Serialized Form

Package org.systemsbiology.gaggle.boss

Class org.systemsbiology.gaggle.boss.GaggleBossTableModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

parentApp

GuiBoss parentApp

applicationNames

java.util.ArrayList<E> applicationNames

listeningState

java.util.ArrayList<E> listeningState

selectionCounts

java.util.ArrayList<E> selectionCounts

appNames

java.lang.String[] appNames

columnNames

java.lang.String[] columnNames

Class org.systemsbiology.gaggle.boss.GuiBoss extends java.rmi.server.UnicastRemoteObject implements Serializable

Serialized Fields

frame

javax.swing.JFrame frame

gooseTable

javax.swing.JTable gooseTable

scrollPane

javax.swing.JScrollPane scrollPane

searchBox

javax.swing.JTextField searchBox

gooseTableModel

GaggleBossTableModel gooseTableModel

serviceName

java.lang.String serviceName

nameHelper

NewNameHelper nameHelper

gooseMap

java.util.HashMap<K,V> gooseMap

gooseListeningMap

java.util.HashMap<K,V> gooseListeningMap

deafGeese

java.util.ArrayList<E> deafGeese

plugins

java.util.ArrayList<E> plugins

outerPanel

javax.swing.JPanel outerPanel

tabbedPanel

javax.swing.JTabbedPane tabbedPanel

frameSizeToggleButton

javax.swing.JButton frameSizeToggleButton

bodyVisible

boolean bodyVisible

config

BossConfig config

Package org.systemsbiology.gaggle.boss.plugins

Class org.systemsbiology.gaggle.boss.plugins.GaggleBossPlugin extends javax.swing.JPanel implements Serializable

Serialized Fields

name

java.lang.String name

Package org.systemsbiology.gaggle.boss.plugins.clipboard

Class org.systemsbiology.gaggle.boss.plugins.clipboard.Clipboard extends GaggleBossPlugin implements Serializable

Serialized Fields

name

java.lang.String name

scrollPane

javax.swing.JScrollPane scrollPane

textArea

javax.swing.JTextArea textArea

gaggleBoss

GuiBoss gaggleBoss

species

java.lang.String species

Package org.systemsbiology.gaggle.boss.plugins.hypothesis

Class org.systemsbiology.gaggle.boss.plugins.hypothesis.HypothesisRecorder extends GaggleBossPlugin implements Serializable

Serialized Fields

name

java.lang.String name

textArea

javax.swing.JTextArea textArea

saveHypothesisButton

javax.swing.JButton saveHypothesisButton

clearTextButton

javax.swing.JButton clearTextButton

gaggleBoss

GuiBoss gaggleBoss

species

java.lang.String species

titleField

javax.swing.JTextField titleField

nameField

javax.swing.JTextField nameField

dateField

javax.swing.JTextField dateField

summaryField

javax.swing.JTextField summaryField

ratingField

javax.swing.JTextField ratingField

Package org.systemsbiology.gaggle.boss.plugins.launcher

Class org.systemsbiology.gaggle.boss.plugins.launcher.Launcher extends GaggleBossPlugin implements Serializable

Serialized Fields

name

java.lang.String name

scrollPane

javax.swing.JScrollPane scrollPane

gaggleBoss

GuiBoss gaggleBoss

species

java.lang.String species

uri

java.lang.String uri

Class org.systemsbiology.gaggle.boss.plugins.launcher.WebPage extends javax.swing.JPanel implements Serializable

Serialized Fields

centerPanel

javax.swing.JPanel centerPanel

urlReadout

javax.swing.JTextField urlReadout

url

java.net.URL url

briefWebSiteName

java.lang.String briefWebSiteName

htmlText

java.lang.String htmlText

fullUrlString

java.lang.String fullUrlString

host

java.lang.String host

protocol

java.lang.String protocol

path

java.lang.String path

file

java.lang.String file

query

java.lang.String query

Package org.systemsbiology.gaggle.boss.plugins.sbeams

Class org.systemsbiology.gaggle.boss.plugins.sbeams.PasswordDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

pressed_OK

boolean pressed_OK

name

javax.swing.JTextField name

pass

javax.swing.JPasswordField pass

okButton

javax.swing.JButton okButton

cancelButton

javax.swing.JButton cancelButton

nameLabel

javax.swing.JLabel nameLabel

passLabel

javax.swing.JLabel passLabel

Class org.systemsbiology.gaggle.boss.plugins.sbeams.SBeamsSearchPanel extends GaggleBossPlugin implements Serializable

Serialized Fields

name

java.lang.String name

targetGoose

java.lang.String targetGoose

scrollPane

javax.swing.JScrollPane scrollPane

searchBox

javax.swing.JTextField searchBox

selectionCountReadout

javax.swing.JTextField selectionCountReadout

retrievedCountReadout

javax.swing.JTextField retrievedCountReadout

sbeamsResultSetTableModel

org.systemsbiology.gaggle.boss.plugins.sbeams.SbeamsResultSetTableModel sbeamsResultSetTableModel

selectionModel

javax.swing.ListSelectionModel selectionModel

sbeamsResultSetTable

javax.swing.JTable sbeamsResultSetTable

broadcastSbeamsSelectionsButton

javax.swing.JButton broadcastSbeamsSelectionsButton

selectAllSbeamsRowsButton

javax.swing.JButton selectAllSbeamsRowsButton

clearAllSbeamsSelectionsButton

javax.swing.JButton clearAllSbeamsSelectionsButton

gaggleBoss

GuiBoss gaggleBoss

species

java.lang.String species

Package org.systemsbiology.gaggle.boss.plugins.tigrAnno

Class org.systemsbiology.gaggle.boss.plugins.tigrAnno.SearchPanel extends GaggleBossPlugin implements Serializable

