addOutgoingLink(DatalinkImpl) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
addOutput(String, int, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity: Creates and adds a new output port with the provided properties.
addOutput(String, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity: Convenience method, creates a new output port with depth and granular depth both set to the value for depth, i.e.
addOutputPort(DataflowOutputPortImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Adds an output port to the DataFlow.
addProcessor(ProcessorImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Adds a processor on the DataFlow.
addProcessorReport(ProcessorReport) - Method in class org.apache.taverna.platform.report.WorkflowReport
addProperties(Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
AddPropertiesMessage(String[], Set<MonitorableProperty<?>>) - Constructor for class org.apache.taverna.monitor.MonitorManager.AddPropertiesMessage
addPropertiesToNode(String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Inject properties into an existing node
addPropertiesToNode(String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.MonitorManager: Push new property get / set methods into the specified node.
addPropertiesToNode(String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
addProvenanceItem(ProvenanceItem) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: Add a ProvenanceItem to the connector
addProxyInput(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity: Add an input to the NonExecutableActivity with the specified name.
addProxyInput(String, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity: Add an input to the NonExecutableActivity with the specified name and depth.
addProxyOutput(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity: Add an output to the NonExecutableActivity with the specified name
addProxyOutput(String, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity: Add an output to the NonExecutableActivity with the specified name and depth
addReportListener(ReportListener) - Method in class org.apache.taverna.platform.report.StatusReport
addResultListener(ResultListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
addResultListener(ResultListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: The result listener is used to handle data tokens produced by the workflow.
addResultListener(ResultListener) - Method in interface org.apache.taverna.workflowmodel.DataflowOutputPort: Add a ResultListener, capable of listening to results being received by the output port
addStrategy(IterationStrategy) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
addTreeModelListener(TypedTreeModelListener<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModel: Adds a listener for the TreeModelEvent posted after the tree changes.
addTrustedCertificate(X509Certificate) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Insert a trusted certificate entry in the Truststore with an alias constructed as: "trustedcert#"#""# "
addTrustedCertificate(X509Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Insert a trusted certificate entry in the Truststore with an alias constructed as: "trustedcert#"#""# "
addUsernameAndPasswordForService(UsernamePassword, URI) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Insert a username and password pair for the given service URI in the Keystore.
addUsernameAndPasswordForService(UsernamePassword, URI) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Insert a username and password pair for the given service URI in the Keystore.
allowsLiteralValues() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort: Literal values are a special case as they are not represented by reference schemes - in rare cases activities may choose to deny literal values, forcing *all* their inputs to be in a particular reference scheme.
allowsLiteralValues() - Method in class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
Annotated<TargetType> - Interface in org.apache.taverna.annotation: Denotes that the object carries workflow object level annotation.
AnnotationAssertion<AnnotationBeanType extends AnnotationBeanSPI> - Interface in org.apache.taverna.annotation: Represents a single assertion of information, providing access to a bean containing the information in the assertion and one specifying the source of the information contained.
AnnotationAssertionImpl - Class in org.apache.taverna.annotation.impl
AnnotationAssertionImpl() - Constructor for class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
AnnotationAssertionImpl(AnnotationBeanSPI, AnnotationRole, List<Person>, AnnotationSourceSPI) - Constructor for class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
AnnotationBeanSPI - Interface in org.apache.taverna.annotation: Marker interface to denote that a bean class is a container for the information encapsulated by an InformationAssertion object
AnnotationChain - Interface in org.apache.taverna.annotation: A fact about an annotated entity is expressed in terms of an annotation chain.
AnnotationChainImpl - Class in org.apache.taverna.annotation.impl
AnnotationChainImpl() - Constructor for class org.apache.taverna.annotation.impl.AnnotationChainImpl
AnnotationPerspective - Interface in org.apache.taverna.annotation: Responsible for the interpretation of an AnnotationChain (which may contain conflicting or disputed information) into a set of AnnotationAssertion instances from that chain which are valid given the chain and some interpretation rule.
AnnotationRole - Enum in org.apache.taverna.annotation: Specifies the role of an AnnotationAssertion within an AnnotationChain
AnnotationSourceSPI - Interface in org.apache.taverna.annotation: A marker interface that specified that the implementation is a bean containing information about a source of annotations.
AnnotationTools - Class in org.apache.taverna.workflowmodel.utils
AnnotationTools() - Constructor for class org.apache.taverna.workflowmodel.utils.AnnotationTools
AppliesTo - Annotation Type in org.apache.taverna.annotation: Annotation to be used on metadata objects to denote which workflow objects they apply to
applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractActivityEdit
applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowEdit
applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowInputPortEdit
applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowOutputPortEdit
applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDatalinkEdit
applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractMergeEdit
applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractProcessorEdit
AsynchronousActivity<ConfigurationType> - Interface in org.apache.taverna.workflowmodel.processor.activity: A concrete invokable activity with an asynchronous invocation API and no knowledge of invocation context.
AsynchronousActivityCallback - Interface in org.apache.taverna.workflowmodel.processor.activity: The callback interface used by instances of AsynchronousActivity to push results and failure messages back to the invocation layer.
augmentationCompleted(Set<ExternalReferenceSPI>) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentorCallback: Called when the augmentation has succeeded
augmentationFailed(ReferenceSetAugmentationException) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentorCallback: Called when the augmentation has failed for some reason
augmentReferenceSet(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
augmentReferenceSet(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentor: Attempts to modify the supplied ReferenceSet such that it contains an implementation of at least one of the ExternalReferenceSPI classes specified.
augmentReferenceSetAsynch(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetAugmentorCallback) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
augmentReferenceSetAsynch(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetAugmentorCallback) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentor: As with ReferenceSetAugmentor.augmentReferenceSet(ReferenceSet, Set, ReferenceContext) but called in an asynchronous fashion.
Author - Class in org.apache.taverna.annotation.annotationbeans: The name of an author of a dataflow held as a String It should allow many but currently only allows one
Author() - Constructor for class org.apache.taverna.annotation.annotationbeans.Author: Default constructor as mandated by java bean specification

B

BAD_WSDL - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
BasicEventForwardingOutputPort - Class in org.apache.taverna.workflowmodel.impl: Extension of AbstractOutputPort implementing EventForwardingOutputPort
BasicEventForwardingOutputPort(String, int, int) - Constructor for class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort: Construct a new abstract output port with event forwarding capability
BlueReference - Class in org.apache.taverna.t2referencetest: BlueReferences carry their data as an internal String and have a resolution cost of 1.0f whatever the value of that string.
BlueReference() - Constructor for class org.apache.taverna.t2referencetest.BlueReference
BlueReference(String) - Constructor for class org.apache.taverna.t2referencetest.BlueReference
BooleanToStringReference - Class in org.apache.taverna.reference.impl.external.object: Convert a java.lang.Boolean to a StringReference.
BooleanToStringReference() - Constructor for class org.apache.taverna.reference.impl.external.object.BooleanToStringReference
buildersUpdated(Object, Map<?, ?>) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
ByteArrayToByteArrayReference - Class in org.apache.taverna.reference.impl.external.object: Convert a byte[] to a ByteArrayReference
ByteArrayToByteArrayReference() - Constructor for class org.apache.taverna.reference.impl.external.object.ByteArrayToByteArrayReference

C

CacheAspect - Class in org.apache.taverna.reference.impl: An aspect used to intercept calls to the various data access objects and divert through a write-through cache provider
CacheAspect() - Constructor for class org.apache.taverna.reference.impl.CacheAspect
cacheSize() - Method in class org.apache.taverna.reference.impl.WriteQueueAspect
cancel(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
cancel() - Method in interface org.apache.taverna.platform.execution.api.Execution: Cancels the execution.
cancel(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Cancels the execution of a workflow.
cancel() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
cancel() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
cancel(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Cancels a running or paused run.
cancel() - Method in class org.apache.taverna.platform.run.impl.Run
cancel(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
cancelWorkflow(String) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop: Cancel the workflow run with the specified id
cancelWorkflowRun() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
cancelWorkflowRun() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Cancel the workflow run corresponding to this facade
canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.file.FileToFileReference
canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.http.UrlToHttpReference: Can convert if the object is an instance of java.net.URL and the protocol is HTTP
canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.BooleanToStringReference: Can convert if the object is an instance of java.lang.Boolean
canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.ByteArrayToByteArrayReference: Can convert if the object is an instance of byte[]
canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.CharacterToStringReference: Can convert if the object is an instance of java.lang.Character
canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.NumberToStringReference: Can convert if the object is an instance of java.lang.Number
canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.StringToStringReference: Can convert if the object is an instance of java.lang.String
canConvert(Object, ReferenceContext) - Method in interface org.apache.taverna.reference.ValueToReferenceConverterSPI: Can this SPI implementation convert the specified object to an ExternalReferenceSPI? This test should be as lightweight as possible, and will usually be based on the Class of the object supplied.
canVisit(Object) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityHealthChecker
canVisit(Object) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker
canVisit(Object) - Method in interface org.apache.taverna.visit.Visitor: Returns true if the visitor can visit the specified object.
canVisit(Object) - Method in class org.apache.taverna.workflowmodel.health.DisabledActivityHealthChecker: The visitor can visit DisabledActivitys.
canVisit(Object) - Method in class org.apache.taverna.workflowmodel.health.UnrecognizedActivityHealthChecker: The visitor can visit UnrecognizedActivitys.
CERTIFICATES_REVOKED_INDICATOR_FILE_NAME - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
changeMasterPassword(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Change the Keystore and the Truststore's master password to the one provided.
changeMasterPassword(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Change the Keystore and the Truststore's master password to the one provided.
CharacterToStringReference - Class in org.apache.taverna.reference.impl.external.object: Convert a Character to a StringReference.
CharacterToStringReference() - Constructor for class org.apache.taverna.reference.impl.external.object.CharacterToStringReference
checkAugmentor() - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl: Check that the reference set augmentor is configured
checkConverterRegistry() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Check whether the converter registry has been defined, throw a ReferenceServiceException if not
checkDao() - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl: Check that the list dao is configured
checkDao() - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl: Check that the list dao is configured
checkDao() - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl: Check that the reference set dao is configured
checkGenerator() - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl: Check that the t2reference generator is configured
checkGenerator() - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl: Check that the t2reference generator is configured
checkGenerator() - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl: Check that the t2reference generator is configured
checkServices() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Throw a ReferenceServiceException if methods in ReferenceService are called without the necessary sub-services configured.
checkValidity() - Method in interface org.apache.taverna.workflowmodel.Dataflow: Triggers a check for various basic potential problems with the workflow, in particular ones related to type checking.
checkValidity() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Run the type check algorithm and return a report on any problems found.
checkValidityImpl() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Works out whether a dataflow is valid.
checkWorkflowFinished(WorkflowInstanceFacadeImpl.WorkflowInstanceFacadeChange) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
childAt(int) - Method in class org.apache.taverna.invocation.TreeCache.NamedNode
childIndices - Variable in class org.apache.taverna.utility.TypedTreeModelEvent
children - Variable in class org.apache.taverna.invocation.TreeCache.NamedNode
children - Variable in class org.apache.taverna.utility.TypedTreeModelEvent
children() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implement TreeNode
children() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: Specialised return type of TreeNode#children()
cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode: Called after a final completion event has been emited for a given owning process, should be used by subclasses to do any tidying required, removing state etc.
cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct
cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.DotProduct
cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.PrefixDotProduct
CLEANUP_DELAY_MS - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
cleanupTimer - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
clear() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
clear() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Clear the child list and parent of this node
clear() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
clear() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: Remove all children nodes and set the parent to null.
clearCachedEndpointStatus() - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker: Clear the cached endpoint statuses.
ClearCachedServiceURIsObserver() - Constructor for class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl.ClearCachedServiceURIsObserver
clone() - Method in class org.apache.taverna.reference.AbstractExternalReference
clone() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI
clone() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
clone() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
clone() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
clone() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
clone() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
clone() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
clone() - Method in class org.apache.taverna.t2referencetest.BlueReference
clone() - Method in class org.apache.taverna.t2referencetest.GreenReference
clone() - Method in class org.apache.taverna.t2referencetest.RedReference
clone() - Method in class org.apache.taverna.t2referencetest.YellowReference
clone() - Method in class org.apache.taverna.visit.VisitReport
clone() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
close() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
close() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
close(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Closes a run.
close(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
CMException - Exception in org.apache.taverna.security.credentialmanager: Represents a (cryptographic or any other) exception thrown by Credential Manager.
CMException() - Constructor for exception org.apache.taverna.security.credentialmanager.CMException: Creates a new CMException.
CMException(String) - Constructor for exception org.apache.taverna.security.credentialmanager.CMException: Creates a new CMException with the specified message.
CMException(String, Throwable) - Constructor for exception org.apache.taverna.security.credentialmanager.CMException: Creates a new CMException with the specified message and cause.
CMException(Throwable) - Constructor for exception org.apache.taverna.security.credentialmanager.CMException: Creates a new CMException with the specified cause throwable.
CMNotInitialisedException - Exception in org.apache.taverna.security.credentialmanager: Represents an exception thrown by Credential Manager if an application tries to invoke certain methods on it before it has been initialised.
CMNotInitialisedException() - Constructor for exception org.apache.taverna.security.credentialmanager.CMNotInitialisedException: Creates a new CMNotInitialisedException.
CMNotInitialisedException(String) - Constructor for exception org.apache.taverna.security.credentialmanager.CMNotInitialisedException: Creates a new CMNotInitialisedException with the specified message.
compare(MasterPasswordProvider, MasterPasswordProvider) - Method in class org.apache.taverna.security.credentialmanager.MasterPasswordProvider.ProviderComparator
compare(NamedWorkflowEntity, NamedWorkflowEntity) - Method in class org.apache.taverna.workflowmodel.utils.NamedWorkflowEntityComparator
compare(Port, Port) - Method in class org.apache.taverna.workflowmodel.utils.PortComparator
compareTo(Invocation) - Method in class org.apache.taverna.platform.report.Invocation
compareTo(TranslationPath) - Method in class org.apache.taverna.reference.impl.TranslationPath: Order by total path cost
Completion - Class in org.apache.taverna.invocation: Contains a (possibly partial) completion event.
Completion(String, int[], InvocationContext) - Constructor for class org.apache.taverna.invocation.Completion: Construct a new optionally partial completion event with the specified owner and completion index
Completion(String, InvocationContext) - Constructor for class org.apache.taverna.invocation.Completion: Construct a new final completion event, equivalent to calling new Completion(owningProcess, new int[0]);
CompletionAwareTreeCache(String, InvocationContext) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer.CompletionAwareTreeCache
completionCreated(Completion) - Method in interface org.apache.taverna.workflowmodel.impl.Crystalizer: Called whenever a completion not corresponding to a node in the cache is generated.
completionCreated(Completion) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorCrystalizerImpl
CompletionHandlingAbstractIterationStrategyNode - Class in org.apache.taverna.workflowmodel.processor.iteration: A superclass for all iteration strategy nodes which are required to propagate final completion events formed from multiple inputs.
CompletionHandlingAbstractIterationStrategyNode() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
CompletionHandlingAbstractIterationStrategyNode.CompletionState - Class in org.apache.taverna.workflowmodel.processor.iteration: Container class for the state of completion for a given process identifier
CompletionState(int) - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode.CompletionState
CompoundEdit - Class in org.apache.taverna.workflowmodel: Implementation of Edit which contains an ordered list of child edits.
CompoundEdit() - Constructor for class org.apache.taverna.workflowmodel.CompoundEdit: Create a new compound edit with no existing Edit objects.
CompoundEdit(List<Edit<?>>) - Constructor for class org.apache.taverna.workflowmodel.CompoundEdit: Create a new compound edit with the specified edits as children.
Condition - Interface in org.apache.taverna.workflowmodel: Defines the base interface for a condition which must be satisfied before a processor can commence invocation.
ConditionCallBack(String) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
conditions - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
conditionsSatisfied(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Called to determine whether all the preconditions for this dispatch stack are satisfied.
Configurable<ConfigurationType> - Interface in org.apache.taverna.workflowmodel: Interface for workflow items that can be configured from a bean.
ConfigurationBean - Annotation Type in org.apache.taverna.workflowmodel.processor.config
ConfigurationException - Exception in org.apache.taverna.platform.capability.api: Thrown when a Configurable cannot be configured by a Configuration.
ConfigurationException() - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
ConfigurationException(String) - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
ConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
ConfigurationException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
ConfigurationException - Exception in org.apache.taverna.workflowmodel: Thrown when attempting to configure a Configurable with an invalid configuration.
ConfigurationException() - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
ConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
ConfigurationException(String) - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
ConfigurationException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
ConfigurationProperty - Annotation Type in org.apache.taverna.workflowmodel.processor.config
ConfigurationProperty.OrderPolicy - Enum in org.apache.taverna.workflowmodel.processor.config
configurationWouldWork() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
configurationWouldWork(Object) - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
configure(JsonNode) - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
configure(JsonNode) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
configure(ConfigurationType) - Method in interface org.apache.taverna.workflowmodel.Configurable: When the item is built from the workflow definition XML the object is first constructed with a default constructor then this method is called, passing in the configuration bean returned by getConfiguration().
configure(ConfigType) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
configure(ConfigType) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity: Called immediately after object construction by the deserialisation framework with a configuration bean built from the auto-generated XML.
configure(ConfigurationType) - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
configure(ActivityAndBeanWrapper) - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
configure(Element) - Method in class org.apache.taverna.workflowmodel.processor.activity.UnrecognizedActivity
configure(Object) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
configure(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
configureFromXML(Element) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl: Configure from an XML element
configurePorts(ActivityPortsDefinitionBean) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity: Simplifies configuring the Activity input and output ports if its ConfigType is an implementation of ActivityPortsDefinitionBean
confirmMasterPassword(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Checks if Keystore's master password is the same as the one provided.
confirmMasterPassword(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Checks if Keystore's master password is the same as the one provided.
connectDefault(NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl: Connect up a new named input port node to the first child of the terminal node.
CONNECTION_PROBLEM - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
CONNECTOR_DERBY - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
CONNECTOR_MYSQL - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
CONNECTOR_TYPE - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
contactEndpoint(Activity<?>, String) - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker: Try to contact the specified endpoint as part of the health-checking of the Activity.
contains(Object) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
containsAll(Collection<?>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
containsErrors() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: Return whether the identified entity either is or contains errors
containsErrors() - Method in interface org.apache.taverna.reference.T2Reference: Error documents always return true, as do any lists where at least one immediate child of the list returns true when this property is evaluated.
containsLocation(int[]) - Method in class org.apache.taverna.invocation.TreeCache: Does the location exist?
containsNestedWorkflow(Processor) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Returns true if processor contains a nested workflow.
contents - Variable in class org.apache.taverna.invocation.TreeCache.NamedNode
context - Variable in class org.apache.taverna.invocation.Event
ContextualizedT2Reference - Interface in org.apache.taverna.reference: Used by the ReferenceService.traverseFrom(T2Reference, int) when traversing a collection structure.
ContextualizedT2ReferenceImpl - Class in org.apache.taverna.reference.impl: Simple implementation of ContextualizedT2Reference
ContextualizedT2ReferenceImpl(T2Reference, int[]) - Constructor for class org.apache.taverna.reference.impl.ContextualizedT2ReferenceImpl
ControlBoundary - Annotation Type in org.apache.taverna.workflowmodel: Denotes that the associated type creates a boundary of control within the dataflow.
controlledConditions - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.file.FileToFileReference: Return a FileReference
convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.http.UrlToHttpReference: Return a new HttpReference constructed from ((URL)o).toExternalForm()
convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.BooleanToStringReference: Return a new InlineStringReference wrapping the supplied String
convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.ByteArrayToByteArrayReference: Return a new InlineByteArrayReference wrapping the supplied byte[]
convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.CharacterToStringReference: Return a new InlineStringReference wrapping the supplied String
convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.NumberToStringReference: Return a new InlineStringReference wrapping the supplied String
convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.StringToStringReference: Return a new InlineStringReference wrapping the supplied String
convert(Object, ReferenceContext) - Method in interface org.apache.taverna.reference.ValueToReferenceConverterSPI: Construct and return a new ExternalReferenceSPI implementation which is in some way equivalent to the supplied object.
convertCertificate(Certificate) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser: Convert the certificate object into an X509Certificate object.
convertCertificate(Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
converters - Variable in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
convertPathToObject(Path) - Static method in class org.apache.taverna.platform.execution.impl.local.T2ReferenceConverter
convertReferenceToPath(Path, T2Reference, InvocationContext) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
CoreDispatchLayerFactory - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Factory for creating core dispatch layers.
CoreDispatchLayerFactory() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
createActivity() - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
createActivity() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
createActivity(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
createActivity(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.ActivityService: Returns the activity for the specified activity type.
createActivity() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory: Creates a new Activity instance.
createActivityInputPort(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Method in interface org.apache.taverna.workflowmodel.Edits: Builds an instance of an InputPort for an Activity.
createActivityInputPort(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl: Builds an instance of ActivityInputPortImpl
createActivityOutputPort(String, int, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Builds an instance of an ActivityOutputPort for an Activity.
createActivityOutputPort(String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl: Builds an instance of ActivityOutputPortImpl
createActivityReport(Activity) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
createActivityReport(Activity) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
createActivityReport(Activity) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
createAnnotationChain() - Method in interface org.apache.taverna.workflowmodel.Edits: Builds a new AnnotationChain.
createAnnotationChain() - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createDataflow(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
createDataflow() - Method in interface org.apache.taverna.workflowmodel.Edits: Build a new Dataflow workflow
createDataflow() - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createDataflowInputPort(String, int, int, Dataflow) - Method in interface org.apache.taverna.workflowmodel.Edits: Builds a new DataflowInputPort.
createDataflowInputPort(String, int, int, Dataflow) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createDataflowOutputPort(String, Dataflow) - Method in interface org.apache.taverna.workflowmodel.Edits: Builds a new DataflowOutputPort.
createDataflowOutputPort(String, Dataflow) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createDatalink(EventForwardingOutputPort, EventHandlingInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Builds a new Datalink with the given source and sink ports
createDatalink(EventForwardingOutputPort, EventHandlingInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createDispatchLayer(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.DispatchLayerService: Returns the dispatch layer for the specified URI.
createDispatchLayer(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
createDispatchLayer(URI) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayerFactory: Creates a new DispatchLayer instance.
createDispatchLayer(URI) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
createExecution(ExecutionEnvironment, WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
createExecution(ExecutionEnvironment, WorkflowBundle, Workflow, Profile, Bundle) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Creates a workflow execution and returns its ID.
createExecutionImpl(WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService: Creates an implementation of an Execution.
createExecutionImpl(WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
createExecutionImpl(WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecutionService
createInputPort(String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Build a new dataflow input port, the granular depth is set for the input port so it can be copied onto the internal output port
createIterationStrategy() - Method in interface org.apache.taverna.workflowmodel.Edits: Builds a new instance of a IterationStrategy.
createIterationStrategy() - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createKeyPairAlias(Key, Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Create a Keystore alias that would be used for adding the given key pair (private and public key) entry to the Keystore.
createKeyPairAlias(Key, Certificate[]) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Create a Keystore alias that would be used for adding the given key pair (private and public key) entry to the Keystore.
createMerge(Dataflow) - Method in interface org.apache.taverna.workflowmodel.Edits
createMerge(Dataflow) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl: Creates a MergeImpl instance.
createMergeInputPort(Merge, String, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Builds a new MergeOutputPort.
createMergeInputPort(Merge, String, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createOutputPort(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Create and return a new DataflowOutputPort in this dataflow
createProcessor(String) - Method in interface org.apache.taverna.workflowmodel.Edits: Builds a new instance of a Processor with the given name.
createProcessor(String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createProcessorInputPort(Processor, String, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Creates a new ProcessorInputPort
createProcessorInputPort(Processor, String, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createProcessorOutputPort(Processor, String, int, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Creates a new ProcessorOutputPort
createProcessorOutputPort(Processor, String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createProcessorReport(Processor) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
createProcessorReport(Processor) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
createProcessorReport(Processor) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputFormat
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputFormat
createReference(InputStream, ReferenceContext) - Method in interface org.apache.taverna.reference.ExternalReferenceBuilderSPI: Given a stream of bytes, build the appropriate target ExternalReferenceSPI implementation which would de-reference to the value of that stream and return it.
createReference(SourceType, ReferenceContext) - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI: Given an existing ExternalReferenceSPI, build the appropriate target ExternalReferenceSPI implementation and return it.
createReference(InputStream, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
createReference(InlineByteArrayReference, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
createReference(InputStream, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
createReference(InlineStringReference, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
createReference(InputStream, ReferenceContext) - Method in class org.apache.taverna.t2referencetest.GreenBuilder: Construct a new GreenReference from the given input stream, ignoring the otherwise helpful context as we don't need any resources from it.
createReference(GreenReference, ReferenceContext) - Method in class org.apache.taverna.t2referencetest.GreenToRed
createRun(RunProfile) - Method in interface org.apache.taverna.platform.run.api.RunService: Creates a new run and returns the ID for the run.
createRun(RunProfile) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
createTrustedCertificateAlias(X509Certificate) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Create a Truststore alias that would be used for adding the given trusted X509 certificate to the Truststore.
createTrustedCertificateAlias(X509Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Create a Truststore alias that would be used for adding the given trusted X509 certificate to the Truststore.
createWorkflowInstanceFacade(Dataflow, InvocationContext, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Build a new WorkflowInstanceFacade using the supplied Dataflow
createWorkflowInstanceFacade(Dataflow, InvocationContext, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
createWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
createWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
createWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
CredentialManager - Interface in org.apache.taverna.security.credentialmanager: Provides a wrapper for Taverna's Keystore and Truststore and implements methods for managing user's credentials (passwords, private/proxy key pairs) and credentials of trusted services and CAs' (i.e.
CredentialManager.KeystoreType - Enum in org.apache.taverna.security.credentialmanager
CredentialManagerAuthenticator - Class in org.apache.taverna.security.credentialmanager.impl: Credential Manager backed Authenticator.
CredentialManagerAuthenticator(CredentialManager) - Constructor for class org.apache.taverna.security.credentialmanager.impl.CredentialManagerAuthenticator
CredentialManagerImpl - Class in org.apache.taverna.security.credentialmanager.impl: Provides an implementation of #CredentialManagerService.
CredentialManagerImpl() - Constructor for class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
CredentialManagerImpl.ClearCachedServiceURIsObserver - Class in org.apache.taverna.security.credentialmanager.impl: Clear the cached service URIs that have username and password associated with them.
CredentialManagerImpl.KeystoreChangedObserver - Class in org.apache.taverna.security.credentialmanager.impl: If any change to the Keystore or Truststore occurs - create the new SSLSocketFactory and set the new default SSLContext which is initialised with the updated Keystore and Truststore material
CrossProduct - Class in org.apache.taverna.workflowmodel.processor.iteration: A cross product node combines its inputs in an 'all against all' manner.
CrossProduct() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct
CrossProduct<E> - Class in org.pingel.util
CrossProduct(List<? extends Iterable<E>>) - Constructor for class org.pingel.util.CrossProduct
CrossProduct(Iterable<E>...) - Constructor for class org.pingel.util.CrossProduct
CrossProductInputFormat - Class in org.apache.taverna.platform.execution.impl.hadoop: An input format that receives an input directory containing a number of directories with input files for each input port to a Taverna processor/activity that will be executed as part of this MapReduce job.
CrossProductInputFormat() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputFormat
CrossProductInputSplit - Class in org.apache.taverna.platform.execution.impl.hadoop
CrossProductInputSplit() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
CrossProductInputSplit(Path, List<Path>) - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
CrossProductRecordReader - Class in org.apache.taverna.platform.execution.impl.hadoop
CrossProductRecordReader() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
CrossProductTest - Class in org.apache.taverna.platform.execution.impl.hadoop
CrossProductTest() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest
CrossProductTest.Map - Class in org.apache.taverna.platform.execution.impl.hadoop
CrossProductTest.Reduce - Class in org.apache.taverna.platform.execution.impl.hadoop
Crystalizer - Interface in org.apache.taverna.workflowmodel.impl: Recieves Job and Completion events and emits Jobs unaltered.
crystalizer - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
Curateable - Interface in org.apache.taverna.annotation: Implemented by objects which can have curation assertions attached to them.
CurationEvent<CurationType extends CurationEventBeanSPI> - Interface in org.apache.taverna.annotation: Represents a single act of curation, parameterized on a bean encapsulating the necessary and sufficient information to describe the specifics of the curation event.
CurationEventBeanSPI - Interface in org.apache.taverna.annotation: Contains the detail for a single curation event.
CurationEventType - Enum in org.apache.taverna.annotation
CURRENT_PORT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
cut(int[]) - Method in class org.apache.taverna.invocation.TreeCache: Chop the cache off at the specified index

