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ABORTED - Static variable in class org.embl.ebi.escience.scufl.ConcurrencyConstraint
Signifies that the processor has failed in some fashion
AboutBox - Class in org.embl.ebi.escience.scuflui.workbench
 
AboutBox() - Constructor for class org.embl.ebi.escience.scuflui.workbench.AboutBox
This method initializes
AbstractArtifactFilter - Class in net.sf.taverna.raven.spi
 
AbstractArtifactFilter() - Constructor for class net.sf.taverna.raven.spi.AbstractArtifactFilter
 
AbstractBufferedImageOp - Class in com.jhlabs.image
A convenience class which implements those methods of BufferedImageOp which are rarely changed.
AbstractBufferedImageOp() - Constructor for class com.jhlabs.image.AbstractBufferedImageOp
 
AbstractCellEditor - Class in org.embl.ebi.escience.treetable
 
AbstractCellEditor() - Constructor for class org.embl.ebi.escience.treetable.AbstractCellEditor
 
AbstractConfiguration - Class in net.sf.taverna.tools
Base class for configuration files.
AbstractConfiguration() - Constructor for class net.sf.taverna.tools.AbstractConfiguration
 
AbstractEFetchWorker - Class in net.sourceforge.taverna.scuflworkers.ncbi
This class provides the basis for all NCBI EFetch Tasks.
AbstractEFetchWorker() - Constructor for class net.sourceforge.taverna.scuflworkers.ncbi.AbstractEFetchWorker
 
AbstractNCBIWorker - Class in net.sourceforge.taverna.scuflworkers.ncbi
This class provides basic common functionality needed by all NCBIWorkers.
AbstractNCBIWorker() - Constructor for class net.sourceforge.taverna.scuflworkers.ncbi.AbstractNCBIWorker
 
AbstractPerspective - Class in net.sf.taverna.perspectives
An abstract implementation of a perspective that handles the storing of the layout XML if modified via the 'update' method, which once set causes this XML to be used rather than the bundled resource.
AbstractPerspective() - Constructor for class net.sf.taverna.perspectives.AbstractPerspective
 
AbstractProcessorAction - Class in org.embl.ebi.escience.scuflui.actions
A simple abstract implementation of the ProcessorActionSPI which allows the extending class to simply specify a JComponent to be created in a standard UIUtils frame.
AbstractProcessorAction() - Constructor for class org.embl.ebi.escience.scuflui.actions.AbstractProcessorAction
 
AbstractRenderer - Class in org.embl.ebi.escience.scuflui.renderers
Abstract rendering class.
AbstractRenderer(String) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer
 
AbstractRenderer(String, Icon) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer
 
AbstractRenderer.ByJavaClass - Class in org.embl.ebi.escience.scuflui.renderers
Accept based on user object type match to a particular Class
AbstractRenderer.ByJavaClass(String) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByJavaClass
 
AbstractRenderer.ByJavaClass(String, Icon) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByJavaClass
 
AbstractRenderer.ByMimeType - Class in org.embl.ebi.escience.scuflui.renderers
Choses to accept a DataThing based upoon its mime type.
AbstractRenderer.ByMimeType(String) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByMimeType
 
AbstractRenderer.ByMimeType(String, Icon) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByMimeType
 
AbstractRenderer.ByPattern - Class in org.embl.ebi.escience.scuflui.renderers
Accept a DataThing based upon the mime type matching a regular expression pattern.
AbstractRenderer.ByPattern(String, Pattern) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByPattern
 
AbstractRenderer.ByPattern(String, Icon, Pattern) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByPattern
 
AbstractRenderer.BySemanticType - Class in org.embl.ebi.escience.scuflui.renderers
 
AbstractRenderer.BySemanticType(String) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.BySemanticType
 
AbstractRenderer.BySemanticType(String, Icon) - Constructor for class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.BySemanticType
 
AbstractRepository - Class in net.sourceforge.taverna.publish
This class provides base-level functionality for repositories.
AbstractRepository() - Constructor for class net.sourceforge.taverna.publish.AbstractRepository
 
AbstractStreamProcessor - Class in net.sourceforge.taverna.io
This class provides a useful extension point for Stream Processors.
AbstractStreamProcessor() - Constructor for class net.sourceforge.taverna.io.AbstractStreamProcessor
 
AbstractStreamTransmitter - Class in net.sourceforge.taverna.io
This class provides the base class for all Stream-based transmitters.
AbstractStreamTransmitter() - Constructor for class net.sourceforge.taverna.io.AbstractStreamTransmitter
 