Serialized Fields

name

java.lang.String name

scrollPane

javax.swing.JScrollPane scrollPane

searchBox

javax.swing.JTextField searchBox

tableModel

org.systemsbiology.gaggle.boss.plugins.tigrAnno.SearchResultsTableModel tableModel

resultsTable

javax.swing.JTable resultsTable

resultSetSizeReadout

javax.swing.JTextField resultSetSizeReadout

broadcastSelectionsButton

javax.swing.JButton broadcastSelectionsButton

selectAllRowsButton

javax.swing.JButton selectAllRowsButton

clearAllSelectionsButton

javax.swing.JButton clearAllSelectionsButton

clearTableButton

javax.swing.JButton clearTableButton

conditionCounterTextField

javax.swing.JTextField conditionCounterTextField

species

java.lang.String species

gaggleBoss

GuiBoss gaggleBoss

annotationUri

java.lang.String annotationUri

searchMap

java.util.HashMap<K,V> searchMap

summaryMap

java.util.HashMap<K,V> summaryMap

Package org.systemsbiology.gaggle.core.datatypes

Class org.systemsbiology.gaggle.core.datatypes.Cluster extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

species

java.lang.String species

rowNames

java.lang.String[] rowNames

columnNames

java.lang.String[] columnNames

metadata

Tuple metadata

Class org.systemsbiology.gaggle.core.datatypes.DataMatrix extends java.lang.Object implements Serializable

Serialization Methods

writeObject

public void writeObject(java.lang.String uri)
                 throws java.io.IOException

Throws:

java.io.IOException

Serialized Fields

name

java.lang.String name

metadata

Tuple metadata

rowTitlesTitle

java.lang.String rowTitlesTitle

columnTitles

java.lang.String[] columnTitles

rowTitles

java.lang.String[] rowTitles

data

double[][] data

uri

java.lang.String uri

fullName

java.lang.String fullName

shortName

java.lang.String shortName

fileExtension

java.lang.String fileExtension

dataTypeBriefName

java.lang.String dataTypeBriefName

species

java.lang.String species

Class org.systemsbiology.gaggle.core.datatypes.GaggleTuple extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

species

java.lang.String species

data

Tuple data

metadata

Tuple metadata

Class org.systemsbiology.gaggle.core.datatypes.Interaction extends java.lang.Object implements Serializable

Serialized Fields

source

java.lang.String source

target

java.lang.String target

interactionType

java.lang.String interactionType

directed

boolean directed

Class org.systemsbiology.gaggle.core.datatypes.Namelist extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

species

java.lang.String species

names

java.lang.String[] names

metadata

Tuple metadata

Class org.systemsbiology.gaggle.core.datatypes.Network extends java.lang.Object implements Serializable

Serialized Fields

interactionList

java.util.List<E> interactionList

nodeAttributes

java.util.Map<K,V> nodeAttributes

edgeAttributes

java.util.Map<K,V> edgeAttributes

nodes

java.util.Set<E> nodes

species

java.lang.String species

name

java.lang.String name

metadata

Tuple metadata

Class org.systemsbiology.gaggle.core.datatypes.Single extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

value

java.io.Serializable value

Class org.systemsbiology.gaggle.core.datatypes.Tuple extends java.lang.Object implements Serializable

Serialized Fields

singleList

java.util.List<E> singleList

name

java.lang.String name

Package org.systemsbiology.gaggle.coreTests

Class org.systemsbiology.gaggle.coreTests.TupleDemo extends java.lang.Object implements Serializable

Package org.systemsbiology.gaggle.experiment.datamatrix

Class org.systemsbiology.gaggle.experiment.datamatrix.LensedDataMatrix extends DataMatrix implements Serializable

Serialized Fields

columnOrder

int[] columnOrder

columnState

boolean[] columnState

rowState

boolean[] rowState

rowMap

int[] rowMap

noExplicitRowSelection

boolean noExplicitRowSelection

underlyingMatrix

DataMatrix underlyingMatrix

nameMap

java.util.Hashtable<K,V> nameMap

Package org.systemsbiology.gaggle.experiment.gui

Class org.systemsbiology.gaggle.experiment.gui.AutoCompletion extends javax.swing.text.PlainDocument implements Serializable

Serialized Fields

comboBox

javax.swing.JComboBox comboBox

model

javax.swing.ComboBoxModel model

editor

javax.swing.text.JTextComponent editor

selecting

boolean selecting

hidePopupOnFocusLoss

boolean hidePopupOnFocusLoss

hitBackspace

boolean hitBackspace

hitBackspaceOnSelection

boolean hitBackspaceOnSelection

editorKeyListener

java.awt.event.KeyListener editorKeyListener

editorFocusListener

java.awt.event.FocusListener editorFocusListener

Class org.systemsbiology.gaggle.experiment.gui.CheckBoxHeader extends javax.swing.JCheckBox implements Serializable

