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

A

ABREV - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
abrev - Variable in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
AbstractAnalysis - Class in org.geworkbench.analysis
Copyright: Copyright (c) 2003
AbstractAnalysis() - Constructor for class org.geworkbench.analysis.AbstractAnalysis
 
AbstractAnalysisLabelComparator - Class in org.geworkbench.analysis
Comparator for AbstraactAnalyses.
AbstractAnalysisLabelComparator() - Constructor for class org.geworkbench.analysis.AbstractAnalysisLabelComparator
 
AbstractCluster - Class in org.geworkbench.bison.model.clusters
Copyright: Copyright (c) 2003
AbstractCluster() - Constructor for class org.geworkbench.bison.model.clusters.AbstractCluster
 
AbstractGridAnalysis - Class in org.geworkbench.analysis
Analyses that have a corresponding (ca)Grid component should extend this abstract class to have the grid analyses exposed.
AbstractGridAnalysis() - Constructor for class org.geworkbench.analysis.AbstractGridAnalysis
 
AbstractResource - Class in org.geworkbench.bison.parsers.resources
Baseline implementation of Resource.
AbstractResource() - Constructor for class org.geworkbench.bison.parsers.resources.AbstractResource
 
AbstractSaveableParameterPanel - Class in org.geworkbench.analysis
This class is used to (1) store the parameters of an analysis, and (2) manage the visual representation (gui) that will be offered to the user in order to provide values for the parameters.
AbstractSaveableParameterPanel() - Constructor for class org.geworkbench.analysis.AbstractSaveableParameterPanel
 
accept(File) - Method in class org.geworkbench.builtin.projects.SaveFileFilterFactory.CsvFileFilter
 
accept(File) - Method in class org.geworkbench.builtin.projects.SaveFileFilterFactory.TabDelimitedFileFilter
 
accept(File) - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat.FASTAFilter
 
accept(File) - Method in class org.geworkbench.util.CsvFileFilter
 
accept(File) - Method in class org.geworkbench.util.sequences.PatFilter
 
AcceptTypes - Annotation Type in org.geworkbench.engine.management
User: matt Date: Oct 14, 2005 Time: 12:45:32 PM
AccessID - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
actionPerformed(ActionEvent) - Method in class org.geworkbench.builtin.projects.RegPanel
 
actionPerformed(ActionEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
activatedArrays - Variable in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
activatedMarkers - Variable in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
activatedMarkers - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
activateLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
activateLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Sets a label's active status to true.
ACTIVATOR - Static variable in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
activeSequenceDB - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
activeSubset() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Gets all the active sub-panels of the panel.
activeSubset() - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Gets all the active sub-panels of the panel.
add(AdjacencyMatrix.Node, AdjacencyMatrix.Node, float, String, Short) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
Adds and edge between geneId1 and geneId2.
add(AdjacencyMatrix.Node, AdjacencyMatrix.Node, float, String) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
Adds and edge between geneId1 and geneId2.
add(AdjacencyMatrix.Node, AdjacencyMatrix.Node, float) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
add(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
add(int, DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
add(T, U) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
add(T) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
Adds a new item to the item list, if it does not already exist.
add(int, T) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
Inserts the item at the specified index.
add(T) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList
Adds the item to the sequential item list.
add(int, T) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList
Adds the item to the sequential item list.
add(T, U) - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSAnnotatedPanel
 
add(DSMatchedSeqPattern) - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternResult
 
add(double) - Method in class org.geworkbench.bison.util.Normal
 
ADD - Static variable in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
add(DSMicroarraySet, AnnotationInformationManager.AnnotationType) - Method in class org.geworkbench.util.AnnotationInformationManager
 
addAcceptor(Class<?>, Class<?>) - Method in class org.geworkbench.engine.management.ComponentRegistry
Adds a type accepter the componentRegistry.
addAll(Collection<? extends T>) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
 
addASequence(T) - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
addASequence(T) - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
addAutoProgressBar() - Method in class org.geworkbench.util.SplashBitmap
Adds a JProgressBar to the splash screen that is automatically updated.
addAutoProgressBarIndeterminate() - Method in class org.geworkbench.util.SplashBitmap
Adds a indeterminate JProgressBar to the splash screen that will be updated while the splash screen is displayed.
Only one progress bar can be added to the splash screen at a time.
addBeforeToHistory(DSExtendable, String) - Static method in class org.geworkbench.builtin.projects.history.HistoryPanel
 
addChangedGenes(String) - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
addChild(DataSetSaveNode) - Method in class org.geworkbench.builtin.projects.DataSetSaveNode
 
addClass(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
addClass(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Adds a class to this context.
addComponentResource(String, ComponentResource) - Method in class org.geworkbench.engine.management.ComponentRegistry
 
addConfidence(double, short) - Method in class org.geworkbench.util.network.InteractionDetail
 
addDataSetNode(DSDataSet<? extends DSBioObject>) - Method in class org.geworkbench.builtin.projects.ProjectPanel
Inserts a new data set as a total level new node in the project tree.
addDataSetSubNode(DSAncillaryDataSet<? extends DSBioObject>) - Method in class org.geworkbench.builtin.projects.ProjectPanel
Inserts a new ancillary data set as a new node in the project tree.
addDirtyRegion(JComponent, int, int, int, int) - Method in class org.geworkbench.util.CheckThreadViolationRepaintManager
 
addDSMicroarraySet(DSMicroarraySet) - Method in class org.geworkbench.builtin.projects.ProjectPanel
 
addEdge(Edge) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeList
 
addEdge(String, String) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeList
 
addExtensionPoint(String) - Method in class org.geworkbench.engine.config.rules.PluginObject
Invoked by the Digester.
addField(Field) - Method in class org.geworkbench.engine.preferences.Preferences
 
addGeneRow(AdjacencyMatrix.Node) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
Add a node only.
addGUIComponent(String) - Method in class org.geworkbench.engine.config.rules.PluginObject
Invoked by the Digester.
addHelpSet(HelpSet) - Static method in class org.geworkbench.engine.config.rules.GeawConfigObject
Append a new help set to the existing ones.
addHistoryDetail(DSExtendable, String) - Static method in class org.geworkbench.builtin.projects.history.HistoryPanel
 
addHost(String) - Method in class org.geworkbench.util.PropertiesMonitor
 
addImageNode(ImageIcon) - Method in class org.geworkbench.builtin.projects.ProjectPanel
Add an image node under the last selected path.
addInvalidComponent(JComponent) - Method in class org.geworkbench.util.CheckThreadViolationRepaintManager
 
addLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
addLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Adds a label to this context.
addManualProgressBar(int, int) - Method in class org.geworkbench.util.SplashBitmap
Adds a JProgressBar to the splash screen that can be updated manually.
Only one progress bar can be added to the splash screen at a time.
addMenuInfo(String, String, String, String, String) - Method in class org.geworkbench.engine.config.ComponentMetadata
 
addMenuItem(JMenuItem) - Method in class org.geworkbench.util.sequences.SequenceViewWidgetPanel
 
addMenuItemInfo(String, String, String, String, String) - Method in class org.geworkbench.engine.config.PluginDescriptor
add menuitem info into an arraylist
addMenuListener(JMenuItem, ActionListener, String) - Method in class org.geworkbench.engine.config.PluginDescriptor
Registers an ActionListener with a JMenuItem.
addModule(String, String) - Method in class org.geworkbench.engine.config.rules.PluginObject
Invoked by the Digester.
addNameValuePair(String, Object) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Adds a new name-value mapping.
addNameValuePair(String, Object) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
addNameValuePair(String, Object) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
addNameValuePair(String, Object) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
addNameValuePair(String, Object) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
addNameValuePair(String, Object) - Method in class org.geworkbench.bison.datastructure.properties.CSExtendable
 
addNameValuePair(String, Object) - Method in interface org.geworkbench.bison.datastructure.properties.DSExtendable
Adds a new name-value mapping.
addNode(Cluster) - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
Adds a Cluster node as a child of this Cluster
addNode(Cluster) - Method in interface org.geworkbench.bison.model.clusters.Cluster
Adds newCluster as a child of this node.
addNode(HierCluster, int) - Method in class org.geworkbench.bison.model.clusters.DefaultHierCluster
Adds Cluster as a child of this node
addNode(HierCluster, int) - Method in interface org.geworkbench.bison.model.clusters.HierCluster
Add the designated node hc in the current cluster, at the designated index position.
addObject(Class<?>, Object) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Adds an object by tag to this data set.
addObject(Class<?>, Object) - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
Stores an arbitrary object by type.
addObserver(Observer) - Method in class org.geworkbench.util.ProgressBar
 
addObserver(Observer) - Method in class org.geworkbench.util.ProgressBarT
 
addPattern(PatternLocations) - Method in class org.geworkbench.util.patterns.PatternSequenceDisplayUtil
 
addPendingNode(GridEndpointReferenceType, String, String, boolean, AbstractGridAnalysis) - Method in class org.geworkbench.builtin.projects.ProjectPanel
Inserts a new pending node in the project tree.
addPlugin(PluginDescriptor) - Static method in class org.geworkbench.engine.config.PluginRegistry
Registers the designated plugin.
addPlugInAtExtension(PluginDescriptor, String) - Static method in class org.geworkbench.engine.config.PluginRegistry
Adds a plugin component descriptor at a named extension point.
addPoint(int) - Method in class org.geworkbench.util.ProgressGraph
 
addProcessedMaSet(DSMicroarraySet) - Method in class org.geworkbench.builtin.projects.ProjectPanel
 
addProgressBarPercent() - Method in class org.geworkbench.util.SplashBitmap
Displays the percentage of progress in the progress bar.
addReferenceGenes(String) - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
addRemotePanel() - Method in class org.geworkbench.builtin.projects.LoadDataDialog
 
addRemoteResource(RemoteResource) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
Add one new resource.
addResultRow(int, String, String, double, double, int, int) - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
addSigGenToPanel(T) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
addSigGenToPanel(T) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
addTask(Runnable, Object, Object, Object) - Method in class org.geworkbench.engine.management.Asynchronous
 
addTask(Runnable, Object, Object, Object) - Method in class org.geworkbench.engine.management.Overflow
 
addTask(Runnable, Object, Object, Object) - Method in class org.geworkbench.engine.management.SwingModel
 
addTask(Runnable, Object, Object, Object) - Method in interface org.geworkbench.engine.management.SynchModel
Called by the ComponentRegistry to add a task to this synch model.
addTask(Runnable, Object, Object, Object) - Method in class org.geworkbench.engine.management.Synchronous
 
addToContainer(String, Component, String, Class<?>) - Method in class org.geworkbench.engine.config.GUIFramework
Adds the visualPlugin to the container identified by the name areaName.
addToContainer(String, Component, String, Class) - Method in class org.geworkbench.engine.skin.Skin
 
addToHistory(DSExtendable, String) - Static method in class org.geworkbench.builtin.projects.history.HistoryPanel
 
addToSortkeyMap(Collator, DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
used for sorting
addToTargetInfoMap(double, DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
used for sorting
addTypeToSubscriptionIgnoreSet(Class<?>) - Method in class org.geworkbench.engine.config.PluginDescriptor
 
addVisualAreaInfo(String, VisualPlugin) - Static method in class org.geworkbench.engine.config.PluginRegistry
 
ADJ_FORMART - Static variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
ADJACENCY_MATRIX_FILE_EXTENSIONS - Static variable in class org.geworkbench.parsers.EdgeListFileFormat
 
AdjacencyMatrix - Class in org.geworkbench.bison.datastructure.biocollections
AdjacencyMatrix.
AdjacencyMatrix(String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
AdjacencyMatrix(String, Map<String, String>) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
AdjacencyMatrix(String, Map<String, String>, Map<String, String>) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
AdjacencyMatrix.Edge - Class in org.geworkbench.bison.datastructure.biocollections
 
AdjacencyMatrix.EdgeInfo - Class in org.geworkbench.bison.datastructure.biocollections
 
AdjacencyMatrix.Node - Class in org.geworkbench.bison.datastructure.biocollections
 
AdjacencyMatrix.Node(DSGeneMarker) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
AdjacencyMatrix.Node(AdjacencyMatrix.NodeType, String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
AdjacencyMatrix.Node(AdjacencyMatrix.NodeType, String, int) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
AdjacencyMatrix.Node(AdjacencyMatrix.NodeType, int) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
AdjacencyMatrix.NodeType - Enum in org.geworkbench.bison.datastructure.biocollections
 
AdjacencyMatrixCancelEvent - Class in org.geworkbench.events
The event for communication from CNKB to cytoscape when you want to cancel the drawing of network.
AdjacencyMatrixCancelEvent(AdjacencyMatrix) - Constructor for class org.geworkbench.events.AdjacencyMatrixCancelEvent
 
AdjacencyMatrixDataSet - Class in org.geworkbench.bison.datastructure.biocollections
 
AdjacencyMatrixDataSet(AdjacencyMatrix, double, String, String, DSMicroarraySet) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
AdjacencyMatrixDataSet(double, String, String, DSMicroarraySet, String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
Constructor that takes a filename to create by reading and parsing the file.
AdjacencyMatrixFileFormat - Class in org.geworkbench.parsers
Handles parsing of ARACNe adjacency matrix .txt files.
AdjacencyMatrixFileFormat() - Constructor for class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
Affy3ExpressionAnnotationParser - Class in org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
 
Affy3ExpressionAnnotationParser() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.Affy3ExpressionAnnotationParser
 
AFFY_DETECTION_CALL_FILTER - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
AffyAnnotationParser - Class in org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
Actual parser of affy annotation.
AffyAnnotationParser() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AffyAnnotationParser
 
AffyAnnotationUtil - Class in org.geworkbench.util
 
AffyAnnotationUtil() - Constructor for class org.geworkbench.util.AffyAnnotationUtil
 
AffyFileFormat - Class in org.geworkbench.parsers
Copyright: Copyright (c) 2003 -2004
AffyFileFormat() - Constructor for class org.geworkbench.parsers.AffyFileFormat
Default constructor.
AffyGeneExonStAnnotationParser - Class in org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
 
AffyGeneExonStAnnotationParser() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AffyGeneExonStAnnotationParser
 
AffymetrixParser - Class in org.geworkbench.bison.parsers
Handles the parsing of single array Affymetrix txt files.
AffymetrixParser(List<String>) - Constructor for class org.geworkbench.bison.parsers.AffymetrixParser
Constructor
AffyParseContext - Class in org.geworkbench.bison.parsers
Copyright: Copyright (c) 2003
AffyParseContext() - Constructor for class org.geworkbench.bison.parsers.AffyParseContext
Default Constructor
AffyParseContext(List<String>) - Constructor for class org.geworkbench.bison.parsers.AffyParseContext
Constructor
AffyResource - Class in org.geworkbench.bison.parsers.resources
Extends Resource to allow handling Affy input files.
AffyResource() - Constructor for class org.geworkbench.bison.parsers.resources.AffyResource
 
affyTxtType - Static variable in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
AlgorithmExecutionResults - Class in org.geworkbench.bison.model.analysis
Copyright: Copyright (c) 2003
AlgorithmExecutionResults(boolean, String, Object) - Constructor for class org.geworkbench.bison.model.analysis.AlgorithmExecutionResults
 
ALIGNMENT_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
ALLELIC_FREQUENCY_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
allMarkers() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
allMarkers() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
allowMultipleValues(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Conjugate method for forceUniqueValue.
allowMultipleValues(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
allowMultipleValues(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
allowMultipleValues(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
allowMultipleValues(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
allowMultipleValues(String) - Method in class org.geworkbench.bison.datastructure.properties.CSExtendable
 
allowMultipleValues(String) - Method in interface org.geworkbench.bison.datastructure.properties.DSExtendable
Conjugate method for forceUniqueValue.
Analysis - Interface in org.geworkbench.bison.model.analysis
Copyright: Copyright (c) 2003
ANALYSIS_PLUGIN_ICON - Static variable in class org.geworkbench.engine.EngineIcons
 
AnalysisAbortEvent - Class in org.geworkbench.events
 
AnalysisAbortEvent(AnalysisInvokedEvent) - Constructor for class org.geworkbench.events.AnalysisAbortEvent
 
AnalysisCompleteEvent - Class in org.geworkbench.events
 
AnalysisCompleteEvent(AnalysisInvokedEvent) - Constructor for class org.geworkbench.events.AnalysisCompleteEvent
 
AnalysisInvokedEvent - Class in org.geworkbench.events
 
AnalysisInvokedEvent(Analysis, String) - Constructor for class org.geworkbench.events.AnalysisInvokedEvent
 
AnalysisParameters - Interface in org.geworkbench.bison.model.analysis
Tagging interface for analysis parameter classes.
AnnotationInformationManager - Class in org.geworkbench.util
 
AnnotationInformationManager.AnnotationType - Enum in org.geworkbench.util
 
AnnotationLookupHelper - Class in org.geworkbench.util
 
AnnotationLookupHelper() - Constructor for class org.geworkbench.util.AnnotationLookupHelper
 
AnnotationManager - Class in org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
 
AnnotationManager() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationManager
 
AnnotationParser - Class in org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
Description:This Class is for retrieving probe annotation information from default annotation files provided by Affymetrix.
AnnotationParser() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
AnnotationsEvent - Class in org.geworkbench.events
Braodcast Event to encapsulate Pathway information retrieved from caBIO queries
AnnotationsEvent(String, Pathway) - Constructor for class org.geworkbench.events.AnnotationsEvent
 
APP_SIZE_FILE - Static variable in class org.geworkbench.engine.skin.Skin
 
approveSelection() - Method in class org.geworkbench.util.OWFileChooser
 
APSerializable - Class in org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
 
APSerializable(DSMicroarraySet, WeakHashMap<DSMicroarraySet, String>, WeakHashMap<DSMicroarraySet, Map<String, AnnotationFields>>, WeakHashMap<String, AnnotationInformationManager.AnnotationType>) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.APSerializable
 
AracneResult - Class in org.geworkbench.bison.datastructure.biocollections
 
AracneResult(AdjacencyMatrix, double, String, String, DSMicroarraySet, List<String>) - Constructor for class org.geworkbench.bison.datastructure.biocollections.AracneResult
 
ASCENDING - Static variable in class org.geworkbench.util.QSort
 
aspp - Variable in class org.geworkbench.analysis.AbstractAnalysis
The parameters panel to be use from within the AnalysisPane in order to collect the analysis parameters from the user.
assignClassToLabel(String, String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
assignClassToLabel(String, String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Assigns a class to a label.
Asynchronous - Class in org.geworkbench.engine.management
Simple asynchronous event synch model.
Asynchronous() - Constructor for class org.geworkbench.engine.management.Asynchronous
 
AVAILABLE_SHAPES - Static variable in class org.geworkbench.util.visualproperties.PanelVisualProperties
 
availableCommands - Variable in class org.geworkbench.util.CommandBase
 

B

bar - Variable in class org.geworkbench.util.SplashBitmap
 
BaseException - Exception in org.geworkbench.util
Base exception class for all application exceptions.
BaseException() - Constructor for exception org.geworkbench.util.BaseException
 
BaseException(String) - Constructor for exception org.geworkbench.util.BaseException
 
BaseRuntimeException - Exception in org.geworkbench.util
Base runtime exception class for all application exceptions.
BaseRuntimeException() - Constructor for exception org.geworkbench.util.BaseRuntimeException
 
BaseRuntimeException(String) - Constructor for exception org.geworkbench.util.BaseRuntimeException
 
BaseRuntimeException(String, Throwable) - Constructor for exception org.geworkbench.util.BaseRuntimeException
 
BasicAuthenticator - Class in org.geworkbench.util
Extends Authenticator to allow for user login *
BasicAuthenticator() - Constructor for class org.geworkbench.util.BasicAuthenticator
Creates a new instance of BasicAuthenticator
begin(String, String, Attributes) - Method in class org.geworkbench.engine.config.rules.PluginRule
 
BinaryEncodeDecode - Class in org.geworkbench.util
Title: Binary Encoder Decoder
BinaryEncodeDecode() - Constructor for class org.geworkbench.util.BinaryEncodeDecode
 
BIOASSAY - Static variable in class org.geworkbench.events.CaArrayEvent
 
BIOASSAY - Static variable in class org.geworkbench.events.CaArrayRequestEvent
 
BLAST_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
BlastObj - Class in org.geworkbench.bison.datastructure.bioobjects.sequence
A class to hold information about each individual hit of a Blast database search.
BlastObj(String, String, String, String, int, int, String, int) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
BOUNDED_TYPE - Static variable in class org.geworkbench.util.ProgressBar
Defines a ProgressBar that has bounds and values shown increment from a minimum to a maximum
BOUNDED_TYPE - Static variable in class org.geworkbench.util.ProgressBarT
Defines a ProgressBarT that has bounds and values shown increment from a minimum to a maximum
BOUNDED_TYPE - Static variable in class org.geworkbench.util.ProgressItem
Defines a ProgressBar that has bounds and values shown increment from a minimum to a maximum
BrowserLauncher - Class in org.geworkbench.util
 
BrowserLauncher() - Constructor for class org.geworkbench.util.BrowserLauncher
 
BUSY_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
BUSY_STATIC_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
BusySwingWorker<T,V> - Class in org.geworkbench.util
An extension of the SwingWorker class that knows how to indicate on a panel that it's busy.
BusySwingWorker() - Constructor for class org.geworkbench.util.BusySwingWorker
 

C

CaArray2Experiment - Class in org.geworkbench.builtin.projects.remoteresources.carraydata
 
CaArray2Experiment(String, String, String, String) - Constructor for class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
CaArrayEvent - Class in org.geworkbench.events
 
CaArrayEvent(String, int) - Constructor for class org.geworkbench.events.CaArrayEvent
 
CaArrayFilteringDialog - Class in org.geworkbench.builtin.projects.remoteresources
 
CaArrayFilteringDialog(Frame, String) - Constructor for class org.geworkbench.builtin.projects.remoteresources.CaArrayFilteringDialog
 
CaARRAYPanel - Class in org.geworkbench.builtin.projects.util
 
CaARRAYPanel() - Constructor for class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
CaArrayQueryEvent - Class in org.geworkbench.events
 
CaArrayQueryEvent(String, int, String, String, String) - Constructor for class org.geworkbench.events.CaArrayQueryEvent
 
CaArrayRequestEvent - Class in org.geworkbench.events
 
CaArrayRequestEvent(String, int, String) - Constructor for class org.geworkbench.events.CaArrayRequestEvent
 
CaArrayRequestHybridizationListEvent - Class in org.geworkbench.events
 
CaArrayRequestHybridizationListEvent(String, int, String, String, CaArray2Experiment) - Constructor for class org.geworkbench.events.CaArrayRequestHybridizationListEvent
 
CaArrayReturnHybridizationListEvent - Class in org.geworkbench.events
 
CaArrayReturnHybridizationListEvent(CaArray2Experiment) - Constructor for class org.geworkbench.events.CaArrayReturnHybridizationListEvent
 
CaArraySuccessEvent - Class in org.geworkbench.events
 
CaArraySuccessEvent(int) - Constructor for class org.geworkbench.events.CaArraySuccessEvent
 
cachedir - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
calcPearsonCorrelation(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Pearson correlation between target and TF
calculateRightSideOneTailedP(int, int, int, int) - Method in class org.geworkbench.util.FishersExactTest
Calculate Right-side one-tailed p-value for Fisher's Exact Test.
CANCEL - Static variable in class org.geworkbench.events.CaArrayRequestEvent
 
cancelAllTasks() - Method in class org.geworkbench.util.ProgressDialog
 
cancelledConnectionInfo - Static variable in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
cancelSelection() - Method in class org.geworkbench.util.OWFileChooser
 
CASE - Static variable in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
categoryList - Static variable in class org.geworkbench.engine.ccm.PluginComponent
 
ccmUpdate() - Method in class org.geworkbench.builtin.projects.ProjectPanel
Force refreshing the visible components.
CCMUpdateEvent - Class in org.geworkbench.events
 
CCMUpdateEvent(Class<? extends DSDataSet>) - Constructor for class org.geworkbench.events.CCMUpdateEvent
 
CEL_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
CELFileFormat - Class in org.geworkbench.parsers
Loads PDB structure format.
CELFileFormat() - Constructor for class org.geworkbench.parsers.CELFileFormat
 
CellularNetWorkElementInformation - Class in org.geworkbench.util.network
It is used to save all celllualr Network information related to a specific marker.
CellularNetWorkElementInformation(DSGeneMarker) - Constructor for class org.geworkbench.util.network.CellularNetWorkElementInformation
 