AbstractTreeTableModel - Class in org.embl.ebi.escience.treetable
 
AbstractTreeTableModel(Object) - Constructor for class org.embl.ebi.escience.treetable.AbstractTreeTableModel
 
accept(FileObject) - Method in interface net.sourceforge.taverna.publish.FileFilter
This method determines whether or not a fileobject meets the selection criteria.
accept(File) - Method in class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellFileFilter
Method for checking whether a file is accepted
accept(File) - Method in class org.embl.ebi.escience.scuflui.shared.ExtensionFileFilter
 
accept(File, String) - Method in class org.embl.ebi.escience.scuflworkers.dependency.DependenciesPanel.FileExtFilter
 
acceptsSource(Object, Object) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel
 
acceptsTarget(Object, Object) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel
 
actionPerformed(ActionEvent) - Method in class net.sf.taverna.zaria.ZPane.ReplaceWithBlankAction
 
actionPerformed(ActionEvent) - Method in class net.sf.taverna.zaria.ZRavenComponent.NameComponentAction
 
actionPerformed(ActionEvent) - Method in class net.sf.taverna.zaria.ZRavenComponent.SelectInstanceAction
 
actionPerformed(ActionEvent) - Method in class net.sf.taverna.zaria.ZRavenComponent.SelectNamedInstanceAction
 
actionPerformed(ActionEvent) - Method in class net.sf.taverna.zaria.ZRavenComponent.SelectSPIAction
 
actionPerformed(ActionEvent) - Method in class net.sf.taverna.zaria.ZRavenComponent.ToggleScrollPaneAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.AddDataConstraintAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.AddInputAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.AddOutputAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.EditMetadataAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.OpenWorkflowFromFileAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.OpenWorkflowFromURLAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.RemoveAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.RenameAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.ResetAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.RunWorkflowAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.SaveWorkflowAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.actions.SetDefaultValueAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench.ExitAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflworkers.dependency.DependenciesPanel.ClassloaderOptions
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction
 
actionPerformed(ActionEvent) - Method in class org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction.OpenNestedWorkflowFromURLAction
 
add(ResultTableCell, ResultThing) - Method in class org.embl.ebi.escience.scuflui.results.ResultTableCellCollection
 
addAlternate(AlternateProcessor) - Method in interface org.embl.ebi.escience.scufl.IProcessor
Add an alternate processor to this processor definition
addAlternate(AlternateProcessor) - Method in class org.embl.ebi.escience.scufl.Processor
Add an alternate processor to this processor definition
addAnnotationTemplate(AnnotationTemplate) - Method in interface org.embl.ebi.escience.scufl.IProcessor
Add an annotation template to this processor
addAnnotationTemplate(AnnotationTemplate) - Method in class org.embl.ebi.escience.scufl.Processor
Add an annotation template to this processor
addArtifact(Artifact) - Method in class net.sf.taverna.raven.repository.impl.EclipseRepository
 
addArtifact(Artifact) - Method in class net.sf.taverna.raven.repository.impl.LocalRepository
 
addArtifact(Artifact) - Method in interface net.sf.taverna.raven.repository.Repository
Add a new artifact to this repository.
addArtifact(Artifact) - Method in class net.sf.taverna.raven.spi.Profile
Allow an artifact to be added to the profile at runtime
addArtifact(Artifact) - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
addArtifactFilterListener(ArtifactFilterListener) - Method in class net.sf.taverna.raven.spi.AbstractArtifactFilter
 
addArtifactFilterListener(ArtifactFilterListener) - Method in interface net.sf.taverna.raven.spi.ArtifactFilter
 
addArtifactsForPlugins(InputStream) - Method in class net.sf.taverna.raven.spi.Profile
Adds artifacts contains in the profile definition for a Plugin.
addBreakpoint() - Method in interface org.embl.ebi.escience.scufl.IProcessor
Add a breakpoint to the processor
addBreakpoint() - Method in class org.embl.ebi.escience.scufl.Processor
Add a breakpoint to the processor
addCellEditorListener(CellEditorListener) - Method in class org.embl.ebi.escience.treetable.AbstractCellEditor
 
addChanges(ScuflModelEvent) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModelChange
 
addColor(String, Color) - Static method in class org.embl.ebi.escience.scuflui.shared.GraphColours
Adds a color to the application color table.
addColumn(FTableColumn) - Method in class org.embl.ebi.escience.scuflui.facets.FTableColumnModel
 
