javax.swing.JLabel title
AbstractClusterNetworksTaskFactory factory
javax.swing.JList<E> moduleList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JSlider intersectonThresholdS
int result
java.util.Vector<E> nodesToExclude
java.util.Vector<E> checkBoxes
java.util.HashMap<K,V> addNodes
java.util.HashMap<K,V> addEdges
java.util.HashMap<K,V> addEdgeNodes
javax.swing.JButton selectdefB
javax.swing.JButton okB
javax.swing.JButton cancelB
AbstractExcludeIntermediateNodesTaskFactory factory
Graph graph
javax.swing.JComboBox<E> networkCB
javax.swing.JList<E> moduleList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JCheckBox nodeIntersectionViewCB
javax.swing.JCheckBox showIntersectionsCB
AbstractModularViewTaskFactory factory
javax.swing.JCheckBox reactionCB
javax.swing.JCheckBox pathwayCB
javax.swing.JCheckBox makeRootPathwayNodeCB
javax.swing.JCheckBox includeNextLinksCB
javax.swing.JCheckBox includePathwaysCB
javax.swing.JCheckBox includeInteractionsCB
javax.swing.JCheckBox proteinCB
javax.swing.JButton okB
javax.swing.JButton cancelB
java.io.File file
java.net.URL url
java.lang.String name
AbstractBioPAXImportTaskFactory factory
javax.swing.JPanel treePane
javax.swing.JPanel listPane
javax.swing.JPanel rightPane
javax.swing.JSplitPane splitPane
BioPAX biopax
javax.swing.JTree jtree
boolean display_all
javax.swing.JLabel whatDisplayed
javax.swing.JButton displayAll
javax.swing.JComboBox<E> clsDescCB
javax.swing.JButton newB
javax.swing.JScrollPane leftSPane
javax.swing.JScrollPane rightSPane
javax.swing.JTabbedPane tabbedPane
boolean display_all
boolean edit_mode
javax.swing.JLabel whatDisplayed
javax.swing.JButton displayAll
javax.swing.JButton edit
java.util.Vector<E> browseStack
int browseCursor
javax.swing.JButton backward
javax.swing.JButton forward
boolean browse_only
boolean registerChange
BioPAXObject bobj
BioPAX biopax
boolean display_all
boolean edit_mode
javax.swing.JPanel viewPanel
BioPAXPropertyBrowserFrame browser_frame
javax.swing.JPanel jContentPane
javax.swing.JLabel jLabelName
javax.swing.JLabel jLabelId
javax.swing.JLabel jLabelX
javax.swing.JLabel jLabelY
javax.swing.JTextField textName
javax.swing.JTextField textId
javax.swing.JTextField textX
javax.swing.JTextField textY
javax.swing.JPanel jPanel
javax.swing.JButton jButtonGET
javax.swing.JButton jButtonADD
javax.swing.JPanel jContentPane
javax.swing.JLabel jLabelName
javax.swing.JLabel jLabelId
javax.swing.JLabel jLabelX
javax.swing.JLabel jLabelY
javax.swing.JTextField textName
javax.swing.JTextField textId
javax.swing.JTextField textX
javax.swing.JTextField textY
javax.swing.JPanel jPanel
javax.swing.JButton jButtonGET
javax.swing.JButton jButtonADD
int result
java.util.Vector<E> constitutiveReactions
java.util.Vector<E> checkBoxes
java.util.HashMap<K,V> addNodes
java.util.HashMap<K,V> addEdges
java.util.HashMap<K,V> addEdgeNodes
javax.swing.JButton selectdefB
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JList<E> familyList
javax.swing.JList<E> memberList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane1
javax.swing.JScrollPane scrollPane2
int result
java.util.HashMap<K,V> tempFamilies
java.util.Vector<E> newFamilies
javax.swing.JRadioButton expandRB
javax.swing.JRadioButton collapseRB
javax.swing.JButton collapseAll
javax.swing.JButton expandAll
javax.swing.JButton selectAll
javax.swing.JButton selectDefault
javax.swing.JButton unselectAll