CellularNetworkPreference - Class in org.geworkbench.util.network
 
CellularNetworkPreference(String) - Constructor for class org.geworkbench.util.network.CellularNetworkPreference
 
centerWindow(Window) - Static method in class org.geworkbench.util.Util
 
changeForUpdate() - Method in class org.geworkbench.builtin.projects.RegPanel
 
checkDirExist(String) - Static method in class org.geworkbench.util.FilePathnameUtils
if directory structure doesn't exist - create
checkFormat(File) - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.AffyFileFormat
In this method, we check that: There is a header line exist (keyword "Probe Set Name" exist) number of columns in header line is same as number of columns in data.
checkFormat(File) - Method in class org.geworkbench.parsers.CELFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.EdgeListFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.ExpressionFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.FileFormat
Checks if the contents of the designated file conform to the format.
checkFormat(File) - Method in class org.geworkbench.parsers.GenePixFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.GeoSeriesMatrixParser
 
checkFormat(File) - Method in class org.geworkbench.parsers.MageTabFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.PatternFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.PDBFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.SOFTFileFormat
 
checkFormat(File) - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
checkMarkerFunctions(DSGeneMarker) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.GeneOntologyUtil
 
checkoutstr - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
checkParentDirExist(String) - Static method in class org.geworkbench.util.FilePathnameUtils
if directory structure doesn't exist - create
CheckThreadViolationRepaintManager - Class in org.geworkbench.util
Adapted from the code from http://www.java2s.com/Code/Java/Swing-JFC/ DetectEventDispatchThreadruleviolations.htm $Id: CheckThreadViolationRepaintManager.java 9758 2012-08-01 14:44:40Z zji $
CheckThreadViolationRepaintManager(boolean) - Constructor for class org.geworkbench.util.CheckThreadViolationRepaintManager
 
CheckThreadViolationRepaintManager() - Constructor for class org.geworkbench.util.CheckThreadViolationRepaintManager
 
checkWspdir() - Static method in class org.geworkbench.builtin.projects.RWspHandler
 
children - Variable in class org.geworkbench.bison.model.clusters.AbstractCluster
Holds all children of this Cluster
CHIPPROVIDER - Static variable in class org.geworkbench.builtin.projects.remoteresources.CaArrayFilteringDialog
 
ChoiceField - Class in org.geworkbench.engine.preferences
 
ChoiceField(String, String[]) - Constructor for class org.geworkbench.engine.preferences.ChoiceField
 
chooseMarkersFromSet(String, JTextField) - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
 
chooseMarkersSet(String, DSPanel<DSGeneMarker>) - Static method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
 
CLASS_CASE - Static variable in class org.geworkbench.bison.annotation.CSAnnotationContext
 
CLASS_CONTROL - Static variable in class org.geworkbench.bison.annotation.CSAnnotationContext
 
CLASS_IGNORE - Static variable in class org.geworkbench.bison.annotation.CSAnnotationContext
 
CLASS_TEST - Static variable in class org.geworkbench.bison.annotation.CSAnnotationContext
 
CLASSES_DIR - Static variable in class org.geworkbench.engine.management.ComponentResource
 
CLASSIFIER_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
ClassifierException - Exception in org.geworkbench.util
Used by classifiers to indicate an exception.
ClassifierException(String) - Constructor for exception org.geworkbench.util.ClassifierException
 
classify(float[]) - Method in class org.geworkbench.bison.algorithm.classification.CSClassifier
Runs a classification on the given object.
classify(float[]) - Method in class org.geworkbench.bison.algorithm.classification.CSVisualClassifier
 
ClassSearcher - Class in org.geworkbench.engine.management
Indexes a classpath so that classes can be searched hierarchically according to class structure.
ClassSearcher(URL[]) - Constructor for class org.geworkbench.engine.management.ClassSearcher
 
cleanCache() - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
cleanUpAnnotatioAfterUnload(DSDataSet<? extends DSBioObject>) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
clear() - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
clear() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
Clears the contents of this item list.
clear() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Clears all data from this panel and all sub-panels.
clearAllVisualProperties() - Method in class org.geworkbench.util.visualproperties.PanelVisualPropertiesManager
 
clearCategoryList() - Static method in class org.geworkbench.engine.ccm.PluginComponent
 
clearConfidenceTypes() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
clearFields() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
clearGridCoordinates() - Method in class org.geworkbench.bison.model.clusters.DefaultSOMCluster
Clear the Grid Coordinates
clearGridCoordinates() - Method in interface org.geworkbench.bison.model.clusters.SOMCluster
Clear the grid coordinateds for this cluster.
clearItemsFromLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
clearItemsFromLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Clears all items from a label.
clearMenuItems() - Method in class org.geworkbench.util.CommandBase
 
clearName(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Removes all values associated with the given name.
clearName(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
clearName(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
clearName(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
clearName(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
clearName(String) - Method in class org.geworkbench.bison.datastructure.properties.CSExtendable
 
clearName(String) - Method in interface org.geworkbench.bison.datastructure.properties.DSExtendable
Removes all values associated with the given name.
clearNodeSelections() - Method in class org.geworkbench.builtin.projects.ProjectSelection
Clears the selections and broadcasts the event
clearPoints() - Method in class org.geworkbench.util.ProgressGraph
 
clearSelections() - Method in class org.geworkbench.util.JAutoList
 
clearVisualProperties(Object) - Method in class org.geworkbench.util.visualproperties.PanelVisualPropertiesManager
 
clone() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
Deep clones this context.
clone() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Deep clones this context.
clone() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
clone() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
clone() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
 
clone() - Method in class org.geworkbench.engine.preferences.ChoiceField
 
clone() - Method in class org.geworkbench.engine.preferences.DoubleField
 
clone() - Method in class org.geworkbench.engine.preferences.Field
 
clone() - Method in class org.geworkbench.engine.preferences.FileField
 
clone() - Method in class org.geworkbench.engine.preferences.IntegerField
 
clone() - Method in class org.geworkbench.engine.preferences.TextField
 
Closable - Interface in org.geworkbench.engine.config
Interface to be implemented by all components that need to do something when application is closing.
close() - Method in class org.geworkbench.util.ResultSetlUtil
 
closing() - Method in interface org.geworkbench.engine.config.Closable
save preference data
Cluster - Interface in org.geworkbench.bison.model.clusters
Copyright: Copyright (c) 2003
ClusteringAnalysis - Interface in org.geworkbench.bison.model.analysis
Tagging interface for clustering analysis algorithms.
ClusterStatistics - Class in org.geworkbench.util.associationdiscovery.statistics
Copyright: Copyright (c) 2002
ClusterStatistics() - Constructor for class org.geworkbench.util.associationdiscovery.statistics.ClusterStatistics
 
colanno - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
colgroup - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
colhist - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
collock - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
colnames - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
ColorContext - Interface in org.geworkbench.bison.util.colorcontext
Decides what color should be used when dispaying a color mosaic representation of a marker value.
ColorScale - Class in org.geworkbench.util
Color scale shown for heat-map type display.
ColorScale(Color, Color, Color) - Constructor for class org.geworkbench.util.ColorScale
Constructor with three color points to control the gradient along the scale.
colprofile - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
columnNames - Static variable in class org.geworkbench.bison.parsers.AffyParseContext
List of possible column names from input file that can be parsed
columnOrder - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
 
coluser - Static variable in class org.geworkbench.builtin.projects.DownloadClient
 
Combinations - Class in org.geworkbench.util
 
Combinations() - Constructor for class org.geworkbench.util.Combinations
 
COMMAND_AREA - Static variable in class org.geworkbench.engine.config.GUIFramework
 
COMMAND_AREA_ICON - Static variable in class org.geworkbench.engine.EngineIcons
 
CommandBase - Class in org.geworkbench.util
Base class for command panels: AnalysisPanel, FilteringPanel, NormalizationPanel
CommandBase(String) - Constructor for class org.geworkbench.util.CommandBase
 
COMMENTS - Static variable in class org.geworkbench.parsers.EdgeListFileFormat
 
CommentsPanel - Class in org.geworkbench.builtin.projects.comments
Copyright: Copyright (c) 2003
CommentsPanel() - Constructor for class org.geworkbench.builtin.projects.comments.CommentsPanel
 
compare(AbstractAnalysis, AbstractAnalysis) - Method in class org.geworkbench.analysis.AbstractAnalysisLabelComparator
 
compare(DSMatchedSeqPattern, DSMatchedSeqPattern) - Method in class org.geworkbench.util.patterns.PatternSorter
 
compareTo(IdeaGLoc) - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
compareTo(IdeaNode) - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
compareTo(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
Implementation of the Comparable interface.
compareTo(CSAffyMarkerValue) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
compareTo(DSMarkerValue) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue
 
compareTo(DSMarkerValue) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
compareTo(HierCluster) - Method in class org.geworkbench.bison.model.clusters.DefaultHierCluster
Comparable method that compares this Cluster to another Hierarchical CLuster node.
compareTo(CaArray2Experiment) - Method in class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
compareTo(Object) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
compareTo(PluginDescriptor) - Method in class org.geworkbench.engine.config.PluginDescriptor
 
compareTo(PatternLocations) - Method in class org.geworkbench.util.patterns.PatternLocations
 
compatibilityLabel - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
 
COMPONENT_DESCRIPTOR_EXTENSION - Static variable in class org.geworkbench.engine.config.rules.PluginObject
 
ComponentClassLoader - Class in org.geworkbench.engine.management
A classloader that allows class definitions in the component to override those of the parent.
ComponentClassLoader(URL[], ComponentResource) - Constructor for class org.geworkbench.engine.management.ComponentClassLoader
 
ComponentClassLoader(URL[], ClassLoader, ComponentResource) - Constructor for class org.geworkbench.engine.management.ComponentClassLoader
 
ComponentConfigurationManager - Class in org.geworkbench.engine.ccm
Manages the dynamic loading and removal of components.
ComponentConfigurationManager2 - Class in org.geworkbench.engine.ccm
Manages the dynamic loading and removal of components.
ComponentConfigurationManagerMenu - Class in org.geworkbench.engine.ccm
A menu for the Component Configuration Manager
ComponentConfigurationManagerMenu() - Constructor for class org.geworkbench.engine.ccm.ComponentConfigurationManagerMenu
 
ComponentConfigurationManagerWindow - Class in org.geworkbench.engine.ccm
This is the main menu for the Component Configuration Manager.
ComponentConfigurationManagerWindow2 - Class in org.geworkbench.engine.ccm
This is a shadow class for ComponentConfigurationManagerWindow to support the component upgrade feature.
ComponentMetadata - Class in org.geworkbench.engine.config
Metadata for a component, such as common name, version, description, etc.
ComponentMetadata(Class<?>, String) - Constructor for class org.geworkbench.engine.config.ComponentMetadata
 
ComponentObjectInputStream - Class in org.geworkbench.engine.management
An object input stream that can load objects using a specific classloader (such as a component's classloader).
ComponentObjectInputStream(InputStream, ClassLoader) - Constructor for class org.geworkbench.engine.management.ComponentObjectInputStream
 
ComponentRegistry - Class in org.geworkbench.engine.management
Component registry implementation.
ComponentResource - Class in org.geworkbench.engine.management
Represents a component (or set of components), their configuration, and required libraries.
ComponentResource(String, boolean) - Constructor for class org.geworkbench.engine.management.ComponentResource
Creates a new component resource rooted in the given directory.
ComponentResource(URLClassLoader) - Constructor for class org.geworkbench.engine.management.ComponentResource
Use this to create the component resource for the built-in components only.
computeSignal() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
Calculate the signal value from the channel values.
computeSignal() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSGenepixMarkerValue
 
CONF_DIR - Static variable in class org.geworkbench.engine.management.ComponentResource
 
confidence - Variable in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
Positive values are normal, negative values are masked.
confirmLoading(String, String) - Method in class org.geworkbench.builtin.projects.WorkspaceHandler
 
contains(Object) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
containsObject(T) - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
containsSupport(CSMatchedPattern<T, R>) - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
contentsChanged(ListDataEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
CONTROL - Static variable in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
convertToDSGeneMarker(List<MindyGeneMarker>) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
convertToHierCluster(Class<?>) - Method in class org.geworkbench.bison.model.clusters.NonRecursiveClusterSet
Create a HierCluster instance from this NonRecursiveClusterSet.
convertToMindyGeneMarker(List<DSGeneMarker>) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
copyFile(InputStream, File) - Static method in class org.geworkbench.util.Util
 
copyValueFrom(Field) - Method in class org.geworkbench.engine.preferences.ChoiceField
 
copyValueFrom(Field) - Method in class org.geworkbench.engine.preferences.DoubleField
 
copyValueFrom(Field) - Method in class org.geworkbench.engine.preferences.Field
 
copyValueFrom(Field) - Method in class org.geworkbench.engine.preferences.FileField
 
copyValueFrom(Field) - Method in class org.geworkbench.engine.preferences.IntegerField
 
copyValueFrom(Field) - Method in class org.geworkbench.engine.preferences.TextField
 
correctMaps() - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
count - Variable in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics
 
countMissing(int) - Method in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
create(int) - Static method in class org.geworkbench.util.ProgressBar
Factory method to create one of the two above defined ProgressBar types
create(int) - Static method in class org.geworkbench.util.ProgressBarT
Factory method to create one of the two above defined ProgressBarT types
create(int) - Static method in class org.geworkbench.util.ProgressDialog
 
createAdjFileFilter() - Static method in class org.geworkbench.builtin.projects.SaveFileFilterFactory
 
createArrayForMindyRun(DSMicroarraySet, DSPanel<DSMicroarray>) - Static method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
createComponent(Class<T>, PluginDescriptor) - Method in class org.geworkbench.engine.management.ComponentRegistry
Creates the component, registering its @Subscribe and @Publish methods.
createConnectonInfo(String, int, String, String) - Static method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
createContext(DSItemList<T>, String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
createContext(DSItemList<T>, String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContextManager
Creates a new context, replacing an existing context if one exists for the same item list and name.
createCsvFileFilter() - Static method in class org.geworkbench.builtin.projects.SaveFileFilterFactory
 
createDSMicroarraySet() - Method in class org.geworkbench.parsers.EfficientMicroarraySet
 
createFASTAfile(File) - Static method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
createGUI(String) - Method in class org.geworkbench.engine.config.rules.GUIWindowObject
 
createHistory() - Method in class org.geworkbench.analysis.AbstractAnalysis
 
createImageIcon(String) - Static method in class org.geworkbench.util.Util
 
createNewInstance(String[]) - Static method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
createPlugin(String, String, String, String) - Method in class org.geworkbench.engine.config.rules.PluginObject
Creates a new plugin in and adds it to the PluginRegistry.
createProgressBar(String, String) - Static method in class org.geworkbench.util.Util
 
createProgressBar(String) - Static method in class org.geworkbench.util.Util
 
createSifFileFilter() - Static method in class org.geworkbench.builtin.projects.SaveFileFilterFactory
 
criterionOption - Variable in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
CSAffyMarkerValue - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
Implementation of AffyMarkerValue.
CSAffyMarkerValue() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
CSAffyMarkerValue(AffyParseContext) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
Constructs a CSAffyMarkerValue object from the contents of the AffyParseContext argument.
CSAlignmentResultSet - Class in org.geworkbench.bison.datastructure.bioobjects.sequence
 
CSAlignmentResultSet(String, List<Vector<BlastObj>>, String, DSSequenceSet<? extends DSSequence>, DSSequenceSet<? extends DSSequence>) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
 
CSAncillaryDataSet<T extends DSBioObject> - Class in org.geworkbench.bison.datastructure.biocollections
 
CSAncillaryDataSet(DSDataSet<T>, String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet
 
CSAnnotationContext<T extends DSNamed> - Class in org.geworkbench.bison.annotation
 
CSAnnotationContext(String, DSItemList<T>) - Constructor for class org.geworkbench.bison.annotation.CSAnnotationContext
 
CSAnnotationContextManager - Class in org.geworkbench.bison.annotation
 
CSAnnotationContextManager.SerializableContexts - Class in org.geworkbench.bison.annotation
 
CSAnnotPanel<T extends DSNamed,U extends java.lang.Comparable<U>> - Class in org.geworkbench.bison.datastructure.complex.panels
Title: Bioworks
CSAnnotPanel(String) - Constructor for class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
CSAnovaResultSet<T extends DSGeneMarker> - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSAnovaResultSet(DSMicroarraySetView<? extends DSGeneMarker, ? extends DSMicroarray>, String, String[], double, String[], double[][]) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
CSClassifier - Class in org.geworkbench.bison.algorithm.classification
Implementing classifiers are able to run classifications on objects.
CSClassifier(DSDataSet<?>, String, String[]) - Constructor for class org.geworkbench.bison.algorithm.classification.CSClassifier
 
CSDataSet<T extends DSBioObject> - Class in org.geworkbench.bison.datastructure.biocollections
An abstract implementation of DSDataSet.
CSDataSet() - Constructor for class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Creates a new data set.
CSDemandResultSet - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSDemandResultSet(DSDataSet<DSMicroarray>, String, Object[][], Object[][], Object[][]) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSDemandResultSet
 
CSExpressionMarker - Class in org.geworkbench.bison.datastructure.bioobjects.markers
Copyright: Copyright (c) 2002
CSExpressionMarker() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
CSExpressionMarker(int) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
CSExpressionMarkerValue - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
Title: Plug And Play
CSExpressionMarkerValue() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue
 
CSExpressionMarkerValue(float) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue
Constructor
CSExpressionMarkerValue(CSExpressionMarkerValue) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue
Constructor
CSExtendable - Class in org.geworkbench.bison.datastructure.properties
Copyright: Copyright (c) 2003
CSExtendable() - Constructor for class org.geworkbench.bison.datastructure.properties.CSExtendable
 
CSGeneMarker - Class in org.geworkbench.bison.datastructure.bioobjects.markers
Title: Bioworks
CSGeneMarker() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
CSGeneMarker(String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
CSGenepixMarkerValue - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
Implementation of GenepixMarkerValue.
CSGenepixMarkerValue(double) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
CSGenepixMarkerValue(CSGenepixMarkerValue) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
CSGenepixMarkerValue(GenepixParseContext) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
Constructs a GenepixMarkerValue object from the contents of the GenepixParseContext argument.
CSGenepixMarkerValue.ComputeSignalMethod - Enum in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSGSEAResultDataSet - Class in org.geworkbench.bison.datastructure.biocollections.gsea
Created by IntelliJ IDEA.
CSGSEAResultDataSet(DSDataSet<? extends DSMicroarray>, String, String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.gsea.CSGSEAResultDataSet
 
CSHierClusterDataSet - Class in org.geworkbench.bison.model.clusters
 
CSHierClusterDataSet(HierCluster[], HierCluster[], boolean, String, DSDataSetView) - Constructor for class org.geworkbench.bison.model.clusters.CSHierClusterDataSet
 
CSItemList<T extends DSNamed> - Class in org.geworkbench.bison.datastructure.complex.panels
A default DSItemList implementation that is backed by an ArrayList and a HashMap.
CSItemList() - Constructor for class org.geworkbench.bison.datastructure.complex.panels.CSItemList
 
CSMarkerValue - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
Title: Plug And Play Framework
CSMarkerValue() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
Default Constructor
CSMarkerValue(CSMarkerValue) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
CSMarkerVector - Class in org.geworkbench.bison.datastructure.biocollections
Copyright: Copyright (c) 2003 -2004
CSMarkerVector() - Constructor for class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
CSMasterRegulatorResultSet<T extends DSGeneMarker> - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSMasterRegulatorResultSet(DSMicroarraySet, String, int) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
CSMasterRegulatorTableResultSet - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSMasterRegulatorTableResultSet(DSMicroarraySet, String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorTableResultSet
 
CSMatchedPattern<T extends DSSequential,R> - Class in org.geworkbench.bison.datastructure.complex.pattern
Title: Bioworks
CSMatchedPattern() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
CSMatchedSeqPattern - Class in org.geworkbench.util.patterns
 
CSMatchedSeqPattern(DSSequenceSet<DSSequence>) - Constructor for class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
CSMatchedSeqPattern(String) - Constructor for class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
CSMatrixReduceExperiment - Class in org.geworkbench.bison.datastructure.complex.pattern.matrix
 
CSMatrixReduceExperiment() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
CSMatrixReduceExperiment(double, double, double, String, String) - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
CSMatrixReduceSet - Class in org.geworkbench.bison.datastructure.complex.pattern.matrix
 
CSMatrixReduceSet(DSDataSet, String) - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceSet
 
CSMicroarray - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSMicroarray(int) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
CSMicroarray(int, int, String, int) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
CSMicroarraySet - Class in org.geworkbench.bison.datastructure.biocollections.microarrays
Title: caWorkbench
CSMicroarraySet() - Constructor for class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
CSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> - Class in org.geworkbench.bison.datastructure.biocollections.views
View of microarray dataset for a given marker subset and a given microarray subset.
CSMicroarraySetView(DSMicroarraySet) - Constructor for class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
CSPanel<T extends DSNamed> - Class in org.geworkbench.bison.datastructure.complex.panels
This class has a really odd design.
CSPanel() - Constructor for class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Constructs a new CSPanel.
CSPanel(String) - Constructor for class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Constructs a new CSPanel with the specified label.
CSPanel(String, String) - Constructor for class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Constructs a new CSPanel with the specified label and sublabel.
CSPanel(DSPanel<T>) - Constructor for class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Creates a CSPanel from an existing panel.
CSPatternMatch<T,R> - Class in org.geworkbench.bison.datastructure.complex.pattern
Title: Bioworks
CSPatternMatch() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.CSPatternMatch
 
CSPatternMatch(T) - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.CSPatternMatch
 
CSPCADataSet - Class in org.geworkbench.bison.datastructure.biocollections.pca
 
CSPCADataSet(DSDataSet<? extends DSMicroarray>, String, String, int, float[][], HashMap<Integer, Double>, HashMap<Integer, List<String>>, HashMap<Integer, String>) - Constructor for class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
 
CSPositionSpecificAffinityMatrix - Class in org.geworkbench.bison.datastructure.complex.pattern.matrix
 
CSPositionSpecificAffinityMatrix() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
CSProbeIntensityArray - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
Stores Probe Intensities as loaded from a CEL file.
CSProbeIntensityArray(DSDataSet<DSBioObject>, String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSProbeIntensityArray
 
CSProbeIntensityArray(DSDataSet<DSBioObject>, String, String, float[][]) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSProbeIntensityArray
 
CSProteinStructure - Class in org.geworkbench.bison.datastructure.bioobjects.structure
 
CSProteinStructure(DSDataSet<DSBioObject>, String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure
 
CSPValued - Class in org.geworkbench.bison.datastructure.complex.pattern.matrix
Title: Bioworks
CSPValued() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPValued
 
CSSeqCmplxRegistration - Class in org.geworkbench.bison.datastructure.complex.pattern.sequence
Title: Bioworks
CSSeqCmplxRegistration() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqCmplxRegistration
 
CSSeqPatternMatch - Class in org.geworkbench.bison.datastructure.complex.pattern.sequence
 
CSSeqPatternMatch() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqPatternMatch
 
CSSeqPatternMatch(DSSequence) - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqPatternMatch
 
CSSeqRegistration - Class in org.geworkbench.bison.datastructure.complex.pattern.sequence
Title: Bioworks
CSSeqRegistration() - Constructor for class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqRegistration
 
CSSequence - Class in org.geworkbench.bison.datastructure.bioobjects.sequence
Title:
CSSequence() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
CSSequence(String, String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
CSSequenceSet<T extends DSSequence> - Class in org.geworkbench.bison.datastructure.biocollections.sequences
 
CSSequenceSet() - Constructor for class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
CSSequentialItemList<T extends DSSequential> - Class in org.geworkbench.bison.datastructure.complex.panels
An item list that maintains a list of items in which each item is aware of its own position in the list.
CSSequentialItemList() - Constructor for class org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList
Create a new CSSequentialItemList.
CSSignificanceResultSet<T extends DSGeneMarker> - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSSignificanceResultSet(DSMicroarraySet, String, String[], String[], double) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
CSSOMClusterDataSet - Class in org.geworkbench.bison.model.clusters
 
CSSOMClusterDataSet(SOMCluster[][], String, DSDataSetView) - Constructor for class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
CSTTestResultSet<T extends DSGeneMarker> - Class in org.geworkbench.bison.datastructure.bioobjects.microarray
 
CSTTestResultSet(DSMicroarraySet, String, String[], String[], double, boolean) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.microarray.CSTTestResultSet
 
CSUnigene - Class in org.geworkbench.bison.datastructure.properties
Title: Bioworks
CSUnigene() - Constructor for class org.geworkbench.bison.datastructure.properties.CSUnigene
 
CsvFileFilter - Class in org.geworkbench.util
 
CsvFileFilter() - Constructor for class org.geworkbench.util.CsvFileFilter
 
CSVisualClassifier - Class in org.geworkbench.bison.algorithm.classification
This class capture the state that represent a VisualGPClassifier object, or just enough to reproduce a VisualGPClassifier object.
CSVisualClassifier(DSDataSet<?>, String, String[], byte[], List<String>, DSPanel<DSMicroarray>, DSPanel<DSMicroarray>) - Constructor for class org.geworkbench.bison.algorithm.classification.CSVisualClassifier
 

D

data - Variable in class org.geworkbench.builtin.projects.RWspHelper.DetailTableModel
 
dataSet - Variable in class org.geworkbench.events.ProjectNodeRenamedEvent
 
DataSetFileFormat - Class in org.geworkbench.parsers
Title: Sequence and Pattern Plugin
DataSetFileFormat() - Constructor for class org.geworkbench.parsers.DataSetFileFormat
 
datasetHistory - Variable in class org.geworkbench.builtin.projects.history.HistoryPanel
 
DataSetNode - Class in org.geworkbench.builtin.projects
Title: Gene Expression Analysis Toolkit
dataSetProperties - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
 
