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Cytoscape 2.8.0 API
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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.ApplyLayoutAction extends CytoscapeAction implements Serializable

serialVersionUID: -576925581582912345L

Serialized Fields

layoutName

String layoutName

alg

CyLayoutAlgorithm alg

applyLayoutButton

JButton applyLayoutButton

Class cytoscape.actions.ApplyVisualStyleAction extends CytoscapeAction implements Serializable

serialVersionUID: 2435881456685787138L

Serialized Fields

styleName

String styleName

Class cytoscape.actions.ArrangeAction extends JMenu implements Serializable

Serialized Fields

cascade

JMenuItem cascade
.

tiled

JMenuItem tiled

horizontal

JMenuItem horizontal

vertical

JMenuItem vertical

bydefault

JMenuItem bydefault

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

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

serialVersionUID: 5033320941306310434L

Class cytoscape.actions.CytoPanelAction extends CytoscapeAction implements Serializable

serialVersionUID: 2069061664423847850L

Serialized Fields

title

String title

position

int position

parent

CytoPanelName parent

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

serialVersionUID: -5887102279435784342L

Serialized Fields

chooser

ExportAsGraphicsFileChooser chooser

defaultFileExt

String defaultFileExt

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.ExportNetworksAsNNFAction 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

helpActionListener

ActionListener helpActionListener

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.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

serialVersionUID: 2309144834195371889L

Class cytoscape.actions.LoggerAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.MemoryUsageAction 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

logger

CyLogger logger

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

serialVersionUID: 3340562148562666874L

Class cytoscape.actions.ShowAllAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ShowCustomGraphicsManagerAction extends CytoscapeAction implements Serializable

serialVersionUID: 5876533870116518191L

Serialized Fields

manager

CustomGraphicsManagerDialog manager

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.command

Class cytoscape.command.CyCommandException extends Exception implements Serializable

Serialized Fields

result

CyCommandResult result
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

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
Deprecated. 

curator

String curator
Deprecated. 

species

String species
Deprecated. 

type

String type
Deprecated. 

hash

HashMap<K,V> hash
Deprecated. 

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

Serialized Fields

species

String species
Deprecated. 

curator

String curator
Deprecated. 

annotationType

String annotationType
Deprecated. 

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

Serialized Fields

curator

String curator
Deprecated. 

ontologyType

String ontologyType
Deprecated. 

termHash

HashMap<K,V> termHash
Deprecated. 

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

Serialized Fields

curator

String curator
Deprecated. 

ontologyType

String ontologyType
Deprecated. 

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

Serialized Fields

name

String name
Deprecated. 

id

int id
Deprecated. 

parents

Vector<E> parents
Deprecated. 

containers

Vector<E> containers
Deprecated. 
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.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

serialVersionUID: 3333726113970459078L

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

cancelFlag

boolean cancelFlag

cancelButton

JButton cancelButton

datasourceComboBox

JComboBox datasourceComboBox

datasourceLabel

JLabel datasourceLabel

mainTabbedPane

JTabbedPane mainTabbedPane

propertyPanel

JPanel propertyPanel

propertyScrollPane

JScrollPane propertyScrollPane

searchButton

JButton searchButton

searchTermScrollPane

JScrollPane searchTermScrollPane

queryTextPane

JTextPane queryTextPane

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

JLabel nameLabel

okButton

JButton okButton

parameterEditorPane

JEditorPane parameterEditorPane

parameterPanel

JPanel parameterPanel

parameterScrollPane

JScrollPane parameterScrollPane

resultPanel

JPanel resultPanel

resultScrollPane

JScrollPane resultScrollPane

serviceLabel

JLabel serviceLabel

titleLabel

JLabel titleLabel

topSeparator

JSeparator topSeparator
Package cytoscape.dialogs

Class cytoscape.dialogs.ColorScaleTable extends JPanel implements Serializable

Class cytoscape.dialogs.EdgeAttributesPopupDetails extends JDialog implements Serializable

Class cytoscape.dialogs.EdgeAttributesPopupDetails.OKAction extends AbstractAction implements Serializable

Serialized Fields

dialog

JDialog dialog

Class cytoscape.dialogs.EditNetworkTitleDialog extends JDialog implements Serializable

Serialized Fields

networkTitle

String networkTitle

btnCancel

JButton btnCancel

btnOK

JButton btnOK

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

tfNetworkTitle

JTextField tfNetworkTitle

Class cytoscape.dialogs.ExportAsGraphicsFileChooser extends JDialog implements Serializable

serialVersionUID: 4895622023575071394L

Serialized Fields

SEPARATOR

String SEPARATOR

selectedFile

File selectedFile

selectedFilter

CyFileFilter selectedFilter

exportTextAsFont

boolean exportTextAsFont

btnPanel

JPanel btnPanel

cancelButton

JButton cancelButton

chkExportTextAsFont

JCheckBox chkExportTextAsFont

chooseFileButton

JButton chooseFileButton

filePathField

JTextField filePathField

formatComboBox

JComboBox formatComboBox

formatLabel

JLabel formatLabel

jSeparator1

JSeparator jSeparator1

okButton

JButton okButton

selectFileLabel

JLabel selectFileLabel

Class cytoscape.dialogs.ExportBitmapOptionsDialog extends JDialog implements Serializable

serialVersionUID: 5333484131669731753L

Serialized Fields

zoomField

JFormattedTextField zoomField

widthInPixelsField

JFormattedTextField widthInPixelsField

heightInPixelsField

JFormattedTextField heightInPixelsField

widthInInchesField

JFormattedTextField widthInInchesField

heightInInchesField

JFormattedTextField heightInInchesField

resolutionComboBox

JComboBox resolutionComboBox

okButton

JButton okButton

originalWidth

int originalWidth

originalHeight

int originalHeight

Class cytoscape.dialogs.ExpressionDataPopupTable extends JDialog implements Serializable

Serialized Fields

mainFrame

Frame mainFrame

popupTable

ExpressionDataPopupTable popupTable

table

JTable table

geneExpressionInfo

ExpressionData geneExpressionInfo

Class cytoscape.dialogs.ExpressionDataPopupTable.OKAction extends AbstractAction implements Serializable

Serialized Fields

dialog

JDialog dialog

Class cytoscape.dialogs.GinyEdgeControlDialog extends JDialog implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

view

GraphView view

edgeNames

String[] edgeNames

edgeNamesHash

HashMap<K,V> edgeNamesHash

selectedTreePaths

TreePath[] selectedTreePaths

edgeAttributes

CyAttributes edgeAttributes

tree

JTree tree

Class cytoscape.dialogs.GinyEdgeControlDialog.OKAction extends AbstractAction implements Serializable

Class cytoscape.dialogs.GraphObjectSelection extends JPanel implements Serializable

Serialized Fields

searchField

JTextField searchField

regexpSearch

JCheckBox regexpSearch

clearSelection

JCheckBox clearSelection

hideFailed

JRadioButton hideFailed

grayFailed

JRadioButton grayFailed

selectPassed

JRadioButton selectPassed

selectedAttributes

JList selectedAttributes

allAttributes

JList allAttributes

cyNetwork

CyNetwork cyNetwork

nodeAttributes

CyAttributes nodeAttributes

edgeAttributes

CyAttributes edgeAttributes

graphView

DingNetworkView graphView

networkView

CyNetworkView networkView

Class cytoscape.dialogs.IconPopupButton extends JPanel implements Serializable

Serialized Fields

title

String title

objectName

String objectName

currentIconName

String currentIconName

currentIcon

Object currentIcon

iconButton

JButton iconButton

iconSelectionForPanel

JLabel iconSelectionForPanel

mainFrame

JFrame mainFrame

mainDialog

JDialog mainDialog

mainPanel

JPanel mainPanel

iconObjectToString

HashMap<K,V> iconObjectToString

stringToIconObject

HashMap<K,V> stringToIconObject

iconList

JList iconList

parentDialog

JDialog parentDialog

alreadyConstructed

boolean alreadyConstructed

Class cytoscape.dialogs.IconPopupButton.ApplyIconAction extends AbstractAction implements Serializable

Class cytoscape.dialogs.IconPopupButton.CancelIconAction extends AbstractAction implements Serializable

Class cytoscape.dialogs.ImportAttributeMatrixDialog extends JDialog implements Serializable

