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

bool

boolean bool

Class cytoscape.actions.BackgroundColorAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.BirdsEyeViewAction extends CytoscapeAction implements Serializable

Serialized Fields

bev

ding.view.BirdsEyeView bev

on

boolean on

Class cytoscape.actions.CheckBoxFileChooser extends JFileChooser implements Serializable

Serialized Fields

jcb

JCheckBox jcb

jcbFlag

boolean jcbFlag

jcbLabel

String jcbLabel

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

cytoPanel

CytoPanel cytoPanel

Reference to our CytoPanel.

cytoPanelPrevState

CytoPanelState cytoPanelPrevState

Maintains state of CytoPanel just prior to being hidden

menuItem

JCheckBoxMenuItem menuItem

Reference to our parent menu.

Class cytoscape.actions.DeleteSelectedAction extends AbstractAction implements Serializable

Serialized Fields

networkView

CyNetworkView networkView

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.DestroySelectedAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.EdgeManipulationAction extends AbstractAction implements Serializable

Serialized Fields

networkView

NetworkView networkView

Class cytoscape.actions.ExitAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ExpFileChooser extends JFileChooser implements Serializable

Serialized Fields

jcb

JCheckBox jcb

copyToAttribs

boolean copyToAttribs

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 AbstractAction implements Serializable

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

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.LayoutAction extends AbstractAction implements Serializable

Serialized Fields

networkView

NetworkView networkView

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.PreferenceAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.PrintAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.RotateSelectedNodesAction extends AbstractAction implements Serializable

Serialized Fields

networkView

NetworkView 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

Class cytoscape.actions.SetVisualPropertiesAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.ShowAllAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.SquiggleAction extends JMenu implements Serializable

Serialized Fields

squiggleMode

JMenuItem squiggleMode

clearSquiggle

JMenuItem clearSquiggle

enabled

boolean enabled

Class cytoscape.actions.ToggleVisualMapperAction extends CytoscapeAction implements Serializable

Class cytoscape.actions.UnHideSelectedAction extends AbstractAction implements Serializable

Serialized Fields

networkView

NetworkView 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

filename

String filename

numGenes

int numGenes

numConds

int numConds

extraTokens

int extraTokens

haveSigValues

boolean haveSigValues

geneNames

Vector geneNames

geneDescripts

Vector geneDescripts

condNames

Vector condNames

geneNameToIndex

Hashtable geneNameToIndex

condNameToIndex

Hashtable condNameToIndex

minExp

double minExp

maxExp

double maxExp

minSig

double minSig

maxSig

double maxSig

allMeasurements

Vector 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 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

attributeLayouter

AttributeLayout attributeLayouter

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 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

jList1

JList jList1

jScrollPane3

JScrollPane jScrollPane3

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 parents

containers

Vector containers

Package cytoscape.data.readers

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

Package cytoscape.data.servers

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

Serialized Fields

annotations

HashMap annotations

thesauri

HashMap 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 gaFiles

nodeAttributes

CyAttributes nodeAttributes

bdsu

BioDataServerUtil bdsu

taxonMap

HashMap taxonMap

nodeSpeciesMap

HashMap nodeSpeciesMap

synoMap

HashMap synoMap

isSpecies

boolean isSpecies

originalSpecies

HashMap 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 labelToCommon

commonToLabel

HashMap commonToLabel

aliasesToLabel

HashMap aliasesToLabel

labelToAll

HashMap 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.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

NetworkView networkView

view

giny.view.GraphView view

edgeNames

String[] edgeNames

edgeNamesHash

HashMap 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 iconObjectToString

stringToIconObject

HashMap 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.ImportNetworkDialog extends JDialog implements Serializable