DataSetSaveNode - Class in org.geworkbench.builtin.projects
A representation of a node for saving to disk.
DataSetSaveNode() - Constructor for class org.geworkbench.builtin.projects.DataSetSaveNode
 
DataSetSaveNode(DSDataSet<? extends DSBioObject>) - Constructor for class org.geworkbench.builtin.projects.DataSetSaveNode
 
DataSetSubNode - Class in org.geworkbench.builtin.projects
Title: Gene Expression Analysis Toolkit
DataSetSubNode(DSAncillaryDataSet) - Constructor for class org.geworkbench.builtin.projects.DataSetSubNode
 
DATASUBSET_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
DataTypeUtils - Class in org.geworkbench.util
 
DataTypeUtils() - Constructor for class org.geworkbench.util.DataTypeUtils
 
deactivateLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
deactivateLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Sets a label's active status to false.
decodeUnsignedInt32(byte[], int, int) - Static method in class org.geworkbench.util.BinaryEncodeDecode
Decode byte array into an int arrray
decodeUnsignedInt32(byte[], int) - Static method in class org.geworkbench.util.BinaryEncodeDecode
 
deepCopy() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
deepCopy() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
deepCopy() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
Make a deep copy of this marker.
deepCopy() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.SequenceMarker
 
deepCopy() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
deepCopy() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue
 
deepCopy() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
deepCopy() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
deepCopy() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
Make a deep copy of the measurements associated with this spot.
deepCopy() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
 
deepCopy() - Method in class org.geworkbench.bison.parsers.AffyParseContext
Generates a deep copy of this parse context
DEFAULT_CONTEXT_NAME - Static variable in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
DEFAULT_OBO_FILE - Static variable in class org.geworkbench.builtin.projects.OboSourcePreference
 
DEFAULT_PAINTS - Static variable in class org.geworkbench.util.visualproperties.PanelVisualProperties
 
DEFAULT_R_LIBPATH - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
DEFAULT_R_LOCATION - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
DEFAULT_RCM_URL - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
DEFAULT_REMOTE_LOCATION - Static variable in class org.geworkbench.builtin.projects.OboSourcePreference
 
DEFAULT_RWSP_URL - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
DEFAULT_TEXT_EDITOR - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
DEFAULT_TEXT_EDITOR_MAC - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
DefaultColorContext - Class in org.geworkbench.bison.util.colorcontext
Default implementation of a color context.
DefaultColorContext() - Constructor for class org.geworkbench.bison.util.colorcontext.DefaultColorContext
 
DefaultHierCluster - Class in org.geworkbench.bison.model.clusters

Generalization of the Cluster contract that encapsulates functionality to handle Clusters generated from the Hierarchical Clustering analysis method

DefaultHierCluster() - Constructor for class org.geworkbench.bison.model.clusters.DefaultHierCluster
 
DefaultIconAssignments - Class in org.geworkbench.builtin.projects
 
DefaultIconAssignments() - Constructor for class org.geworkbench.builtin.projects.DefaultIconAssignments
 
DefaultSOMCluster - Class in org.geworkbench.bison.model.clusters
Copyright: Copyright (c) 2003
DefaultSOMCluster() - Constructor for class org.geworkbench.bison.model.clusters.DefaultSOMCluster
 
DEFAULTTYPE - Static variable in class org.geworkbench.util.patterns.PatternLocations
 
DEL - Static variable in class org.geworkbench.util.ResultSetlUtil
 
DELETE - Static variable in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
DELETE - Static variable in class org.geworkbench.events.SubpanelChangedEvent
 
deleteDirectory(File) - Static method in class org.geworkbench.util.Util
 
deleteParameters(String) - Method in class org.geworkbench.analysis.AbstractAnalysis
 
deleteParameters(String) - Method in interface org.geworkbench.bison.model.analysis.Analysis
 
deleteRemoteResource(RemoteResource) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
Delete one resource object
deleteRemoteResource(int) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
Delete one resource based on its index position.
deleteRemoteResource(String) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
Delete one resource based on its shortname.
delUserFromWorkspace(String) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
DENDOGRAM_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
DependencyManager - Class in org.geworkbench.engine.ccm
The utility to ask for user's confirmation for load/unload dependent components.
DESCENDING - Static variable in class org.geworkbench.util.QSort
 
description - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Used in the implementation of the Describable interface.
DESCRIPTION - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
description - Variable in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
description - Variable in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
Used in the implementation of the Describable interface.
description - Variable in class org.geworkbench.builtin.projects.ProjectTreeNode
 
deserializeNamedParameterSet(String) - Method in class org.geworkbench.analysis.AbstractAnalysis
Returns the parameters panel populated with the parameter values that where stored under the designated 'name'.
deserializeNamedParameterSetPanel(String) - Method in class org.geworkbench.analysis.AbstractAnalysis
Returns the parameters panel populated with the parameter values that where stored under the designated 'name'.
DETECTION_ABSENT - Static variable in class org.geworkbench.bison.parsers.AffymetrixParser
 
DETECTION_MARGINAL - Static variable in class org.geworkbench.bison.parsers.AffymetrixParser
 
DETECTION_PRESENT - Static variable in class org.geworkbench.bison.parsers.AffymetrixParser
 
DEVIATION_BASED_FILTER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
dirPropertyKey - Variable in class org.geworkbench.builtin.projects.ProjectTreeNode
 
dirty - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
DirtyID - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
disableDoubleBuffering(Component) - Static method in class org.geworkbench.util.PrintUtils
 
disableFocusMenuItems() - Method in class org.geworkbench.engine.config.PluginDescriptor
Invoked when the plugin (which must implement the VisualPlugin interface) looses the keyboard focus.
DISCOVER - Static variable in class org.geworkbench.bison.datastructure.complex.pattern.PatternResult
 
display(LoadDataDialog, String) - Method in class org.geworkbench.builtin.projects.remoteresources.CaArrayFilteringDialog
 
displayPreferencesDialog() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
displaySequenceDB - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
dispose() - Method in class org.geworkbench.util.ProgressBar
Hides the ProgressBar
dispose() - Method in class org.geworkbench.util.ProgressBarT
Hides the ProgressBarT
dispose() - Method in class org.geworkbench.util.ProgressDialog
Hides the ProgressDialog
dispose() - Method in class org.geworkbench.util.ProgressItem
Hides the ProgressBar
DO_NOT_CREATE_VALUE_OBJECT - Static variable in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
Documentation - Annotation Type in org.geworkbench.engine.management
Annotation to provide RUNTIME access to JavaDoc for use with the caSCRIPT mechanism, similar to xdoclethttp://xdoclet.sourceforge.net/xdoclet/index.html functionality
doInBackground() - Method in class org.geworkbench.builtin.projects.RWspHelper.AccessRemoteTask
 
doInBackground() - Method in class org.geworkbench.builtin.projects.RWspHelper.RemoveRemoteTask
 
doInBackground() - Method in class org.geworkbench.builtin.projects.RWspHelper.UploadNewTask
 
doInBackground() - Method in class org.geworkbench.builtin.projects.WorkspaceHandler.OpenTask
 
doInBackground() - Method in class org.geworkbench.builtin.projects.WorkspaceHandler.SaveTask
 
doMergeSets(DSMicroarraySet[]) - Static method in class org.geworkbench.builtin.projects.FileOpenHandler
Merger an array of MSMicroarraySets and create a new dataset node.
done() - Method in class org.geworkbench.builtin.projects.RWspHelper.AccessRemoteTask
 
done() - Method in class org.geworkbench.builtin.projects.RWspHelper.CheckOpenRemoteTask
 
done() - Method in class org.geworkbench.builtin.projects.RWspHelper.CheckReleaseRemoteTask
 
done() - Method in class org.geworkbench.builtin.projects.RWspHelper.CheckUpdateRemoteTask
 
done() - Method in class org.geworkbench.builtin.projects.RWspHelper.RemoveRemoteTask
 
done() - Method in class org.geworkbench.builtin.projects.WorkspaceHandler.OpenTask
 
done() - Method in class org.geworkbench.builtin.projects.WorkspaceHandler.SaveTask
 
doSaveLocal(boolean) - Static method in class org.geworkbench.builtin.projects.RWspHandler
 
DoubleField - Class in org.geworkbench.engine.preferences
 
DoubleField(String) - Constructor for class org.geworkbench.engine.preferences.DoubleField
 
DownloadClient - Class in org.geworkbench.builtin.projects
Client for retrieving remote workspace
DownloadClient() - Constructor for class org.geworkbench.builtin.projects.DownloadClient
 
downloadGEARFromServer(String) - Method in class org.geworkbench.engine.ccm.ComponentConfigurationManager2
 
DSAffyMarkerValue - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
Copyright: Copyright (c) 2003
DSAlignmentResultSet - Interface in org.geworkbench.bison.datastructure.bioobjects.sequence
 
DSAncillaryDataSet<T extends DSBioObject> - Interface in org.geworkbench.bison.datastructure.biocollections
Extends the notion of a data set by adding access to parent dataset.
DSAnnotated - Interface in org.geworkbench.bison.datastructure.properties
 
DSAnnotatedPanel<T extends DSNamed,U> - Interface in org.geworkbench.bison.datastructure.complex.panels
Title: Bioworks
DSAnnotationContext<T extends DSNamed> - Interface in org.geworkbench.bison.annotation
This defines the contract for a context of annotations, labels and classifications for a DSItemList.
DSAnnotationContextManager - Interface in org.geworkbench.bison.annotation
This defines the contract for a manager of contexts for the annotation, labelling and classification of the items of a DSItemList.
DSAnovaResultSet<T extends DSGeneMarker> - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
 
DSBioObject - Interface in org.geworkbench.bison.datastructure.bioobjects
Implementing classes store biological data (such as a sequence or a microarray).
DSClassification<T extends DSNamed> - Interface in org.geworkbench.bison.datastructure.bioobjects
Implementing classifications have the notion of a classification and its associated confidence value (p-value).
DSClusterDataSet - Interface in org.geworkbench.bison.model.clusters
Represents
DSDataSet<T extends DSBioObject> - Interface in org.geworkbench.bison.datastructure.biocollections
Implementing classes store sets of biological data (such as a set of microarrays or sequences).
DSDataSetView<Q extends DSBioObject> - Interface in org.geworkbench.bison.datastructure.biocollections.views
Dataset view only from package org.geworkbench.bison.model.clusters.
DSDemandResultSet - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
 
DSDescribable - Interface in org.geworkbench.bison.datastructure.properties
Copyright: Copyright (c) 2003
DSExtendable - Interface in org.geworkbench.bison.datastructure.properties
Copyright: Copyright (c) 2003
DSGeneMarker - Interface in org.geworkbench.bison.datastructure.bioobjects.markers
This class is used to represent any arbitrary genetic marker, such as an Affy probe, a DNA sequence, etc.
DSGenepixMarkerValue - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
Copyright: Copyright (c) 2003
DSGSEAResultDataSet - Interface in org.geworkbench.bison.datastructure.biocollections.gsea
Created by IntelliJ IDEA.
DSHierClusterDataSet - Interface in org.geworkbench.bison.model.clusters
 
DSIdentifiable - Interface in org.geworkbench.bison.datastructure.properties
Allows the association of an ID with an object.
DSItemList<T extends DSNamed> - Interface in org.geworkbench.bison.datastructure.complex.panels
Specifies a list of DSNamed objects, accessible by label.
DSMarkerValue - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
Model of the data collected for a single spot (feature) on a microarray.
DSMasterRagulatorResultSet<T extends DSGeneMarker> - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
 
DSMasterRegulatorTableResultSet - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
 
DSMatchedPattern<T,R> - Interface in org.geworkbench.bison.datastructure.complex.pattern
Title: Bioworks
DSMatchedSeqPattern - Interface in org.geworkbench.bison.datastructure.complex.pattern.sequence
Title:
DSMatrixReduceExperiment - Interface in org.geworkbench.bison.datastructure.complex.pattern.matrix
 
DSMatrixReduceSet - Interface in org.geworkbench.bison.datastructure.complex.pattern.matrix
 
DSMicroarray - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
The microarray abstraction.
DSMicroarraySet - Interface in org.geworkbench.bison.datastructure.biocollections.microarrays
Defines a generic set of Microarrays.
DSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> - Interface in org.geworkbench.bison.datastructure.biocollections.views
Interface of the view of microarray dataset for a given marker subset and a given microarray subset.
DSMutableMarkerValue - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
Model of mutable behavior of data collected for a single spot (feature) on a microarray.
DSNamed - Interface in org.geworkbench.bison.datastructure.properties
Specifies an object that has a mutable name or label.
DSPanel<T extends DSNamed> - Interface in org.geworkbench.bison.datastructure.complex.panels
Implementing classes are activatable/deactivatable item lists.
DSPatternMatch<T,R> - Interface in org.geworkbench.bison.datastructure.complex.pattern
Title: Bioworks
DSPCADataSet - Interface in org.geworkbench.bison.datastructure.biocollections.pca
 
DSPositionSpecificAffintyMatrix - Interface in org.geworkbench.bison.datastructure.complex.pattern.matrix
Stores a position-specific affinity matrix (for example-- as produced by MatrixREDUCE).
DSProbeIntensityArray - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
User: mhall Date: Mar 13, 2006 Time: 11:43:13 AM
DSProteinStructure - Interface in org.geworkbench.bison.datastructure.bioobjects.structure
User: mhall Date: Mar 13, 2006 Time: 11:43:13 AM
DSPValue - Interface in org.geworkbench.bison.util
Title: Bioworks
DSPValued - Interface in org.geworkbench.bison.datastructure.bioobjects
Implementing classes have a notion of an object and an associated 'confidence' value (p-value) for that object.
DSRangeMarker - Interface in org.geworkbench.bison.datastructure.bioobjects.markers
Title: Plug And Play
DSSeqPatternMatch - Interface in org.geworkbench.bison.datastructure.complex.pattern.sequence
Title: Bioworks
DSSequence - Interface in org.geworkbench.bison.datastructure.bioobjects.sequence
This interface defines a generic sequence.
DSSequenceSet<T extends DSSequence> - Interface in org.geworkbench.bison.datastructure.biocollections.sequences
 
DSSequential - Interface in org.geworkbench.bison.datastructure.properties
Implementing classes are ordered according to an index value, or serial.
DSSignificanceResultSet<T extends DSGeneMarker> - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
 
DSSOMClusterDataSet - Interface in org.geworkbench.bison.model.clusters
 
DSTTestResultSet<T extends DSGeneMarker> - Interface in org.geworkbench.bison.datastructure.bioobjects.microarray
 
DSUnigene - Interface in org.geworkbench.bison.datastructure.properties
 
DynamicMenuItemException - Exception in org.geworkbench.engine.config.rules
Thrown when the menu path specified within some <menu-item> block of the configuration file, is in conflict with the already existing menu structure.
DynamicMenuItemException() - Constructor for exception org.geworkbench.engine.config.rules.DynamicMenuItemException
 
DynamicMenuItemException(String) - Constructor for exception org.geworkbench.engine.config.rules.DynamicMenuItemException
 

E

Edge - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
Edge(String, String) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.Edge
 
EDGE_LIST_FILE_EXTENSIONS - Static variable in class org.geworkbench.parsers.EdgeListFileFormat
 
EdgeList - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
EdgeList() - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeList
 
EdgeList(int) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeList
 
EDGELIST_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
EdgeListDataSet - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
EdgeListDataSet(String, EdgeList, String) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeListDataSet
 
EdgeListFileFormat - Class in org.geworkbench.parsers
 
EdgeListFileFormat() - Constructor for class org.geworkbench.parsers.EdgeListFileFormat
Default constructor.
EdgeListResource - Class in org.geworkbench.bison.parsers.resources
 
EdgeListResource() - Constructor for class org.geworkbench.bison.parsers.resources.EdgeListResource
 
EDIT - Static variable in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
EfficientMicroarraySet - Class in org.geworkbench.parsers
An memory-efficient representation, and the parser of .exp file.
EfficientMicroarraySet(File) - Constructor for class org.geworkbench.parsers.EfficientMicroarraySet
 
elementClicked(int, MouseEvent) - Method in class org.geworkbench.util.JAutoList
Does nothing by default.
elementDoubleClicked(int, MouseEvent) - Method in class org.geworkbench.util.JAutoList
Does nothing by default.
elementRightClicked(int, MouseEvent) - Method in class org.geworkbench.util.JAutoList
Does nothing by default.
enableDoubleBuffering(Component) - Static method in class org.geworkbench.util.PrintUtils
 
enableFocusMenuItems() - Method in class org.geworkbench.engine.config.PluginDescriptor
Invoked when the plugin (which must implement the VisualPlugin interface) gains the keyboard focus.
enableWelcomeScreenMenu(boolean) - Static method in class org.geworkbench.engine.config.rules.GeawConfigObject
 
encodeUnsignedInt32(byte[], int, int) - Static method in class org.geworkbench.util.BinaryEncodeDecode
Encodes a int into a byte array starting at index.
encodeUnsignedInt32(int[]) - Static method in class org.geworkbench.util.BinaryEncodeDecode
Encode an int array into a byte array
encrypt(String) - Static method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
EngineIcons - Class in org.geworkbench.engine
Icons used by the application framework.
EngineIcons() - Constructor for class org.geworkbench.engine.EngineIcons
 
ENTREZ_GENE - Static variable in class org.geworkbench.util.network.InteractionDetail
 
ENTREZ_ID - Static variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
enumerateCombinations(int, int, int[]) - Static method in class org.geworkbench.util.Combinations
 
equals(Object) - Method in class org.geworkbench.analysis.ParameterKey
 
equals(Object) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
equals(Object) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.EdgeInfo
 
equals(Object) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
equals(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
equals(Object) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
Program that use equals() method will automatically use this one instead of the above method.
equals(Object) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
equals(Object) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
equals(DSMarkerValue) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
Tests if two markers are equal
equals(Object) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
Compares two expression markers
equals(Object) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
Tests if two markers are equal
equals(Object) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
 
equals(Object) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
 
equals(Object) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Two panels are equal if their labels are identical.
equals(Object) - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
equals(Object) - Method in class org.geworkbench.builtin.projects.ImageData
 
equals(Object) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
Use shortname as the Key for every object.
equals(Object) - Method in class org.geworkbench.engine.ccm.PluginComponent
 
equals(Object) - Method in class org.geworkbench.engine.config.PluginDescriptor
Definition of equality for PluginDescriptor objects.
equals(Object) - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
equals(Object) - Method in class org.geworkbench.util.network.InteractionDetail
 
equals(Object) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.Edge
 
equals(String, String) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.Edge
 
escapedMenuItemDelimiter - Static variable in class org.geworkbench.engine.config.rules.PluginObject
 
Event - Class in org.geworkbench.engine.config.events
Base class for all application events.
Event(Object) - Constructor for class org.geworkbench.engine.config.events.Event
 
EventException - Exception in org.geworkbench.engine.management
 
EventException() - Constructor for exception org.geworkbench.engine.management.EventException
 
EventException(String) - Constructor for exception org.geworkbench.engine.management.EventException
 
EventException(String, Throwable) - Constructor for exception org.geworkbench.engine.management.EventException
 
EventException(Throwable) - Constructor for exception org.geworkbench.engine.management.EventException
 
evidenceId - Variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.EdgeInfo
 
execute(Object) - Method in interface org.geworkbench.bison.model.analysis.Analysis
invokes the actual service
execute(Object) - Method in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
executeQuery(String, String) - Static method in class org.geworkbench.util.ResultSetlUtil
 
executeQueryWithUserInfo(String, String, String) - Static method in class org.geworkbench.util.ResultSetlUtil
 
executeTask(ProgressTask<?, ?>) - Method in class org.geworkbench.util.ProgressDialog
 
EXHAUSTIVE - Static variable in class org.geworkbench.bison.datastructure.complex.pattern.PatternResult
 
expectedType() - Method in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
expectedTypeName - Variable in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
EXPERIMENT - Static variable in class org.geworkbench.events.CaArrayEvent
 
EXPERIMENT - Static variable in class org.geworkbench.events.CaArrayRequestEvent
 
experimentInfo - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Stores the experiment information (if any) associated with the microarray set.
ExperimentInformationPanel - Class in org.geworkbench.builtin.projects.experimentinformation
This application component is responsible for displaying the exepriment information (if any) associated with a microarray set.
ExperimentInformationPanel() - Constructor for class org.geworkbench.builtin.projects.experimentinformation.ExperimentInformationPanel
 
experimentsLoaded - Variable in class org.geworkbench.builtin.projects.util.CaARRAYPanel
Used to avoid querying the server for all experiments all the time.
expPvalueType - Static variable in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
EXPRESSION_THRESHOLD_FILTER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
ExpressionFileFormat - Class in org.geworkbench.parsers
Title: Sequence and Pattern Plugin
ExpressionFileFormat() - Constructor for class org.geworkbench.parsers.ExpressionFileFormat
 
ExpressionPValueColorContext - Class in org.geworkbench.bison.util.colorcontext
'Relative' color preference.
ExpressionPValueColorContext() - Constructor for class org.geworkbench.bison.util.colorcontext.ExpressionPValueColorContext
 
ExpressionResource - Class in org.geworkbench.parsers
Title: Sequence and Pattern Plugin
ExpressionResource() - Constructor for class org.geworkbench.parsers.ExpressionResource
 
extend - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Used in the implementation of the Extendable interface.
extend - Variable in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
Used in the implementation of the Extendable interface.

F

Field - Class in org.geworkbench.engine.preferences
 
Field(String) - Constructor for class org.geworkbench.engine.preferences.Field
 
file - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
 
FILE_SEPARATOR - Static variable in class org.geworkbench.util.FilePathnameUtils
 
FileField - Class in org.geworkbench.engine.preferences
 
FileField(String) - Constructor for class org.geworkbench.engine.preferences.FileField
 
FileField(String, FileFilter) - Constructor for class org.geworkbench.engine.preferences.FileField
 
FileFormat - Class in org.geworkbench.parsers
Copyright: Copyright (c) 2003
FileFormat() - Constructor for class org.geworkbench.parsers.FileFormat
 
FileFormatHelp - Class in org.geworkbench.parsers
This is a dummy class only for the purpose to facilitate a help topic.
FileFormatHelp() - Constructor for class org.geworkbench.parsers.FileFormatHelp
 
filename - Variable in class org.geworkbench.builtin.projects.WorkspaceHandler.OpenTask
 
filename - Variable in class org.geworkbench.builtin.projects.WorkspaceHandler.SaveTask
 
FileOpenHandler - Class in org.geworkbench.builtin.projects
This class is refactored out of ProjectPanel to handle the file open action, especially tackles the progress bar requirement for multiple files.
FilePathnameUtils - Class in org.geworkbench.util
Part of the API for accessing file system by geworkbench components.
FilePathnameUtils() - Constructor for class org.geworkbench.util.FilePathnameUtils
 
fill(DSMatchedSeqPattern, DSSequenceSet<? extends DSSequence>) - Static method in class org.geworkbench.util.patterns.PatternOperations
 
fillDefaultValues(Map<Serializable, Serializable>) - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
For the parameter fields that are not in the input map, add them as default value
fillPreferences(Class<?>, Preferences) - Method in class org.geworkbench.engine.preferences.PreferencesManager
Fills out the preferences (which should contain default values) with saved preferences values, if there are any.
filter(String, String) - Static method in class org.geworkbench.util.Util
Filters the string by removing those patterns that match the regex.
FilteringAnalysis - Class in org.geworkbench.bison.model.analysis
Abstract class to tag filtering analysis and defines common methods for filtering.
FilteringAnalysis() - Constructor for class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
FilteringAnalysis.CriterionOption - Enum in org.geworkbench.bison.model.analysis
 
FilteringEvent - Class in org.geworkbench.events
Application event thrown in order to communicate the results of a normalization operation.
FilteringEvent(DSMicroarraySet, DSMicroarraySet, String) - Constructor for class org.geworkbench.events.FilteringEvent
 
findNext(boolean) - Method in class org.geworkbench.util.JAutoList
Override to customize the result of the 'next' button being clicked (or ENTER being pressed in text field).
finish() - Static method in class org.geworkbench.engine.config.rules.GeawConfigObject
Executed at the end of parsing.
finish() - Method in class org.geworkbench.engine.config.rules.GeawConfigRule
Overrides the corresponding method from ObjectCreateRule.
finish() - Method in class org.geworkbench.engine.config.rules.PluginObject
Invoked at the end of parsing, for: setting up the coupled event relationships, attach a focus handler to the GUI representation of this plugin.
fireModelChangedEvent() - Method in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
FishersExactTest - Class in org.geworkbench.util
Fisher's Exact Test
FishersExactTest(int) - Constructor for class org.geworkbench.util.FishersExactTest
 
focusGained(FocusEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
focusLost(FocusEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
FOLD_CHANGE_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
FoldChangeResult - Class in org.geworkbench.bison.datastructure.bioobjects
Result of Fold Change analysis.
FoldChangeResult(DSMicroarraySet, String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.FoldChangeResult
 
forceUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Forces that the name be associated with at most one value.
forceUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
forceUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
forceUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
forceUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
forceUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.properties.CSExtendable
 
forceUniqueValue(String) - Method in interface org.geworkbench.bison.datastructure.properties.DSExtendable
Forces that the name be associated with at most one value.
formatDateStandard(Date) - Static method in class org.geworkbench.util.Util
 
formatName - Variable in class org.geworkbench.parsers.FileFormat
The display name of the format.
formatter - Static variable in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue
Formats values to be displayed
fromIndex(int) - Static method in enum org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue.ComputeSignalMethod
 
fromString(String) - Method in class org.geworkbench.engine.preferences.ChoiceField
 
fromString(String) - Method in class org.geworkbench.engine.preferences.DoubleField
 
fromString(String) - Method in class org.geworkbench.engine.preferences.Field
 
fromString(String) - Method in class org.geworkbench.engine.preferences.FileField
 
fromString(String) - Method in class org.geworkbench.engine.preferences.IntegerField
 
fromString(String) - Method in class org.geworkbench.engine.preferences.TextField
 