addColumn(int, FTableColumn) - Method in class org.embl.ebi.escience.scuflui.facets.FTableColumnModel
 
addConcurrencyConstraint(ConcurrencyConstraint) - Method in class org.embl.ebi.escience.scufl.ScuflModel
Add a concurrency constraint to the model
addDataConstraint(DataConstraint) - Method in class org.embl.ebi.escience.scufl.ScuflModel
Add a data constraint to the model
AddDataConstraintAction - Class in org.embl.ebi.escience.scuflui.actions
COMMENT
AddDataConstraintAction(ScuflModel, Port, Port) - Constructor for class org.embl.ebi.escience.scuflui.actions.AddDataConstraintAction
 
addEdge(Object) - Method in class org.embl.ebi.escience.scuflui.graph.GraphSpanningTree
 
addElement(String, String, Element) - Method in class org.embl.ebi.escience.scuflworkers.rserv.RservXMLHandler
 
addField(JPanel, String, JTextField) - Method in class org.embl.ebi.escience.scuflworkers.rserv.RservConfigPanel
 
addFilter(ArtifactFilter) - Method in class net.sf.taverna.raven.spi.SpiRegistry
Add a new ArtifactFilter
addFromScavengerHelpers() - Method in class org.embl.ebi.escience.scuflui.workbench.DefaultScavengerTree
 
addFTableColumnModelListener(FTableColumnModelListener) - Method in class org.embl.ebi.escience.scuflui.facets.FTableColumnModel
 
addGraphModelListener(GraphModelListener) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel
 
addInput(ResultSource) - Method in class org.embl.ebi.escience.scuflui.results.ResultSource
 
addInput(ResultThing) - Method in class org.embl.ebi.escience.scuflui.results.ResultThing
Adds a ResultThing as an input to this result.
AddInputAction - Class in org.embl.ebi.escience.scuflui.actions
COMMENT
AddInputAction(ScuflModel) - Constructor for class org.embl.ebi.escience.scuflui.actions.AddInputAction
 
addListener(WorkflowEventListener) - Method in class org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher
 
addListener(ScuflModelEventListener) - Method in class org.embl.ebi.escience.scufl.ScuflModel
Add a new ScuflModelEventListener to the listener list.
addListener(ScuflModelSet.ScuflModelSetListener) - Method in class org.embl.ebi.escience.scuflui.shared.ScuflModelSet
 
addLiteral(String) - Method in class org.embl.ebi.escience.scufl.AnnotationTemplate
Add a new text literal to the template
addMIMEType(String) - Method in class org.embl.ebi.escience.scufl.PortSemanticMarkup
Add a MIME type
addMIMEType(String) - Method in class org.embl.ebi.escience.scufl.SemanticMarkup
Add a MIME type
addModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.shared.ScuflModelSet
 
addModelListener(ModelMap.ModelChangeListener) - Method in class org.embl.ebi.escience.scuflui.shared.ModelMap
 
AddNestedWorkflowAction - Class in org.embl.ebi.escience.scuflworkers.workflow
 
AddNestedWorkflowAction() - Constructor for class org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction
 
AddNestedWorkflowAction.OpenNestedWorkflowFromURLAction - Class in org.embl.ebi.escience.scuflworkers.workflow
 
AddNestedWorkflowAction.OpenNestedWorkflowFromURLAction() - Constructor for class org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction.OpenNestedWorkflowFromURLAction
 
addNewArtifact(Artifact) - Method in class net.sf.taverna.raven.spi.SpiRegistry
 
addNonTreeEdge(Object) - Method in class org.embl.ebi.escience.scuflui.graph.GraphSpanningTree
 
addNonTreeEdge(Object) - Method in class org.embl.ebi.escience.scuflui.graph.PositionLayout
 
addNonTreeEdge(Object) - Method in class org.embl.ebi.escience.scuflui.graph.RowLayout
 
addOutput(ResultSource) - Method in class org.embl.ebi.escience.scuflui.results.ResultSource
 
addOutput(ResultThing) - Method in class org.embl.ebi.escience.scuflui.results.ResultThing
Adds a ResultThing as an output to this result.
AddOutputAction - Class in org.embl.ebi.escience.scuflui.actions
COMMENT
AddOutputAction(ScuflModel) - Constructor for class org.embl.ebi.escience.scuflui.actions.AddOutputAction
 
addOutputProcessor(Processor) - Method in class org.embl.ebi.escience.scuflui.results.ResultSource
 