javax.swing.JButton addNewFamily
boolean blockMemberUpdate
Graph network
java.util.Vector<E> selectedNodes
javax.swing.JList<E> sourceList
javax.swing.JList<E> targetList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JCheckBox goUpstreamCB
javax.swing.JCheckBox goDownstreamCB
javax.swing.JCheckBox checkHUGOatt
javax.swing.JTextField searchRadius
javax.swing.JTextField minimumNumberOfGenes
javax.swing.JComboBox<E> netwAddCB
javax.swing.JList<E> netwUpdateList
javax.swing.JRadioButton FirstOrderConnection
javax.swing.JRadioButton FirstOrderConnectionsWithComplexes
javax.swing.JRadioButton SecondOrderConnections
javax.swing.JRadioButton AddFirstNeighbours
javax.swing.JRadioButton ConnectByShortestPath
javax.swing.JCheckBox TestComponentSignificance
javax.swing.JCheckBox MakeConnectivityTable
javax.swing.JComboBox<E> NumberOfPermutations
javax.swing.JCheckBox MakeSizeSignificanceTest
javax.swing.JComboBox<E> NumberOfPermutationsForSizeTest
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JTextArea fixedNodeList
javax.swing.JTextArea sizesToTest
javax.swing.JList<E> sourceList
javax.swing.JList<E> targetList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JCheckBox directedGraphCB
javax.swing.JRadioButton shortestPathRB
javax.swing.JRadioButton suboptimalShortestPathRB
javax.swing.JRadioButton allPathRB
javax.swing.JRadioButton outputCurrentNetworkRB
javax.swing.JRadioButton outputNewNetworkRB
javax.swing.JCheckBox limitationRadius
javax.swing.JTextField searchRadius
javax.swing.JList<E> sourceList
javax.swing.JList<E> targetList
javax.swing.JList<E> sideList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JRadioButton shortestPathRB
javax.swing.JRadioButton suboptimalShortestPathRB
javax.swing.JRadioButton allPathRB
javax.swing.JRadioButton bergeRB
javax.swing.JRadioButton partialRB
javax.swing.JCheckBox limitationRadius
javax.swing.JTextField searchRadius
javax.swing.JTextField maxSetNb
javax.swing.JTextField maxSetSize
javax.swing.JTextField maxSetSizeBerge
javax.swing.JPanel panel
java.util.Vector<E> nodeList
javax.swing.JComboBox<E> attNames
java.lang.String selectedAttributeName
java.util.HashMap<K,V> nodeID2attribute
DataPathConsistencyAnalyzer analyzer
int result
javax.swing.JTextArea textArea
javax.swing.JFileChooser fc
DataPathConsistencyAnalyzer dpc
javax.swing.JList<E> sourceList
javax.swing.JList<E> targetList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JCheckBox directedGraphCB
javax.swing.JRadioButton shortestPathRB
javax.swing.JRadioButton suboptimalShortestPathRB
javax.swing.JRadioButton allPathRB
javax.swing.JCheckBox limitationRadius
javax.swing.JTextField searchRadius
javax.swing.JList<E> sourceList
javax.swing.JList<E> targetList
javax.swing.JPanel panel
javax.swing.JTextField numberOfPermutations
DataPathConsistencyAnalyzer analyzer
javax.swing.JRadioButton permuteActiveNodesRB
javax.swing.JRadioButton permuteAllNodesRB
javax.swing.JList<E> sourceList
javax.swing.JList<E> targetList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
javax.swing.JCheckBox directedGraphCB
javax.swing.JRadioButton shortestPathRB
javax.swing.JRadioButton suboptimalShortestPathRB
javax.swing.JRadioButton allPathRB
javax.swing.JButton advancedB
javax.swing.JButton infTableB
javax.swing.JComboBox<E> ActivityAttrbuteCB
javax.swing.JButton updateActivityAttributeB
javax.swing.JCheckBox limitationRadius