D

DaoException - Exception in org.apache.taverna.reference: Thrown by the Data Access Object interface methods, wrapping any underlying exception.
DaoException() - Constructor for exception org.apache.taverna.reference.DaoException
DaoException(String) - Constructor for exception org.apache.taverna.reference.DaoException
DaoException(Throwable) - Constructor for exception org.apache.taverna.reference.DaoException
DaoException(String, Throwable) - Constructor for exception org.apache.taverna.reference.DaoException
data - Variable in class org.apache.taverna.activities.testutils.DummyCallback
DatabaseConfiguration - Interface in org.apache.taverna.configuration.database
DatabaseConfigurationImpl - Class in org.apache.taverna.configuration.database.impl: Configuration for the reference service and provenance.
DatabaseConfigurationImpl(ConfigurationManager) - Constructor for class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
DatabaseManager - Interface in org.apache.taverna.configuration.database
DatabaseManagerImpl - Class in org.apache.taverna.configuration.database.impl: A set of utility methods related to basic data management.
DatabaseManagerImpl(ApplicationConfiguration, DatabaseConfiguration) - Constructor for class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
Dataflow - Interface in org.apache.taverna.workflowmodel: Top level definition object for a dataflow workflow.
DataflowActivity - Class in org.apache.taverna.activities.dataflow: An Activity providing nested Dataflow functionality.
DataflowActivity() - Constructor for class org.apache.taverna.activities.dataflow.DataflowActivity
DataflowActivityFactory - Class in org.apache.taverna.activities.dataflow: An ActivityFactory for creating DataflowActivity.
DataflowActivityFactory() - Constructor for class org.apache.taverna.activities.dataflow.DataflowActivityFactory
DataflowActivityHealthChecker - Class in org.apache.taverna.activities.dataflow
DataflowActivityHealthChecker() - Constructor for class org.apache.taverna.activities.dataflow.DataflowActivityHealthChecker
DataflowCollation - Class in org.apache.taverna.visit: This visit kind is a dummy for collecting together the information associated with a nested workflow.
DataflowCollation() - Constructor for class org.apache.taverna.visit.DataflowCollation
DataflowImpl - Class in org.apache.taverna.workflowmodel.impl: Implementation of Dataflow including implementation of the dataflow level type checker.
DataflowImpl() - Constructor for class org.apache.taverna.workflowmodel.impl.DataflowImpl: Protected constructor, assigns a default name.
DataflowInputPort - Interface in org.apache.taverna.workflowmodel: An input port on a Dataflow contains a nested output port within it.
DataflowInputPortImpl - Class in org.apache.taverna.workflowmodel.impl
DataflowOutputPort - Interface in org.apache.taverna.workflowmodel: Output port of a DataFlow, exposes an internal EventHandlingInputPort into which the internal workflow logic pushes data to be exposed outside the workflow boundary.
DataflowPort - Interface in org.apache.taverna.workflowmodel: Defines that the implementing port belongs to a Dataflow
DataflowRunComplete - Class in org.apache.taverna.provenance.item: Informs the ProvenanceConnector that a workflow has been run to completion.
DataflowRunComplete() - Constructor for class org.apache.taverna.provenance.item.DataflowRunComplete
DataflowValidationReport - Interface in org.apache.taverna.workflowmodel: Contains a validation report from a dataflow validation check.
DataflowValidationReportImpl - Class in org.apache.taverna.workflowmodel.impl: Simple implementation of the DataflowValidationReport interface
Datalink - Interface in org.apache.taverna.workflowmodel: A single point to point data link from an instance of EventForwardingOutputPort to an instance of EventHandlingInputPort
DataProvenanceItem - Class in org.apache.taverna.provenance.item: Contains references to data which a workflow has used or created.
DataProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.DataProvenanceItem
DATATYPE_SOURCE - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
DEFAULT_VALUE - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
defaultConfig() - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
DefaultMasterPasswordProvider - Class in org.apache.taverna.security.credentialmanager.impl
DefaultMasterPasswordProvider() - Constructor for class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
defaultTrustStorePasswords - Static variable in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Various passwords to try for the Java's default truststore.
delete(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
delete() - Method in interface org.apache.taverna.platform.execution.api.Execution: Deletes the execution.
delete(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Deletes the execution of a workflow.
delete() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
delete() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
delete(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Deletes a run.
delete() - Method in class org.apache.taverna.platform.run.impl.Run: Deletes a run.
delete(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
delete(ErrorDocument) - Method in interface org.apache.taverna.reference.ErrorDocumentDao
delete(T2Reference) - Method in interface org.apache.taverna.reference.ErrorDocumentService
delete(T2Reference) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
delete(ErrorDocument) - Method in class org.apache.taverna.reference.impl.InMemoryErrorDocumentDao
delete(IdentifiedList<T2Reference>) - Method in class org.apache.taverna.reference.impl.InMemoryListDao
delete(ReferenceSet) - Method in class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
delete(T2Reference) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
delete(List<T2Reference>) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
delete(T2Reference) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
delete(T2Reference) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
delete(IdentifiedList<T2Reference>) - Method in interface org.apache.taverna.reference.ListDao
delete(T2Reference) - Method in interface org.apache.taverna.reference.ListService
delete(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceService
delete(List<T2Reference>) - Method in interface org.apache.taverna.reference.ReferenceService
delete(ReferenceSet) - Method in interface org.apache.taverna.reference.ReferenceSetDao
delete(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceSetService
deleteData() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
deleteData() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
deleteErrorDocumentsForWFRun(String) - Method in interface org.apache.taverna.reference.ErrorDocumentDao
deleteErrorDocumentsForWFRun(String) - Method in class org.apache.taverna.reference.impl.InMemoryErrorDocumentDao
deleteErrorDocumentsForWorkflowRun(String) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Delete all ErrorDocumentS used by the specific workflow run.
deleteErrorDocumentsForWorkflowRun(String) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
deleteIdentifiedListsForWFRun(String) - Method in class org.apache.taverna.reference.impl.InMemoryListDao
deleteIdentifiedListsForWFRun(String) - Method in interface org.apache.taverna.reference.ListDao
deleteIdentifiedListsForWorkflowRun(String) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
deleteIdentifiedListsForWorkflowRun(String) - Method in interface org.apache.taverna.reference.ListService: Delete all IdentifiedListS used by the specific workflow run.
DeleteIdentifiedOperation - Annotation Type in org.apache.taverna.reference.annotations: Applied to methods in Dao implementations which delete data in the backing store.
deleteKeyPair(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Delete a key pair entry from the Keystore given its alias.
deleteKeyPair(Key, Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Delete a key pair entry from the Keystore given its private and public key parts.
deleteKeyPair(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Delete a key pair entry from the Keystore given its alias.
deleteKeyPair(Key, Certificate[]) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Delete a key pair entry from the Keystore given its private and public key parts.
deleteReferenceSetsForWFRun(String) - Method in class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
deleteReferenceSetsForWFRun(String) - Method in interface org.apache.taverna.reference.ReferenceSetDao
deleteReferenceSetsForWorkflowRun(String) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
deleteReferenceSetsForWorkflowRun(String) - Method in interface org.apache.taverna.reference.ReferenceSetService: Delete all ReferenceSetS used by the specific workflow run.
deleteReferencesForWorkflowRun(String) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
deleteReferencesForWorkflowRun(String) - Method in interface org.apache.taverna.reference.ReferenceService
deleteRevokedCertificates() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
deleteRun(String) - Method in interface org.apache.taverna.workflowmodel.RunDeletionListener
deleteTrustedCertificate(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Delete a trusted certificate entry from the Truststore given its alias.
deleteTrustedCertificate(X509Certificate) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Delete a trusted certificate entry from the Truststore given the certificate.
deleteTrustedCertificate(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Delete a trusted certificate entry from the Truststore given its alias.
deleteTrustedCertificate(X509Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Delete a trusted certificate entry from the Truststore given the certificate.
deleteUsernameAndPasswordForService(URI) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Delete a username and password pair for the given service URI from the Keystore.
deleteUsernameAndPasswordForService(URI) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Delete a username and password pair for the given service URI from the Keystore.
deleteUsernameAndPasswordForService(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Deprecated.
Use CredentialManagerImpl.deleteUsernameAndPasswordForService(URI serviceURI) instead.
depth - Variable in class org.apache.taverna.workflowmodel.AbstractPort
DereferenceException - Exception in org.apache.taverna.reference: Thrown when a problem occurs during de-reference of an ExternalReferenceSPI implementation.
DereferenceException() - Constructor for exception org.apache.taverna.reference.DereferenceException
DereferenceException(String) - Constructor for exception org.apache.taverna.reference.DereferenceException
DereferenceException(Throwable) - Constructor for exception org.apache.taverna.reference.DereferenceException
DereferenceException(String, Throwable) - Constructor for exception org.apache.taverna.reference.DereferenceException
deregisterNode(String[]) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Request the removal of the specified node from the monitor tree.
deregisterNode(String) - Method in class org.apache.taverna.monitor.MonitorManager: Remove the specified node from the monitor.
deregisterNode(String[]) - Method in class org.apache.taverna.monitor.MonitorManager: Remove the specified node from the monitor.
deregisterNode(String[]) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
DeregisterNodeMessage(String[]) - Constructor for class org.apache.taverna.monitor.MonitorManager.DeregisterNodeMessage
DescriptiveTitle - Class in org.apache.taverna.annotation.annotationbeans: The descriptive title of a dataflow held as a String
DescriptiveTitle() - Constructor for class org.apache.taverna.annotation.annotationbeans.DescriptiveTitle: Default constructor as mandated by java bean specification
DeserializationException - Exception in org.apache.taverna.workflowmodel.serialization
DeserializationException(String) - Constructor for exception org.apache.taverna.workflowmodel.serialization.DeserializationException
DeserializationException(String, Exception) - Constructor for exception org.apache.taverna.workflowmodel.serialization.DeserializationException
DeserializeParam(String) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
disableAutoSave() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
disableAutoSave() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
DISABLED - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
DisabledActivity - Class in org.apache.taverna.workflowmodel.processor.activity: A disabled activity is a wrapper for an Activity that is offline or similarly disabled.
DisabledActivity(Class<? extends Activity<?>>, Object) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity: Create a DisabledActivity that represents an offline activity of the specified class with the specified configuration.
DisabledActivity(Activity<?>, Object) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity: Create a DisabledActivity that represents a specific Activity with its configuration.
DisabledActivity(Activity<?>) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity: Create a DisabledActivity that represents a specific Activity that is now disabled e.g.
DisabledActivityHealthChecker - Class in org.apache.taverna.workflowmodel.health: Check on the health of a DisabledActivity
DisabledActivityHealthChecker() - Constructor for class org.apache.taverna.workflowmodel.health.DisabledActivityHealthChecker
DispatchCompletionEvent - Class in org.apache.taverna.workflowmodel.processor.dispatch.events: Dispatch event containing detailing a (potentially partial) completion of a stream of streaming result events.
DispatchCompletionEvent(String, int[], InvocationContext) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchCompletionEvent: Construct a new dispatch result completion event
DispatchErrorEvent - Class in org.apache.taverna.workflowmodel.processor.dispatch.events: Message within the dispatch stack representing a single error report.
DispatchErrorEvent(String, int[], InvocationContext, String, Throwable, DispatchErrorType, Activity<?>) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent: Create a new error event
DispatchErrorType - Enum in org.apache.taverna.workflowmodel.processor.dispatch.events: A simple enumeration of possible failure classes, used to determine whether fault handling dispatch layers should attempt to handle a given failure message.
DispatchJobEvent - Class in org.apache.taverna.workflowmodel.processor.dispatch.events: An event within the dispatch stack containing a single job's worth of data along with an ordered list of Activity instances.
DispatchJobEvent(String, int[], InvocationContext, Map<String, T2Reference>, List<? extends Activity<?>>) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent: Create a new job event, specifying a complete set of input data and a list of activities which could potentially consume this data
DispatchJobQueueEvent - Class in org.apache.taverna.workflowmodel.processor.dispatch.events: A message within the dispatch stack containing a single reference to the job queue from the iteration system along with an ordered list of Activity instances.
DispatchJobQueueEvent(String, InvocationContext, BlockingQueue<IterationInternalEvent<? extends IterationInternalEvent<?>>>, List<? extends Activity<?>>) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent: Create a new job queue event, specifying the queue of Completion and Job objects and the list of activities which will be used to process the corresponding dispatch events
DispatchLayer<ConfigurationType> - Interface in org.apache.taverna.workflowmodel.processor.dispatch: Layers within the dispatch stack define a control flow to handle dispatch of jobs from a queue (generated by the iteration system) to appropriate activities.
DispatchLayerConfigurationException - Exception in org.apache.taverna.platform.capability.api: Thrown when a dispatch layer's configuration is incorrect.
DispatchLayerConfigurationException() - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerConfigurationException
DispatchLayerConfigurationException(String) - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerConfigurationException
DispatchLayerConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerConfigurationException
DispatchLayerConfigurationException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerConfigurationException
DispatchLayerErrorReaction - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description: Describes how a dispatch layer reacts to an error message
dispatchLayerExists(URI) - Method in interface org.apache.taverna.platform.capability.api.DispatchLayerService: Returns true iff a dispatch layer exists for the specified URI.
dispatchLayerExists(URI) - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
dispatchLayerExists(URI) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns true iff a dispatch layer exists for the specified URI in this ExecutionEnvironment.
dispatchLayerExists(URI) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
DispatchLayerFactory - Interface in org.apache.taverna.workflowmodel.processor.dispatch: Factory for creating DispatchLayer instances.
DispatchLayerJobQueueReaction - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description: Describes how a dispatch layer reacts to a Job Queue message
DispatchLayerJobReaction - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description: Describes how a dispatch layer reacts to a Job message
DispatchLayerNotFoundException - Exception in org.apache.taverna.platform.capability.api: Thrown when a dispatch layer is not found.
DispatchLayerNotFoundException() - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerNotFoundException
DispatchLayerNotFoundException(String) - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerNotFoundException
DispatchLayerNotFoundException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerNotFoundException
DispatchLayerNotFoundException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.DispatchLayerNotFoundException
DispatchLayerResultCompletionReaction - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description: Describes how a dispatch layer reacts to a result completion message
DispatchLayerResultReaction - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description: Describes how a dispatch layer responds to a result message
DispatchLayerService - Interface in org.apache.taverna.platform.capability.api: Service for discovering available dispatch layers and the properties required to configure the layers.
DispatchLayerServiceImpl - Class in org.apache.taverna.platform.capability.dispatch.impl
DispatchLayerServiceImpl() - Constructor for class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
DispatchLayerStateEffect - Enum in org.apache.taverna.workflowmodel.processor.dispatch.description: Describes the effect of a message on the state of a dispatch layer, used by DispatchLayerReaction.
DispatchMessageType - Enum in org.apache.taverna.workflowmodel.processor.dispatch.description: Enumeration of the possible message types passed between layers of the dispatch stack.
DispatchResultEvent - Class in org.apache.taverna.workflowmodel.processor.dispatch.events: Dispatch event containing the results from an invocation.
DispatchResultEvent(String, int[], InvocationContext, Map<String, T2Reference>, boolean) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent: Construct a new dispatch result event, specifying the data and whether the result is part of a stream of multiple results events from a single invocation
dispatchStack - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
dispatchStack - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
DispatchStack - Interface in org.apache.taverna.workflowmodel.processor.dispatch: The dispatch stack is responsible for consuming a queue of jobs from the iteration strategy and dispatching those jobs through a stack based control flow to an appropriate invocation target.
DispatchStackImpl - Class in org.apache.taverna.workflowmodel.processor.dispatch.impl: The dispatch stack is responsible for consuming a queue of jobs from the iteration strategy and dispatching those jobs through a stack based control flow to an appropriate invocation target.
DispatchStackImpl() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
DispatchStackImpl.TopLayer - Class in org.apache.taverna.workflowmodel.processor.dispatch.impl
DisputeEvent - Class in org.apache.taverna.annotation.impl
DisputeEvent() - Constructor for class org.apache.taverna.annotation.impl.DisputeEvent
DisputeEvent(DisputeEventDetails, CurationEventType, Curateable) - Constructor for class org.apache.taverna.annotation.impl.DisputeEvent
DisputeEventDetails - Class in org.apache.taverna.annotation.impl
DisputeEventDetails() - Constructor for class org.apache.taverna.annotation.impl.DisputeEventDetails
DistinguishedNameParser - Interface in org.apache.taverna.security.credentialmanager: Methods for parsing Distinguished Names and various associated utility methods.
DistinguishedNameParserImpl - Class in org.apache.taverna.security.credentialmanager.impl: Utility methods for Credential Manager and security-related stuff.
DistinguishedNameParserImpl() - Constructor for class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
DocumentationUrl - Class in org.apache.taverna.annotation.annotationbeans: A link to documentation for the target element contained at a particular Uniform Resource Locator (URL)
DocumentationUrl() - Constructor for class org.apache.taverna.annotation.annotationbeans.DocumentationUrl: Default constructor as mandated by java bean specification
doEdit() - Method in class org.apache.taverna.workflowmodel.CompoundEdit: Attempts to call the doEdit method of all child edits.
doEdit() - Method in interface org.apache.taverna.workflowmodel.Edit: Perform the edit
doEdit() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit
doEditAction(AbstractActivity<T>) - Method in class org.apache.taverna.workflowmodel.impl.AbstractActivityEdit: Do the actual edit here
doEditAction(DataflowImpl) - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowEdit: Do the actual edit here
doEditAction(DataflowInputPortImpl) - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowInputPortEdit: Do the actual edit here
doEditAction(DataflowOutputPortImpl) - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowOutputPortEdit: Do the actual edit here
doEditAction(DatalinkImpl) - Method in class org.apache.taverna.workflowmodel.impl.AbstractDatalinkEdit: Do the actual edit here
doEditAction(MergeImpl) - Method in class org.apache.taverna.workflowmodel.impl.AbstractMergeEdit
doEditAction(ProcessorImpl) - Method in class org.apache.taverna.workflowmodel.impl.AbstractProcessorEdit: Do the actual edit here
doEditAction(DispatchStackImpl) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit: Do the actual edit here
DotProduct - Class in org.apache.taverna.workflowmodel.processor.iteration: The dot product matches jobs by index array, when a job is received a job is emited if and only if the index array of the new job is matched exactly by index arrays of one job in each other input index.
DotProduct() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.DotProduct
DotProductTest - Class in org.apache.taverna.platform.execution.impl.hadoop
DotProductTest() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest
DotProductTest.Map - Class in org.apache.taverna.platform.execution.impl.hadoop
DotProductTest.Reduce - Class in org.apache.taverna.platform.execution.impl.hadoop
doTranslation(ReferenceSet, ReferenceContext) - Method in class org.apache.taverna.reference.impl.TranslationPath
doTypeCheck() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
doTypeCheck() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl: When called this method configures input port filters and the crystalizer, pushing cardinality information into outgoing datalinks.
doTypeCheck() - Method in interface org.apache.taverna.workflowmodel.TokenProcessingEntity: Run a collection level based type check on the token processing entity
DRIVER_CLASS_NAME - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
DummyCallback - Class in org.apache.taverna.activities.testutils: A DummyCallback to aid with testing Activities.
DummyCallback(ReferenceService) - Constructor for class org.apache.taverna.activities.testutils.DummyCallback
DummyReferenceSet - Class in org.apache.taverna.t2referencetest
DummyReferenceSet(ExternalReferenceSPI) - Constructor for class org.apache.taverna.t2referencetest.DummyReferenceSet

E

Edit<TargetType> - Interface in org.apache.taverna.workflowmodel: The workflow object model exposed by this API is read only.
EditException - Exception in org.apache.taverna.workflowmodel: Superclass of all exceptions thrown when altering the workflow model through the edit manager.
EditException(String) - Constructor for exception org.apache.taverna.workflowmodel.EditException
EditException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.EditException
EditException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.EditException
Edits - Interface in org.apache.taverna.workflowmodel: Defines the set of all available edit actions over a workflow model.
EditsImpl - Class in org.apache.taverna.workflowmodel.impl: Implementation of Edits
EditsImpl() - Constructor for class org.apache.taverna.workflowmodel.impl.EditsImpl
EmptyReferenceContext - Class in org.apache.taverna.reference.impl: A trivial implementation of ReferenceContext, used if the context parameter to any service method is null.
EmptyReferenceContext() - Constructor for class org.apache.taverna.reference.impl.EmptyReferenceContext
ENABLE_PROVENANCE - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
enableAutoSave() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
enableAutoSave() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
ENDPOINT_EXPIRY_MILLIS - Static variable in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
equals(Object) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
equals(Object) - Method in class org.apache.taverna.reference.impl.external.file.FileReference
equals(Object) - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
equals(Object) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
equals(Object) - Method in class org.apache.taverna.workflowmodel.OrderedPair: A pair of objects (a,b) is equal to another pair (c,d) if and only if a, b, c and d are all the same type and the condition (a.equals(c) & b.equals(d)) is true.
ErrorBounce - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Receives job events, checks to see whether any parameters in the job are error tokens or collections which contain errors.
ErrorBounce() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
ErrorBounce.ErrorBounceState - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
ErrorBounceState() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce.ErrorBounceState
errorDao - Variable in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
ErrorDocument - Interface in org.apache.taverna.reference: Contains the definition of an error token within the workflow system.
ErrorDocumentDao - Interface in org.apache.taverna.reference: Data access object handling ErrorDocument instances.
ErrorDocumentImpl - Class in org.apache.taverna.reference.impl: Simple bean implementation of ErrorDocument
ErrorDocumentImpl() - Constructor for class org.apache.taverna.reference.impl.ErrorDocumentImpl
ErrorDocumentService - Interface in org.apache.taverna.reference: Provides facilities to register list of T2References, register empty lists at any given depth and to resolve appropriate T2Reference instances back to these lists.
errorDocumentService - Variable in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
ErrorDocumentServiceCallback - Interface in org.apache.taverna.reference: Callback interface used by asynchronous methods in the ErrorDocumentService interface
ErrorDocumentServiceException - Exception in org.apache.taverna.reference: RuntimeException subclass thrown by the error document service layer interfaces.
ErrorDocumentServiceException() - Constructor for exception org.apache.taverna.reference.ErrorDocumentServiceException
ErrorDocumentServiceException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ErrorDocumentServiceException
ErrorDocumentServiceException(String) - Constructor for exception org.apache.taverna.reference.ErrorDocumentServiceException
ErrorDocumentServiceException(Throwable) - Constructor for exception org.apache.taverna.reference.ErrorDocumentServiceException
ErrorDocumentServiceImpl - Class in org.apache.taverna.reference.impl: Implementation of ErrorDocumentService, inject with an appropriate ErrorDocumentDao and T2ReferenceGenerator to enable.
ErrorDocumentServiceImpl() - Constructor for class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
ErrorProvenanceItem - Class in org.apache.taverna.provenance.item: When an error is received in the dispatch stack, one of these is created and sent across to the ProvenanceConnector.
ErrorProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.ErrorProvenanceItem
errorRetrievalFailed(ErrorDocumentServiceException) - Method in interface org.apache.taverna.reference.ErrorDocumentServiceCallback: Called if the retrieval failed for some reason
errorRetrieved(ErrorDocument) - Method in interface org.apache.taverna.reference.ErrorDocumentServiceCallback: Called when the requested ReferenceSet has been successfully retrieved.
Event<EventType extends Event<?>> - Class in org.apache.taverna.invocation: Abstract superclass of all 'event' types within a workflow invocation.
Event(String, int[], InvocationContext) - Constructor for class org.apache.taverna.invocation.Event
EVENT_TOPIC_ROOT - Static variable in interface org.apache.taverna.platform.run.api.RunService
eventAdded(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
eventAdded(String) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.NotifiableLayer: Called when a new Job or Completion is added to a queue within the dispatch stack
EventForwardingOutputPort - Interface in org.apache.taverna.workflowmodel: An extension of OutputPort defining a set of target EventReceivingInputPorts to which internally generated events will be relayed.
EventHandlingInputPort - Interface in org.apache.taverna.workflowmodel: Input port capable of receiving and reacting to workflow events.
ExampleValue - Class in org.apache.taverna.annotation.annotationbeans: A String containing an example or a description of an example
ExampleValue() - Constructor for class org.apache.taverna.annotation.annotationbeans.ExampleValue: Default constructor as mandated by java bean specification
executeAsynch(Map<String, T2Reference>, AsynchronousActivityCallback) - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
executeAsynch(Map<String, T2Reference>, AsynchronousActivityCallback) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
executeAsynch(Map<String, T2Reference>, AsynchronousActivityCallback) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity: Request an asynchronous invocation of the activity on the specified data.
executeAsynch(Map<String, T2Reference>, AsynchronousActivityCallback) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivity: Invoke the activity in an asynchronous manner.
executeAsynch(Map<String, T2Reference>, AsynchronousActivityCallback) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity: Attempting to run a NonExecutableActivity will always fail.
executeAsynchWithMonitoring(Map<String, T2Reference>, AsynchronousActivityCallback) - Method in interface org.apache.taverna.workflowmodel.processor.activity.MonitorableAsynchronousActivity: This has the same invocation semantics as AsynchronousActivity.executeAsynch and all implementations should also implement that method, with the difference that this one returns immediately with a set of monitorable properties which represent monitorable or steerable state within the invocation itself.
executeRunnable(Runnable) - Method in class org.apache.taverna.reference.impl.AbstractServiceImpl: Schedule a runnable for execution - current naive implementation uses a new thread and executes immediately, but this is where any thread pool logic would go if we wanted to add that.
Execution - Interface in org.apache.taverna.platform.execution.api: Interface for a single execution of a Taverna workflow.
ExecutionEnvironment - Interface in org.apache.taverna.platform.execution.api: The ExecutionEnvironment specifies the capabilities of a workflow execution environment.
ExecutionEnvironmentService - Interface in org.apache.taverna.platform.execution.api: Service for finding ExecutionEnvironments.
ExecutionEnvironmentServiceImpl - Class in org.apache.taverna.platform.execution.impl: Implementation of the ExecutionEnvironmentService.
ExecutionEnvironmentServiceImpl() - Constructor for class org.apache.taverna.platform.execution.impl.ExecutionEnvironmentServiceImpl
ExecutionService - Interface in org.apache.taverna.platform.execution.api: Service for executing Taverna workflows.
exportKeyPair(String, Path, String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Export a key entry containing private key and public key certificate chain from the Keystore to a PKCS #12 file.
exportKeyPair(String, Path, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Export a key entry containing private key and public key certificate chain from the Keystore to a PKCS #12 file.
EXPOSE_DATANATURE - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
ExternalReferenceBuilderSPI<TargetType extends ExternalReferenceSPI> - Interface in org.apache.taverna.reference: Constructs an ExternalReferenceSPI instance from a byte stream.
ExternalReferenceConstructionException - Exception in org.apache.taverna.reference: Thrown when an exception occurs during construction of an ExternalReferenceSPI instance.
ExternalReferenceConstructionException() - Constructor for exception org.apache.taverna.reference.ExternalReferenceConstructionException
ExternalReferenceConstructionException(String) - Constructor for exception org.apache.taverna.reference.ExternalReferenceConstructionException
ExternalReferenceConstructionException(Throwable) - Constructor for exception org.apache.taverna.reference.ExternalReferenceConstructionException
ExternalReferenceConstructionException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ExternalReferenceConstructionException
ExternalReferenceSPI - Interface in org.apache.taverna.reference: A reference to a single piece of data.
ExternalReferenceTranslatorSPI<SourceType extends ExternalReferenceSPI,TargetType extends ExternalReferenceSPI> - Interface in org.apache.taverna.reference: Constructs an ExternalReference instance from an existing ExternalReference, most usually of a different type.
ExternalReferenceValidationException - Exception in org.apache.taverna.reference: Thrown by setter methods and constructors of ExternalReferenceSPI implementations when fed parameters which cause some kind of format or validation error.
ExternalReferenceValidationException() - Constructor for exception org.apache.taverna.reference.ExternalReferenceValidationException
ExternalReferenceValidationException(String) - Constructor for exception org.apache.taverna.reference.ExternalReferenceValidationException
ExternalReferenceValidationException(Throwable) - Constructor for exception org.apache.taverna.reference.ExternalReferenceValidationException
ExternalReferenceValidationException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ExternalReferenceValidationException

F

FacadeListener - Interface in org.apache.taverna.facade: Used to communicate a failure of the overall workflow to interested parties.
facadeListeners - Variable in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
FacadeResultListener(Dataflow, WorkflowProvenanceItem) - Constructor for class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.FacadeResultListener
fail(String, Throwable) - Method in class org.apache.taverna.activities.testutils.DummyCallback
fail(String) - Method in class org.apache.taverna.activities.testutils.DummyCallback
fail(String, Throwable, DispatchErrorType) - Method in class org.apache.taverna.activities.testutils.DummyCallback
fail(String, Throwable, DispatchErrorType) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: If the job fails (as opposed to succeeding and sending an error for which the receiveResult method is used) this method will cause an error to be sent up the dispatch stack, triggering any appropriate handling methods such as retry, failover etc.
fail(String, Throwable) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: If the job fails (as opposed to succeeding and sending an error for which the receiveResult method is used) this method will cause an error to be sent up the dispatch stack, triggering any appropriate handling methods such as retry, failover etc.
fail(String) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: If the job fails (as opposed to succeeding and sending an error for which the receiveResult method is used) this method will cause an error to be sent up the dispatch stack, triggering any appropriate handling methods such as retry, failover etc.
fail(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
fail(String, Throwable) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
fail(String, Throwable, DispatchErrorType) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
fail(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
fail(String, Throwable) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
fail(String, Throwable, DispatchErrorType) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
failed - Variable in class org.apache.taverna.activities.testutils.DummyCallback
Failover - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Failure handling dispatch layer, consumes job events with multiple activities and emits the same job but with only the first activity.
Failover() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
failures - Variable in class org.apache.taverna.activities.testutils.DummyCallback
FailureTransmitter - Interface in org.apache.taverna.workflowmodel: Used to message interested parties when a top level failure occurs within a Dataflow
FileReference - Class in org.apache.taverna.reference.impl.external.file: Implementation of ExternalReference used to refer to data held in a locally accessible file.
FileReference() - Constructor for class org.apache.taverna.reference.impl.external.file.FileReference: Explicitly declare default constructor, will be used by hibernate when constructing instances of this bean from the database.
FileReference(File) - Constructor for class org.apache.taverna.reference.impl.external.file.FileReference: Construct a file reference pointed at the specified file and with no character set defined.
FileToFileReference - Class in org.apache.taverna.reference.impl.external.file: Converts java.lang.File instances to FileReference reference type
FileToFileReference() - Constructor for class org.apache.taverna.reference.impl.external.file.FileToFileReference
FilteringInputPort - Interface in org.apache.taverna.workflowmodel: A filtering input port is one capable of filtering events to only pass through data events at a certain depth.
finalize() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
findAncestor(List<Object>, Class<?>) - Static method in class org.apache.taverna.visit.VisitReport: Find the most recent ancestor (earliest in the list) of a given class from the list of ancestors
findEventHandlingInputPort(List<Edit<?>>, Dataflow, InputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Find (and possibly create) an EventHandlingInputPort.
findEventHandlingOutputPort(List<Edit<?>>, Dataflow, OutputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Find (and possibly create) an EventForwardingOutputPort.
findIntermediateProvenance() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
finishedWith(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
finishedWith(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: Clear cached state for the specified process when notified by the dispatch stack
finishedWith(String) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer: Called when there will be no more events with the specified process identifier, can be used to purge cached state from layers within the stack
finishedWith(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Called when the specified owning process is finished with, that is to say all invocation has been performed and any layer state caches have been purged.
finishedWith(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
finishedWith(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance: A set of provenance events for a particular owning process has been finished with so you can remove all the IterationProvenanceItems from the map
finishedWith(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
finishedWith(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
fire() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
fire() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Where a workflow has no inputs this method will cause it to start processing.
fire(String, InvocationContext) - Method in interface org.apache.taverna.workflowmodel.Dataflow: A dataflow with no inputs cannot be driven by the supply of data tokens as it has nowhere to receive such tokens.
fire(String, InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
fire(String, InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
fire(String, InvocationContext) - Method in interface org.apache.taverna.workflowmodel.Processor: A processor with no inputs cannot be driven by the supply of data tokens as it has nowhere to receive such tokens.
firstLayer() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
forget(String, int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: Remove the specified pending retry job from the cache
FreeTextDescription - Class in org.apache.taverna.annotation.annotationbeans: An unconstrained textual description held as a String
FreeTextDescription() - Constructor for class org.apache.taverna.annotation.annotationbeans.FreeTextDescription: Default constructor as mandated by java bean specification