Serialized Fields

status

boolean status

currentKeyAttributeName

String currentKeyAttributeName

keyAttributeModel

DefaultComboBoxModel keyAttributeModel

keyAttributeBox

JComboBox keyAttributeBox

cancelButton

JButton cancelButton

importButton

JButton importButton

jSeparator1

JSeparator jSeparator1

attributeMatrixFileNameTextField

JTextField attributeMatrixFileNameTextField

attributeSelectionSliderLabel

JLabel attributeSelectionSliderLabel

selectAttributeMatrixFileButton

JButton selectAttributeMatrixFileButton

titleLabel

JLabel titleLabel

Class cytoscape.dialogs.ImportNetworkDialog extends JDialog implements Serializable

Serialized Fields

status

boolean status

networkFiles

File[] networkFiles

theBookmarks

Bookmarks theBookmarks

bookmarkCategory

String bookmarkCategory

URLstr

String URLstr

bookmarkEditor

cytoscape.dialogs.ImportNetworkDialog.BookmarkComboBoxEditor bookmarkEditor

pleaseMessage

String pleaseMessage

cancelButton

JButton cancelButton

importButton

JButton importButton

radioButtonPanel

JPanel radioButtonPanel

selectButton

JButton selectButton

buttonGroup1

ButtonGroup buttonGroup1

networkFileComboBox

JComboBox networkFileComboBox

titleLabel

JLabel titleLabel

remoteRadioButton

JRadioButton remoteRadioButton

localRadioButton

JRadioButton localRadioButton

networkFileTextField

JTextField networkFileTextField

titleSeparator

JSeparator titleSeparator

Class cytoscape.dialogs.IntegerEntryField extends JPanel implements Serializable

Serialized Fields

sizeField

JTextField sizeField

sizeLabel

JLabel sizeLabel

mainFrame

JFrame mainFrame

mainPanel

JPanel mainPanel

Class cytoscape.dialogs.JointIntegerEntry extends JPanel implements Serializable

Serialized Fields

field1

IntegerEntryField field1

field2

IntegerEntryField field2

constraintLabel

JLabel constraintLabel

constraintBox

JCheckBox constraintBox

mainFrame

JFrame mainFrame

mainPanel

JPanel mainPanel

field1Name

String field1Name

field2Name

String field2Name

fieldName

String fieldName

locked

boolean locked

Class cytoscape.dialogs.LabelTextPanel extends JPanel implements Serializable

Serialized Fields

attributeNames

String[] attributeNames

nodeLabelKey

MutableString nodeLabelKey

theBox

JComboBox theBox

Class cytoscape.dialogs.LabelTextPanel.BoxAction extends AbstractAction implements Serializable

Class cytoscape.dialogs.NetworkMetaDataDialog extends JDialog implements Serializable

Serialized Fields

metaTM

NetworkMetaDataTableModel metaTM

mdp

MetadataParser mdp

network

CyNetwork network

description

String description

logger

CyLogger logger

okButton

JButton okButton

cancelButton

JButton cancelButton

descriptionTextArea

JTextArea descriptionTextArea

titleLabel

JLabel titleLabel

jPanel1

JPanel jPanel1

metadataTableScrollPane

JScrollPane metadataTableScrollPane

descriptionScrollPane

JScrollPane descriptionScrollPane

mainSplitPane

JSplitPane mainSplitPane

metadataTable

JTable metadataTable

Class cytoscape.dialogs.NetworkMetaDataTableModel extends DefaultTableModel implements Serializable

Serialized Fields

network

CyNetwork network

dataArray

Object[][] dataArray

data

Map<K,V> data

description

String description

mdp

MetadataParser mdp

Class cytoscape.dialogs.NewSlider extends JPanel implements Serializable

Serialized Fields

minimum

int minimum

maximum

int maximum

current

int current

sigFigs

int sigFigs

myTitle

JLabel myTitle

myMin

JLabel myMin

myMax

JLabel myMax

myTextbox

NewSlider.MJTextField myTextbox

title

String title

mySlider

NewSlider.MJSlider mySlider

attributeName

String attributeName

Class cytoscape.dialogs.NewSlider.MJSlider extends JSlider implements Serializable

Serialized Fields

test

String test

Class cytoscape.dialogs.NewSlider.MJTextField extends JTextField implements Serializable

Class cytoscape.dialogs.NewStringPopupDialog extends JDialog implements Serializable

Serialized Fields

theString

String theString

textField

JTextField textField

Class cytoscape.dialogs.NewStringPopupDialog.CancelAction extends AbstractAction implements Serializable

Class cytoscape.dialogs.NewStringPopupDialog.OkAction extends AbstractAction implements Serializable

Class cytoscape.dialogs.PopupTextArea extends JDialog implements Serializable

Serialized Fields

popupTextArea

PopupTextArea popupTextArea

location

Point location

Class cytoscape.dialogs.PopupTextArea.OKAction extends AbstractAction implements Serializable

Class cytoscape.dialogs.SetNestedNetworkDialog extends JDialog implements Serializable

Serialized Fields

nodeView

NodeView nodeView
Creates a new EditNetworkTitleDialog object.

btnCancel

JButton btnCancel

btnOK

JButton btnOK

jScrollPane1

JScrollPane jScrollPane1

lbTitle

JLabel lbTitle

lstNetwork

JList lstNetwork

pnlButtons

JPanel pnlButtons

selectedNetwork

CyNetwork selectedNetwork

Class cytoscape.dialogs.ShrinkExpandGraph extends CytoscapeAction implements Serializable

Serialized Fields

m

double m
Package cytoscape.dialogs.logger

Class cytoscape.dialogs.logger.LoggerDialog extends JDialog implements Serializable

Serialized Fields

messageMap

Map<K,V> messageMap

logTabMap

Map<K,V> logTabMap

messageAdded

boolean messageAdded

clearButton

JButton clearButton

closeButton

JButton closeButton

logTabs

JTabbedPane logTabs
Package cytoscape.dialogs.plugins

Class cytoscape.dialogs.plugins.LicenseDialog extends JDialog implements Serializable

Serialized Fields

acceptRadio

JRadioButton acceptRadio

buttonPane

JPanel buttonPane

cancelButton

JButton cancelButton

declineRadio

JRadioButton declineRadio

licenseLabel

JLabel licenseLabel

licensePanel

JEditorPane licensePanel

licenseScrollPane

JScrollPane licenseScrollPane

licenseSplitPane

JSplitPane licenseSplitPane

okButton

JButton okButton

pluginList

JList pluginList

pluginListScrollPane

JScrollPane pluginListScrollPane

listModel

cytoscape.dialogs.plugins.LicenseDialog.LicenseListModel listModel

Class cytoscape.dialogs.plugins.PluginManageDialog extends JDialog implements Serializable

Serialized Fields

currentPluginSiteURL

String currentPluginSiteURL

HOWTOSEARCH

String HOWTOSEARCH

baseSiteLabel

String baseSiteLabel

availablePluginsLabel

JLabel availablePluginsLabel

bottomPane

JPanel bottomPane

btnAddSite

JButton btnAddSite

btnClear

JButton btnClear

btnDeleteSite

JButton btnDeleteSite

btnEditSite

JButton btnEditSite

btnSearch

JButton btnSearch

buttonPanel

JPanel buttonPanel

closeButton

JButton closeButton

downloadLocText

JLabel downloadLocText

infoScrollPane

JScrollPane infoScrollPane

infoTextPane

JEditorPane infoTextPane

installDeleteButton

JButton installDeleteButton

jLabel3

JLabel jLabel3

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

jScrollPane1

JScrollPane jScrollPane1

jSplitPane1

JSplitPane jSplitPane1

jSplitPane2

JSplitPane jSplitPane2

jTabbedPane1

JTabbedPane jTabbedPane1

lbSearchTitle

JLabel lbSearchTitle

lstDownloadSites

JList lstDownloadSites

msgLabel

JLabel msgLabel

msgPanel

JTextArea msgPanel

pluginTree

JTree pluginTree

pnlSearch

JPanel pnlSearch

pnlSettings

JPanel pnlSettings

sitePanel

JPanel sitePanel

tfSearch

JTextField tfSearch

topPane

JPanel topPane

treeScrollPane

JScrollPane treeScrollPane

versionCheck

JCheckBox versionCheck

rootTreeNode

TreeNode rootTreeNode

installedNode

TreeNode installedNode

availableNode

TreeNode availableNode

treeModel

ManagerModel treeModel

treeRenderer

TreeCellRenderer treeRenderer

hiddenNodes

HashMap<K,V> hiddenNodes

bookmarkCategory

String bookmarkCategory

theBookmarks

Bookmarks theBookmarks

Class cytoscape.dialogs.plugins.PluginUpdateDialog extends JDialog implements Serializable