javax.swing.JTextField searchRadius
javax.swing.JPanel panel
javax.swing.JPanel panelAct
java.util.Vector<E> activeNodes
java.util.Vector<E> dataActive
java.util.Vector<E> targetNodes
java.util.Vector<E> dataTarget
DataPathConsistencyAnalyzer analyzer
int result
javax.swing.JList<E> pathwayList
javax.swing.JList<E> activeNodeList
javax.swing.JList<E> pathList
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JButton reportB
javax.swing.JButton makeTargetNetworkB
javax.swing.JButton makeNodeNetworkB
javax.swing.JButton makePathNetworkB
javax.swing.JButton significanceTestB
javax.swing.JButton selectAllPathB
javax.swing.JButton showMostSignificantB
javax.swing.JButton DesInconsistentNodesB
javax.swing.JButton DesInconsistentPathsB
javax.swing.JButton DesInactivePathsB
javax.swing.JTextField pathActivityThresh
javax.swing.JScrollPane scrollPane
javax.swing.JCheckBox useSignAlgebra
javax.swing.JCheckBox useAllnodesAttributes
DataPathConsistencyAnalyzer analyzer
int result
javax.swing.JLabel labelTargetInfo
javax.swing.JLabel labelNodeInfo
javax.swing.JLabel labelPathInfo
javax.swing.JPanel panel
javax.swing.JList<E> netwList
java.util.Vector<E> netwV
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JScrollPane scrollPane
BioPAX biopax
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton showAllEntityNamesB
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JTextField biopaxField
javax.swing.JButton browseBioPAX
javax.swing.JTextField indexField
javax.swing.JButton browseIndex
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JTextField accNumField
javax.swing.JButton browseAccNum
javax.swing.JTextField indexField
javax.swing.JButton browseIndex
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JTextArea textArea
javax.swing.JRadioButton currentNetworkRB
javax.swing.JRadioButton listOfNamesRB
javax.swing.JRadioButton selectAllTypeRB
javax.swing.JRadioButton selectOfTypeRB
javax.swing.JRadioButton selectExceptTypeRB
javax.swing.JRadioButton outputCurrentNetworkRB
javax.swing.JRadioButton outputNewNetworkRB
javax.swing.JList<E> listOfTypes
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JRadioButton outputCurrentNetworkRB
javax.swing.JRadioButton outputNewNetworkRB
javax.swing.JRadioButton allNodesRB
javax.swing.JRadioButton selectedNodesRB
javax.swing.JCheckBox selectComplex
javax.swing.JRadioButton complexExpand
javax.swing.JRadioButton complexNoExpand
javax.swing.JCheckBox selectSpecies
javax.swing.JCheckBox selectReactions
javax.swing.JRadioButton reactionConnecting
javax.swing.JRadioButton reactionAll
javax.swing.JRadioButton reactionComplete
javax.swing.JCheckBox selectPublications
javax.swing.JCheckBox cbchangeSpeciesCoordinates
javax.swing.JCheckBox cbPutCytoscapeColorsOnSpecies
javax.swing.JCheckBox cbPutCytoscapeColorsOnReactions
javax.swing.JCheckBox cbMakeReactionsGrey
javax.swing.JCheckBox cbmergeIfFileExists
javax.swing.JCheckBox cbremoveLineBreakPoints
javax.swing.JCheckBox cbinsertHypotheticalInfluences_complexMutualInhibition
javax.swing.JCheckBox cbinsertHypotheticalInfluences_inhCatalysisReactant
javax.swing.JCheckBox cbremoveComplexNames
javax.swing.JCheckBox cbremoveResiduesNames
javax.swing.JTextField tfscaleFactor
javax.swing.JRadioButton rbScalingPosition
javax.swing.JRadioButton rbScalingShape
javax.swing.JTextField tfFontSize
javax.swing.JCheckBox cbChangeFontSize
