Serialized Form

Package fr.curie.BiNoM.cytoscape.analysis

Class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

moduleList

javax.swing.JList moduleList

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

scrollPane

javax.swing.JScrollPane scrollPane

intersectonThresholdS

javax.swing.JSlider intersectonThresholdS

Class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

netwAddCB

javax.swing.JComboBox netwAddCB

netwUpdateList

javax.swing.JList netwUpdateList

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

scrollPane

javax.swing.JScrollPane scrollPane

Class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

sourceList

javax.swing.JList sourceList

targetList

javax.swing.JList targetList

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

scrollPane

javax.swing.JScrollPane scrollPane

directedGraphCB

javax.swing.JCheckBox directedGraphCB

shortestPathRB

javax.swing.JRadioButton shortestPathRB

suboptimalShortestPathRB

javax.swing.JRadioButton suboptimalShortestPathRB

allPathRB

javax.swing.JRadioButton allPathRB

outputCurrentNetworkRB

javax.swing.JRadioButton outputCurrentNetworkRB

outputNewNetworkRB

javax.swing.JRadioButton outputNewNetworkRB

limitationRadius

javax.swing.JCheckBox limitationRadius

searchRadius

javax.swing.JTextField searchRadius

Class fr.curie.BiNoM.cytoscape.analysis.ModularViewDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

networkCB

javax.swing.JComboBox networkCB

moduleList

javax.swing.JList moduleList

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

scrollPane

javax.swing.JScrollPane scrollPane

nodeIntersectionViewCB

javax.swing.JCheckBox nodeIntersectionViewCB

showIntersectionsCB

javax.swing.JCheckBox showIntersectionsCB

Class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

sourceList

javax.swing.JList sourceList

targetList

javax.swing.JList targetList

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

scrollPane

javax.swing.JScrollPane scrollPane

directedGraphCB

javax.swing.JCheckBox directedGraphCB

shortestPathRB

javax.swing.JRadioButton shortestPathRB

suboptimalShortestPathRB

javax.swing.JRadioButton suboptimalShortestPathRB

allPathRB

javax.swing.JRadioButton allPathRB

limitationRadius

javax.swing.JCheckBox limitationRadius

searchRadius

javax.swing.JTextField searchRadius

Package fr.curie.BiNoM.cytoscape.biopax

Class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

reactionCB

javax.swing.JCheckBox reactionCB

pathwayCB

javax.swing.JCheckBox pathwayCB

makeRootPathwayNodeCB

javax.swing.JCheckBox makeRootPathwayNodeCB

includeNextLinksCB

javax.swing.JCheckBox includeNextLinksCB

includePathwaysCB

javax.swing.JCheckBox includePathwaysCB

includeInteractionsCB

javax.swing.JCheckBox includeInteractionsCB

proteinCB

javax.swing.JCheckBox proteinCB

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

file

java.io.File file

url

java.net.URL url

name

java.lang.String name

Class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworksDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

netwList

javax.swing.JList netwList

netwV

java.util.Vector<E> netwV

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

scrollPane

javax.swing.JScrollPane scrollPane

biopax

BioPAX biopax

Package fr.curie.BiNoM.cytoscape.biopax.propedit

Class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTreeFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

treePane

javax.swing.JPanel treePane

listPane

javax.swing.JPanel listPane

rightPane

javax.swing.JPanel rightPane

splitPane

javax.swing.JSplitPane splitPane

biopax

BioPAX biopax

jtree

javax.swing.JTree jtree

display_all

boolean display_all

whatDisplayed

javax.swing.JLabel whatDisplayed

displayAll

javax.swing.JButton displayAll

clsDescCB

javax.swing.JComboBox clsDescCB

newB

javax.swing.JButton newB

leftSPane

javax.swing.JScrollPane leftSPane

rightSPane

javax.swing.JScrollPane rightSPane

Class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

tabbedPane

javax.swing.JTabbedPane tabbedPane

display_all

boolean display_all

edit_mode

boolean edit_mode

whatDisplayed

javax.swing.JLabel whatDisplayed

displayAll

javax.swing.JButton displayAll

edit

javax.swing.JButton edit

browseStack

java.util.Vector<E> browseStack

browseCursor

int browseCursor

backward

javax.swing.JButton backward

forward

javax.swing.JButton forward

browse_only

boolean browse_only

registerChange

boolean registerChange

Class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel extends javax.swing.JScrollPane implements Serializable