G

GeawConfigObject - Class in org.geworkbench.engine.config.rules
Describes the object that is pushed on the UILauncher stack when processing the top-most tag, namely the pattern "geaw-config".
GeawConfigObject() - Constructor for class org.geworkbench.engine.config.rules.GeawConfigObject
 
GeawConfigRule - Class in org.geworkbench.engine.config.rules
Invoked to process the top-most tag, namely the pattern "geaw-config".
GeawConfigRule(String) - Constructor for class org.geworkbench.engine.config.rules.GeawConfigRule
 
GENE_NAME - Static variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
GENE_NAME_GENE_ID_DELIMITER - Static variable in class org.geworkbench.parsers.EdgeListFileFormat
 
GENE_ONTOLOGY_BIOLOGICAL_PROCESS - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
GENE_ONTOLOGY_CELLULAR_COMPONENT - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
GENE_ONTOLOGY_MOLECULAR_FUNCTION - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
GENE_SYMBOL - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
GeneChromosomeMatcher - Class in org.geworkbench.util.sequences
Title:
GeneChromosomeMatcher(boolean, String, int, int, String) - Constructor for class org.geworkbench.util.sequences.GeneChromosomeMatcher
 
geneId - Variable in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
geneIds - Variable in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
GeneOntologyTree - Class in org.geworkbench.bison.datastructure.bioobjects.markers.goterms
Represents the Gene Ontology Tree and provides methods to access it.
GeneOntologyUtil - Class in org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
 
GeneOntologyUtil() - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.GeneOntologyUtil
 
GENEPIX_FlAGS_FILTER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
GENEPIX_VALUES - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
GenePixFileFormat - Class in org.geworkbench.parsers
Handles the parsing of Affymetrix .txt files (MAS 5.0).
GenePixFileFormat() - Constructor for class org.geworkbench.parsers.GenePixFileFormat
Default constructor.
genepixGPRType - Static variable in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
GenepixParseContext - Class in org.geworkbench.bison.parsers
Parse context to customize parsing of Genepix files.
GenepixParseContext(List<String>) - Constructor for class org.geworkbench.bison.parsers.GenepixParseContext
Constructor
GenePixParser - Class in org.geworkbench.bison.parsers
A parser of GenePix gpr file.
GenePixParser(List<String>) - Constructor for class org.geworkbench.bison.parsers.GenePixParser
 
GenepixResource - Class in org.geworkbench.bison.parsers.resources
Extends Resource to allow handling Genepix input files.
GenepixResource() - Constructor for class org.geworkbench.bison.parsers.resources.GenepixResource
 
generateHistoryForMaSetView(DSMicroarraySetView<DSGeneMarker, DSMicroarray>) - Method in class org.geworkbench.analysis.AbstractAnalysis
 
generateHistoryStringForGeneralDataSet(DSDataSet) - Method in class org.geworkbench.analysis.AbstractAnalysis
 
GENERIC_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
GeneSelectorEvent - Class in org.geworkbench.events
Title: Sequence and Pattern Plugin
GeneSelectorEvent(DSPanel<DSGeneMarker>) - Constructor for class org.geworkbench.events.GeneSelectorEvent
 
GeneSelectorEvent(DSGeneMarker) - Constructor for class org.geworkbench.events.GeneSelectorEvent
 
GeneTaggedEvent - Class in org.geworkbench.events
Event published from gene panel to update visualization of cytoscape.
GeneTaggedEvent(DSPanel<DSGeneMarker>) - Constructor for class org.geworkbench.events.GeneTaggedEvent
 
GeneTaggedEvent(DSPanel<DSGeneMarker>, int) - Constructor for class org.geworkbench.events.GeneTaggedEvent
 
GeneTaggedEvent(DSPanel<DSGeneMarker>, int, int) - Constructor for class org.geworkbench.events.GeneTaggedEvent
 
GeoSeriesMatrixParser - Class in org.geworkbench.parsers
 
GeoSeriesMatrixParser() - Constructor for class org.geworkbench.parsers.GeoSeriesMatrixParser
 
get(DSGeneMarker, DSMicroarraySet) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
Returns a map with all the edges to geneId.
get(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
get(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
get(String) - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
get(int) - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
get(int) - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
get(int) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
get(String) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
Gets an item by label, using the HashMap.
get(int) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Gets the item from by index.
get(String) - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSItemList
Gets an item by label.
get(int) - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
get(int) - Method in interface org.geworkbench.bison.datastructure.complex.pattern.DSMatchedPattern
 
get(Object) - Method in class org.geworkbench.engine.management.TypeMap
 
get(int) - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
get(String, String) - Method in class org.geworkbench.util.PropertiesMonitor
 
getAccelerator() - Method in class org.geworkbench.engine.config.MenuItemInfo
 
getAcceptors(Class<?>) - Method in class org.geworkbench.engine.management.ComponentRegistry
Gets the acceptors for the given type.
getAccessions() - Method in class org.geworkbench.bison.parsers.AffymetrixParser
Retrives the accession values preprocessed from the input datafile
getAccessions() - Method in class org.geworkbench.bison.parsers.GenePixParser
Retrieve the accession values pre-processed from the input datafile
getAction() - Method in class org.geworkbench.events.ImageSnapshotEvent
 
getActionListener(String) - Method in class org.geworkbench.builtin.projects.ProjectPanel
Interface MenuListener method that returns the appropriate ActionListener to handle MenuEvent generated by MenuItem referenced by menuKey attribute
getActionListener(String) - Method in class org.geworkbench.engine.ccm.ComponentConfigurationManagerMenu
 
getActionListener(String) - Method in interface org.geworkbench.engine.config.MenuListener
Returns an ActionListener that will be listening to a menu item.
getActionListener(String) - Method in class org.geworkbench.engine.config.PreferencesMenu
 
getActionListener(String) - Method in class org.geworkbench.engine.skin.ShortCutMenu
 
getActionListener(String) - Method in class org.geworkbench.util.CommandBase
 
getActivatedItemsForClass(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getActivatedItemsForClass(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves all items for the class that are in activated panels.
getActivators() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getActivators() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getActiveItems() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getActiveItems() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves all items that are associated with at least one active label.
getActiveSequenceSet(DSPanel<? extends DSGeneMarker>) - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getActualFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getActualSource() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getAddr1() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getAddr2() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getAdjacencyMatrix() - Method in class org.geworkbench.events.AdjacencyMatrixCancelEvent
 
getAdjPValue(T) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getAdjPValue(T) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAnovaResultSet
 
getAgg() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getAlignedSeq() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
getAlignmentLength() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
getAllAncestorGoTerms(String) - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getAllContexts(DSItemList<T>) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
getAllContexts(DSItemList<T>) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContextManager
Retrieves an array of all contexts for the given item list.
getAllowedValues() - Method in class org.geworkbench.engine.preferences.ChoiceField
 
getAllTerms() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getAnalysis() - Method in class org.geworkbench.events.AnalysisInvokedEvent
 
getAnalysisName() - Method in class org.geworkbench.analysis.AbstractGridAnalysis
Analyses extending this class will implement this method, setting the name of the service.
getAnalysisType() - Method in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
getAncestors(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
Gets all the ancestor terms for the term with the given ID.
getAncillaryDataSet() - Method in class org.geworkbench.events.ProjectNodeAddedEvent
 
getAncillaryDataSet() - Method in class org.geworkbench.events.ProjectNodePostCompletedEvent
 
getAncillaryDataSet() - Method in class org.geworkbench.events.ProjectNodeRemovedEvent
 
getAnnotatedGenes(int) - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
getAnnotatedGenes(DSMicroarraySet, int) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationManager
 
getAnnotation() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
getAnnotation() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
 
getAnnotationFileName() - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getAnnotationFileName() - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
getAnnotationType() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.Affy3ExpressionAnnotationParser
 
getAnnotationType() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AffyGeneExonStAnnotationParser
 
getApplicationTitle() - Method in class org.geworkbench.engine.skin.Skin
 
getArrayForMindyRun() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
getArraySet() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaData
 
getArraySet() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
getASCII() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.sequence.DSMatchedSeqPattern
 
getASCII() - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
getAscii() - Method in class org.geworkbench.util.patterns.PatternLocations
 
getAsciiLength() - Method in class org.geworkbench.util.patterns.PatternLocations
 
getAssayNameFilter() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getAssayType() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getAttribute(String) - Method in interface org.geworkbench.bison.datastructure.properties.DSAnnotated
 
getAuthor() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getAuthorUrl() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getBase() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getBigDecimal(String) - Method in class org.geworkbench.util.ResultSetlUtil
 
getBigDecimal(int) - Method in class org.geworkbench.util.ResultSetlUtil
 
getBinNumber() - Static method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getBisonParameters() - Method in class org.geworkbench.analysis.AbstractGridAnalysis
This method should be implmented to obtain the user input (which is stored as BISON parameters), convert it to caGrid parameters, and return a map with caGrid parameter values keyed by parameter names.
getBisonReturnType() - Method in class org.geworkbench.analysis.AbstractGridAnalysis
 
getBlastDataSet() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
 
getBlastDataSet() - Method in interface org.geworkbench.bison.datastructure.bioobjects.sequence.DSAlignmentResultSet
 
getBlastedParentDataSet() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
 
getBlastedParentDataSet() - Method in interface org.geworkbench.bison.datastructure.bioobjects.sequence.DSAlignmentResultSet
 
getBonferroni() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getBonferroni() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getBound() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getCaArray2Experiment() - Method in class org.geworkbench.events.CaArrayReturnHybridizationListEvent
 
getCaArrayDisplayPanel() - Method in class org.geworkbench.builtin.projects.LoadDataDialog
 
getCalledFromProgramFlag() - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
getCasePanel() - Method in class org.geworkbench.bison.algorithm.classification.CSVisualClassifier
 
getCasePanel() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getCellLine() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getCenterColor() - Method in class org.geworkbench.util.ColorScale
 
getCh1Bg() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
Gets the Background Value at 635 nm wavelength
getCh1Bg() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSGenepixMarkerValue
Gets the Channel 1 background value
getCh1Fg() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
Gets the Signal Value at 635 nm wavelength
getCh1Fg() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSGenepixMarkerValue
Gets the Channel 1 foreground value
getCh2Bg() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
Gets the Background Value at 532 nm wavelength
getCh2Bg() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSGenepixMarkerValue
Gets the Channel 2 background value
getCh2Fg() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
Gets the Signal Value at 532 nm wavelength
getCh2Fg() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSGenepixMarkerValue
Gets the Channel 2 foreground value
getChains() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure
 
getChains() - Method in interface org.geworkbench.bison.datastructure.bioobjects.structure.DSProteinStructure
 
getChangedGenes() - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
getCheckout() - Method in class org.geworkbench.builtin.projects.SaveTree
 
getChildren(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
Gets all the children terms for the term with the given ID.
getChildren() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
getChildren() - Method in class org.geworkbench.builtin.projects.DataSetSaveNode
 
getChildrenNodes() - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
Gets all the children Cluster nodes of this node
getChildrenNodes() - Method in interface org.geworkbench.bison.model.clusters.Cluster
Returns the children nodes of this node.
getChipType(DSMicroarraySet) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
getChipType() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSProbeIntensityArray
 
getChr() - Method in class org.geworkbench.util.sequences.GeneChromosomeMatcher
 
getChrBand() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getCity() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getClass(int) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getClass(int) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves a class by index.
getClassForItem(T) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getClassForItem(T) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the class for a given item.
getClassForLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getClassForLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the class assigned to a label.
getClassification() - Method in interface org.geworkbench.bison.datastructure.bioobjects.DSClassification
Gets the classification of this object.
getClassifications() - Method in class org.geworkbench.bison.algorithm.classification.CSClassifier
The array of class names that this classifier supports.
getClassifications() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getClassifiedObject() - Method in interface org.geworkbench.bison.datastructure.bioobjects.DSClassification
Gets the object that was classified.
getClassLoader() - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getClassLoader() - Method in class org.geworkbench.engine.management.ComponentResource
 
getClassName() - Method in class org.geworkbench.analysis.ParameterKey
 
getClassSearcher() - Method in class org.geworkbench.engine.management.ComponentResource
Gets the class searcher for the component resource.
getClazz() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getCluster(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 
getCluster(int, int) - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 
getCluster(int) - Method in class org.geworkbench.bison.model.clusters.CSHierClusterDataSet
 
getCluster(int) - Method in class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
getCluster(int, int) - Method in class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
getCluster(int) - Method in interface org.geworkbench.bison.model.clusters.DSClusterDataSet
 
getCluster(int) - Method in interface org.geworkbench.bison.model.clusters.DSHierClusterDataSet
 
getCluster(int, int) - Method in interface org.geworkbench.bison.model.clusters.DSSOMClusterDataSet
 
getClusterBy() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResult
 
getClusters() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 
getClusters() - Method in class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
getClusters() - Method in interface org.geworkbench.bison.model.clusters.DSSOMClusterDataSet
 
getClusterSet() - Method in class org.geworkbench.events.HierClusterModelEvent
 
getCoeff() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getCoeff() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getCoeff() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSMatrixReduceExperiment
 
getCoeff() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getColor() - Method in class org.geworkbench.events.ProgressBarEvent
 
getColor() - Method in class org.geworkbench.util.visualproperties.PanelVisualProperties
 
getColorContextClass() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getColumnClass(int) - Method in class org.geworkbench.builtin.projects.RWspHelper.WspTableModel
 
getColumnCount() - Method in class org.geworkbench.builtin.projects.RWspHelper.DetailTableModel
 
getColumnCount() - Method in class org.geworkbench.util.sequences.PatternTableModel
See javax.swing.table.TableModel
getColumnName(int) - Method in class org.geworkbench.builtin.projects.RWspHelper.DetailTableModel
 
getColumnName(int) - Method in class org.geworkbench.util.sequences.PatternTableModel
See javax.swing.table.TableModel
getColumnNames() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getColumnOrder() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
 
getColumnOrder() - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
 
getColumns() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 
getColumns() - Method in class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
getColumns() - Method in interface org.geworkbench.bison.model.clusters.DSSOMClusterDataSet
 
getColumnsToUse() - Method in class org.geworkbench.bison.parsers.AffyParseContext
Gets the columns to use for parsing
getColumnsToUse() - Method in class org.geworkbench.bison.parsers.GenepixParseContext
Gets the columns to use for parsing
getColumNum(String) - Method in class org.geworkbench.util.ResultSetlUtil
 
getCommandByName(String) - Method in class org.geworkbench.util.CommandBase
 
getCompatibilityLabel() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Gets a string describing the compatibility of this data set.
getCompatibilityLabel() - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
Gets a string describing the compatibility of this data set.
getCompatibilityLabel() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
getCompatibilityLabel
getComponent() - Method in class org.geworkbench.builtin.projects.comments.CommentsPanel
 
getComponent() - Method in class org.geworkbench.builtin.projects.experimentinformation.ExperimentInformationPanel
 
getComponent() - Method in class org.geworkbench.builtin.projects.history.HistoryPanel
 
getComponent() - Method in class org.geworkbench.builtin.projects.InformationPanel
 
getComponent() - Method in class org.geworkbench.builtin.projects.ProjectPanel
Interface VisualPlugin method that returns a Component which is the visual representation of the this plugin.
getComponent() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getComponent() - Method in interface org.geworkbench.engine.config.VisualPlugin
Return the Component that is the visual representation of the implementing plugin.
getComponent() - Method in class org.geworkbench.engine.preferences.PreferencesDialog.FileFieldComponent
 
getComponent() - Method in class org.geworkbench.engine.WelcomeScreen
 
getComponent() - Method in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
getComponent
getComponentConfigurationSettingsDir(String) - Static method in class org.geworkbench.util.FilePathnameUtils
will create absolute path starting with home directory as a root for configuration settings directory
getComponentResource() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getComponentResource() - Method in class org.geworkbench.engine.management.ComponentClassLoader
 
getComponentResourceByName(String) - Method in class org.geworkbench.engine.management.ComponentRegistry
 
getComponentsDirectory() - Static method in class org.geworkbench.engine.config.UILauncher
 
getComponentsList() - Method in class org.geworkbench.engine.management.ComponentRegistry
 
getComponentVector() - Static method in class org.geworkbench.engine.config.PluginRegistry
 
getComputePValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getComputeSignalMethod() - Static method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
getConfidence() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
getConfidence() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
getConfidence() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
A value indicating our confidence in the measured signal.
getConfidenceTypeList() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getConfidenceTypes() - Method in class org.geworkbench.util.network.InteractionDetail
 
getConfidenceValue(int) - Method in class org.geworkbench.util.network.InteractionDetail
 
getConfirmPasswd() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getConfusedData() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
getConn() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getConnection(String) - Static method in class org.geworkbench.util.ResultSetlUtil
 
getConnectionNo() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getConnectProtocal() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
getConnType() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaModule
 
getConsensusSequence() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getConsensusSequence() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getContent() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure
 
getContext(DSItemList<T>, String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
getContext(DSItemList<T>, int) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
getContext(DSItemList<T>, String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContextManager
Gets a context by name for the given item list.
getContext(DSItemList<T>, int) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContextManager
Retrieves a context by index.
getContext() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getContextsForSerialization(DSItemList<T>) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
getControlPanel() - Method in class org.geworkbench.bison.algorithm.classification.CSVisualClassifier
 
getControlPanel() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getCorrelation(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Pearson correlation between the transcription factor and the target gene.
getCount() - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
getCount() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics
Get the count (M#).
getCountSeq() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getCreatedat() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getCriticalPValue() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getCriticalPValue() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getCriticalPValue() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
getCurrentContext(DSItemList<T>) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
getCurrentContext(DSItemList<T>) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContextManager
Retrieves the currently-selected context for the given item list.
getCurrentPassword() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getCurrentPortnumber() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getCurrentProgress() - Method in class org.geworkbench.util.BusySwingWorker
 
getCurrentResourceName() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getCurrentResourceName() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getCurrentURL() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getCurrentUser() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getD() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getData() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaDataSet
 
getData() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getData() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorTableResultSet
 
getData() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRegulatorTableResultSet
 
getData() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getData() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeListDataSet
 
getData() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyDataSet
 
getData() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo
 
getData() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostDataSet
 
getDatabaseID() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
Returns the database name of the hit sequence stored in this BlastObj.
getDataFile(File) - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
getDataFile(File) - Method in class org.geworkbench.parsers.AffyFileFormat
getDataFile
getDataFile(File, String) - Method in class org.geworkbench.parsers.AffyFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.AffyFileFormat
getDataFile
getDataFile(File) - Method in class org.geworkbench.parsers.CELFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.CELFileFormat
getDataFile
getDataFile(File) - Method in class org.geworkbench.parsers.DataSetFileFormat
 
getDataFile(File, String) - Method in class org.geworkbench.parsers.DataSetFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.DataSetFileFormat
 
getDataFile(File) - Method in class org.geworkbench.parsers.EdgeListFileFormat
getDataFile
getDataFile(File[]) - Method in class org.geworkbench.parsers.EdgeListFileFormat
getDataFile
getDataFile(File, String) - Method in class org.geworkbench.parsers.ExpressionFileFormat
 
getDataFile(File) - Method in class org.geworkbench.parsers.ExpressionFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.ExpressionFileFormat
getDataFile
getDataFile(File) - Method in class org.geworkbench.parsers.GenePixFileFormat
getDataFile
getDataFile(File[]) - Method in class org.geworkbench.parsers.GenePixFileFormat
getDataFile
getDataFile(File) - Method in class org.geworkbench.parsers.MageTabFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.MageTabFileFormat
 
getDataFile(File) - Method in class org.geworkbench.parsers.PatternFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.PatternFileFormat
 
getDataFile(File) - Method in class org.geworkbench.parsers.PDBFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.PDBFileFormat
getDataFile
getDataFile(File) - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat
 
getDataFile(File) - Method in class org.geworkbench.parsers.SOFTFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.SOFTFileFormat
 
getDataFile(File) - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
getDataFile(File, String) - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
getDataFile(File[]) - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
getDataFilesDirPath() - Static method in class org.geworkbench.util.FilePathnameUtils
will create absolute path starting with the user current working directory as it is used to read data files that come with geworkbench distribution.
getDataFileSkipAnnotation(File) - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
getDataSet() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getDataSet() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSDataSetView
Get the DSDataSet object underlying this is view
getDataset() - Method in class org.geworkbench.builtin.projects.DataSetNode
 
getDataSet() - Method in class org.geworkbench.builtin.projects.DataSetSaveNode
 
getDataset() - Method in class org.geworkbench.builtin.projects.DataSetSubNode
 
getDataSet() - Method in class org.geworkbench.builtin.projects.ProjectPanel
 
getDataSet() - Method in class org.geworkbench.builtin.projects.ProjectSelection
 
getDataset() - Method in class org.geworkbench.builtin.projects.ProjectTreeNode
 
getDataSet() - Method in class org.geworkbench.events.HistoryEvent
 
getDataSet() - Method in class org.geworkbench.events.PhenotypeSelectorEvent
 
getDataSet() - Method in class org.geworkbench.events.ProjectEvent
 
getDataSet() - Method in class org.geworkbench.events.ProjectNodeAddedEvent
 
getDataSet() - Method in class org.geworkbench.events.ProjectNodeRemovedEvent
 
getDataSet() - Method in class org.geworkbench.events.ProjectNodeRenamedEvent
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSProbeIntensityArray
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.MarkUsResultDataSet
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.PudgeResultSet
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.SkybaseResultSet
 
getDataSetFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.SkyLineResultDataSet
 
getDataSetFile() - Method in class org.geworkbench.builtin.projects.ImageData
 
getDataSetHistory() - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
 
getDataSetName() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
The name of data set.
getDataSetName() - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
The name of data set.
getDataSetName() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getDataSetName() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
getDataSetName
getDataSetName() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternResult
 
getDataSetName() - Method in class org.geworkbench.builtin.projects.ImageData
 
getDataSetName() - Method in class org.geworkbench.events.AnalysisInvokedEvent
 
getDataSetType() - Method in class org.geworkbench.events.CCMUpdateEvent
 
getDataSetView() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 
getDataSetView() - Method in class org.geworkbench.bison.model.clusters.CSHierClusterDataSet
 
getDataSetView() - Method in class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
getDataSetView() - Method in interface org.geworkbench.bison.model.clusters.DSClusterDataSet
 
getDataSize() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
getDataSize() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo
 
getDataSubSet() - Method in class org.geworkbench.builtin.projects.ProjectSelection
 
getDatavisibility() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getDate() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getDbar() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getDbSource() - Method in class org.geworkbench.util.network.InteractionDetail
 
getDefaultClass() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getDefaultClass() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the default class.
getDefaultVisualProperties(int) - Method in class org.geworkbench.util.visualproperties.PanelVisualPropertiesManager
 
getDefinition() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
getDefPath() - Method in class org.geworkbench.util.PropertiesMonitor
 
getDeltaInc() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getDeltaMax() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getDeltaMi() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
getDepth(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
Returns the depth of the term for the given ID.
getDepth() - Method in class org.geworkbench.bison.model.clusters.DefaultHierCluster
Gets the Combinatorial Depth of this Cluster
getDepth() - Method in interface org.geworkbench.bison.model.clusters.HierCluster
Returns the combinatorial depth of this node in the Hierachical cluster tree i.e.
getDescription() - Method in class org.geworkbench.analysis.AbstractAnalysis
 
getDescription() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
getDescription() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Get all available descriptions in the form of an array of strings.
getDescription() - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getDescription() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getDescription() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
getLabel
getDescription() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
Returns the textual description of this Marker
getDescription() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getDescription() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
Returns the description of the hit protein sequence stored in this BlastObj.
getDescription() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
getDescription() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure
 
getDescription() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Gets all descriptions for the panel.
getDescription() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getDescription() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getDescription() - Method in interface org.geworkbench.bison.datastructure.properties.DSDescribable
Get the description..
getDescription() - Method in class org.geworkbench.builtin.projects.DataSetSaveNode
 
getDescription() - Method in class org.geworkbench.builtin.projects.ProjectTreeNode
 
getDescription() - Method in class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
getDescription() - Method in class org.geworkbench.builtin.projects.SaveFileFilterFactory.CsvFileFilter
 
getDescription() - Method in class org.geworkbench.builtin.projects.SaveFileFilterFactory.TabDelimitedFileFilter
 
getDescription() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getDescription() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getDescription() - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat.FASTAFilter
 