AddParserAction - Class in org.biomoby.client.taverna.plugin
An action to add a parser from within the Workflow editor
AddParserAction() - Constructor for class org.biomoby.client.taverna.plugin.AddParserAction
 
addPlugin(Plugin) - Method in class net.sf.taverna.update.plugin.PluginManager
 
addPluginListener(PluginListener) - Method in class net.sf.taverna.update.plugin.Plugin
Adds a PluginListener.
addPluginManagerListener(PluginManagerListener) - Static method in class net.sf.taverna.update.plugin.PluginManager
 
addPluginSite(PluginSite) - Method in class net.sf.taverna.update.plugin.PluginManager
Adds a PluginSite.
AddPluginSiteFrame - Class in net.sf.taverna.update.plugin.ui
 
AddPluginSiteFrame(JDialog) - Constructor for class net.sf.taverna.update.plugin.ui.AddPluginSiteFrame
This method initializes
addPort(Port) - Method in interface org.embl.ebi.escience.scufl.IProcessor
Add a new port to this processor
addPort(Port) - Method in class org.embl.ebi.escience.scufl.Processor
Add a new port to this processor
addPortReference(Port) - Method in class org.embl.ebi.escience.scufl.AnnotationTemplate
Add a new port reference to this template
addProcessor(Processor) - Method in class org.embl.ebi.escience.scufl.ScuflModel
Add a processor to the model.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.embl.ebi.escience.scuflui.facets.FTableColumn
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.embl.ebi.escience.scuflui.facets.FTableColumn
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.embl.ebi.escience.scuflui.facets.PropertyFetcher.Closure
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.embl.ebi.escience.scuflui.facets.PropertyFetcher.Closure
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.embl.ebi.escience.scuflui.facets.RegexScanner.PatternEditor
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.embl.ebi.escience.scuflui.facets.RegexScanner.Scanner
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.embl.ebi.escience.scuflui.facets.RegexScanner.Scanner
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface org.embl.ebi.escience.scuflui.spi.FacetFinderSPI.ColumnID
Add a property change listener that will be informed whenever any property of the column alters that could affect the data the column would return.
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface org.embl.ebi.escience.scuflui.spi.FacetFinderSPI.ColumnID
 
addRegistryListener(InstanceRegistryListener) - Method in class net.sf.taverna.raven.spi.InstanceRegistry
Add a new registry listener to be notified of any updates to this SpiRegistry
addRegistryListener(RegistryListener) - Method in class net.sf.taverna.raven.spi.SpiRegistry
Add a new registry listener to be notified of any updates to this SpiRegistry
addRegistryListener(RegistryListener) - Method in class org.embl.ebi.escience.utils.TavernaSPIRegistry
 
addRemoteRepository(URL) - Method in class net.sf.taverna.raven.repository.impl.EclipseRepository
 
addRemoteRepository(URL) - Method in class net.sf.taverna.raven.repository.impl.LocalRepository
 
addRemoteRepository(URL) - Method in interface net.sf.taverna.raven.repository.Repository
Add a reference to a remote repository to be used to fetch pom and jar files.
addRepositoryListener(RepositoryListener) - Method in class net.sf.taverna.raven.repository.impl.EclipseRepository
 
addRepositoryListener(RepositoryListener) - Method in class net.sf.taverna.raven.repository.impl.LocalRepository
Add a new repository listener to be notified of status changes within this Repository implementation
addRepositoryListener(RepositoryListener) - Method in interface net.sf.taverna.raven.repository.Repository
Add a listener to be notified on changes to the repository status
addScavenger(Scavenger) - Method in class org.embl.ebi.escience.scuflui.workbench.DefaultScavengerTree
 
addScavenger(Scavenger) - Method in interface org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Add a new scavenger to the tree, firing appropriate model events as we do.
addScavengerHelper(ScavengerHelper) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerHelperThreadPool
Adds a new scavenger helper, and creates a thread for it to load the default scavengers.
addScavengerHelperForModel(ScavengerHelper, ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerHelperThreadPool
Scavengers over a ScuflModel for processors that are understood by the scavenger helper.
addScavengersFromModel() - Method in class org.embl.ebi.escience.scuflui.workbench.DefaultScavengerTree
 
addScavengersFromModel() - Method in interface org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Examine the model, create any scavengers that would have been required to populate the model with its existing processors.
addService(String) - Method in class org.embl.ebi.escience.scuflworkers.soaplab.SoaplabCategory
 
addSource(ResultSource) - Method in class org.embl.ebi.escience.scuflui.results.ResultTableColumn
 
