Serialized Form

Package cytoscape.actions

Class cytoscape.actions.AlignHorizontalAction extends AbstractAction implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

Class cytoscape.actions.AlignVerticalAction extends AbstractAction implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

Class cytoscape.actions.AlphabeticalSelectionAction extends CytoscapeAction implements Serializable

Serialized Fields

dialog

JDialog dialog

search

JButton search

cancel

JButton cancel

searchField

JTextField searchField

Class cytoscape.actions.AnimatedLayoutAction extends AbstractAction implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

Deprecated.

bool

boolean bool

Deprecated.

Class cytoscape.actions.ArrangeAction extends JMenu implements Serializable

Serialized Fields

cascade

JMenuItem cascade

.

tiled

JMenuItem tiled

horizontal

JMenuItem horizontal

vertical

JMenuItem vertical

Class cytoscape.actions.BackgroundColorAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.BendSelectedEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.BirdsEyeViewAction extends CytoscapeAction implements Serializable

Serialized Fields

bev

ding.view.BirdsEyeView bev

Deprecated.

on

boolean on

Deprecated.

Class cytoscape.actions.BookmarkAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.CheckBoxFileChooser extends JFileChooser implements Serializable

Serialized Fields

jcb

JCheckBox jcb

Deprecated.

jcbFlag

boolean jcbFlag

Deprecated.

jcbLabel

String jcbLabel

Deprecated.

Class cytoscape.actions.CloneGraphInNewWindowAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.CreateNetworkViewAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.CytoPanelAction extends CytoscapeAction implements Serializable

Serialized Fields

title

String title

position

int position

Class cytoscape.actions.DeleteAction extends CytoscapeAction implements Serializable

serialVersionUID: -5769255815829787466L

Serialized Fields

graphObj

GraphObject graphObj

Class cytoscape.actions.DeselectAllAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.DeSelectAllEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.DeSelectAllNodesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.DestroyNetworkAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.DestroyNetworkViewAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.EdgeManipulationAction extends AbstractAction implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

Class cytoscape.actions.ExitAction extends CytoscapeAction implements Serializable

Serialized Fields

returnVal

int returnVal

Class cytoscape.actions.ExpFileChooser extends JFileChooser implements Serializable

Serialized Fields

jcb

JCheckBox jcb

Deprecated.

copyToAttribs

boolean copyToAttribs

Deprecated.

Class cytoscape.actions.ExportAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExportAsGMLAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExportAsGraphicsAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExportAsInteractionsAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExportAsXGMMLAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExportEdgeAttributesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExportNodeAttributesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExportVizmapAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.FitContentAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.GraphObjectSelectionAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.HelpAboutAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.HelpContactHelpDeskAction extends CytoscapeAction implements Serializable

Serialized Fields

helpDeskURL

String helpDeskURL

Class cytoscape.actions.HelpContentsAction extends CytoscapeAction implements Serializable

Serialized Fields

csh

javax.help.CSH.DisplayHelpFromSource csh

Class cytoscape.actions.HideSelectedAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.HideSelectedEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.HideSelectedNodesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ImportBioDataServerAction extends CytoscapeAction implements Serializable

Serialized Fields

wiz

GeneOntologyWizard wiz

Class cytoscape.actions.ImportEdgeAttributesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ImportExpressionMatrixAction extends CytoscapeAction implements Serializable

Serialized Fields

windowMenu

CyMenus windowMenu

Class cytoscape.actions.ImportGraphFileAction extends CytoscapeAction implements Serializable

Serialized Fields

windowMenu

CyMenus windowMenu

Class cytoscape.actions.ImportNodeAttributesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ImportVizmapAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.InvertSelectedEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.InvertSelectedNodesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ListFromFileSelectionAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.MapOntologyAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.NewNetworkAction extends CytoscapeAction implements Serializable

serialVersionUID: -5729080768973677821L

Class cytoscape.actions.NewSessionAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.NewWindowSelectedNodesEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.NewWindowSelectedNodesOnlyAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.OpenSessionAction extends CytoscapeAction implements Serializable

Serialized Fields

windowMenu

CyMenus windowMenu

Class cytoscape.actions.PluginManagerAction extends CytoscapeAction implements Serializable

Serialized Fields

bookmarkCategory

String bookmarkCategory

Class cytoscape.actions.PluginUpdateAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.PreferenceAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.PrintAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ProxyServerAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.RotateSelectedNodesAction extends AbstractAction implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