getDescription() - Method in class org.geworkbench.util.CsvFileFilter
 
getDescription() - Method in class org.geworkbench.util.ProgressGraph
 
getDescription() - Method in class org.geworkbench.util.sequences.PatFilter
 
getDescriptionSortKey() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyGeneMarker
 
getDescriptorForPlugin(Object) - Method in class org.geworkbench.engine.management.ComponentRegistry
 
getDescriptorForPluginClass(Class<?>) - Method in class org.geworkbench.engine.management.ComponentRegistry
 
getDetailedAlignment() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
getDeviation(T, String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getDeviation(T, String) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAnovaResultSet
 
getDimensionality() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
This method returns the dimensionality of the marker.
getDimensionality() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue
This method returns the dimensionality of the marker.
getDimensionality() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
This method returns the dimensionality of the marker.
getDimensionality() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
This method returns the dimensionality of the marker.
getDir() - Method in class org.geworkbench.engine.management.ComponentResource
 
getDirty() - Method in class org.geworkbench.builtin.projects.SaveTree
 
getDisplaySelectedInteractionTypes() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getDisplayValue() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
getDistribution(List<String>, short, double) - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getDocumentation() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getDouble(String) - Method in class org.geworkbench.util.ResultSetlUtil
 
getDouble(int) - Method in class org.geworkbench.util.ResultSetlUtil
 
getDrug1() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getDrug2() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getDSDataSet() - Method in class org.geworkbench.builtin.projects.PendingTreeNode
 
getdSGeneId() - Method in class org.geworkbench.util.network.InteractionDetail
 
getdSGeneMarker() - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getdSGeneName() - Method in class org.geworkbench.util.network.InteractionDetail
 
getDuration() - Method in class org.geworkbench.util.ProgressBar
Gets time period of animation
getDuration() - Method in class org.geworkbench.util.ProgressBarT
Gets time period of animation
getDuration() - Method in class org.geworkbench.util.ProgressItem
Gets time period of animation
getEdge() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSDemandResultSet
 
getEdge() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSDemandResultSet
 
getEdge(int) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeList
 
getEdges() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getEdges(AdjacencyMatrix.Node) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getEigenValues() - Method in class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
 
getEigenValues() - Method in interface org.geworkbench.bison.datastructure.biocollections.pca.DSPCADataSet
 
getEigenVectors() - Method in class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
 
getEigenVectors() - Method in interface org.geworkbench.bison.datastructure.biocollections.pca.DSPCADataSet
 
getEmail() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getEncodedChars(char[]) - Static method in class org.geworkbench.builtin.projects.RegPanel
Encode clear text char[] to digested String
getEncryptedPassword() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
getEndNode() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.Edge
 
getEndPoint() - Method in class org.geworkbench.util.sequences.GeneChromosomeMatcher
 
getEntrezId(DSMicroarraySet, String) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationManager
 
getErrorMessage() - Method in class org.geworkbench.events.CaArrayEvent
 
getErrorMessage() - Static method in class org.geworkbench.util.ValidationUtils
 
getEvalue() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
Returns the e-value of the alignment of query and protein sequence hit in this BlastObj.
getEvidenceId() - Method in class org.geworkbench.util.network.InteractionDetail
 
getExact() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getExactTokens() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getExperiment() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getExperiment() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getExperiment() - Method in class org.geworkbench.events.CaArrayRequestHybridizationListEvent
 
getExperimentID() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getExperimentID() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getExperimentInfo() - Method in class org.geworkbench.bison.parsers.AffymetrixParser
Returns the experiment execution information as it was found at the preamble of the input file.
getExperimentInformation() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Returns the experiment information associated with the microarray set.
getExperimentInformation() - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
Returns the experiment information associated with the data set.
getExperimentInformation() - Method in class org.geworkbench.builtin.projects.LoadDataDialog
Returns the experiment information for the most recently selected remote file.
getExperimentReferenceId() - Method in class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
getExperiments(ActionEvent) - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getExperiments() - Method in class org.geworkbench.events.CaArrayEvent
 
getExportName(AdjacencyMatrix.Node) - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
getExtension() - Method in class org.geworkbench.builtin.projects.SaveFileFilterFactory.CsvFileFilter
 
getExtension() - Method in class org.geworkbench.builtin.projects.SaveFileFilterFactory.CustomFileFilter
 
getExtension() - Method in class org.geworkbench.builtin.projects.SaveFileFilterFactory.TabDelimitedFileFilter
 
getFASTAFileName() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getFdr() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getFeatureNames() - Method in class org.geworkbench.bison.algorithm.classification.CSVisualClassifier
 
getFeaturesFile() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getField(String) - Method in class org.geworkbench.engine.preferences.Preferences
 
getFields() - Method in class org.geworkbench.engine.preferences.Preferences
 
getFile() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
The underlying file associated with this data set.
getFile() - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
The underlying file associated with this data set.
getFile() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getFile() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
getFile
getFile() - Method in class org.geworkbench.builtin.projects.ImageData
 
getFileExtensions() - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.AffyFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.CELFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.EdgeListFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.ExpressionFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.FileFormat
Return the list of extensions (if any) for the files following this format.
getFileExtensions() - Method in class org.geworkbench.parsers.GenePixFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.MageTabFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.PatternFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.PDBFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.SOFTFileFormat
 
getFileExtensions() - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.AffyFileFormat
Return the FileFilter defined for Affy files.
getFileFilter() - Method in class org.geworkbench.parsers.CELFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.EdgeListFileFormat
Return the FileFilter defined for Edge List files.
getFileFilter() - Method in class org.geworkbench.parsers.ExpressionFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.FileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.GenePixFileFormat
Return the FileFilter defined for Genepix files.
getFileFilter() - Method in class org.geworkbench.parsers.MageTabFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.PatternFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.PDBFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.SOFTFileFormat
 
getFileFilter() - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
getFilename() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaDataSet
 
getFilename() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeListDataSet
 
getFilename() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyDataSet
 
getFilename() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostDataSet
 
getFilter() - Method in class org.geworkbench.engine.preferences.FileField
 
getFilterCrit() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getFilteredDataSize() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
getFilteredMASet() - Method in class org.geworkbench.events.FilteringEvent
Gets the microarraySet that was the result of the filtering operation.
getFilteredStatistics(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
getFirstItemName() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
getFristItem
getFlag() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
getFlag() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSGenepixMarkerValue
Gets the flag value
getFName() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getFold() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getFoldChange(T) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getFoldChange(T) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
getFormatName() - Method in class org.geworkbench.parsers.FileFormat
 
getFrame() - Static method in class org.geworkbench.engine.config.GUIFramework
 
getfreeVariableNames() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getFStatistic(T) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getFStatistic(T) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAnovaResultSet
 
getGene() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getGene1() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
getGene1() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaModule
 
getGene2() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
getGene2() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaModule
 
getGeneDetail(DSMicroarraySet) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationManager
 
getGeneDetail(DSMicroarraySet, String) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationManager
 
getGeneId() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
getGeneId() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
getGeneId() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
Returns a unique identifier that represent this piece of genetic information
getGeneIds() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
getGeneIds() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
getGeneIds() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
return all entrez ID's for this 'marker' (probe set) from annotation file
getGeneIDs(String) - Static method in class org.geworkbench.util.AnnotationLookupHelper
 
getGeneIdToMarkerMapping(DSMicroarraySet) - Static method in class org.geworkbench.util.AnnotationLookupHelper
 
getGeneMarker() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyGeneMarker
 
getGeneName() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
getGeneName() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
 
getGeneNameSortKey(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Gene name CollationKey that is used for sorting
getGeneNameToMarkerIDMapping(DSMicroarraySet) - Static method in class org.geworkbench.util.AnnotationLookupHelper
 
getGeneNameToMarkerMapping(DSMicroarraySet) - Static method in class org.geworkbench.util.AnnotationLookupHelper
 
getGenepixComputationMethod() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getGeneRankingMap() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getGenericMarker() - Method in class org.geworkbench.events.GeneSelectorEvent
 
getGenesInRegulon(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getGenesInRegulon(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getGenesInTargetList(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getGenesInTargetList(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getGeneType() - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getGenomeBuildNumber() - Method in class org.geworkbench.util.sequences.GeneChromosomeMatcher
 
getGlobalConfigurationSettingsDir() - Static method in class org.geworkbench.util.FilePathnameUtils
will create absolute path starting with home directory as a root for configuration settings directory
getGLoc() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaModule
 
getGoc() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getGoCEs() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getGoCHits() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getGocList() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaResultDataSet
 
getGoCNes() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getGoInfoStr() - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getGoTermName(int) - Static method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
return GO term name for a given GO term ID
getGoTermToGene(DSMicroarraySet) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationManager
 
getGridEpr() - Method in class org.geworkbench.builtin.projects.PendingTreeNode
Get underlying GridEndpointReferenceType.
getGridEpr() - Method in class org.geworkbench.events.PendingNodeCancelledEvent
 
getGridEprs() - Method in class org.geworkbench.events.PendingNodeLoadedFromWorkspaceEvent
 
getGroupingN() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getGroupingType() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getGuiWindow() - Static method in class org.geworkbench.engine.config.rules.GeawConfigObject
Return the top level window for the application.
getHeight() - Method in class org.geworkbench.bison.model.clusters.DefaultHierCluster
Gets the Algorithmic Height of this Cluster
getHeight() - Method in interface org.geworkbench.bison.model.clusters.HierCluster
Returns the Height of this node
getHelpMenu() - Static method in class org.geworkbench.engine.config.rules.GeawConfigObject
Returns a handle to the help menu.
getHelpSet() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getHighlightedIndex() - Method in class org.geworkbench.util.JAutoList
 
getHistory(DSExtendable) - Static method in class org.geworkbench.builtin.projects.history.HistoryPanel
 
getHitCount() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
 
getHitCount() - Method in interface org.geworkbench.bison.datastructure.bioobjects.sequence.DSAlignmentResultSet
 
getHosts() - Method in class org.geworkbench.util.PropertiesMonitor
Get the set of hosts.
getHostSelected() - Method in class org.geworkbench.util.PropertiesMonitor
 
getHousekeepingnormalizerSettingsPath() - Static method in class org.geworkbench.util.FilePathnameUtils
 
getHybridizations() - Method in class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
getIcon() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getIcon() - Method in class org.geworkbench.engine.config.MenuItemInfo
 
getID() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
 
getId() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
getID() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getID() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
getID() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
Gets the ID for this object.
getID() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Returns the ID for this panel.
getID() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getID() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getID() - Method in interface org.geworkbench.bison.datastructure.properties.DSIdentifiable
Return the ID of the implementing object.
getID() - Static method in class org.geworkbench.bison.util.RandomNumberGenerator
 
getID() - Method in class org.geworkbench.engine.config.IdentifiableImpl
 
getIDEASettingsPath() - Static method in class org.geworkbench.util.FilePathnameUtils
 
getIdentity() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
getIdForDisplay() - Method in class org.geworkbench.util.patterns.PatternLocations
 
getImage() - Method in class org.geworkbench.events.ImageSnapshotEvent
 
getImageIcon() - Method in class org.geworkbench.builtin.projects.ImageData
 
getInclude() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
Returns whether this BlastObj is included to add to the project.
getIncrement() - Method in class org.geworkbench.util.ProgressBar.IncrementModel
 
getIncrement() - Method in class org.geworkbench.util.ProgressBarT.IncrementModel
 
getIncrement() - Method in class org.geworkbench.util.ProgressItem.IncrementModel
 
getInfo(String, String) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
This method returns required annotation field for a given affymatrix marker ID .
getInfo(DSMicroarraySet, String, String) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
getInformation() - Method in class org.geworkbench.events.FilteringEvent
Gets the information about the filter used
getInfoType() - Method in class org.geworkbench.events.CaArrayEvent
 
getInfoType() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
getInputFile() - Method in class org.geworkbench.bison.parsers.resources.AffyResource
Return the name of the input file from which this resource is generated
getInputFile() - Method in class org.geworkbench.bison.parsers.resources.EdgeListResource
Return the name of the input file from which this resource is generated
getInputFile() - Method in class org.geworkbench.bison.parsers.resources.GenepixResource
Return the name of the input file from which this resource is generated
getInputFileName() - Method in class org.geworkbench.parsers.ExpressionResource
Return the name of the input file from which this resource is generated
getInputFileName() - Method in class org.geworkbench.parsers.sequences.SequenceResource
Return the name of the input file from which this resource is generated
getInputName() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getInstance() - Static method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
getInstance() - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getInstance() - Static method in class org.geworkbench.builtin.projects.OboSourcePreference
 
getInstance() - Static method in class org.geworkbench.builtin.projects.ProjectPanel
 
getInstance() - Static method in class org.geworkbench.engine.ccm.ComponentConfigurationManager
 
getInstance() - Static method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getInstance() - Static method in class org.geworkbench.engine.properties.PropertiesManager
 
getInstance() - Static method in class org.geworkbench.util.AnnotationInformationManager
 
getInstance() - Static method in class org.geworkbench.util.visualproperties.PanelVisualPropertiesManager
 
getInstanceUntilAvailable() - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getInteractionDistribution(String, short, double) - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getInteractionEvidenceMap() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getInteractionGene() - Method in class org.geworkbench.util.network.InteractionDetail
 
getInteractionNum(String) - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getInteractionType() - Method in class org.geworkbench.util.network.InteractionDetail
 
getInteractionTypeMap() - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
getInteractionTypeSifMap() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getInvokeEvent() - Method in class org.geworkbench.events.AnalysisAbortEvent
 
getInvokeEvent() - Method in class org.geworkbench.events.AnalysisCompleteEvent
 
getIsLogNormalized() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getIsLogNormalized() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSTTestResultSet
 
getIsLogNormalized() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
getItemList() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getItemList() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the underlying data set on which this context is based.
getItemPanel() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getItemPanel() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
Assigns a specific item panel selection.
getItems() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
 
getItemsForClass(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getItemsForClass(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves all items for the class.
getItemsWithAllLabels(String...) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getItemsWithAllLabels(String...) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves those items that hold all of the specified labels.
getItemsWithAnyLabel(String...) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getItemsWithAnyLabel(String...) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves all items that hold at least one of the specified labels.
getItemsWithLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getItemsWithLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the items for a label.
getItemsWithoutLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getItemsWithoutLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the items that do not have the specified label.
getIter() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getLabAffliation() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getLabel() - Method in class org.geworkbench.analysis.AbstractAnalysis
 
getLabel(int) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getLabel(int) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves a label by index.
getLabel() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getLabel() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Gets the label for this data set.
getLabel() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getLabel() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
getAccession
getLabel() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getLabel() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
getLabel() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Gets the label for this panel.
getLabel() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
getLabel() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getLabel() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getLabel() - Method in interface org.geworkbench.bison.datastructure.properties.DSNamed
Gets the label for this object.
getLabel() - Method in class org.geworkbench.engine.config.IdentifiableImpl
 
getLabels(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getLabels(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getLabels(int) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
getLabelsForClass(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getLabelsForClass(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves all the labels that have been assigned to a class.
getLabelsForItem(T) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getLabelsForItem(T) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the labels for a given item.
getLabelTree() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getLabelTree() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Gets all labels and the items contained within each.
getLastAnnotationFileName() - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
getLastchange() - Method in class org.geworkbench.builtin.projects.SaveTree
 
getLastDataDirectory() - Static method in class org.geworkbench.builtin.projects.LoadDataDialog
 
getLastDataFormat() - Static method in class org.geworkbench.builtin.projects.LoadDataDialog
 
getLastSavedParameterSetName() - Method in class org.geworkbench.analysis.AbstractAnalysis
 
getLeadingEdge(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorTableResultSet
 
getLeadingEdge(String) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRegulatorTableResultSet
 
getLeafChildren() - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
Gets all the children of this Cluster that are also leaves
getLeafChildren() - Method in interface org.geworkbench.bison.model.clusters.Cluster
Returns only the children nodes that are leafs.
getLeafChildrenCount() - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
Gets the number of children of this Cluster that are also leaves
getLeafChildrenCount() - Method in interface org.geworkbench.bison.model.clusters.Cluster
Returns the number of leaf children for this node.
getLeafChildrenCountMap() - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
 
getLeafChildrenCountMap() - Method in interface org.geworkbench.bison.model.clusters.Cluster
Returns a map of cluster to number of leaf children for that cluster.
getLength() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.sequence.DSMatchedSeqPattern
 
getLength() - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
getLevelTwoIds() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getLicense() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getList() - Method in class org.geworkbench.util.JAutoList
 
getLName() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getLoadByDefault() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getLoc() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getLoCEs() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getLoCHits() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getLockedWorkspaceList(String) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
getLocList() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaResultDataSet
 
getLoCNes() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getLogdata() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getMarker() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
getMarker() - Method in class org.geworkbench.events.MarkerSelectedEvent
 
getMarkerByUniqueIdentifier(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
getMarkerCluster() - Method in class org.geworkbench.events.HierClusterModelEvent
Gets the MarkerHierCluster node resulting from Hierarchical Clustering Analysis representing Genetic Marker clusters
getMarkerCount() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getMarkerCount() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getMarkerInfo() - Method in class org.geworkbench.bison.model.clusters.LeafSOMCluster
Gets the DSMarker contained in this LeafSOMCluster
getMarkerInfo() - Method in class org.geworkbench.bison.model.clusters.MarkerHierCluster
Gets the DSMarker associated with this node
getMarkerList() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getMarkerList() - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
getMarkerLoadOptions() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getMarkerNo() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getMarkerNo() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
Returns the number of features in the chip
getMarkerPanel() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getMarkerPanel() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
Allows to retrieve the marker panel selection
getMarkers() - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getMarkers() - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
get the marker list
getMarkersForGivenGeneId(DSMicroarraySet, String) - Static method in class org.geworkbench.util.AnnotationLookupHelper
 
getMarkersForGivenGeneName(DSMicroarraySet, String) - Static method in class org.geworkbench.util.AnnotationLookupHelper
 
getMarkersToBeRemoved(DSMicroarraySet) - Method in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
getMarkerValue(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getMarkerValue(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getMarkerValue(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
 
getMarkerValue(int) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
 
getMarkerValueColor(DSMarkerValue, DSGeneMarker, float) - Method in interface org.geworkbench.bison.util.colorcontext.ColorContext
 
getMarkerValueColor(DSMarkerValue, DSGeneMarker, float) - Method in class org.geworkbench.bison.util.colorcontext.DefaultColorContext
 
getMarkerValueColor(DSMarkerValue, DSGeneMarker, float) - Method in class org.geworkbench.bison.util.colorcontext.ExpressionPValueColorContext
 
getMarkerValues() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getMarkerValues() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
 
getMArraySet(File) - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
getMArraySet(File) - Method in class org.geworkbench.parsers.AffyFileFormat
 
getMArraySet(File) - Method in class org.geworkbench.parsers.GeoSeriesMatrixParser
 
getMArraySet(File) - Method in class org.geworkbench.parsers.SampleFileParser
 
getMaSet() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResult
 
getMaSet() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getMatchIndex() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getMatchIndex() - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
getMatchingMarkers(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
getMatchingMarkers(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector
 
getMatrix() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
getMatrixReduceExperiments() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceSet
 
getMatrixReduceExperiments() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSMatrixReduceSet
 
getMax() - Method in class org.geworkbench.events.ProgressBarEvent
 
getMAX_INTERACTION_NUMBER() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getMaxColor() - Method in class org.geworkbench.util.ColorScale
 
getMaxColorValue(float) - Method in interface org.geworkbench.bison.util.colorcontext.ColorContext
Returns the color corresponding to the maxiumum value possible at this intensity.
getMaxColorValue(float) - Method in class org.geworkbench.bison.util.colorcontext.DefaultColorContext
 
getMaxColorValue(float) - Method in class org.geworkbench.bison.util.colorcontext.ExpressionPValueColorContext
 
getMaxConfidenceValue(Short) - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getMaxConfidenceValueMap() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getMaxGap() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getMaxHeight() - Method in class org.geworkbench.bison.model.clusters.DefaultHierCluster
Returns the Maximum Algorithmic Height of any Cluster in the Hierarchical Cluster Tree that this Cluster is a part of
getMaxHeight() - Method in interface org.geworkbench.bison.model.clusters.HierCluster
Maximum height that any leaf posseses in the tree
getMaxKer() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getMaxLength() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getMaxLength() - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
getMaxLength() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.sequence.DSMatchedSeqPattern
 
getMaxLength() - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
getMaxPatternNo() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMaxRunTime() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMaxValue() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getMaxValue() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getMean(T, String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getMean(T, String) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAnovaResultSet
 
getMean() - Method in class org.geworkbench.bison.util.Normal
 
getMeanValue(DSGeneMarker, int) - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getMeanValue(DSGeneMarker, int) - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
getMeanValue(T, int) - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getMeanValue(T, int) - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
getMeasurement() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getMedusaCommand() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaData
 
getMenuBar() - Static method in class org.geworkbench.engine.config.rules.GeawConfigObject
Return the menu bar for the top level window of the application.
getMenuInfoList() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getMenuItemInfos() - Method in class org.geworkbench.engine.config.PluginDescriptor
returns the menuitem infos
getMessage() - Method in class org.geworkbench.bison.model.analysis.AlgorithmExecutionResults
Gets any error message provided by the algorithm execution
getMessage() - Method in class org.geworkbench.bison.model.analysis.ParamValidationResults
Get the error message provided (if any).
getMessage() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getMessage() - Method in class org.geworkbench.events.AnnotationsEvent
The message that this Event was constructed with
getMessage() - Method in class org.geworkbench.events.ImageSnapshotEvent
 
getMessage() - Method in class org.geworkbench.events.ProgressBarEvent
 
getMessage() - Method in class org.geworkbench.events.ProjectNodeAddedEvent
 
getMessage() - Method in class org.geworkbench.events.ProjectNodeRenamedEvent
 
getMessage() - Method in class org.geworkbench.events.SingleMicroarrayEvent
 
getMessage() - Method in class org.geworkbench.util.ProgressItem
 
getMi() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
getMicroarray() - Method in class org.geworkbench.bison.model.clusters.MicroarrayHierCluster
Gets the Microarray associated with this node
getMicroarray() - Method in class org.geworkbench.bison.parsers.AffymetrixParser
Returns the microarray produced by reading the input file.
getMicroarray() - Method in class org.geworkbench.bison.parsers.GenePixParser
Returns the microarray produced by reading the input file.
getMicroarray() - Method in class org.geworkbench.events.SingleMicroarrayEvent
 
getMicroarrayCluster() - Method in class org.geworkbench.events.HierClusterModelEvent
Gets the MicroarrayHierCluster node resulting from Hierarchical Clustering Analysis representing Microarray clusters
getMicroarraySet() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getMicroarraySet() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
getMicroarraySet() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getMicroarraySet() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getMicroarraySet() - Method in class org.geworkbench.events.HierClusterModelEvent
Gets the MicroarraySet used for Hierarchical Clustering Analysis
getMicroarrayWithId(String) - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getMiddleColorValue(float) - Method in interface org.geworkbench.bison.util.colorcontext.ColorContext
Returns the color that indicates a value between the minimum and maximum values.
getMiddleColorValue(float) - Method in class org.geworkbench.bison.util.colorcontext.DefaultColorContext
 
getMiddleColorValue(float) - Method in class org.geworkbench.bison.util.colorcontext.ExpressionPValueColorContext
 
getMin() - Method in class org.geworkbench.events.ProgressBarEvent
 
getMinColor() - Method in class org.geworkbench.util.ColorScale
 
getMinColorValue(float) - Method in interface org.geworkbench.bison.util.colorcontext.ColorContext
Returns the color corresponding to the minimum value possible at this intensity.
getMinColorValue(float) - Method in class org.geworkbench.bison.util.colorcontext.DefaultColorContext
 
getMinColorValue(float) - Method in class org.geworkbench.bison.util.colorcontext.ExpressionPValueColorContext
 
getMinGap() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getMinKer() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getMinMax() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSProbeIntensityArray
 
getMinPatternNo() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMinPer100Support() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMinPValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMinSupport() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMinTokens() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMinValue() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getMinValue() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getMinWTokens() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getMode(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getMode(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getMode() - Method in class org.geworkbench.engine.config.MenuItemInfo
 
getMode() - Method in class org.geworkbench.events.SubpanelChangedEvent
 
getModel() - Method in class org.geworkbench.util.JAutoList
 
getModelFileContent() - Method in class org.geworkbench.bison.algorithm.classification.CSVisualClassifier
 
getModelFileContent() - Method in class org.geworkbench.bison.datastructure.biocollections.PredictionModel
 
getModels() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
getModStat() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo
 
getModulator() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyResultRow
Get the modulator in this MINDY result row.
getModulatorInfoMap() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
getModulators() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get the list of mondulators.
getModule() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSDemandResultSet
 
getModule() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSDemandResultSet
 
getModule(String) - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getModuleID(String) - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getModuleList() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaResultDataSet
 
getModules(Class<T>) - Method in class org.geworkbench.engine.management.ComponentRegistry
 
getMover() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics
Get the mover (M+)
getMunder() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics
Get the munder (M-)
getName() - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
 
getName() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getName() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the name of this context.
getName() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
getName() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
getName() - Method in class org.geworkbench.builtin.projects.experimentinformation.ExperimentInformationPanel
 