G

generateWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
get(int[]) - Method in class org.apache.taverna.invocation.TreeCache: Get the job object at the specified index array
get(T2Reference) - Method in interface org.apache.taverna.reference.ErrorDocumentDao: Retrieves a named and populated ErrorDocument
get(int) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
get(T2Reference) - Method in class org.apache.taverna.reference.impl.InMemoryErrorDocumentDao
get(T2Reference) - Method in class org.apache.taverna.reference.impl.InMemoryListDao
get(T2Reference) - Method in class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
get(T2Reference) - Method in class org.apache.taverna.reference.impl.SimpleCacheProviderImpl
get(T2Reference) - Method in interface org.apache.taverna.reference.ListDao: Retrieves a named and populated IdentifiedList of T2Reference from the database by T2Reference
get(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceServiceCacheProvider: Called before an attempt is made to retrieve an item from the backing store
get(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceSetDao: Fetch a reference set by id
getA() - Method in class org.apache.taverna.workflowmodel.OrderedPair: Return object a
getAbove() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
getActivities() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent: Returns a list of activity instances which can be applied to the data contained by this job event.
getActivities() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
getActivities() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Override to return the list of activities to be used by this dispatch stack.
getActivity() - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
getActivity() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
getActivity() - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
getActivity() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
getActivityConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
getActivityConfigurationSchema() - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
getActivityConfigurationSchema() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
getActivityConfigurationSchema(URI) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
getActivityConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.capability.api.ActivityService: Returns the JSON Schema for the configuration required by an activity.
getActivityConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns a JSON Schema for the configuration required by an activity.
getActivityConfigurationSchema(URI) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
getActivityConfigurationSchema(URI) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
getActivityConfigurationSchema(URI) - Method in interface org.apache.taverna.services.ServiceRegistry: Returns the JSON Schema for the configuration required by an activity.
getActivityConfigurationSchema() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory: Returns the JSON Schema for the configuration required by the Activity.
getActivityInputPort(Activity<?>, String) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getActivityInputPorts(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
getActivityInputPorts(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.ActivityService: Returns the input ports that the activity type requires to be present in order to execute with the specified configuration.
getActivityInputPorts(URI, JsonNode) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
getActivityInputPorts(URI, JsonNode) - Method in interface org.apache.taverna.services.ServiceRegistry: Returns the input ports that the activity type requires to be present in order to execute with the specified configuration.
getActivityList() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getActivityList() - Method in interface org.apache.taverna.workflowmodel.Processor: A processor contains zero or more activities in an ordered list.
getActivityOutputPort(Activity<?>, String) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getActivityOutputPorts(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
getActivityOutputPorts(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.ActivityService: Returns the output ports that the activity type requires to be present in order to execute with the specified configuration.
getActivityOutputPorts(URI, JsonNode) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
getActivityOutputPorts(URI, JsonNode) - Method in interface org.apache.taverna.services.ServiceRegistry: Returns the output ports that the activity type requires to be present in order to execute with the specified configuration.
getActivityProvenanceItem() - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
getActivityReports() - Method in class org.apache.taverna.platform.report.ProcessorReport
getActivityType() - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
getActivityType() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
getActivityType() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory: What type of Activitys can this factory create?
getActivityTypes() - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
getActivityTypes() - Method in interface org.apache.taverna.platform.capability.api.ActivityService: Returns the available activity types.
getActivityTypes() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns the activity types available in this ExecutionEnvironment.
getActivityTypes() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
getActivityTypes() - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
getActivityTypes() - Method in interface org.apache.taverna.services.ServiceRegistry: Returns the activity types in the registry.
getAddActivityEdit(Processor, Activity<?>) - Method in interface org.apache.taverna.workflowmodel.Edits: Add an Activity implementation to the set of activities within a Processor
getAddActivityEdit(Processor, Activity<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to add an ActivityInputPort to an Activity.
getAddActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddActivityInputPortMappingEdit(Activity<?>, String, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to add a ProcessorInputPort to ActivityInputPort mapping to an Activity.
getAddActivityInputPortMappingEdit(Activity<?>, String, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to add an ActivityOutputPort to an Activity.
getAddActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddActivityOutputPortMappingEdit(Activity<?>, String, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to add a ProcessorOutputPort to OutputPort mapping to an Activity.
getAddActivityOutputPortMappingEdit(Activity<?>, String, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddAnnotationAssertionEdit(AnnotationChain, AnnotationAssertion<?>) - Method in interface org.apache.taverna.workflowmodel.Edits: Add an AnnotationAssertion to an AnnotationChain
getAddAnnotationAssertionEdit(AnnotationChain, AnnotationAssertion<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddAnnotationBean(AnnotationAssertion<T>, AnnotationBeanSPI) - Method in interface org.apache.taverna.workflowmodel.Edits: Add an AnnotationBeanSPI to an AnnotationAssertion
getAddAnnotationBean(AnnotationAssertion, AnnotationBeanSPI) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddAnnotationChainEdit(Annotated<?>, AnnotationBeanSPI) - Method in interface org.apache.taverna.workflowmodel.Edits: Returnes an edit that creates an AnnotationAssertion, adds the AnnotationAssertion to an AnnotationChain and adds the AnnotationChain to the Annotated.
getAddAnnotationChainEdit(Annotated<?>, AnnotationBeanSPI) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddAnnotationEdit(AnnotationChain) - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing
getAddAnnotationEdit(AnnotationChain) - Method in interface org.apache.taverna.annotation.Annotated: Add new workflow object metadata to this annotated entity
getAddAnnotationRole(AnnotationAssertion<T>, AnnotationRole) - Method in interface org.apache.taverna.workflowmodel.Edits
getAddAnnotationRole(AnnotationAssertion, AnnotationRole) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddAnnotationSource(AnnotationAssertion<T>, AnnotationSourceSPI) - Method in interface org.apache.taverna.workflowmodel.Edits
getAddAnnotationSource(AnnotationAssertion, AnnotationSourceSPI) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddCreator(AnnotationAssertion<T>, Person) - Method in interface org.apache.taverna.workflowmodel.Edits
getAddCreator(AnnotationAssertion, Person) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddCurationEvent(AnnotationAssertion<T>, CurationEvent<S>) - Method in interface org.apache.taverna.workflowmodel.Edits
getAddCurationEvent(AnnotationAssertion, CurationEvent) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to add a DataflowInputPort to a Dataflow.
getAddDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to add a DataflowOutputPort to a Dataflow.
getAddDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddDispatchLayerEdit(DispatchStack, DispatchLayer<?>, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Add a new layer to the specified dispatch stack
getAddDispatchLayerEdit(DispatchStack, DispatchLayer<?>, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddIterationStrategyEdit(IterationStrategyStack, IterationStrategy) - Method in interface org.apache.taverna.workflowmodel.Edits
getAddIterationStrategyEdit(IterationStrategyStack, IterationStrategy) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddIterationStrategyInputNodeEdit(IterationStrategy, NamedInputPortNode) - Method in interface org.apache.taverna.workflowmodel.Edits
getAddIterationStrategyInputNodeEdit(IterationStrategy, NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddMergeEdit(Dataflow, Merge) - Method in interface org.apache.taverna.workflowmodel.Edits
getAddMergeEdit(Dataflow, Merge) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddMergeInputPortEdit(Merge, MergeInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to add a MergeInputPort to a Merge.
getAddMergeInputPortEdit(Merge, MergeInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddProcessorEdit(Dataflow, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits: Provides an edit object responsible for adding a Processor to a Dataflow
getAddProcessorEdit(Dataflow, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Provides an Edit to add an input port a processor, creating matching ports in the iteration strategy or strategies as a side effect.
getAddProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAddProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Provides an Edit to add a new output port on a processor
getAddProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getAliases(CredentialManager.KeystoreType) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get all the aliases from the Keystore/Truststore or null if there was some error while accessing it.
getAliases(CredentialManager.KeystoreType) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get all the aliases from the Keystore/Truststore or null if there was some error while accessing it.
getAllowsChildren() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implement TreeNode
getAllowsChildren() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode: These nodes can never have children
getAllowsLiteralValues() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
getAnnotatingClasses(List<AnnotationBeanSPI>, Annotated<?>) - Method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
getAnnotation(Annotated<?>, Class<?>) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
getAnnotationBeanClasses(List<AnnotationBeanSPI>, Class<T>) - Method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
getAnnotations() - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing: Return the set of annotations bound to this annotated object, the set returned is an unmodifiable copy of the internal annotation set, if you need to modify the annotations you should use the get methods for Edit objects to do so.
getAnnotations() - Method in interface org.apache.taverna.annotation.Annotated: Each annotated object contains a bag of metadata object instances
getAnnotations(AnnotationChain) - Method in interface org.apache.taverna.annotation.AnnotationPerspective: Evaluate the annotations and their curation events in the specified chain, resolve conflicts if possible and return the resultant set of annotations
getAnnotationString(Annotated<?>, Class<?>, String) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
getApproximateSizeInBytes() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI: Approximate size of the stored data or -1 if we do not know.
getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl
getApproximateSizeInBytes() - Method in interface org.apache.taverna.reference.ReferenceSet: Get approximate size of the data pointed to by this ReferenceSet.
getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.BlueReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.DummyReferenceSet
getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.GreenReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.RedReference
getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.YellowReference
getAsImpl(T2Reference) - Static method in class org.apache.taverna.reference.impl.T2ReferenceImpl
getAssertions() - Method in interface org.apache.taverna.annotation.AnnotationChain: Returns the ordered list of AnnotationAssertions.
getAssertions() - Method in class org.apache.taverna.annotation.impl.AnnotationChainImpl
getAuthenticator() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
getAuthenticator() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
getB() - Method in class org.apache.taverna.workflowmodel.OrderedPair: Return object b
getBackoffFactor() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig: Factor by which the initial delay is multiplied for each retry after the first, this allows for exponential backoff of retry times up to a certain ceiling
getBean() - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
getBelow() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
getBuilders() - Method in class org.apache.taverna.reference.impl.TranslationPath
getC() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
getC() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
getCancelledDate() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the date that the status changed to CANCELLED.
getCancelledWorkflowRunId() - Method in class org.apache.taverna.facade.WorkflowRunCancellation
getCardinality() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode: Each node defines the level of collection depth for that input port
getCategory() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getCategory() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getCause() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
getCause() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent: Return the throwable behind this error, or null if there was no exception raised to create it.
getCertificate(CredentialManager.KeystoreType, String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get certificate entry from the Keystore or Truststore.
getCertificate(CredentialManager.KeystoreType, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get certificate entry from the Keystore or Truststore.
getChangeDataflowInputPortDepthEdit(DataflowInputPort, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to change the depth of a DataflowInputPort.
getChangeDataflowInputPortDepthEdit(DataflowInputPort, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getChangeDataflowInputPortGranularDepthEdit(DataflowInputPort, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to change the granular depth of a DataflowInputPort.
getChangeDataflowInputPortGranularDepthEdit(DataflowInputPort, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getCharset() - Method in class org.apache.taverna.reference.AbstractExternalReference: Default to returning null for charset
getCharset() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI: For textual data return the character set that should be used to pull data into a java String object.
getCharset() - Method in class org.apache.taverna.reference.impl.external.file.FileReference: Default to returning null for charset
getCharset() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
getCharset() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference: Character encoding set to 'UTF-8' by default
getCharset() - Method in class org.apache.taverna.t2referencetest.BlueReference: Character encoding set to 'UTF-8'
getCharset() - Method in class org.apache.taverna.t2referencetest.GreenReference: Character encoding set to 'UTF-8'
getCharset() - Method in class org.apache.taverna.t2referencetest.RedReference: Character encoding set to 'UTF-8'
getCharset() - Method in class org.apache.taverna.t2referencetest.YellowReference: Character encoding set to 'UTF-8'
getCheckTime() - Method in class org.apache.taverna.visit.VisitReport
getChild(T2Reference) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Return the T2Reference for the sole child of an error document identifier.
getChild(T2Reference) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
getChild(NodeType, int) - Method in interface org.apache.taverna.utility.TypedTreeModel: Returns the child of parent at index 'index' in the parent's child array.
getChildAt(int) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implement TreeNode
getChildAt(int) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: Specialised return type of TreeNode#getChildAt(int)
getChildCount(NodeType) - Method in interface org.apache.taverna.utility.TypedTreeModel: Returns the number of children of parent.
getChildCount() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implement TreeNode
getChildEdits() - Method in class org.apache.taverna.workflowmodel.CompoundEdit
getChildIndices() - Method in class org.apache.taverna.utility.TypedTreeModelEvent: Returns the values of the child indexes.
getChildren() - Method in class org.apache.taverna.utility.TypedTreeModelEvent: Returns the objects that are children of the node identified by getPath at the locations specified by getChildIndices.
getChildren() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implements IterationStrategyNode
getChildren() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: Return a copy of the list of children nodes, or an empty list if TreeNode.getAllowsChildren() is false.
getClassName() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
getClassName() - Method in interface org.apache.taverna.reference.StackTraceElementBean: Returns the fully qualified name of the class containing the execution point represented by this stack trace element.
getClearIterationStrategyStackEdit(IterationStrategyStack) - Method in interface org.apache.taverna.workflowmodel.Edits
getClearIterationStrategyStackEdit(IterationStrategyStack) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getCN() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
getCN() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
getCollections() - Method in class org.pingel.util.CrossProduct
getCompactForm() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
getCompletedDate() - Method in class org.apache.taverna.platform.report.Invocation: Returns the date that the status changed to COMPLETED.
getCompletedDate() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the date that the status changed to COMPLETED.
getCompletionState(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
getCondition() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
getConfiguration() - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
getConfiguration() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
getConfiguration() - Method in interface org.apache.taverna.workflowmodel.Configurable: Each item stores configuration within a bean of type ConfigurationType, this method returns the configuration.
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity: Get a configuration bean representing the definition of the activity.
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.UnrecognizedActivity
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
getConfigureActivityEdit(Activity<ConfigurationBean>, ConfigurationBean) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an Edit that is responsible for configuring an Activity with a given configuration bean.
getConfigureActivityEdit(Activity<T>, T) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getConfigureEdit(Configurable<ConfigurationType>, ConfigurationType) - Method in interface org.apache.taverna.workflowmodel.Edits: Return an Edit that can configure a Configurable (such as an Activity or DispatchLayer with a given configuration bean.
getConfigureEdit(Configurable<T>, T) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getConnectDatalinkEdit(Datalink) - Method in interface org.apache.taverna.workflowmodel.Edits: Connect a datalink to its source and sink.
getConnectDatalinkEdit(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getConnection() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
getConnection() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
getConnectMergedDatalinkEdit(Merge, EventForwardingOutputPort, EventHandlingInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Creates and returns an instance of an Edit that is responsible for generating the links to an from the Merge instance to link together the source and sink port via the merge instance.
getConnectMergedDatalinkEdit(Merge, EventForwardingOutputPort, EventHandlingInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getConnectorType() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getConnectorType() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getConnectProcessorOutputEdit(Processor, String, EventHandlingInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Connect the output port of the specified processor to a target input port.
getConnectProcessorOutputEdit(Processor, String, EventHandlingInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getConstructionCost() - Method in interface org.apache.taverna.reference.ExternalReferenceBuilderSPI: Return an approximate complexity cost of the reference construction.
getConstructionCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
getConstructionCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
getConstructionCost() - Method in class org.apache.taverna.t2referencetest.GreenBuilder: Construction cost fixed at 1.5f
getContainsErrors() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: Property accessor for Hibernate, complies with java bean spec
getContent() - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
getContents() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
getContents() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference: Get the 'value' of this reference as a string, really just returns the internal string representation.
getContents() - Method in class org.apache.taverna.t2referencetest.BlueReference: Get the 'value' of this reference as a string, really just returns the internal string representation.
getContents() - Method in class org.apache.taverna.t2referencetest.GreenReference: Get the 'value' of this reference as a string, really just returns the internal string representation.
getContents() - Method in class org.apache.taverna.t2referencetest.RedReference: Get the 'value' of this reference as a string, really just returns the internal string representation.
getContents() - Method in class org.apache.taverna.t2referencetest.YellowReference: Get the 'value' of this reference as a string, really just returns the internal string representation.
getContext() - Method in class org.apache.taverna.activities.testutils.DummyCallback
getContext() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
getContext() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Return the invocation context used by this facade
getContext() - Method in class org.apache.taverna.invocation.Event
getContext() - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: The invocation context contains resources such as data managers, security agents and provenance consumers to be used by the Activity as it runs.
getContext() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
getContext() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
getControl() - Method in interface org.apache.taverna.workflowmodel.Condition
getControlledPreconditionList() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getControlledPreconditionList() - Method in interface org.apache.taverna.workflowmodel.Processor: A processor may control zero or more other processors within the same level of the workflow through preconditions.
getCreateAndConnectDatalinkEdit(Dataflow, EventForwardingOutputPort, EventHandlingInputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Creates an Edit that creates a Datalink between a source and sink port and connects the Datalink.
getCreateAndConnectDatalinkEdit(Dataflow, OutputPort, InputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Get an Edit that will link the given output port to the given input port.
getCreateConditionEdit(Processor, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits: Create a condition governing execution of the target processor.
getCreateConditionEdit(Processor, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getCreateDataflowInputPortEdit(Dataflow, String, int, int) - Method in interface org.apache.taverna.workflowmodel.Edits: Add an input port to a dataflow.
getCreateDataflowInputPortEdit(Dataflow, String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getCreateDataflowOutputPortEdit(Dataflow, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Add an output port to a dataflow.
getCreateDataflowOutputPortEdit(Dataflow, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getCreatedDate() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the date that the status was set to CREATED.
getCreationDate() - Method in interface org.apache.taverna.annotation.Curateable: All curation events are marked with their creation date, this is the date at which the curation event was associated with its target.
getCreationDate() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
getCreationDate() - Method in interface org.apache.taverna.monitor.MonitorNode: Each node has a creation date
getCreators() - Method in interface org.apache.taverna.annotation.Curateable: Each curateable has a list of people associated with it, frequently one person and in some cases none, although this should be avoided if possible.
getCreators() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
getCredentialManagerDefaultDirectory(ApplicationConfiguration) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser: Get the configuration directory where the security stuff will be/is saved to.
getCredentialManagerDefaultDirectory(ApplicationConfiguration) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
getCurationAssertions() - Method in interface org.apache.taverna.annotation.Curateable: Curateable instances have a list of curation events which are used to determine whether the implementing object is valid given a particular interpretive context.
getCurationAssertions() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
getCurrentKey() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
getCurrentKey() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
getCurrentPort() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getCurrentPort() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getCurrentValue() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
getCurrentValue() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
getData() - Method in class org.apache.taverna.invocation.WorkflowDataToken: Return the ID of the data this event represents
getData() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
getData() - Method in class org.apache.taverna.workflowmodel.processor.activity.Job: The actual data carried by this (partial) Job object is in the form of a map, where the keys of the map are Strings identifying the named input and the values are Strings containing valid data identifiers within the context of a visible DataManager object (see CloudOne specification for further information on the DataManager system)
getData() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent: The actual data carried by this dispatch job event object is in the form of a map, where the keys of the map are Strings identifying the named input and the values are Strings containing valid data identifiers within the context of a visible DataManager object (see CloudOne specification for further information on the DataManager system)
getData() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent: The result contains a map of named EntityIdentifier instances corresponding to the result data.
getDatabaseContext() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getDatabaseContext() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getDataBundle() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
getDataBundle() - Method in interface org.apache.taverna.platform.execution.api.Execution: Returns the Bundle containing the data values for the Workflow.
getDataBundle() - Method in class org.apache.taverna.platform.report.WorkflowReport
getDataBundle() - Method in class org.apache.taverna.platform.run.api.RunProfile: Returns the Bundle containing the data values for the Workflow.
getDataBundle(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Returns the Bundle containing the data values of the run.
getDataBundle() - Method in class org.apache.taverna.platform.run.impl.Run: Returns the Bundle containing the data values of the run.
getDataBundle(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getDataflow() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
getDataflow() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Return the dataflow this facade facades
getDataflow(Workflow) - Method in interface org.apache.taverna.platform.execution.api.WorkflowCompiler: Convert a workflow into a dataflow.
getDataflow(WorkflowBundle) - Method in interface org.apache.taverna.platform.execution.api.WorkflowCompiler: Convert a workflow bundle into a dataflow.
getDataflow(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
getDataflow(WorkflowBundle) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
getDataflow(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
getDataflow() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
getDataflow() - Method in interface org.apache.taverna.workflowmodel.DataflowPort: Get the parent DataFlow to which this port belongs
getDataflow() - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
getDataflow() - Method in exception org.apache.taverna.workflowmodel.InvalidDataflowException: Get the Dataflow that is not valid.
getDataflowActivity(Activity) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
getDataflowID() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
getDataflowProcessor(Processor) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
getDataflowValidationReport() - Method in exception org.apache.taverna.workflowmodel.InvalidDataflowException: Get the validation report for the failing dataflow.
getDataMap() - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
getDataNature() - Method in class org.apache.taverna.reference.AbstractExternalReference: Default to returning DataReferenceNature.UNKNOWN
getDataNature() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI: Determine, if possible, whether the data this reference refers to is textual or binary in nature.
getDataNature() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
getDataNature() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference: Data nature set to 'ReferencedDataNature.TEXT'
getDataNature() - Method in class org.apache.taverna.t2referencetest.BlueReference: Data nature set to 'ReferencedDataNature.TEXT'
getDataNature() - Method in class org.apache.taverna.t2referencetest.GreenReference: Data nature set to 'ReferencedDataNature.TEXT'
getDataNature() - Method in class org.apache.taverna.t2referencetest.RedReference: Data nature set to 'ReferencedDataNature.TEXT'
getDataNature() - Method in class org.apache.taverna.t2referencetest.YellowReference: Data nature set to 'ReferencedDataNature.TEXT'
getDataNatureName() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
getDataSource() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
getDataSource() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
getDate(JsonNode, String) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
getDefaultDispatchStackEdit(Processor) - Method in interface org.apache.taverna.workflowmodel.Edits: Provides an edit that setup the default dispatch stack on a raw processor.
getDefaultDispatchStackEdit(Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getDefaultPropertyMap() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getDefaultPropertyMap() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getDeleteDispatchLayerEdit(DispatchStack, DispatchLayer<?>) - Method in interface org.apache.taverna.workflowmodel.Edits: Remove a dispatch layer from its dispatch stack
getDeleteDispatchLayerEdit(DispatchStack, DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getDepth() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: Get the depth of the entity referred to by this reference
getDepth() - Method in interface org.apache.taverna.reference.T2Reference: All entities identified by a T2Reference have a conceptual depth.
getDepth() - Method in class org.apache.taverna.workflowmodel.AbstractPort
getDepth() - Method in interface org.apache.taverna.workflowmodel.Port
getDepth() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
getDereferenceBasedPaths(ReferenceSet) - Method in class org.apache.taverna.reference.impl.TranslationPath: Return a list of translation paths based on this one but which start at an existing reference within the supplied reference set.
getDescription() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
getDescription() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
getDescription() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns a description of this ExecutionEnvironment.
getDescription() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Returns a description of this ExecutionService.
getDesiredCardinalities() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
getDesiredCardinalities() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategy: Return a map of port name -> desired cardinality for this iteration strategy
getDetail() - Method in interface org.apache.taverna.annotation.AnnotationAssertion: Each annotation assertion contains a bean specifying the actual annotation, varying from a simple string for a free text description to more sophisticated semantic annotations or controlled vocabularies.
getDetail() - Method in interface org.apache.taverna.annotation.CurationEvent
getDetail() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
getDetail() - Method in class org.apache.taverna.annotation.impl.DisputeEvent
getDisconnectDatalinkAndRemovePortsEdit(Datalink, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getDisconnectDatalinkEdit(Datalink) - Method in interface org.apache.taverna.workflowmodel.Edits: Disconnect a datalink from its source and sink.
getDisconnectDatalinkEdit(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getDispatchLayerConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.capability.api.DispatchLayerService: Returns the JSON Schema for the configuration required by a dispatch layer.
getDispatchLayerConfigurationSchema(URI) - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
getDispatchLayerConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns a JSON Schema for the configuration required by a dispatch layer.
getDispatchLayerConfigurationSchema(URI) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
getDispatchLayerConfigurationSchema(URI) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayerFactory: Returns the JSON Schema for the configuration required by the DispatchLayer.
getDispatchLayerConfigurationSchema(URI) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
getDispatchLayerTypes() - Method in interface org.apache.taverna.platform.capability.api.DispatchLayerService: Returns the available dispatch layer types.
getDispatchLayerTypes() - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
getDispatchLayerTypes() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns the dispatch layer types available in this ExecutionEnvironment.
getDispatchLayerTypes() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
getDispatchLayerTypes() - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayerFactory: Returns the types of the DispatchLayers that this factory can create.
getDispatchLayerTypes() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
getDispatchStack() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getDispatchStack() - Method in interface org.apache.taverna.workflowmodel.Processor: The dispatch stack pulls jobs from the queue generated by the iteration system and handles the dispatch of these jobs to appropriate activity workers
getDisplayName() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getDisplayName() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getDocumentationURL() - Method in class org.apache.taverna.annotation.annotationbeans.DocumentationUrl
getDriverClassName() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getDriverClassName() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getEdits() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
getEmailAddress() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
getEmailAddress() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
getEmptyJob(String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer
getEmptyJob(String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorCrystalizerImpl
getEnableDisabledActivityEdit(Processor, DisabledActivity, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getEnactmentEnded() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getEnactmentStarted() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getEndpointExpiryInMilliseconds() - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
getEntities(Class<T>) - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
getEntities(Class<T>) - Method in class org.apache.taverna.reference.impl.EmptyReferenceContext: Return an empty entity set for all queries.
getEntities(Class<T>) - Method in interface org.apache.taverna.reference.ReferenceContext: Return a list of all entities in the resolution context which match the supplied entity type argument.
getEntities(Class<T>) - Method in interface org.apache.taverna.workflowmodel.Dataflow: Get all workflow entities with the specified type restriction, this allows retrieval of Processor, Merge, a mix of the two or any other future entity to be added to the workflow model without a significant change in this part of the API.
getEntities(Class<T>) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Gets all workflow entities of the specified type and returns as an unmodifiable list of that type
getError(T2Reference) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Retrieve a previously named and registered ErrorDocument from the backing store
getError(T2Reference) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
getErrorAsynch(T2Reference, ErrorDocumentServiceCallback) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Functionality the same as getError but in asynchronous mode, returning immediately and using the supplied callback to communicate its results.
getErrorAsynch(T2Reference, ErrorDocumentServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
getErrorDocumentService() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
getErrorDocumentService() - Method in interface org.apache.taverna.reference.ReferenceService: Returns the ErrorDocumentService this ReferenceService uses, use this when you need functionality from that service explicitly.
getErrorItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getErrorReferences() - Method in interface org.apache.taverna.reference.ErrorDocument: If the error document is created from set of references that contain error documents, this method returns them.
getErrorReferences() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
getErrorReferenceSet() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl: Used by Hibernate to bodge around problems with interface types in the API
getErrorType() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
getEventType() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.InputDataProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.OutputDataProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
getEventType() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: What type of information does the item contain.
getEventType() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
getEventType() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
getExceptionMessage() - Method in interface org.apache.taverna.reference.ErrorDocument: If the error document is created from a Throwable, this contains the message part of the Throwable.
getExceptionMessage() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
getExecution(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
getExecutionEnvironment() - Method in class org.apache.taverna.platform.run.api.RunProfile: Returns the ExecutionEnvironment used to execute the Workflow.
getExecutionEnvironments() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironmentService: Returns the available ExecutionEnvironments.
getExecutionEnvironments(Profile) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironmentService: Returns the ExecutionEnvironments that can execute the specified Profile.
getExecutionEnvironments() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Returns the ExecutionEnvironments available for this ExecutionService.
getExecutionEnvironments() - Method in class org.apache.taverna.platform.execution.impl.ExecutionEnvironmentServiceImpl
getExecutionEnvironments(Profile) - Method in class org.apache.taverna.platform.execution.impl.ExecutionEnvironmentServiceImpl
getExecutionEnvironments() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
getExecutionEnvironments() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecutionService
getExecutionEnvironments() - Method in interface org.apache.taverna.platform.run.api.RunService: Returns the available ExecutionEnvironments.
getExecutionEnvironments(WorkflowBundle) - Method in interface org.apache.taverna.platform.run.api.RunService: Returns the ExecutionEnvironments that can execute the specified WorkflowBundle using its default Profile.
getExecutionEnvironments(Profile) - Method in interface org.apache.taverna.platform.run.api.RunService: Returns the ExecutionEnvironments that can execute the specified Profile.
getExecutionEnvironments() - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getExecutionEnvironments(WorkflowBundle) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getExecutionEnvironments(Profile) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getExecutionService() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
getExecutionService() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns the ExecutionService that provides this ExecutionEnvironment.
getExternalReferences() - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl
getExternalReferences() - Method in interface org.apache.taverna.reference.ReferenceSet: The reference set contains a set of ExternalReferenceSPI instances, all of which point to byte equivalent data.
getExternalReferences() - Method in class org.apache.taverna.t2referencetest.DummyReferenceSet
getExtraDescription() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
getFacadeID() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem: As WorkflowInstanceFacades are created for a Processor the details are appended to the owning process identifier.
getFailedActivity() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent: Return the Activity instance which failed to produce this error message
getFailedDate() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the date that the status changed to FAILED.
getFailedEntities() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport: The workflow will be marked as invalid if any entity fails to type check.
getFailedEntities() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
getFailureTransmitter() - Method in interface org.apache.taverna.workflowmodel.Dataflow: The failure transmitter contains event listeners to be notified of workflow level failures - these occur when an error bubbles up to the top of the dispatch stack in a processor and is not handled by conversion to an error token within the data stream.
getFailureTransmitter() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
getFailureType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent: Return the type of failure, this is used by upstream dispatch layers to determine whether they can reasonably handle the error message
getFile() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
getFileName() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
getFileName() - Method in interface org.apache.taverna.reference.StackTraceElementBean: Returns the name of the source file containing the execution point represented by this stack trace element.
getFilePath() - Method in class org.apache.taverna.reference.impl.external.file.FileReference: Getter used by hibernate to retrieve the file path string property
getFilePrefix() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getFilePrefix() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getFilterDepth() - Method in interface org.apache.taverna.workflowmodel.FilteringInputPort: Set the depth at which to filter events.
getFilterDepth() - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
getFirstProcessorWithActivityInputPort(Dataflow, ActivityInputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Find the first processor that contains an activity that has the given activity input port.
getFirstProcessorWithActivityOutputPort(Dataflow, ActivityOutputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getFragmentMappedURIsForAllUsernameAndPasswordPairs() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
getGranularDepth() - Method in class org.apache.taverna.workflowmodel.AbstractOutputPort
getGranularDepth() - Method in interface org.apache.taverna.workflowmodel.OutputPort: The granular depth is the depth of the finest grained item that can be emitted from this output port.
getGranularDepth() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean
getGranularInputDepth() - Method in interface org.apache.taverna.workflowmodel.DataflowInputPort: Define the finest grained item that will be sent to this input port.
getGranularInputDepth() - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
getHandledReferenceSchemes() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort: Declares that the DataDocument instances fed as input data (either directly or as elements of a collection) to this input port must contain at least one of the specified ReferenceScheme types.
getHandledReferenceSchemes() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
getHandledReferenceSchemes() - Method in class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
getHibernateDialect() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getHibernateDialect() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getHttpUrl() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
getHttpUrlString() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference: Getter used by hibernate to retrieve the file path string property
getID() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
getID() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
getID() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
getID() - Method in interface org.apache.taverna.platform.execution.api.Execution: Returns the identifier for this execution.
getID() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns the identifier for this ExecutionEnvironment.
getID() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Returns the identifier for this ExecutionService.
getId() - Method in class org.apache.taverna.platform.report.Invocation: Returns the identifier for this invocation by prepending the identifier of the parent invocation.
getID() - Method in class org.apache.taverna.platform.run.impl.Run: Returns the identifier for this Run.
getId() - Method in interface org.apache.taverna.reference.Identified: Return an appropriately configured instance of T2Reference for this identified object.
getId() - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
getId() - Method in class org.apache.taverna.t2referencetest.DummyReferenceSet
getIdentification() - Method in class org.apache.taverna.annotation.annotationbeans.IdentificationAssertion
GetIdentifiedOperation - Annotation Type in org.apache.taverna.reference.annotations: Applied to methods in Dao implementations which fetch data from the backing store by ID
getIdentifier() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
getIdentifier() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: An identifier that is unique to this facade.
getIdentifier() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
getIdentifier() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: The unique identifier for this item
getIdentifier() - Method in interface org.apache.taverna.workflowmodel.Dataflow: An identifier that is unique to this dataflow and its current state.
getIdentifier() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
getIncomingLink() - Method in interface org.apache.taverna.workflowmodel.EventHandlingInputPort: If this port is connected to a Datalink return the link, otherwise return null
getIncomingLink() - Method in class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
getIndex() - Method in class org.apache.taverna.invocation.Event: Events have an index placing them in a conceptual tree structure.
getIndex() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
getIndex() - Method in class org.apache.taverna.platform.report.Invocation
getIndex() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
getIndex() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
getIndex() - Method in interface org.apache.taverna.reference.ContextualizedT2Reference
getIndex() - Method in class org.apache.taverna.reference.impl.ContextualizedT2ReferenceImpl
getIndex(TreeNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implement TreeNode
getIndexesByProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
getIndexLength() - Method in class org.apache.taverna.invocation.TreeCache: The length of index arrays of jobs within the TreeCache.
getIndexOfChild(NodeType, NodeType) - Method in interface org.apache.taverna.utility.TypedTreeModel: Returns the index of child in parent.
getInitialBuilder() - Method in class org.apache.taverna.reference.impl.TranslationPath
getInitialDelay() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig: Delay in milliseconds between the initial failure message and the first attempt to retry the failed job
getInputDataItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getInputPortDefinitions() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
getInputPortDirectories() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
getInputPortMapping() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
getInputPortMapping() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity: A processor may have different input port names to the activity or activities it contains.
getInputPorts(JsonNode) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
getInputPorts(JsonNode) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
getInputPorts() - Method in interface org.apache.taverna.workflowmodel.Dataflow: Dataflows have a list of input ports.
getInputPorts() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Return a copy of the list of dataflow input ports for this dataflow
getInputPorts() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getInputPorts() - Method in interface org.apache.taverna.workflowmodel.Merge: The Merge object contains an ordered list of InputPort objects.
getInputPorts() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
getInputPorts() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity: An Activity contains a set of named input ports.
getInputPorts(JsonNode) - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory: Returns the ActivityInputPorts that the Activity requires to be present in order to execute with the specified configuration.
getInputPorts() - Method in interface org.apache.taverna.workflowmodel.Processor: Each processor has a list of zero or more input ports.
getInputPorts() - Method in interface org.apache.taverna.workflowmodel.TokenProcessingEntity
getInputPortWithName(String) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getInputs() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
getInputs() - Method in class org.apache.taverna.platform.report.Invocation: Returns a map of input port names to values.
getInstance() - Static method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Get the MonitorImpl singleton
getInstance() - Static method in class org.apache.taverna.monitor.MonitorManager: Get the MonitorManager singleton instance.
getInstance() - Static method in class org.apache.taverna.visit.DataflowCollation
getInstance() - Static method in class org.apache.taverna.workflowmodel.health.HealthCheck
getInternalId() - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
getInternalInputPort() - Method in interface org.apache.taverna.workflowmodel.DataflowOutputPort: Get the internal input port for this workflow output
getInternalOutputPort() - Method in interface org.apache.taverna.workflowmodel.DataflowInputPort: Return the internal output port.
getInternalOutputPort() - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
getInvalidDataflows() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport: An entity will be marked invalid if it depends on a nested dataflow which itself is invalid.
getInvalidDataflows() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
getInvocation(String) - Method in class org.apache.taverna.platform.report.StatusReport: Get an invocation with a given name.