Serialized Fields

closeButton

JButton closeButton

infoScrollPane

JScrollPane infoScrollPane

infoTextPane

JEditorPane infoTextPane

jSplitPane1

JSplitPane jSplitPane1

msgLabel

JLabel msgLabel

pluginTree

JTree pluginTree

treeScrollPane

JScrollPane treeScrollPane

updateAllButton

JButton updateAllButton

updateLabel

JLabel updateLabel

updateSelectedButton

JButton updateSelectedButton

rootTreeNode

TreeNode rootTreeNode

treeModel

ManagerModel treeModel

Class cytoscape.dialogs.plugins.PluginUrlDialog extends JDialog implements Serializable

Serialized Fields

bookmarkCategory

String bookmarkCategory

theBookmarks

Bookmarks theBookmarks

parentDialog

PluginManageDialog parentDialog

editSiteButton

JButton editSiteButton

cancelButton

JButton cancelButton

jPanel1

JPanel jPanel1

label

JLabel label

labelPanel

JPanel labelPanel

okButton

JButton okButton

urlComboBox

JComboBox urlComboBox

Class cytoscape.dialogs.plugins.TreeCellRenderer extends DefaultTreeCellRenderer implements Serializable

Serialized Fields

warningIcon

Icon warningIcon

okIcon

Icon okIcon

Class cytoscape.dialogs.plugins.TreeNode extends DefaultMutableTreeNode implements Serializable

Serialized Fields

children

Vector<E> children

infoObj

DownloadableInfo infoObj

title

String title

parent

TreeNode parent

childAllowed

boolean childAllowed

visible

boolean visible
Package cytoscape.dialogs.preferences

Class cytoscape.dialogs.preferences.BookmarkDialog extends JDialog implements Serializable

Serialized Fields

bookmarkCategory

String bookmarkCategory

theBookmarks

Bookmarks theBookmarks

bookmarkCategories

String[] bookmarkCategories

btnAddBookmark

JButton btnAddBookmark

btnDeleteBookmark

JButton btnDeleteBookmark

btnEditBookmark

JButton btnEditBookmark

btnOK

JButton btnOK

cmbCategory

JComboBox cmbCategory

jPanel1

JPanel jPanel1

jScrollPane1

JScrollPane jScrollPane1

listBookmark

JList listBookmark

Class cytoscape.dialogs.preferences.EditBookmarkDialog extends JDialog implements Serializable

Serialized Fields

cancelButton

JButton cancelButton

categoryLabel

JLabel categoryLabel

jLabel1

JLabel jLabel1

jLabel3

JLabel jLabel3

jLabel4

JLabel jLabel4

nameTextField

JTextField nameTextField

okButton

JButton okButton

urlTextField

JTextField urlTextField

parent

JDialog parent

bookmarks

Bookmarks bookmarks

categoryName

String categoryName

mode

String mode

dataSource

DataSource dataSource

Class cytoscape.dialogs.preferences.PluginsTableModel extends AbstractTableModel implements Serializable

Serialized Fields

properties

Properties properties
Deprecated. 

pluginsSet

TreeSet<E> pluginsSet
Deprecated. 

pluginsFromCommandLineLoadedAndSaved

boolean pluginsFromCommandLineLoadedAndSaved
Deprecated. 

Class cytoscape.dialogs.preferences.PreferencesDialog extends JDialog implements Serializable

Serialized Fields

selection

int[] selection

propsTablePane

JScrollPane propsTablePane

prefsTable

JTable prefsTable

propBtnPane

JPanel propBtnPane

okButtonPane

JPanel okButtonPane

vizmapPane

JPanel vizmapPane

cyPropsPane

JPanel cyPropsPane

saveVizmapBtn

JCheckBox saveVizmapBtn

saveCyPropsBtn

JCheckBox saveCyPropsBtn

vizmapText

JTextArea vizmapText

cyPropsText

JTextArea cyPropsText

addPropBtn

JButton addPropBtn

deletePropBtn

JButton deletePropBtn

modifyPropBtn

JButton modifyPropBtn

okButton

JButton okButton

cancelButton

JButton cancelButton

prefsTM

PreferenceTableModel prefsTM

lsm

ListSelectionModel lsm

saveCyPropsAsDefault

boolean saveCyPropsAsDefault

saveVizmapAsDefault

boolean saveVizmapAsDefault

Class cytoscape.dialogs.preferences.PreferenceTableModel extends AbstractTableModel implements Serializable

Serialized Fields

properties

Properties properties

propertiesList

Vector<E> propertiesList

Class cytoscape.dialogs.preferences.PreferenceValueDialog extends JDialog implements Serializable

Serialized Fields

preferenceName

String preferenceName

preferenceValue

String preferenceValue

title

String title

preferenceNameL

JLabel preferenceNameL

value

JTextField value

okButton

JButton okButton

cancelButton

JButton cancelButton

tableModel

TableModel tableModel

callerRef

PreferencesDialog callerRef

Class cytoscape.dialogs.preferences.ProxyServerDialog extends JDialog implements Serializable

serialVersionUID: -2693844068486336199L

Serialized Fields

btnCancel

JButton btnCancel

btnUpdate

JButton btnUpdate

chbUseProxy

JCheckBox chbUseProxy

cmbType

JComboBox cmbType

jPanel1

JPanel jPanel1

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

lbHost

JLabel lbHost

lbPort

JLabel lbPort

lbType

JLabel lbType

lbUseProxy

JLabel lbUseProxy

tfHost

JTextField tfHost

tfPort

JTextField tfPort

_lastUseProxy

boolean _lastUseProxy

_lastProxyHost

String _lastProxyHost

_lastProxyPort

String _lastProxyPort

_lastProxyType

String _lastProxyType
Package cytoscape.geom.rtree

Class cytoscape.geom.rtree.RTree extends Object implements Serializable

Serialized Fields

m_MBR

float[] m_MBR

m_maxBranches

int m_maxBranches

m_minBranches

int m_minBranches

m_root

cytoscape.geom.rtree.RTree.Node m_root

m_entryMap

IntObjHash m_entryMap

m_deletedEntry

Object m_deletedEntry

m_deletedEntries

int m_deletedEntries

m_mapExpansionThreshold

int m_mapExpansionThreshold

m_objKeyBuff

int[] m_objKeyBuff

m_childrenBuff

cytoscape.geom.rtree.RTree.Node[] m_childrenBuff

m_xMinBuff

float[] m_xMinBuff

m_yMinBuff

float[] m_yMinBuff

m_xMaxBuff

float[] m_xMaxBuff

m_yMaxBuff

float[] m_yMaxBuff

m_tempBuff1

float[] m_tempBuff1

m_tempBuff2

float[] m_tempBuff2

m_extentsStack

float[] m_extentsStack

m_nodeStack

cytoscape.geom.rtree.ObjStack m_nodeStack
Package cytoscape.layout.ui

Class cytoscape.layout.ui.DynamicLayoutMenu extends JMenu implements Serializable

Serialized Fields

layout

CyLayoutAlgorithm layout

selectedNodes

Set<E> selectedNodes

Class cytoscape.layout.ui.DynamicLayoutMenu.LayoutAttributeMenuItem extends JMenuItem implements Serializable

Serialized Fields

selectedOnly

boolean selectedOnly

Class cytoscape.layout.ui.LayoutMenu extends JMenu implements Serializable

Serialized Fields

subMenuList

List<E> subMenuList

Class cytoscape.layout.ui.LayoutSettingsDialog extends JDialog implements Serializable

Serialized Fields

currentLayout

CyLayoutAlgorithm currentLayout

titleLabel

JLabel titleLabel

mainPanel

JPanel mainPanel

buttonBox

JPanel buttonBox

algorithmSelector

JComboBox algorithmSelector

algorithmPanel

JPanel algorithmPanel

Class cytoscape.layout.ui.SettingsAction extends CytoscapeAction implements Serializable

Class cytoscape.layout.ui.StaticLayoutMenu extends JMenuItem implements Serializable

Serialized Fields

layout

CyLayoutAlgorithm layout
Package cytoscape.plugin

Class cytoscape.plugin.DuplicatePluginClassException extends PluginException implements Serializable

Class cytoscape.plugin.InvalidDownloadable extends PluginException implements Serializable

Class cytoscape.plugin.ManagerException extends PluginException implements Serializable

Class cytoscape.plugin.NotAPluginException extends PluginException implements Serializable

Class cytoscape.plugin.PluginException extends Exception implements Serializable

Class cytoscape.plugin.PluginProperties extends Properties implements Serializable

Serialized Fields

configFileName

String configFileName

packageName

String packageName

errorMsg

String errorMsg

Class cytoscape.plugin.TrackerException extends PluginException implements Serializable

Class cytoscape.plugin.WebstartException extends PluginException implements Serializable

Package cytoscape.task.ui

Class cytoscape.task.ui.JErrorPanel extends JPanel implements Serializable

serialVersionUID: 333614801L

Serialized Fields

t

Throwable t
The Error Object

userErrorMessage

String userErrorMessage
A Human Readable Error Message

tip

String tip
Hint to user as to how to fix the error.

showDetails

boolean showDetails
Flag to Show/Hide Error Details.

detailsButton

JButton detailsButton
Show/Hide Details Button.

detailsPane

JScrollPane detailsPane
Scroll Pane used to display Stack Trace Elements.

owner

JDialog owner
JDialog Owner.