Class cytoscape.actions.SaveSessionAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SaveSessionAsAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectAdjacentEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectAllAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectAllEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectAllNodesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectConnectedNodesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectFirstNeighborsAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectionModeAction extends JMenu implements Serializable

Serialized Fields

nodes

JCheckBoxMenuItem nodes

Creates a new SelectionModeAction object.

edges

JCheckBoxMenuItem edges

nodesAndEdges

JCheckBoxMenuItem nodesAndEdges

Class cytoscape.actions.SetVisualPropertiesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ShowAllAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ShowGraphicsDetailsAction extends CytoscapeAction implements Serializable

Serialized Fields

showFlag

boolean showFlag

Class cytoscape.actions.StraightenSelectedEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ToggleVisualMapperAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.UnHideSelectedAction extends AbstractAction implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

Class cytoscape.actions.UnHideSelectedEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.UnHideSelectedNodesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.WebServiceNetworkImportAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ZoomAction extends CytoscapeAction implements Serializable

Serialized Fields

factor

double factor

Class cytoscape.actions.ZoomSelectedAction extends CytoscapeAction implements Serializable

Package cytoscape.data

Class cytoscape.data.AttributeSaverDialog extends JDialog implements Serializable

Serialized Fields

state

cytoscape.data.AttributeSaverState state

The state associated with the attribute table, keeps track of the attribute, filename and booleans. Edited through the jtable

attributeTable

JTable attributeTable

JTable for displaying boolean, attribute and filename

saveButton

JButton saveButton

Class cytoscape.data.ExpressionData extends Object implements Serializable

Serialized Fields

taskMonitor

cytoscape.task.TaskMonitor taskMonitor

significanceType

int significanceType

keyAttributeName

String keyAttributeName

mappingByAttribute

boolean mappingByAttribute

filename

String filename

numGenes

int numGenes

numConds

int numConds

extraTokens

int extraTokens

haveSigValues

boolean haveSigValues

geneNames

Vector<E> geneNames

geneDescripts

Vector<E> geneDescripts

condNames

Vector<E> condNames

geneNameToIndex

Hashtable<K,V> geneNameToIndex

condNameToIndex

Hashtable<K,V> condNameToIndex

minExp

double minExp

maxExp

double maxExp

minSig

double minSig

maxSig

double maxSig

allMeasurements

Vector<E> allMeasurements

Class cytoscape.data.mRNAMeasurement extends Object implements Serializable

Serialized Fields

expressionRatio

double expressionRatio

significance

double significance

Package cytoscape.data.annotation

Class cytoscape.data.annotation.Annotation extends Object implements Serializable

Serialized Fields

ontology

Ontology ontology

curator

String curator

species

String species

type

String type

hash

HashMap<K,V> hash

Class cytoscape.data.annotation.AnnotationDescription extends Object implements Serializable

Serialized Fields

species

String species

curator

String curator

annotationType

String annotationType

Class cytoscape.data.annotation.AnnotationGui extends CytoscapeAction implements Serializable

Serialized Fields

dataServer

BioDataServer dataServer

defaultSpecies

String defaultSpecies

annotationDescriptions

AnnotationDescription[] annotationDescriptions

availableAnnotationsTree

JTree availableAnnotationsTree

currentAnnotationsTree

JTree currentAnnotationsTree

actionListBox

JList actionListBox

actionListModel

DefaultListModel actionListModel

actionListBoxCurrentSelection

int actionListBoxCurrentSelection

annotationPath

TreePath annotationPath

currentAnnotationCategory

String currentAnnotationCategory

mainDialog

JDialog mainDialog

annotateNodesButton

JButton annotateNodesButton

layoutByAnnotationButton

JButton layoutByAnnotationButton

addSharedAnnotationEdgesButton

JButton addSharedAnnotationEdgesButton

deleteCreatedObjectsButton

JButton deleteCreatedObjectsButton

networkView

CyNetworkView networkView

network

CyNetwork network

Class cytoscape.data.annotation.AnnotationGui.Gui extends JDialog implements Serializable

Class cytoscape.data.annotation.AnnotationGui.Gui.DeleteCreatedObjectsAction extends AbstractAction implements Serializable

Class cytoscape.data.annotation.AnnotationGui.Gui.DrawSharedEdgesAnnotationAction extends AbstractAction implements Serializable

Class cytoscape.data.annotation.AnnotationGui.Gui.LayoutByAnnotationAction extends AbstractAction implements Serializable

Class cytoscape.data.annotation.AnnotationGui.Gui.OKAction extends AbstractAction implements Serializable