getName() - Method in class org.geworkbench.builtin.projects.history.HistoryPanel
 
getName() - Method in class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
getName() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getName() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getName() - Method in class org.geworkbench.engine.management.ComponentResource
 
getName() - Method in class org.geworkbench.engine.preferences.Field
 
getName() - Method in class org.geworkbench.util.sequences.GeneChromosomeMatcher
 
getNamedParameterSet(String) - Method in class org.geworkbench.analysis.AbstractAnalysis
Returns the parameter values that were stored (in parameterHash in memory) under the designated name.
getNameMap(String) - Static method in class org.geworkbench.engine.config.PluginRegistry
 
getNamesOfStoredParameterSets() - Method in class org.geworkbench.analysis.AbstractAnalysis
Returns the names of the parameter sets that were saved through a call to saveParameters(String filename).
getNameSortKey() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyGeneMarker
 
getNamespaceIds() - Static method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
getNes() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getNES(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getNES(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getNetworkName() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
getNewMarkerOrder() - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getNewMarkerOrder() - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
getNewName() - Method in class org.geworkbench.events.ProjectNodeRenamedEvent
 
getNode(int) - Method in class org.geworkbench.bison.model.clusters.DefaultHierCluster
Gets a particular child from a known index
getNode(int) - Method in interface org.geworkbench.bison.model.clusters.HierCluster
Return the node at the designated index position.
getNodeList() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaResultDataSet
 
getNodeNumber() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
 
getNodes() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix
Return the starting nodes of all edges.
getNodesCount() - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
Gets the number of children of this Cluster
getNodesCount() - Method in interface org.geworkbench.bison.model.clusters.Cluster
Returns the number of children for this node.
getNodeType() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
getNumberOfClasses() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getNumberOfClasses() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the number of classes in this context.
getNumberOfClusters() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 
getNumberOfClusters() - Method in class org.geworkbench.bison.model.clusters.CSHierClusterDataSet
 
getNumberOfClusters() - Method in class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
getNumberOfClusters() - Method in interface org.geworkbench.bison.model.clusters.DSClusterDataSet
 
getNumberOfContexts(DSItemList<T>) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
getNumberOfContexts(DSItemList<T>) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContextManager
Gets the count of contexts for the given item list.
getNumberOfLabels() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
getNumberOfLabels() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the number of labels in this context.
getNumberOfPages() - Method in class org.geworkbench.util.PrintUtils
 
getNumberOfProperItems() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
 
getNumberOfProperItems() - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Gets the number of proper items in this panel.
getNumberOfRoots() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getNumPCs() - Method in class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
 
getNumPCs() - Method in interface org.geworkbench.bison.datastructure.biocollections.pca.DSPCADataSet
 
getObject(Class<?>) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Gets an object by the provided tag.
getObject(Class<?>) - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
Gets an object by the specified type.
getObject(T) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
getObject(int) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
getObject(int) - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSAnnotatedPanel
 
getObject(T) - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSAnnotatedPanel
 
getObject() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSPatternMatch
 
getObject() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.DSPatternMatch
 
getObject() - Method in class org.geworkbench.events.PhenotypeSelectedEvent
 
getOddRatio(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getOddRatio(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getOffset(int) - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
getOldName() - Method in class org.geworkbench.events.ProjectNodeRenamedEvent
 
getOldPasswd() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getOntologyChildren(int) - Static method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
return list of child IDs for a GO term ID
getOrganism() - Method in class org.geworkbench.bison.datastructure.properties.CSUnigene
 
getOrganism() - Method in interface org.geworkbench.bison.datastructure.properties.DSUnigene
 
getOriginalMASet() - Method in class org.geworkbench.events.FilteringEvent
Gets the microarraySet that was the input to the filtering operation.
getOrigIndx() - Method in class org.geworkbench.util.QSort
 
getOutputMode() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getOutputName() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getOutputPath() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaDataSet
 
getPageFormat(int) - Method in class org.geworkbench.util.PrintUtils
 
getPanel(T) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
getPanel(T) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Get the panel that contains the given item.
getPanel(T) - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Gets the sub-panel that contains the given item.
getPanel() - Method in class org.geworkbench.events.GeneSelectorEvent
 
getPanel() - Method in class org.geworkbench.events.GeneTaggedEvent
 
getPanel() - Method in class org.geworkbench.events.SubpanelChangedEvent
 
getPanelIndex() - Method in class org.geworkbench.events.GeneTaggedEvent
 
getParameterName() - Method in class org.geworkbench.analysis.ParameterKey
 
getParameterPanel() - Method in class org.geworkbench.analysis.AbstractAnalysis
 
getParameterPanel() - Method in interface org.geworkbench.bison.model.analysis.Analysis
returns a GUI for entering analysis-specific parameter values.
getParameters() - Method in class org.geworkbench.analysis.AbstractAnalysis
 
getParameters() - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
Implement this method to let others get current parameters from current parameter panel.
getParameters() - Method in interface org.geworkbench.bison.model.analysis.Analysis
 
getParametersFromPanel() - Method in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
getParent() - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
Gets the Cluster which contains this Cluster as a child.
getParent() - Method in interface org.geworkbench.bison.model.clusters.Cluster
Returns the Cluster node that is the parent of this cluster.
getParentDataSet() - Method in class org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet
 
getParentDataSet() - Method in interface org.geworkbench.bison.datastructure.biocollections.DSAncillaryDataSet
Gets the parent data set for this ancillary data set.
getParentDataSet() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getParentDataSet() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
getParentDataSet() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.PudgeResultSet
 
getParentDataSet() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.SkybaseResultSet
 
getParentNode() - Method in class org.geworkbench.events.ProjectNodePostCompletedEvent
 
getParentPanel() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getParents() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
getParentSequenceSet() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternResult
 
getPasswd() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getPassword() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getPassword() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getPassword() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
getPassword() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
getPassword() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getPassword() - Method in class org.geworkbench.events.CaArrayRequestHybridizationListEvent
 
getPasswordAuthentication() - Method in class org.geworkbench.util.BasicAuthenticator
 
getPath() - Method in class org.geworkbench.engine.config.MenuItemInfo
 
getPathway() - Method in class org.geworkbench.events.AnnotationsEvent
Gets the Pathway object associated with this Event
getPathwayDiagram() - Method in interface org.geworkbench.util.annotation.Pathway
Gets the PathwayDiagram contained in the Pathway instance
getPathwayId() - Method in interface org.geworkbench.util.annotation.Pathway
Gets the Pathway Identifier of the Pathway instance
getPathwayName() - Method in interface org.geworkbench.util.annotation.Pathway
Gets the name of the Pathway contained in this instance
getPattern(int) - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternResult
 
getPattern(int) - Method in class org.geworkbench.util.sequences.PatternTableModel
Get the pattern at the index row.
getPatternColor(int) - Static method in class org.geworkbench.util.patterns.PatternOperations
 
getPatternFound() - Method in class org.geworkbench.events.ProgressChangeEvent
Returns the number of patterns found.
getPatternNo() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternResult
 
getPatternType() - Method in class org.geworkbench.util.patterns.PatternLocations
 
getPercentAligned() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
Returns the percentage of the query that's aligned with protein sequence hit in this BlastObj.
getPercentDone() - Method in class org.geworkbench.events.ProgressBarEvent
 
getPercentVars() - Method in class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
 
getPercentVars() - Method in interface org.geworkbench.bison.datastructure.biocollections.pca.DSPCADataSet
 
getPhoneNumber() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getPlugin() - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getPluginClass() - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getPluginDescriptor(String) - Static method in class org.geworkbench.engine.config.PluginRegistry
 
getPort() - Method in class org.geworkbench.events.CaArrayEvent
 
getPort() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
getPort() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getPort() - Method in class org.geworkbench.events.CaArrayRequestHybridizationListEvent
 
getPort() - Method in class org.geworkbench.util.PropertiesMonitor
 
getPortnumber() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
getPortnumber() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getPosition() - Method in class org.geworkbench.util.patterns.PatternOfflet
 
getPredictionModel() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getPredModelFile() - Method in class org.geworkbench.bison.datastructure.biocollections.PredictionModel
 
getPrefDir() - Method in class org.geworkbench.engine.preferences.PreferencesManager
 
getPreferencesManager() - Static method in class org.geworkbench.engine.preferences.PreferencesManager
 
getPreferredOrder() - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getPreviousResourceName() - Static method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getPrintable(int) - Method in class org.geworkbench.util.PrintUtils
 
getPrintDetails() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getProbe() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
getProbe1() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
getProbe2() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
getProbeIntensities() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSProbeIntensityArray
 
getProgressBarValue() - Method in class org.geworkbench.util.SplashBitmap
Gets the current value of the progress bar in this splash screen.
getProgressItem() - Method in class org.geworkbench.util.ProgressTask
 
getProgressMax() - Method in class org.geworkbench.util.BusySwingWorker
 
getProperItem(int) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
 
getProperItem(int) - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Gets a proper item by index.
getPropertiesMonitor() - Static method in class org.geworkbench.util.PropertiesMonitor
This method returns and instance to a shared PropertiesMonitor object.
getProperty(String) - Method in class org.geworkbench.bison.parsers.AffymetrixParser
Gets property based on experiment information
getProperty(Class<?>, String, String) - Method in class org.geworkbench.engine.properties.PropertiesManager
 
getPsamId() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getPsamId() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSMatrixReduceExperiment
 
getPssmLength() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
getPublicIdentifier() - Method in class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
getPValue() - Method in interface org.geworkbench.bison.datastructure.bioobjects.DSPValued
Get the p-value for this object.
getPvalue() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaResultDataSet
 
getPValue(T) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getPValue(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getPValue(T) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAnovaResultSet
 
getPValue(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getPvalue() - Method in class org.geworkbench.bison.datastructure.bioobjects.SamResultData
 
getPValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
getPValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSPatternMatch
 
getPValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getPValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getPValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPValued
 
getPValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqRegistration
 
getPValue() - Method in interface org.geworkbench.bison.util.DSPValue
 
getPValues() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getQType() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getQuantitationTypes() - Method in class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment
 
getQueries() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
getQueryPairs() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
getRange() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
 
getRange() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSRangeMarker
 
getRank(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getRank(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getRawMarkerData() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getRawMarkerData() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
 
getRCM_URL() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getReader() - Method in class org.geworkbench.bison.parsers.resources.AbstractResource
 
getReader() - Method in interface org.geworkbench.bison.parsers.resources.Resource
Return the Reader modelled by this resource.
getReferenceGenes() - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
getRegistration() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSPatternMatch
 
getRegistration() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.DSPatternMatch
 
getRegistration() - Method in class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqPatternMatch
 
getRegistration() - Method in class org.geworkbench.util.patterns.PatternLocations
 
getRegistry() - Static method in class org.geworkbench.engine.management.ComponentRegistry
Gets an instance of the ComponentRegistry.
getRegulators() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaData
 
getRegulon(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorTableResultSet
 
getRegulon(String) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRegulatorTableResultSet
 
getRelated() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getRemoteResourceManager() - Static method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getReportFile() - Method in class org.geworkbench.bison.datastructure.biocollections.gsea.CSGSEAResultDataSet
 
getReportFile() - Method in interface org.geworkbench.bison.datastructure.biocollections.gsea.DSGSEAResultDataSet
 
getRepressors() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getRepressors() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getRequestItem() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getRequired() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getResource() - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getResource(String) - Method in class org.geworkbench.engine.management.ComponentClassLoader
 
getResource(File) - Method in class org.geworkbench.parsers.AffyFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.CELFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.EdgeListFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.GenePixFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.MageTabFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.PatternFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.PDBFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.SOFTFileFormat
 
getResource(File) - Method in class org.geworkbench.parsers.TabDelimitedDataMatrixFileFormat
 
getResourceNames() - Static method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
getResult() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSDemandResultSet
 
getResult() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSDemandResultSet
 
getResult() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.MarkUsResultDataSet
 
getResult() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.PudgeResultSet
 
getResult() - Method in class org.geworkbench.bison.datastructure.bioobjects.structure.SkyLineResultDataSet
 
getResult() - Method in class org.geworkbench.builtin.projects.RWspHelper.AccessRemoteTask
 
getResult() - Method in class org.geworkbench.util.visualproperties.JShapeDialog
 
getResult2DArray() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getResult2DArray() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAnovaResultSet
 
getResultAsArray() - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
getResultList() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResult
 
getResults() - Method in class org.geworkbench.bison.model.analysis.AlgorithmExecutionResults
The Object containing the results of the algorithm execution
getReverseIndex() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getReverseIndex() - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
getRightSideOneTailedP(int, int, int, int) - Static method in class org.geworkbench.util.FishersExactTest
 
getRLibPath() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getRLocation() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getRoot(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getRoot(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getRow(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getRow(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
getRow(int) - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getRow(int) - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
Return the numeric value of a given row, namely the (gene) marker of a given index.
getRow(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo
 
getRowAsString(int) - Method in class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
 
getRowCount() - Method in class org.geworkbench.builtin.projects.RWspHelper.DetailTableModel
 
getRowCount() - Method in class org.geworkbench.util.sequences.PatternTableModel
See javax.swing.table.TableModel
getRowNames() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getRows() - Method in class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 
getRows() - Method in class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet
 
getRows() - Method in interface org.geworkbench.bison.model.clusters.DSSOMClusterDataSet
 
getRows(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get the list of MINDY result rows
getRows(DSGeneMarker, List<DSGeneMarker>) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get the list of MINDY result rows
getRunLog() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceSet
 
getRunLog() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSMatrixReduceSet
 
getRWSP_URL() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getSatus() - Method in class org.geworkbench.events.StatusBarEvent
Gets a status message.
getSavedWorkspace(String) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
getSavedWorkspaceInfo(String) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
getSavedWorkspaceList(String) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
getSavedWorkspaceStatus(String, int, String) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
getScore(DSGeneMarker, DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get the score
getScore() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyResultRow
Get the score in this MINDY result row.
getScore(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo
 
getScores() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getScores() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getScores() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
getSeedSequence() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getSeedSequence() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getSelected() - Method in class org.geworkbench.builtin.projects.SaveTree
 
getSelectedCluster(int) - Method in class org.geworkbench.bison.model.clusters.CSHierClusterDataSet
 
getSelectedCluster(int) - Method in interface org.geworkbench.bison.model.clusters.DSHierClusterDataSet
 
getSelectedConfidenceType() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getSelectedDataSetNode() - Method in class org.geworkbench.builtin.projects.ProjectSelection
 
getSelectedDataSetSubNode() - Method in class org.geworkbench.builtin.projects.ProjectSelection
 
getSelectedIndices() - Method in class org.geworkbench.util.JAutoList
 
getSelectedInteractions(List<String>, short) - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getSelectedInteractions(String, short) - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getSelectedMarkerCluster() - Method in class org.geworkbench.events.HierClusterModelEvent
 
getSelectedMicroarrayCluster() - Method in class org.geworkbench.events.HierClusterModelEvent
 
getSelectedNode() - Method in class org.geworkbench.builtin.projects.ProjectSelection
 
getSelectedResouceByName(String) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
 
getSelectedSequence() - Method in class org.geworkbench.util.sequences.SequenceViewWidget
 
getSelectedSequence() - Method in class org.geworkbench.util.sequences.SequenceViewWidgetPanel
 
getSelection() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
getSelection() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Gets the special 'selection' panel.
getSelection() - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Gets the selected sub-panel.
getSelection() - Method in class org.geworkbench.builtin.projects.ProjectPanel
 
getSelection() - Method in class org.geworkbench.engine.preferences.ChoiceField
 
getSelectionAsString() - Method in class org.geworkbench.engine.preferences.ChoiceField
 
getSelectionEnabled() - Method in class org.geworkbench.bison.model.clusters.CSHierClusterDataSet
 
getSelectionEnabled() - Method in interface org.geworkbench.bison.model.clusters.DSHierClusterDataSet
 
getSelectionEnabled() - Method in class org.geworkbench.events.HierClusterModelEvent
 
getSelectionLastSelected(DSDataSet<? extends DSBioObject>) - Method in class org.geworkbench.engine.skin.Skin
 
getSelectionSelected() - Method in class org.geworkbench.builtin.projects.DataSetSaveNode
 
getSelectorMarkerOrder() - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getSelectorMarkerOrder() - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
getSequence(int) - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getSequence(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getSequence(int) - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
getSequence() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
getSequence() - Method in interface org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence
Gets the sequence as a String.
getSequenceDB(File) - Static method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getSequenceNo() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
getSequenceNo() - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
getSequences() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceSet
 
getSequences() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSMatrixReduceSet
 
getSeqURL() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
getSeqViewWPanel() - Method in class org.geworkbench.util.sequences.SequenceViewWidget
 
getSeqXclickPoint() - Method in class org.geworkbench.util.sequences.SequenceViewWidgetPanel
 
getSerial() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
getSerial
getSerial() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getSerial() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
getSerial() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Gets the index of this object in its ordered container.
getSerial() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getSerial() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getSerial() - Method in interface org.geworkbench.bison.datastructure.properties.DSSequential
Gets the serial for this object.
getSerializable() - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
getSetFraction() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get the fraction of the sample to display on the heat map.
getShape() - Method in class org.geworkbench.util.visualproperties.PanelVisualProperties
 
getShapeIndex() - Method in class org.geworkbench.util.visualproperties.PanelVisualProperties
 
getShortName() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
getShortName() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
 
getShortname() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
getShortNames() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
getShortNames() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
return all gene symbols for this 'marker' (probe set) from annotation file
getSigma() - Method in class org.geworkbench.bison.util.Normal
 
getSignificance(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getSignificance(T) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getSignificance(T) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
Gets the significance value for the marker.
getSignificantMarkers() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
getSignificantMarkers() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getSignificantMarkers() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
getSimilarityMatrix() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getSimilarityThreshold() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getSmallestIncrement() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getSorted() - Method in class org.geworkbench.util.QSort
 
getSortedDouble() - Method in class org.geworkbench.util.QSort
 
getSortMode() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getSourceLocation() - Method in class org.geworkbench.builtin.projects.OboSourcePreference
 
getSourceType() - Method in class org.geworkbench.builtin.projects.OboSourcePreference
 
getStartNode() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.Edge
 
getStartPoint() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
 
getStartPoint() - Method in class org.geworkbench.util.sequences.GeneChromosomeMatcher
 
getState() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getStatistics(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get the statics for the specified modulator.
getStatusAsChar() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
getStatusAsChar() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
getStopNotifyAnalysisPanelTemporaryFlag() - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
 
getString(String) - Method in class org.geworkbench.util.ResultSetlUtil
 
getString(int) - Method in class org.geworkbench.util.ResultSetlUtil
 
getStringId() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
getSubLabel() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Gets the sub-label for this panel.
getSubLabel() - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Gets the sub-label for this DSPanel.
getSubSequence(int, int) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
getSummary() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
 
getSummary() - Method in interface org.geworkbench.bison.datastructure.bioobjects.sequence.DSAlignmentResultSet
 
getSupport() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
getSupport() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.DSMatchedPattern
 
getSupport() - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
getTabDelimitedFileFilter() - Static method in class org.geworkbench.builtin.projects.SaveFileFilterFactory
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.geworkbench.builtin.projects.RWspHelper.ColorRenderer
 
getTaggedItemSetTree() - Method in class org.geworkbench.events.PhenotypeSelectorEvent
 
getTarget() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyResultRow
Get the target in this MINDY result row.
getTargets() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaData
 
getTargets(DSGeneMarker) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get a list of targets for one modulator
getTargets(List<DSGeneMarker>) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get a list of targets for all modulator in the list
getTemporaryFilesDirectoryPath() - Static method in class org.geworkbench.util.FilePathnameUtils
will create absolute path starting with home directory as a root for temporary files directory if "temporary.files.directory" property is not set will use DEFAULT_TEMP_FILE_DIR
getTerm(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getTestLoss() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
getTestPredResultModel() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getText() - Method in class org.geworkbench.bison.datastructure.bioobjects.SelectorResult
 
getTextEditor() - Method in class org.geworkbench.engine.preferences.GlobalPreferences
 
getTFs() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getTFs() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getThreadId() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getThreadNo() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getThreshold() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
getThreshold() - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
getTissue() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
getTitle() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getTitrationId() - Method in class org.geworkbench.events.TitrationCurveEvent
 
getToken() - Method in class org.geworkbench.util.patterns.PatternOfflet
 
getToolUrl() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getTopLevelDataSetNodes() - Method in class org.geworkbench.builtin.projects.ProjectPanel
 
getTotalArrays() - Method in class org.geworkbench.events.CaArraySuccessEvent
 
getTrainingProgressListener() - Method in interface org.geworkbench.util.TrainingTask
 
getTrainLoss() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
getTrainPredResultModel() - Method in class org.geworkbench.bison.datastructure.biocollections.SVMResultSet
 
getTranscriptionFactor() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Get the transcription factor specified for MINDY data.
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.geworkbench.builtin.projects.TreeNodeRenderer
Component used for rendering on the ProjectTree based on type and selection
getTreeModel() - Method in class org.geworkbench.builtin.projects.ProjectPanel
 
getTreeNode() - Method in class org.geworkbench.events.ProjectEvent
 
getTreeSet() - Method in class org.geworkbench.util.patterns.PatternSequenceDisplayUtil
 
getTutorialUrl() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getTValue(T) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet
 
getTValue(T) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
 
getTValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getTValue() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getTValue() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSMatrixReduceExperiment
 
getTValue() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
getType() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getType() - Method in class org.geworkbench.events.GeneTaggedEvent
 
getType() - Method in class org.geworkbench.events.ProgressBarEvent
 
getType() - Method in class org.geworkbench.events.SubpanelChangedEvent
 
getUMatrix() - Method in class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
 
getUMatrix() - Method in interface org.geworkbench.bison.datastructure.biocollections.pca.DSPCADataSet
 
getUnigene() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
getUnigene() - Method in interface org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker
 
getUnigeneAsString() - Method in class org.geworkbench.bison.datastructure.properties.CSUnigene
 
getUnigeneAsString() - Method in interface org.geworkbench.bison.datastructure.properties.DSUnigene
 
getUnigeneId() - Method in class org.geworkbench.bison.datastructure.properties.CSUnigene
 
getUnigeneId() - Method in interface org.geworkbench.bison.datastructure.properties.DSUnigene
 
getUniqueMarkers() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getUniqueMarkers() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
getUniqueName(String, Set<String>) - Static method in class org.geworkbench.util.Util
Generates a unique name given a desired name and a set of existing names.
getUniqueSupport() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
getUniqueSupport() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.DSMatchedPattern
 
getUniqueSupport() - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
getUri() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
getUrl() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getUrl() - Method in class org.geworkbench.events.CaArrayEvent
 
getUrl() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
getUrl() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getUrl() - Method in class org.geworkbench.events.CaArrayRequestHybridizationListEvent
 
getUrl() - Static method in class org.geworkbench.util.ResultSetlUtil
 
getURLProperty() - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
getUsedIds() - Static method in class org.geworkbench.engine.config.PluginDescriptor
 
getUsedIds() - Static method in class org.geworkbench.engine.config.PluginRegistry
 
getUser() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
getUserInfo() - Method in class org.geworkbench.builtin.projects.RWspHandler
 
getUsername() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getUsername() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
getUsername() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
getUsername() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
getUsername() - Method in class org.geworkbench.events.CaArrayRequestHybridizationListEvent
 
getUserName() - Method in class org.geworkbench.util.PropertiesMonitor
 
getUserSettingDirectoryPath() - Static method in class org.geworkbench.util.FilePathnameUtils
will create absolute path starting with home directory as a root for user setting directory if "user.setting.directory" property is not set will use DEFAULT_USER_SETTING_DIR
getUserSettingsFilePath() - Static method in class org.geworkbench.util.FilePathnameUtils
will create absolute path starting with home directory as a root for user settings file, if "userSettings" property is not set will use DEFAULT_USERSETTINGS_FILE
getValue(DSGeneMarker, int) - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getValue(int, int) - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
getValue(int, int) - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
getValue(DSGeneMarker, int) - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
getValue(int, int) - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getValue(T, int) - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
getValue(int, int) - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
getValue(T, int) - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
getValue() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue
 
getValue() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
getValue(DSGeneMarker) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet
 
getValue() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
Return the signal measurement for this spot.
getValue(DSGeneMarker) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet
 
getValue() - Method in class org.geworkbench.engine.preferences.DoubleField
 
getValue() - Method in class org.geworkbench.engine.preferences.FileField
 
getValue() - Method in class org.geworkbench.engine.preferences.IntegerField
 
getValue() - Method in class org.geworkbench.engine.preferences.PreferencesDialog.FileFieldComponent
 
getValue() - Method in class org.geworkbench.engine.preferences.TextField
 
getValueAt(int, int) - Method in class org.geworkbench.builtin.projects.RWspHelper.DetailTableModel
 
getValueAt(int, int) - Method in class org.geworkbench.builtin.projects.RWspHelper.WspTableModel
 
getValueAt(int, int) - Method in class org.geworkbench.util.sequences.PatternTableModel
 
getValuesForName(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Returns all values mapped to the designated name.
getValuesForName(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
getValuesForName(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
getValuesForName(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
getValuesForName(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
getValuesForName(String) - Method in class org.geworkbench.bison.datastructure.properties.CSExtendable
 
getValuesForName(String) - Method in interface org.geworkbench.bison.datastructure.properties.DSExtendable
Returns all values mapped to the designated name.
getVar() - Method in class org.geworkbench.engine.config.MenuItemInfo
 
getVariables() - Method in class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
 
getVariables() - Method in interface org.geworkbench.bison.datastructure.biocollections.pca.DSPCADataSet
 
getVariances() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
getVersion() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
getVersion() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
getVersion() - Method in class org.geworkbench.engine.config.ComponentMetadata
 
getVersion() - Method in class org.geworkbench.util.network.CellularNetworkPreference
 
getVisualArea(Component) - Method in class org.geworkbench.engine.config.GUIFramework
get the infomation about the visual area the visualPlugin was plugged into
getVisualArea(Component) - Method in class org.geworkbench.engine.skin.Skin
 
getVisualAreaMap() - Static method in class org.geworkbench.engine.config.PluginRegistry
 
getVisualLastSelected(DSDataSet<? extends DSBioObject>) - Method in class org.geworkbench.engine.skin.Skin
 
getVisualLocation() - Method in class org.geworkbench.engine.config.PluginDescriptor
 
getVisualProperties(Object) - Method in class org.geworkbench.util.visualproperties.PanelVisualPropertiesManager
 
getVisualProperties() - Method in class org.geworkbench.util.visualproperties.VisualPropertiesDialog
 
getVisualSelected() - Method in class org.geworkbench.builtin.projects.DataSetSaveNode
 
getWholeSeq() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj
getWholeSeq
getWindow() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
getWorkspacePath() - Method in class org.geworkbench.builtin.projects.WorkspaceHandler
 
getWorkTitle() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getWriter() - Method in class org.geworkbench.bison.parsers.resources.AbstractResource
 
getWriter() - Method in interface org.geworkbench.bison.parsers.resources.Resource
Return the Writer modelled by this resource.
getWspId() - Method in class org.geworkbench.builtin.projects.SaveTree
 
getXCoordinate() - Method in class org.geworkbench.bison.model.clusters.DefaultSOMCluster
Gets the X Coordinate of the Grid this SOMCluster represents
getXCoordinate() - Method in interface org.geworkbench.bison.model.clusters.SOMCluster
Gets the x coordinate for this cluster
getYCoordinate() - Method in class org.geworkbench.bison.model.clusters.DefaultSOMCluster
Gets the Y Coordinate of the Grid this SOMCluster represents
getYCoordinate() - Method in interface org.geworkbench.bison.model.clusters.SOMCluster
Gets the y coordinate for this cluster
getZipCode() - Method in class org.geworkbench.builtin.projects.RegisterBean
 
getzScore() - Method in class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
GLOBAL_PROPERTIES - Static variable in class org.geworkbench.engine.properties.PropertiesManager
 