addSystemArtifact(Artifact) - Method in class net.sf.taverna.raven.spi.Profile
 
addSystemArtifact(String, String, String) - Static method in class net.sf.taverna.tools.Bootstrap
 
addSystemLoaderArtifacts() - Static method in class net.sf.taverna.tools.Bootstrap
 
addTableModelListener(TableModelListener) - Method in class org.embl.ebi.escience.scuflui.results.ResultTableModel
 
addTableSelectionListener(ResultTable.TableSelectionListener) - Method in class org.embl.ebi.escience.scuflui.results.ResultTable
Shockingly, this adds a TableSelectionListener to this table.
addThread(ScavengerHelperThreadPool.ScavengerHelperThread) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerHelperThreadPool
 
addTreeEdge(Object) - Method in class org.embl.ebi.escience.scuflui.graph.GraphSpanningTree
 
addTreeModelListener(TreeModelListener) - Method in class org.embl.ebi.escience.treetable.AbstractTreeTableModel
 
addUndoableEditListener(UndoableEditListener) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel
 
addURL(URL) - Method in class net.sf.taverna.tools.BootstrapClassLoader
 
addWorkflowStateListener(WorkflowStateListener) - Method in class org.embl.ebi.escience.scufl.enactor.implementation.WorkflowInstanceImpl
Register the specified listener with the engine for this instance and use the internal workflow ID
AdvancedModelExplorer - Class in org.embl.ebi.escience.scuflui
An amalgam of the ScuflModelExplorerTreeTable and the IterationStrategyControl panels linked such that selection of a Processor node in the model explorer leads to context sensitive options appearing in a properties tab.
AdvancedModelExplorer() - Constructor for class org.embl.ebi.escience.scuflui.AdvancedModelExplorer
 
AdvancedModelExplorer.WorkflowMetadata - Class in org.embl.ebi.escience.scuflui
 
AdvancedModelExplorer.WorkflowMetadata() - Constructor for class org.embl.ebi.escience.scuflui.AdvancedModelExplorer.WorkflowMetadata
 
AdvancedModelExplorerFactory - Class in org.embl.ebi.escience.scuflui
 
AdvancedModelExplorerFactory() - Constructor for class org.embl.ebi.escience.scuflui.AdvancedModelExplorerFactory
 
AggregatingClassLoader - Class in net.sf.taverna.raven.repository
ClassLoader implementation as a convenience to allow searching of multiple artifact based classloaders.
AggregatingClassLoader(Repository, List<Artifact>, ClassLoader) - Constructor for class net.sf.taverna.raven.repository.AggregatingClassLoader
 
AggregatingClassLoader(Repository, List<Artifact>) - Constructor for class net.sf.taverna.raven.repository.AggregatingClassLoader
 
ALL - Static variable in class org.embl.ebi.escience.scufl.view.DotView
 
allScavengersAsXML() - Static method in class net.sf.taverna.tools.Scavengers
Represent as XML all the installed scavengers and their factories.
alphaLevel - Variable in class net.sf.taverna.zaria.progress.InfiniteProgressPanel
 
AlternateProcessor - Class in org.embl.ebi.escience.scufl
Represents an alternate processor to be used in case of failures in the primary.
AlternateProcessor(Processor) - Constructor for class org.embl.ebi.escience.scufl.AlternateProcessor
 
AlternateProcessScheduled - Class in org.embl.ebi.escience.scufl.provenance.process
Event corresponding to an alternate processor instance being created by the enactor's scheduling mechanism.
AlternateProcessScheduled() - Constructor for class org.embl.ebi.escience.scufl.provenance.process.AlternateProcessScheduled
Create a new event with no information about the processor being scheduled.
AlternateProcessScheduled(Processor) - Constructor for class org.embl.ebi.escience.scufl.provenance.process.AlternateProcessScheduled
Create a new event corresponding to the scheduling of the specified processor
alternates - Variable in class org.embl.ebi.escience.scufl.Processor
 
animals - Static variable in class org.embl.ebi.escience.baclava.iterator.IteratorNodeTests
 
animation - Variable in class net.sf.taverna.zaria.progress.InfiniteProgressPanel
 
AnnotationTemplate - Class in org.embl.ebi.escience.scufl
An AnnotationTemplate object represents a single possible RDF statement that may be generated as a side effect of the invocation of a processor task instance.
AnnotationTemplate() - Constructor for class org.embl.ebi.escience.scufl.AnnotationTemplate
Create a blank annotation template object
AnnotationTemplate(Element) - Constructor for class org.embl.ebi.escience.scufl.AnnotationTemplate
Create an annotation template object from a JDOM Element, the element being the <template> tag.
APConfigPanel - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
The configuration panel for abstract processors
APConfigPanel(APProcessor) - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APConfigPanel
Create a new rserv configuration panel applying to the processor specified in the constructor
APEditor - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
class for editing the abstract processors
APEditor() - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APEditor
 