Serialized Fields

column

int column

Class org.systemsbiology.gaggle.experiment.gui.DataMatrixTableModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

columnNames

java.lang.String[] columnNames

savedRowIndices

int[] savedRowIndices

newRowIndices

int[] newRowIndices

data

java.lang.Object[][] data

columnWidths

int[] columnWidths

defaultColumnWidth

int defaultColumnWidth

preferredTableWidth

int preferredTableWidth

Class org.systemsbiology.gaggle.experiment.gui.DataMatrixViewer extends javax.swing.JPanel implements Serializable

Serialized Fields

tabbedPane

javax.swing.JTabbedPane tabbedPane

currentDirectory

java.io.File currentDirectory

nameHelper

NameHelper nameHelper

metaData

java.util.ArrayList<E> metaData

navigator

MetaDataNavigator navigator

matrices

DataMatrix[] matrices

matrixList

java.util.ArrayList<E> matrixList

controlPanel

javax.swing.JPanel controlPanel

movieController

javax.swing.JPanel movieController

butNameType

javax.swing.JButton butNameType

toolbar

javax.swing.JToolBar toolbar

lastModificationTime

java.util.Date lastModificationTime

allViews

java.util.ArrayList<E> allViews

plotTabNames

java.util.HashMap<K,V> plotTabNames

widgets

java.util.HashMap<K,V> widgets

currentTabIndex

int currentTabIndex

Class org.systemsbiology.gaggle.experiment.gui.LoadMatrixProjectDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ok

boolean ok

checkBox

javax.swing.JCheckBox checkBox

list

javax.swing.JList list

Class org.systemsbiology.gaggle.experiment.gui.LoadMatrixProjectListModel extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

projects

MatrixProject[] projects

Class org.systemsbiology.gaggle.experiment.gui.MatrixSpreadsheet extends javax.swing.JPanel implements Serializable

Serialized Fields

matrix

DataMatrix matrix

tableModel

DataMatrixTableModel tableModel

name

java.lang.String name

lens

LensedDataMatrix lens

nameHelper

NameHelper nameHelper

matrixViewCoordinator

MatrixViewCoordinator matrixViewCoordinator

table

javax.swing.JTable table

selectionCountTextField

javax.swing.JTextField selectionCountTextField

nameTypeButton

javax.swing.JButton nameTypeButton

rowSelectionListeningDisabled

boolean rowSelectionListeningDisabled

sortOrderAscending

boolean sortOrderAscending

calculateByDataWidth

boolean calculateByDataWidth

navigator

MetaDataNavigator navigator

columnCheckBoxHeaderMap

java.util.HashMap<K,V> columnCheckBoxHeaderMap

buttonPanel

javax.swing.JPanel buttonPanel

controlPanel

javax.swing.JPanel controlPanel

movieController

javax.swing.JPanel movieController

volcanoPlotButton

javax.swing.JButton volcanoPlotButton

companionMatrixID

int companionMatrixID

rowHeader

MutableList rowHeader

preferredTableWidth

int preferredTableWidth

preferredTableHeight

int preferredTableHeight

widgets

java.util.HashMap<K,V> widgets

Class org.systemsbiology.gaggle.experiment.gui.MetaDataViewer extends javax.swing.JDialog implements Serializable

Serialized Fields

experimentChooser

javax.swing.JComboBox experimentChooser

experiments

java.util.Map<K,V> experiments

textArea

javax.swing.JTextArea textArea

Class org.systemsbiology.gaggle.experiment.gui.MutableList extends javax.swing.JList implements Serializable

Serialized Fields

originalValues

java.util.Vector<E> originalValues

originalNames

java.util.Vector<E> originalNames

nameMap

java.util.Hashtable<K,V> nameMap

indexMap

java.util.Hashtable<K,V> indexMap

Class org.systemsbiology.gaggle.experiment.gui.SaveMatrixProjectDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

nameField

javax.swing.JTextField nameField

descriptionField

javax.swing.JTextArea descriptionField

ok

boolean ok

Class org.systemsbiology.gaggle.experiment.gui.SearchDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ok

boolean ok

tag1

javax.swing.JComboBox tag1

tag2

javax.swing.JComboBox tag2

tag3

javax.swing.JComboBox tag3

allTags

java.lang.String[] allTags

Class org.systemsbiology.gaggle.experiment.gui.SearchResultsFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

tags

java.lang.String[] tags

results

Condition[] results

resultNames

java.lang.String[] resultNames

tdv

TreeDataViewer tdv

table

javax.swing.JTable table

Class org.systemsbiology.gaggle.experiment.gui.SearchResultsTableModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

results

Condition[] results

Class org.systemsbiology.gaggle.experiment.gui.TreeDataViewer extends java.lang.Object implements Serializable

Serialized Fields

perst

java.util.List<E> perst

currentTreeSelection

java.util.ArrayList<E> currentTreeSelection

dataMatrixViewer

DataMatrixViewer dataMatrixViewer

experimentNavigator

MetaDataNavigator experimentNavigator

currentlySelectedExperiments

java.util.ArrayList<E> currentlySelectedExperiments

experiments

java.util.ArrayList<E> experiments

jframe

javax.swing.JFrame jframe

menubar

javax.swing.JMenuBar menubar

toolbar

javax.swing.JToolBar toolbar

extraToolbar

javax.swing.JToolBar extraToolbar

toolbarEtcPanel

javax.swing.JPanel toolbarEtcPanel

treePane

javax.swing.JScrollPane treePane

resultsPanel

javax.swing.JPanel resultsPanel

outerSplitPane

javax.swing.JSplitPane outerSplitPane

treeWidget

javax.swing.JTree treeWidget

newRepositoryButton

javax.swing.JButton newRepositoryButton

saveAllButton

javax.swing.JButton saveAllButton

loadSelectedConditionsButton

javax.swing.JButton loadSelectedConditionsButton

showHideWorkFramesButton

javax.swing.JButton showHideWorkFramesButton

followExperimentLinksButton

javax.swing.JButton followExperimentLinksButton

selectedExperimentInfoUrls

java.util.HashMap<K,V> selectedExperimentInfoUrls

exitListeners

java.util.HashSet<E> exitListeners

workFramesVisible

boolean workFramesVisible

conditionCounterTextField

javax.swing.JTextField conditionCounterTextField

dataBrowserHasEntireWindow

boolean dataBrowserHasEntireWindow

settings

Settings settings

selectedConditionCount

int selectedConditionCount

movieController

MovieController movieController

repository

java.lang.String repository

experimentDetailsAction

org.systemsbiology.gaggle.experiment.gui.TreeDataViewer.ExperimentDetailsAction experimentDetailsAction

closeAllTabsAction

org.systemsbiology.gaggle.experiment.gui.TreeDataViewer.CloseAllTabsAction closeAllTabsAction

treeCollapsed

boolean treeCollapsed

Package org.systemsbiology.gaggle.experiment.gui.actions

Class org.systemsbiology.gaggle.experiment.gui.actions.CorrelationFinderDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

parentSpreadsheet

MatrixSpreadsheet parentSpreadsheet

matrix

DataMatrix matrix

lens

LensedDataMatrix lens

finder

CorrelationFinder finder

currentCorrelationThreshold

double currentCorrelationThreshold

namesOfCorrelatedNodes

java.util.ArrayList<E> namesOfCorrelatedNodes

namesOfReferenceNodes

java.lang.String[] namesOfReferenceNodes

correlatedCountTextField

javax.swing.JTextField correlatedCountTextField

thresholdTextField

javax.swing.JTextField thresholdTextField

correlationMode

java.lang.String correlationMode

Class org.systemsbiology.gaggle.experiment.gui.actions.CorrelationFinderDialog.DismissAction extends javax.swing.AbstractAction implements Serializable

Class org.systemsbiology.gaggle.experiment.gui.actions.CreateNewMatrixFromSelection extends javax.swing.AbstractAction implements Serializable

Serialized Fields

parent

MatrixSpreadsheet parent

mvc

MatrixViewCoordinator mvc

Class org.systemsbiology.gaggle.experiment.gui.actions.DataMatrixMovieDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

mainPanel

javax.swing.JPanel mainPanel

edgedPanel

javax.swing.JPanel edgedPanel

conditionsPanel

javax.swing.JPanel conditionsPanel

speedPanel

javax.swing.JPanel speedPanel

playPanel

javax.swing.JPanel playPanel

statusPanel

javax.swing.JPanel statusPanel

loopPanel

javax.swing.JPanel loopPanel

buttonPanel

javax.swing.JPanel buttonPanel

dismissPanel

javax.swing.JPanel dismissPanel

fileLabel

javax.swing.JLabel fileLabel

speedLabel

javax.swing.JLabel speedLabel

conditionLabels

javax.swing.JLabel[] conditionLabels

fileField

javax.swing.JTextField fileField

browseButton

javax.swing.JButton browseButton

conditionsSlider

javax.swing.JSlider conditionsSlider

speedSlider

javax.swing.JSlider speedSlider

conditionsListener

org.systemsbiology.gaggle.experiment.gui.actions.DataMatrixMovieDialog.ConditionsSliderListener conditionsListener

playButton

javax.swing.JButton playButton

stopButton

javax.swing.JButton stopButton

pauseButton

javax.swing.JButton pauseButton

dismissButton

javax.swing.JButton dismissButton

loop

javax.swing.JCheckBox loop

pBar

javax.swing.JProgressBar pBar

lenses

LensedDataMatrix[] lenses

attributeNames

java.lang.String[] attributeNames

maxConditions

int maxConditions

cytoscapeWindow

CytoscapeWindow cytoscapeWindow

timer

javax.swing.Timer timer

startLabelText

java.lang.String startLabelText

movieState

int movieState

movieFrame

int movieFrame

loopMovie

boolean loopMovie

Class org.systemsbiology.gaggle.experiment.gui.actions.MathematicalOperations extends javax.swing.AbstractAction implements Serializable

Serialized Fields

parentSpreadsheet

MatrixSpreadsheet parentSpreadsheet

opName

java.lang.String opName

averageCount

int averageCount

andCount

int andCount

orCount

int orCount

Class org.systemsbiology.gaggle.experiment.gui.actions.MatrixExporter extends javax.swing.AbstractAction implements Serializable

Serialized Fields

parentSpreadsheet

MatrixSpreadsheet parentSpreadsheet

currentDirectory

java.io.File currentDirectory

Class org.systemsbiology.gaggle.experiment.gui.actions.MatrixExporterDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ok

boolean ok

exportAllRowsCheckbox

javax.swing.JCheckBox exportAllRowsCheckbox

transposeMatrixCheckbox

javax.swing.JCheckBox transposeMatrixCheckbox

Class org.systemsbiology.gaggle.experiment.gui.actions.ThresholdSelectorDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

parentSpreadsheet

MatrixSpreadsheet parentSpreadsheet

matrix

DataMatrix matrix

lens

LensedDataMatrix lens

sortedRows

double[][] sortedRows

matrixMin

double matrixMin

matrixMax

double matrixMax

currentThreshold

double currentThreshold

namesOfRowsAboveThreshold

java.util.ArrayList<E> namesOfRowsAboveThreshold

decimalFormatter

java.text.DecimalFormat decimalFormatter

selectionCountTextField

javax.swing.JTextField selectionCountTextField

thresholdTextField

javax.swing.JTextField thresholdTextField

Class org.systemsbiology.gaggle.experiment.gui.actions.ThresholdSelectorDialog.DismissAction extends javax.swing.AbstractAction implements Serializable

Package org.systemsbiology.gaggle.experiment.gui.movie

Class org.systemsbiology.gaggle.experiment.gui.movie.MovieControllerInfoDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

lenses

LensedDataMatrix[] lenses

saveChangesButton

javax.swing.JButton saveChangesButton

allTables

javax.swing.JTable[] allTables

Class org.systemsbiology.gaggle.experiment.gui.movie.MovieControllerInfoDialog.DismissAction extends javax.swing.AbstractAction implements Serializable

Class org.systemsbiology.gaggle.experiment.gui.movie.MovieControllerInfoDialog.SaveChangesAction extends javax.swing.AbstractAction implements Serializable

Package org.systemsbiology.gaggle.experiment.gui.plotters.matrix

Class org.systemsbiology.gaggle.experiment.gui.plotters.matrix.MatrixPlotter extends javax.swing.JPanel implements Serializable

Serialized Fields

dataMatrix

DataMatrix dataMatrix

xAxisLabel

java.lang.String xAxisLabel

yAxisLabel

java.lang.String yAxisLabel

preferredWidth

int preferredWidth

preferredHeight

int preferredHeight

seriesHash

java.util.HashMap<K,V> seriesHash

dataset

XYSeriesCollection dataset

plot

XYPlot plot

renderer

StandardXYItemRenderer renderer

showConditionsToggleButton

javax.swing.JButton showConditionsToggleButton

xAxisConditionNames

java.lang.String[] xAxisConditionNames

nameHelper

NameHelper nameHelper

settings

Settings settings

Class org.systemsbiology.gaggle.experiment.gui.plotters.matrix.SelectableMatrixPlotter extends javax.swing.JPanel implements Serializable

Serialized Fields

matrixPlotter

MatrixPlotter matrixPlotter

selectionListBox

javax.swing.JList selectionListBox

currentSelection

java.util.ArrayList<E> currentSelection

rowNames

java.lang.String[] rowNames

selectionToggleButton

javax.swing.JButton selectionToggleButton

selectionToggleState

boolean selectionToggleState

selectionCountTextField

javax.swing.JTextField selectionCountTextField

namesToDisplay

java.lang.String namesToDisplay

Package org.systemsbiology.gaggle.experiment.gui.plotters.scatter

Class org.systemsbiology.gaggle.experiment.gui.plotters.scatter.ScatterPlotter extends javax.swing.JPanel implements Serializable

Serialized Fields

pointNames

java.lang.String[] pointNames

xVector

double[] xVector

yVector

double[] yVector

title

java.lang.String title

xAxisLabel

java.lang.String xAxisLabel

yAxisLabel

java.lang.String yAxisLabel

mainPanel

javax.swing.JPanel mainPanel

xyPairsList

java.util.ArrayList<E> xyPairsList

chartDataSet

XYSeriesCollection chartDataSet

chartPanel

SelectableChartPanel chartPanel

dragActionComboBox

javax.swing.JComboBox dragActionComboBox

selectionReadout

javax.swing.JTextField selectionReadout

dragMeaning

int dragMeaning

currentSelection

java.util.ArrayList<E> currentSelection

Package org.systemsbiology.gaggle.experiment.metadata

Class org.systemsbiology.gaggle.experiment.metadata.Condition extends java.lang.Object implements Serializable

Serialized Fields

alias

java.lang.String alias

variables

java.util.ArrayList<E> variables

Class org.systemsbiology.gaggle.experiment.metadata.DataSetDescription extends java.lang.Object implements Serializable

Serialized Fields

uri

java.lang.String uri

status

java.lang.String status

type

java.lang.String type

Class org.systemsbiology.gaggle.experiment.metadata.MetaData extends java.lang.Object implements Serializable

Serialized Fields

title

java.lang.String title

date

java.lang.String date

uri

java.lang.String uri

predicates

java.util.HashMap<K,V> predicates

links

java.util.HashMap<K,V> links

dataSetDescriptions

java.util.ArrayList<E> dataSetDescriptions

conditions

java.util.ArrayList<E> conditions

constants

java.util.List<E> constants

treePaths

java.util.List<E> treePaths

variableSummary

java.util.HashMap<K,V> variableSummary

selectionCriteria

java.util.HashMap<K,V> selectionCriteria

Class org.systemsbiology.gaggle.experiment.metadata.Variable extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

value

java.lang.String value

units

java.lang.String units

Package org.systemsbiology.gaggle.geese.annotation

Class org.systemsbiology.gaggle.geese.annotation.AnnotationGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

gooseName

java.lang.String gooseName

boss

Boss boss

gaggleConnector

RmiGaggleConnector gaggleConnector

factory

GuiWidgetFactory factory

scrollPane

javax.swing.JScrollPane scrollPane

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

remoteObj

java.rmi.Remote remoteObj

column

int column

searchBox

javax.swing.JTextField searchBox

tableModel

org.systemsbiology.gaggle.geese.annotation.SearchResultsTableModel tableModel

resultsTable

SelfAdjustingJTable resultsTable

broadcastSelectionsButton

javax.swing.JButton broadcastSelectionsButton

broadcastListButton

javax.swing.JButton broadcastListButton

selectAllRowsButton

javax.swing.JButton selectAllRowsButton

clearAllSelectionsButton

javax.swing.JButton clearAllSelectionsButton

clearTableButton

javax.swing.JButton clearTableButton

conditionCounterTextField

javax.swing.JTextField conditionCounterTextField

status

javax.swing.JTextField status

selectionCountReadout

javax.swing.JTextField selectionCountReadout

retrievedCountReadout

javax.swing.JTextField retrievedCountReadout

columnMenu

javax.swing.JMenu columnMenu

species

java.lang.String species

index

Index index

summaryMap

java.util.HashMap<K,V> summaryMap

broadcastSelectionAction

org.systemsbiology.gaggle.geese.annotation.AnnotationGoose.BroadcastSelectionAction broadcastSelectionAction

anchorTagPattern

java.util.regex.Pattern anchorTagPattern

activeGooseNames

java.lang.String[] activeGooseNames

Class org.systemsbiology.gaggle.geese.annotation.LoadAnnotationDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ok

boolean ok

speciesComboBox

javax.swing.JComboBox speciesComboBox

uriTextField

javax.swing.JTextField uriTextField

okAction

javax.swing.Action okAction

appendCheckBox

javax.swing.JCheckBox appendCheckBox

knownSpeciesSet

java.util.TreeSet<E> knownSpeciesSet

knownAnnotationFiles

java.util.HashMap<K,V> knownAnnotationFiles

map from species name to the uri of an annotation file, if any preloaded annotation files are present.

Class org.systemsbiology.gaggle.geese.annotation.SelfAdjustingJTable extends javax.swing.JTable implements Serializable

Package org.systemsbiology.gaggle.geese.common.actions

Class org.systemsbiology.gaggle.geese.common.actions.ConnectToBossAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

connector

RmiGaggleConnector connector

Class org.systemsbiology.gaggle.geese.common.actions.DisconnectFromBossAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

connector

RmiGaggleConnector connector

Class org.systemsbiology.gaggle.geese.common.actions.HideGooseAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

boss

Boss boss

targetGoose

java.lang.String targetGoose

Class org.systemsbiology.gaggle.geese.common.actions.ShowGooseAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

boss

Boss boss

targetGoose

java.lang.String targetGoose

Class org.systemsbiology.gaggle.geese.common.actions.UpdateGooseChooserAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

gooseChooser

GooseChooserComboBox gooseChooser

Package org.systemsbiology.gaggle.geese.common.gui

Class org.systemsbiology.gaggle.geese.common.gui.GaggleMenu extends javax.swing.JMenu implements Serializable

Serialized Fields

connector

RmiGaggleConnector connector

Class org.systemsbiology.gaggle.geese.common.gui.GooseChooserComboBox extends javax.swing.JComboBox implements Serializable

Serialized Fields

boss

Boss boss

goose

Goose goose

Package org.systemsbiology.gaggle.geese.cy.fly

Class org.systemsbiology.gaggle.geese.cy.fly.ControlPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

toolbar

javax.swing.JToolBar toolbar

gridbagLayout

java.awt.GridBagLayout gridbagLayout

nodeSelectionTextField

javax.swing.JTextField nodeSelectionTextField

movieConditionReadout

javax.swing.JTextField movieConditionReadout

cw

CytoscapeWindow cw

dataServer

BioDataServer dataServer

graphHider

UndoableGraphHider graphHider

myGaggleName

java.lang.String myGaggleName

boss

Boss boss

connector

RmiGaggleConnector connector

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

confidenceReadout

javax.swing.JTextField confidenceReadout

confidenceThreshold

double confidenceThreshold

decimalFormatter

java.text.DecimalFormat decimalFormatter

species

java.lang.String species

Package org.systemsbiology.gaggle.geese.cy.inferelator

Class org.systemsbiology.gaggle.geese.cy.inferelator.ControlPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

toolbar

javax.swing.JToolBar toolbar

gridbagLayout

java.awt.GridBagLayout gridbagLayout

nodeSelectionTextField

javax.swing.JTextField nodeSelectionTextField

nodeInClusterSelectionTextField

javax.swing.JTextField nodeInClusterSelectionTextField

targetGoose

java.lang.String targetGoose

gooseChooser

javax.swing.JComboBox gooseChooser

connectButton

javax.swing.JButton connectButton

disconnectButton

javax.swing.JButton disconnectButton

activeGooseNames

java.lang.String[] activeGooseNames

cw

CytoscapeWindow cw

dataServer

BioDataServer dataServer

graphHider

UndoableGraphHider graphHider

myGaggleName

java.lang.String myGaggleName

connector

RmiGaggleConnector connector

boss

Boss boss

residualsReadout

javax.swing.JTextField residualsReadout

motifPValsReadout

javax.swing.JTextField motifPValsReadout

regulatorWeightsReadout

javax.swing.JTextField regulatorWeightsReadout

regulatorWeightsThreshold

double regulatorWeightsThreshold

motifPValsThreshold

double motifPValsThreshold

residualsThreshold

double residualsThreshold

decimalFormatter

java.text.DecimalFormat decimalFormatter

species

java.lang.String species

Package org.systemsbiology.gaggle.geese.cy.ip

Class org.systemsbiology.gaggle.geese.cy.ip.ControlPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

activeGooseNames

java.lang.String[] activeGooseNames

toolbar

javax.swing.JToolBar toolbar

connectButton

javax.swing.JButton connectButton

disconnectButton

javax.swing.JButton disconnectButton

gridbagLayout

java.awt.GridBagLayout gridbagLayout

nodeSelectionTextField

javax.swing.JTextField nodeSelectionTextField

probabilityThresholdReadout

javax.swing.JTextField probabilityThresholdReadout

probabilityThreshold

double probabilityThreshold

peptideMinCountThresholdReadout

javax.swing.JTextField peptideMinCountThresholdReadout

peptideMinCountThreshold

int peptideMinCountThreshold

peptideMaxCountThresholdReadout

javax.swing.JTextField peptideMaxCountThresholdReadout

peptideMaxCountThreshold

int peptideMaxCountThreshold

cw

CytoscapeWindow cw

dataServer

BioDataServer dataServer

graphHider

UndoableGraphHider graphHider

myGaggleName

java.lang.String myGaggleName

gaggleBoss

Boss gaggleBoss

connector

RmiGaggleConnector connector

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

gagglePopupMenu

javax.swing.JPopupMenu gagglePopupMenu

defaultCursor

java.awt.Cursor defaultCursor

busyCursor

java.awt.Cursor busyCursor

geneFindingDistanceReadout

javax.swing.JTextField geneFindingDistanceReadout

zoomFactorReadout

javax.swing.JTextField zoomFactorReadout

ratioThresholdReadout

javax.swing.JTextField ratioThresholdReadout

lambdaThresholdReadout

javax.swing.JTextField lambdaThresholdReadout

residualsReadout

javax.swing.JTextField residualsReadout

motifPValsReadout

javax.swing.JTextField motifPValsReadout

zoomFactor

double zoomFactor

ratioThreshold

double ratioThreshold

lambdaThreshold

double lambdaThreshold

geneFindingDistance

int geneFindingDistance

decimalFormatter

java.text.DecimalFormat decimalFormatter

motifPValsThreshold

double motifPValsThreshold

residualsThreshold

double residualsThreshold

species

java.lang.String species

lastSelection

java.lang.String[] lastSelection

selectedNodeIndex

int selectedNodeIndex

Package org.systemsbiology.gaggle.geese.cy.jdrf

Class org.systemsbiology.gaggle.geese.cy.jdrf.ControlPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

nodeSelectionTextField

javax.swing.JTextField nodeSelectionTextField

movieConditionReadout

javax.swing.JTextField movieConditionReadout

cw

CytoscapeWindow cw

dataServer

BioDataServer dataServer

graphHider

UndoableGraphHider graphHider

myGaggleName

java.lang.String myGaggleName

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

gaggleBoss

Boss gaggleBoss

connector

RmiGaggleConnector connector

correlationReadout

javax.swing.JTextField correlationReadout

correlationThreshold

double correlationThreshold

decimalFormatter

java.text.DecimalFormat decimalFormatter

species

java.lang.String species

Package org.systemsbiology.gaggle.geese.cy.prolinks

Class org.systemsbiology.gaggle.geese.cy.prolinks.ControlPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

toolbar

javax.swing.JToolBar toolbar

gridbagLayout

java.awt.GridBagLayout gridbagLayout

nodeSelectionTextField

javax.swing.JTextField nodeSelectionTextField

movieConditionReadout

javax.swing.JTextField movieConditionReadout

nodeInClusterSelectionTextField

javax.swing.JTextField nodeInClusterSelectionTextField

connectButton

javax.swing.JButton connectButton

disconnectButton

javax.swing.JButton disconnectButton

targetGoose

java.lang.String targetGoose

gooseChooser

javax.swing.JComboBox gooseChooser

cw

CytoscapeWindow cw

dataServer

BioDataServer dataServer

graphHider

UndoableGraphHider graphHider

myGaggleName

java.lang.String myGaggleName

connector

RmiGaggleConnector connector

boss

Boss boss

activeGooseNames

java.lang.String[] activeGooseNames

residualsReadout

javax.swing.JTextField residualsReadout

pValsReadout

javax.swing.JTextField pValsReadout

confidenceReadout

javax.swing.JTextField confidenceReadout

confidenceThreshold

double confidenceThreshold

pValsThreshold

double pValsThreshold

residualsThreshold

double residualsThreshold

decimalFormatter

java.text.DecimalFormat decimalFormatter

species

java.lang.String species

Package org.systemsbiology.gaggle.geese.cy.tileViewer

Class org.systemsbiology.gaggle.geese.cy.tileViewer.ControlPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