Serialized Fields

bobj

BioPAXObject bobj

biopax

BioPAX biopax

display_all

boolean display_all

edit_mode

boolean edit_mode

viewPanel

javax.swing.JPanel viewPanel

browser_frame

BioPAXPropertyBrowserFrame browser_frame

Package fr.curie.BiNoM.cytoscape.biopax.query

Class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfoDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

biopax

BioPAX biopax

okB

javax.swing.JButton okB

Class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

biopax

BioPAX biopax

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

biopaxField

javax.swing.JTextField biopaxField

browseBioPAX

javax.swing.JButton browseBioPAX

indexField

javax.swing.JTextField indexField

browseIndex

javax.swing.JButton browseIndex

Class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

biopax

BioPAX biopax

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

accNumField

javax.swing.JTextField accNumField

browseAccNum

javax.swing.JButton browseAccNum

indexField

javax.swing.JTextField indexField

browseIndex

javax.swing.JButton browseIndex

Class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

biopax

BioPAX biopax

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

textArea

javax.swing.JTextArea textArea

currentNetworkRB

javax.swing.JRadioButton currentNetworkRB

listOfNamesRB

javax.swing.JRadioButton listOfNamesRB

selectAllTypeRB

javax.swing.JRadioButton selectAllTypeRB

selectOfTypeRB

javax.swing.JRadioButton selectOfTypeRB

selectExceptTypeRB

javax.swing.JRadioButton selectExceptTypeRB

outputCurrentNetworkRB

javax.swing.JRadioButton outputCurrentNetworkRB

outputNewNetworkRB

javax.swing.JRadioButton outputNewNetworkRB

listOfTypes

javax.swing.JList listOfTypes

Class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

biopax

BioPAX biopax

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

outputCurrentNetworkRB

javax.swing.JRadioButton outputCurrentNetworkRB

outputNewNetworkRB

javax.swing.JRadioButton outputNewNetworkRB

allNodesRB

javax.swing.JRadioButton allNodesRB

selectedNodesRB

javax.swing.JRadioButton selectedNodesRB

selectComplex

javax.swing.JCheckBox selectComplex

complexExpand

javax.swing.JRadioButton complexExpand

complexNoExpand

javax.swing.JRadioButton complexNoExpand

selectSpecies

javax.swing.JCheckBox selectSpecies

selectReactions

javax.swing.JCheckBox selectReactions

reactionConnecting

javax.swing.JRadioButton reactionConnecting

reactionAll

javax.swing.JRadioButton reactionAll

reactionComplete

javax.swing.JRadioButton reactionComplete

selectPublications

javax.swing.JCheckBox selectPublications

Class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLogDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

textArea

javax.swing.JTextArea textArea

Package fr.curie.BiNoM.cytoscape.lib

Class fr.curie.BiNoM.cytoscape.lib.MLLabel extends javax.swing.JPanel implements Serializable

Serialized Fields

text

java.lang.String text

splitLen

int splitLen

label_v

java.util.Vector<E> label_v

Package fr.curie.BiNoM.cytoscape.netwop

Class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifferenceDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

netw1CB

javax.swing.JComboBox netw1CB

netw2CB

javax.swing.JComboBox netw2CB

diff1TF

javax.swing.JTextField diff1TF

diff2TF

javax.swing.JTextField diff2TF

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

Class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateConfirmDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

mainPanel

javax.swing.JPanel mainPanel

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

netwAdd

cytoscape.CyNetwork netwAdd

netwSup

cytoscape.CyNetwork netwSup

networks

cytoscape.CyNetwork[] networks

cbs

javax.swing.JCheckBox[] cbs

Class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

netwAddCB

javax.swing.JComboBox netwAddCB

netwSupCB

javax.swing.JComboBox netwSupCB

netwUpdateList

javax.swing.JList netwUpdateList

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

scrollPane

javax.swing.JScrollPane scrollPane

Package fr.curie.BiNoM.cytoscape.utils

Class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

nodeCB

fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog.Component[] nodeCB

edgeCB

fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog.Component[] edgeCB

edgeNodeCB

fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog.Component[] edgeNodeCB

addNodes

java.util.HashMap<K,V> addNodes

addEdges

java.util.HashMap<K,V> addEdges

addEdgeNodes

java.util.HashMap<K,V> addEdgeNodes

selectdefB

javax.swing.JButton selectdefB

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

cbNodeMap

java.util.HashMap<K,V> cbNodeMap

cbEdgeMap

java.util.HashMap<K,V> cbEdgeMap

Class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

addNodes

java.util.HashMap<K,V> addNodes

addEdges

java.util.HashMap<K,V> addEdges

addEdgeNodes

java.util.HashMap<K,V> addEdgeNodes