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

C

CACHE_PART_DATATYPES - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

An ID used in CacheImpl.removeFromCache(java.lang.String) indicating data types part.

CACHE_PART_SERVICES - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

An ID used in CacheImpl.removeFromCache(java.lang.String) indicating services part.

CACHE_PROP_COUNT - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

CACHE_PROP_LOCATION - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

CACHE_PROP_NAME - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

CACHE_PROP_OLDEST - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

CACHE_PROP_SIZE - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

CACHE_PROP_YOUNGEST - Static variable in class org.biomoby.client.taverna.plugin.CacheImpl

CacheImpl - Class in org.biomoby.client.taverna.plugin

An implementation of CentralAll, allowing to cache locally results of the cumulative methods so it does not need to access Moby registry all the time.

CacheImpl(String) - Constructor for class org.biomoby.client.taverna.plugin.CacheImpl

Create an instance that will access a default Moby registry and will cache results in the 'cacheDir' directory.

CacheImpl(String, String, String) - Constructor for class org.biomoby.client.taverna.plugin.CacheImpl

Create an instance that will access a Moby registry defined by its 'endpoint' and 'namespace', and will cache results in the 'cacheDir' directory.

called - Variable in class net.sf.taverna.t2.lang.observer.ObserverTest.SelvRemovingObserver

callWebService(String, String) - Static method in class org.embl.ebi.escience.scuflworkers.soaplab.Soap

Invoke the web service, passing no parameters, and return the result.

callWebService(String, String, String) - Static method in class org.embl.ebi.escience.scuflworkers.soaplab.Soap

Invoke the web service, passing a single String parameter, and return the result.

callWebService(String, String, Object[]) - Static method in class org.embl.ebi.escience.scuflworkers.soaplab.Soap

Invoke the web service and return the result.

cancelCellEditing() - Method in class org.embl.ebi.escience.treetable.AbstractCellEditor

cancelExecution() - Method in class org.embl.ebi.escience.scufl.enactor.implementation.WorkflowInstanceImpl

cancelExecution() - Method in interface org.embl.ebi.escience.scufl.enactor.WorkflowInstance

Cancel the currently running workflow, freeing any resources used

canDrop(DropTargetDragEvent) - Method in class org.embl.ebi.escience.scuflui.WorkflowInputMapBuilder.TreeTransferHandler

canHandle(Processor) - Method in class org.biomoby.client.taverna.plugin.AddParserAction

canHandle(Processor) - Method in class org.biomoby.client.taverna.plugin.BiomobyAction

canHandle(Processor) - Method in class org.biomoby.client.taverna.plugin.BiomobyObjectAction

canHandle(Scavenger) - Method in class org.biomoby.client.taverna.plugin.BiomobyScavengerAction

canHandle(Processor) - Method in class org.biomoby.client.taverna.plugin.BiomobyWidgetAction

canHandle(Processor) - Method in class org.biomoby.client.taverna.plugin.ConfigureMobyServiceAction

canHandle(Processor) - Method in class org.embl.ebi.escience.scuflui.actions.SetBoringAction

canHandle(Processor) - Method in class org.embl.ebi.escience.scuflui.actions.UnsetBoringAction

canHandle(RendererRegistry, DataThing) - Method in class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByJavaClass

canHandle(RendererRegistry, DataThing) - Method in class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.ByMimeType

canHandle(RendererRegistry, DataThing) - Method in class org.embl.ebi.escience.scuflui.renderers.AbstractRenderer.BySemanticType

canHandle(RendererRegistry, Object, Class) - Method in class org.embl.ebi.escience.scuflui.renderers.AWTComponentRenderer

canHandle(RendererRegistry, DataThing) - Method in class org.embl.ebi.escience.scuflui.renderers.CollectionAsTable

canHandle(RendererRegistry, Object, String) - Method in class org.embl.ebi.escience.scuflui.renderers.JMolRenderer

canHandle(RendererRegistry, DataThing) - Method in class org.embl.ebi.escience.scuflui.renderers.LabelRenderer

canHandle(RendererRegistry, Object, String) - Method in class org.embl.ebi.escience.scuflui.renderers.SeqVistaRenderer

canHandle(String, Object) - Method in interface org.embl.ebi.escience.scuflui.shared.ModelMap.ModelChangeListener