getInvocationContext() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: Get the InvocationContext that this reporter should be using if it needs to dereference any data
getInvocationEnded() - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
getInvocationProcessId() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
getInvocations() - Method in class org.apache.taverna.platform.report.Invocation: Returns the child invocations.
getInvocations() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the invocations.
getInvocationStarted() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
getInvocationStarted() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
getIteration() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct
getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.DotProduct
getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl: The iteration depth here is calculated by taking first the top iteration strategy and applying the actual input types to it, then for each subsequent strategy in the stack using the 'desired cardinality' of the input nodes for each layer to work out the increase in index array length.
getIterationDepth(Map<String, Integer>) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategy: The iteration strategy results in a set of job objects with a particular job index.
getIterationDepth(Map<String, Integer>) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: In the context of an enclosing iteration strategy each node should be able to return the iteration depth, i.e.
getIterationDepth(Map<String, Integer>) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyStack: Calculate the depth of the iteration strategy stack as a whole given a set of named inputs and their cardinalities.
getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode: Iteration depth is the difference between the supplied input depth and the desired one.
getIterationProvenanceItem() - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
getIterationProvItem(Event<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
getIterationStrategy() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getIterationStrategy() - Method in interface org.apache.taverna.workflowmodel.Processor: The iteration strategy is responsible for combining input data events into jobs which are then queued for execution through the dispatch stack
getJavaTruststorePassword() - Method in interface org.apache.taverna.security.credentialmanager.JavaTruststorePasswordProvider: Get the Java truststore password.
getJavaTruststorePasswordProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get the Java truststore password providers for providing the password to encrypt/decrypt the Java's default truststore.
getJDBCUri() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getJDBCUri() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getJobsCompleted() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
getJobsCompleted() - Method in class org.apache.taverna.platform.report.ProcessorReport: Returns the number of jobs that the processor has completed.
getJobsCompletedWithErrors() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
getJobsCompletedWithErrors() - Method in class org.apache.taverna.platform.report.ProcessorReport: Returns the number of jobs that completed with an error.
getJobsCopy(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: Get a copy of the list of AbstractErrorHandlerLayer.JobStates for the owning process, or an empty list if the owning process is unknown or have been forgotten.
getJobsDefault(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: Get the list of AbstractErrorHandlerLayer.JobStates for the owning process, creating and adding it to the state map if necessary.
getJobsQueued() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
getJobsQueued() - Method in class org.apache.taverna.platform.report.ProcessorReport: Returns the number of jobs queued by the processor.
getJobsStarted() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
getJobsStarted() - Method in class org.apache.taverna.platform.report.ProcessorReport: Returns the number of jobs that the processor has started processing.
getJTree() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Returns a tree view over the monitor.
getKeyPairsCertificateChain(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get certificate chain for the key pair entry from the Keystore given its alias.
getKeyPairsCertificateChain(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get certificate chain for the key pair entry from the Keystore.
getKeyPairsPrivateKey(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get the private key part of a key pair entry from the Keystore given its alias.
getKeyPairsPrivateKey(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get the private key part of a key pair entry from the Keystore given its alias.
getKind() - Method in class org.apache.taverna.visit.VisitReport
getL() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
getL() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
getLastModified() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
getLastModified() - Method in interface org.apache.taverna.monitor.MonitorableProperty: Get the last update date for this property, if the property is immutable then this should be set to the date at which the implementation is created.
getLastModified() - Method in class org.apache.taverna.platform.execution.impl.local.StaticProperty
getLastWorkingConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
getLayers() - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack: The DispatchStack consists of an ordered list of DispatchLayer instances where the DispatchLayer at index zero is at the bottom of the stack and is almost always an invocation layer of some kind (in any working dispatch stack configuration)
getLayers() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
getLength() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
getLineNumber() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
getLineNumber() - Method in interface org.apache.taverna.reference.StackTraceElementBean: Returns the line number of the source line containing the execution point represented by this stack trace element.
getLinks() - Method in interface org.apache.taverna.workflowmodel.Dataflow: The dataflow is largely defined by the links between processors and other entities within its scope.
getLinks() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: For each processor input, merge input and workflow output get the incoming link and, if non null, add to a list and return the entire list.
getList(T2Reference) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
getList(T2Reference) - Method in interface org.apache.taverna.reference.ListService: Retrieve a previously named and registered list of T2Reference instances identified by the specified T2Reference (which must be of type T2ReferenceType.IdentifiedList)
getListAsynch(T2Reference, ListServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl
getListAsynch(T2Reference, ListServiceCallback) - Method in interface org.apache.taverna.reference.ListService: Functionality the same as getList but in asynchronous mode, returning immediately and using the supplied callback to communicate its results.
getListContents() - Method in class org.apache.taverna.reference.impl.T2ReferenceListImpl: This is only called from Hibernate, outside of test code, so is relatively safe to leave unchecked.
getListService() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
getListService() - Method in interface org.apache.taverna.reference.ReferenceService: Returns the ListService this ReferenceService uses, use this when you need functionality from that service explicitly.
getLocalName() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Return the local name of this workflow
getLocalName() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getLocalName() - Method in interface org.apache.taverna.workflowmodel.NamedWorkflowEntity: Every workflow level entity has a name which is unique within the workflow in which it exists.
getLocalPart() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: Get the local part of the URI for this reference
getLocalPart() - Method in interface org.apache.taverna.reference.T2Reference: In addition to the namespace the T2Reference contains a local identifier.
getLocations() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
getLowerNumericValue() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
getMapProcessorPortsForActivityEdit(Processor) - Method in interface org.apache.taverna.workflowmodel.Edits: Provides an edit that will configure the processors ports to map to those of its internal Activity.
getMapProcessorPortsForActivityEdit(Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getMasterPassword(boolean) - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
getMasterPassword(boolean) - Method in interface org.apache.taverna.security.credentialmanager.MasterPasswordProvider: Get the master password for the Credential Manager.
getMasterPasswordProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get the master password providers for providing the master password to encrypt/decrypt the Credential Maager's Keystore and Truststore.
getMaxDelay() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig: Maximum delay in milliseconds between failure reception and retry.
getMaximumJobs() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ParallelizeConfig
getMaxRetries() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig: Maximum number of retries for a failing process
getMerge() - Method in interface org.apache.taverna.workflowmodel.MergePort
getMerges() - Method in interface org.apache.taverna.workflowmodel.Dataflow: Dataflows also contain a set of merge operations, this method returns an unmodifiable copy of the set.
getMerges() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Return the list of all merge operations within the dataflow
getMessage() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
getMessage() - Method in interface org.apache.taverna.reference.ErrorDocument: Error documents can carry an arbitrary string message, this returns it.
getMessage() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
getMessage() - Method in class org.apache.taverna.visit.VisitReport
getMessage() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent: Return the textual message representing this error
getMessageDigestAsFormattedString(byte[], String) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
getMessageDigestAsFormattedString(byte[], String) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl: Get the message digest of the given byte array as a string of hexadecimal characters in the form XX:XX:XX...
getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.AbstractDispatchEvent: Return the DispatchMessageType for this event object
getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchCompletionEvent: DispatchMessageType.RESULT_COMPLETION
getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent
getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent
getMethodName() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
getMethodName() - Method in interface org.apache.taverna.reference.StackTraceElementBean: Returns the name of the method containing the execution point represented by this stack trace element.
getMimeType() - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
getMimeTypes() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
getMonitorTree() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
getMoveDatalinkSinkEdit(Dataflow, Datalink, EventHandlingInputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getName() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
getName() - Method in interface org.apache.taverna.monitor.MonitorableProperty: Return the name of this property, names are heirarchical in nature and are defined as an array of String objects.
getName() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
getName() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
getName() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment: Returns the name of this ExecutionEnvironment.
getName() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Returns the name of this ExecutionService.
getName() - Method in class org.apache.taverna.platform.execution.impl.local.StaticProperty
getName() - Method in class org.apache.taverna.platform.report.Invocation: Returns the name for this invocation.
getName() - Method in class org.apache.taverna.workflowmodel.AbstractPort
getName() - Method in interface org.apache.taverna.workflowmodel.Port
getName() - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
getName() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
getNamespace() - Method in class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator: Get the namespace for identifiers generated by this class
getNamespace() - Method in class org.apache.taverna.reference.impl.UUIDT2ReferenceGenerator
getNamespace() - Method in interface org.apache.taverna.reference.T2ReferenceGenerator: All T2Reference objects will have this namespace
getNamespacePart() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: Get the namespace part of the URI for this reference
getNamespacePart() - Method in interface org.apache.taverna.reference.T2Reference: T2Reference instances retain a reference to the reference manager which created them in the form of a namespace.
getNestedDataflow() - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
getNestedDataflow() - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflow
getNestedDataflow() - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflowSource
getNestedPathForProcessor(Processor, Dataflow) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Return a path of processors where the last element is this processor and previous ones are nested processors that contain this one all the way to the top but excluding the top level workflow as this is only a list of processors.
getNestedWorkflowReport() - Method in class org.apache.taverna.platform.report.ActivityReport
getNewProperties() - Method in class org.apache.taverna.monitor.MonitorManager.AddPropertiesMessage
getNextLocalPart() - Method in class org.apache.taverna.reference.impl.AbstractT2ReferenceGenerator: Generate a new local part for a new reference.
getNextLocalPart() - Method in class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator
getNextLocalPart() - Method in class org.apache.taverna.reference.impl.UUIDT2ReferenceGenerator
getNodeRemovalDelay() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
getNumericValue() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericValueAssertion
getO() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
getO() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
getObject(ProceedingJoinPoint) - Method in class org.apache.taverna.reference.impl.CacheAspect: Handle a 'get by T2Reference' operation on a Dao
getObject() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
getObject(ProceedingJoinPoint) - Method in class org.apache.taverna.reference.impl.WriteQueueAspect: Handle a 'get by T2Reference' operation on a Dao
getObservers() - Method in class org.apache.taverna.lang.observer.MultiCaster: A list of all the classes currently registered with this MultiCaster
getObservers() - Method in interface org.apache.taverna.lang.observer.Observable: A list of all the currently registered Observers
getObservers() - Method in class org.apache.taverna.monitor.MonitorManager: A list of all the currently registered Observers
getObservers() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get all current observers of changes to the Keystore or Truststore.
getObservers() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get all current observers of changes to the Keystore or Truststore.
getObservers() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getOU() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
getOU() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
getOutgoingLinks() - Method in interface org.apache.taverna.workflowmodel.EventForwardingOutputPort: The set of datalinks for which this output port is the source of events
getOutgoingLinks() - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort: Implements EventForwardingOutputPort
getOutputDataItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getOutputPort() - Method in interface org.apache.taverna.workflowmodel.Merge: The Merge object has a single output port through which modified events are emitted as described in the javadoc for getInputPorts
getOutputPortDefinitions() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
getOutputPortMapping() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
getOutputPortMapping() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity: Outputs of the activity may be named differently to those of the processor.
getOutputPorts(JsonNode) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
getOutputPorts(JsonNode) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.Dataflow: Dataflows have a list of output ports.
getOutputPorts() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Return all dataflow output ports
getOutputPorts() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getOutputPorts() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity: An Activity contains a set of named output ports.
getOutputPorts(JsonNode) - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory: Returns the ActivityOutputPorts that the Activity requires to be present in order to execute with the specified configuration.
getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.Processor: Each processor has a list of zero or more output ports.
getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.TokenProcessingEntity
getOutputPortWithName(String) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getOutputs() - Method in class org.apache.taverna.platform.report.Invocation: Returns a map of output port names to values.
getOwningProcess() - Method in class org.apache.taverna.invocation.Event: The event has an owner, this is represented as a String object but the ownership is hierarchical in nature.
getOwningProcess() - Method in class org.apache.taverna.monitor.MonitorManager.MonitorMessage
getOwningProcess() - Method in interface org.apache.taverna.monitor.MonitorNode: Each monitor node has an identity corresponding to the identifier stack of the data flowing through the workflow object that created it.
getOwningProcess() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
getOwningProcess() - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
getParent() - Method in class org.apache.taverna.platform.report.Invocation: Returns the parent invocation.
getParent() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implement TreeNode
getParent() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: Specialised return type of TreeNode#getParent()
getParentDataflow() - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflowSource
getParentId() - Method in class org.apache.taverna.platform.report.Invocation
getParentId() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
getParentId() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: Who is the parent of this item?
getParentIterationItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
getParentProcessIdentifier() - Method in class org.apache.taverna.activities.testutils.DummyCallback
getParentProcessIdentifier() - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: For activities which are going to establish state below the invoke node in the monitor tree this method returns the owning process identifier allocated to the invoke node.
getParentProcessIdentifier() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
getParentProcessIdentifier() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
getParentReport() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the parent report.
getPassword() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getPassword() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getPassword() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
getPasswordAsString() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
getPasswordAuthentication() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerAuthenticator
getPathCost() - Method in class org.apache.taverna.reference.impl.TranslationPath: Sum of translation costs of all translators in path
getPausedDate() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the date that the status last changed to PAUSED.
getPausedDates() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the dates that the status changed to PAUSED.
getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToBooleanConverter
getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToByteArrayConverter
getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToDoubleConverter
getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToIntegerConverter
getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToStringConverter
getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToVMObjectReferenceConverter
getPojoClass() - Method in interface org.apache.taverna.reference.StreamToValueConverterSPI: The class of objects which this builder can construct from a stream
getPoolMaxActive() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getPoolMaxActive() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getPoolMaxIdle() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getPoolMaxIdle() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getPoolMinIdle() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getPoolMinIdle() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getPoppedIndex() - Method in class org.apache.taverna.invocation.IterationInternalEvent: Helper method for the popIndex operation, returns the modified index array.
getPort() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getPort() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getPortName() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
getPortName() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode: Each node maps to a single named input port within the processor
getPossibleServiceURIsToLookup(URI, boolean) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
getPreconditionList() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
getPreconditionList() - Method in interface org.apache.taverna.workflowmodel.Processor: A processor has zero or more preconditions explicitly declared.
getPrimaryKey() - Method in class org.apache.taverna.reference.AbstractExternalReference: Used by Hibernate internally to establish a foreign key relationship between this abstract superclass and tables corresponding to implementations of the ExternalReference interface.
getProcessId() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
getProcessId() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: Get the enactor supplie identifier
getProcessName() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Defines the enclosing process name, usually Processor.getName() on the parent
getProcessor() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
getProcessor() - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack: The dispatch stack is contained within a processor, this can be null if the stack is being used out of this context but layers may be relying on this link to get information about the processor input ports and their annotations for various reasons.
getProcessor() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
getProcessor() - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
getProcessor() - Method in interface org.apache.taverna.workflowmodel.ProcessorPort: Get the Processor to which this port belongs
getProcessorId(String[]) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
getProcessorID() - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
getProcessorInputPort(Processor, Activity<?>, InputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getProcessorOutputPort(Processor, Activity<?>, OutputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getProcessorProvenanceItem() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
getProcessorReports() - Method in class org.apache.taverna.platform.report.WorkflowReport
getProcessors() - Method in interface org.apache.taverna.workflowmodel.Dataflow: A Dataflow consists of a set of named Processor instances.
getProcessors() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Return the list of all processors within the dataflow
getProcessorsWithActivity(Dataflow, Activity<?>) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getProcessorsWithActivityInputPort(Dataflow, ActivityInputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getProcessorsWithActivityOutputPort(Dataflow, OutputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getProfile() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
getProfile() - Method in interface org.apache.taverna.platform.execution.api.Execution: Returns the Profile to use when executing the Workflow.
getProfile(String) - Method in interface org.apache.taverna.platform.run.api.RunService
getProfile() - Method in class org.apache.taverna.platform.run.impl.Run
getProfile(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getProfileName() - Method in class org.apache.taverna.platform.run.api.RunProfile: Returns the name of the Profile to use when running the Workflow.
getProgress() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
getProgress() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
getProperties() - Method in class org.apache.taverna.monitor.MonitorManager.RegisterNodeMessage
getProperties() - Method in interface org.apache.taverna.monitor.MonitorNode: Each monitor node exposes a set of properties, which may or may not be mutable
getProperties() - Method in class org.apache.taverna.visit.VisitReport
getProperties() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
getProperty(String) - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
getProperty(String) - Method in class org.apache.taverna.platform.report.ProcessorReport
getProperty(String) - Method in class org.apache.taverna.visit.VisitReport
getPropertyKeys() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
getPropertyKeys() - Method in class org.apache.taverna.platform.report.ProcessorReport
getProvenanceCollection() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: Get all the ProvenanceItems that the connector currently knows about
getProvenanceReporter() - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
getProvenanceReporter() - Method in interface org.apache.taverna.invocation.InvocationContext
getProviderPriority() - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
getProviderPriority() - Method in interface org.apache.taverna.security.credentialmanager.MasterPasswordProvider: Get the priority of this provider.
getPushedDataMap() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
getPushedDataMap() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Return a map of the data pushed on the named port
getPushedOwningProcess() - Method in class org.apache.taverna.invocation.IterationInternalEvent: Helper method for the pushIndex operation
getQueue() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
getReference() - Method in interface org.apache.taverna.reference.ContextualizedT2Reference
getReference() - Method in class org.apache.taverna.reference.impl.ContextualizedT2ReferenceImpl
getReferenceService() - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
getReferenceService() - Method in interface org.apache.taverna.invocation.InvocationContext: Return the reference service to be used within this invocation context
getReferenceService() - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
getReferenceService() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
getReferenceService() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: Get the ReferenceService in use by this connector
getReferenceSet(T2Reference) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
getReferenceSet(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceSetService: Get a previously registered ReferenceSet by T2Reference.
getReferenceSetAsynch(T2Reference, ReferenceSetServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
getReferenceSetAsynch(T2Reference, ReferenceSetServiceCallback) - Method in interface org.apache.taverna.reference.ReferenceSetService: Functionality the same as getReferenceSet but in asynchronous mode, returning immediately and using the supplied callback to communicate its results.
getReferenceSetService() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
getReferenceSetService() - Method in interface org.apache.taverna.reference.ReferenceService: Returns the ReferenceSetService this ReferenceService uses, use this when you need functionality from that service explicitly.
getReferenceSetWithAugmentation(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
getReferenceSetWithAugmentation(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceSetService: Functionality the same as getReferenceSet but with the additional option to specify a set of ExternalReferenceSPI classes.
getReferenceSetWithAugmentationAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl: Functionality as getReferenceSetWithAugmentation but with the addition of a callback interface to report the result or failure of the method.
getReferenceSetWithAugmentationAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetServiceCallback) - Method in interface org.apache.taverna.reference.ReferenceSetService: Functionality as getReferenceSetWithAugmentation but with the addition of a callback interface to report the result or failure of the method.
getReferenceType() - Method in interface org.apache.taverna.reference.ExternalReferenceBuilderSPI: Expose the type of the ExternalReferenceSPI that this builder can construct
getReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
getReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
getReferenceType() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: Get the type of the entity to which this reference refers
getReferenceType() - Method in interface org.apache.taverna.reference.T2Reference: To determine the entity that this reference points to we use an enumeration of possible entity types
getReferenceType() - Method in class org.apache.taverna.t2referencetest.GreenBuilder
getRemoveActivityEdit(Processor, Activity<?>) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove an Activity from a Processor
getRemoveActivityEdit(Processor, Activity<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove an ActivityInputPort from an Activity.
getRemoveActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveActivityInputPortMappingEdit(Activity<?>, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove a ProcessorInputPort to ActivityInputPort mapping from an Activity.
getRemoveActivityInputPortMappingEdit(Activity<?>, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove an OutputPort from an Activity.
getRemoveActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveActivityOutputPortMappingEdit(Activity<?>, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove a ProcessorOutputPort to OutputPort mapping from an Activity.
getRemoveActivityOutputPortMappingEdit(Activity<?>, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveAnnotationEdit(AnnotationChain) - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing
getRemoveAnnotationEdit(AnnotationChain) - Method in interface org.apache.taverna.annotation.Annotated: Remove an annotation object from the this annotated entity
getRemoveConditionEdit(Processor, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits: Remove a condition previously applied to the specified pair of Processor instances
getRemoveConditionEdit(Processor, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove a DataflowInputPort from a Dataflow.
getRemoveDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove a DataflowOutputPort from a Dataflow.
getRemoveDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveMergeEdit(Dataflow, Merge) - Method in interface org.apache.taverna.workflowmodel.Edits: Removes a merge from the dataflow.
getRemoveMergeEdit(Dataflow, Merge) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveProcessorEdit(Dataflow, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to remove a Processor from a Dataflow.
getRemoveProcessorEdit(Dataflow, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits: Removes a Processor input port.
getRemoveProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveProcessorInputPortEdit(ProcessorInputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getRemoveProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
getRemoveProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRemoveProcessorOutputPortEdit(ProcessorOutputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getRenameDataflowInputPortEdit(DataflowInputPort, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Rename a dataflow input port
getRenameDataflowInputPortEdit(DataflowInputPort, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRenameDataflowOutputPortEdit(DataflowOutputPort, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Rename a dataflow output port
getRenameDataflowOutputPortEdit(DataflowOutputPort, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRenameMergeEdit(Merge, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Rename a merge
getRenameMergeEdit(Merge, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getRenameProcessorEdit(Processor, String) - Method in interface org.apache.taverna.workflowmodel.Edits: Rename a processor
getRenameProcessorEdit(Processor, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getReorderMergeInputPortsEdit(Merge, List<MergeInputPort>) - Method in interface org.apache.taverna.workflowmodel.Edits: Returns an edit to reorder the list of MergeInputPortS in a Merge.
getReorderMergeInputPortsEdit(Merge, List<MergeInputPort>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getReplacementActivity() - Method in interface org.apache.taverna.workflowmodel.processor.activity.SupersededActivity
getReport() - Method in class org.apache.taverna.platform.report.Invocation
getReporter() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
getResolutionCost() - Method in class org.apache.taverna.reference.AbstractExternalReference: Default to a value of 0.0f for the resolution cost, but implementations should at least attempt to set this to a more sensible level!
getResolutionCost() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI: Resolution cost is an informal guide to how costly the process of de-referencing this reference would be.
getResolutionCost() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
getResolutionCost() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
getResolutionCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference: Default resolution cost of 0.0f whatever the contents
getResolutionCost() - Method in class org.apache.taverna.t2referencetest.BlueReference: Default resolution cost of 1.0f whatever the contents
getResolutionCost() - Method in class org.apache.taverna.t2referencetest.GreenReference: Default resolution cost of 1.0f whatever the contents
getResolutionCost() - Method in class org.apache.taverna.t2referencetest.RedReference: Default resolution cost of 1.0f whatever the contents
getResolutionCost() - Method in class org.apache.taverna.t2referencetest.YellowReference: Default resolution cost of 1.0f whatever the contents
getResolvedDepth() - Method in interface org.apache.taverna.workflowmodel.Datalink: Each datalink has a resolved depth, this being the constant sum of index array length + item depth for all tokens exchanged along this link.
getResultId() - Method in class org.apache.taverna.visit.VisitReport
getResumedDate() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the date that the status last changed form PAUSED to RUNNING.
getResumedDates() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the dates that the status changed from PAUSED to RUNNING.
getRole() - Method in interface org.apache.taverna.annotation.AnnotationAssertion: The annotation assertion plays one of several roles within the annotation chain, either an initial assertion, a refinement of a previous assertion or a replacement of a previous assertion.
getRole() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
getRoot() - Method in interface org.apache.taverna.utility.TypedTreeModel: Returns the root of the tree.
getRunName(String) - Method in interface org.apache.taverna.platform.run.api.RunService
getRunName(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getRuns() - Method in interface org.apache.taverna.platform.run.api.RunService: Returns the list of runs that this service is managing.
getRuns() - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getServiceURIsForAllUsernameAndPasswordPairs() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get service URIs associated with all username/password pairs currently in the Keystore.
getServiceURIsForAllUsernameAndPasswordPairs() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get service URIs associated with all username/password pairs currently in the Keystore.
getServiceURLsforAllUsernameAndPasswordPairs() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Deprecated.
getServiceUsernameAndPassword(URI, String) - Method in interface org.apache.taverna.security.credentialmanager.ServiceUsernameAndPasswordProvider: Get the username and password pair for the given service URI.
getServiceUsernameAndPasswordProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get the providers of username and passwords for services.
getSessionID() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: What is the unique identifier used by this connector
getSetIterationStrategyStackEdit(Processor, IterationStrategyStack) - Method in interface org.apache.taverna.workflowmodel.Edits: Provide an edit that will configure a processors's iteration strategy stack to the one provided.
getSetIterationStrategyStackEdit(Processor, IterationStrategyStack) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getSink() - Method in interface org.apache.taverna.workflowmodel.Datalink: Get the sink for events flowing through this link
getSource() - Method in interface org.apache.taverna.annotation.Curateable: Each annotation or curation has a resource from which the event is inherently derived, for example if the annotation was created manually after reading a paper the source would unambiguously specify the publication.
getSource() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
getSource() - Method in class org.apache.taverna.utility.TypedTreeModelEvent: The object on which the Event initially occurred.
getSource() - Method in interface org.apache.taverna.workflowmodel.Datalink: Get the source for events flowing through this link
getSourceReference() - Method in class org.apache.taverna.reference.impl.TranslationPath
getSourceReferenceType() - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI: Return the type of external reference that this translator consumes.
getSourceReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
getSourceReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
getSourceReferenceType() - Method in class org.apache.taverna.t2referencetest.GreenToRed
getSourceType() - Method in class org.apache.taverna.reference.impl.TranslationPath
getSplits(JobContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputFormat
getST() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
getST() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
getStackTraceElementString(StackTraceElementBean) - Static method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
getStackTraceList() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl: Used by Hibernate to bodge around problems with interface types in the API
getStackTraceStrings() - Method in interface org.apache.taverna.reference.ErrorDocument: If the error document is created from a Throwable it will have a stack trace, in this case the stack trace is represented as a list of StackTraceElement beans
getStackTraceStrings() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl: From interface, not used by hibernate internally
getStartedDate() - Method in class org.apache.taverna.platform.report.Invocation: Returns the date that the status changed to RUNNING.
getStartedDate() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the date that the status changed to RUNNING.
getStartInternalDerbyServer() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getStartInternalDerbyServer() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getState() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
getState() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Return the current workflow WorkflowInstanceFacade.State.
getState() - Method in class org.apache.taverna.platform.report.Invocation: Returns the current State of the invocation.
getState() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the current State.
getState(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Returns the current state of the run.
getState() - Method in class org.apache.taverna.platform.run.impl.Run: Returns the current State of the Run.
getState(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getState() - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
getStateModel() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
getStateModel() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Workflow state is available through a sub-tree of the monitor tree.
getStateObject(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: Generate an appropriate state object from the specified job event.
getStateObject(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
getStateObject(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
getStatus() - Method in class org.apache.taverna.visit.VisitReport: Determines the overall Status.
getStrategies() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
getStrategies() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyStack: The iteration strategy stack consists of an ordered list of iteration strategies.
getStringValue() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
getSubject() - Method in class org.apache.taverna.platform.report.StatusReport: Returns the subject of this report.
getSubject() - Method in class org.apache.taverna.visit.VisitReport
getSubject() - Method in class org.apache.taverna.workflowmodel.CompoundEdit: There is no explicit subject for a compound edit, so this method always returns null.
getSubject() - Method in interface org.apache.taverna.workflowmodel.Edit: Return the object to which this edit applies
getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractActivityEdit
getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowEdit
getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowInputPortEdit
getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowOutputPortEdit
getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDatalinkEdit
getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractMergeEdit
getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractProcessorEdit
getSubject() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit
getSubjectURI() - Method in class org.apache.taverna.platform.report.StatusReport
getSubReports() - Method in class org.apache.taverna.visit.VisitReport: Provides a list of sub reports.
getTarget() - Method in interface org.apache.taverna.annotation.CurationEvent: The curation event applies to a specific other event, either another curation event or an annotation assertion.
getTarget() - Method in class org.apache.taverna.annotation.impl.DisputeEvent
getTarget() - Method in interface org.apache.taverna.workflowmodel.Condition
getTargetReferenceType() - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI: Return the type of external reference this translator constructs.
getTargetReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
getTargetReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
getTargetReferenceType() - Method in class org.apache.taverna.t2referencetest.GreenToRed
getTargetType() - Method in class org.apache.taverna.reference.impl.TranslationPath
getTavernaSSLSocketFactory() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get Taverna's SSLSocketFactory backed by Credential Manager's Keystore and Truststore.
getTavernaSSLSocketFactory() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
getTemporaryDerbyJDBC() - Method in class org.apache.taverna.platform.spring.jdbc.TemporaryJDBC
getTerminalNode() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
getTerminalNode() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategy
getText() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractTextualValueAssertion
getText() - Method in class org.apache.taverna.annotation.annotationbeans.MimeType: Return the MIME type as a string, mime types look like 'part/part'.
getTheCredentialManagerDefaultDirectory(ApplicationConfiguration) - Static method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl: Get the configuration directory where the security stuff will be/is saved to.
getTimeoutInSeconds() - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
getTokenProcessingEntityWithEventForwardingOutputPort(EventForwardingOutputPort, Dataflow) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Get the TokenProcessingEntity (Processor, Merge or Dataflow) from the workflow that contains the given EventForwardingOutputPort.
getTokenProcessingEntityWithEventHandlingInputPort(EventHandlingInputPort, Dataflow) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Get the TokenProcessingEntity (Processor, Merge or Dataflow) from the workflow that contains the given target EventHandlingInputPort.
getTranslatedElementClass() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort: The Java object type desired when the input data reference is converted to an object.
getTranslatedElementClass() - Method in class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
getTranslatedElementType() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
getTranslationCost() - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI: Return an approximate complexity cost of the translation.
getTranslationCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
getTranslationCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
getTranslationCost() - Method in class org.apache.taverna.t2referencetest.GreenToRed
getTranslators() - Method in class org.apache.taverna.reference.impl.TranslationPath
getTreePath() - Method in class org.apache.taverna.utility.TypedTreeModelEvent: For all events, except treeStructureChanged, returns the parent of the changed nodes.
getTrustConfirmationProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get the providers of trust confirmation for HTTPS connections to external services/sites
getType() - Method in interface org.apache.taverna.annotation.CurationEvent: The curation event type specifies whether this curation event is a validation, repudiation or neither of its target.
getType() - Method in class org.apache.taverna.annotation.impl.DisputeEvent
getTypedId() - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl: Used because technically you can't accept and return implementation types in the methods on a bean which implements an interface, but Hibernate needs to construct concrete input and output types!
getUniqueMergeInputPortName(Merge, String, int) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
getUnresolvedOutputs() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport: The workflow will be marked as invalid if any of the dataflow output ports can't be typed based on incoming links.
getUnresolvedOutputs() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
getUnsatisfiedEntities() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport: The workflow will be marked as invalid if there are entities with unlinked input ports or where there are cycles causing the type checking algorithm to give up.
getUnsatisfiedEntities() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
getUpdateDataflowInternalIdentifierEdit(Dataflow, String) - Method in interface org.apache.taverna.workflowmodel.Edits
getUpdateDataflowInternalIdentifierEdit(Dataflow, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getUpdateDataflowNameEdit(Dataflow, String) - Method in interface org.apache.taverna.workflowmodel.Edits
getUpdateDataflowNameEdit(Dataflow, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
getUpperNumericValue() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
getUri() - Method in class org.apache.taverna.annotation.impl.URISource
getUsername() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getUsername() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getUsername() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
getUsernameAndPasswordForService(URI, boolean, String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Get a username and password pair for the given service's URI, or null if it does not exit.
getUsernameAndPasswordForService(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Deprecated.
Use CredentialManagerImpl.getUsernameAndPasswordForService(URI, boolean, String) instead
getUsernameAndPasswordForService(URI, boolean, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Get a username and password pair for the given service's URI, or null if it does not exit.
getUUID() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
getUUID() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
getUuid() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference: Getter used by hibernate to retrieve the object uuid property.
getValue() - Method in class org.apache.taverna.activities.stringconstant.StringConstantConfigurationBean
getValue() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
getValue() - Method in interface org.apache.taverna.monitor.MonitorableProperty: Return the value of this property
getValue() - Method in class org.apache.taverna.platform.execution.impl.local.StaticProperty
getValue() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
getValue() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
getValue() - Method in interface org.apache.taverna.reference.ValueCarryingExternalReference: Returns the value
getValueType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
getValueType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
getValueType() - Method in interface org.apache.taverna.reference.ValueCarryingExternalReference: Returns the type of the inlined value
getVisitorClass() - Method in class org.apache.taverna.visit.DataflowCollation
getVisitorClass() - Method in class org.apache.taverna.visit.VisitKind: The class that all visitors that extend/implement if they make this type of visit.
getVisitorClass() - Method in class org.apache.taverna.workflowmodel.health.HealthCheck: Sub-classes of HealthChecker are used to perform HealthCheck visits.
getWorkflow() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
getWorkflow() - Method in interface org.apache.taverna.platform.execution.api.Execution: Returns the Workflow to execute.
getWorkflow(Dataflow) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
getWorkflow(String) - Method in interface org.apache.taverna.platform.run.api.RunService
getWorkflow() - Method in class org.apache.taverna.platform.run.impl.Run
getWorkflow(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getWorkflowActivity(Activity<?>) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
getWorkflowBundle() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
getWorkflowBundle() - Method in interface org.apache.taverna.platform.execution.api.Execution: Returns the WorkflowBundle containing the Workflows required for execution.
getWorkflowBundle() - Method in class org.apache.taverna.platform.run.api.RunProfile: Returns the WorkflowBundle.
getWorkflowId() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
getWorkflowId() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: The uuid that belongs to the actual dataflow
getWorkflowName() - Method in class org.apache.taverna.platform.run.api.RunProfile: Returns the name of the Workflow to run.
getWorkflowObject() - Method in class org.apache.taverna.monitor.MonitorManager.RegisterNodeMessage
getWorkflowObject() - Method in interface org.apache.taverna.monitor.MonitorNode: Each monitor node can reference zero or one workflow object.
getWorkflowProcessor(Processor) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
getWorkflowReport() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
getWorkflowReport(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
getWorkflowReport() - Method in interface org.apache.taverna.platform.execution.api.Execution: Returns the WorkflowReport for the execution.
getWorkflowReport(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Returns the workflow report for the specified execution.
getWorkflowReport(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Returns the status report for the run.
getWorkflowReport() - Method in class org.apache.taverna.platform.run.impl.Run: Returns the status report for the run.
getWorkflowReport(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
getWorkflowRunId() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
getWorkflowRunId() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Get the unique id of the wf run inside the facede.
getWorkflowRunId() - Method in class org.apache.taverna.reference.WorkflowRunIdEntity
getWorstStatus(Collection<VisitReport>) - Static method in class org.apache.taverna.visit.VisitReport: Determine the worst status from a collection of reports
granularDepth - Variable in class org.apache.taverna.workflowmodel.AbstractOutputPort
GreenBuilder - Class in org.apache.taverna.t2referencetest: Trivially build a GreenReference from an InputStream, implementing the ExternalReferenceBuilderSPI interface.
GreenBuilder() - Constructor for class org.apache.taverna.t2referencetest.GreenBuilder
GreenReference - Class in org.apache.taverna.t2referencetest: GreenReferences carry their data as an internal String and have a resolution cost of 1.1f whatever the value of that string.
GreenReference() - Constructor for class org.apache.taverna.t2referencetest.GreenReference
GreenReference(String) - Constructor for class org.apache.taverna.t2referencetest.GreenReference
GreenToRed - Class in org.apache.taverna.t2referencetest
GreenToRed() - Constructor for class org.apache.taverna.t2referencetest.GreenToRed

H

handleError() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer.JobState: Called when the layer below pushes an error up and where the error index and owning process matches that of this state object.
hasEntryWithAlias(CredentialManager.KeystoreType, String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Check if the Keystore/Truststore contains an entry with the given alias.
hasEntryWithAlias(CredentialManager.KeystoreType, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Check if the Keystore/Truststore contains an entry with the given alias.
hasExpired() - Method in interface org.apache.taverna.monitor.MonitorNode: Nodes can persist in the tree after they have expired, in which case this will return true.
hashCode() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
hashCode() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
hashCode() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
hashCode() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
hashCode() - Method in class org.apache.taverna.workflowmodel.OrderedPair
hasKeyPair(Key, Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Checks if the Keystore contains the given key pair entry (private key and its corresponding public key certificate chain).
hasKeyPair(Key, Certificate[]) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Checks if the Keystore contains the given key pair entry (private key and its corresponding public key certificate chain).
hasTrustedCertificate(Certificate) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Checks if the Truststore contains the given public key certificate.
hasTrustedCertificate(Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Checks if the Truststore contains the given public key certificate.
hasUsernamePasswordForService(URI) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Checks if the Keystore contains a username and password for the given service URI.
hasUsernamePasswordForService(URI) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Checks if the Keystore contains a username and password for the given service URI.
HealthCheck - Class in org.apache.taverna.workflowmodel.health: A HealthCheck is a kind of visit that determines if the corresponding object in a workflow (normally an Activity) will work during a workflow run.
HealthCheck() - Constructor for class org.apache.taverna.workflowmodel.health.HealthCheck
HealthChecker<T> - Interface in org.apache.taverna.workflowmodel.health: An SPI interface whose implementation performs a health check on an arbitrary instance.
HIBERNATE_CONTEXT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
HIBERNATE_DIALECT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
HibernateComponentClass - Interface in org.apache.taverna.reference.h3: A marker used to denote that the class should be pre-loaded into hibernate's class mapping.
HibernateMappedEntity - Interface in org.apache.taverna.reference.h3: A marker interface used to denote that the component should be registered with the Hibernate ORM system prior to any ExternalReferenceSPI implementations.
HierarchyRole - Enum in org.apache.taverna.annotation: Possible relationships between entities in a hierarchical context.
HierarchyTraversal - Annotation Type in org.apache.taverna.annotation: Applied to getFoo methods to indicate that the returned type is related to the annotated type by some hierarchical relationship, either parent or child.
HierarchyTraverser - Class in org.apache.taverna.visit: A HierarchyTraverser allows the traversal of the parent -> child hierarchy (as indicated by annotations) and performs visits conforming to the set of VisitKinds.
HierarchyTraverser(Set<Visitor<?>>) - Constructor for class org.apache.taverna.visit.HierarchyTraverser: Create a HierarchyTraverser that can perform visits of the specified set of VisitKind.
HIGH_PORT_DEPTH - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
HostInstitution - Class in org.apache.taverna.annotation.annotationbeans: The host institution for an activity implementation
HostInstitution() - Constructor for class org.apache.taverna.annotation.annotationbeans.HostInstitution: Default constructor as mandated by java bean specification
HttpReference - Class in org.apache.taverna.reference.impl.external.http: Implementation of ExternalReference used to refer to data held in a locally accessible file.
HttpReference() - Constructor for class org.apache.taverna.reference.impl.external.http.HttpReference: Explicitly declare default constructor, will be used by hibernate when constructing instances of this bean from the database.

I

IdentificationAssertion - Class in org.apache.taverna.annotation.annotationbeans: An IdentificationAssertion is used to hold previous identifications of an object.
IdentificationAssertion() - Constructor for class org.apache.taverna.annotation.annotationbeans.IdentificationAssertion
Identified - Interface in org.apache.taverna.reference: Interface for any object that has an associated T2Reference
IdentifiedArrayList<T> - Class in org.apache.taverna.reference.impl: Implementation of IdentifiedList which delegates to an ArrayList for its storage functionality.
IdentifiedArrayList() - Constructor for class org.apache.taverna.reference.impl.IdentifiedArrayList
IdentifiedArrayList(Collection<T>) - Constructor for class org.apache.taverna.reference.impl.IdentifiedArrayList
IdentifiedArrayList(int) - Constructor for class org.apache.taverna.reference.impl.IdentifiedArrayList
IdentifiedList<T> - Interface in org.apache.taverna.reference: An identified list is a list which is identified by a T2Reference.
identifierResolved(Identified) - Method in interface org.apache.taverna.reference.ReferenceServiceResolutionCallback: Called when the resolution process has completed
IN_MEMORY - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
IN_MEMORY_CONTEXT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
incomingJobs - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
INCOMPATIBLE_MIMETYPES - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
index - Variable in class org.apache.taverna.invocation.Event
indexOf(Object) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
initialize(InputSplit, TaskAttemptContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
initialize(InputSplit, TaskAttemptContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
initializeSSL() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Set the default SSLContext to use Credential Manager's Keystore and Truststore for managing SSL connections from Taverna and also set HttpsURLConnection's default SSLSocketFactory to use the one from the just configured SSLContext, i.e.
initializeSSL() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
injectPropertiesFor(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce: Two properties, dispatch.errorbounce.reflected(integer) is the number of incoming jobs which have been bounced back as results with errors, dispatch.errorbounce.translated(integer) is the number of failures from downstream in the stack that have been re-written as complete results containing error documents.
injectPropertiesFor(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize: Injects the following properties into its parent processor's property set: dispatch.parallelize.queuesize [Integer]
The current size of the incomming job queue, or -1 if the state isn't defined for the registered process identifier (which will be the case if the process hasn't started or has had its state purged after a final completion of some kind.
injectPropertiesFor(String) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.PropertyContributingDispatchLayer: Inject properties for the specified owning process into the parent dispatch stack.
InlineByteArrayReference - Class in org.apache.taverna.reference.impl.external.object: A reference implementation that inlines an array of bytes.
InlineByteArrayReference() - Constructor for class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
InlineByteArrayReferenceBuilder - Class in org.apache.taverna.reference.impl.external.object: Build an InlineByteArrayReference from an InputStream
InlineByteArrayReferenceBuilder() - Constructor for class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
InlineByteToInlineStringTranslator - Class in org.apache.taverna.reference.impl.external.object
InlineByteToInlineStringTranslator() - Constructor for class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
InlineStringReference - Class in org.apache.taverna.reference.impl.external.object: Contains and references a String value
InlineStringReference() - Constructor for class org.apache.taverna.reference.impl.external.object.InlineStringReference
InlineStringReferenceBuilder - Class in org.apache.taverna.reference.impl.external.object: Build an InlineStringReference from an InputStream
InlineStringReferenceBuilder() - Constructor for class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
InlineStringToInlineByteTranslator - Class in org.apache.taverna.reference.impl.external.object
InlineStringToInlineByteTranslator() - Constructor for class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
InMemoryErrorDocumentDao - Class in org.apache.taverna.reference.impl: A trivial in-memory implementation of ErrorDocumentDao for either testing or very lightweight embedded systems.
InMemoryErrorDocumentDao() - Constructor for class org.apache.taverna.reference.impl.InMemoryErrorDocumentDao
InMemoryListDao - Class in org.apache.taverna.reference.impl: A trivial in-memory implementation of ListDao for either testing or very lightweight embedded systems.
InMemoryListDao() - Constructor for class org.apache.taverna.reference.impl.InMemoryListDao
InMemoryReferenceSetDao - Class in org.apache.taverna.reference.impl: A trivial in-memory implementation of ReferenceSetDao for either testing or very lightweight embedded systems.
InMemoryReferenceSetDao() - Constructor for class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
innerReceiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
innerReceiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct
innerReceiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.DotProduct: Delegate to the superclass to propogate completion events if and only if the completion event is a final one.
innerReceiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
innerReceiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct: Receive a job, emit jobs corresponding to the orthogonal join of the new job with all jobs in all other input lists.
innerReceiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.DotProduct
innerReceiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.PrefixDotProduct
inputComplete - Variable in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode.CompletionState
InputDataProvenanceItem - Class in org.apache.taverna.provenance.item: Contains details of port names and the input data they receive.
InputDataProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.InputDataProvenanceItem
InputPort - Interface in org.apache.taverna.workflowmodel: Marker interface denoting that the instance is an input port.
inputPortMapping - Variable in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
inputPorts - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
inputPorts - Variable in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
insert(MutableTreeNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
insert(MutableTreeNode, int) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
insert(MutableTreeNode) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: Insert a new child node.
insert(MutableTreeNode, int) - Method in class org.apache.taverna.workflowmodel.processor.iteration.TerminalNode
insertJob(Job) - Method in class org.apache.taverna.invocation.TreeCache: Add a job to the cache, the job is inserted at a position corresponding to its index array property
insertJob(Job) - Method in class org.apache.taverna.invocation.TreeCache.NamedNode
installAuthenticator() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Connects this credential manager to the Java HTTP authenticator mechanism.
IntermediateProvenance - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Sits above the Invoke layer and collects information about the current workflow run to be stored by the ProvenanceConnector.
IntermediateProvenance() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
internalClone(VisitReport) - Method in class org.apache.taverna.visit.VisitReport
internalIdentifier - Variable in class org.apache.taverna.workflowmodel.impl.DataflowImpl
internalOutput - Variable in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
INVALID_CONFIGURATION - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
INVALID_SCRIPT - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
INVALID_URL - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
InvalidConfigurationException - Exception in org.apache.taverna.services: Thrown when a Configuration is not valid for a Configurable.
InvalidConfigurationException() - Constructor for exception org.apache.taverna.services.InvalidConfigurationException
InvalidConfigurationException(String) - Constructor for exception org.apache.taverna.services.InvalidConfigurationException
InvalidConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.services.InvalidConfigurationException
InvalidConfigurationException(Throwable) - Constructor for exception org.apache.taverna.services.InvalidConfigurationException
InvalidDataflowException - Exception in org.apache.taverna.workflowmodel: Thrown if attempting to use a workflow that is not valid.
InvalidDataflowException(Dataflow, DataflowValidationReport) - Constructor for exception org.apache.taverna.workflowmodel.InvalidDataflowException
InvalidExecutionIdException - Exception in org.apache.taverna.platform.execution.api: Thrown when an executionID is not valid for an ExecutionService.
InvalidExecutionIdException() - Constructor for exception org.apache.taverna.platform.execution.api.InvalidExecutionIdException
InvalidExecutionIdException(String) - Constructor for exception org.apache.taverna.platform.execution.api.InvalidExecutionIdException
InvalidExecutionIdException(String, Throwable) - Constructor for exception org.apache.taverna.platform.execution.api.InvalidExecutionIdException
InvalidExecutionIdException(Throwable) - Constructor for exception org.apache.taverna.platform.execution.api.InvalidExecutionIdException
InvalidRunIdException - Exception in org.apache.taverna.platform.run.api: Thrown when a runID is not valid for the RunService.
InvalidRunIdException() - Constructor for exception org.apache.taverna.platform.run.api.InvalidRunIdException
InvalidRunIdException(String) - Constructor for exception org.apache.taverna.platform.run.api.InvalidRunIdException
InvalidRunIdException(String, Throwable) - Constructor for exception org.apache.taverna.platform.run.api.InvalidRunIdException
InvalidRunIdException(Throwable) - Constructor for exception org.apache.taverna.platform.run.api.InvalidRunIdException
InvalidWorkflowException - Exception in org.apache.taverna.platform.execution.api: Thrown when a Workflow fails to validate.
InvalidWorkflowException() - Constructor for exception org.apache.taverna.platform.execution.api.InvalidWorkflowException
InvalidWorkflowException(String, Throwable) - Constructor for exception org.apache.taverna.platform.execution.api.InvalidWorkflowException
InvalidWorkflowException(String) - Constructor for exception org.apache.taverna.platform.execution.api.InvalidWorkflowException
InvalidWorkflowException(Throwable) - Constructor for exception org.apache.taverna.platform.execution.api.InvalidWorkflowException
Invocation - Class in org.apache.taverna.platform.report: A single invocation of a workflow, processor or activity.
Invocation(String, Invocation, StatusReport<?, ?>) - Constructor for class org.apache.taverna.platform.report.Invocation
Invocation(String, int[], Invocation, StatusReport<?, ?>) - Constructor for class org.apache.taverna.platform.report.Invocation
invocationContext - Variable in class org.apache.taverna.activities.testutils.DummyCallback
InvocationContext - Interface in org.apache.taverna.invocation: Carries the context of a workflow invocation, the necessary data manager, security agents and any other resource shared across the invocation such as provenance injectors.
InvocationContextImpl - Class in org.apache.taverna.invocation.impl
InvocationContextImpl(ReferenceService, ProvenanceReporter) - Constructor for class org.apache.taverna.invocation.impl.InvocationContextImpl
invocationProcessIdentifier - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
InvocationStartedProvenanceItem - Class in org.apache.taverna.provenance.item
InvocationStartedProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
Invoke - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Context free invoker layer, does not pass index arrays of jobs into activity instances.
Invoke() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
invoke(DispatchJobEvent, AsynchronousActivity<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
Invoke.InvokeCallBack - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
invokeAsyncActivity(AbstractAsynchronousActivity<?>, Map<String, Object>, Map<String, Class<?>>) - Static method in class org.apache.taverna.activities.testutils.ActivityInvoker: Invokes an AsynchronousActivity with a given set of input Objects and returns a Map of requested output values.
InvokeCallBack(DispatchJobEvent, ReferenceService, String, AsynchronousActivity<?>) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
IO_PROBLEM - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
isApplied() - Method in class org.apache.taverna.workflowmodel.CompoundEdit
isApplied() - Method in interface org.apache.taverna.workflowmodel.Edit: Has the edit been applied yet?
isApplied() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit
isAutoSave() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
isAutoSave() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
isComplete() - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode.CompletionState: Return true iff all inputs have completed
isDisputed(AnnotationChain) - Method in interface org.apache.taverna.annotation.AnnotationPerspective: Annotation chains may be in a disputed state if there are conflicting mutually exclusive events within them under the interpretation imposed by the annotation perspective and the perspective is unable to sensibly reconcile them.
isEmpty() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
isEnabled(ReferenceContext) - Method in interface org.apache.taverna.reference.ExternalReferenceBuilderSPI: Because the reference builder may rely on facilities provided to it through the context this method is available to check whether these facilities are sufficient.
isEnabled(ReferenceContext) - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI: Because the reference translator may rely on facilities provided to it through the context this method is available to check whether these facilities are sufficient.
isEnabled(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
isEnabled(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
isEnabled(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
isEnabled(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
isEnabled(ReferenceContext) - Method in class org.apache.taverna.t2referencetest.GreenBuilder: Doesn't use any context resources so is always enabled
isEnabled(ReferenceContext) - Method in class org.apache.taverna.t2referencetest.GreenToRed
isExposeDatanature() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
isExposeDatanature() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
isFinal() - Method in class org.apache.taverna.invocation.Event: An event is final if its index array is zero length
isFinal() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
isFinal() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
isInMemory() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
isInMemory() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
isInput() - Method in class org.apache.taverna.provenance.item.DataProvenanceItem: Is this ProvenanceItem for input or output data
isInput() - Method in class org.apache.taverna.provenance.item.InputDataProvenanceItem: Used when generating the xml version by the DataProvenanceItem.
isInput() - Method in class org.apache.taverna.provenance.item.OutputDataProvenanceItem: Used when generating the xml version by the DataProvenanceItem.
isInputPort() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
isInputPortConnected(DataflowInputPort) - Method in interface org.apache.taverna.workflowmodel.Dataflow: Check if the given input port is connected to anything in the workflow.
isInputPortConnected(DataflowInputPort) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
isKeyEntry(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Check if the given alias identifies a key entry in the Keystore.
isKeyEntry(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Check if the given alias identifies is a key entry in the Keystore.
isLeaf(NodeType) - Method in interface org.apache.taverna.utility.TypedTreeModel: Returns true if node is a leaf.
isLeaf() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implement TreeNode
isLeaf() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode: These nodes correspond to inputs to the iteration strategy and are always leaf nodes as a result.
isProvenanceEnabled() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
isProvenanceEnabled() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
isRunFirst() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
isRunning() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
isRunning() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
isSatisfied(String) - Method in interface org.apache.taverna.workflowmodel.Condition
isShouldSave() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
isSplitable(JobContext, Path) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputFormat
isSplitable(JobContext, Path) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputFormat
isStreamingEvent() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent: If this result is part of a stream, that is to say multiple result events from a single job event, then return true otherwise return false.
isTimeConsuming() - Method in class org.apache.taverna.activities.dataflow.DataflowActivityHealthChecker
isTimeConsuming() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker
isTimeConsuming() - Method in interface org.apache.taverna.visit.Visitor: An indication if the visit would take sufficient time that it should only be run upon user request
isTimeConsuming() - Method in class org.apache.taverna.workflowmodel.health.DisabledActivityHealthChecker: The check is not time consuming as it simply constructs a VisitReport
isTimeConsuming() - Method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker: A remote health-check is time consuming as it tries to contact an external resource.
isTimeConsuming() - Method in class org.apache.taverna.workflowmodel.health.UnrecognizedActivityHealthChecker: The check is not time consuming as it simply constructs a VisitReport
isValid() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport: Overall validity - if the workflow is valid it can be run, otherwise there are problems somewhere and a facade can't be created from it.
isValid() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
isWorkflowIncomplete() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport: Whether the workflow is incomplete, i.e.
isWorkflowIncomplete() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
IterationInternalEvent<EventType extends IterationInternalEvent<?>> - Class in org.apache.taverna.invocation: Abstract superclass for event types which have to pass through the iteration system.
IterationInternalEvent(String, int[], InvocationContext) - Constructor for class org.apache.taverna.invocation.IterationInternalEvent: Protected constructor for the minimum fields required by all Event subclasses
IterationProvenanceItem - Class in org.apache.taverna.provenance.item: One of these is created for each iteration inside an enacted activity.
IterationProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.IterationProvenanceItem
iterationStack - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
IterationStrategy - Interface in org.apache.taverna.workflowmodel.processor.iteration
IterationStrategyImpl - Class in org.apache.taverna.workflowmodel.processor.iteration.impl: A single layer of iteration strategy, consuming individual named inputs and combining these into Job objects to be consumed by the dispatch stack
IterationStrategyImpl() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
IterationStrategyImpl.TerminalNodeImpl - Class in org.apache.taverna.workflowmodel.processor.iteration.impl: The terminal node is used internally as the root of the iteration strategy tree, it is responsible for forwarding all events up to the iteration strategy itself which can then propogate them to the strategy stack.
IterationStrategyNode - Interface in org.apache.taverna.workflowmodel.processor.iteration: Interface for nodes within an iteration strategy layer
IterationStrategyStack - Interface in org.apache.taverna.workflowmodel.processor.iteration: Stack of iteration strategy containers.
IterationStrategyStackImpl - Class in org.apache.taverna.workflowmodel.processor.iteration.impl: Contains an ordered list of IterationStrategyImpl objects.
IterationStrategyStackImpl() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
IterationTypeMismatchException - Exception in org.apache.taverna.workflowmodel.processor.iteration: Thrown during the typecheck phase when an iteration strategy is configured such that at runtime it would fail.
IterationTypeMismatchException() - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.IterationTypeMismatchException
IterationTypeMismatchException(String) - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.IterationTypeMismatchException
IterationTypeMismatchException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.IterationTypeMismatchException
IterationTypeMismatchException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.IterationTypeMismatchException
iterator() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
iterator() - Method in class org.apache.taverna.reference.impl.TranslationPath: Wrap translator list iterator for convenience
iterator() - Method in class org.pingel.util.CrossProduct

J

JavaTruststorePasswordProvider - Interface in org.apache.taverna.security.credentialmanager: Defines an interface for providing a password for Java's default truststore located in JAVA_HOME/lib/security/cacerts.
JDBC_URI - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
JNDI_NAME - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
Job - Class in org.apache.taverna.workflowmodel.processor.activity: Contains a (possibly partial) job description.
Job(String, int[], Map<String, T2Reference>, InvocationContext) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.Job: Create a new Job object with the specified owning process (colon separated 'list' of process identifiers), index array and data map
jobCreated(Job) - Method in interface org.apache.taverna.workflowmodel.impl.Crystalizer: This method is called when a new Job has been handled by the AbstractCrystalizer, either by direct passthrough or by list registration.
jobCreated(Job) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorCrystalizerImpl
jobEvent - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer.JobState
jobEvent - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
JobState(DispatchJobEvent) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer.JobState
jobsWithPrefix(int[]) - Method in class org.apache.taverna.invocation.TreeCache: Recursively fetch contents of all nodes under the specified index array, used by the prefix matching iteration strategy

K

KEYSTORE_FILE_NAME - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
KeystoreChangedEvent - Class in org.apache.taverna.security.credentialmanager: An event given to CredentialManagerOld observers registered using Observable#addObserver(org.apache.taverna.lang.observer.Observer) to let them know the Keystore or Truststore have been changed.
KeystoreChangedEvent(CredentialManager.KeystoreType) - Constructor for class org.apache.taverna.security.credentialmanager.KeystoreChangedEvent
KeystoreChangedObserver() - Constructor for class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl.KeystoreChangedObserver
keystoreType - Variable in class org.apache.taverna.security.credentialmanager.KeystoreChangedEvent

L

lastIndexOf(Object) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
layerAbove(DispatchLayer<?>) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack: Return the layer above (lower index!) the specified layer, or a reference to the internal top layer dispatch layer if there is no layer above the specified one.
layerAbove(DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Return the layer above (lower index!) the specified layer, or a reference to the internal top layer dispatch layer if there is no layer above the specified one.
layerBelow(DispatchLayer<?>) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack: Return the layer below (higher index) the specified layer, or null if there is no layer below this one.
layerBelow(DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Return the layer below (higher index) the specified layer, or null if there are no layers below this one
layerBelow(IterationStrategyImpl) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl: Return the layer below the specified one, or null if there is no lower layer
link(String, String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Create a new datalink between two entities within the workflow
listDao - Variable in class org.apache.taverna.reference.impl.AbstractListServiceImpl
ListDao - Interface in org.apache.taverna.reference: Data access object handling NamedLists of T2Reference instances.
listDelegate - Variable in class org.apache.taverna.reference.impl.IdentifiedArrayList
listIterator() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
listIterator(int) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
listRetrievalFailed(ListServiceException) - Method in interface org.apache.taverna.reference.ListServiceCallback: Called if the retrieval failed for some reason
listRetrieved(IdentifiedList<T2Reference>) - Method in interface org.apache.taverna.reference.ListServiceCallback: Called when the requested ReferenceSet has been successfully retrieved.
listService - Variable in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
ListService - Interface in org.apache.taverna.reference: Provides facilities to register list of T2References, register empty lists at any given depth and to resolve appropriate T2Reference instances back to these lists.
ListServiceCallback - Interface in org.apache.taverna.reference: Callback interface used by asynchronous methods in the ListService interface
ListServiceException - Exception in org.apache.taverna.reference: Thrown by methods in the ListService interface if anything goes wrong with list registration or retrieval.
ListServiceException() - Constructor for exception org.apache.taverna.reference.ListServiceException
ListServiceException(String) - Constructor for exception org.apache.taverna.reference.ListServiceException
ListServiceException(Throwable) - Constructor for exception org.apache.taverna.reference.ListServiceException
ListServiceException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ListServiceException
ListServiceImpl - Class in org.apache.taverna.reference.impl: Implementation of ListService, inject with an appropriate ListDao and T2ReferenceGenerator to enable.
ListServiceImpl() - Constructor for class org.apache.taverna.reference.impl.ListServiceImpl
load(Bundle) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
load(Path, WorkflowBundle) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
loadPKCS12Keystore(Path, String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Load a PKCS12-type keystore from a file using the supplied password.
loadPKCS12Keystore(Path, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Load a PKCS12-type keystore from a file using the supplied password.
loadWorkflowReportJson(Path) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
LocalExecution - Class in org.apache.taverna.platform.execution.impl.local: An Execution for executing Taverna workflows on a local Taverna Dataflow Engine.
LocalExecution(WorkflowBundle, Workflow, Profile, Bundle, ReferenceService, Edits, ActivityService, DispatchLayerService) - Constructor for class org.apache.taverna.platform.execution.impl.local.LocalExecution: Constructs an Execution for executing Taverna workflows on a local Taverna Dataflow Engine.
LocalExecutionEnvironment - Class in org.apache.taverna.platform.execution.impl.local: Execution Environment for a local Taverna Dataflow Engine
LocalExecutionEnvironment(LocalExecutionService, ActivityService, DispatchLayerService) - Constructor for class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
LocalExecutionMonitor - Class in org.apache.taverna.platform.execution.impl.local: A workflow monitor for local executions.
LocalExecutionMonitor(WorkflowReport, Bundle, WorkflowToDataflowMapper, String) - Constructor for class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
LocalExecutionService - Class in org.apache.taverna.platform.execution.impl.local: Service for executing Taverna workflows on a local Taverna Dataflow Engine.
LocalExecutionService() - Constructor for class org.apache.taverna.platform.execution.impl.local.LocalExecutionService: Constructs an execution service that executes workflows using the T2 dataflow engine.
LocalProcessorReport - Class in org.apache.taverna.platform.execution.impl.local: ProcessorReport implementation based on MonitorableProperty objects.
LocalProcessorReport(Processor) - Constructor for class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
LocationConstants - Interface in org.apache.taverna.activities.testutils: A definition of constants for base locations of external resources used for testing.
LockedNestedDataflow - Interface in org.apache.taverna.workflowmodel.processor.activity: A LockedNestedDataflow is intended to be unchangeable.
Loop - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: A layer that allows while-style loops.
Loop() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
Loop.ConditionCallBack - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
LOOP_CONNECTION - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
LOOP_PORT - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
LoopConfiguration - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Configuration bean for the Loop.
LoopConfiguration() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration

M

main(String[]) - Static method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest
main(String[]) - Static method in class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest
main(String[]) - Static method in class org.apache.taverna.platform.execution.impl.hadoop.Test
main(String[]) - Static method in class org.pingel.util.CrossProduct
makeExecutionThread(Runnable) - Method in class org.apache.taverna.reference.impl.AbstractServiceImpl
makeObjectMapperForLoad() - Static method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
makeObjectMapperForSave() - Static method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
Map() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest.Map
map(Text, TextArrayWritable, Mapper<Text, TextArrayWritable, Text, TextArrayWritable>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest.Map
Map() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest.Map
map(LongWritable, MapWritable, Mapper<LongWritable, MapWritable, LongWritable, MapWritable>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest.Map
map(int[], Map<String, Path>, Mapper<int[], Map<String, Path>, Object, Object>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaMapper
MasterPasswordProvider - Interface in org.apache.taverna.security.credentialmanager: Defines an interface for providing a master password for the Credential Manager.
MasterPasswordProvider.ProviderComparator - Class in org.apache.taverna.security.credentialmanager: Set the provider's priority that determines the order in which various master password providers will be invoked.
Merge - Interface in org.apache.taverna.workflowmodel: Allows multiple outputs to be routed to a single input within the dataflow.
MergeInputPort - Interface in org.apache.taverna.workflowmodel: Input port on a Merge object
MergeOutputPort - Interface in org.apache.taverna.workflowmodel: An EventForwardingOutputPort that is associated with Merge instances.
MergePort - Interface in org.apache.taverna.workflowmodel: An input or output Port for a Merge.
MimeType - Class in org.apache.taverna.annotation.annotationbeans: A single MIME type, intended to be used to annotate an input or output port within the workflow to denote the type within that system of data produced or consumed by the port.
MimeType() - Constructor for class org.apache.taverna.annotation.annotationbeans.MimeType: Default constructor as mandated by java bean specification
MISSING_CLASS - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
MISSING_DEPENDENCY - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
MissingIterationInputException - Exception in org.apache.taverna.workflowmodel.processor.iteration: Thrown when an attempt is made to evaluate the type of the iteration strategy but one or more input ports aren't defined in the input array of types.
MissingIterationInputException() - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.MissingIterationInputException
MissingIterationInputException(String) - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.MissingIterationInputException
MissingIterationInputException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.MissingIterationInputException
MissingIterationInputException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.iteration.MissingIterationInputException
MonitorableAsynchronousActivity<ConfigType> - Interface in org.apache.taverna.workflowmodel.processor.activity: An extension of AsynchronousActivity with the additional stipulation that implementing classes must return a set of monitorable properties for the activity invocation instance when invoked.
MonitorableProperty<T> - Interface in org.apache.taverna.monitor: A single readable property contained by a Monitorable.
monitorables - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
MonitorManager - Class in org.apache.taverna.monitor: Manages a list of monitors implementations that get notified to register and deregister nodes (ie.
MonitorManager() - Constructor for class org.apache.taverna.monitor.MonitorManager: Protected constructor, use singleton access MonitorManager.getInstance() instead.
MonitorManager.AddPropertiesMessage - Class in org.apache.taverna.monitor: Message indicating that new properties have been added to a node identified by given owning process.
MonitorManager.DeregisterNodeMessage - Class in org.apache.taverna.monitor: Message indicating that the node of the given owning process is to be deregistered.
MonitorManager.MonitorMessage - Class in org.apache.taverna.monitor: Common abstract superclass for all monitor messages.
MonitorManager.RegisterNodeMessage - Class in org.apache.taverna.monitor: Message indicating that the node of the given owning process is to be registered.
MonitorMessage(String[]) - Constructor for class org.apache.taverna.monitor.MonitorManager.MonitorMessage
MonitorNode - Interface in org.apache.taverna.monitor: A single node in the Monitor tree, containing an optional arbitrary workflow object and a set of properties which may or may not be mutable.
MonitorTreeModel - Class in org.apache.taverna.monitor.impl: A relatively naive Monitor interface which holds all state in a tree model.
MonitorTreeModel() - Constructor for class org.apache.taverna.monitor.impl.MonitorTreeModel: Protected constructor, use singleton access MonitorTreeModel.getInstance() instead.
MultiCaster<Message> - Class in org.apache.taverna.lang.observer: Send notifications to registered observers about changes to models
MultiCaster(Observable<Message>) - Constructor for class org.apache.taverna.lang.observer.MultiCaster: Set the MultiCaster.observable ie.
multiCaster - Variable in class org.apache.taverna.monitor.MonitorManager