Class cytoscape.task.ui.JTask extends JDialog implements Serializable

serialVersionUID: 333614801L

Serialized Fields

pBar

JProgressBar pBar
ProgressBar UI component.

descriptionValue

JLabel descriptionValue
Description value label.

statusValue

JTextArea statusValue
Status value label.

timeRemainingValue

JLabel timeRemainingValue
Time remaining label.

timeElapsedValue

JLabel timeElapsedValue
Time elapsed label.

progressValue

JLabel progressValue
Progress Value.

timer

Timer timer
Internal Timer.

cancelButton

JButton cancelButton
Cancel Button.

closeButton

JButton closeButton
Close Button.

startTime

Date startTime
Time Stamp when Component was constructed.

taskTitle

String taskTitle
Title Value.

config

JTaskConfig config
Used to Configure the JTask UI.

task

Task task
Task we are monitoring.

progressPanel

JPanel progressPanel
Contains all the Progress Fields.

haltRequested

boolean haltRequested
Flag to Indicate that user has requested that task halt.

errorOccurred

boolean errorOccurred
Flag to Indicate that error has occurred within task.

timeRemaining

long timeRemaining
Estimated Time Remaining.

Package cytoscape.util

Class cytoscape.util.CytoscapeAction extends AbstractAction implements Serializable

Serialized Fields

preferredMenu

String preferredMenu

preferredButtonGroup

String preferredButtonGroup

menuIndex

Integer menuIndex

acceleratorSet

boolean acceleratorSet

keyModifiers

int keyModifiers

keyCode

int keyCode

consoleName

String consoleName

useCheckBoxMenuItem

boolean useCheckBoxMenuItem

Class cytoscape.util.CytoscapeMenuBar extends JMenuBar implements Serializable

Serialized Fields

defaultMenuSpecifier

String defaultMenuSpecifier

actionMembersSet

Set<E> actionMembersSet

actionMenuItemMap

Map<K,V> actionMenuItemMap

menuMap

Map<K,V> menuMap

menuEffectiveLastIndexMap

Map<K,V> menuEffectiveLastIndexMap
The Menu->Integer "effective last index" Map for Menus with menu items that want to be at the end.

identifier

String identifier

Class cytoscape.util.CytoscapeProgressMonitor extends JFrame implements Serializable

Serialized Fields

pMonitor

ProgressMonitor pMonitor

timer

Timer timer

parentComponent

Component parentComponent

monitoredTask

MonitoredTask monitoredTask

Class cytoscape.util.CytoscapeToolBar extends JToolBar implements Serializable

Serialized Fields

actionButtonMap

Map<K,V> actionButtonMap

actionMembersSet

Set<E> actionMembersSet

Class cytoscape.util.IndeterminateProgressBar extends JDialog implements Serializable

Serialized Fields

mainPanel

JPanel mainPanel

labelPanel

JPanel labelPanel

barPanel

JPanel barPanel

label

JLabel label

labelText

String labelText

pBar

JProgressBar pBar
Package cytoscape.util.intr

Class cytoscape.util.intr.IntArray extends Object implements Serializable

Serialized Fields

m_arr

int[] m_arr

Class cytoscape.util.intr.IntBTree extends Object implements Serializable

Serialized Fields

m_maxBranches

int m_maxBranches

m_minBranches

int m_minBranches

m_root

cytoscape.util.intr.IntBTree.Node m_root

Class cytoscape.util.intr.IntHash extends Object implements Serializable

Serialized Fields

m_arr

int[] m_arr

m_elements

int m_elements

m_size

int m_size

m_thresholdSize

int m_thresholdSize

m_dump

int[] m_dump

Class cytoscape.util.intr.IntIntHash extends Object implements Serializable

Serialized Fields

m_keys

int[] m_keys

m_vals

int[] m_vals

m_elements

int m_elements

m_size

int m_size

m_thresholdSize

int m_thresholdSize

m_prevKey

int m_prevKey

m_prevInx

int m_prevInx

m_keyDump

int[] m_keyDump

m_valDump

int[] m_valDump

Class cytoscape.util.intr.IntObjHash extends Object implements Serializable

Serialized Fields

m_keys

int[] m_keys

m_vals

Object[] m_vals

m_elements

int m_elements

m_thresholdSize

int m_thresholdSize

m_prevKey

int m_prevKey

m_prevInx

int m_prevInx

Class cytoscape.util.intr.IntQueue extends Object implements Serializable

Serialized Fields

m_queue

int[] m_queue

m_head

int m_head

m_tail

int m_tail

Class cytoscape.util.intr.IntStack extends Object implements Serializable

Serialized Fields

m_stack

int[] m_stack

m_currentSize

int m_currentSize

Class cytoscape.util.intr.IntTHash extends Object implements Serializable

Serialized Fields

m_keys

int[] m_keys

m_vals

List<E> m_vals

m_elements

int m_elements

m_thresholdSize

int m_thresholdSize

m_prevKey

int m_prevKey

m_prevInx

int m_prevInx

Class cytoscape.util.intr.LongLongHash extends Object implements Serializable

Serialized Fields

m_keys

long[] m_keys

m_vals

long[] m_vals

m_elements

int m_elements

m_size

int m_size

m_thresholdSize

int m_thresholdSize

m_prevKey

long m_prevKey

m_prevInx

int m_prevInx

m_keyDump

long[] m_keyDump

m_valDump

long[] m_valDump

Class cytoscape.util.intr.MinIntHeap extends Object implements Serializable

Serialized Fields

m_heap

int[] m_heap

m_currentSize

int m_currentSize

m_orderOK

boolean m_orderOK
Package cytoscape.util.swing

Class cytoscape.util.swing.AboutDialog extends JDialog implements Serializable

Serialized Fields

mainEditorPane

JEditorPane mainEditorPane

mainScrollPane

JScrollPane mainScrollPane

titleLabel

JLabel titleLabel

titlePanel

JPanel titlePanel

mainPanel

JPanel mainPanel

Class cytoscape.util.swing.AttributeImportPanel extends JPanel implements Serializable

serialVersionUID: 876173290119736978L

Serialized Fields

panelTitle

String panelTitle

logo

Icon logo

attributePanelTitle

String attributePanelTitle

attributeComboBox

JComboBox attributeComboBox

attributeLabel

JLabel attributeLabel

attributePanel

JPanel attributePanel

attributeTypeComboBox

JComboBox attributeTypeComboBox

attributeTypeLabel

JLabel attributeTypeLabel

cancelButton

JButton cancelButton

databaseComboBox

JComboBox databaseComboBox

databasePanel

JPanel databasePanel

attrListPanel

JPanel attrListPanel

availableAttrPanel

JPanel availableAttrPanel

availableAttrScrollPane

JScrollPane availableAttrScrollPane

importButton

JButton importButton

titleLabel

JLabel titleLabel

resetButton

JButton resetButton

attrList

CheckBoxJList attrList

model

DefaultListModel model

Class cytoscape.util.swing.CheckBoxJList extends JList implements Serializable

Serialized Fields

selectionCache

HashSet<E> selectionCache

Class cytoscape.util.swing.CyCollapsiblePanel extends JPanel implements Serializable

Serialized Fields

border

cytoscape.util.swing.CyCollapsiblePanel.CollapsableTitledBorder border

collapsedBorderLine

Border collapsedBorderLine

expandedBorderLine

Border expandedBorderLine

titleComponent

AbstractButton titleComponent

iconArrow

ImageIcon[] iconArrow

arrow

JButton arrow

panel

JPanel panel

collapsed

boolean collapsed

Class cytoscape.util.swing.DropDownMenuButton extends JButton implements Serializable

Serialized Fields

buttonIcon

Icon buttonIcon

Class cytoscape.util.swing.FilterHistoryJList extends JList implements Serializable

Serialized Fields

filterField

cytoscape.util.swing.FilterHistoryJList.FilterField filterField

DEFAULT_FIELD_WIDTH

int DEFAULT_FIELD_WIDTH

Class cytoscape.util.swing.JStatusBar extends JPanel implements Serializable

Serialized Fields

leftLabel

JLabel leftLabel

centerLabel

JLabel centerLabel

rightLabel

JLabel rightLabel

leftPanel

JPanel leftPanel

centerPanel

JPanel centerPanel

rightPanel

JPanel rightPanel

Class cytoscape.util.swing.JTreeTable extends JTable implements Serializable

serialVersionUID: -505249707913524363L

Serialized Fields

tree

JTreeTable.TreeTableCellRenderer tree
A subclass of JTree.