Class cytoscape.data.annotation.Ontology extends Object implements Serializable

Serialized Fields

curator

String curator

ontologyType

String ontologyType

termHash

HashMap<K,V> termHash

Class cytoscape.data.annotation.OntologyDescription extends Object implements Serializable

Serialized Fields

curator

String curator

ontologyType

String ontologyType

Class cytoscape.data.annotation.OntologyMapperDialog extends JDialog implements Serializable

Serialized Fields

dataServer

BioDataServer dataServer

defaultSpecies

String defaultSpecies

annotationDescriptions

AnnotationDescription[] annotationDescriptions

annotationPath

TreePath annotationPath

currentAnnotationCategory

String currentAnnotationCategory

networkView

CyNetworkView networkView

network

CyNetwork network

nodeAttributes

CyAttributes nodeAttributes

addEdgesButton

JButton addEdgesButton

applyAllButton

JButton applyAllButton

applyButton

JButton applyButton

buttonPanel

JPanel buttonPanel

deleteCreatedButton

JButton deleteCreatedButton

goAttributeScrollPane

JScrollPane goAttributeScrollPane

goAttributeTree

JTree goAttributeTree

goServerScrollPane

JScrollPane goServerScrollPane

goServerTree

JTree goServerTree

layoutButton

JButton layoutButton

okButton

JButton okButton

removeAllButton

JButton removeAllButton

removeButton

JButton removeButton

contextMenu

JPopupMenu contextMenu

amigoLink

JMenuItem amigoLink

Class cytoscape.data.annotation.OntologyTerm extends Object implements Serializable

Serialized Fields

name

String name

id

int id

parents

Vector<E> parents

containers

Vector<E> containers

Package cytoscape.data.readers

Class cytoscape.data.readers.GMLException extends RuntimeException implements Serializable

Class cytoscape.data.readers.XGMMLException extends RuntimeException implements Serializable

Package cytoscape.data.servers

Class cytoscape.data.servers.BioDataServerRmi extends UnicastRemoteObject implements Serializable

Serialized Fields

annotations

HashMap<K,V> annotations

thesauri

HashMap<K,V> thesauri

startTime

Date startTime

lastAccessTime

Date lastAccessTime

Package cytoscape.data.servers.ui

Class cytoscape.data.servers.ui.AnotationPanel extends JPanel implements Serializable

Serialized Fields

LS

String LS

columnNames

String[] columnNames

oboFile

File oboFile

gaFiles

HashMap<K,V> gaFiles

nodeAttributes

CyAttributes nodeAttributes

bdsu

BioDataServerUtil bdsu

taxonMap

HashMap<K,V> taxonMap

nodeSpeciesMap

HashMap<K,V> nodeSpeciesMap

synoMap

HashMap<K,V> synoMap

isSpecies

boolean isSpecies

originalSpecies

HashMap<K,V> originalSpecies

headerScrollPane

JScrollPane headerScrollPane

oboButton

JButton oboButton

gaButton

JButton gaButton

flipCheckBox

JCheckBox flipCheckBox

speciesComboBox

JComboBox speciesComboBox

headerEditorPane

JEditorPane headerEditorPane

jLabel1

JLabel jLabel1

nodeNameList

JList nodeNameList

gaList

JList gaList

jPanel1

JPanel jPanel1

jPanel2

JPanel jPanel2

upperPanel

JPanel upperPanel

jScrollPane2

JScrollPane jScrollPane2

jScrollPane3

JScrollPane jScrollPane3

jSeparator1

JSeparator jSeparator1

jSplitPane1

JSplitPane jSplitPane1

previewTable

JTable previewTable

oboTextField

JTextField oboTextField

previewScrollPane

JScrollPane previewScrollPane

speciesCheckBox

JCheckBox speciesCheckBox

gaListModel

DefaultListModel gaListModel

previewTableModel

DefaultTableModel previewTableModel

Class cytoscape.data.servers.ui.ManifestfileSelectionPanel extends JPanel implements Serializable