GlobalPreferences - Class in org.geworkbench.engine.preferences
 
GoAnalysisResult - Class in org.geworkbench.bison.datastructure.biocollections
Go Terms Analysis Result.
GoAnalysisResult(DSDataSet<DSMicroarray>, String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult
Constructor for a result not populated yet.
GOTERM - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
GOTerm - Class in org.geworkbench.bison.datastructure.bioobjects.markers.goterms
Represents a Gene Ontology Term.
GOTerm(int) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
GOTEXPERIMENTS - Static variable in class org.geworkbench.events.CaArrayQueryEvent
 
GOTVALIDVALUES - Static variable in class org.geworkbench.events.CaArrayQueryEvent
 
GUIFramework - Class in org.geworkbench.engine.config
Base class for the top-level window of an application.
GUIFramework() - Constructor for class org.geworkbench.engine.config.GUIFramework
 
GUIWindowObject - Class in org.geworkbench.engine.config.rules
Describes the object that is pushed on the UILauncher stack when processing the pattern "geaw-config/gui-window".
GUIWindowObject() - Constructor for class org.geworkbench.engine.config.rules.GUIWindowObject
 

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handleBisonInputs(DSMicroarraySetView<DSGeneMarker, DSMicroarray>, DSDataSet<?>) - Method in class org.geworkbench.analysis.AbstractGridAnalysis
Packs the bison inputs (including parameters) for the grid service.
handleMouseEvent(MouseEvent) - Method in class org.geworkbench.util.JAutoList
 
handleSubscription(String, String) - Method in class org.geworkbench.engine.config.rules.PluginObject
 
hasAttribute(String) - Method in interface org.geworkbench.bison.datastructure.properties.DSAnnotated
 
hasChanged() - Method in class org.geworkbench.util.ProgressBar
 
hasChanged() - Method in class org.geworkbench.util.ProgressBarT
 
hasContext(DSItemList<T>, String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContextManager
 
hasContext(DSItemList<T>, String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContextManager
Checks for the existence of a named context for an item list.
hashCode() - Method in class org.geworkbench.analysis.ParameterKey
 
hashCode() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
hashCode() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.EdgeInfo
 
hashCode() - Method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
hashCode() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
hashCode() - Method in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GOTerm
 
hashCode() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSItemList
 
hashCode() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
 
hashCode() - Method in class org.geworkbench.bison.datastructure.complex.pattern.PatternDiscoveryParameters
 
hashCode() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
hashCode() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
hashCode() - Method in class org.geworkbench.engine.config.PluginDescriptor
 
hashCode() - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
hashCode() - Method in class org.geworkbench.util.network.InteractionDetail
 
hashCode() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.Edge
 
hasHistory(DSExtendable) - Static method in class org.geworkbench.builtin.projects.history.HistoryPanel
 
hasLabel(T, String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
hasLabel(T, String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Returns true if the item has the specified label, false otherwise.
hasParametersToSave() - Method in class org.geworkbench.bison.model.analysis.ParameterPanel
 
hasParametersToSave(boolean) - Method in class org.geworkbench.bison.model.analysis.ParameterPanel
 
hasPattern() - Method in class org.geworkbench.util.patterns.PatternSequenceDisplayUtil
 
hideDialog() - Method in class org.geworkbench.util.CommandBase
 
hideFrame() - Method in class org.geworkbench.builtin.projects.RegPanel
 
hideOnClick() - Method in class org.geworkbench.util.SplashBitmap
Tells this splash screen to close when being clicked.
hideOnTimeout(int) - Method in class org.geworkbench.util.SplashBitmap
Tells this splash screen to close after a certain time has passed.
hideSplash() - Method in class org.geworkbench.util.SplashBitmap
Hides this splash screen and stops all running timers.
hideWelcomeScreen() - Method in class org.geworkbench.engine.skin.Skin
 
HIERARCHICAL_CLUSTERING_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
HierCluster - Interface in org.geworkbench.bison.model.clusters
Copyright (c) 2006 Columbia University Defines a Generalization of a Cluster that would be obtained from a Hierarchical Clustering Analysis
hierClusterModelChange(HierClusterModelEvent) - Method in interface org.geworkbench.events.HierClusterModelEventListener
 
HierClusterModelEvent - Class in org.geworkbench.events
Copyright: Copyright (c) 2003
HierClusterModelEvent(Object) - Constructor for class org.geworkbench.events.HierClusterModelEvent
Constructor
HierClusterModelEvent(Object, DSHierClusterDataSet) - Constructor for class org.geworkbench.events.HierClusterModelEvent
Constructor
HierClusterModelEventListener - Interface in org.geworkbench.events
Copyright: Copyright (c) 2003
HIGHLIGHT - Static variable in class org.geworkbench.events.GeneTaggedEvent
 
HighlightCurrentParameterThread - Class in org.geworkbench.analysis
We use this class as a call back function
HighlightCurrentParameterThread(ReHighlightable) - Constructor for class org.geworkbench.analysis.HighlightCurrentParameterThread
Pass in the analysis panel needs to be refreshed.
HISTORY - Static variable in class org.geworkbench.builtin.projects.history.HistoryPanel
Used as the "name" in the name-value pair that keeps track of the history of changes that a given dataset is being submitted to.
HISTORYDETAIL - Static variable in class org.geworkbench.builtin.projects.history.HistoryPanel
 
HistoryEvent - Class in org.geworkbench.events
 
HistoryEvent(DSDataSet<? extends DSBioObject>) - Constructor for class org.geworkbench.events.HistoryEvent
 
HistoryPanel - Class in org.geworkbench.builtin.projects.history
This application component is responsible for displaying the history of modifications (editing, normalization, filtering, etc) that a microarray set has undergone.
HistoryPanel() - Constructor for class org.geworkbench.builtin.projects.history.HistoryPanel
 
historyPanel - Variable in class org.geworkbench.builtin.projects.history.HistoryPanel
 
historyTextArea - Variable in class org.geworkbench.builtin.projects.history.HistoryPanel
 
HOUSEKEEPINGGENES_VALUE_NORMALIZER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 

I

Icons - Class in org.geworkbench.builtin.projects
 
Icons() - Constructor for class org.geworkbench.builtin.projects.Icons
 
id - Variable in class org.geworkbench.builtin.projects.RWspHelper.AccessRemoteTask
 
id - Variable in class org.geworkbench.engine.config.IdentifiableImpl
Stores a unique id.
id - Variable in class org.geworkbench.util.pathwaydecoder.RankSorter
 
IdeaGLoc - Class in org.geworkbench.bison.datastructure.bioobjects
 
IdeaGLoc(String, String, String, String, double, double, double) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.IdeaGLoc
 
IdeaModule - Class in org.geworkbench.bison.datastructure.bioobjects
 
IdeaModule(String, String, String, String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.IdeaModule
 
IdeaNode - Class in org.geworkbench.bison.datastructure.bioobjects
 
IdeaNode(String, String, String, int, double, int, int, double, double, int, int, double, double) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.IdeaNode
 
IdeaResultDataSet - Class in org.geworkbench.bison.datastructure.bioobjects
Result of IDEA analysis.
IdeaResultDataSet(DSMicroarraySet, String, List<IdeaGLoc>, List<IdeaGLoc>, List<IdeaNode>, List<IdeaModule>, double) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.IdeaResultDataSet
 
IdentifiableImpl - Class in org.geworkbench.engine.config
This class provides an implementation of the Identifiable interface to be used with PluginDescriptor objects.
IdentifiableImpl() - Constructor for class org.geworkbench.engine.config.IdentifiableImpl
Default constructor
IdentifiableImpl(String) - Constructor for class org.geworkbench.engine.config.IdentifiableImpl
Instantiates using the prescribed id.
IdentifiableImpl(String, String) - Constructor for class org.geworkbench.engine.config.IdentifiableImpl
Instantiates using the prescribed id and name
idExists(String) - Static method in class org.geworkbench.engine.config.IdentifiableImpl
 
IdID - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
IGNORE_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
image - Variable in class org.geworkbench.builtin.projects.ImageNode
ImageIcon that this ImageNode refers to
IMAGE_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
ImageData - Class in org.geworkbench.builtin.projects
Title: Bioworks
ImageData(File) - Constructor for class org.geworkbench.builtin.projects.ImageData
 
ImageNode - Class in org.geworkbench.builtin.projects
Copyright: Copyright (c) 2003
ImageNode(ImageData) - Constructor for class org.geworkbench.builtin.projects.ImageNode
Constructor
ImageSnapshotEvent - Class in org.geworkbench.events
Copyright: Copyright (c) 2003
ImageSnapshotEvent(String, ImageIcon, ImageSnapshotEvent.Action) - Constructor for class org.geworkbench.events.ImageSnapshotEvent
 
ImageSnapshotEvent.Action - Enum in org.geworkbench.events
 
INDETERMINATE_TYPE - Static variable in class org.geworkbench.util.ProgressBar
Defines a ProgressBar that animates cyclically till asked to stop
INDETERMINATE_TYPE - Static variable in class org.geworkbench.util.ProgressBarT
Defines a ProgressBarT that animates cyclically till asked to stop
INDETERMINATE_TYPE - Static variable in class org.geworkbench.util.ProgressItem
Defines a ProgressBar that animates cyclically till asked to stop
indexOf(Object) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
 
indexOfLabel(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
indexOfLabel(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Returns the index of the label in this context.
info - Variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Edge
 
InformationPanel - Class in org.geworkbench.builtin.projects
The new panel that is shown in visualization area and contains the three panels that used to be in command area: CommentsPanel, HistoryPanel, and ExperimentInformationPanel.
InformationPanel() - Constructor for class org.geworkbench.builtin.projects.InformationPanel
 
init(AffyParseContext) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
Initializes class attributes from the contents of the AffyParseContext argument.
init(Map) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
init() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceManager
A default setup when no property file is found.
initFilteredModulatorInfoMap() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
initFrame() - Method in class org.geworkbench.builtin.projects.RegPanel
 
initialize() - Method in class org.geworkbench.engine.management.Asynchronous
 
initialize() - Method in class org.geworkbench.engine.management.Overflow
 
initialize() - Method in class org.geworkbench.engine.management.SwingModel
 
initialize() - Method in interface org.geworkbench.engine.management.SynchModel
 
initialize() - Method in class org.geworkbench.engine.management.Synchronous
 
INITIALIZE - Static variable in class org.geworkbench.events.ProgressBarEvent
Event types
initialize(HashMap<CSSequence, PatternSequenceDisplayUtil>, DSSequenceSet<? extends DSSequence>, boolean) - Method in class org.geworkbench.util.sequences.SequenceViewWidgetPanel
New Initialization method.
initializeDefaultIconAssignments() - Static method in class org.geworkbench.builtin.projects.DefaultIconAssignments
 
initializeExperimentTree() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
initializeMarkerVector(int) - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
initializeMarkerVector(int) - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
 
initializePhenotypeContext(DSAnnotationContext<T>) - Static method in class org.geworkbench.bison.annotation.CSAnnotationContext
Initializes a context to have typical values for describing phenotypes.
initPanelView() - Method in class org.geworkbench.util.sequences.SequenceViewWidget
Initiate the Panel, which should be used as the entry point.
initWelcomeScreen() - Method in class org.geworkbench.engine.skin.Skin
 
InputFileFormatException - Exception in org.geworkbench.parsers
Thrown when attempting to open an input file that does not comply with a user-designated format.
InputFileFormatException() - Constructor for exception org.geworkbench.parsers.InputFileFormatException
 
InputFileFormatException(String) - Constructor for exception org.geworkbench.parsers.InputFileFormatException
 
insertRow(MindyResultRow) - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo
 
installComponents() - Method in class org.geworkbench.engine.ccm.ComponentConfigurationManager2
 
instance - Static variable in class org.geworkbench.util.PropertiesMonitor
 
IntegerField - Class in org.geworkbench.engine.preferences
 
IntegerField(String) - Constructor for class org.geworkbench.engine.preferences.IntegerField
 
InteractionDetail - Class in org.geworkbench.util.network
The deatil of one interaction.
InteractionDetail(String, String, String, String, String, Short) - Constructor for class org.geworkbench.util.network.InteractionDetail
 
INTERACTIONS_SERVLET_CONNECTION_TIMEOUT - Static variable in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
INTERACTIONS_SERVLET_URL - Static variable in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
intervalAdded(ListDataEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
intervalRemoved(ListDataEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
intId - Variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
is3Prime(DSMicroarraySet) - Method in class org.geworkbench.util.AnnotationInformationManager
 
isAbsent() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
isAbsent() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
isAbsent() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAffyMarkerValue
Utility method converse of AffyMarkerValue#isPresent
isActive() - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Gets the activation status of the data set.
isActive() - Method in interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
Gets the activation status of the data set.
isActive() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Obtains the activation state of this Panel
isActive() - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Active panels are used by the visual displays.
isActive() - Method in class org.geworkbench.util.pathwaydecoder.RankSorter
 
isAnnotated() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
isAuthorizationRequired() - Method in class org.geworkbench.analysis.AbstractGridAnalysis
Authorization is required unless the sub-class overwrite this.
isBoundary(int) - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
 
isBoundary(int) - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Used to determine if the current index is a sub-panel boundary
isCancelled() - Method in interface org.geworkbench.util.TrainingTask
 
isCompleteCheck() - Method in class org.geworkbench.util.CheckThreadViolationRepaintManager
 
isConnectionSuccess() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
isDirty() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
isDirty() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
isDirty
isDirty() - Method in class org.geworkbench.builtin.projects.ImageData
 
isDirty() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
isDirty() - Method in class org.geworkbench.util.network.CellularNetWorkElementInformation
 
isDNA() - Method in class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet
 
isDNA() - Method in interface org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet
 
isDrawBorder() - Method in class org.geworkbench.util.visualproperties.JShapeButton
 
isEditable() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResource
 
isEmpty() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeList
 
isEmpty() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
isEmpty() - Method in class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
isExecutionSuccessful() - Method in class org.geworkbench.bison.model.analysis.AlgorithmExecutionResults
Gets the status of the algorithn execution
isExperimental() - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
isExperimental(boolean) - Method in class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
isExperimentsLoaded() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
isFiltered() - Method in class org.geworkbench.util.pathwaydecoder.RankSorter
 
isFirstTime() - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
 
isFromGear() - Method in class org.geworkbench.engine.management.ComponentResource
 
isGeneEntrezId() - Method in class org.geworkbench.util.network.InteractionDetail
 
isInitial() - Method in class org.geworkbench.events.ProgressChangeEvent
Whether this event is the one for initially adding listener.
isInSubscriptionIgnoreSet(Class<?>) - Method in class org.geworkbench.engine.config.PluginDescriptor
 
isLabelActive(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
isLabelActive(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Retrieves the active status value of a label.
isLeaf() - Method in class org.geworkbench.bison.model.clusters.AbstractCluster
Specifes if this Cluster is a leaf.
isLeaf() - Method in interface org.geworkbench.bison.model.clusters.Cluster
Returns true if this node has no children.
isLineView - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
isLogNormalized() - Method in interface org.geworkbench.bison.model.analysis.ParameterPanelIncludingNormalized
 
isMarginal() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
isMarginal() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
isMarginal() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAffyMarkerValue
Tests the Marginality of this MarkerValue in the containing Microarray
isMarkerUndefined(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
isMarkerUndefined(int) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
Convenience method to access the undefined status of the i-th feature directly
isMarkerValid(int) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
isMarkerValid(int) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray
Convenience method to access the valid status of the i-th feature directly
isMasked() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
isMasked() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
This method returns whether this marker should be temporarily ignored by analytical tools
isMenuListener() - Method in class org.geworkbench.engine.config.PluginDescriptor
Checks if the plugin implements the MenuListener interface.
isMergeSupported() - Method in class org.geworkbench.parsers.AdjacencyMatrixFileFormat
 
isMergeSupported() - Method in class org.geworkbench.parsers.CELFileFormat
 
isMergeSupported() - Method in class org.geworkbench.parsers.FileFormat
 
isMergeSupported() - Method in class org.geworkbench.parsers.MageTabFileFormat
 
isMergeSupported() - Method in class org.geworkbench.parsers.PatternFileFormat
 
isMergeSupported() - Method in class org.geworkbench.parsers.PDBFileFormat
 
isMergeSupported() - Method in class org.geworkbench.parsers.sequences.SequenceFileFormat
 
isMergeSupported() - Method in class org.geworkbench.parsers.SOFTFileFormat
 
isMissing() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
isMissing() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
Check if the mesurement for this spot is classified as "missing".
isMissing(int, int) - Method in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
isMustAccept() - Method in class org.geworkbench.engine.ccm.PluginComponent
 
isPlotted() - Method in class org.geworkbench.util.pathwaydecoder.RankSorter
 
isPopulated() - Method in class org.geworkbench.events.CaArrayEvent
 
isPopulated() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
isPopulated() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
isPositiveStrandDirection() - Method in class org.geworkbench.util.sequences.GeneChromosomeMatcher
 
isPrefixMode() - Method in class org.geworkbench.util.JAutoList
 
isPresent() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue
 
isPresent() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
isPresent() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAffyMarkerValue
Tests the Detection Status of this MarkerValue in the containing Microarray
isPropertiesChanged() - Method in class org.geworkbench.util.visualproperties.VisualPropertiesDialog
 
isQueryExperiment() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
isReverseComplement() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
isRunningOnAMac() - Static method in class org.geworkbench.util.Util
 
isShowProgress() - Method in class org.geworkbench.util.BusySwingWorker
 
isSourceDirty() - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
isStillWaitForConnecting() - Method in class org.geworkbench.builtin.projects.util.CaARRAYPanel
 
isSucceed() - Method in class org.geworkbench.events.CaArrayEvent
 
isSucceed() - Method in class org.geworkbench.events.CaArrayQueryEvent
 
isSucceed() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
isTrailingStrand() - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
isTrailingStrand() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.matrix.DSPositionSpecificAffintyMatrix
 
isUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
Check if forceUniqueValue() is in effect for the designated name.
isUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray
 
isUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
isUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment
 
isUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix
 
isUniqueValue(String) - Method in class org.geworkbench.bison.datastructure.properties.CSExtendable
 
isUniqueValue(String) - Method in interface org.geworkbench.bison.datastructure.properties.DSExtendable
Check if forceUniqueValue() is in effect for the designated name.
isUnsupervised() - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
isUnsupervised() - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Returns true if there are no items labelled 'class'.
isUseFilterCrit() - Method in class org.geworkbench.events.CaArrayRequestEvent
 
isUsingDimers() - Method in class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
isValid() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
isValid() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
This method returns whether the marker is both unmasked and not undefined.
isValid() - Method in class org.geworkbench.bison.model.analysis.ParamValidationResults
Return the parameter validation outcome.
isValid(StringBuffer) - Method in class org.geworkbench.builtin.projects.RegPanel
 
isValidDNASeqForBLAST(DSSequence) - Static method in class org.geworkbench.bison.util.SequenceUtils
Check if the DSSequence argument represents a well formed DNA sequence for the purpose of a BLAST submission.
isVisualPlugin() - Method in class org.geworkbench.engine.config.PluginDescriptor
Checks if the plugin implements the VisualPlugin interface.
items() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
items() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
ix - Variable in class org.geworkbench.util.pathwaydecoder.RankSorter
 
iy - Variable in class org.geworkbench.util.pathwaydecoder.RankSorter
 

J

jAllSequenceCheckBox - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
JAutoList - Class in org.geworkbench.util
A list control that supports interactive text search.
JAutoList(ListModel) - Constructor for class org.geworkbench.util.JAutoList
 
jButton6_actionPerformed(ActionEvent) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
jComboBox1_actionPerformed(ActionEvent) - Method in class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
 
jScrollPane1 - Variable in class org.geworkbench.builtin.projects.history.HistoryPanel
 
JShapeButton - Class in org.geworkbench.util.visualproperties
A component that displays a shape and allows the user to click on it.
JShapeButton(Shape, Paint) - Constructor for class org.geworkbench.util.visualproperties.JShapeButton
 
JShapeDialog - Class in org.geworkbench.util.visualproperties
Dialog that displays some shapes and allows one to be chosen.
JShapeDialog(Dialog, String, Shape[], Paint, int) - Constructor for class org.geworkbench.util.visualproperties.JShapeDialog
 
jToolBar1 - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
jToolBar3 - Variable in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
jViewComboBox - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 

K

keyPressed(KeyEvent) - Method in class org.geworkbench.util.JAutoList
Override to customize the result of a key being typed in the search field.
KMeansResult - Class in org.geworkbench.bison.datastructure.bioobjects
Result of K-Means Clustering analysis.
KMeansResult(DSMicroarraySet, String, SOMCluster[][], int, ArrayList<List<String[]>>) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.KMeansResult
 
KMeansResultMarkers - Class in org.geworkbench.bison.datastructure.bioobjects
 
KMeansResultMarkers(DSMicroarraySet, String, DSMicroarraySetView<? extends DSGeneMarker, ? extends DSMicroarray>, SOMCluster[][], int, ArrayList<List<String[]>>) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers
 

L

label - Variable in class org.geworkbench.bison.datastructure.biocollections.CSDataSet
 
label - Variable in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
labelExists(String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
labelExists(String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
 
labelItem(T, String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
labelItem(T, String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Applies a label to an item.
labelItems(List<T>, String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
labelItems(T[], String) - Method in class org.geworkbench.bison.annotation.CSAnnotationContext
 
labelItems(List<T>, String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Applies a label to a list of items.
labelItems(T[], String) - Method in interface org.geworkbench.bison.annotation.DSAnnotationContext
Applies a label to a array of items.
lastchange - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
LastChangeID - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
LastSyncID - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
LDHeight - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
LDWidth - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
LeafSOMCluster - Class in org.geworkbench.bison.model.clusters
Copyright: Copyright (c) 2003
LeafSOMCluster(DSGeneMarker) - Constructor for class org.geworkbench.bison.model.clusters.LeafSOMCluster
The DSMarker that this SOMCluster represents
length() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
length() - Method in interface org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence
Gets the length of the sequence.
length() - Method in class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqRegistration
 
LIB_DIR - Static variable in class org.geworkbench.engine.management.ComponentResource
 
LincsDataSet - Class in org.geworkbench.bison.datastructure.biocollections.lincs
 
LincsDataSet(DSMicroarraySet, String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet
 