Class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer extends JTree implements Serializable

Serialized Fields

visibleRow

int visibleRow
Last table/tree row asked to renderer.

Class cytoscape.util.swing.NetworkSelectorPanel extends JPanel implements Serializable

serialVersionUID: 8694272457769377810L

Serialized Fields

networkComboBox

JComboBox networkComboBox

Class cytoscape.util.swing.TreeTableModelAdapter extends AbstractTableModel implements Serializable

serialVersionUID: 4492106324533343342L

Serialized Fields

tree

JTree tree

treeTableModel

TreeTableModel treeTableModel

Class cytoscape.util.swing.WidestStringComboBoxModel extends DefaultComboBoxModel implements Serializable

Serialized Fields

widest

String widest

widestValid

boolean widestValid
Package cytoscape.util.undo

Class cytoscape.util.undo.CyAbstractEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

desc

String desc

Class cytoscape.util.undo.RedoAction extends CytoscapeAction implements Serializable

Class cytoscape.util.undo.UndoAction extends CytoscapeAction implements Serializable

Package cytoscape.view

Class cytoscape.view.CytoscapeDesktop extends JFrame implements Serializable

serialVersionUID: 2986320083629749014L

Serialized Fields

lastPluginRegistryUpdate

long lastPluginRegistryUpdate

returnVal

int returnVal

defaultVisualStyle

VisualStyle defaultVisualStyle

networkPanel

NetworkPanel networkPanel
The network panel that sends out events when a network is selected from the Tree that it contains.

cyMenus

CyMenus cyMenus
The CyMenus object provides access to the all of the menus and toolbars that will be needed.

networkViewManager

NetworkViewManager networkViewManager
The NetworkViewManager can support three types of interfaces. Tabbed/InternalFrame/ExternalFrame

pcs

SwingPropertyChangeSupport pcs
provides support for property change events

graphViewController

GraphViewController graphViewController
The GraphViewController for all NetworkViews that we know about

vmm

VisualMappingManager vmm
Provides Operations for Mapping Data Attributes of CyNetworks to CyNetworkViews

vizmapperUI

VizMapperMainPanel vizmapperUI
New VizMapper UI

currentNetworkID

String currentNetworkID
Current network and view.

currentNetworkViewID

String currentNetworkViewID

cytoPanelWest

CytoPanelImp cytoPanelWest

cytoPanelEast

CytoPanelImp cytoPanelEast

cytoPanelSouth

CytoPanelImp cytoPanelSouth

cytoPanelSouthWest

CytoPanelImp cytoPanelSouthWest

statusBar

JLabel statusBar

main_panel

JPanel main_panel

styleBoxIndex

int styleBoxIndex

bevh

cytoscape.view.BirdsEyeViewHandler bevh

defaultControlPanelWidth

int defaultControlPanelWidth

defaultDataPanelHeight

int defaultDataPanelHeight

topRightPane

BiModalJSplitPane topRightPane

rightPane

BiModalJSplitPane rightPane

masterPane

BiModalJSplitPane masterPane

Class cytoscape.view.InternalFrameComponent extends JComponent implements Serializable

serialVersionUID: -6037450600865410121L

Serialized Fields

layeredPane

JLayeredPane layeredPane
ref to the JInternalFrame's JLayeredPane

backgroundCanvas

DingCanvas backgroundCanvas
ref to background canvas

networkCanvas

DingCanvas networkCanvas
ref to network canvas

foregroundCanvas

DingCanvas foregroundCanvas
ref to foreground canvas

Class cytoscape.view.NetworkPanel extends JPanel implements Serializable

serialVersionUID: -7102083850894612840L

Serialized Fields

pcs

SwingPropertyChangeSupport pcs

treeTable

JTreeTable treeTable

root

NetworkTreeNode root

navigatorPanel

JPanel navigatorPanel

networkTreePanel

JPanel networkTreePanel

popup

JPopupMenu popup

popupActionListener

cytoscape.view.PopupActionListener popupActionListener

createViewItem

JMenuItem createViewItem

destroyViewItem

JMenuItem destroyViewItem

destroyNetworkItem

JMenuItem destroyNetworkItem

editNetworkTitle

JMenuItem editNetworkTitle

applyVisualStyleMenu

JMenuItem applyVisualStyleMenu

split

BiModalJSplitPane split

treeTableModel

NetworkTreeTableModel treeTableModel

cytoscapeDesktop

CytoscapeDesktop cytoscapeDesktop

doNotEnterValueChanged

boolean doNotEnterValueChanged

Class cytoscape.view.NetworkTreeNode extends DefaultMutableTreeNode implements Serializable

serialVersionUID: -1504239724666254584L

Serialized Fields

network_uid

String network_uid

Class cytoscape.view.TreeCellRenderer extends DefaultTreeCellRenderer implements Serializable

serialVersionUID: -678559990857492912L

Package cytoscape.view.cytopanels

Class cytoscape.view.cytopanels.BiModalJSplitPane extends JSplitPane implements Serializable

Serialized Fields

frame

JFrame frame
Reference application frame.

currentMode

int currentMode
The current mode.

defaultDividerSize

int defaultDividerSize
The default divider size.

dividerLocation

int dividerLocation
The saved divider location.

Class cytoscape.view.cytopanels.CytoPanelImp extends JPanel implements Serializable

serialVersionUID: 8431678873343221338L

Serialized Fields

tabbedPane

JTabbedPane tabbedPane
The JTabbedPane we hide.

cytoPanelState

CytoPanelState cytoPanelState
Our state.

compassDirection

int compassDirection
Our compass direction.

cytoPanelListenerList

ArrayList<E> cytoPanelListenerList
An array of CytoPanelListeners

NOTIFICATION_STATE_CHANGE

int NOTIFICATION_STATE_CHANGE
Notification state change.

NOTIFICATION_COMPONENT_SELECTED

int NOTIFICATION_COMPONENT_SELECTED
Notification component selected.

NOTIFICATION_COMPONENT_ADDED

int NOTIFICATION_COMPONENT_ADDED
Notification component added.

NOTIFICATION_COMPONENT_REMOVED

int NOTIFICATION_COMPONENT_REMOVED
Notification component removed.

cytoPanelContainer

CytoPanelContainer cytoPanelContainer
Reference to CytoPanelContainer we live in.

externalFrame

JDialog externalFrame
External window used to hold the floating CytoPanel.

floatIcon

ImageIcon floatIcon
The float icon.

dockIcon

ImageIcon dockIcon
The dock icon.

floatLabel

JLabel floatLabel
The label which contains the tab title - not sure if its needed.

floatButton

JButton floatButton
The float/dock button.

FLOAT_PANEL_SCALE_FACTOR

int FLOAT_PANEL_SCALE_FACTOR
The float/dock button.

FLOAT_PANEL_COLOR

Color FLOAT_PANEL_COLOR
Color of the dock/float button panel.

Package cytoscape.visual

Class cytoscape.visual.Arrow extends Object implements Serializable

Serialized Fields

arrowColor

Color arrowColor

shape

ArrowShape shape

size

int size

Class cytoscape.visual.DuplicateCalculatorNameException extends RuntimeException implements Serializable

Package cytoscape.visual.calculators

Class cytoscape.visual.calculators.AbstractCalculator.CalculatorUI extends JPanel implements Serializable

Serialized Fields

myGBG

GridBagGroup myGBG
Deprecated. 
Remember the grid bag group in case the mapper UI needs to be updated.

Package cytoscape.visual.customgraphic.ui

Class cytoscape.visual.customgraphic.ui.CustomGraphicsBrowser extends org.jdesktop.swingx.JXList implements Serializable

serialVersionUID: -8342056297304400824L

Serialized Fields

model

DefaultListModel model

pool

CustomGraphicsManager pool

Class cytoscape.visual.customgraphic.ui.CustomGraphicsCellRenderer extends JPanel implements Serializable

serialVersionUID: 8040076496780883222L

Serialized Fields

panelMap

Map<K,V> panelMap

Class cytoscape.visual.customgraphic.ui.CustomGraphicsDetailPanel extends JPanel implements Serializable

serialVersionUID: -412539582192509545L

Serialized Fields

cg

CyCustomGraphics cg

heightLabel

JLabel heightLabel

heightTextField

JTextField heightTextField

imageViewPanel

org.jdesktop.swingx.JXImageView imageViewPanel

infoPanel

JPanel infoPanel

lockCheckBox

JCheckBox lockCheckBox

modifyPanel

JPanel modifyPanel

nameLabel

JLabel nameLabel

nameTextField

JTextField nameTextField

resetButton

JButton resetButton

tagLabel

JLabel tagLabel

tagTextField

JTextField tagTextField

widthLabel

JLabel widthLabel

widthTextField

JTextField widthTextField

searchButton

JButton searchButton

Class cytoscape.visual.customgraphic.ui.CustomGraphicsManagerDialog extends JDialog implements Serializable

serialVersionUID: 7681270324415099781L

Serialized Fields

browser

CustomGraphicsBrowser browser

detail

CustomGraphicsDetailPanel detail

manager

CustomGraphicsManager manager

addButton

JButton addButton

buttonPanel

JPanel buttonPanel

deleteButton

JButton deleteButton

leftScrollPane

JScrollPane leftScrollPane

mainSplitPane

JSplitPane mainSplitPane

rightScrollPane

JScrollPane rightScrollPane

Class cytoscape.visual.customgraphic.ui.CyCustomGraphicsTableCellRenderer extends DefaultTableCellRenderer implements Serializable

serialVersionUID: -5155795609971962107L

Class cytoscape.visual.customgraphic.ui.CyCustomGraphicsTreeCellRenderer extends DefaultTreeCellRenderer implements Serializable

serialVersionUID: -5155795609971962107L

Package cytoscape.visual.mappings

Class cytoscape.visual.mappings.LegendTable extends JPanel implements Serializable

Serialized Fields

legendTable

JTable legendTable
Package cytoscape.visual.mappings.continuous

Class cytoscape.visual.mappings.continuous.ContinuousLegend extends JPanel implements Serializable

Serialized Fields

points

List<E> points

type

VisualPropertyType type

legend

JLabel legend

width

int width

height

int height

yoff

int yoff
Package cytoscape.visual.mappings.discrete

Class cytoscape.visual.mappings.discrete.DiscreteLegend extends JPanel implements Serializable

Package cytoscape.visual.ui

Class cytoscape.visual.ui.DefaultAppearenceBuilder extends JDialog implements Serializable

serialVersionUID: 596165395462496156L

Serialized Fields

applyButton

JButton applyButton

cancelButton

JButton cancelButton

nodeScrollPane

JScrollPane nodeScrollPane

edgeScrollPane

JScrollPane edgeScrollPane

globalScrollPane

JScrollPane globalScrollPane

dependencyScrollPane

JScrollPane dependencyScrollPane

defaultObjectTabbedPane

JTabbedPane defaultObjectTabbedPane

nodeList

org.jdesktop.swingx.JXList nodeList

edgeList

org.jdesktop.swingx.JXList edgeList

globalList

org.jdesktop.swingx.JXList globalList

dependencyPanel

JPanel dependencyPanel

jXPanel1

org.jdesktop.swingx.JXPanel jXPanel1

dependencyCheckBoxMap

Map<K,V> dependencyCheckBoxMap

jXTitledPanel1

org.jdesktop.swingx.JXTitledPanel jXTitledPanel1

mainView

DefaultViewPanel mainView

Class cytoscape.visual.ui.DefaultViewPanel extends JPanel implements Serializable

Serialized Fields

background

Color background

Class cytoscape.visual.ui.FontChooser extends JPanel implements Serializable

Serialized Fields

selectedFont

Font selectedFont

fontFaceModel

DefaultComboBoxModel fontFaceModel

face

JComboBox face

Class cytoscape.visual.ui.FontRenderer extends DefaultListCellRenderer implements Serializable

Class cytoscape.visual.ui.LabelPlacerGraphic extends JPanel implements Serializable

Serialized Fields

lp

LabelPosition lp
Deprecated. 

default_xy

int default_xy
Deprecated. 

xy

int xy
Deprecated. 

center

int center
Deprecated. 

offsetRatio

float offsetRatio
Deprecated. 

nxy

int nxy
Deprecated. 

npoints

int[] npoints
Deprecated. 

lx

int lx
Deprecated. 

ly

int ly
Deprecated. 

lxpoints

int[] lxpoints
Deprecated. 

lypoints

int[] lypoints
Deprecated. 

dot

int dot
Deprecated. 

xPos

int xPos
Deprecated. 

yPos

int yPos
Deprecated. 

bestLabelX

int bestLabelX
Deprecated. 

bestLabelY

int bestLabelY
Deprecated. 

bestNodeX

int bestNodeX
Deprecated. 

bestNodeY

int bestNodeY
Deprecated. 

beenDragged

boolean beenDragged
Deprecated. 

canOffsetDrag

boolean canOffsetDrag
Deprecated. 

xClickOffset

int xClickOffset
Deprecated. 

yClickOffset

int yClickOffset
Deprecated. 

xOffset

int xOffset
Deprecated. 

yOffset

int yOffset
Deprecated. 

justify

int justify
Deprecated. 

transparentRed

Color transparentRed
Deprecated. 

transparentBlue

Color transparentBlue
Deprecated. 

transparentMagenta

Color transparentMagenta
Deprecated. 

renderDetail

boolean renderDetail
Deprecated. 

label

String label
Deprecated. 

node

String node
Deprecated. 

click

String click
Deprecated. 

labelLen

int labelLen
Deprecated. 

nodeLen

int nodeLen
Deprecated. 

clickLen

int clickLen
Deprecated. 

ascent

int ascent
Deprecated. 

detailStrokeWidth

int detailStrokeWidth
Deprecated. 

lowStrokeWidth

int lowStrokeWidth
Deprecated. 

detailStroke

Stroke detailStroke
Deprecated. 

lowStroke

Stroke lowStroke
Deprecated. 

gravityDistance

double gravityDistance
Deprecated. 

Class cytoscape.visual.ui.LegendDialog extends JDialog implements Serializable

Serialized Fields

visualStyle

VisualStyle visualStyle

jPanel1

JPanel jPanel1

jButton1

JButton jButton1

jButton2

JButton jButton2

jScrollPane1

JScrollPane jScrollPane1

parent

Component parent

Class cytoscape.visual.ui.ObjectPlacerControl extends JPanel implements Serializable

serialVersionUID: 3875032897986523443L

Serialized Fields

lp

ObjectPosition lp

justifyCombo

JComboBox justifyCombo

xoffsetBox

JTextField xoffsetBox

yoffsetBox

JTextField yoffsetBox

nodeAnchors

JComboBox nodeAnchors

labelAnchors

JComboBox labelAnchors

ignoreEvents

boolean ignoreEvents

Class cytoscape.visual.ui.ObjectPlacerGraphic extends JPanel implements Serializable

serialVersionUID: -1091948204116900740L

Serialized Fields

p

ObjectPosition p

xy

int xy

center

int center

offsetRatio

float offsetRatio

nxy

int nxy

npoints

int[] npoints

lx

int lx

ly

int ly

lxpoints

int[] lxpoints

lypoints

int[] lypoints

dot

int dot

xPos

int xPos

yPos

int yPos

bestLabelX

int bestLabelX

bestLabelY

int bestLabelY

bestNodeX

int bestNodeX

bestNodeY

int bestNodeY

beenDragged

boolean beenDragged

canOffsetDrag

boolean canOffsetDrag

xClickOffset

int xClickOffset

yClickOffset

int yClickOffset

xOffset

int xOffset

yOffset

int yOffset

justify

Justification justify

renderDetail

boolean renderDetail

objectLabel

String objectLabel

targetLabel

String targetLabel

click

String click

labelLen

int labelLen

clickLen

int clickLen

ascent

int ascent

detailStrokeWidth

int detailStrokeWidth

lowStrokeWidth

int lowStrokeWidth

detailStroke

Stroke detailStroke

lowStroke

Stroke lowStroke

objectSize

Dimension objectSize

targetSize

Dimension targetSize

Class cytoscape.visual.ui.PopupFontChooser extends JDialog implements Serializable

Serialized Fields

font

Font font

chooser

FontChooser chooser

Class cytoscape.visual.ui.PopupIconChooser.ApplyIconAction extends AbstractAction implements Serializable

Class cytoscape.visual.ui.PopupIconChooser.CancelIconAction extends AbstractAction implements Serializable

Class cytoscape.visual.ui.PopupObjectPositionChooser extends JDialog implements Serializable

serialVersionUID: 7146654020668346430L

Serialized Fields

position

ObjectPosition position

newPosition

ObjectPosition newPosition

targetType

VisualPropertyType targetType

Class cytoscape.visual.ui.ValueSelectDialog extends JDialog implements Serializable

serialVersionUID: 1201804212862509435L

Serialized Fields

type

VisualPropertyType type

iconMap

Map<K,V> iconMap

orderedKeyList

List<E> orderedKeyList

originalValue

Object originalValue

canceled

boolean canceled

height

int height

listTitle

String listTitle

applyButton

JButton applyButton

cancelButton

JButton cancelButton

iconList

org.jdesktop.swingx.JXList iconList

iconListScrollPane

JScrollPane iconListScrollPane

mainPanel

org.jdesktop.swingx.JXTitledPanel mainPanel

model

DefaultListModel model

Class cytoscape.visual.ui.VizMapperMainPanel extends JPanel implements Serializable

serialVersionUID: 2010449914223315524L

Serialized Fields

vmm

VisualMappingManager vmm

propertyMap

Map<K,V> propertyMap

discMapBuffer

Map<K,V> discMapBuffer

lastVSName

String lastVSName

noMapListScrollPane

JScrollPane noMapListScrollPane

noMapping

List<E> noMapping

buttonPanel

JPanel buttonPanel

addButton

JButton addButton

bottomPanel

JPanel bottomPanel

editorWindowManager

Map<K,V> editorWindowManager

defaultImageManager

Map<K,V> defaultImageManager

ignore

boolean ignore

logger

CyLogger logger

hiddenProperties

Set<E> hiddenProperties

defaultAppearencePanel

JPanel defaultAppearencePanel

mainSplitPane

JSplitPane mainSplitPane

listSplitPane

JSplitPane listSplitPane

optionButton

DropDownMenuButton optionButton

visualPropertySheetPanel

com.l2fprod.common.propertysheet.PropertySheetPanel visualPropertySheetPanel

vsNameComboBox

JComboBox vsNameComboBox

vsSelectPanel

JPanel vsSelectPanel

nodeAttrEditor

CyComboBoxPropertyEditor nodeAttrEditor

edgeAttrEditor

CyComboBoxPropertyEditor edgeAttrEditor

nodeNumericalAttrEditor

CyComboBoxPropertyEditor nodeNumericalAttrEditor

edgeNumericalAttrEditor

CyComboBoxPropertyEditor edgeNumericalAttrEditor

mappingTypeEditor

CyComboBoxPropertyEditor mappingTypeEditor

rendReg

com.l2fprod.common.propertysheet.PropertyRendererRegistry rendReg

editorReg

com.l2fprod.common.propertysheet.PropertyEditorRegistry editorReg

rendFactory

CellRendererFactory rendFactory

editorFactory

CellEditorFactory editorFactory

discretePropSetter

DiscretePropertySetter discretePropSetter

Class cytoscape.visual.ui.VizMapperMainPanel.CopyStyleListener extends AbstractAction implements Serializable

serialVersionUID: 4741684758183028809L

Class cytoscape.visual.ui.VizMapperMainPanel.CreateLegendListener extends AbstractAction implements Serializable

Class cytoscape.visual.ui.VizMapperProperty extends com.l2fprod.common.propertysheet.DefaultProperty implements Serializable

serialVersionUID: -9103147252041414576L

Serialized Fields

hiddenObject

Object hiddenObject
Package cytoscape.visual.ui.editors.continuous

Class cytoscape.visual.ui.editors.continuous.BelowAndAbovePanel extends JPanel implements Serializable

Serialized Fields

type

VisualPropertyType type

boxColor

Color boxColor

below

boolean below

value

Object value

Class cytoscape.visual.ui.editors.continuous.C2CMappingEditor extends ContinuousMappingEditorPanel implements Serializable

serialVersionUID: -3555354576428996187L

Class cytoscape.visual.ui.editors.continuous.C2DMappingEditor extends ContinuousMappingEditorPanel implements Serializable

serialVersionUID: 2146889489175240626L

Class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel extends JDialog implements Serializable

serialVersionUID: -2558647616344119220L

Serialized Fields

type

VisualPropertyType type

calculator

Calculator calculator

mapping

ContinuousMapping mapping

allPoints

List<E> allPoints

spinnerModel

SpinnerNumberModel spinnerModel

below

Object below

above

Object above

attrs

CyAttributes attrs

lastSpinnerNumber

double lastSpinnerNumber

addButton

JButton addButton

attrNameLabel

JLabel attrNameLabel

colorButton

JButton colorButton

deleteButton

JButton deleteButton

iconPanel

JPanel iconPanel

pivotLabel

JLabel pivotLabel

rangeEditorPanel

JPanel rangeEditorPanel

rangeSettingPanel

JPanel rangeSettingPanel

slider

org.jdesktop.swingx.JXMultiThumbSlider<E> slider

valueSpinner

JSpinner valueSpinner

visualPropertyLabel

JLabel visualPropertyLabel

rotaryEncoder

org.jdesktop.swingx.JXMultiThumbSlider<E> rotaryEncoder

minMaxButton

JButton minMaxButton

abovePanel

BelowAndAbovePanel abovePanel

belowPanel

BelowAndAbovePanel belowPanel

Class cytoscape.visual.ui.editors.continuous.ContinuousTrackRenderer extends JComponent implements Serializable

Serialized Fields

TITLE_FONT

Font TITLE_FONT

smallFont

Font smallFont

defFont

Font defFont

valueMap

Map<K,V> valueMap

trackHeight

int trackHeight

arrowBarPosition

int arrowBarPosition

min

float min

max

float max

clickFlag

boolean clickFlag

dragFlag

boolean dragFlag

curPoint

Point curPoint

slider

org.jdesktop.swingx.JXMultiThumbSlider<E> slider

listener

cytoscape.visual.ui.editors.continuous.ContinuousTrackRenderer.CMouseListener listener

verticesList

Map<K,V> verticesList

selectedIdx

int selectedIdx

dragOrigin

Point dragOrigin

type

VisualPropertyType type

cMapping

ContinuousMapping cMapping

title

String title

below

Number below

above

Number above

values

List<E> values

valueArea

Polygon valueArea

belowSquare

Point belowSquare

aboveSquare

Point aboveSquare

Class cytoscape.visual.ui.editors.continuous.CyGradientTrackRenderer extends JComponent implements Serializable

Serialized Fields

trackHeight

int trackHeight

SMALL_FONT

Font SMALL_FONT

TITLE_FONT

Font TITLE_FONT

slider

org.jdesktop.swingx.JXMultiThumbSlider<E> slider

below

Color below

above

Color above

attrName

String attrName

type

VisualPropertyType type

Class cytoscape.visual.ui.editors.continuous.DiscreteTrackRenderer extends JComponent implements Serializable

serialVersionUID: 5024551458030362213L

Serialized Fields

trackHeight

int trackHeight

arrowBarYPosition

int arrowBarYPosition

smallIconSize

int smallIconSize

below

Object below

above

Object above

type

VisualPropertyType type

title

String title

rangeObjects

List<E> rangeObjects

slider

org.jdesktop.swingx.JXMultiThumbSlider<E> slider

Class cytoscape.visual.ui.editors.continuous.GradientEditorPanel extends ContinuousMappingEditorPanel implements Serializable

serialVersionUID: -7645303507318540305L

Class cytoscape.visual.ui.editors.continuous.MinMaxDialog extends JDialog implements Serializable

serialVersionUID: 7350824820761046009L

Serialized Fields

min

Double min

max

Double max

attr

CyAttributes attr

attrName

String attrName

cancelButton

JButton cancelButton

maxLabel

JLabel maxLabel

maxTextField

JTextField maxTextField

minLabel

JLabel minLabel

minTextField

JTextField minTextField

okButton

JButton okButton

titleLabel

JLabel titleLabel

titlePanel

JPanel titlePanel

restoreButton

JButton restoreButton

Class cytoscape.visual.ui.editors.continuous.TriangleThumbRenderer extends JComponent implements Serializable

Serialized Fields

slider

org.jdesktop.swingx.JXMultiThumbSlider<E> slider

selected

boolean selected

Class cytoscape.visual.ui.editors.continuous.YValueLegendPanel extends JPanel implements Serializable

Serialized Fields

type

VisualPropertyType type
Package cytoscape.visual.ui.editors.discrete

Class cytoscape.visual.ui.editors.discrete.CustomGraphicsCellRenderer extends com.l2fprod.common.swing.renderer.DefaultCellRenderer implements Serializable

serialVersionUID: 381040361846340312L

Serialized Fields

iconMap

Map<K,V> iconMap

Class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer extends com.l2fprod.common.swing.renderer.DefaultCellRenderer implements Serializable

Class cytoscape.visual.ui.editors.discrete.FontCellRenderer extends com.l2fprod.common.swing.renderer.DefaultCellRenderer implements Serializable

Class cytoscape.visual.ui.editors.discrete.ObjectPositionCellRenderer extends com.l2fprod.common.swing.renderer.DefaultCellRenderer implements Serializable

serialVersionUID: -7898871787941450155L

Class cytoscape.visual.ui.editors.discrete.ShapeCellRenderer extends com.l2fprod.common.swing.renderer.DefaultCellRenderer implements Serializable

Serialized Fields

icons

Map<K,V> icons

type

VisualPropertyType type
Package cytoscape.visual.ui.icon

Class cytoscape.visual.ui.icon.ArrowIcon extends VisualPropertyIcon implements Serializable

Serialized Fields

arrow

ArrowShape arrow

Class cytoscape.visual.ui.icon.LineTypeIcon extends VisualPropertyIcon implements Serializable

Serialized Fields

stroke

Stroke stroke

g2d

Graphics2D g2d

superimposedText

String superimposedText

textFont

Font textFont

textColor

Color textColor

Class cytoscape.visual.ui.icon.NodeIcon extends VisualPropertyIcon implements Serializable

serialVersionUID: -7589422578478706397L

Serialized Fields

newShape

Shape newShape

g2d

Graphics2D g2d

Class cytoscape.visual.ui.icon.VisualPropertyIcon extends ImageIcon implements Serializable

serialVersionUID: 8512931880283553107L

Serialized Fields

height

int height

width

int width

color

Color color

shape

Shape shape

name

String name

leftPad

int leftPad

bottomPad

int bottomPad
Package ding.view

Class ding.view.ArbitraryGraphicsCanvas extends DingCanvas implements Serializable

Serialized Fields

m_graphPerspective

GraphPerspective m_graphPerspective
Our reference to the GraphPerspective our view belongs to

m_dGraphView

DGraphView m_dGraphView
Our reference to the DGraphView we live within

m_innerCanvas

InnerCanvas m_innerCanvas
Our reference to the inner canvas

m_componentToNodeMap

Map<K,V> m_componentToNodeMap

Class ding.view.BirdsEyeView extends Component implements Serializable

Serialized Fields

m_extents

double[] m_extents

m_view

DGraphView m_view

m_cLis

ContentChangeListener m_cLis

m_vLis

ViewportChangeListener m_vLis

m_img

Image m_img

m_contentChanged

boolean m_contentChanged

m_myXCenter

double m_myXCenter

m_myYCenter

double m_myYCenter

m_myScaleFactor

double m_myScaleFactor

m_viewWidth

int m_viewWidth

m_viewHeight

int m_viewHeight

m_viewXCenter

double m_viewXCenter

m_viewYCenter

double m_viewYCenter

m_viewScaleFactor

double m_viewScaleFactor

m_desktopView

Component m_desktopView

m_currMouseButton

int m_currMouseButton

m_lastXMousePos

int m_lastXMousePos

m_lastYMousePos

int m_lastYMousePos

Class ding.view.DingCanvas extends JComponent implements Serializable

serialVersionUID: 4138104679262169265L

Serialized Fields

m_img

Image m_img
ref to image we maintain

m_backgroundColor

Color m_backgroundColor
ref to our background color

m_isVisible

boolean m_isVisible
ref to visibility boolean

m_isOpaque

boolean m_isOpaque
ref to opaque boolean

Class ding.view.InnerCanvas extends DingCanvas implements Serializable

serialVersionUID: 6219424955453507079L

Serialized Fields

m_ptBuff

double[] m_ptBuff

m_extentsBuff2

float[] m_extentsBuff2

m_floatBuff1

float[] m_floatBuff1

m_floatBuff2

float[] m_floatBuff2

m_line

Line2D.Float m_line

m_path

GeneralPath m_path

m_path2

GeneralPath m_path2

m_stack

IntStack m_stack

m_stack2

IntStack m_stack2

m_lock

Object m_lock

m_view

DGraphView m_view

m_lod

GraphLOD[] m_lod

m_hash

IntHash m_hash

m_grafx

GraphGraphics m_grafx

m_xCenter

double m_xCenter

m_yCenter

double m_yCenter

m_scaleFactor

double m_scaleFactor

m_lastRenderDetail

int m_lastRenderDetail

m_selectionRect

Rectangle m_selectionRect

m_undoable_edit

ViewChangeEdit m_undoable_edit

isPrinting

boolean isPrinting

m_fontMetrics

FontMetrics m_fontMetrics

NodeMovement

boolean NodeMovement

dropTarget

DropTarget dropTarget

selecting

boolean selecting

listeners

Vector<E> listeners

transferComponents

Vector<E> transferComponents

nodeContextMenuListeners

Vector<E> nodeContextMenuListeners
Listeners for node right-click menu

edgeContextMenuListeners

Vector<E> edgeContextMenuListeners
Listeners for edge right-click menu.

m_currMouseButton

int m_currMouseButton

m_lastXMousePos

int m_lastXMousePos

m_lastYMousePos

int m_lastYMousePos

m_button1NodeDrag

boolean m_button1NodeDrag

Class ding.view.InnerCanvasEvent extends EventObject implements Serializable

Class ding.view.ViewChangeEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

origState

ding.view.ViewState origState

newState

ding.view.ViewState newState

m_view

DGraphView m_view

m_label

String m_label

m_savedObjs

ViewChangeEdit.SavedObjs m_savedObjs
Package giny.model

Class giny.model.GraphPerspectiveChangeEvent extends EventObject implements Serializable

Class giny.model.NestedNetworkChangeEvent extends EventObject implements Serializable

serialVersionUID: -4279473805735358503L

Serialized Fields

parentNode

Node parentNode

graphView

GraphView graphView

Class giny.model.RootGraphChangeEvent extends EventObject implements Serializable

Package giny.view

Class giny.view.GraphViewChangeEvent extends EventObject implements Serializable

Package org.apache.commons.cli

Class org.apache.commons.cli.AlreadySelectedException extends ParseException implements Serializable

Class org.apache.commons.cli.MissingArgumentException extends ParseException implements Serializable

Class org.apache.commons.cli.MissingOptionException extends ParseException implements Serializable

Class org.apache.commons.cli.ParseException extends Exception implements Serializable

Class org.apache.commons.cli.UnrecognizedOptionException extends ParseException implements Serializable

Package org.cytoscape.equations

Class org.cytoscape.equations.BooleanList extends ArrayList<Boolean> implements Serializable

serialVersionUID: -39245160342061982L

Class org.cytoscape.equations.DoubleList extends ArrayList<Double> implements Serializable

serialVersionUID: 9241560324069182L

Class org.cytoscape.equations.FunctionError extends Exception implements Serializable

serialVersionUID: -2671219600906051276L

Serialized Fields

argNumber

int argNumber

Class org.cytoscape.equations.LongList extends ArrayList<Long> implements Serializable

serialVersionUID: -245160324069812L

Class org.cytoscape.equations.StringList extends ArrayList<String> implements Serializable

serialVersionUID: -4245160342069182L

Package phoebe

Class phoebe.PhoebeCanvasDropEvent extends AWTEvent implements Serializable

serialVersionUID: 1213746928492377L

Serialized Fields

transferable

Transferable transferable

location

Point location

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