N

name - Variable in class org.apache.taverna.workflowmodel.AbstractPort
name - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
NamedInputPortNode - Class in org.apache.taverna.workflowmodel.processor.iteration: Acts as the input to a stage within the iteration strategy, passes all jobs straight through.
NamedInputPortNode(String, int) - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
NamedNode() - Constructor for class org.apache.taverna.invocation.TreeCache.NamedNode
NamedWorkflowEntity - Interface in org.apache.taverna.workflowmodel: Entities existing directly within a workflow such as Processors, Merge operators and other potential future extensions exist within a naming scheme.
NamedWorkflowEntityComparator - Class in org.apache.taverna.workflowmodel.utils: Compare two named workflow entities (such as a Processor) by their local name.
NamedWorkflowEntityComparator() - Constructor for class org.apache.taverna.workflowmodel.utils.NamedWorkflowEntityComparator
NamingException - Exception in org.apache.taverna.workflowmodel: Potentially thrown when an edit fails due to naming of entities created or modified by the edit.
NamingException(String) - Constructor for exception org.apache.taverna.workflowmodel.NamingException
NamingException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.NamingException
NamingException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.NamingException
NESTED_ISSUES - Static variable in class org.apache.taverna.visit.DataflowCollation
NestedDataflow - Interface in org.apache.taverna.workflowmodel.processor.activity: Nested workflows/dataflows can come in many shapes and sizes - in-line, url etc.
NestedDataflowSource<T extends NestedDataflow> - Interface in org.apache.taverna.workflowmodel.processor.activity
nextErrorDocumentReference(int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.AbstractT2ReferenceGenerator
nextErrorDocumentReference(int, ReferenceContext) - Method in interface org.apache.taverna.reference.T2ReferenceGenerator: Create a new and otherwise unused T2Reference to an ErrorDocument.
nextKeyValue() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
nextKeyValue() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
nextListReference(boolean, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.AbstractT2ReferenceGenerator
nextListReference(boolean, int, ReferenceContext) - Method in interface org.apache.taverna.reference.T2ReferenceGenerator: Create a new and otherwise unused T2Reference to an IdentifiedList.
nextReferenceSetReference(ReferenceContext) - Method in class org.apache.taverna.reference.impl.AbstractT2ReferenceGenerator
nextReferenceSetReference(ReferenceContext) - Method in interface org.apache.taverna.reference.T2ReferenceGenerator: Create a new and otherwise unused T2Reference to a ReferenceSet.
NO_CONFIGURATION - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
NO_ENDPOINTS - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
NO_PROBLEM - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
nodeAt(int[]) - Method in class org.apache.taverna.invocation.TreeCache
nodeAtProcessPath(String[], int) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Return the node pointed to by the first 'limit' number of elements in the owning process string array.
NonExecutableActivity<T> - Class in org.apache.taverna.workflowmodel.processor.activity: A non-executable activity is a wrapper for an Activity that cannot be executed, for example because it is offline or unrecognized.
NonExecutableActivity() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity: It is not possible to create a "naked" NonExecutableActivity.
normalize() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
normalize() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategy
normalizeServiceURI(URI) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Normalize an URI for insertion as the basis for path-recursive lookups, ie.
NoSuchPropertyException - Exception in org.apache.taverna.monitor: Thrown when an attempt is made to access a monitorable property which is no longer current.
NoSuchPropertyException() - Constructor for exception org.apache.taverna.monitor.NoSuchPropertyException
NoSuchPropertyException(String, Throwable) - Constructor for exception org.apache.taverna.monitor.NoSuchPropertyException
NoSuchPropertyException(String) - Constructor for exception org.apache.taverna.monitor.NoSuchPropertyException
NoSuchPropertyException(Throwable) - Constructor for exception org.apache.taverna.monitor.NoSuchPropertyException
NOT_HTTP - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
NOT_IMPLEMENTED - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
NotifiableLayer - Interface in org.apache.taverna.workflowmodel.processor.dispatch: If a layer requires notification of the arrival of new items to the event queues within the dispatcher it should implement this interface.
notify(Message) - Method in class org.apache.taverna.lang.observer.MultiCaster: Tell all the registered observers about the change to the model
notify(Observable<Message>, Message) - Method in interface org.apache.taverna.lang.observer.Observer: Called by the Observable to notify the implementing class of changes
notify(Observable<Message>, Message) - Method in class org.apache.taverna.lang.observer.SwingAwareObserver
notify(Observable<MonitorManager.MonitorMessage>, MonitorManager.MonitorMessage) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Called by the Observable to notify the implementing class of changes
notify(Observable<MonitorManager.MonitorMessage>, MonitorManager.MonitorMessage) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
notify(Observable<KeystoreChangedEvent>, KeystoreChangedEvent) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl.ClearCachedServiceURIsObserver
notify(Observable<KeystoreChangedEvent>, KeystoreChangedEvent) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl.KeystoreChangedObserver
notifySwing(Observable<Message>, Message) - Method in class org.apache.taverna.lang.observer.SwingAwareObserver
NULL_DATATYPE - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
NULL_VALUE - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
NumberToStringReference - Class in org.apache.taverna.reference.impl.external.object: Convert a java.lang.Number to a StringReference.
NumberToStringReference() - Constructor for class org.apache.taverna.reference.impl.external.object.NumberToStringReference

O

Observable<Message> - Interface in org.apache.taverna.lang.observer: Implements this if you want to notify other classes about changes
Observer<Message> - Interface in org.apache.taverna.lang.observer: Implement if you want to register with an Observable
observers - Variable in class org.apache.taverna.lang.observer.MultiCaster
OLD_T2TRUSTSTORE_FILE - Static variable in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
OLD_TRUSTSTORE_PASSWORD - Static variable in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
open(Path) - Method in interface org.apache.taverna.platform.run.api.RunService: Opens a run and returns the ID for the run.
open(Path) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
openStream(ReferenceContext) - Method in interface org.apache.taverna.reference.ExternalReferenceSPI: Open and return an InputStream to the data referenced using, if required, any facilities within the supplied context.
openStream(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.file.FileReference: Open and return an InputStream to the data referenced using, if required, any facilities within the supplied context.
openStream(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.http.HttpReference: Return the data at the URL represented by this external reference
openStream(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
openStream(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference: Fakes a de-reference operation, returning a byte stream over the string data.
openStream(ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
openStream(ReferenceContext) - Method in class org.apache.taverna.t2referencetest.BlueReference: Fakes a de-reference operation, returning a byte stream over the string data.
openStream(ReferenceContext) - Method in class org.apache.taverna.t2referencetest.GreenReference: Fakes a de-reference operation, returning a byte stream over the string data.
openStream(ReferenceContext) - Method in class org.apache.taverna.t2referencetest.RedReference: Fakes a de-reference operation, returning a byte stream over the string data.
openStream(ReferenceContext) - Method in class org.apache.taverna.t2referencetest.YellowReference: Fakes a de-reference operation, returning a byte stream over the string data.
Optional - Class in org.apache.taverna.annotation.annotationbeans: A declaration that the bound input port is optional, if this annotation is refuted then the interpretation should be that the input port is required.
Optional() - Constructor for class org.apache.taverna.annotation.annotationbeans.Optional: Default constructor as mandated by java bean specification
OrderedPair<T> - Class in org.apache.taverna.workflowmodel: A simple generic class to hold a pair of same type objects.
OrderedPair(T, T) - Constructor for class org.apache.taverna.workflowmodel.OrderedPair: Build a new ordered pair with the specified objects.
org.apache.taverna.activities.dataflow - package org.apache.taverna.activities.dataflow
org.apache.taverna.activities.stringconstant - package org.apache.taverna.activities.stringconstant: Contains the activity classes required in the execution of Beanshell scripts.
org.apache.taverna.activities.testutils - package org.apache.taverna.activities.testutils
org.apache.taverna.annotation - package org.apache.taverna.annotation: Entities within the workflow object model may be marked as annotated.
org.apache.taverna.annotation.annotationbeans - package org.apache.taverna.annotation.annotationbeans
org.apache.taverna.annotation.impl - package org.apache.taverna.annotation.impl
org.apache.taverna.configuration.database - package org.apache.taverna.configuration.database
org.apache.taverna.configuration.database.impl - package org.apache.taverna.configuration.database.impl
org.apache.taverna.facade - package org.apache.taverna.facade: Facade interfaces to represent a workflow instance within the enactor.
org.apache.taverna.facade.impl - package org.apache.taverna.facade.impl
org.apache.taverna.invocation - package org.apache.taverna.invocation: Contains classes supporting workflow invocation.
org.apache.taverna.invocation.impl - package org.apache.taverna.invocation.impl
org.apache.taverna.lang.observer - package org.apache.taverna.lang.observer: Implementation of the observer pattern.
org.apache.taverna.monitor - package org.apache.taverna.monitor: Defines the API for the monitoring and steering system.
org.apache.taverna.monitor.impl - package org.apache.taverna.monitor.impl
org.apache.taverna.platform.capability.activity.impl - package org.apache.taverna.platform.capability.activity.impl
org.apache.taverna.platform.capability.api - package org.apache.taverna.platform.capability.api
org.apache.taverna.platform.capability.dispatch.impl - package org.apache.taverna.platform.capability.dispatch.impl
org.apache.taverna.platform.execution.api - package org.apache.taverna.platform.execution.api
org.apache.taverna.platform.execution.impl - package org.apache.taverna.platform.execution.impl
org.apache.taverna.platform.execution.impl.hadoop - package org.apache.taverna.platform.execution.impl.hadoop
org.apache.taverna.platform.execution.impl.local - package org.apache.taverna.platform.execution.impl.local
org.apache.taverna.platform.execution.impl.remote - package org.apache.taverna.platform.execution.impl.remote
org.apache.taverna.platform.report - package org.apache.taverna.platform.report
org.apache.taverna.platform.run.api - package org.apache.taverna.platform.run.api
org.apache.taverna.platform.run.impl - package org.apache.taverna.platform.run.impl
org.apache.taverna.platform.spring.jdbc - package org.apache.taverna.platform.spring.jdbc: Extensions to the JDBC parts of Spring, and support for proxying of JDBC drivers so we can load them dynamically from raven artifacts.
org.apache.taverna.provenance.item - package org.apache.taverna.provenance.item
org.apache.taverna.provenance.reporter - package org.apache.taverna.provenance.reporter
org.apache.taverna.provenance.vocabulary - package org.apache.taverna.provenance.vocabulary
org.apache.taverna.reference - package org.apache.taverna.reference: Interfaces for the Taverna 2 reference manager.
org.apache.taverna.reference.annotations - package org.apache.taverna.reference.annotations: Annotations to make methods in the data access object implementations for cache injection.
org.apache.taverna.reference.h3 - package org.apache.taverna.reference.h3: Contains the marker interfaces used by the implementation package to ensure that all appropriate classes are mapped in hibernate before implementations of classes that depend upon them, and to ensure that 'static' classes such as the implementations of reference set etc are mapped correctly.
org.apache.taverna.reference.impl - package org.apache.taverna.reference.impl: Implementation of the reference manager APIs backed by Hibernate.
org.apache.taverna.reference.impl.external.file - package org.apache.taverna.reference.impl.external.file: Support for references to a file on a local (or otherwise mounted) filesystem
org.apache.taverna.reference.impl.external.http - package org.apache.taverna.reference.impl.external.http: Support for references to a URL with the HTTP protocol
org.apache.taverna.reference.impl.external.object - package org.apache.taverna.reference.impl.external.object: Support for representation of inlined objects as references.
org.apache.taverna.security.credentialmanager - package org.apache.taverna.security.credentialmanager
org.apache.taverna.security.credentialmanager.impl - package org.apache.taverna.security.credentialmanager.impl
org.apache.taverna.services - package org.apache.taverna.services
org.apache.taverna.services.impl - package org.apache.taverna.services.impl
org.apache.taverna.t2referencetest - package org.apache.taverna.t2referencetest
org.apache.taverna.utility - package org.apache.taverna.utility: Utility classes, currently consists of a generic type safe alternative to TreeModel along with an adapter class to allow it to be used where a TreeModel is required (i.e.
org.apache.taverna.visit - package org.apache.taverna.visit
org.apache.taverna.workflowmodel - package org.apache.taverna.workflowmodel: Defines classes and interfaces for workflow level entities and events.
org.apache.taverna.workflowmodel.health - package org.apache.taverna.workflowmodel.health: A package that contains a set of classes to be used in testing a Dataflow prior to invocation.
These can carry our various tests such as a service endpoint being accessible.
org.apache.taverna.workflowmodel.impl - package org.apache.taverna.workflowmodel.impl: Implementation package for workflow entities
org.apache.taverna.workflowmodel.processor.activity - package org.apache.taverna.workflowmodel.processor.activity: Provides definitions for a single Activity to be contained within a Processor.
org.apache.taverna.workflowmodel.processor.activity.config - package org.apache.taverna.workflowmodel.processor.activity.config: A set of helper classes to aid in defining how Activities are configured.
org.apache.taverna.workflowmodel.processor.activity.impl - package org.apache.taverna.workflowmodel.processor.activity.impl: Contains specific implementations of the Activity Ports, together with an implementation of ActivityPortBuilder which is responsible for building them.
org.apache.taverna.workflowmodel.processor.config - package org.apache.taverna.workflowmodel.processor.config
org.apache.taverna.workflowmodel.processor.dispatch - package org.apache.taverna.workflowmodel.processor.dispatch: Definition and support classes for the Dispatch Stack.
org.apache.taverna.workflowmodel.processor.dispatch.description - package org.apache.taverna.workflowmodel.processor.dispatch.description: Annotations and enumerations used to describe dispatch layers, specifically the types of messages they can consume and their reactions to those messages.
org.apache.taverna.workflowmodel.processor.dispatch.events - package org.apache.taverna.workflowmodel.processor.dispatch.events
org.apache.taverna.workflowmodel.processor.dispatch.impl - package org.apache.taverna.workflowmodel.processor.dispatch.impl: Implementation package for the dispatch stack interfaces.
org.apache.taverna.workflowmodel.processor.dispatch.layers - package org.apache.taverna.workflowmodel.processor.dispatch.layers: Contains implementations of DispatchLayer defined by the core Taverna 2 specification.
org.apache.taverna.workflowmodel.processor.iteration - package org.apache.taverna.workflowmodel.processor.iteration: Object model and enactment logic for the iteration strategy component of a Processor
org.apache.taverna.workflowmodel.processor.iteration.impl - package org.apache.taverna.workflowmodel.processor.iteration.impl: Implementation logic for the iteration system.
org.apache.taverna.workflowmodel.serialization - package org.apache.taverna.workflowmodel.serialization
org.apache.taverna.workflowmodel.utils - package org.apache.taverna.workflowmodel.utils
org.pingel.util - package org.pingel.util
outgoingJobs - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
outgoingLinks - Variable in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
outputAdded(Path, String, int[]) - Method in interface org.apache.taverna.platform.report.ReportListener
outputAdded(Path, String, int[]) - Method in class org.apache.taverna.platform.report.StatusReport: Informs the report that an output value has been added.
OutputDataProvenanceItem - Class in org.apache.taverna.provenance.item: Contains details of port names and the output data they receive.
OutputDataProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.OutputDataProvenanceItem
OutputPort - Interface in org.apache.taverna.workflowmodel: Port representing the output of an activity, processor or workflow.
outputPortMapping - Variable in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
outputPorts - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
outputPorts - Variable in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
owner - Variable in class org.apache.taverna.invocation.Event
owningProcessId - Static variable in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl

P

Parallelize - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Dispatch layer which consumes a queue of events and fires off a fixed number of simultaneous jobs to the layer below.
Parallelize() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
Parallelize(int) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize: Test constructor, only used by unit tests, should probably not be public access here?
ParallelizeConfig - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Bean to hold the configuration for the parallelize layer, specifically a single int property defining the number of concurrent jobs in that processor instance per owning process ID.
ParallelizeConfig() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.ParallelizeConfig
parseActivityReport(JsonNode, Path, ProcessorReport, WorkflowBundle) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
parseDates(JsonNode, StatusReport) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
ParsedDistinguishedName - Interface in org.apache.taverna.security.credentialmanager: A parsed Distinguished Name with getters for parts.
ParsedDistinguishedNameImpl - Class in org.apache.taverna.security.credentialmanager.impl: Parses a Distinguished Name and stores the parts for retreival.
ParsedDistinguishedNameImpl(String) - Constructor for class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl: Parses a DN string and fills in fields with DN parts.
parseDN(String) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser: Parses a DN string and fills in fields with DN parts.
parseDN(String) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl: Parses a DN string and fills in fields with DN parts.
parseInvocation(JsonNode, Path, StatusReport) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
parseProcessorReport(JsonNode, Path, WorkflowReport, WorkflowBundle) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
parseValues(JsonNode, Path) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
parseWorkflowReport(JsonNode, Path, ActivityReport, WorkflowBundle) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
PASSWORD - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
path - Variable in class org.apache.taverna.utility.TypedTreeModelEvent
pathSteps() - Method in class org.apache.taverna.reference.impl.TranslationPath
pause(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
pause() - Method in interface org.apache.taverna.platform.execution.api.Execution: Pauses the execution.
pause(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Pauses the execution of a workflow.
pause() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
pause() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
pause(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Pauses a running run.
pause() - Method in class org.apache.taverna.platform.run.impl.Run
pause(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
pauseWorkflow(String) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop: Pause the workflow run with the specified id
pauseWorkflowRun() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
pauseWorkflowRun() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Pause the workflow run corresponding to this facade
Person - Interface in org.apache.taverna.annotation: All metadata assertions and curation assertions have a person who is ultimately responsible for the assertion (although this may not necessarily imply that the assertion was created interactively).
PersonImpl - Class in org.apache.taverna.annotation.impl
PersonImpl(String) - Constructor for class org.apache.taverna.annotation.impl.PersonImpl
POOL_MAX_ACTIVE - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
POOL_MAX_IDLE - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
POOL_MIN_IDLE - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
popIndex() - Method in class org.apache.taverna.invocation.Completion: Pull the index array previous pushed to the owning process name and prepend it to the current index array
popIndex() - Method in class org.apache.taverna.invocation.IterationInternalEvent: Pop a previously pushed index array off the process name and append the current index array to create the new index array.
popIndex() - Method in class org.apache.taverna.workflowmodel.processor.activity.Job: Pull the index array previous pushed to the owning process name and prepend it to the current index array
popOwner() - Method in class org.apache.taverna.invocation.Event: Helper method for implementations of popOwningProcess, this constructs the appropriate process identifier after the leaf has been removed and returns it.
popOwningProcess() - Method in class org.apache.taverna.invocation.Completion
popOwningProcess() - Method in class org.apache.taverna.invocation.Event: Return a copy of the event subclass with the last owning process removed from the owning process list.
popOwningProcess() - Method in class org.apache.taverna.invocation.WorkflowDataToken
popOwningProcess() - Method in class org.apache.taverna.workflowmodel.processor.activity.Job
popOwningProcess() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchCompletionEvent
popOwningProcess() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
popOwningProcess() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent
popOwningProcess() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
popOwningProcess() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent
PORT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
Port - Interface in org.apache.taverna.workflowmodel: Named port which receives events from some other entity and handles them appropriately.
PortComparator - Class in org.apache.taverna.workflowmodel.utils: Compare two workflow ports by their name.
PortComparator() - Constructor for class org.apache.taverna.workflowmodel.utils.PortComparator
PrefixDotProduct - Class in org.apache.taverna.workflowmodel.processor.iteration: Matches jobs where the index array of the job on index 0 is the prefix of the index array of the job on index 1.
PrefixDotProduct() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.PrefixDotProduct
printProcess(String[]) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
ProcessIdentifierException - Exception in org.apache.taverna.invocation: Thrown when attempting to create an invalid process identifier, either by popping an empty one (this by definition has no parents) or by pushing a local name including a colon ':' character.
ProcessIdentifierException() - Constructor for exception org.apache.taverna.invocation.ProcessIdentifierException
ProcessIdentifierException(String, Throwable) - Constructor for exception org.apache.taverna.invocation.ProcessIdentifierException
ProcessIdentifierException(String) - Constructor for exception org.apache.taverna.invocation.ProcessIdentifierException
ProcessIdentifierException(Throwable) - Constructor for exception org.apache.taverna.invocation.ProcessIdentifierException
Processor - Interface in org.apache.taverna.workflowmodel: A single node within the dataflow digraph, the Processor is the basic functional unit within a Taverna workflow.
ProcessorCrystalizerImpl - Class in org.apache.taverna.workflowmodel.impl: AbstractCrystalizer bound to a specific ProcessorImpl
ProcessorCrystalizerImpl(ProcessorImpl) - Constructor for class org.apache.taverna.workflowmodel.impl.ProcessorCrystalizerImpl: Create and bind to the specified ProcessorImpl
ProcessorFinishedEvent - Class in org.apache.taverna.workflowmodel: An event saying that a processor with a given owning process has finished with execution (that includes the whole dispatch stack - iterations of the processor and all).
ProcessorFinishedEvent(Processor, String) - Constructor for class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
ProcessorImpl - Class in org.apache.taverna.workflowmodel.impl: Implementation of Processor
ProcessorImpl() - Constructor for class org.apache.taverna.workflowmodel.impl.ProcessorImpl: Create a new processor implementation with default blank iteration strategy and dispatch stack.
ProcessorInputPort - Interface in org.apache.taverna.workflowmodel: Input port on a Processor, is both a filtering input port and a processor port
ProcessorOutputPort - Interface in org.apache.taverna.workflowmodel: Input port on a Processor, is both an event forwarding output port and a processor port
ProcessorPort - Interface in org.apache.taverna.workflowmodel: An ProcessorInputPort or ProcessorOutputPort belonging to a Processor.
ProcessorProvenanceItem - Class in org.apache.taverna.provenance.item: Each Processor inside a workflow will have one of these for each provenance run.
ProcessorProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.ProcessorProvenanceItem
ProcessorReport - Class in org.apache.taverna.platform.report: Report about the State of a Processor invocation.
ProcessorReport(Processor) - Constructor for class org.apache.taverna.platform.report.ProcessorReport: Constructs a new ProcessorReport.
ProcessProvenanceItem - Class in org.apache.taverna.provenance.item: Each time a job is received by the dispatch stack one of these will be created.
ProcessProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.ProcessProvenanceItem
PROPERTY_KEYSTORE - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PROPERTY_KEYSTORE_PASSWORD - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PROPERTY_KEYSTORE_PROVIDER - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PROPERTY_KEYSTORE_TYPE - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PROPERTY_TRUSTSTORE - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PROPERTY_TRUSTSTORE_PASSWORD - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PROPERTY_TRUSTSTORE_PROVIDER - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PROPERTY_TRUSTSTORE_TYPE - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
PropertyContributingDispatchLayer<ConfigType> - Interface in org.apache.taverna.workflowmodel.processor.dispatch: Used by dispatch layers which can contribute property information to their parent processor instance.
ProvenanceItem - Interface in org.apache.taverna.provenance.item: Used to store some enactment information during a workflow run
ProvenanceReporter - Interface in org.apache.taverna.provenance.reporter
ProviderComparator() - Constructor for class org.apache.taverna.security.credentialmanager.MasterPasswordProvider.ProviderComparator
pruneAnnotations(Annotated<?>, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools: Remove out of date annotations unless many of that class are allowed, or it is explicitly not pruned
pushCompletion(String, String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort: Action to take when the filter pushes a completion event out
pushCompletion(Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Push the specified completion event to the parent node
pushData(WorkflowDataToken, String) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
pushData(WorkflowDataToken, String) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Push a data token into the specified port.
pushData(String, String, int[], T2Reference, InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort: Action to take when a data event is created by the filter
pushEvent(IterationInternalEvent<? extends IterationInternalEvent<?>>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Called when an event (Completion or Job) hits the top of the dispatch stack and needs to be pushed out of the processor
pushIndex() - Method in class org.apache.taverna.invocation.Completion: Push the index array onto the owning process name and return the new Job object.
pushIndex() - Method in class org.apache.taverna.invocation.IterationInternalEvent: Push the index array onto the owning process name and return the new Event subclass object.
pushIndex() - Method in class org.apache.taverna.workflowmodel.processor.activity.Job: Push the index array onto the owning process name and return the new Job object.
pushJob(Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Push the specified job up to the parent node in the iteration strategy.
pushOwner(String) - Method in class org.apache.taverna.invocation.Event: Helper method for implementations of pushOwningProcess, appends the specified local name to the current owning process identifier and returns the new id.
pushOwningProcess(String) - Method in class org.apache.taverna.invocation.Completion
pushOwningProcess(String) - Method in class org.apache.taverna.invocation.Event: Return a copy of the event subclass with the specified local process name appended to the owning process identifier field.
pushOwningProcess(String) - Method in class org.apache.taverna.invocation.WorkflowDataToken
pushOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.Job
pushOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchCompletionEvent
pushOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
pushOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent
pushOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
pushOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent
pushToken(WorkflowDataToken, String, int) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
put(Identified) - Method in class org.apache.taverna.reference.impl.SimpleCacheProviderImpl
put(Identified) - Method in interface org.apache.taverna.reference.ReferenceServiceCacheProvider: Called after an Identified has been written to the backing store, either for the first time or after modification.
PutIdentifiedOperation - Annotation Type in org.apache.taverna.reference.annotations: Applied to methods in Dao implementations which store or update data in the backing store.
putObject(ProceedingJoinPoint) - Method in class org.apache.taverna.reference.impl.CacheAspect: Called around a write or update operation on the backing store, writes through to the cache after modifying the state of the backing store and before returning from the dao method
putObject(ProceedingJoinPoint) - Method in class org.apache.taverna.reference.impl.WriteQueueAspect: Called around a write or update operation on the backing store, writes through to the cache after modifying the state of the backing store and before returning from the dao method