APIConsumerDefinition - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
Definition for an APIConsumer processor or factory
APIConsumerDefinition(String, String, String[], String[], int[], String, int, String, boolean, boolean) - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerDefinition
 
APIConsumerDefinition(Element) - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerDefinition
 
APIConsumerEditor - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
 
APIConsumerEditor() - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerEditor
 
APIConsumerProcessor - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
Processor for the API consumer worker
APIConsumerProcessor(ScuflModel, String, APIConsumerDefinition) - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerProcessor
 
APIConsumerProcessorFactory - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
APIConsumer factory
APIConsumerProcessorFactory(APIConsumerDefinition) - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerProcessorFactory
public APIConsumerProcessorFactory(Element e) { String methodName = e.getAttributeValue("name","No method!"); setName(methodName); Element descriptionElement = e.getChild("Description"); if (descriptionElement != null) { setDescription(descriptionElement.getTextTrim()); } }
APIConsumerProcessorInfoBean - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
Provides information about the APIConsumner Processor plugin, using taverna.properties, identified by the tag 'apiconsumer'
APIConsumerProcessorInfoBean() - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerProcessorInfoBean
 
APIConsumerScavenger - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
Scavenger driven off an XML file created by the APIConsumer tool.
APIConsumerScavenger(URL) - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerScavenger
 
APIConsumerScavengerHelper - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
Create a new APIConsumerScavenger from a file dialog
APIConsumerScavengerHelper() - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerScavengerHelper
 
APIConsumerTask - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
A task to invoke a APIConsumerProcessor
APIConsumerTask(Processor) - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerTask
 
APIConsumerXMLHandler - Class in org.embl.ebi.escience.scuflworkers.apiconsumer
Handles XML store and load for the APIConsumer processor
APIConsumerXMLHandler() - Constructor for class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerXMLHandler
 
APPLICATION - Static variable in class net.sf.taverna.tools.Bootstrap
 
APProcessor - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
The abstract processor is a processor that contains a set of input ports and output ports and a brief description what it should do If the processor has an alternate, it executes the alternate, otherwise it does nothing
APProcessor(ScuflModel, String) - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APProcessor
Constructor of the abstract processor
APProcessorFactory - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
Class for constructing the abstract processor
APProcessorFactory() - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APProcessorFactory
 
APProcessorInfoBean - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
 
APProcessorInfoBean() - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APProcessorInfoBean
 
APScavenger - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
The scavanger for abstract processors
APScavenger() - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APScavenger
Constructor for creating the RshellScavenger
APTask - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
Class for executing the abstract process The process executes it's alternate, if it has one, otherwise it shows its content
APTask(Processor) - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APTask
Constructor of the task object
APXMLHandler - Class in nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor
Class for handling the xml belonging to the abstract processor
APXMLHandler() - Constructor for class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APXMLHandler
 
arrayList - Static variable in class org.biomoby.client.taverna.plugin.CreateMobySimple
 
ARROW_DOWN - Static variable in class org.embl.ebi.escience.scuflui.shared.CArrowImage
 
ARROW_LEFT - Static variable in class org.embl.ebi.escience.scuflui.shared.CArrowImage
 
ARROW_RIGHT - Static variable in class org.embl.ebi.escience.scuflui.shared.CArrowImage
 
ARROW_UP - Static variable in class org.embl.ebi.escience.scuflui.shared.CArrowImage
 
Artifact - Interface in net.sf.taverna.raven.repository
A single code artifact (jar) within a maven2 repository either remote or local.
artifactDependencies - Variable in class org.embl.ebi.escience.scuflworkers.dependency.DependencyProcessor
Artifact dependencies.
ArtifactDownloadDialog - Class in net.sf.taverna.zaria.raven
 
artifactExistsInProfile(Artifact) - Method in class net.sf.taverna.zaria.ZPane
Determines whether an artifact exists in the profile, if one exists.
ArtifactFilter - Interface in net.sf.taverna.raven.spi
Filter a set of Artifact objects according to some criteria
ArtifactFilterListener - Interface in net.sf.taverna.raven.spi
 
artifactForClass(Class) - Method in class net.sf.taverna.raven.repository.impl.EclipseRepository
 
artifactForClass(Class) - Method in class net.sf.taverna.raven.repository.impl.LocalRepository
Given a Class object return the Artifact whose LocalArtifactClassLoader created it.
artifactForClass(Class) - Method in interface net.sf.taverna.raven.repository.Repository
Given a Class object return the Artifact whose LocalArtifactClassLoader created it.
artifactId - Variable in class net.sf.taverna.raven.repository.BasicArtifact
 
ArtifactImpl - Class in net.sf.taverna.raven.repository.impl
A single Maven2 artifact with group, artifact and version
ArtifactNotFoundException - Exception in net.sf.taverna.raven.repository
Thrown when an attempt to locate a remote module in a repository fails for some reason or when a reference is made to an Artifact that cannot be resolved within the current local repository.
ArtifactNotFoundException() - Constructor for exception net.sf.taverna.raven.repository.ArtifactNotFoundException
 
ArtifactNotFoundException(String) - Constructor for exception net.sf.taverna.raven.repository.ArtifactNotFoundException
 
ArtifactStateException - Exception in net.sf.taverna.raven.repository
Thrown when an operation attempt to perform on an artifact that isn't in the right state relative to a particular repository
ArtifactStateException(ArtifactStatus, ArtifactStatus[]) - Constructor for exception net.sf.taverna.raven.repository.ArtifactStateException
 
ArtifactStatus - Enum in net.sf.taverna.raven.repository
Enumeration of the possible states a dependency may occupy during the resolution, fetch and verify process.
AskWorker - Class in net.sourceforge.taverna.scuflworkers.ui
This processor creates a Dialog with a text box for user input.
AskWorker() - Constructor for class net.sourceforge.taverna.scuflworkers.ui.AskWorker
 
asObject(boolean) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
Convert primitive type to the proper Object instance.
asObject(byte) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
 
asObject(char) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
 
asObject(double) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
 
asObject(float) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
 
asObject(int) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
 
asObject(long) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
 
asObject(short) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
 
asObjectList(Object) - Static method in class org.embl.ebi.escience.scufl.tools.Lang
Convert arrays containing primitive types such as int[] into a List containing the Object version of the primitive type.
AssigningServiceClient - Class in org.embl.ebi.escience.baclava.lsid
An implementation of the LSIDProvider interface which connects through to an instance of the LSID assigning service to acquire LSIDs
AssigningServiceClient() - Constructor for class org.embl.ebi.escience.baclava.lsid.AssigningServiceClient
Default constructor so an instance can be created for use by the enactor framework.
asXML() - Method in class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerDefinition
 
attachToModel(ScuflModel) - Method in class net.sourceforge.taverna.scuflworkers.bsf.BSFConfigPanel
 
attachToModel(ScuflModel) - Method in class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APConfigPanel
 
attachToModel(ScuflModel) - Method in class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellConfigPanel
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scufl.view.TreeModelView
Bind to a ScuflModel
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.AdvancedModelExplorer
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.DotTextArea
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.graph.WorkflowEditor
 
attachToModel(Processor) - Method in class org.embl.ebi.escience.scuflui.IterationStrategyEditor
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.ScavengerTreePanel
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.ScuflDiagramPanel
 
attachToModel(SemanticMarkup) - Method in class org.embl.ebi.escience.scuflui.ScuflSemanticMarkupEditor
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.ScuflSVGDiagram
 
attachToModel(Processor) - Method in interface org.embl.ebi.escience.scuflui.spi.ProcessorViewSPI
Directs the implementing component to bind to the specified Processor instance, refresh its internal state from the model and commence listening to events, maintaining its state as these events dictate.
attachToModel(SemanticMarkup) - Method in interface org.embl.ebi.escience.scuflui.spi.SemanticMarkupViewSPI
Directs the implementing component to bind to the specified SemanticMarkup instance, refresh its internal state from the model and commence listening to events, maintaining its state as these events dictate.
attachToModel(ScuflModel) - Method in interface org.embl.ebi.escience.scuflui.spi.WorkflowModelViewSPI
Directs the implementing component to bind to the specified ScuflModel instance, refresh its internal state from the model and commence listening to events, maintaining its state as these events dictate.
attachToModel(Processor) - Method in class org.embl.ebi.escience.scuflui.TemplateEditor
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.treeview.ScuflModelExplorer
Bind this view onto a ScuflModel instance, this registers the view to receive events and thus keep up to date.
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.treeview.ScuflModelTreeTable
Bind this view onto a ScuflModel instance, this registers the view to receive events and thus keep up to date.
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.DefaultScavengerTree
Listen for model bind requests to set the internal ScuflModel field
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.WorkflowInputMapBuilder
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.XScuflTextArea
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.XScuflTree
 
autoscroll(Point) - Method in class org.embl.ebi.escience.scuflui.IterationStrategyEditor
 
AWTComponentRenderer - Class in org.embl.ebi.escience.scuflui.renderers
Class that renders objects which have a Java Component subclass as their user object
AWTComponentRenderer() - Constructor for class org.embl.ebi.escience.scuflui.renderers.AWTComponentRenderer
 

B

backoff - Variable in class org.embl.ebi.escience.scufl.Processor
 
BaclavaDataService - Interface in org.embl.ebi.escience.baclava.store
Defines the API that a concrete backing store must implement.
BaclavaDataServiceFactory - Class in org.embl.ebi.escience.baclava.store
 
BaclavaDataServiceFactory() - Constructor for class org.embl.ebi.escience.baclava.store.BaclavaDataServiceFactory
 
BaclavaIterator - Class in org.embl.ebi.escience.baclava.iterator
This provides an Iterator interface with a single additional method to allow reset of the iterator to its starting state.
BaclavaIterator(Collection) - Constructor for class org.embl.ebi.escience.baclava.iterator.BaclavaIterator
 
BaclavaIterator(Collection, List) - Constructor for class org.embl.ebi.escience.baclava.iterator.BaclavaIterator
 
BaclavaIterator(DataThing, Collection, List) - Constructor for class org.embl.ebi.escience.baclava.iterator.BaclavaIterator
Construct an iterator from a list of non data thing objects, a reference to the parent DataThing which contains them and an explicit index list.
BaclavaIteratorNode - Class in org.embl.ebi.escience.baclava.iterator
A DefaultMutableTreeNode implementing ResumableIterator by wrapping a BaclavaIterator.
BaclavaIteratorNode(BaclavaIterator, String) - Constructor for class org.embl.ebi.escience.baclava.iterator.BaclavaIteratorNode
A TreeNode that contains a BaclavaIterator.
bake(Object) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingFactory
 
bake(String) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingFactory
Easy for String objects, everything already recognizes them so no custom code required.
bake(String[]) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingFactory
For String arrays convert the array to a List and store that.
bake(byte[]) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingFactory
For byte arrays store the byte array as is
bake(byte[][]) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingFactory
For arrays of byte arrays store each byte array in a List
bakeForSoaplab(List) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingFactory
Bake a List of Lists into a List of byte[]
bakeInputMap() - Method in class org.embl.ebi.escience.scuflui.WorkflowInputMapBuilder
 
barsCount - Variable in class net.sf.taverna.zaria.progress.InfiniteProgressPanel
 
Base64 - Class in net.iharder
Encodes and decodes to and from Base64 notation.
Base64 - Class in org.embl.ebi.escience.baclava
Encodes and decodes to and from Base64 notation.
Base64.InputStream - Class in net.iharder
A Base64#InputStream will read data from another InputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.
Base64.InputStream(InputStream) - Constructor for class net.iharder.Base64.InputStream
Constructs a Base64#InputStream in DECODE mode.
Base64.InputStream(InputStream, int) - Constructor for class net.iharder.Base64.InputStream
Constructs a Base64#InputStream in either ENCODE or DECODE mode.
Base64.InputStream - Class in org.embl.ebi.escience.baclava
A {#InputStream} will read data from another InputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.
Base64.InputStream(InputStream) - Constructor for class org.embl.ebi.escience.baclava.Base64.InputStream
Constructs a {#InputStream} in DECODE mode.
Base64.InputStream(InputStream, int) - Constructor for class org.embl.ebi.escience.baclava.Base64.InputStream
Constructs a {#InputStream} in either ENCODE or DECODE mode.
Base64.OutputStream - Class in net.iharder
A Base64#OutputStream will write data to another OutputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.
Base64.OutputStream(OutputStream) - Constructor for class net.iharder.Base64.OutputStream
Constructs a Base64#OutputStream in ENCODE mode.
Base64.OutputStream(OutputStream, int) - Constructor for class net.iharder.Base64.OutputStream
Constructs a Base64#OutputStream in either ENCODE or DECODE mode.
Base64.OutputStream - Class in org.embl.ebi.escience.baclava
A {#OutputStream} will write data to another OutputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.
Base64.OutputStream(OutputStream) - Constructor for class org.embl.ebi.escience.baclava.Base64.OutputStream
Constructs a {#Outp