Serialized Fields

status

boolean status

cancelButton

JButton cancelButton

importButton

JButton importButton

jSeparator1

JSeparator jSeparator1

networkFileNameTextField

JTextField networkFileNameTextField

selectNetworkFileButton

JButton selectNetworkFileButton

titleLabel

JLabel titleLabel

vsBuilderCheckBox

JCheckBox vsBuilderCheckBox

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

XGMML_PACKAGE

String XGMML_PACKAGE

DEFAULT_ABOUT

String DEFAULT_ABOUT

metaTM

NetworkMetaDataTableModel metaTM

lsm

ListSelectionModel lsm

selection

int[] selection

network

CyNetwork network

description

String description

okButton

JButton okButton

cancelButton

JButton cancelButton

descriptionEditorPane

JEditorPane descriptionEditorPane

titleLabel

JLabel titleLabel

jPanel1

JPanel jPanel1

jScrollPane1

JScrollPane jScrollPane1

jScrollPane2

JScrollPane jScrollPane2

jSplitPane1

JSplitPane jSplitPane1

jTable1

JTable jTable1

metadataTable

JTable metadataTable

Class cytoscape.dialogs.NetworkMetaDataTableModel extends DefaultTableModel implements Serializable

Serialized Fields

network

CyNetwork network

dataVector

Object[][] dataVector

data

HashMap data

description

String description

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.VisualStyleBuilderDialog extends JDialog implements Serializable

Serialized Fields

mapperSuffix

String mapperSuffix

VSName

String VSName

gmlReader

GMLReader2 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

Package cytoscape.dialogs.preferences

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

Serialized Fields

properties

Properties properties

pluginsSet

TreeSet pluginsSet

pluginsFromCommandLineLoadedAndSaved

boolean pluginsFromCommandLineLoadedAndSaved

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

Serialized Fields

pluginTypes

String[] pluginTypes

selection

int[] selection

propsTablePane

JScrollPane propsTablePane

pluginsTablePane

JScrollPane pluginsTablePane

pluginsTable

JTable pluginsTable

prefsTable

JTable prefsTable

propBtnPane

JPanel propBtnPane

pluginBtnPane

JPanel pluginBtnPane

okButtonPane

JPanel okButtonPane

vizmapPane

JPanel vizmapPane

cyPropsPane

JPanel cyPropsPane

saveVizmapBtn

JCheckBox saveVizmapBtn

saveCyPropsBtn

JCheckBox saveCyPropsBtn

vizmapText

JTextArea vizmapText

cyPropsText

JTextArea cyPropsText

pluginTypesComboBox

JComboBox pluginTypesComboBox

addPluginBtn

JButton addPluginBtn

deletePluginBtn

JButton deletePluginBtn

addPropBtn

JButton addPropBtn

deletePropBtn

JButton deletePropBtn

modifyPropBtn

JButton modifyPropBtn

okButton

JButton okButton

cancelButton

JButton cancelButton

prefsTM

PreferenceTableModel prefsTM

pluginsTM

PluginsTableModel pluginsTM

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 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

browseButton

JButton browseButton

okButton

JButton okButton

cancelButton

JButton cancelButton

tableModel

TableModel tableModel

includeBrowseBtn

boolean includeBrowseBtn

callerRef

PreferencesDialog callerRef

Package cytoscape.plugin

Class cytoscape.plugin.NotAPluginException extends Exception 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

Class cytoscape.util.CytoscapeMenuBar extends JMenuBar implements Serializable

Serialized Fields

defaultMenuSpecifier

String defaultMenuSpecifier

actionMembersSet

Set actionMembersSet

actionMenuItemMap

Map actionMenuItemMap

menuMap

Map menuMap

menuEffectiveLastIndexMap

Map menuEffectiveLastIndexMap

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 actionButtonMap

actionMembersSet

Set 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

Class cytoscape.util.UndoManager.RedoAction extends AbstractAction implements Serializable

Class cytoscape.util.UndoManager.UndoAction extends AbstractAction implements Serializable

