Serialized Form

Package cytoscape.task.ui

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

Serialized Fields

t

Throwable t

The Error Object

userErrorMessage

String userErrorMessage

A Human Readable Error Message

showDetails

boolean showDetails

Flag to Show/Hide Error Details.

detailsButton

JButton detailsButton

Show/Hide Details Button.

detailsPane

JScrollPane detailsPane

Scroll Pane used to display Stack Trace Elements.

owner

JDialog owner

JDialog Owner.

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

Serialized Fields

pBar

JProgressBar pBar

ProgressBar UI component.

descriptionValue

JLabel descriptionValue

Description value label.

statusValue

JTextArea statusValue

Status value label.

timeRemainingValue

JLabel timeRemainingValue

Time remaining label.

timeElapsedValue

JLabel timeElapsedValue

Time elapsed label.

progressValue

JLabel progressValue

Progress Value.

timer

Timer timer

Internal Timer.

cancelButton

JButton cancelButton

Cancel Button.

closeButton

JButton closeButton

Close Button.

startTime

Date startTime

Time Stamp when Component was constructed.

taskTitle

String taskTitle

Title Value.

config

JTaskConfig config

Used to Configure the JTask UI.

task

Task task

Task we are monitoring.

progressPanel

JPanel progressPanel

Contains all the Progress Fields.

haltRequested

boolean haltRequested

Flag to Indicate that user has requested that task halt.

errorOccurred

boolean errorOccurred

Flag to Indicate that error has occurred within task.

timeRemaining

long timeRemaining

Estimated Time Remaining.

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.util.swing.BioDataServerPanel1 extends JPanel implements Serializable

Serialized Fields

blankSpace

JLabel blankSpace

anotherBlankSpace

JLabel anotherBlankSpace

yetAnotherBlankSpace1

JLabel yetAnotherBlankSpace1

yetAnotherBlankSpace2

JLabel yetAnotherBlankSpace2

jLabel1

JLabel jLabel1

jLabel2

JLabel jLabel2

jLabel9

JLabel jLabel9

welcomeTitle

JLabel welcomeTitle

contentPanel

JPanel contentPanel

iconLabel

JLabel iconLabel

icon

ImageIcon icon

oldFileRadioButton

JRadioButton oldFileRadioButton

newFileRadioButton

JRadioButton newFileRadioButton

connectorGroup

ButtonGroup connectorGroup

yetAnotherBlankSpace3

JLabel yetAnotherBlankSpace3

yetAnotherBlankSpace4

JLabel yetAnotherBlankSpace4

yetAnotherBlankSpace8

JLabel yetAnotherBlankSpace8

yetAnotherBlankSpace7

JLabel yetAnotherBlankSpace7

yetAnotherBlankSpace6

JLabel yetAnotherBlankSpace6

yetAnotherBlankSpace5

JLabel yetAnotherBlankSpace5

yetAnotherBlankSpace9

JLabel yetAnotherBlankSpace9

yetAnotherBlankSpace10

JLabel yetAnotherBlankSpace10

yetAnotherBlankSpace11

JLabel yetAnotherBlankSpace11

yetAnotherBlankSpace12

JLabel yetAnotherBlankSpace12

yetAnotherBlankSpace13

JLabel yetAnotherBlankSpace13

noteLabel

JLabel noteLabel

noteLabel1

JLabel noteLabel1

noteLabel2

JLabel noteLabel2

noteLabel3

JLabel noteLabel3

Class cytoscape.util.swing.BioDataServerPanel2 extends JPanel implements Serializable

Serialized Fields

anotherBlankSpace

JLabel anotherBlankSpace

blankSpace

JLabel blankSpace

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

jPanel2

JPanel jPanel2

panelTitle

JLabel panelTitle

contentPanel

JPanel contentPanel

iconLabel

JLabel iconLabel

separator

JSeparator separator

textLabel

JLabel textLabel

titlePanel

JPanel titlePanel

jc1

JFileChooser jc1

oboFileName

JTextField oboFileName

gaFileName

JTextField gaFileName

selectOboFile

JButton selectOboFile

selectGaFile

JButton selectGaFile

jPanel3

Container jPanel3

jc2

JFileChooser jc2

flipCheck

JCheckBox flipCheck

start

File start

Class cytoscape.util.swing.BioDataServerPanel3 extends JPanel implements Serializable

Serialized Fields

anotherBlankSpace

JLabel anotherBlankSpace

blankSpace

JLabel blankSpace

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

progressDescription

JLabel progressDescription

progressSent

JProgressBar progressSent

contentPanel

JPanel contentPanel

iconLabel

JLabel iconLabel

separator

JSeparator separator

textLabel

JLabel textLabel

titlePanel

JPanel titlePanel

jLabel2

JLabel jLabel2

jLabel3

JLabel jLabel3

spList

JComboBox spList

start

File start

species

String species

taxonNameBox

JTextField taxonNameBox

setButton

JButton setButton

selectionType

ButtonGroup selectionType

comboBoxButton

JRadioButton comboBoxButton

textBoxButton

JRadioButton textBoxButton

currentSpBox

JTextField currentSpBox

FS

String FS

TAXON_FILE

String TAXON_FILE

See Also:

Constant Field Values

yetAnotherBlankSpace1

JLabel yetAnotherBlankSpace1

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

jPanel4

JPanel jPanel4

jLabel4

JLabel jLabel4

jLabel5

JLabel jLabel5

yetAnotherBlankSpace2

JLabel yetAnotherBlankSpace2

yetAnotherBlankSpace3

Component yetAnotherBlankSpace3

Class cytoscape.util.swing.BioDataServerPanel4 extends JPanel implements Serializable

Serialized Fields

anotherBlankSpace

JLabel anotherBlankSpace

blankSpace

JLabel blankSpace

connectorGroup

ButtonGroup connectorGroup

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

progressDescription

JLabel progressDescription

progressSent

JProgressBar progressSent

welcomeTitle

JLabel welcomeTitle

yetAnotherBlankSpace1

JLabel yetAnotherBlankSpace1

contentPanel

JPanel contentPanel

iconLabel

JLabel iconLabel

separator

JSeparator separator

textLabel

JLabel textLabel

titlePanel

JPanel titlePanel

jLabel2

JLabel jLabel2

jLabel3

JLabel jLabel3

spList

JComboBox spList

start

File start

species

String species

taxonNameBox

JTextField taxonNameBox

setButton

JButton setButton

selectionType

ButtonGroup selectionType

comboBoxButton

JRadioButton comboBoxButton

textBoxButton

JRadioButton textBoxButton

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

currentSpBox

JTextField currentSpBox

manifestFileName

JTextField manifestFileName

selectManifestFile

JButton selectManifestFile

manifestName

String manifestName

jc1

JFileChooser jc1

FS

String FS

Class cytoscape.util.swing.BioDataServerPanel5 extends JPanel implements Serializable

Serialized Fields

anotherBlankSpace

JLabel anotherBlankSpace

blankSpace

JLabel blankSpace

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

jPanel2

JPanel jPanel2

panelTitle

JLabel panelTitle

contentPanel

JPanel contentPanel

iconLabel

JLabel iconLabel

separator

JSeparator separator

textLabel

JLabel textLabel

titlePanel

JPanel titlePanel

jc1

JFileChooser jc1

oboFileName

JTextField oboFileName

gaFileName

JTextField gaFileName

selectOboFile

JButton selectOboFile

selectGaFile

JButton selectGaFile

jPanel3

Container jPanel3

jc2

JFileChooser jc2

flipCheck

JCheckBox flipCheck

start

File start

FS

String FS

TAXON_FILE

String TAXON_FILE

See Also:

Constant Field Values

Class cytoscape.util.swing.BioDataServerPanel6 extends JPanel implements Serializable

Serialized Fields

start

File start

FS

String FS

TAXON_FILE

String TAXON_FILE

See Also:

Constant Field Values

taxonFileLocation

String taxonFileLocation

bdsUtil

BioDataServerUtil bdsUtil

gaFileSelectedFlag

boolean gaFileSelectedFlag

overwriteCheckBox

JCheckBox overwriteCheckBox

jTextPane1

JTextPane jTextPane1

oboPanel

JPanel oboPanel

oboFileName

JTextField oboFileName

gaPanel

JPanel gaPanel

overwritePanel

JPanel overwritePanel

overwriteComboBox

JComboBox overwriteComboBox

selectOboButton

JButton selectOboButton

jPanel1

JPanel jPanel1

addGAButton

JButton addGAButton

gaFileList

JList gaFileList

jPanel2

JPanel jPanel2

titlePanel

JPanel titlePanel

textLabel

JLabel textLabel

jScrollPane

JScrollPane jScrollPane

gaListItems

Vector gaListItems

messageArea2

JTextArea messageArea2

jLabel

JLabel jLabel

flipCheckBox

JCheckBox flipCheckBox

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.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.

See Also:

Constant Field Values

NOTIFICATION_COMPONENT_SELECTED

int NOTIFICATION_COMPONENT_SELECTED

Notification component selected.

See Also:

Constant Field Values

NOTIFICATION_COMPONENT_ADDED

int NOTIFICATION_COMPONENT_ADDED

Notification component added.

See Also:

Constant Field Values

NOTIFICATION_COMPONENT_REMOVED

int NOTIFICATION_COMPONENT_REMOVED

Notification component removed.

See Also:

Constant Field Values

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.

See Also:

Constant Field Values

FLOAT_PANEL_COLOR

Color FLOAT_PANEL_COLOR

Color of the dock/float button panel.

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

reidentificationEnabled

boolean reidentificationEnabled

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

cytoscape.view.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

cytoscape.view.NetworkViewManager networkViewManager

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

cyHelpBroker

cytoscape.view.CyHelpBroker cyHelpBroker

The HelpBroker provides access to JavaHelp

pcs

SwingPropertyChangeSupport pcs

provides support for property change events

graphViewController

cytoscape.view.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

cytoscape.visual.ui.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

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.data.ExpressionData extends Object implements Serializable

Serialized Fields

taskMonitor

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.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.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.plugin.NotAPluginException extends Exception implements Serializable

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

Serialized Fields

tree

JTree tree

treeTableModel

TreeTableModel treeTableModel