Return true if the listener can handle events for the given modelname and model.

canHandle(Processor) - Method in interface org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI

Can this action handle the specified processor? Return true if this action is applicable.

canHandle(RendererRegistry, DataThing) - Method in interface org.embl.ebi.escience.scuflui.spi.RendererSPI

Return true if this SPI can handle the given object with the given mime type, false otherwise.

canHandle(Scavenger) - Method in interface org.embl.ebi.escience.scuflui.workbench.scavenger.spi.ScavengerActionSPI

Can this action handle the specified scavenger? Return true if this action is applicable.

canHandle(String, Object) - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench.CurrentWorkflowListener

canHandle(String, Object) - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench.DebugListener

canHandle(String, Object) - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench.WorkflowInstanceListener

canHandle(String, Object) - Method in class org.embl.ebi.escience.scuflui.workbench.WorkbenchPerspectives.CurrentPerspectiveListener

canHandle(Processor) - Method in class org.embl.ebi.escience.scuflworkers.java.actions.FlattenListEditAction

Only handles LocalServiceProcessor based on FlattenList

canHandle(Processor) - Method in class org.embl.ebi.escience.scuflworkers.java.actions.SliceListEditAction

Only handles LocalServiceProcessor based on SliceList

canHandle(Processor) - Method in class org.embl.ebi.escience.scuflworkers.soaplab.SoaplabDescriberPanel

canHandle(Processor) - Method in class org.embl.ebi.escience.scuflworkers.workflow.WorkflowEditProcessorAction

canMakeFacets(DataThing) - Method in class org.embl.ebi.escience.scuflui.facets.PropertyFetcher

canMakeFacets(DataThing) - Method in class org.embl.ebi.escience.scuflui.facets.RegexScanner

canMakeFacets(DataThing) - Method in class org.embl.ebi.escience.scuflui.facets.Self

canMakeFacets(DataThing) - Method in class org.embl.ebi.escience.scuflui.facets.ToString

canMakeFacets(DataThing) - Method in interface org.embl.ebi.escience.scuflui.spi.FacetFinderSPI

Indicate if this facet finder can decompose this DataThing.

cantFindClass() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

CArrowImage - Class in net.sf.taverna.t2.lang.ui

A BufferedImage of one of four types of arrow (up, down, left or right) drawn to the size specified on the constructor.

CArrowImage(int) - Constructor for class net.sf.taverna.t2.lang.ui.CArrowImage

CArrowImage(int, int, int) - Constructor for class net.sf.taverna.t2.lang.ui.CArrowImage

CArrowImage - Class in org.embl.ebi.escience.scuflui.shared

A BufferedImage of one of four types of arrow (up, down, left or right) drawn to the size specified on the constructor.

CArrowImage(int) - Constructor for class org.embl.ebi.escience.scuflui.shared.CArrowImage

CArrowImage(int, int, int) - Constructor for class org.embl.ebi.escience.scuflui.shared.CArrowImage

changeOutputPortTaskData(String, String, Object) - Method in class org.embl.ebi.escience.scufl.enactor.implementation.WorkflowInstanceImpl

changeOutputPortTaskData(String, String, Object) - Method in interface org.embl.ebi.escience.scufl.enactor.WorkflowInstance

Changes intermediate output data on the output porttask.

changeProxySettings(Properties) - Method in class net.sf.taverna.raven.launcher.LauncherHttpProxyConfiguration

Change the System Proxy settings according to the property values specified.

characters(char[], int, int) - Method in class net.sourceforge.taverna.biojava.StringXMLEmitter

checkFactories() - Method in class net.sf.taverna.t2.util.beanable.BeanableFactoryRegistry

Find all the BeanableFactorys and log any problems

checkForUpdates() - Method in class net.sf.taverna.raven.plugins.PluginManager

Checks the PluginSites to find updates for installed plugins.

checkForUpdates() - Method in class net.sf.taverna.update.plugin.PluginManager

Checks the PluginSites to find updates for installed plugins.

checkUpdated() - Method in class org.embl.ebi.escience.scuflui.AdvancedModelExplorer.WorkflowMetadata

checkValidWorkflow(ScuflModel, Component) - Static method in class org.embl.ebi.escience.scuflui.WorkflowInputPanelFactory

childIterator() - Method in class org.embl.ebi.escience.baclava.DataThing

Iterate over all imediate children.