Serialized Fields

anotherBlankSpace

JLabel anotherBlankSpace

blankSpace

JLabel blankSpace

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

contentPanel

JPanel contentPanel

iconLabel

JLabel iconLabel

separator

JSeparator separator

textLabel

JLabel textLabel

titlePanel

JPanel titlePanel

jLabel3

JLabel jLabel3

spList

JComboBox spList

start

File start

species

String species

taxonNameBox

JTextField taxonNameBox

manifestFileName

JTextField manifestFileName

selectManifestFile

JButton selectManifestFile

manifestName

String manifestName

jc1

JFileChooser jc1

Class cytoscape.data.servers.ui.OboPanel extends JPanel implements Serializable

Serialized Fields

LS

String LS

oboFile

File oboFile

headerEditorPane

JEditorPane headerEditorPane

headerScrollPane1

JScrollPane headerScrollPane1

jSeparator1

JSeparator jSeparator1

messageEditorPane

JEditorPane messageEditorPane

messageScrollPane

JScrollPane messageScrollPane

oboFileNameTextField

JTextField oboFileNameTextField

selectButton

JButton selectButton

titleLabel

JLabel titleLabel

Class cytoscape.data.servers.ui.SelectFormatPanel extends JPanel implements Serializable

Serialized Fields

fileTypeButtonGroup

ButtonGroup fileTypeButtonGroup

descriptionEditorPane

JEditorPane descriptionEditorPane

titleLabel

JLabel titleLabel

messageLabel

JLabel messageLabel

bdsRadioButton

JRadioButton bdsRadioButton

oboRadioButton

JRadioButton oboRadioButton

htmlScrollPane

JScrollPane htmlScrollPane

jSeparator1

JSeparator jSeparator1

Class cytoscape.data.servers.ui.SpeciesPanel extends JPanel implements Serializable

Serialized Fields

currentSpeciesName

String currentSpeciesName

overwriteComboBox

JComboBox overwriteComboBox

jLabel1

JLabel jLabel1

jSeparator1

JSeparator jSeparator1

overwriteCheckBox

JCheckBox overwriteCheckBox

messageEditorPane

JEditorPane messageEditorPane

messageScrollPane

JScrollPane messageScrollPane

Package cytoscape.data.synonyms

Class cytoscape.data.synonyms.Thesaurus extends Object implements Serializable

Serialized Fields

species

String species

labelToCommon

HashMap<K,V> labelToCommon

commonToLabel

HashMap<K,V> commonToLabel

aliasesToLabel

HashMap<K,V> aliasesToLabel

labelToAll

HashMap<K,V> labelToAll

Package cytoscape.data.webservice

Class cytoscape.data.webservice.CyWebServiceEvent extends EventObject implements Serializable

Serialized Fields

type

CyWebServiceEvent.WSEventType type

parameter

Object parameter

nextMove

CyWebServiceEvent.WSEventType nextMove

Class cytoscape.data.webservice.CyWebServiceException extends Exception implements Serializable

Serialized Fields

ec

CyWebServiceException.WSErrorCode ec

Class cytoscape.data.webservice.WebServiceClientImpl extends Object implements Serializable

Serialized Fields

clientStub

Object clientStub

clientID

String clientID

displayName

String displayName

type

WebServiceClientManager.ClientType[] type

props

ModuleProperties props

availableMethods

Collection<E> availableMethods

description

String description

Class cytoscape.data.webservice.WebServiceClientImplWithGUI extends WebServiceClientImpl<S> implements Serializable

Serialized Fields

gui

Container gui

Package cytoscape.data.webservice.ui

Class cytoscape.data.webservice.ui.UnifiedNetworkImportDialog extends JDialog implements Serializable

Serialized Fields

selectedClientID

String selectedClientID

task

cytoscape.data.webservice.ui.UnifiedNetworkImportDialog.WSNetworkImportTask task

clientNames

Map<K,V> clientNames

serviceUIPanels

Map<K,V> serviceUIPanels

numDataSources

int numDataSources

numClients

int numClients

cancelButton

JButton cancelButton

datasourceComboBox

JComboBox datasourceComboBox

datasourceLabel

JLabel datasourceLabel

mainPanel

JPanel mainPanel

mainTabbedPane

JTabbedPane mainTabbedPane

propertyPanel

JPanel propertyPanel

propertyScrollPane

JScrollPane propertyScrollPane

resetButton

JButton resetButton

searchButton

JButton searchButton

searchTermScrollPane

JScrollPane searchTermScrollPane

searchTermTextPane

JTextPane searchTermTextPane

titleLabel

JLabel titleLabel

aboutButton

JButton aboutButton

buttonPanel

JPanel buttonPanel

queryPanel

JPanel queryPanel

installPanel

JPanel installPanel

clearButton

JButton clearButton

dataQueryPanel

JPanel dataQueryPanel

datasourcePanel

JPanel datasourcePanel

titleIconLabel

JLabel titleIconLabel

titlePanel

JPanel titlePanel

Class cytoscape.data.webservice.ui.WSImportResultDialog extends JDialog implements Serializable

Serialized Fields

basePanel

JPanel basePanel

nameLabel