LINEVIEW - Static variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
list - Variable in class org.geworkbench.util.JAutoList
 
listContent - Static variable in class org.geworkbench.builtin.projects.remoteresources.CaArrayFilteringDialog
 
listDialog - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
listeners - Variable in class org.geworkbench.util.CommandBase
 
listLock() - Static method in class org.geworkbench.builtin.projects.RWspHelper
 
listWsp(boolean) - Method in class org.geworkbench.builtin.projects.RWspHandler
 
LkUsrID - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
load(ComponentConfigurationManagerMenu) - Static method in class org.geworkbench.engine.ccm.ComponentConfigurationManagerWindow
Load method
load() - Static method in class org.geworkbench.engine.ccm.ComponentConfigurationManagerWindow2
Load method
load(ComponentConfigurationManagerMenu) - Static method in class org.geworkbench.engine.ccm.ComponentConfigurationManagerWindow2
Load method
loadAllComponentFolders(File) - Method in class org.geworkbench.engine.ccm.ComponentConfigurationManager
.cwb.xml files decides which rows should be displayed in the CCM window.
loadAnnotationFile(DSMicroarraySet, File, AffyAnnotationParser) - Static method in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
loadClass(String) - Method in class org.geworkbench.engine.management.ComponentClassLoader
 
loadClass(String, boolean) - Method in class org.geworkbench.engine.management.ComponentClassLoader
Attempts to load the class in this classloader before deferring to parent.
LoadDataDialog - Class in org.geworkbench.builtin.projects
Popup to select a file (local or remote) to open.
LoadDataDialog() - Constructor for class org.geworkbench.builtin.projects.LoadDataDialog
 
loadSavedParameterSets() - Method in class org.geworkbench.analysis.AbstractAnalysis
load all saved parameter sets in tmpDir
loadSelectedComponents() - Method in class org.geworkbench.engine.ccm.ComponentConfigurationManager
 
LocalDataFilesHelp - Class in org.geworkbench.builtin.projects
This is a dummy class only for the purpose to facilitate a help topic.
LocalDataFilesHelp() - Constructor for class org.geworkbench.builtin.projects.LocalDataFilesHelp
 
LocalID - Static variable in class org.geworkbench.builtin.projects.RWspHandler
 
LOCUSLINK - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
LOG_TRANSFORMATION_NORMALIZER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
logBinomialDistribution(int, int, double) - Static method in class org.geworkbench.util.associationdiscovery.statistics.ClusterStatistics
 

M

m_threshold - Static variable in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
MageTabFileFormat - Class in org.geworkbench.parsers
 
MageTabFileFormat() - Constructor for class org.geworkbench.parsers.MageTabFileFormat
 
main(String[]) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
main(String[]) - Static method in class org.geworkbench.engine.config.UILauncher
The application start point.
main(String[]) - Static method in class org.geworkbench.engine.management.Overflow
Testing.
main(String[]) - Static method in class org.geworkbench.engine.preferences.PreferencesDialog
 
main(String[]) - Static method in class org.geworkbench.util.Combinations
 
main(String[]) - Static method in class org.geworkbench.util.JAutoList
Test program for JAutoList
main(String[]) - Static method in class org.geworkbench.util.ProgressGraph
 
main(String[]) - Static method in class org.geworkbench.util.QSort
 
main(String[]) - Static method in class org.geworkbench.util.ResultSetlUtil
 
main(String[]) - Static method in class org.geworkbench.util.visualproperties.JShapeButton
 
MAIN_DELIMITER - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
 
mainPanel - Variable in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
makeCopy() - Method in class org.geworkbench.engine.preferences.Preferences
 
MalformedMenuItemException - Exception in org.geworkbench.engine.config.rules
Thrown when the string describing a menu item within a <menu-item> block of the configuration file, is not correctly formed.
MalformedMenuItemException() - Constructor for exception org.geworkbench.engine.config.rules.MalformedMenuItemException
 
MalformedMenuItemException(String) - Constructor for exception org.geworkbench.engine.config.rules.MalformedMenuItemException
 
manager - Variable in class org.geworkbench.engine.ccm.ComponentConfigurationManagerWindow
 
MARGIN - Static variable in class org.geworkbench.engine.preferences.PreferencesDialog
 
marker - Variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node
 
MARKER_LOAD_VALUES - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
MARKER_MEAN_MEDIAN_CENTERING_NORMALIZER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MARKER_MEAN_VARIANCE_NORMALIZER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MARKER_SELECTION - Static variable in class org.geworkbench.events.GeneSelectorEvent
 
MarkerHierCluster - Class in org.geworkbench.bison.model.clusters
Generalization of DefaultHierCluster that contains a org.geworkbench.bison.model.microarray.DSMarker that contains a reference to a Genetic Marker defined by org.geworkbench.bison.model.microarray.MarkerValue.
MarkerHierCluster() - Constructor for class org.geworkbench.bison.model.clusters.MarkerHierCluster
 
markerId - Variable in class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
 
markers() - Method in class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView
 
markers() - Method in interface org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView
 
markers - Variable in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
MarkerSelectedEvent - Class in org.geworkbench.events
Title: Sequence and Pattern Plugin
MarkerSelectedEvent(DSGeneMarker) - Constructor for class org.geworkbench.events.MarkerSelectedEvent
 
MARKUS_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MarkUsResultDataSet - Class in org.geworkbench.bison.datastructure.bioobjects.structure
A class to contain returned result from MarkUs analysis.
MarkUsResultDataSet(DSDataSet<DSBioObject>, String) - Constructor for class org.geworkbench.bison.datastructure.bioobjects.structure.MarkUsResultDataSet
 
maSet - Variable in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
maSetView - Variable in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
mask() - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
 
mask() - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMutableMarkerValue
Sets the mask bit to be temporarily ignored by analyses methods
MASK - Static variable in class org.geworkbench.util.BinaryEncodeDecode
 
mask(int[], boolean) - Method in class org.geworkbench.util.sequences.PatternTableModel
Mask the patterns of this model
maskRepeats() - Method in class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence
 
matchAffyAnnotationFile(DSMicroarraySet) - Static method in class org.geworkbench.util.AffyAnnotationUtil
 
matches - Variable in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
matches() - Method in class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
 
matches() - Method in interface org.geworkbench.bison.datastructure.complex.pattern.DSMatchedPattern
 
matches() - Method in class org.geworkbench.util.patterns.CSMatchedSeqPattern
 
matrix - Variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
max - Variable in class org.geworkbench.bison.util.Range
 
MAX_INTERACTION_NUM - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
MAX_NETWORK_OBJECT_NUMBER - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
MAX_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MEAN_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MEDIAN_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MEDUSA_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MedusaCommand - Class in org.geworkbench.bison.datastructure.biocollections.medusa
A command object to pass around with medusa parameters.
MedusaCommand() - Constructor for class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand
 
MedusaData - Class in org.geworkbench.bison.datastructure.biocollections.medusa
 
MedusaData(DSMicroarraySet, ArrayList<DSGeneMarker>, ArrayList<DSGeneMarker>, MedusaCommand) - Constructor for class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaData
 
MedusaDataSet - Class in org.geworkbench.bison.datastructure.biocollections.medusa
 
MedusaDataSet(DSDataSet<DSMicroarray>, String, MedusaData, String) - Constructor for class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaDataSet
 
menuBarHelp - Class in org.geworkbench.builtin.projects
This is a dummy class only for the purpose to facilitate a help topic.
menuBarHelp() - Constructor for class org.geworkbench.builtin.projects.menuBarHelp
 
menuItemDelimiter - Static variable in class org.geworkbench.engine.config.rules.GeawConfigObject
The character that delimits the menu items within the 'path' attribute of the <menu-item> element in the application configuration file.
MenuItemInfo - Class in org.geworkbench.engine.config
Holds information pertaining to a main menu item for a component.
MenuItemInfo(String, String, String, String, String) - Constructor for class org.geworkbench.engine.config.MenuItemInfo
 
MenuListener - Interface in org.geworkbench.engine.config
Interface to be implemented by all plugin components that want to register listeners for menu items from the menu bar.
merge(HashMap<CSSequence, PatternSequenceDisplayUtil>, HashMap<CSSequence, PatternSequenceDisplayUtil>) - Static method in class org.geworkbench.util.patterns.PatternOperations
 
mergeMicroarraySet(DSMicroarraySet) - Method in class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
 
mergeMicroarraySet(DSMicroarraySet) - Method in interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
Merges another MicroarraySet into this one
mergePatternSequenceDisplayUtil(PatternSequenceDisplayUtil) - Method in class org.geworkbench.util.patterns.PatternSequenceDisplayUtil
 
message - Variable in class org.geworkbench.events.ProjectNodeRenamedEvent
 
microarray - Variable in class org.geworkbench.bison.model.clusters.MicroarrayHierCluster
Stores the microarray associated with this cluster.
MICROARRAY_MEAN_MEDIAN_CENTERING_NORMALIZER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MicroarrayHierCluster - Class in org.geworkbench.bison.model.clusters
Copyright: Copyright (c) 2003
MicroarrayHierCluster() - Constructor for class org.geworkbench.bison.model.clusters.MicroarrayHierCluster
 
MICROARRAYS_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
MicroarraySetParser - Class in org.geworkbench.parsers
Parser of .exp file.
MicroarraySetParser() - Constructor for class org.geworkbench.parsers.MicroarraySetParser
 
microarraySetViewSetter(DSMicroarraySetView<? extends DSGeneMarker, ? extends DSMicroarray>) - Method in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet
 
microarraySetViewSetter(DSMicroarraySetView<? extends DSGeneMarker, ? extends DSMicroarray>) - Method in interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSAnovaResultSet
 
MicroarrayViewEventBase - Class in org.geworkbench.util.microarrayutils
 
MicroarrayViewEventBase() - Constructor for class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 
min - Variable in class org.geworkbench.bison.util.Range
 
MIN_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MindyData - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
Class containing MINDY run results.
MindyData(CSMicroarraySet, ArrayList<DSMicroarray>, float, DSGeneMarker) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
 
MindyData(CSMicroarraySet, List<MindyResultRow>, float) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
Constructor.
MindyDataSet - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
MindyDataSet(DSMicroarraySet, String, MindyData, String) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyDataSet
 
MindyGeneMarker - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
MindyGeneMarker(DSGeneMarker, CollationKey, CollationKey) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyGeneMarker
 
MindyResultRow - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
Represents a row in the MINDY result data.
MindyResultRow(DSGeneMarker, DSGeneMarker, float) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyResultRow
Constructor.
mInfo - Variable in class org.geworkbench.bison.model.clusters.MarkerHierCluster
Stores the marker associated with this cluster.
MISSING - Static variable in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
Value which is assigned to the field confidence to indicate that the marker value is marked as "missing".
MISSING_VALUE_NORMALIZER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MISSING_VALUES_FILTER_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
MODAL_TYPE - Static variable in class org.geworkbench.util.ProgressDialog
 
modifySavedWorkspace(String, String, String, String, String) - Static method in class org.geworkbench.builtin.projects.DownloadClient
 
ModulatorInfo - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
ModulatorInfo() - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo
 
ModulatorStatistics - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
Represents the statistics of a modulator.
ModulatorStatistics(int, int, int) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics
Constructor.
Module - Annotation Type in org.geworkbench.engine.management
Date: Apr 25, 2005 Time: 5:11:31 PM Company: Columbia University Author: John Watkinson
mouseClicked(MouseEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
mouseEntered(MouseEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
mouseExited(MouseEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
mousePressed(MouseEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
mouseReleased(MouseEvent) - Method in class org.geworkbench.events.listeners.ParameterActionListener
 
mover - Variable in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics
 
MRA_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
munder - Variable in class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics
 

N

name - Variable in class org.geworkbench.engine.config.IdentifiableImpl
Stores a (not necessarily unique) name.
NETBOOST_TYPE - Static variable in class org.geworkbench.analysis.AbstractAnalysis
 
NetBoostData - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
NetBoostData(String, String, String) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData
 
NetBoostDataSet - Class in org.geworkbench.util.pathwaydecoder.mutualinformation
 
NetBoostDataSet(DSDataSet<DSBioObject>, String, NetBoostData, String) - Constructor for class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostDataSet
 
NETWORK_ICON - Static variable in class org.geworkbench.builtin.projects.Icons
 
NEW - Static variable in class org.geworkbench.events.SubpanelChangedEvent
 
newName - Variable in class org.geworkbench.events.ProjectNodeRenamedEvent
 
next() - Method in class org.geworkbench.util.ResultSetlUtil
 
NEXT_BUTTON_TEXT - Static variable in class org.geworkbench.util.JAutoList
 
node1 - Variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Edge
 
node2 - Variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Edge
 
NONMODAL_TYPE - Static variable in class org.geworkbench.util.ProgressDialog
 
NonRecursiveClusterSet - Class in org.geworkbench.bison.model.clusters
An serial implementation of cluster set so that no recursive operation is needed to traverse.
NonRecursiveClusterSet(HierCluster, Class<?>) - Constructor for class org.geworkbench.bison.model.clusters.NonRecursiveClusterSet
 
norm - Variable in class org.geworkbench.bison.util.Range
 
Normal - Class in org.geworkbench.bison.util
Title: Plug And Play
Normal() - Constructor for class org.geworkbench.bison.util.Normal
 
NormalizingAnalysis - Interface in org.geworkbench.bison.model.analysis
Tagging interface for filtering analysis algorithms.
notifyAnalysisPanel() - Method in class org.geworkbench.analysis.AbstractSaveableParameterPanel
Notify AnalysisPanel to refresh high lighted group
NotMenuListenerException - Exception in org.geworkbench.engine.config.rules
Thrown when a plugin that does not implement interface MenuListener attempts to register an ActionListener with a menu item in the application configuration file.
NotMenuListenerException() - Constructor for exception org.geworkbench.engine.config.rules.NotMenuListenerException
 
NotMenuListenerException(String) - Constructor for exception org.geworkbench.engine.config.rules.NotMenuListenerException
 
NotVisualPluginException - Exception in org.geworkbench.engine.config.rules
Thrown when a plugin that does not implement interface VisualPlugin attempts to register an ActionListener with a menu item in the application configuration file, requsting to be notified only when the plugin has the focus.
NotVisualPluginException() - Constructor for exception org.geworkbench.engine.config.rules.NotVisualPluginException
 
NotVisualPluginException(String) - Constructor for exception org.geworkbench.engine.config.rules.NotVisualPluginException
 
NULL_BIGDECIMAL - Static variable in class org.geworkbench.util.ResultSetlUtil
 
NULL_STR - Static variable in class org.geworkbench.util.ResultSetlUtil
 
numberThreshold - Variable in class org.geworkbench.bison.model.analysis.FilteringAnalysis
 
numMarkersSelectedLabel - Variable in class org.geworkbench.util.microarrayutils.MicroarrayViewEventBase
 

O

object - Variable in class org.geworkbench.bison.datastructure.complex.pattern.CSPatternMatch
 
objects - Variable in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
OBO_FILENAME - Static variable in class org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
 
OboSourceDialog - Class in org.geworkbench.builtin.projects
 
OboSourcePreference - Class in org.geworkbench.builtin.projects
 
OboSourcePreference.Source - Enum in org.geworkbench.builtin.projects
 
offsets - Variable in class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqCmplxRegistration
 
oldName - Variable in class org.geworkbench.events.ProjectNodeRenamedEvent
 
open(String) - Method in class org.geworkbench.builtin.projects.WorkspaceHandler
Prompt the user to open a saved workspace.
openFiles() - Method in class org.geworkbench.builtin.projects.FileOpenHandler
 
openURL(String) - Static method in class org.geworkbench.util.BrowserLauncher
Attempts to open the default web browser to the given URL.
org.geworkbench.analysis - package org.geworkbench.analysis
 
org.geworkbench.bison.algorithm.classification - package org.geworkbench.bison.algorithm.classification
 
org.geworkbench.bison.annotation - package org.geworkbench.bison.annotation
 
org.geworkbench.bison.datastructure.biocollections - package org.geworkbench.bison.datastructure.biocollections
 
org.geworkbench.bison.datastructure.biocollections.gsea - package org.geworkbench.bison.datastructure.biocollections.gsea
 
org.geworkbench.bison.datastructure.biocollections.lincs - package org.geworkbench.bison.datastructure.biocollections.lincs
 
org.geworkbench.bison.datastructure.biocollections.medusa - package org.geworkbench.bison.datastructure.biocollections.medusa
 
org.geworkbench.bison.datastructure.biocollections.microarrays - package org.geworkbench.bison.datastructure.biocollections.microarrays
 
org.geworkbench.bison.datastructure.biocollections.pca - package org.geworkbench.bison.datastructure.biocollections.pca
 
org.geworkbench.bison.datastructure.biocollections.sequences - package org.geworkbench.bison.datastructure.biocollections.sequences
 
org.geworkbench.bison.datastructure.biocollections.views - package org.geworkbench.bison.datastructure.biocollections.views
 
org.geworkbench.bison.datastructure.bioobjects - package org.geworkbench.bison.datastructure.bioobjects
 
org.geworkbench.bison.datastructure.bioobjects.markers - package org.geworkbench.bison.datastructure.bioobjects.markers
 
org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser - package org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
 
org.geworkbench.bison.datastructure.bioobjects.markers.goterms - package org.geworkbench.bison.datastructure.bioobjects.markers.goterms
 
org.geworkbench.bison.datastructure.bioobjects.microarray - package org.geworkbench.bison.datastructure.bioobjects.microarray
 
org.geworkbench.bison.datastructure.bioobjects.sequence - package org.geworkbench.bison.datastructure.bioobjects.sequence
 
org.geworkbench.bison.datastructure.bioobjects.structure - package org.geworkbench.bison.datastructure.bioobjects.structure
 
org.geworkbench.bison.datastructure.complex.panels - package org.geworkbench.bison.datastructure.complex.panels
 
org.geworkbench.bison.datastructure.complex.pattern - package org.geworkbench.bison.datastructure.complex.pattern
 
org.geworkbench.bison.datastructure.complex.pattern.matrix - package org.geworkbench.bison.datastructure.complex.pattern.matrix
 
org.geworkbench.bison.datastructure.complex.pattern.sequence - package org.geworkbench.bison.datastructure.complex.pattern.sequence
 
org.geworkbench.bison.datastructure.properties - package org.geworkbench.bison.datastructure.properties
 
org.geworkbench.bison.model.analysis - package org.geworkbench.bison.model.analysis
 
org.geworkbench.bison.model.clusters - package org.geworkbench.bison.model.clusters
 
org.geworkbench.bison.parsers - package org.geworkbench.bison.parsers
 
org.geworkbench.bison.parsers.resources - package org.geworkbench.bison.parsers.resources
 
org.geworkbench.bison.util - package org.geworkbench.bison.util
 
org.geworkbench.bison.util.colorcontext - package org.geworkbench.bison.util.colorcontext
 
org.geworkbench.builtin.projects - package org.geworkbench.builtin.projects
 
org.geworkbench.builtin.projects.comments - package org.geworkbench.builtin.projects.comments
 
org.geworkbench.builtin.projects.experimentinformation - package org.geworkbench.builtin.projects.experimentinformation
 
org.geworkbench.builtin.projects.history - package org.geworkbench.builtin.projects.history
 
org.geworkbench.builtin.projects.remoteresources - package org.geworkbench.builtin.projects.remoteresources
 
org.geworkbench.builtin.projects.remoteresources.carraydata - package org.geworkbench.builtin.projects.remoteresources.carraydata
 
org.geworkbench.builtin.projects.util - package org.geworkbench.builtin.projects.util
 
org.geworkbench.engine - package org.geworkbench.engine
 
org.geworkbench.engine.ccm - package org.geworkbench.engine.ccm
 
org.geworkbench.engine.config - package org.geworkbench.engine.config
 
org.geworkbench.engine.config.events - package org.geworkbench.engine.config.events
 
org.geworkbench.engine.config.rules - package org.geworkbench.engine.config.rules
 
org.geworkbench.engine.management - package org.geworkbench.engine.management
 
org.geworkbench.engine.preferences - package org.geworkbench.engine.preferences
 
org.geworkbench.engine.properties - package org.geworkbench.engine.properties
 
org.geworkbench.engine.skin - package org.geworkbench.engine.skin
 
org.geworkbench.events - package org.geworkbench.events
 
org.geworkbench.events.listeners - package org.geworkbench.events.listeners
 
org.geworkbench.parsers - package org.geworkbench.parsers
 
org.geworkbench.parsers.sequences - package org.geworkbench.parsers.sequences
 
org.geworkbench.util - package org.geworkbench.util
 
org.geworkbench.util.annotation - package org.geworkbench.util.annotation
 
org.geworkbench.util.associationdiscovery.statistics - package org.geworkbench.util.associationdiscovery.statistics
 
org.geworkbench.util.microarrayutils - package org.geworkbench.util.microarrayutils
 
org.geworkbench.util.network - package org.geworkbench.util.network
 
org.geworkbench.util.pathwaydecoder - package org.geworkbench.util.pathwaydecoder
 
org.geworkbench.util.pathwaydecoder.mutualinformation - package org.geworkbench.util.pathwaydecoder.mutualinformation
 
org.geworkbench.util.patterns - package org.geworkbench.util.patterns
 
org.geworkbench.util.sequences - package org.geworkbench.util.sequences
 
org.geworkbench.util.visualproperties - package org.geworkbench.util.visualproperties
 
organism - Variable in class org.geworkbench.bison.datastructure.properties.CSUnigene
 
ORGANISM - Static variable in class org.geworkbench.builtin.projects.remoteresources.CaArrayFilteringDialog
 
organisms - Static variable in class org.geworkbench.bison.datastructure.properties.CSUnigene
 
orgSequenceDB - Variable in class org.geworkbench.util.sequences.SequenceViewWidget
 
ORIGINAL - Static variable in class org.geworkbench.engine.preferences.GlobalPreferences
 
OTHER - Static variable in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
 
Overflow - Class in org.geworkbench.engine.management
Asynchronous event synch model that "overflows".
Overflow() - Constructor for class org.geworkbench.engine.management.Overflow
 
OWFileChooser - Class in org.geworkbench.util
 
OWFileChooser() - Constructor for class org.geworkbench.util.OWFileChooser
 
OWFileChooser(String) - Constructor for class org.geworkbench.util.OWFileChooser
 
OWFileChooser(File) - Constructor for class org.geworkbench.util.OWFileChooser
 

P

p_threshold - Static variable in class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
Used to define how present/marginal/absent calls should be made based on the call p-value: p-value < p_threshold --> Present p_threshold <= p-values < m_threshold --> Marginal p-value >= m_threshold --> Absent
paint(Graphics) - Method in class org.geworkbench.util.ProgressGraph
 
paint(Graphics) - Method in class org.geworkbench.util.visualproperties.JShapeButton
 
paintComponent(Graphics) - Method in class org.geworkbench.util.sequences.SequenceViewWidget.JDetailPanel
 
paintComponent(Graphics) - Method in class org.geworkbench.util.sequences.SequenceViewWidgetPanel
 
PANEL_SELECTION - Static variable in class org.geworkbench.events.GeneSelectorEvent
 
panels() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel
 
panels() - Method in class org.geworkbench.bison.datastructure.complex.panels.CSPanel
Get all sub-panels for this panel.
panels() - Method in interface org.geworkbench.bison.datastructure.complex.panels.DSPanel
Gets all the sub-panels of the panel.
PanelVisualProperties - Class in org.geworkbench.util.visualproperties
Keeps track of the visual display properties of panels.
PanelVisualProperties(int, Color) - Constructor for class org.geworkbench.util.visualproperties.PanelVisualProperties
 
PanelVisualPropertiesManager - Class in org.geworkbench.util.visualproperties
Maintains visual properties for panels.
PanelVisualPropertiesManager() - Constructor for class org.geworkbench.util.visualproperties.PanelVisualPropertiesManager
 
ParameterActionListener - Class in org.geworkbench.events.listeners
 
ParameterActionListener(AbstractSaveableParameterPanel) - Constructor for class org.geworkbench.events.listeners.ParameterActionListener
 
parameterHash - Variable in class org.geworkbench.analysis.AbstractAnalysis
Contains indices that are used in order to recover the set of named parameter settings that have been saved for a particular analysis.
ParameterKey - Class in org.geworkbench.analysis
Represents the saved parameters for a specific analysis.
ParameterKey(String, String) - Constructor for class org.geworkbench.analysis.ParameterKey
 
ParameterPanel - Class in org.geworkbench.bison.model.analysis
Copyright: Copyright (c) 2003
ParameterPanel() - Constructor for class org.geworkbench.bison.model.analysis.ParameterPanel
 
ParameterPanelIncludingNormalized - Interface in org.geworkbench.bison.model.analysis
 
parameterSetExist(Map<Serializable, Serializable>) - Method in class org.geworkbench.analysis.AbstractAnalysis
Check if the inputed parameterSet already exist in memory or not.
ParamValidationResults - Class in org.geworkbench.bison.model.analysis
Return value for calls to Analysis.validateParameters().
ParamValidationResults(boolean, String) - Constructor for class org.geworkbench.bison.model.analysis.ParamValidationResults
Constructor.
parent - Variable in class org.geworkbench.bison.model.clusters.AbstractCluster
Reference to Cluster which contains this Cluster as a child
parseAdjacencyMatrix(String, DSMicroarraySet, Map<String, String>, String, String, boolean) - Static method in class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet