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.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.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.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.SelectAllAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectAllEdgesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SelectAllNodesAction 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.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.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

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

Class cytoscape.data.servers.BioDataServerRmi_Stub extends RemoteStub implements Serializable

serialVersionUID: 2L

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.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

Serialized Fields

filePathField

JTextField filePathField

formatComboBox

JComboBox formatComboBox

okButton

JButton okButton

selectedFile

File selectedFile

Class cytoscape.dialogs.ExportBitmapOptionsDialog extends JDialog implements Serializable

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

cytoscape.bookmarks.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

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.ShrinkExpandGraph extends CytoscapeAction implements Serializable

Serialized Fields

m

double m

Class cytoscape.dialogs.URLimportAdvancedDialog extends JDialog implements Serializable

Serialized Fields

parent

JDialog parent

bookmarkCategory

String bookmarkCategory

theBookmarks

cytoscape.bookmarks.Bookmarks theBookmarks

bookmarkPanel

JPanel bookmarkPanel

btnAddBookmark

JButton btnAddBookmark

btnDeleteBookmark

JButton btnDeleteBookmark

btnEditBookmark

JButton btnEditBookmark

btnOK

JButton btnOK

btnPanelBookmark

JPanel btnPanelBookmark

btnSetProxy

JButton btnSetProxy

cmbProxyType

JComboBox cmbProxyType

jLabel3

JLabel jLabel3

jPanel2

JPanel jPanel2

jScrollPane1

JScrollPane jScrollPane1

lbBookmarkTitle

JLabel lbBookmarkTitle

lbHostName

JLabel lbHostName

lbPort

JLabel lbPort

lbProxyServer

JLabel lbProxyServer

lbProxyTitle

JLabel lbProxyTitle

lbType

JLabel lbType

proxyPanel

JPanel proxyPanel

tfHost

JTextField tfHost

tfPort

JTextField tfPort

bookmarkList

JList bookmarkList

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

Serialized Fields

name

String name

URLstr

String URLstr

parent

JDialog parent

theBookmarks

cytoscape.bookmarks.Bookmarks theBookmarks

categoryName

String categoryName

bookmarkURL

URL bookmarkURL

mode

String mode

dataSource

cytoscape.bookmarks.DataSource dataSource

btnCancel

JButton btnCancel

btnOK

JButton btnOK

jPanel1

JPanel jPanel1

lbName

JLabel lbName

lbURL

JLabel lbURL

tfName

JTextField tfName

tfURL

JTextField tfURL

Class cytoscape.dialogs.VisualStyleBuilderDialog extends JDialog implements Serializable

Serialized Fields

mapperSuffix

String mapperSuffix

VSName

String VSName

gmlReader

GMLReader gmlReader

generateButton

JButton generateButton

jSeparator1

JSeparator jSeparator1

mapperLabel

JLabel mapperLabel

mapperTextField

JTextField mapperTextField

messageEditorPane

JEditorPane messageEditorPane

messageScrollPane

JScrollPane messageScrollPane

styleNameLabel

JLabel styleNameLabel

styleNameTextField

JTextField styleNameTextField

titleLabel

JLabel titleLabel

skipButton

JButton skipButton

Package cytoscape.dialogs.plugins

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

Serialized Fields

agreeRadio

JRadioButton agreeRadio

cancelButton

JButton cancelButton

declineRadio

JRadioButton declineRadio

finishButton

JButton finishButton

jScrollPane1

JScrollPane jScrollPane1

licenseEditorPane

JEditorPane licenseEditorPane

pluginLicenseLabel

JLabel pluginLicenseLabel

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

Serialized Fields

baseSiteLabel

String baseSiteLabel

availablePluginsLabel

JLabel availablePluginsLabel

changeSiteButton

JButton changeSiteButton

closeButton

JButton closeButton

deleteButton

JButton deleteButton

installButton

JButton installButton

infoScrollPane

JScrollPane infoScrollPane

infoTextPane

JEditorPane infoTextPane

jSplitPane1

JSplitPane jSplitPane1

msgLabel

JLabel msgLabel

pluginTree

JTree pluginTree

treeScrollPane

JScrollPane treeScrollPane

rootTreeNode

TreeNode rootTreeNode

installedNode

TreeNode installedNode

availableNode

TreeNode availableNode

treeModel

ManagerModel treeModel

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

cytoscape.bookmarks.Bookmarks theBookmarks

parentDialog

PluginManageDialog parentDialog

addSiteButton

JButton addSiteButton

cancelButton

JButton cancelButton

jPanel1

JPanel jPanel1

label

JLabel label

labelPanel

JPanel labelPanel

okButton

JButton okButton

urlComboBox

JComboBox urlComboBox

Package cytoscape.dialogs.preferences

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

Serialized Fields

bookmarkCategory

String bookmarkCategory

theBookmarks

cytoscape.bookmarks.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.BookmarkDialog.EditBookmarkDialog extends JDialog implements Serializable

Serialized Fields

name

String name

URLstr

String URLstr

parent

JDialog parent

theBookmarks

cytoscape.bookmarks.Bookmarks theBookmarks

categoryName

String categoryName

bookmarkURL

URL bookmarkURL

mode

String mode

dataSource

cytoscape.bookmarks.DataSource dataSource

btnCancel

JButton btnCancel

btnOK

JButton btnOK

jPanel1

JPanel jPanel1

lbCategory

JLabel lbCategory

lbCategoryValue

JLabel lbCategoryValue

lbName

JLabel lbName

lbURL

JLabel lbURL

tfName

JTextField tfName

tfURL

JTextField tfURL

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

lsmA

ListSelectionModel lsmA

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

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.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.WebstartException extends PluginException implements Serializable

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.swing

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

Serialized Fields

selectionCache

HashSet<E> selectionCache

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

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.TreeTableModelAdapter extends AbstractTableModel implements Serializable

Serialized Fields

tree

JTree tree

treeTableModel

TreeTableModel treeTableModel

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

Serialized Fields

lastPluginRegistryUpdate

long lastPluginRegistryUpdate

returnVal

int returnVal

viewType

int viewType

The type of view, should be considered final

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

vizMapper

VisualMappingManager vizMapper

Provides Operations for Mapping Data Attributes of CyNetworks to CyNetworkViews

vizMapUI

VizMapUI vizMapUI

Deprecated. Use VizMapperMainPanel instead.

user interface to the VisualMappingManager vizMapper.

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

vsAssociationMap

HashMap<K,V> vsAssociationMap

main_panel

JPanel main_panel

currentStyleBox

JComboBox currentStyleBox

styleBoxIndex

int styleBoxIndex

Class cytoscape.view.InternalFrameComponent extends JComponent implements Serializable

Serialized Fields

layeredPane

JLayeredPane layeredPane

ref to the JInternalFrame's JLayeredPane

backgroundCanvas

ding.view.DingCanvas backgroundCanvas

ref to background canvas

networkCanvas

ding.view.DingCanvas networkCanvas

ref to network canvas

foregroundCanvas

ding.view.DingCanvas foregroundCanvas

ref to foreground canvas

Class cytoscape.view.NetworkPanel extends JPanel implements Serializable

Serialized Fields

pcs

SwingPropertyChangeSupport pcs

treeTable

JTreeTable treeTable

root

NetworkPanel.NetworkTreeNode root

navigatorPanel

JPanel navigatorPanel

popup

JPopupMenu popup

popupActionListener

cytoscape.view.PopupActionListener popupActionListener

createViewItem

JMenuItem createViewItem

destroyViewItem

JMenuItem destroyViewItem

destroyNetworkItem

JMenuItem destroyNetworkItem

editNetworkTitle

JMenuItem editNetworkTitle

split

BiModalJSplitPane split

treeTableModel

cytoscape.view.NetworkPanel.NetworkTreeTableModel treeTableModel

cytoscapeDesktop

CytoscapeDesktop cytoscapeDesktop

Class cytoscape.view.NetworkPanel.NetworkTreeNode extends DefaultMutableTreeNode implements Serializable

Serialized Fields

network_uid

String network_uid

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

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

JFrame 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

name

String name

Deprecated.

Class cytoscape.visual.DuplicateCalculatorNameException extends RuntimeException implements Serializable

Class cytoscape.visual.LineType extends Object implements Serializable

Serialized Fields

name

String name

Deprecated.

stroke

Stroke stroke

Deprecated.

type

LineStyle type

Deprecated.

width

Float width

Deprecated.

Package cytoscape.visual.calculators

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

Serialized Fields

myGBG

GridBagGroup myGBG

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

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

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

Serialized Fields

components

ArrayList<E> components

Deprecated.

defaultObject

Object defaultObject

Deprecated.

parentDialog

JDialog parentDialog

Deprecated.

cm

ContinuousMapping cm

Deprecated.

Package cytoscape.visual.mappings.discrete

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

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

Serialized Fields

parentDialog

JDialog parentDialog

network

CyNetwork network

attrName

String attrName

mappedKeys

TreeSet<E> mappedKeys

dm

DiscreteMapping dm

defaultObject

Object defaultObject

mapType

byte mapType

buttonPanel

JPanel buttonPanel

listScrollPane

JScrollPane listScrollPane

buttonPositions

HashMap<K,V> buttonPositions

Package cytoscape.visual.ui

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

Serialized Fields

nac

NodeAppearanceCalculator nac

applyButton

JButton applyButton

cancelButton

JButton cancelButton

lockNodeSizeCheckBox

JCheckBox lockNodeSizeCheckBox

nodeScrollPane

JScrollPane nodeScrollPane

edgeScrollPane

JScrollPane edgeScrollPane

globalScrollPane

JScrollPane globalScrollPane

defaultObjectTabbedPane

JTabbedPane defaultObjectTabbedPane

nodeList

org.jdesktop.swingx.JXList nodeList

edgeList

org.jdesktop.swingx.JXList edgeList

globalList

org.jdesktop.swingx.JXList globalList

jXPanel1

org.jdesktop.swingx.JXPanel jXPanel1

jXTitledPanel1

org.jdesktop.swingx.JXTitledPanel jXTitledPanel1

mainView

DefaultViewPanel mainView

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

Serialized Fields

vmm

VisualMappingManager vmm

Deprecated.

backColor

ValueDisplayer backColor

Deprecated.

selectedNodeColor

ValueDisplayer selectedNodeColor

Deprecated.

reverseSelectedNodeColor

ValueDisplayer reverseSelectedNodeColor

Deprecated.

selectedEdgeColor

ValueDisplayer selectedEdgeColor

Deprecated.

reverseSelectedEdgeColor

ValueDisplayer reverseSelectedEdgeColor

Deprecated.

parentDialog

VizMapUI parentDialog

Deprecated.

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

Serialized Fields

view

CyNetworkView view

oldView

CyNetworkView oldView

background

Color background

canvas

Component canvas

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

default_xy

int default_xy

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

canDrag

boolean canDrag

canOffsetDrag

boolean canOffsetDrag

xClickOffset

int xClickOffset

yClickOffset

int yClickOffset

xOffset

int xOffset

yOffset

int yOffset

justify

int justify

transparentRed

Color transparentRed

transparentBlue

Color transparentBlue

renderDetail

boolean renderDetail

label

String label

node

String node

click

String click

labelLen

int labelLen

nodeLen

int nodeLen

clickLen

int clickLen

ascent

int ascent

detailStrokeWidth

int detailStrokeWidth

lowStrokeWidth

int lowStrokeWidth

detailStroke

Stroke detailStroke

lowStroke

Stroke lowStroke

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.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.PopupLabelPositionChooser extends JDialog implements Serializable

Serialized Fields

lp

LabelPosition lp

newlp

LabelPosition newlp

Class cytoscape.visual.ui.ValueDisplayer extends JButton implements Serializable

Serialized Fields

dispType

byte dispType

Deprecated.

Holds the type of UI this ValueDisplayer will pop up.

inputObj

Object inputObj

Deprecated.

Holds the object inputted by the user.

title

String title

Deprecated.

Input dialog title

parent

JDialog parent

Deprecated.

Parent dialog

inputListener

ActionListener inputListener

Deprecated.

ActionListener that triggers input UI

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

Serialized Fields

type

VisualPropertyType type

shapeMap

Map<K,V> shapeMap

orderedKeyList

List<E> orderedKeyList

originalValue

Object originalValue

canceled

boolean canceled

applyButton

JButton applyButton

cancelButton

JButton cancelButton

iconList

JList iconList

iconListScrollPane

JScrollPane iconListScrollPane

mainPanel

org.jdesktop.swingx.JXTitledPanel mainPanel

model

DefaultListModel model

Class cytoscape.visual.ui.ValueSelectDialog.IconCellRenderer extends JLabel implements Serializable

Serialized Fields

SELECTED_FONT

Font SELECTED_FONT

NORMAL_FONT

Font NORMAL_FONT

SELECTED_COLOR

Color SELECTED_COLOR

SELECTED_FONT_COLOR

Color SELECTED_FONT_COLOR

icons

List<E> icons

Class cytoscape.visual.ui.VizMapAttrTab extends VizMapTab implements Serializable

Serialized Fields

catalog

CalculatorCatalog catalog

Deprecated.

reference to calculator catalog

VMM

VisualMappingManager VMM

Deprecated.

VisualMappingManager for the window

type

byte type

Deprecated.

The type of this VizMapAttrTab. This should be one of the constants defined in VizMapUI that identifies a particular visual attribute. Utility methods in VizUIUtilites are used to convert this type into a particular object or method of the current visual style.

currentCalculator

Calculator currentCalculator

Deprecated.

The calculator whose UI is being displayed by this tab. Note that this duplicates the calculator reference held by the current visual style. This is done for convenience, rather than continually using a utility method to figure out which calculator corresponds to the type field of this object. It is the responsibility of every method in this class to make sure this field is synchronized with the current state of the current visual style. This field should only be changed via the setCurrentCalculator method of this class, which additionally ensures that the proper listener is attached to the current calculator.

mainUIDialog

VizMapUI mainUIDialog

Deprecated.

the parent JDialog

defaultValueDisplayer

ValueDisplayer defaultValueDisplayer

Deprecated.

Default ValueDisplayer

calcComboBox

JComboBox calcComboBox

Deprecated.

Combo box for calculator selection

mapPanelGBG

GridBagGroup mapPanelGBG

Deprecated.

Calculator UI

calcContainer

JPanel calcContainer

Deprecated.

calcPanel

JPanel calcPanel

Deprecated.

the panel containing the calculator-specific UI provided by the currently selected calculator

calcListener

cytoscape.visual.ui.VizMapAttrTab.CalculatorUIListener calcListener

Deprecated.

Listener for calculator UI changes

Class cytoscape.visual.ui.VizMapFontTab extends VizMapTab implements Serializable

Serialized Fields

faceTab

VizMapAttrTab faceTab

Deprecated.

sizeTab

VizMapAttrTab sizeTab

Deprecated.

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

Serialized Fields

vmm

VisualMappingManager vmm

propertyMap

Map<K,V> propertyMap

lastVSName

String lastVSName

noMapListScrollPane

JScrollPane noMapListScrollPane

noMapping

List<E> noMapping

buttonPanel

JPanel buttonPanel

addButton

JButton addButton

deleteButton

JButton deleteButton

bottomPanel

JPanel bottomPanel

editorWindowManager

Map<K,V> editorWindowManager

defaultImageManager

Map<K,V> defaultImageManager

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

defCellRenderer

DefaultTableCellRenderer defCellRenderer

stringCellEditor

CyStringPropertyEditor stringCellEditor

collorCellRenderer

CyColorCellRenderer collorCellRenderer

colorCellEditor

CyColorPropertyEditor colorCellEditor

shapeCellRenderer

ShapeCellRenderer shapeCellRenderer

shapeCellEditor

CyComboBoxPropertyEditor shapeCellEditor

lineCellRenderer

ShapeCellRenderer lineCellRenderer

lineCellEditor

CyComboBoxPropertyEditor lineCellEditor

arrowCellEditor

CyComboBoxPropertyEditor arrowCellEditor

arrowShapeCellRenderer

ShapeCellRenderer arrowShapeCellRenderer

numberCellEditor

CyDoublePropertyEditor numberCellEditor

fontCellEditor

CyFontPropertyEditor fontCellEditor

fontCellRenderer

FontCellRenderer fontCellRenderer

labelPositionRenderer

LabelPositionCellRenderer labelPositionRenderer

labelPositionEditor

CyLabelPositionPropertyEditor labelPositionEditor

emptyBoxRenderer

DefaultTableCellRenderer emptyBoxRenderer

filledBoxRenderer

DefaultTableCellRenderer filledBoxRenderer

continuousRenderer

DefaultTableCellRenderer continuousRenderer

discreteRenderer

DefaultTableCellRenderer discreteRenderer

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

addMappingButton

JButton addMappingButton

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

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

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

Serialized Fields

hiddenObject

Object hiddenObject

Class cytoscape.visual.ui.VizMapSizeTab extends VizMapTab implements Serializable

Serialized Fields

hwPanel

JPanel hwPanel

lockPanel

JPanel lockPanel

mainPanel

JPanel mainPanel

height

VizMapAttrTab height

width

VizMapAttrTab width

size

VizMapAttrTab size

VMM

VisualMappingManager VMM

nodeCalc

NodeAppearanceCalculator nodeCalc

mainUIDialog

VizMapUI mainUIDialog

locked

boolean locked

lockBox

JCheckBox lockBox

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

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

Serialized Fields

VMM

VisualMappingManager VMM

Deprecated.

mainPane

JPanel mainPane

Deprecated.

The content pane for the dialog

actionButtonsPanel

JPanel actionButtonsPanel

Deprecated.

attrSelectorPanel

JPanel attrSelectorPanel

Deprecated.

tabPaneContainer

JPanel tabPaneContainer

Deprecated.

The content pane for the JTabbedPanes

tabs

List<E> tabs

Deprecated.

Keeps track of contained tabs

styles

Collection<E> styles

Deprecated.

All known VisualStyles

styleSelector

VizMapUI.StyleSelector styleSelector

Deprecated.

StyleSelector sub-dialog

initialized

boolean initialized

Deprecated.

Class cytoscape.visual.ui.VizMapUI.StyleSelector extends JDialog implements Serializable

Serialized Fields

catalog

CalculatorCatalog catalog

Reference to catalog

styleComboModel

DefaultComboBoxModel styleComboModel

Model for combo boxes

styleComboBox

JComboBox styleComboBox

Combo box for style selection

styleComboBoxDupe

JComboBox styleComboBoxDupe

Duplicate combo box for style selection - used in toolbar

styleGBG

GridBagGroup styleGBG

GridBagGroup for layout

currentStyle

VisualStyle currentStyle

Currently selected style

styleDefUI

VizMapUI styleDefUI

Reference to style definition UI

myself

VizMapUI.StyleSelector myself

Reference back to self for action listeners

styleDefNeedsUpdate

boolean styleDefNeedsUpdate

Lazily create visual style parameter UI.

rebuilding

boolean rebuilding

Flag to trap events triggered by myself

mainFrame

JFrame mainFrame

Class cytoscape.visual.ui.VizMapUI.StyleSelector.DefStyleListener extends AbstractAction implements Serializable

Class cytoscape.visual.ui.VizMapUI.StyleSelector.DupeStyleListener extends AbstractAction implements Serializable

Class cytoscape.visual.ui.VizMapUI.StyleSelector.LegendListener extends AbstractAction implements Serializable

Serialized Fields

parent

JDialog parent

Class cytoscape.visual.ui.VizMapUI.StyleSelector.NewStyleListener extends AbstractAction implements Serializable

Class cytoscape.visual.ui.VizMapUI.StyleSelector.RemoveStyleListener extends AbstractAction implements Serializable

Class cytoscape.visual.ui.VizMapUI.StyleSelector.RenameStyleListener extends AbstractAction implements Serializable

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

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

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

Serialized Fields

type

VisualPropertyType type

calculator

Calculator calculator

mapping

ContinuousMapping mapping

maxValue

double maxValue

minValue

double minValue

valRange

double valRange

allPoints

ArrayList<E> allPoints

spinnerModel

SpinnerNumberModel spinnerModel

below

Object below

above

Object above

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

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

valueRange

double valueRange

minValue

double minValue

maxValue

double maxValue

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

minValue

double minValue

maxValue

double maxValue

range

double range

below

Color below

above

Color above

attrName

String attrName

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

Serialized Fields

TITLE_FONT

Font TITLE_FONT

SMALL_ICON_SIZE

int SMALL_ICON_SIZE

valueRange

double valueRange

minValue

double minValue

maxValue

double maxValue

below

Object below

above

Object above

type

VisualPropertyType type

title

String title

rangeObjects

List<E> rangeObjects

lastObject

Object lastObject

rangeTooltips

List<E> rangeTooltips

slider

org.jdesktop.swingx.JXMultiThumbSlider<E> slider

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

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.CyColorCellRenderer extends com.l2fprod.common.swing.renderer.DefaultCellRenderer implements Serializable

Class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor.Renderer extends DefaultListCellRenderer implements Serializable

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

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

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

g2d

Graphics2D g2d

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

Serialized Fields

stroke

BasicStroke stroke

g2d

Graphics2D g2d

superimposedText

String superimposedText

textFont

Font textFont

textColor

Color textColor

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

Serialized Fields

newShape

Shape newShape

g2d

Graphics2D g2d

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

Serialized Fields

height

int height

width

int width

color

Color color

shape

Shape shape

name

String name

leftPad

int leftPad

bottomPad

int bottomPad