Package cytoscape.util.swing

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.view

Class cytoscape.view.CytoscapeDesktop extends JFrame implements Serializable

Serialized Fields

lastPluginRegistryUpdate

long lastPluginRegistryUpdate

VIEW_TYPE

int VIEW_TYPE

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

cyHelpBroker

CyHelpBroker cyHelpBroker

The HelpBroker provides access to JavaHelp

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

user interface to the VisualMappingManager vizMapper.

currentNetworkID

String currentNetworkID

currentNetworkViewID

String currentNetworkViewID

cytoPanelWest

CytoPanelImp cytoPanelWest

cytoPanelEast

CytoPanelImp cytoPanelEast

cytoPanelSouth

CytoPanelImp cytoPanelSouth

statusBar

JLabel statusBar

vsAssociationMap

HashMap vsAssociationMap

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

JSplitPane 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 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

name

String name

Class cytoscape.visual.DuplicateCalculatorNameException extends RuntimeException implements Serializable

Class cytoscape.visual.LineType extends Object implements Serializable

Serialized Fields

name

String name

stroke

Stroke stroke

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.continuous

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

Serialized Fields

components

ArrayList components

defaultObject

Object defaultObject

parentDialog

JDialog parentDialog

network

CyNetwork network

cm

ContinuousMapping cm

Package cytoscape.visual.mappings.discrete

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

Serialized Fields

parentDialog

JDialog parentDialog

network

CyNetwork network

attrName

String attrName

mappedKeys

TreeSet mappedKeys

dm

DiscreteMapping dm

defaultObject

Object defaultObject

mapType

byte mapType

buttonPanel

JPanel buttonPanel

listScrollPane

JScrollPane listScrollPane

buttonPositions

HashMap buttonPositions

Package cytoscape.visual.ui

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

Serialized Fields

vmm

VisualMappingManager vmm

backColor

ValueDisplayer backColor

parentDialog

VizMapUI parentDialog

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

Serialized Fields

selectedFont

Font selectedFont

displayFonts

Font[] displayFonts

fontFaceModel

DefaultComboBoxModel fontFaceModel

face

JComboBox face

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

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

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

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

Serialized Fields

dispType

byte dispType

Holds the type of UI this ValueDisplayer will pop up.

inputObj

Object inputObj

Holds the object inputted by the user.

title

String title

Input dialog title

parent

JDialog parent

Parent dialog

inputListener

ActionListener inputListener

ActionListener that triggers input UI

enabled

boolean enabled

Enable/disable mouse listeners

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

Serialized Fields

catalog

CalculatorCatalog catalog

reference to calculator catalog

VMM

VisualMappingManager VMM

VisualMappingManager for the window

type

byte type

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

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

the parent JDialog

defaultValueDisplayer

ValueDisplayer defaultValueDisplayer

Default ValueDisplayer

calcComboBox

JComboBox calcComboBox

Combo box for calculator selection

mapPanelGBG

GridBagGroup mapPanelGBG

Calculator UI

calcContainer

JPanel calcContainer

calcPanel

JPanel calcPanel

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

calcListener

VizMapAttrTab.CalculatorUIListener calcListener

Listener for calculator UI changes

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

Serialized Fields

faceTab

VizMapAttrTab faceTab

sizeTab

VizMapAttrTab sizeTab

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

mainPane

JPanel mainPane

The content pane for the dialog

mainGBG

GridBagGroup mainGBG

actionButtonsPanel

JPanel actionButtonsPanel

attrSelectorPanel

JPanel attrSelectorPanel

tabPaneContainer

JPanel tabPaneContainer

The content pane for the JTabbedPanes

tabs

VizMapTab[] tabs

Keeps track of contained tabs

styles

Collection styles

All known VisualStyles

styleSelector

VizMapUI.StyleSelector styleSelector

StyleSelector sub-dialog

initialized

boolean initialized

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

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.NewStyleListener extends AbstractAction implements Serializable

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

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