ChooseWorker - Class in net.sourceforge.taverna.scuflworkers.ui

This processor allows the user to select an option from a list of radio buttons.

ChooseWorker() - Constructor for class net.sourceforge.taverna.scuflworkers.ui.ChooseWorker

circleDown(float) - Static method in class com.jhlabs.image.ImageMath

A "circle down" function.

circleUp(float) - Static method in class com.jhlabs.image.ImageMath

A "circle up" function.

clamp(float, float, float) - Static method in class com.jhlabs.image.ImageMath

Clamp a value to an interval.

clamp(int, int, int) - Static method in class com.jhlabs.image.ImageMath

Clamp a value to an interval.

classIcon - Static variable in class org.embl.ebi.escience.scuflui.TavernaIcons

ClassLocation - Class in net.sf.taverna.raven.prelauncher

Given a Class, find the directory/JAR it was loaded from.

ClassLocation() - Constructor for class net.sf.taverna.raven.prelauncher.ClassLocation

classLocationAnonymousClass() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationClasses() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationClassesWithSpaces() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationDirClasses() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationDirClassesWithSpaces() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationDirJar() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationDirJarWithSpaces() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationInnerClass() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationJar() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationJarWithSpaces() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationMe() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationURIClasses() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationURIClassesWithSpaces() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationURIJar() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

classLocationURIJarWithSpaces() - Method in class net.sf.taverna.raven.prelauncher.TestClassLocation

clean() - Method in class net.sf.taverna.raven.repository.impl.LocalRepository

Clean the local repository by removing invalid artifacts and directories.

cleanEmpty() - Method in class net.sf.taverna.raven.repository.impl.LocalRepositoryTest

clear() - Method in class net.sf.taverna.t2.partition.HashSetModel

clear() - Method in class org.embl.ebi.escience.scufl.ScuflModel

Clear the model, retaining any existing listeners but removing all model data.

clearFilters() - Method in class net.sf.taverna.raven.spi.SpiRegistry

Clear all ArtifactFilter objects

clearMIMETypes() - Method in class org.embl.ebi.escience.scufl.PortSemanticMarkup

Clear the array of MIME types

clearMIMETypes() - Method in class org.embl.ebi.escience.scufl.SemanticMarkup

Clear the array of MIME types

clone() - Method in class org.embl.ebi.escience.baclava.DataThing

clone() - Method in class org.embl.ebi.escience.scufl.ScuflModel

cloneCells(Object[]) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel

close() - Method in class net.iharder.Base64.OutputStream

Flushes and closes (I think, in the superclass) the stream.

close() - Method in class org.embl.ebi.escience.baclava.Base64.OutputStream

Flushes and closes (I think, in the superclass) the stream.

closeWorkflow() - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench

Close the current workflow.

closeWorkflow(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench

Close the given workflow.

collectAllProcessors(Map, String) - Method in class org.embl.ebi.escience.scufl.ScuflModel

Crawl down the workflow locating all processors and expanding nested workflow processors recursively to get a complete list of all (non workflow) processors in the workflow.