javax.swing.ButtonGroup bgtypeOfScaling
javax.swing.JButton okB
javax.swing.JButton cancelB
java.io.File cdfile
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JTextField accNumField
javax.swing.JButton browseAccNum
javax.swing.JTextField indexField
javax.swing.JButton browseIndex
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JTextField indexField
javax.swing.JButton browseIndex
javax.swing.JCheckBox formatAnnotations
javax.swing.JCheckBox allAnnotations
javax.swing.JCheckBox guessIdentifiers
javax.swing.JCheckBox removeEmptySections
javax.swing.JCheckBox removeInvalidTags
javax.swing.JCheckBox moveNonannotatedTextToReferenceSection
javax.swing.JCheckBox useHUGOIdsForModuleIdentification
javax.swing.JCheckBox insertMapsTagBeforeModules
javax.swing.JTextField gmtFileField
javax.swing.JButton browseGMTIndex
javax.swing.JFileChooser fc
javax.swing.JTextField field1
javax.swing.JTextField field2
javax.swing.JCheckBox mergeImages
javax.swing.JTextField imageZoomLevel
javax.swing.JLabel lab1
javax.swing.JButton b1
javax.swing.JButton b2
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JTextField datatableField
javax.swing.JButton browseDatatable
javax.swing.JTextField celldesignerField
javax.swing.JButton browseCellDesigner
javax.swing.JTextField pngField
javax.swing.JButton browsePng
javax.swing.JTextField proteinGroupField
javax.swing.JButton browseProteinGroup
javax.swing.JCheckBox normalizeToZValues
javax.swing.JCheckBox useModuleDefinitionsFromCellDesignerFile
javax.swing.JCheckBox useProteinNameIfHUGOisntFound
javax.swing.JTextField influenceRadius
javax.swing.JTextField thresholdForComputingGradient
javax.swing.JTextField gridSizeX
javax.swing.JTextField gridSizeY
BioPAX biopax
javax.swing.JButton okB
javax.swing.JButton cancelB
javax.swing.JTextField wordPressURL
javax.swing.JTextField wordPressUser
javax.swing.JTextField wordPressPassw
javax.swing.JButton browseAccNum
javax.swing.JTextField configFile
javax.swing.JButton browseIndex
javax.swing.JCheckBox produceBrowseOnlyVersion
java.awt.Container container
int width
int heightByLine
javax.swing.JButton okBouton
javax.swing.JButton cancelBouton
boolean ok
javax.swing.JComboBox<E>[] comboBoxes
java.util.ArrayList<E> fields
java.util.ArrayList<E> datas
javax.swing.JTextArea textArea
GraphDocument _graphDoc
Graph _graph
org.sbml.x2001.ns.celldesigner.SbmlDocument _sbmlobject
java.util.HashMap<K,V> _sbmlObjectMap
BioPAX _biopaxobject
boolean showOnlyEntityNames
boolean showAlsoSynonyms
javax.swing.JTextArea textArea
GraphDocument _graphDoc
org.sbml.x2001.ns.celldesigner.SbmlDocument _sbmlobject
java.util.HashMap<K,V> _sbmlObjectMap
BioPAX _biopaxobject
fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog.Component[] nodeCB
fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog.Component[] edgeCB
fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog.Component[] edgeNodeCB
java.util.HashMap<K,V> addNodes
java.util.HashMap<K,V> addEdges
java.util.HashMap<K,V> addEdgeNodes
javax.swing.JButton selectdefB
javax.swing.JButton okB
javax.swing.JButton cancelB
java.util.HashMap<K,V> cbNodeMap
java.util.HashMap<K,V> cbEdgeMap
PavingData pd
double maxAbsVal
fr.curie.BiNoM.cytoscape.utils.PavingDialog.TextBox textbox
javax.swing.JPanel pan
int side
boolean stateNotValue
boolean blueWhiteRed
int wGap
javax.swing.JComboBox<E> listOfAtributes
javax.swing.JTextField subString
Graph _graph