R

ReactionTo - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description: Describes the type of message to which the various DispatchLayerFooReaction classes are referring
readFields(DataInput) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
receiveBypassCompletion(Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
receiveCompletion(int[]) - Method in class org.apache.taverna.activities.testutils.DummyCallback
receiveCompletion(int[]) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: If (and only if) the activity is streaming data then this method can be called to signal a (possibly partial) completion of the stream.
receiveCompletion(int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
receiveCompletion(int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
receiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
receiveCompletion(String, String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
receiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
receiveCompletion(String, String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
receiveCompletion(int, Completion) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: Nodes can also receive completion events, the simplest being one declaring that no further input is expected on the given input, or partial completion events which are interpreted as 'no event with an index array prefixed by the specified completion index array will be received on the specified index'
receiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode: Completion events are passed straight through the same as jobs
receiveData(String, String, int[], T2Reference, InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl: Receive a single data event from an upstream process.
receiveData(String, String, int[], T2Reference, InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
receivedCompletion - Variable in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode.CompletionState
receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: If an error occurs we can either handle the error or send it to the layer above for further processing.
receiveError(DispatchErrorEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer: Receive a single error reference from the layer below
receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce: Always send the error document job result on receiving a failure, at least for now! This should be configurable, in effect this is the part that ensures the processor never sees a top level failure.
receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance: Create an ErrorProvenanceItem and send across to the ProvenanceConnector
receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
receiveEvent(WorkflowDataToken) - Method in interface org.apache.taverna.workflowmodel.EventHandlingInputPort: Receive an arbitrary workflow event.
receiveEvent(IterationInternalEvent<?>) - Method in class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer: Receive a Job or Completion, Jobs are emitted unaltered and cached, Completion events trigger registration of a corresponding list - this may be recursive in nature if the completion event's index implies nested lists which have not been registered.
receiveEvent(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
receiveEvent(IterationInternalEvent<? extends IterationInternalEvent<?>>) - Method in interface org.apache.taverna.workflowmodel.impl.Crystalizer: Receive a Job or Completion, Jobs are emitted unaltered and cached, Completion events trigger registration of a corresponding list - this may be recursive in nature if the completion event's index implies nested lists which have not been registered.
receiveEvent(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl: Receive an input event, relay it through the internal output port to all connected entities
receiveEvent(WorkflowDataToken) - Method in interface org.apache.taverna.workflowmodel.MergeInputPort: Receive an arbitrary workflow event.
receiveEvent(IterationInternalEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Receive an event to be fed into the top layer of the dispatch stack for processing.
receiveEvent(IterationInternalEvent<?>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl: Receive a single job from an upstream IterationStrategyImpl in the stack.
receiveEventFromStrategy(IterationInternalEvent<? extends IterationInternalEvent<?>>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl: Called by the final iteration strategy to push events onto the dispatcher's queue
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: Receive a job from the layer above, store it for later retries and pass it down to the next layer
receiveJob(DispatchJobEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer: Receive a single job and associated set of activities from the layer above
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce: If the job contains errors, or collections which contain errors themselves then bounce a result message with error documents in back up to the layer above
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover: Receive a job from the layer above, store it in the state map then relay it to the layer below with a modified activity list containing only the activity at index 0
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance: Create the ProvenanceItems and send them all across to the ProvenanceConnector except for the IterationProvenanceItem, this one is told what it's inputs are but has to wait until the results are received before being sent across.
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke: Receive a job from the layer above and pick the first concrete activity from the list to invoke.
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
receiveJob(Job, List<? extends Activity<?>>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
receiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
receiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
receiveJob(int, Job) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode: The nodes within the iteration strategy, a tree structure, are event based.
receiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode: If this node receives a job it will always be pushed without modification up to the parent
receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
receiveJobQueue(DispatchJobQueueEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer: Receive a pointer to the job queue along with a set of activities, this is received from the layer above in the dispatch stack or from the DispatchStackImpl object itself if this is the top layer.
receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
receiveMonitorableProperty(MonitorableProperty<?>, String) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack: The dispatch stack acts as an aggregator for monitorable properties exposed by the dispatch layers.
receiveResult(Map<String, T2Reference>, int[]) - Method in class org.apache.taverna.activities.testutils.DummyCallback
receiveResult(Map<String, T2Reference>, int[]) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: Push a map of named identifiers out to the invocation layer which is then responsible for wrapping them up into an appropriate Job object and sending it up the dispatch stack.
receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: If we see a result with an index matching one of those in the current retry state we can safely forget that state object
receiveResult(DispatchResultEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer: Receive a result from the layer below
receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance: Populate an OutputDataProvenanceItem with the results and attach it to the appropriate IterationProvenanceItem.
receiveResult(Map<String, T2Reference>, int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
receiveResult(Map<String, T2Reference>, int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer: If we see a completion event with an index matching one of those in the current retry state we can safely forget that state object
receiveResultCompletion(DispatchCompletionEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer: Receive a (possibly partial) completion event from the layer below.
receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize: Only going to receive this if the activity invocation was streaming, in which case we need to handle all completion events and pass them up the stack.
receiveToken(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
recordIdentifier() - Method in interface org.apache.taverna.workflowmodel.Dataflow
recordIdentifier() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
RedReference - Class in org.apache.taverna.t2referencetest: RedReferences carry their data as an internal String and have a resolution cost of 0.9f whatever the value of that string.
RedReference() - Constructor for class org.apache.taverna.t2referencetest.RedReference
RedReference(String) - Constructor for class org.apache.taverna.t2referencetest.RedReference
Reduce() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest.Reduce
reduce(Text, Iterable<TextArrayWritable>, Reducer<Text, TextArrayWritable, Text, Text>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest.Reduce
Reduce() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest.Reduce
reduce(LongWritable, Iterable<MapWritable>, Reducer<LongWritable, MapWritable, LongWritable, Text>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest.Reduce
reduce(int[], Iterable<Map<String, Path>>, Reducer<int[], Map<String, Path>, Object, Object>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaReducer
REFERENCE_SERVICE_CONTEXT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
ReferenceContext - Interface in org.apache.taverna.reference: Many operations over the reference manager require access to an appropriate context.
ReferencedDataNature - Enum in org.apache.taverna.reference: Where possible ExternalReferenceSPI implementations should be able to determine whether the data they refer to is textual or binary in nature.
referenceFromString(String) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl: Parse the reference contained in the string and return a T2Reference with the correct properties
referenceFromString(String) - Method in interface org.apache.taverna.reference.ReferenceService: Given a string representation of a T2Reference create a new T2Reference with the correct depth etc.
referenceService - Variable in class org.apache.taverna.activities.testutils.DummyCallback
ReferenceService - Interface in org.apache.taverna.reference: Top level access point to the reference manager for client code which is aware of references and error documents.
ReferenceServiceCacheProvider - Interface in org.apache.taverna.reference: A simple interface to be implemented by data access object cache providers, intended to be used to inject cache implementations through AoP
ReferenceServiceException - Exception in org.apache.taverna.reference: Thrown by methods in the ReferenceService, used to wrap any underlying exceptions from lower layers.
ReferenceServiceException() - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
ReferenceServiceException(String) - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
ReferenceServiceException(Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
ReferenceServiceException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
ReferenceServiceImpl - Class in org.apache.taverna.reference.impl: Implementation of ReferenceService, inject with ReferenceSetService, ErrorDocumentService and ListService to enable.
ReferenceServiceImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceServiceImpl
ReferenceServiceResolutionCallback - Interface in org.apache.taverna.reference: Used by the asynchronous form of the resolveIdentifier method in ReferenceService
ReferenceSet - Interface in org.apache.taverna.reference: A set of ExternalReferenceSPI instances, all of which point to the same (byte equivalent) data.
ReferenceSetAugmentationException - Exception in org.apache.taverna.reference: Thrown when the reference set augmentor is unable to provide at least one of the desired types for any reason.
ReferenceSetAugmentationException() - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
ReferenceSetAugmentationException(String) - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
ReferenceSetAugmentationException(Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
ReferenceSetAugmentationException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
referenceSetAugmentor - Variable in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
ReferenceSetAugmentor - Interface in org.apache.taverna.reference: Provides a framework to find and engage appropriate instances of ExternalReferenceTranslatorSPI and ExternalReferenceBuilderSPI to build external references from, respectively, other external references and from streams.
ReferenceSetAugmentorCallback - Interface in org.apache.taverna.reference: Callback interface used when augmenting a ReferenceSet in an asynchronous fashion through augmentReferenceSetAsynch in ReferenceSetAugmentor.
ReferenceSetAugmentorImpl - Class in org.apache.taverna.reference.impl: Implementation of ReferenceSetAugmentor using Dijkstra's shortest path algorithm over a type graph built from SPI instance registries of reference builders and reference translators.
ReferenceSetAugmentorImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl: Default constructor to make life easier when using Spring.
referenceSetDao - Variable in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
ReferenceSetDao - Interface in org.apache.taverna.reference: Data Access Object interface for ReferenceSet.
ReferenceSetImpl - Class in org.apache.taverna.reference.impl: An implementation of ReferenceSet with the additional methods and metadata required by Hibernate3 to allow it to be persisted in a relational store.
ReferenceSetImpl(Set<ExternalReferenceSPI>, T2ReferenceImpl) - Constructor for class org.apache.taverna.reference.impl.ReferenceSetImpl: Construct a new ReferenceSetImpl with the given set of external references and identifier.
ReferenceSetImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceSetImpl: Default constructor, used by Hibernate when reconstructing this bean from the database.
referenceSetRetrievalFailed(ReferenceSetServiceException) - Method in interface org.apache.taverna.reference.ReferenceSetServiceCallback: Called if the retrieval failed for some reason
referenceSetRetrieved(ReferenceSet) - Method in interface org.apache.taverna.reference.ReferenceSetServiceCallback: Called when the requested ReferenceSet has been successfully retrieved.
referenceSetService - Variable in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
ReferenceSetService - Interface in org.apache.taverna.reference: Provides facilities to register sets of ExternalReferenceSPI implementations within the reference manager and to retrieve these sets by T2Reference either as stored or with translation support.
ReferenceSetServiceCallback - Interface in org.apache.taverna.reference: Callback interface used by asynchronous methods in the ReferenceSetService interface
ReferenceSetServiceException - Exception in org.apache.taverna.reference: RuntimeException subclass thrown by the reference set service layer interfaces.
ReferenceSetServiceException() - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
ReferenceSetServiceException(String) - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
ReferenceSetServiceException(Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
ReferenceSetServiceException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
ReferenceSetServiceImpl - Class in org.apache.taverna.reference.impl: Implementation of ReferenceSetService, inject with an appropriate ReferenceSetDao to enable.
ReferenceSetServiceImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
refreshInternalIdentifier() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
refService - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
register(Object, int, boolean, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl: The top level registration method is used to register either as yet unregistered ErrorDocuments and ReferenceSets (if these are passed in and already have an identifier this call does nothing) and arbitrarily nested Lists of the same.
register(Object, int, boolean, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceService: The top level registration method is used to register either as yet unregistered ErrorDocuments and ReferenceSets (if these are passed in and already have an identifier this call does nothing) and arbitrarily nested Lists of the same.
registerEmptyList(int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
registerEmptyList(int, ReferenceContext) - Method in interface org.apache.taverna.reference.ListService: Register a new empty list with the specified depth.
registerError(String, Throwable, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Register a new error document.
registerError(String, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Equivalent to registerError(message, null, depth, context).
registerError(Throwable, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Equivalent to registerError("", t, depth, context).
registerError(String, Set<T2Reference>, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService: Register a new error document.
registerError(String, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
registerError(Throwable, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
registerError(String, Throwable, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl: Register the specified error and any child errors (which have the same namespace and local part but a lower depth, down to depth of zero
registerError(String, Set<T2Reference>, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
registerList(List<T2Reference>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
registerList(List<T2Reference>, ReferenceContext) - Method in interface org.apache.taverna.reference.ListService: Register a new list of T2References.
registerNode(Object, String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Create a new node in the monitor
registerNode(Object, String) - Method in class org.apache.taverna.monitor.MonitorManager: Register a new node with this monitor.
registerNode(Object, String, Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.MonitorManager: Register a new node with this monitor.
registerNode(Object, String[]) - Method in class org.apache.taverna.monitor.MonitorManager: Register a new node with this monitor.
registerNode(Object, String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.MonitorManager: Register a new node with this monitor.
registerNode(Object, String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
RegisterNodeMessage(Object, String[], Set<MonitorableProperty<?>>) - Constructor for class org.apache.taverna.monitor.MonitorManager.RegisterNodeMessage
registerReferenceSet(Set<ExternalReferenceSPI>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
registerReferenceSet(Set<ExternalReferenceSPI>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceSetService: Register a set of ExternalReferenceSPI instances, all of which should point to byte equivalent data, and return the newly created ReferenceSet.
RemoteExecution - Class in org.apache.taverna.platform.execution.impl.remote: An Execution for executing a Taverna workflow on a Taverna Server.
RemoteExecution(WorkflowBundle, Workflow, Profile, Bundle) - Constructor for class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
RemoteExecutionService - Class in org.apache.taverna.platform.execution.impl.remote: Service for executing Taverna workflows on a Taverna Server.
RemoteExecutionService() - Constructor for class org.apache.taverna.platform.execution.impl.remote.RemoteExecutionService
RemoteHealthChecker - Class in org.apache.taverna.workflowmodel.health: A RemoteHealthChecker performs a visit to an Activity by trying to contact a specific endpoint
RemoteHealthChecker() - Constructor for class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
remove(Object) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
remove(int) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
remove(int) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
remove(MutableTreeNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
removeAll(Collection<?>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
removeAnnotationAssertion(AnnotationAssertion<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationChainImpl
removeAnnotationBean() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
removeAnnotationRole() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
removeAnnotationSource() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
removeCreator(Person) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
removeCurationEvent(CurationEvent<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
removeDataflowInputPort(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Remove the named dataflow input port
removeDataflowInputPort(DataflowInputPort) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Remove the specified input port from this dataflow
removeDataflowOutputPort(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Remove the named dataflow output port
removeDataflowOutputPort(DataflowOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Remove the specified output port from this dataflow
removeEntity(Object) - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
removeFacadeListener(FacadeListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
removeFacadeListener(FacadeListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Remove a previously registered failure listener
removeFromParent() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
removeInput(NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
removeInputByName(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
removeInputs() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity: Remove existing input ports
removeJob(String, AbstractErrorHandlerLayer<ConfigurationType>.JobState) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
removeLayer(DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
removeMerge(Merge) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
removeObserver(Observer<Message>) - Method in class org.apache.taverna.lang.observer.MultiCaster: Remove the observer and no longer send out any notifications about it
removeObserver(Observer<Message>) - Method in interface org.apache.taverna.lang.observer.Observable: Remove a class who is currently observing
removeObserver(Observer<MonitorManager.MonitorMessage>) - Method in class org.apache.taverna.monitor.MonitorManager: Remove a class who is currently observing
removeObserver(Observer<KeystoreChangedEvent>) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Remove an observer of the changes to the Keystore or Truststore.
removeObserver(Observer<KeystoreChangedEvent>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Remove an observer of the changes to the Keystore or Truststore.
removeObserver(Observer<ProcessorFinishedEvent>) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
removeOutgoingLink(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
removeOutputs() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity: Remove existing output ports.
removeProcessor(Processor) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
removeReportListener(ReportListener) - Method in class org.apache.taverna.platform.report.StatusReport
removeResultListener(ResultListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
removeResultListener(ResultListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Remove a previously registered result listener
removeResultListener(ResultListener) - Method in interface org.apache.taverna.workflowmodel.DataflowOutputPort: Remove a ResultListener
removeStrategy(IterationStrategy) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
removeTreeModelListener(TypedTreeModelListener<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModel: Removes a listener previously added with addTreeModelListener.
renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToBooleanConverter
renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToByteArrayConverter
renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToDoubleConverter
renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToIntegerConverter
renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToStringConverter
renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToVMObjectReferenceConverter
renderFrom(InputStream, ReferencedDataNature, String) - Method in interface org.apache.taverna.reference.StreamToValueConverterSPI: Render the stream to the target object type
renderIdentifier(T2Reference, Class<?>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
renderIdentifier(T2Reference, Class<?>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceService: Resolve the given identifier, building a POJO structure where the non-list items are of the desired class.
ReportListener - Interface in org.apache.taverna.platform.report
requestRun(Runnable) - Method in class org.apache.taverna.activities.testutils.DummyCallback
requestRun(Runnable) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback: If an activity proxy wants to create a new thread of activity it should use this method unless there is a very good reason not to.
requestRun(Runnable) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
requestRun(Runnable) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
resetAuthCache() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Reset the JVMs cache for authentication like HTTP Basic Auth.
resetAuthCache() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Reset the JVMs cache for authentication like HTTP Basic Auth.
resetPassword() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
resolutionFailed(ReferenceServiceException) - Method in interface org.apache.taverna.reference.ReferenceServiceResolutionCallback: Called when the resolution process has failed
resolveAt(String, int[]) - Method in class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer.CompletionAwareTreeCache
resolveIdentifier(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl: Perform recursive identifier resolution, building a collection structure of Identified objects, any collection elements being IdentifiedLists of Identified subclasses.
resolveIdentifier(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceService: Perform recursive identifier resolution, building a collection structure of Identified objects, any collection elements being IdentifiedLists of Identified subclasses.
resolveIdentifierAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceServiceResolutionCallback) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Wraps the synchronous form, using the executeRunnable method to schedule it.
resolveIdentifierAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceServiceResolutionCallback) - Method in interface org.apache.taverna.reference.ReferenceService: As resolveIdentifier but using a callback object and returning immediately
ResultListener - Interface in org.apache.taverna.facade: Implement and use with the WorkflowInstanceFacade to listen for data production events from the underlying workflow instance
resultListeners - Variable in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
resultTokenProduced(WorkflowDataToken, String) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.FacadeResultListener
resultTokenProduced(WorkflowDataToken, String) - Method in interface org.apache.taverna.facade.ResultListener: Called when a new result token is produced by the workflow instance.
resultTokenProduced(WorkflowDataToken, String) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
resultWrappingDepth - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
resume(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
resume() - Method in interface org.apache.taverna.platform.execution.api.Execution: Resumes a paused execution.
resume(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Resumes the execution of a paused workflow.
resume() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
resume() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
resume(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Resumes a paused run.
resume() - Method in class org.apache.taverna.platform.run.impl.Run
resume(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
resumeWorkflow(String) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop: Resume the workflow run with the specified id
resumeWorkflowRun() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
resumeWorkflowRun() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade: Resume the workflow run corresponding to this facade
retainAll(Collection<?>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
Retry - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: Implements retry policy with delay between retries and exponential backoff
Retry() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
Retry(int, int, int, double) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
RetryConfig - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
RetryConfig() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
run(String[]) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest
run(String[]) - Method in class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest
run(String[]) - Method in class org.apache.taverna.platform.execution.impl.hadoop.Test
Run - Class in org.apache.taverna.platform.run.impl: A single run of a Workflow.
Run(RunProfile) - Constructor for class org.apache.taverna.platform.run.impl.Run: Constructs a Run from the specified RunProfile.
Run(String, Bundle) - Constructor for class org.apache.taverna.platform.run.impl.Run
RUN_CLOSED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RUN_CREATED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RUN_DELETED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RUN_OPENED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RUN_PAUSED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RUN_RESUMED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RUN_STARTED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RUN_STOPPED - Static variable in interface org.apache.taverna.platform.run.api.RunService
RunDeletionListener - Interface in org.apache.taverna.workflowmodel: A RunDeletionListener is notified when a run is deleted.
RunProfile - Class in org.apache.taverna.platform.run.api: A RunProfile specifies the parameters required to run a Workflow.
RunProfile(ExecutionEnvironment, WorkflowBundle, Bundle) - Constructor for class org.apache.taverna.platform.run.api.RunProfile: Constructs a RunProfile that specifies the parameters required to run a Workflow.
RunProfile(ExecutionEnvironment, WorkflowBundle, String, String, Bundle) - Constructor for class org.apache.taverna.platform.run.api.RunProfile: Constructs a RunProfile that specifies the parameters required to run a Workflow.
RunProfileException - Exception in org.apache.taverna.platform.run.api: Thrown when a RunProfile doesn't contain the correct components to run a workflow.
RunProfileException() - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
RunProfileException(String, Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
RunProfileException(String) - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
RunProfileException(Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
RunService - Interface in org.apache.taverna.platform.run.api: Service for managing runs of Taverna workflows.
RunServiceImpl - Class in org.apache.taverna.platform.run.impl: Implementation of the RunService.
RunServiceImpl() - Constructor for class org.apache.taverna.platform.run.impl.RunServiceImpl
RunStateException - Exception in org.apache.taverna.platform.run.api: Thrown when an operation is attempted when a workflow is in the wrong state, e.g., resuming a workflow that is not paused.
RunStateException() - Constructor for exception org.apache.taverna.platform.run.api.RunStateException
RunStateException(String, Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunStateException
RunStateException(String) - Constructor for exception org.apache.taverna.platform.run.api.RunStateException
RunStateException(Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunStateException

S

sanitiseName(String) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Checks that the name does not have any characters that are invalid for a Taverna name.
satisfyConditions(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl: Called when a set of conditions which were unsatisfied in the context of a given owning process become satisfied.
save(String, Path) - Method in interface org.apache.taverna.platform.run.api.RunService: Saves a run.
save(String, Path) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
save(WorkflowReport, Path) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
save(WorkflowReport, Bundle) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
saveProperties() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
saveUsernameAndPasswordForService(String, String, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Deprecated.
Use CredentialManagerImpl.addUsernameAndPasswordForService(UsernamePassword, URI) instead
SemanticAnnotation - Class in org.apache.taverna.annotation.annotationbeans: A SemanticAssertion holds a String which contains RDF about an Object
SemanticAnnotation() - Constructor for class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
sendEvent(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort: Forward the specified event to all targets
sentJob - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
SerializationException - Exception in org.apache.taverna.workflowmodel.serialization
SerializationException(String, Exception) - Constructor for exception org.apache.taverna.workflowmodel.serialization.SerializationException
SerializationException(String) - Constructor for exception org.apache.taverna.workflowmodel.serialization.SerializationException
SerializeParam(Object) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
ServiceRegistry - Interface in org.apache.taverna.services: Register of Taverna services.
ServiceRegistryImpl - Class in org.apache.taverna.services.impl: Simple implementation of a ServiceRegistry that discovers available services from the ActivityService.
ServiceRegistryImpl() - Constructor for class org.apache.taverna.services.impl.ServiceRegistryImpl
ServiceUsernameAndPasswordProvider - Interface in org.apache.taverna.security.credentialmanager: Defines an interface for providing a username and password for a service to be invoked as part of a workflow run.
set(int, T) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
setActivity(Activity<?>) - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
setActivity(Activity<?>) - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
setActivity(Activity<?>) - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
setActivityFactories(List<ActivityFactory>) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl: Sets the list of available ActivityFactorys.
setActivityProvenanceItem(ActivityProvenanceItem) - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
setActivityService(ActivityService) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService: Sets the service for creating activities.
setActivityService(ActivityService) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
setAllowsLiteralValues(boolean) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
setAnnotationBean(AnnotationBeanSPI) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
setAnnotationRole(AnnotationRole) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
setAnnotations(Set<AnnotationChain>) - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing: Set the annotation chains associated with this annotated object.
setAnnotations(Set<AnnotationChain>) - Method in interface org.apache.taverna.annotation.Annotated
setAnnotationSource(AnnotationSourceSPI) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
setAnnotationString(Annotated<?>, Class<?>, String, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
setApplicationConfiguration(ApplicationConfiguration) - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl: Sets the applicationConfiguration.
setApplicationConfiguration(ApplicationConfiguration) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Sets the applicationConfiguration.
setApplicationConfiguration(ApplicationConfiguration) - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider: Sets the applicationConfiguration.
setApproximateSizeInBytes(Long) - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl
setBackoffFactor(float) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
setBean(Object) - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
setBuilders(List<ExternalReferenceBuilderSPI<?>>) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl: Inject a list containing all known implementations of ExternalReferenceBuilderSPI.
setBuilders(List<ExternalReferenceBuilderSPI<?>>) - Method in class org.apache.taverna.reference.impl.TranslationPath
setCacheProvider(ReferenceServiceCacheProvider) - Method in class org.apache.taverna.reference.impl.CacheAspect: Inject an instance of ReferenceServiceCacheProvider
setCancelledDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the date that the status changed to CANCELLED.
setCause(Throwable) - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
setCharset(String) - Method in class org.apache.taverna.reference.impl.external.file.FileReference: Setter used by hibernate to set the charset property of the file reference
setCheckTime(long) - Method in class org.apache.taverna.visit.VisitReport
setClassName(String) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
setCompletedDate(Date) - Method in class org.apache.taverna.platform.report.Invocation: Sets the date that the status changed to COMPLETED.
setCompletedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the date that the status changed to COMPLETED.
setCondition(Activity<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
setConfigurationDirectoryPath(Path) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager: Set the directory where Credential Manager's Keystore and Truststore files will be read from.
setConfigurationDirectoryPath(Path) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Set the directory where Credential Manager's Keystore and Truststore files will be read from.
setContainsErrors(boolean) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: This method is only ever called from within Hibernate when re-constructing the identifier component to set the error property of the identifier.
setContent(String) - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
setContents(String) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
setContents(String) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference: Set the 'value' of this reference as a string.
setContents(String) - Method in class org.apache.taverna.t2referencetest.BlueReference: Set the 'value' of this reference as a string.
setContents(String) - Method in class org.apache.taverna.t2referencetest.GreenReference: Set the 'value' of this reference as a string.
setContents(String) - Method in class org.apache.taverna.t2referencetest.RedReference: Set the 'value' of this reference as a string.
setContents(String) - Method in class org.apache.taverna.t2referencetest.YellowReference: Set the 'value' of this reference as a string.
setConverters(List<ValueToReferenceConverterSPI>) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Inject value to reference convertor SPI
setCreatedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the date that the status was set to CREATED.
setCreators(List<Person>) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
setCredentialManager(CredentialManager) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerAuthenticator
setCurationEventType(CurationEventType) - Method in class org.apache.taverna.annotation.impl.DisputeEvent
setCurrentPort(int) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setCurrentPort(int) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setData(T2Reference) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
setDatabaseConfiguration(DatabaseConfiguration) - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl: Sets the databaseConfiguration.
setDataBundle(Bundle) - Method in class org.apache.taverna.platform.report.WorkflowReport
setDataBundle(Bundle) - Method in class org.apache.taverna.platform.run.api.RunProfile: Sets the Bundle containing the data values for the Workflow.
setDataflow(Dataflow) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
setDataflowID(String) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
setDataMap(Map<String, T2Reference>) - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
setDataNature(ReferencedDataNature) - Method in class org.apache.taverna.reference.impl.external.file.FileReference
setDataNatureName(String) - Method in class org.apache.taverna.reference.impl.external.file.FileReference
setDate(Date) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
setDepth(int) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: This method is only ever called from within Hibernate when re-constructing the identifier component to set the depth of the identifier.
setDepth(int) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
setDepth(int) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
setDispatchLayerFactories(List<DispatchLayerFactory>) - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl: Sets the list of available DispatchLayerFactorys.
setDispatchLayerService(DispatchLayerService) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService: Sets the service for creating dispatch layers.
setDispatchStack(DispatchStack) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
setDispatchStack(DispatchStack) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer: Set the parent dispatch stack of this layer, this is called when a layer is added to the dispatch stack and can be safely ignored by end users of this API
setDisputeEventDetails(DisputeEventDetails) - Method in class org.apache.taverna.annotation.impl.DisputeEvent
setDocumentationURL(URL) - Method in class org.apache.taverna.annotation.annotationbeans.DocumentationUrl
setDriverClassName(String) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setDriverClassName(String) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setEdits(Edits) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
setEdits(Edits) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
setEdits(Edits) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService: Sets the Edits Service for creating Taverna Dataflows.
setEdits(Edits) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
setEdits(Edits) - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
setEnactmentEnded(Timestamp) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
setEnactmentStarted(Timestamp) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
setEndpointExpiryInMilliseconds(int) - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
setErrorDao(ErrorDocumentDao) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl: Inject the error document data access object.
setErrorDocumentService(ErrorDocumentService) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Inject error document service
setErrorItem(ErrorProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
setErrorReferenceSet(Set) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl: Used by Hibernate to bodge around problems with interface types in the API
setErrorType(String) - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
setEventAdmin(EventAdmin) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
setExceptionMessage(String) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
setExecutionEnvironment(ExecutionEnvironment) - Method in class org.apache.taverna.platform.run.api.RunProfile: Sets the ExecutionEnvironment used to execute the Workflow.
setExecutionEnvironmentService(ExecutionEnvironmentService) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
setExecutionServices(Set<ExecutionService>) - Method in class org.apache.taverna.platform.execution.impl.ExecutionEnvironmentServiceImpl: Sets the ExecutionServices that will be used to find ExecutionEnvironments.
setExposeDatanature(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setExposeDatanature(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setExternalReferences(Set<ExternalReferenceSPI>) - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl: This method is only ever called from within Hibernate, and is used to initialize the set of external references.
setFacadeID(String) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
setFailedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the date that the status changed to FAILED.
setFileName(String) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
setFilePath(String) - Method in class org.apache.taverna.reference.impl.external.file.FileReference: Setter used by hibernate to set the file path property of the file reference
setFilterDepth(int) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
setFinal(boolean) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
setFinal(boolean) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
setFragmentForURI(URI, String) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
setFragmentForURI(URI, String) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
setGranularDepth(int) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
setGranularDepth(int) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean
setHandledReferenceSchemes(List<Class<? extends ExternalReferenceSPI>>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
setHttpUrlString(String) - Method in class org.apache.taverna.reference.impl.external.http.HttpReference: Setter used by hibernate to set the file path property of the file reference
setIdentification(String) - Method in class org.apache.taverna.annotation.annotationbeans.IdentificationAssertion
setIdentifier(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
setIdentifier(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: A unique id for this event.
setImmutable() - Method in interface org.apache.taverna.workflowmodel.Dataflow: Mark this dataflow as immutable.
setImmutable() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
setIncomingLink(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
setIndex(int[]) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
setIndex(int[]) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
setInitialBuilder(ExternalReferenceBuilderSPI<?>) - Method in class org.apache.taverna.reference.impl.TranslationPath
setInitialDelay(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
setInMemory(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setInMemory(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setInput(String, Path) - Method in class org.apache.taverna.platform.report.Invocation: Sets the value of an input port.
setInputDataItem(InputDataProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
setInputPort(boolean) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
setInputPortDefinitions(List<ActivityInputPortDefinitionBean>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
setInputs(Map<String, Path>) - Method in class org.apache.taverna.platform.report.Invocation: Sets the values of input ports.
setInstance(MonitorManager) - Static method in class org.apache.taverna.monitor.MonitorManager: Set the MonitorManager singleton instance.
setInternalId(String) - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
setInvocationContext(InvocationContext) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: Set the InvocationContext that this reporter should be using
setInvocationEnded(Timestamp) - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
setInvocationProcessId(String) - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
setInvocationStarted(Date) - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
setInvocationStarted(Timestamp) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
setIteration(int[]) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
setIterationProvenanceItem(IterationProvenanceItem) - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
setIterationStrategyStack(IterationStrategyStackImpl) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
setJavaTruststorePassword(String) - Method in interface org.apache.taverna.security.credentialmanager.JavaTruststorePasswordProvider: Set the Java truststore password.
setJavaTruststorePasswordProviders(List<JavaTruststorePasswordProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Set the Java truststore password providers for providing the password to encrypt/decrypt the Java's default truststore.
setJDBCUri(String) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setJDBCUri(String) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setJobsCompleted(int) - Method in class org.apache.taverna.platform.report.ProcessorReport: Set the number of completed jobs.
setJobsCompletedWithErrors(int) - Method in class org.apache.taverna.platform.report.ProcessorReport: Set the number of jobs that have completed, but with errors.
setJobsQueued(int) - Method in class org.apache.taverna.platform.report.ProcessorReport: Set the number of queued jobs.
setJobsStarted(int) - Method in class org.apache.taverna.platform.report.ProcessorReport: Set the number of started jobs.
setKind(VisitKind) - Method in class org.apache.taverna.visit.VisitReport
setLineNumber(int) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
setListContents(List) - Method in class org.apache.taverna.reference.impl.T2ReferenceListImpl: This is only called from Hibernate, outside of test code, so is relatively safe to leave unchecked.
setListDao(ListDao) - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl: Inject the list data access object.
setListService(ListService) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Inject list service
setLocalName(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Sets the local name for the dataflow
setLocalPart(String) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: This method is only ever called from within Hibernate when re-constructing the identifier component to set the local part of the identifier.
setLowerNumericValue(NumericType) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
setMasterPassword(String) - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
setMasterPassword(String) - Method in interface org.apache.taverna.security.credentialmanager.MasterPasswordProvider: Set the master password.
setMasterPasswordProviders(List<MasterPasswordProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Set the master password providers for providing the master password to encrypt/decrypt the Credential Maager's Keystore and Truststore.
setMaxDelay(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
setMaximumJobs(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ParallelizeConfig
setMaxRetries(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
setMessage(String) - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
setMessage(String) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
setMessage(String) - Method in class org.apache.taverna.visit.VisitReport: Sets the message
setMethodName(String) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
setMimeType(String) - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
setMimeTypes(List<String>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
setMimeTypes(Set<URI>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
setName(String) - Method in class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
setName(String) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
setName(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
setName(String) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
setName(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
setName(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
setNamespace(String) - Method in class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator: Set the namespace for identifiers generated by this class as a string
setNamespace(String) - Method in class org.apache.taverna.reference.impl.UUIDT2ReferenceGenerator: Set the namespace for identifiers generated by this class as a string
setNamespacePart(String) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: This method is only ever called from within Hibernate when re-constructing the identifier component to set the namespace part of the identifier.
setNestedDataflow(Dataflow) - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
setNestedDataflow(Dataflow) - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflow
setNestedWorkflowReport(WorkflowReport) - Method in class org.apache.taverna.platform.report.ActivityReport
setNodeRemovalDelay(long) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Nodes will be removed at least delayTime milliseconds after their initial deregistration request, this allows UI components to show nodes which would otherwise vanish almost instantaneously.
setNumericValue(NumericType) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericValueAssertion
setObject(Object) - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
setOutput(String, Path) - Method in class org.apache.taverna.platform.report.Invocation: Sets the value of an output port.
setOutputDataItem(OutputDataProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
setOutputPortDefinitions(List<ActivityOutputPortDefinitionBean>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
setOutputs(Map<String, Path>) - Method in class org.apache.taverna.platform.report.Invocation: Sets the values of input ports.
setOwningProcess(String) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
setOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
setParent(MutableTreeNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode: Implements IterationStrategyNode
setParentId(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
setParentId(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: The parent of this provenance Item.
setParentIterationItem(IterationProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
setParentReport(PARENT) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the parent report.
setPassword(char[]) - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
setPausedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the date that the status last changed to PAUSED.
setPort(int) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setPort(String) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setPort(int) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setPort(String) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setPortName(String) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
setPrimaryKey(int) - Method in class org.apache.taverna.reference.AbstractExternalReference: Used by Hibernate internally to establish a foreign key relationship between this abstract superclass and tables corresponding to implementations of the ExternalReference interface.
setProcessId(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
setProcessId(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: The workflow model id that is supplied during enactment eg facade0:dataflow2:processor1
setProcessor(Processor) - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
setProcessorProvenanceItem(ProcessorProvenanceItem) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
setProfileName(String) - Method in class org.apache.taverna.platform.run.api.RunProfile: Sets the name of the Profile to use when running the Workflow.
setProperties(Properties) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
setProperty(T) - Method in interface org.apache.taverna.monitor.SteerableProperty: Set the property value
setProperty(String, Object) - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
setProperty(String, Object) - Method in class org.apache.taverna.platform.report.ProcessorReport: Set an additional property
setProperty(String, Object) - Method in class org.apache.taverna.visit.VisitReport
setProvenanceEnabled(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setProvenanceEnabled(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setReferenceService(ReferenceService) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService: Sets the reference service.
setReferenceService(ReferenceService) - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
setReferenceService(ReferenceService) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
setReferenceService(ReferenceService) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: Tell the connector what ReferenceService it should use when trying to dereference data items inside ProvenanceItems
setReferenceSetAugmentor(ReferenceSetAugmentor) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl: Inject the ReferenceSetAugmentor used to translate or construct new ExternalReferenceSPI instances within a ReferenceSet
setReferenceSetDao(ReferenceSetDao) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl: Inject the reference set data access object.
setReferenceSetService(ReferenceSetService) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Inject reference set service
setReferenceType(T2ReferenceType) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: This method is only ever called from within Hibernate when re-constructing the identifier component to set the reference type property of the identifier.
setReporter(ProvenanceReporter) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance: Tell this layer what ProvenanceConnector implementation is being used to capture the ProvenanceItems.
setResultId(int) - Method in class org.apache.taverna.visit.VisitReport
setResumedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the date that the status last changed form PAUSED to RUNNING.
setRunFirst(boolean) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
setServiceUsernameAndPassword(URI, UsernamePassword) - Method in interface org.apache.taverna.security.credentialmanager.ServiceUsernameAndPasswordProvider: Set the username and password pair for the given service URI.
setServiceUsernameAndPasswordProviders(List<ServiceUsernameAndPasswordProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Set the providers of username and passwords for services.
setSessionID(String) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter: A unique identifier for this run of provenance, should correspond to the initial WorkflowProvenanceItem idenifier that gets sent through
setShouldSave(boolean) - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
setSourceReference(ExternalReferenceSPI) - Method in class org.apache.taverna.reference.impl.TranslationPath
setStackTraceList(List) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl: Used by Hibernate to bodge around problems with interface types in the API
setStartedDate(Date) - Method in class org.apache.taverna.platform.report.Invocation: Sets the date that the status changed to RUNNING.
setStartedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport: Sets the date that the status changed to RUNNING.
setStartInternalDerbyServer(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
setStartInternalDerbyServer(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
setState(WorkflowInstanceFacade.State) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
setState(State) - Method in class org.apache.taverna.platform.report.StatusReport
setState(WorkflowInstanceFacade.State) - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
setStatus(VisitReport.Status) - Method in class org.apache.taverna.visit.VisitReport: Sets the status of this report.
setSubject(Object) - Method in class org.apache.taverna.visit.VisitReport
setSubReports(Collection<VisitReport>) - Method in class org.apache.taverna.visit.VisitReport: Replaces the List of sub reports with those provided.
setT2ReferenceGenerator(T2ReferenceGenerator) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl: Inject the T2Reference generator used to allocate new IDs when registering ErrorDocuments
setT2ReferenceGenerator(T2ReferenceGenerator) - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl: Inject the T2Reference generator used to allocate new IDs when registering lists of T2Reference
setT2ReferenceGenerator(T2ReferenceGenerator) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl: Inject the T2Reference generator used to allocate new IDs when registering sets of ExternalReferenceSPI
setTargetEvent(Curateable) - Method in class org.apache.taverna.annotation.impl.DisputeEvent
setText(String) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractTextualValueAssertion
setTimeoutInSeconds(int) - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
setTranslatedElementType(Class<?>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
setTranslators(List<ExternalReferenceTranslatorSPI<?, ?>>) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl: Inject a list containing all known implementations of ExternalReferenceTranslatorSPI.
setTranslators(List<ExternalReferenceTranslatorSPI<?, ?>>) - Method in class org.apache.taverna.reference.impl.TranslationPath
setTrustConfirmationProviders(List<TrustConfirmationProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl: Set the providers of trust confirmation for HTTPS connections to external services/sites.
setTypedId(T2ReferenceImpl) - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl: This method is only ever called from within Hibernate, and is used to initialize the unique ID of this reference set.
setup(Mapper<int[], Map<String, Path>, Object, Object>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaMapper
setup(Reducer<int[], Map<String, Path>, Object, Object>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaReducer
setUpperNumericValue(NumericType) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
setUri(URI) - Method in class org.apache.taverna.annotation.impl.URISource
setUserInfoForURI(URI, String) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
setUserInfoForURI(URI, String) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
setUsername(String) - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
setUserObject(Object) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
setUuid(String) - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference: Setter used by hibernate to set the object uuid property.
setValue(String) - Method in class org.apache.taverna.activities.stringconstant.StringConstantConfigurationBean
setValue(byte[]) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
setValueBuilders(List<StreamToValueConverterSPI>) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl: Inject stream to value converter SPI
setWasTimeConsuming(boolean) - Method in class org.apache.taverna.visit.VisitReport
setWorkflow(WorkflowProvenanceItem) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance: So that the ProvenanceItems know which Dataflow has been enacted this layer has to know about the WorkflowProvenanceItem
setWorkflowBundle(WorkflowBundle) - Method in class org.apache.taverna.platform.run.api.RunProfile: Sets the WorkflowBundle containing the Workflow to run.
setWorkflowBundleIO(WorkflowBundleIO) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
setWorkflowId(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
setWorkflowId(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem: The uuid that belongs to the actual dataflow
setWorkflowName(String) - Method in class org.apache.taverna.platform.run.api.RunProfile: Sets the name of the Workflow to run.
setWorkflowRunId(String) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
setWorkflowRunId(String) - Method in class org.apache.taverna.reference.WorkflowRunIdEntity
SharedVocabulary - Enum in org.apache.taverna.provenance.vocabulary: Static strings which identify all the ProvenanceItems and ProvenanceEventTypes
shouldTrustCertificate(X509Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.TrustConfirmationProvider: If the given public key certificate should be trusted or not.
showMonitorFrame() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel: Very simple UI!
SimpleCacheProviderImpl - Class in org.apache.taverna.reference.impl: Completely naive cache provider that just stores everything in a map.
SimpleCacheProviderImpl() - Constructor for class org.apache.taverna.reference.impl.SimpleCacheProviderImpl
SimpleT2ReferenceGenerator - Class in org.apache.taverna.reference.impl: Simple implementation of T2ReferenceGenerator intended to be injected into the service layers for integration testing.
SimpleT2ReferenceGenerator() - Constructor for class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator
size() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
source - Variable in class org.apache.taverna.utility.TypedTreeModelEvent
stack - Variable in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
StackTraceElementBean - Interface in org.apache.taverna.reference: Used by the ErrorDocument interface to represent a frame within a stack trace
StackTraceElementBeanImpl - Class in org.apache.taverna.reference.impl: Simple bean implementation of StackTraceElement for Hibernate
StackTraceElementBeanImpl() - Constructor for class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
start(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
start() - Method in interface org.apache.taverna.platform.execution.api.Execution: Starts the execution.
start(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService: Starts the execution of a workflow.
start() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
start() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
start(String) - Method in interface org.apache.taverna.platform.run.api.RunService: Starts a run.
start() - Method in class org.apache.taverna.platform.run.impl.Run
start(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
START_INTERNAL_DERBY - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
startDerbyNetworkServer() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
startDerbyNetworkServer() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
State - Enum in org.apache.taverna.platform.report: Valid states for status reports.
stateChange(WorkflowInstanceFacade, WorkflowInstanceFacade.State, WorkflowInstanceFacade.State) - Method in interface org.apache.taverna.facade.FacadeListener
stateChanged(State, State) - Method in interface org.apache.taverna.platform.report.ReportListener
stateLastModified - Variable in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
StateProperty() - Constructor for class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
StaticProperty - Class in org.apache.taverna.platform.execution.impl.local: A MonitorableProperty with fixed values.
StaticProperty(MonitorableProperty<?>) - Constructor for class org.apache.taverna.platform.execution.impl.local.StaticProperty: Records the state of the MonitorableProperty.
StatusReport<SUBJECT extends Ported,PARENT extends StatusReport<?,?>> - Class in org.apache.taverna.platform.report: Report about the State of a workflow component.
StatusReport(SUBJECT) - Constructor for class org.apache.taverna.platform.report.StatusReport: Constructs a new StatusReport for the subject and sets the created date to the current date.
SteerableProperty<T> - Interface in org.apache.taverna.monitor: Some monitorable properties are mutable and can be written to by steering agents or other clients.
Stop - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers: This layer allows for the cancellation, pausing and resuming of workflow runs.
Stop() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
stopDerbyNetworkServer() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
stopDerbyNetworkServer() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
store() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
store(ErrorDocument) - Method in interface org.apache.taverna.reference.ErrorDocumentDao: Store a named ErrorDocument to the database.
store(ErrorDocument) - Method in class org.apache.taverna.reference.impl.InMemoryErrorDocumentDao
store(IdentifiedList<T2Reference>) - Method in class org.apache.taverna.reference.impl.InMemoryListDao
store(ReferenceSet) - Method in class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
store(IdentifiedList<T2Reference>) - Method in interface org.apache.taverna.reference.ListDao: Store a named and populated IdentifiedList of T2Reference to the database.
store(ReferenceSet) - Method in interface org.apache.taverna.reference.ReferenceSetDao: Store the specified new reference set
StreamToBooleanConverter - Class in org.apache.taverna.reference.impl.external.object
StreamToBooleanConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToBooleanConverter
StreamToByteArrayConverter - Class in org.apache.taverna.reference.impl.external.object: Build a byte[] from an InputStream
StreamToByteArrayConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToByteArrayConverter
StreamToDoubleConverter - Class in org.apache.taverna.reference.impl.external.object
StreamToDoubleConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToDoubleConverter
StreamToIntegerConverter - Class in org.apache.taverna.reference.impl.external.object
StreamToIntegerConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToIntegerConverter
StreamToStringConverter - Class in org.apache.taverna.reference.impl.external.object: Build a String from an InputStream
StreamToStringConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToStringConverter
StreamToValueConverterSPI<T> - Interface in org.apache.taverna.reference: SPI for objects that can render a POJO from an InputStream
StreamToVMObjectReferenceConverter - Class in org.apache.taverna.reference.impl.external.object: Builds a VMObjectReference from an InputStream.
StreamToVMObjectReferenceConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToVMObjectReferenceConverter
StringConstantActivity - Class in org.apache.taverna.activities.stringconstant: An Activity that holds a constant string value.
StringConstantActivity() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantActivity
StringConstantActivityFactory - Class in org.apache.taverna.activities.stringconstant: An ActivityFactory for creating StringConstantActivity.
StringConstantActivityFactory() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
StringConstantActivityHealthChecker - Class in org.apache.taverna.activities.stringconstant
StringConstantActivityHealthChecker() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker
StringConstantConfigurationBean - Class in org.apache.taverna.activities.stringconstant: Configuration bean for setting up a StringConstantActivity.
The only thing to be configured is the string value, since the ports are fixed.
StringConstantConfigurationBean() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantConfigurationBean
StringToStringReference - Class in org.apache.taverna.reference.impl.external.object: Convert a String to a StringReference
StringToStringReference() - Constructor for class org.apache.taverna.reference.impl.external.object.StringToStringReference
subList(int, int) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
SupersededActivity<ConfigurationType> - Interface in org.apache.taverna.workflowmodel.processor.activity: A superseded activity is one which has been replaced be another activity type of similar functionality but different configuration and name
SupportsStreamedResult - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description: Declares that a dispatch layer can handle streamed result data correctly, if this annotation is attached to a DispatchLayer implementation that implementation must be able to correctly handle the result completion message type.
SwingAwareObserver<Message> - Class in org.apache.taverna.lang.observer: Implementation of an Observer that adds calls to notify to the AWT event dispatching thread.
SwingAwareObserver() - Constructor for class org.apache.taverna.lang.observer.SwingAwareObserver

T

T2Reference - Interface in org.apache.taverna.reference: The T2Reference is used within the workflow system to refer to any entity within the reference management system, whether reference set, list or error document.
T2ReferenceConverter - Class in org.apache.taverna.platform.execution.impl.local
T2ReferenceConverter() - Constructor for class org.apache.taverna.platform.execution.impl.local.T2ReferenceConverter
t2ReferenceGenerator - Variable in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
t2ReferenceGenerator - Variable in class org.apache.taverna.reference.impl.AbstractListServiceImpl
t2ReferenceGenerator - Variable in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
T2ReferenceGenerator - Interface in org.apache.taverna.reference: Provides new unique T2Reference instances.
T2ReferenceImpl - Class in org.apache.taverna.reference.impl: An implementation of T2Reference specific to the ReferenceSetImpl.
T2ReferenceImpl() - Constructor for class org.apache.taverna.reference.impl.T2ReferenceImpl
T2ReferenceListImpl - Class in org.apache.taverna.reference.impl: Simple extension of IdentifiedArrayList<T2Reference> exposing get and set methods for the list contents so we can map it in hibernate.
T2ReferenceListImpl() - Constructor for class org.apache.taverna.reference.impl.T2ReferenceListImpl
T2ReferenceType - Enum in org.apache.taverna.reference: The T2Reference interface is used to identify several different kinds of information, namely ReferenceSet, IdentifiedList and ErrorDocument.
TavernaInputFormat - Class in org.apache.taverna.platform.execution.impl.hadoop
TavernaInputFormat() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputFormat
TavernaInputSplit - Class in org.apache.taverna.platform.execution.impl.hadoop
TavernaInputSplit(int[], Map<String, Path>, long, String[]) - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
TavernaMapper - Class in org.apache.taverna.platform.execution.impl.hadoop
TavernaMapper() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.TavernaMapper
TavernaRecordReader - Class in org.apache.taverna.platform.execution.impl.hadoop
TavernaRecordReader() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
TavernaReducer - Class in org.apache.taverna.platform.execution.impl.hadoop
TavernaReducer() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.TavernaReducer
TemporaryJDBC - Class in org.apache.taverna.platform.spring.jdbc: Create JDBC connection strings for temporary use (ie.
TemporaryJDBC() - Constructor for class org.apache.taverna.platform.spring.jdbc.TemporaryJDBC
TerminalNode - Class in org.apache.taverna.workflowmodel.processor.iteration: The terminal node is the root of the iteration strategy tree, it is responsible for forwarding all events up to the iteration strategy itself which can then propogate them to the strategy stack.
TerminalNode() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.TerminalNode
TerminalNodeImpl() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
Test - Class in org.apache.taverna.platform.execution.impl.hadoop
Test() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.Test
TextArrayWritable - Class in org.apache.taverna.platform.execution.impl.hadoop
TextArrayWritable() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.TextArrayWritable
thread - Variable in class org.apache.taverna.activities.testutils.DummyCallback
TIME_OUT - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
TIMEOUT - Static variable in class org.apache.taverna.activities.testutils.ActivityInvoker: Timeout in seconds
toArray() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
toArray(U[]) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
TokenOrderException - Exception in org.apache.taverna.invocation: Thrown when tokens are supplied in an invalid order.
TokenOrderException() - Constructor for exception org.apache.taverna.invocation.TokenOrderException
TokenOrderException(String, Throwable) - Constructor for exception org.apache.taverna.invocation.TokenOrderException
TokenOrderException(String) - Constructor for exception org.apache.taverna.invocation.TokenOrderException
TokenOrderException(Throwable) - Constructor for exception org.apache.taverna.invocation.TokenOrderException
TokenProcessingEntity - Interface in org.apache.taverna.workflowmodel: Superinterface for all classes within the workflow model which consume and emit workflow data tokens.
tokenReceived(String, InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl: Called when a token is received or the dataflow is fired, checks to see whether the process identifier is already known (in which case we assume it's been registered and can ignore it) or registers it with the monitor along with all child entities.
Tools - Class in org.apache.taverna.workflowmodel.utils: Various workflow model tools that can be helpful when constructing a dataflow.
Tools() - Constructor for class org.apache.taverna.workflowmodel.utils.Tools
TopLayer() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
toString() - Method in class org.apache.taverna.invocation.Completion
toString() - Method in class org.apache.taverna.invocation.Event
toString() - Method in class org.apache.taverna.invocation.TreeCache: Show the tree structure, printing each node recursively
toString() - Method in class org.apache.taverna.invocation.WorkflowDataToken: Show the owner, index array and data map in textual form for debugging and any other purpose.
toString() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
toString() - Method in class org.apache.taverna.platform.report.Invocation
toString() - Method in class org.apache.taverna.platform.report.WorkflowReport
toString() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
toString() - Method in class org.apache.taverna.reference.impl.ContextualizedT2ReferenceImpl
toString() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
toString() - Method in class org.apache.taverna.reference.impl.external.file.FileReference: Human readable string form for debugging, should not be regarded as stable.
toString() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference: Human readable string form for debugging, should not be regarded as stable.
toString() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference: String representation for testing, returns string{CONTENTS}
toString() - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl: For debugging purposes, prints a summary of the contents and identifier of this reference set.
toString() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: By default when printing an identifier we use T2ReferenceImpl.toUri().
toString() - Method in class org.apache.taverna.reference.impl.T2ReferenceListImpl: Print the contents of this list for vaguely human readable debug purposes.
toString() - Method in class org.apache.taverna.reference.impl.TranslationPath: Return a human readable representation of this translation path, used by the logging methods to print trace information.
toString() - Method in class org.apache.taverna.t2referencetest.BlueReference: String representation for testing, returns blue{CONTENTS}
toString() - Method in class org.apache.taverna.t2referencetest.GreenReference: String representation for testing, returns green{CONTENTS}
toString() - Method in class org.apache.taverna.t2referencetest.RedReference: String representation for testing, returns red{CONTENTS}
toString() - Method in class org.apache.taverna.t2referencetest.YellowReference: String representation for testing, returns yellow{CONTENTS}
toString() - Method in class org.apache.taverna.utility.TypedTreeModelEvent: Returns a string that displays and identifies this object's properties.
toString() - Method in class org.apache.taverna.visit.VisitReport
toString() - Method in class org.apache.taverna.workflowmodel.AbstractPort
toString() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
toString() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
toString() - Method in class org.apache.taverna.workflowmodel.processor.activity.Job: Show the owner, index array and data map in textual form for debugging and any other purpose.
toString() - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflowSource
toString() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
toUri() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl: Returns the identifier expressed as a URI, constructed based on the reference type.
toUri() - Method in interface org.apache.taverna.reference.T2Reference: All T2Reference instances can be represented as a URI.
transformOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort: Override this to transform owning process identifiers as they pass through the filter, by default this is the identity transformation
TranslationPath - Class in org.apache.taverna.reference.impl: A path from one external reference to another along with a total estimated path cost through one or more reference translators.
TranslationPath() - Constructor for class org.apache.taverna.reference.impl.TranslationPath
translatorsUpdated(Object, Map<?, ?>) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
traverse(Object, List, Set<VisitReport>, boolean) - Method in class org.apache.taverna.visit.HierarchyTraverser: Carry out the appropriate visits on an object and then traverse down the hierarchy of its children.
traverseFrom(T2Reference, int) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl: Initiates a traversal of the specified t2reference, traversing to whatever level of depth is required such that all identifiers returned within the iterator have the specified depth.
traverseFrom(T2Reference, int) - Method in interface org.apache.taverna.reference.ReferenceService: Initiates a traversal of the specified t2reference, traversing to whatever level of depth is required such that all identifiers returned within the iterator have the specified depth.
TreeCache - Class in org.apache.taverna.invocation: Tree cache for jobs waiting to be combined and dispatched down the iteration system
TreeCache() - Constructor for class org.apache.taverna.invocation.TreeCache
TreeCache.NamedNode - Class in org.apache.taverna.invocation
TreeModelAdapter - Class in org.apache.taverna.utility: Wraps a typed tree model up in a standard tree model for use with JTree and friends.
treeNodesChanged(TypedTreeModelEvent<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModelListener: Invoked after a node (or a set of siblings) has changed in some way.
treeNodesInserted(TypedTreeModelEvent<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModelListener: Invoked after nodes have been inserted into the tree.
treeNodesRemoved(TypedTreeModelEvent<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModelListener: Invoked after nodes have been removed from the tree.
treeStructureChanged(TypedTreeModelEvent<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModelListener: Invoked after the tree has drastically changed structure from a given node down.
TrustConfirmationProvider - Interface in org.apache.taverna.security.credentialmanager: Defines an interface for providing ways to confirm/decline trust in a given service (i.e.
TRUSTSTORE_FILE_NAME - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
TypedTreeModel<NodeType> - Interface in org.apache.taverna.utility: A replacement for TreeModel where nodes are typed rather than being generic objects.
TypedTreeModelEvent<NodeType> - Class in org.apache.taverna.utility: Type aware version of TreeModelEvent
TypedTreeModelEvent(Object, NodeType[]) - Constructor for class org.apache.taverna.utility.TypedTreeModelEvent: Used to create an event when the node structure has changed in some way, identifying the path to the root of a modified subtree as an array of Objects.
TypedTreeModelEvent(Object, TreePath) - Constructor for class org.apache.taverna.utility.TypedTreeModelEvent: Used to create an event when the node structure has changed in some way, identifying the path to the root of the modified subtree as a TreePath object.
TypedTreeModelEvent(Object, TreePath, int[], NodeType[]) - Constructor for class org.apache.taverna.utility.TypedTreeModelEvent: Used to create an event when nodes have been changed, inserted, or removed, identifying the path to the parent of the modified items as a TreePath object.
TypedTreeModelEvent(Object, NodeType[], int[], NodeType[]) - Constructor for class org.apache.taverna.utility.TypedTreeModelEvent: Used to create an event when nodes have been changed, inserted, or removed, identifying the path to the parent of the modified items as an array of Objects.
TypedTreeModelListener<NodeType> - Interface in org.apache.taverna.utility: Equivalent to TreeModelListener for use with the TypedTreeModel

U

undo() - Method in class org.apache.taverna.workflowmodel.CompoundEdit: Rolls back all child edits in reverse order
undo() - Method in interface org.apache.taverna.workflowmodel.Edit: Deprecated.
undo() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit
undoEditAction(DispatchStackImpl) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit: Undo any edit effects here
uniqueObjectName(String, Set<String>) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
uniquePortName(String, Collection<? extends Port>) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Find a unique port name given a list of existing ports.
uniqueProcessorName(String, Dataflow) - Static method in class org.apache.taverna.workflowmodel.utils.Tools: Find a unique processor name for the supplied Dataflow, based upon the preferred name.
UNKNOWN_OPERATION - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
UNMANAGED_LOCATION - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
UNRECOGNIZED - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
UnrecognizedActivity - Class in org.apache.taverna.workflowmodel.processor.activity: An unrecognized activity is an activity that was not recognized when the workflow was opened.
UnrecognizedActivity(Element) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.UnrecognizedActivity
UnrecognizedActivityHealthChecker - Class in org.apache.taverna.workflowmodel.health: Check on the health of a UnrecognizedActivity
UnrecognizedActivityHealthChecker() - Constructor for class org.apache.taverna.workflowmodel.health.UnrecognizedActivityHealthChecker
UNSUPPORTED_STYLE - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
untypedView(TypedTreeModel<NodeType>) - Static method in class org.apache.taverna.utility.TreeModelAdapter: Return an untyped TreeModel wrapper around the specified TypedTreeModel
update(ReferenceSet) - Method in class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
update() - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
update(ReferenceSet) - Method in interface org.apache.taverna.reference.ReferenceSetDao: Update a pre-existing entry in the database
URI - Static variable in class org.apache.taverna.activities.dataflow.DataflowActivity
URI - Static variable in class org.apache.taverna.activities.stringconstant.StringConstantActivity
URI - Static variable in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
URI - Static variable in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity
URI - Static variable in class org.apache.taverna.workflowmodel.processor.activity.UnrecognizedActivity
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
URI - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
URISource - Class in org.apache.taverna.annotation.impl
URISource() - Constructor for class org.apache.taverna.annotation.impl.URISource
URISource(URI) - Constructor for class org.apache.taverna.annotation.impl.URISource
UrlToHttpReference - Class in org.apache.taverna.reference.impl.external.http: Convert a URL with http protocol to a HttpReference reference type
UrlToHttpReference() - Constructor for class org.apache.taverna.reference.impl.external.http.UrlToHttpReference
USER_SET_MASTER_PASSWORD_INDICATOR_FILE_NAME - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
USERNAME - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
USERNAME_AND_PASSWORD_SEPARATOR_CHARACTER - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
UsernamePassword - Class in org.apache.taverna.security.credentialmanager
UsernamePassword() - Constructor for class org.apache.taverna.security.credentialmanager.UsernamePassword
UsernamePassword(String, String) - Constructor for class org.apache.taverna.security.credentialmanager.UsernamePassword
UTF_8 - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
UUIDT2ReferenceGenerator - Class in org.apache.taverna.reference.impl: A T2ReferenceGenerator based on UUIDs.
UUIDT2ReferenceGenerator() - Constructor for class org.apache.taverna.reference.impl.UUIDT2ReferenceGenerator

V

valueBuilders - Variable in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
ValueCarryingExternalReference<T> - Interface in org.apache.taverna.reference: Specialization of ExternalReferenceSPI for reference types which carry a value type internally.
valueForPathChanged(TreePath, Object) - Method in interface org.apache.taverna.utility.TypedTreeModel: Messaged when the user has altered the value for the item identified by path to newValue.
valueOf(String) - Static method in enum org.apache.taverna.annotation.AnnotationRole: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.annotation.CurationEventType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.annotation.HierarchyRole: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.facade.WorkflowInstanceFacade.State: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.platform.report.State: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.provenance.vocabulary.SharedVocabulary: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.reference.ReferencedDataNature: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.reference.T2ReferenceType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.security.credentialmanager.CredentialManager.KeystoreType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.visit.VisitReport.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.workflowmodel.processor.dispatch.description.DispatchLayerStateEffect: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.workflowmodel.processor.dispatch.description.DispatchMessageType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorType: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.apache.taverna.annotation.AnnotationRole: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.annotation.CurationEventType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.annotation.HierarchyRole: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.facade.WorkflowInstanceFacade.State: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.platform.report.State: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.provenance.vocabulary.SharedVocabulary: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.reference.ReferencedDataNature: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.reference.T2ReferenceType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.security.credentialmanager.CredentialManager.KeystoreType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.visit.VisitReport.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.workflowmodel.processor.dispatch.description.DispatchLayerStateEffect: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.workflowmodel.processor.dispatch.description.DispatchMessageType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorType: Returns an array containing the constants of this enum type, in the order they are declared.
ValueToReferenceConversionException - Exception in org.apache.taverna.reference: Thrown by instances of ValueToReferenceConvertor when trying to convert an object to an instance of ExternalReferenceSPI if the conversion process fails for some reason.
ValueToReferenceConversionException() - Constructor for exception org.apache.taverna.reference.ValueToReferenceConversionException
ValueToReferenceConversionException(String) - Constructor for exception org.apache.taverna.reference.ValueToReferenceConversionException
ValueToReferenceConversionException(Throwable) - Constructor for exception org.apache.taverna.reference.ValueToReferenceConversionException
ValueToReferenceConversionException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ValueToReferenceConversionException
ValueToReferenceConverterSPI - Interface in org.apache.taverna.reference: SPI for components that can convert an arbitrary object to an ExternalReferenceSPI representing the value of that object.
visit(DataflowActivity, List<Object>) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityHealthChecker
visit(StringConstantActivity, List<Object>) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker
visit(T, List<Object>) - Method in interface org.apache.taverna.visit.Visitor: Visit an object which has the specified ancestry (list of parents) and possibly return a VisitReport detailing the result of the visit.
visit(DisabledActivity, List<Object>) - Method in class org.apache.taverna.workflowmodel.health.DisabledActivityHealthChecker: The result of the visit is simply a VisitReport to state that the service is not available.
visit(UnrecognizedActivity, List<Object>) - Method in class org.apache.taverna.workflowmodel.health.UnrecognizedActivityHealthChecker: The result of the visit is simply a VisitReport to state that the service is not available.
VisitKind - Class in org.apache.taverna.visit: A type of visit that can be made e.g.
VisitKind() - Constructor for class org.apache.taverna.visit.VisitKind
Visitor<T> - Interface in org.apache.taverna.visit: A Visitor can perform a visit of a VisitKind on a object.
visitors - Variable in class org.apache.taverna.visit.HierarchyTraverser: The set of visitors that can perform visits of one or more of a set of VisitKind.
VisitReport - Class in org.apache.taverna.visit
VisitReport(VisitKind, Object, String, int, VisitReport.Status) - Constructor for class org.apache.taverna.visit.VisitReport: Constructs the Visit Report.
VisitReport() - Constructor for class org.apache.taverna.visit.VisitReport: Used internally by VisitReport.clone().
VisitReport(VisitKind, Object, String, int, VisitReport.Status, Collection<VisitReport>) - Constructor for class org.apache.taverna.visit.VisitReport: Constructs the Visit Report
VisitReport(VisitKind, Object, String, int, Collection<VisitReport>) - Constructor for class org.apache.taverna.visit.VisitReport
VisitReport.Status - Enum in org.apache.taverna.visit: Enumeration of the possible status's in increasing severity: OK, WARNING,SEVERE
visitReportToStringBuffer(StringBuffer, String) - Method in class org.apache.taverna.visit.VisitReport
VMObjectReference - Class in org.apache.taverna.reference.impl.external.object: Implementation of ExternalReferenceSPI used to refer to objects in the local virtual machine.
VMObjectReference() - Constructor for class org.apache.taverna.reference.impl.external.object.VMObjectReference

W

wasTimeConsuming() - Method in class org.apache.taverna.visit.VisitReport
WorkflowCompiler - Interface in org.apache.taverna.platform.execution.api: A workflow compilation service converts a workflow (in a WorkflowBundle) into a dataflow.
WorkflowDataProvenanceItem - Class in org.apache.taverna.provenance.item: When the WorkflowInstanceFacade for a processor receives a data token one of these is created.
WorkflowDataProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
WorkflowDataToken - Class in org.apache.taverna.invocation: A single data token passed between processors in a workflow.
WorkflowDataToken(String, int[], T2Reference, InvocationContext) - Constructor for class org.apache.taverna.invocation.WorkflowDataToken: Construct a new data token with the specified owning process, conceptual index array and data reference
workflowFailed(WorkflowInstanceFacade, String, Throwable) - Method in interface org.apache.taverna.facade.FacadeListener: Called if the workflow fails in a critical and fundamental way.
WorkflowInstanceFacade - Interface in org.apache.taverna.facade: The interaction point with a workflow instance.
WorkflowInstanceFacade.State - Enum in org.apache.taverna.facade
WorkflowInstanceFacadeImpl - Class in org.apache.taverna.facade.impl: Implementation of WorkflowInstanceFacade
WorkflowInstanceFacadeImpl(Dataflow, InvocationContext, String) - Constructor for class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
WorkflowInstanceFacadeImpl.FacadeResultListener - Class in org.apache.taverna.facade.impl
WorkflowInstanceFacadeImpl.StateProperty - Class in org.apache.taverna.facade.impl
WorkflowItem - Interface in org.apache.taverna.workflowmodel: An item that forms a structural part of a Workflow.
WorkflowProvenanceItem - Class in org.apache.taverna.provenance.item: The first ProvenanceItem that the ProvenanceConnector will receive for a workflow run.
WorkflowProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.WorkflowProvenanceItem
WorkflowReport - Class in org.apache.taverna.platform.report: Report about the State of a Workflow run.
WorkflowReport(Workflow) - Constructor for class org.apache.taverna.platform.report.WorkflowReport
WorkflowReportJSON - Class in org.apache.taverna.platform.run.impl
WorkflowReportJSON() - Constructor for class org.apache.taverna.platform.run.impl.WorkflowReportJSON
WorkflowRunCancellation - Class in org.apache.taverna.facade: A WorkflowRunCancellation is passed to listeners when a workflow run is cancelled.
WorkflowRunCancellation(String) - Constructor for class org.apache.taverna.facade.WorkflowRunCancellation
workflowRunFacades - Static variable in interface org.apache.taverna.facade.WorkflowInstanceFacade: A weak hash map of all workflow run IDs mapped against the corresponding WorkflowInstanceFacadeS.
WorkflowRunIdEntity - Class in org.apache.taverna.reference: Entity that wraps workflow run id and can be passed through ( ReferenceContext to be used by T2ReferenceGenerator to generate references that are specific for a workflow run.
WorkflowRunIdEntity(String) - Constructor for class org.apache.taverna.reference.WorkflowRunIdEntity
WorkflowStructureException - Exception in org.apache.taverna.workflowmodel: Thrown predominantly at runtime under circumstances that suggest an inconsistancy in the workflow model.
WorkflowStructureException(String) - Constructor for exception org.apache.taverna.workflowmodel.WorkflowStructureException
WorkflowToDataflowMapper - Class in org.apache.taverna.platform.execution.impl.local: Translates a scufl2 Workflow into a Dataflow.
WorkflowToDataflowMapper(WorkflowBundle, Profile, Edits, ActivityService, DispatchLayerService) - Constructor for class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
write(DataOutput) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
WriteQueueAspect - Class in org.apache.taverna.reference.impl: An aspect used to intercept calls to the various data access objects and execute data writes on a thread limited executer with an unbounded blocking queue.
WriteQueueAspect() - Constructor for class org.apache.taverna.reference.impl.WriteQueueAspect
WriteQueueAspect(int) - Constructor for class org.apache.taverna.reference.impl.WriteQueueAspect
WSDL_TEST_BASE - Static variable in interface org.apache.taverna.activities.testutils.LocationConstants

Y

YellowReference - Class in org.apache.taverna.t2referencetest: YellowReferences carry their data as an internal String and have a resolution cost of 1.0f whatever the value of that string.
YellowReference() - Constructor for class org.apache.taverna.t2referencetest.YellowReference
YellowReference(String) - Constructor for class org.apache.taverna.t2referencetest.YellowReference

A B C D E F G H I J K L M N O P R S T U V W Y