CollectionAsTable - Class in org.embl.ebi.escience.scuflui.renderers

CollectionAsTable() - Constructor for class org.embl.ebi.escience.scuflui.renderers.CollectionAsTable

collectionConstructed(CollectionConstructionEvent) - Method in class org.embl.ebi.escience.scufl.enactor.WorkflowEventAdapter

collectionConstructed(CollectionConstructionEvent) - Method in interface org.embl.ebi.escience.scufl.enactor.WorkflowEventListener

Called when a data item is wrapped up inside a default collection prior to being passed to a service expecting a higher cardinality version of the same input type

CollectionConstructionEvent - Class in org.embl.ebi.escience.scufl.enactor.event

CollectionConstructionEvent(WorkflowInstance, String[], String) - Constructor for class org.embl.ebi.escience.scufl.enactor.event.CollectionConstructionEvent

colorSpline(float, int, int[]) - Static method in class com.jhlabs.image.ImageMath

Compute a Catmull-Rom spline for RGB values.

colorSpline(int, int, int[], int[]) - Static method in class com.jhlabs.image.ImageMath

Compute a Catmull-Rom spline for RGB values, but with variable knot spacing.

colour() - Method in interface org.embl.ebi.escience.scuflworkers.ProcessorInfoBean

colour() - Method in class org.embl.ebi.escience.scuflworkers.ProcessorInfoBeanHelper

colours - Static variable in class org.embl.ebi.escience.baclava.iterator.IteratorNodeTests

columnAdded(FTableColumnModelEvent) - Method in interface org.embl.ebi.escience.scuflui.facets.FTableColumnModelListener

columnChanged(FTableColumnModelEvent) - Method in interface org.embl.ebi.escience.scuflui.facets.FTableColumnModelListener

columnIterator() - Method in class org.embl.ebi.escience.scuflui.facets.FTableColumnModel

columnMoved(FTableColumnModelEvent) - Method in interface org.embl.ebi.escience.scuflui.facets.FTableColumnModelListener

columnRemoved(FTableColumnModelEvent) - Method in interface org.embl.ebi.escience.scuflui.facets.FTableColumnModelListener

columnSelectionChanged(ListSelectionEvent) - Method in class org.embl.ebi.escience.scuflui.results.ResultTable

com.jhlabs.image - package com.jhlabs.image

compareTo(Plugin) - Method in class net.sf.taverna.raven.plugins.Plugin

compareTo(Object) - Method in class net.sf.taverna.raven.repository.BasicArtifact

Compare with another object.

compareTo(Plugin) - Method in class net.sf.taverna.update.plugin.Plugin

compareTo(Object) - Method in class org.embl.ebi.escience.scufl.DataConstraint

Use the toString as the comparable

compareVersion(Plugin) - Method in class net.sf.taverna.raven.plugins.Plugin

compareVersion(Plugin) - Method in class net.sf.taverna.update.plugin.Plugin

Compatibility - Interface in net.sf.taverna.x2008.xml.plugins

An XML Compatibility(@http://taverna.sf.net/2008/xml/plugins).

Compatibility.Factory - Class in net.sf.taverna.x2008.xml.plugins

A factory class with static methods for creating instances of this type.

CompatibilityImpl - Class in net.sf.taverna.x2008.xml.plugins.impl

An XML Compatibility(@http://taverna.sf.net/2008/xml/plugins).

CompatibilityImpl(SchemaType) - Constructor for class net.sf.taverna.x2008.xml.plugins.impl.CompatibilityImpl

compatible - Variable in class net.sf.taverna.raven.plugins.Plugin

compatible - Variable in class net.sf.taverna.update.plugin.Plugin

compileWorkflow(ScuflModel, Map, UserContext) - Method in interface org.embl.ebi.escience.scufl.enactor.EnactorProxy

Submit a workflow to the enactor represented by this proxy.

compileWorkflow(ScuflModel, UserContext) - Method in interface org.embl.ebi.escience.scufl.enactor.EnactorProxy

Submit to the enactor represented by this proxy for compilation the workflow submission.

compileWorkflow(ScuflModel, Map, UserContext) - Method in class org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy

compileWorkflow(ScuflModel, UserContext) - Method in class org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy

COMPLETED - Static variable in class org.embl.ebi.escience.scufl.ConcurrencyConstraint

Signifies that the processor has completed

ConcatenateFileListWorker - Class in net.sourceforge.taverna.scuflworkers.io

This processor concatenates a series of text files and saves the results into the output file.

ConcatenateFileListWorker() - Constructor for class net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker

ConcatenateFileListWorkerTest - Class in net.sourceforge.taverna.scuflworkers.io

This class Last edited by $Author: sowen70 $

ConcatenateFileListWorkerTest() - Constructor for class net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorkerTest

ConcurrencyConstraint - Class in org.embl.ebi.escience.scufl

Represents a concurrency constraint between two processors

ConcurrencyConstraint(ScuflModel, String, Processor, Processor, int, int, int) - Constructor for class org.embl.ebi.escience.scufl.ConcurrencyConstraint

Create a new concurrency constraint.

ConcurrencyConstraintCreationException - Exception in org.embl.ebi.escience.scufl

Thrown by the ConcurrencyConstraint constructor if the arguments passed in are invalid.

ConcurrencyConstraintCreationException(String) - Constructor for exception org.embl.ebi.escience.scufl.ConcurrencyConstraintCreationException

concurrencyTest() - Method in class net.sf.taverna.t2.lang.observer.ObserverTest

configure(Element) - Method in class net.sf.taverna.zaria.ZBasePane

Automatically intializes the repository with any named components that aren't already there.

configure(Element) - Method in class net.sf.taverna.zaria.ZBlankComponent

configure(Element) - Method in class net.sf.taverna.zaria.ZRavenComponent

configure(Element) - Method in class net.sf.taverna.zaria.ZSplitPane

configure(Element) - Method in class net.sf.taverna.zaria.ZTabbedPane

configure(Element) - Method in interface net.sf.taverna.zaria.ZTreeNode

Set current state of this node, including construction of nested containers, from the specified JDOM Element

configureDataThing(Element, DataThing) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingXMLFactory

Build a DataThing from the supplied Element object, the Element in this case is the 'myGridDataDocument' element.

configuredForUpdates() - Method in class net.sf.taverna.raven.appconfig.bootstrap.RavenProperties

Indicates whether the system is configured to allow updates (using a profilelist) or not (using a forced profile).

configuredForUpdates() - Method in class net.sf.taverna.tools.RavenProperties

Indicates whether the system is configured to allow updates (using a profilelist) or not (using a forced profile).

configureFromElement(Element) - Method in class org.embl.ebi.escience.scufl.PortSemanticMarkup

Configure this markup object from the supplied XML element.

configureFromElement(Element) - Method in class org.embl.ebi.escience.scufl.SemanticMarkup

Configure this markup object from the supplied XML element.

ConfigureMobyServiceAction - Class in org.biomoby.client.taverna.plugin

ConfigureMobyServiceAction() - Constructor for class org.biomoby.client.taverna.plugin.ConfigureMobyServiceAction

connect() - Method in class org.embl.ebi.escience.scuflworkers.rserv.RservTask

connectToWorkflow(String) - Method in interface org.embl.ebi.escience.scufl.enactor.ResumableEnactorProxy

Get a WorkflowInstance implementation corresponding to the running workflow with the supplied identifier.

console - Static variable in class net.sf.taverna.raven.log.ConsoleLog

Where to print log messages.

ConsoleLog - Class in net.sf.taverna.raven.log

Implementation of LogInterface for simple System.err based printouts.

ConsoleLog() - Constructor for class net.sf.taverna.raven.log.ConsoleLog

ConsoleLog(Class) - Constructor for class net.sf.taverna.raven.log.ConsoleLog

constraintIcon - Static variable in class org.embl.ebi.escience.scuflui.TavernaIcons

ConstructingIterator - Class in org.embl.ebi.escience.scufl.provenance.process

Event corresponding to the generation of an implicit iterator.

ConstructingIterator(IterationStrategy) - Constructor for class org.embl.ebi.escience.scufl.provenance.process.ConstructingIterator

ConstructingIterator() - Constructor for class org.embl.ebi.escience.scufl.provenance.process.ConstructingIterator

consumeXML(Element) - Method in class org.embl.ebi.escience.scuflworkers.java.FlattenList

Extract the <flattenlist depth="X" /> number from the element.

consumeXML(Element) - Method in class org.embl.ebi.escience.scuflworkers.java.SliceList

Extract the <slicelist depth="X" /> number from the element.

consumeXML(Element) - Method in interface org.embl.ebi.escience.scuflworkers.java.XMLExtensible

consumeXML(Element) - Method in class org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter

Generates the TypeDescriptor structure, and then the relevant inputs from the XML element provided.

consumeXML(Element) - Method in class org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter

Generates the TypeDescriptor structure, and then the relevant outputs from the XML element provided.

contains(Object) - Method in class org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel

containsSecondaries() - Method in class org.biomoby.client.taverna.plugin.BiomobyProcessor

contextItemsForPort(Port) - Method in class org.embl.ebi.escience.scuflworkers.java.XMLSplitterScuflContextMenuFactory

Generates a List of JMenuItems, if appropriate, for the given port

contextMenuItems() - Method in class org.embl.ebi.escience.scuflworkers.java.XMLSplittableInputPort

contextMenuItems() - Method in class org.embl.ebi.escience.scuflworkers.java.XMLSplittableOutputPort

Generates the menu items for the port if applicable, otherwise returns an empty List

contextMenuItems() - Method in interface org.embl.ebi.escience.scuflworkers.ScuflContextMenuAware

Creates a list, in order, of the JMenuItems to be added to the ScuflContextMenu

convert(String) - Static method in class org.embl.ebi.escience.scufl.AnnotationTemplate

Take an input string and return the string with all less than characters replaced with the appropriate XML literal

convertCoords(String) - Method in class net.sourceforge.taverna.scuflworkers.io.DataRangeTask

This method converts comma-delimited

convertObject(Object) - Static method in class org.embl.ebi.escience.baclava.factory.DataThingFactory

copyIcon - Static variable in class org.embl.ebi.escience.scuflui.TavernaIcons

copyMetadataFrom(DataThing) - Method in class org.embl.ebi.escience.baclava.DataThing

Copy the markup from the supplied DataThing object to this one.

CopyOfBiomobyTask - Class in org.biomoby.client.taverna.plugin

CopyOfBiomobyTask(Processor) - Constructor for class org.biomoby.client.taverna.plugin.CopyOfBiomobyTask

createCollectionFromListOfSimples(String, List<Element>) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createCompatibleDestImage(BufferedImage, ColorModel) - Method in class com.jhlabs.image.AbstractBufferedImageOp

createConnection(RshellConnectionSettings) - Method in class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellConnectionManager

Methos for creating a new r shell connection

createDomDocument() - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createEmpty() - Method in class net.sf.taverna.raven.repository.impl.LocalRepositoryTest

createFrame(ScuflModel, UIComponentSPI, int, int, int, int) - Static method in class org.embl.ebi.escience.scuflui.shared.UIUtils

Create a top level window using the configured default frame creator.

createFrame(JComponent, int, int, int, int) - Static method in class org.embl.ebi.escience.scuflui.shared.UIUtils

As for the method above but allows a non-ScuflUIComponent JComponent.

createFrame(ScuflModel, UIComponentSPI, int, int, int, int) - Method in interface org.embl.ebi.escience.scuflui.shared.UIUtils.FrameCreator

createFromBean(BeanType) - Method in class net.sf.taverna.t2.util.beanable.BeanableFactory

Construct a Beanable (an instance of the class returned from BeanableFactory.getBeanableType()) loaded from the given bean.

createHomes(InputStream) - Static method in class org.biomoby.client.taverna.plugin.TreeUtils

createLoaderMethod(List<URL>, List<URL>) - Static method in class net.sf.taverna.raven.appconfig.bootstrap.Bootstrap

createLoaderMethod(List<URL>, List<URL>) - Static method in class net.sf.taverna.tools.Bootstrap

CreateMobyCollection - Class in org.biomoby.client.taverna.plugin

A local processor to construct a biomoby data packet from either an ID or a string content

CreateMobyCollection() - Constructor for class org.biomoby.client.taverna.plugin.CreateMobyCollection

CreateMobyData - Class in org.biomoby.client.taverna.plugin

A local processor to construct a biomoby data packet from either an ID or a string content

CreateMobyData() - Constructor for class org.biomoby.client.taverna.plugin.CreateMobyData

CreateMobyData - Class in org.embl.ebi.escience.scuflworkers.biomoby

A local processor to construct a biomoby data packet from either an ID or a string content

CreateMobyData() - Constructor for class org.embl.ebi.escience.scuflworkers.biomoby.CreateMobyData

createMobyDataElementWrapper(Element, String, Element) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createMobyDataElementWrapper(String) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createMobyDataElementWrapper(Element) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createMobyDataElementWrapper(String, String) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createMobyDataElementWrapper(String, String, Element) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createMobyDataWrapper(String, Element) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

CreateMobySimple - Class in org.biomoby.client.taverna.plugin

A local processor to construct a biomoby data packet from either an ID or a string content

CreateMobySimple() - Constructor for class org.biomoby.client.taverna.plugin.CreateMobySimple

createMultipleInvokations(Element[]) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createMultipleInvokations(String[]) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createProcessor(String, ScuflModel) - Method in class org.embl.ebi.escience.scuflworkers.ProcessorFactory

Instantiate a new processor with the supplied name and bind it to the specified model.

createServiceInput(String[], String) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createServiceInput(Element[], String) - Static method in class org.biomoby.client.taverna.plugin.XMLUtilities

createTempDirectory() - Method in class net.sf.taverna.raven.LoaderTest

createTempDirectory() - Static method in class net.sf.taverna.raven.repository.impl.LocalRepositoryTest

createTempDirectory() - Static method in class net.sf.taverna.raven.repository.impl.PomPropertiesTest

createWorkbenchClass(String, Method) - Static method in class net.sf.taverna.raven.appconfig.bootstrap.Bootstrap

createWorkbenchClass(String, Method) - Static method in class net.sf.taverna.tools.Bootstrap

CrossNode - Class in org.embl.ebi.escience.scufl

A cross product node in an iterator tree model

CrossNode() - Constructor for class org.embl.ebi.escience.scufl.CrossNode

CTransferableTreePath - Class in net.sf.taverna.t2.lang.ui

This represents a TreePath (a node in a JTree) that can be transferred between a drag source and a drop target.

CTransferableTreePath(TreePath) - Constructor for class net.sf.taverna.t2.lang.ui.CTransferableTreePath

Constructs a transferrable tree path object for the specified path.

CTransferableTreePath - Class in org.embl.ebi.escience.scuflui.shared

This represents a TreePath (a node in a JTree) that can be transferred between a drag source and a drop target.

CTransferableTreePath(TreePath) - Constructor for class org.embl.ebi.escience.scuflui.shared.CTransferableTreePath

Constructs a transferrable tree path object for the specified path.

CURRENT_PERSPECTIVE - Static variable in class org.embl.ebi.escience.scuflui.shared.ModelMap

Used as a modelName for setModel() and getNamedModel() - notes the current active perspective in the GUI.

CURRENT_PROFILE - Static variable in class net.sf.taverna.raven.appconfig.bootstrap.ProfileSelector

CURRENT_PROFILE - Static variable in class net.sf.taverna.tools.ProfileSelector

CURRENT_WORKFLOW - Static variable in class org.embl.ebi.escience.scuflui.shared.ModelMap

Used as a modelName for setModel() and getNamedModel() - notes the current active workflow in the GUI.

CustomPartitionAlgorithm - Class in net.sf.taverna.t2.partition.algorithms

Takes a custom search term and checks against the properties eg "operation" of each of the available items.

CustomPartitionAlgorithm() - Constructor for class net.sf.taverna.t2.partition.algorithms.CustomPartitionAlgorithm

CustomPartitionAlgorithm(String) - Constructor for class net.sf.taverna.t2.partition.algorithms.CustomPartitionAlgorithm

CustomPerspective - Class in net.sf.taverna.perspectives

User generated perspective.

CustomPerspective(Element) - Constructor for class net.sf.taverna.perspectives.CustomPerspective

CustomPerspectiveFactory - Class in net.sf.taverna.perspectives

CustomPerspectiveFactory() - Constructor for class net.sf.taverna.perspectives.CustomPerspectiveFactory