activeGooseNames

java.lang.String[] activeGooseNames

connectButton

javax.swing.JButton connectButton

disconnectButton

javax.swing.JButton disconnectButton

tileNavigationToolbar

javax.swing.JToolBar tileNavigationToolbar

gridbagLayout

java.awt.GridBagLayout gridbagLayout

nodeSelectionTextField

javax.swing.JTextField nodeSelectionTextField

nodeInClusterSelectionTextField

javax.swing.JTextField nodeInClusterSelectionTextField

cw

CytoscapeWindow cw

dataServer

BioDataServer dataServer

graphHider

UndoableGraphHider graphHider

myGaggleName

java.lang.String myGaggleName

targetGoose

java.lang.String targetGoose

gaggleBoss

Boss gaggleBoss

connector

RmiGaggleConnector connector

gagglePopupMenu

javax.swing.JPopupMenu gagglePopupMenu

geneFinder

GeneFinder geneFinder

gooseChooser

javax.swing.JComboBox gooseChooser

defaultCursor

java.awt.Cursor defaultCursor

busyCursor

java.awt.Cursor busyCursor

geneFindingDistanceReadout

javax.swing.JTextField geneFindingDistanceReadout

zoomFactorReadout

javax.swing.JTextField zoomFactorReadout

ratioThresholdReadout

javax.swing.JTextField ratioThresholdReadout

lambdaThresholdReadout

javax.swing.JTextField lambdaThresholdReadout

residualsReadout

javax.swing.JTextField residualsReadout

motifPValsReadout

javax.swing.JTextField motifPValsReadout

zoomFactor

double zoomFactor

ratioThreshold

double ratioThreshold

lambdaThreshold

double lambdaThreshold

geneFindingDistance

int geneFindingDistance

decimalFormatter

java.text.DecimalFormat decimalFormatter

motifPValsThreshold

double motifPValsThreshold

residualsThreshold

double residualsThreshold

species

java.lang.String species

lastSelection

java.lang.String[] lastSelection

selectedNodeIndex

int selectedNodeIndex

Package org.systemsbiology.gaggle.geese.diag

Class org.systemsbiology.gaggle.geese.diag.DiagGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

myGaggleName

java.lang.String myGaggleName

boss

Boss boss

connector

RmiGaggleConnector connector

scrollPane

javax.swing.JScrollPane scrollPane

textArea

javax.swing.JTextArea textArea

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

Package org.systemsbiology.gaggle.geese.dmv

Class org.systemsbiology.gaggle.geese.dmv.GaggledTreeDataViewer extends java.lang.Object implements Serializable

Serialized Fields

myGaggleName

java.lang.String myGaggleName

tdv

TreeDataViewer tdv

movieController

MovieController movieController

boss

Boss boss

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

activeGooseNames

java.lang.String[] activeGooseNames

getGeeseNamesButton

javax.swing.JButton getGeeseNamesButton

showGooseButton

javax.swing.JButton showGooseButton

hideGooseButton

javax.swing.JButton hideGooseButton

broadcastListButton

javax.swing.JButton broadcastListButton

broadcastClusterButton

javax.swing.JButton broadcastClusterButton

broadcastMatrixButton

javax.swing.JButton broadcastMatrixButton

gaggleConnector

RmiGaggleConnector gaggleConnector

factory

GuiWidgetFactory factory

Package org.systemsbiology.gaggle.geese.echo

Class org.systemsbiology.gaggle.geese.echo.EchoGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

connector

RmiGaggleConnector connector

myGaggleName

java.lang.String myGaggleName

boss

Boss boss

Package org.systemsbiology.gaggle.geese.ihop

Class org.systemsbiology.gaggle.geese.ihop.IHopGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

myGaggleName

java.lang.String myGaggleName

connector

RmiGaggleConnector connector

boss

Boss boss

scrollPane

javax.swing.JScrollPane scrollPane

textArea

javax.swing.JTextArea textArea

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

Package org.systemsbiology.gaggle.geese.lister

Class org.systemsbiology.gaggle.geese.lister.GaggledLister extends java.lang.Object implements Serializable

Serialized Fields

myName

java.lang.String myName

lister

Lister lister

connector

RmiGaggleConnector connector

gaggleBoss

Boss gaggleBoss

species

java.lang.String species

Class org.systemsbiology.gaggle.geese.lister.GaggledLister.BroadcastSelectionAction extends javax.swing.AbstractAction implements Serializable

Class org.systemsbiology.gaggle.geese.lister.Lister extends javax.swing.JFrame implements Serializable

Serialized Fields

listData

java.lang.String[] listData

listbox

javax.swing.JList listbox

lsm

javax.swing.ListSelectionModel lsm

toolbar

javax.swing.JToolBar toolbar

currentSelection

java.util.ArrayList<E> currentSelection

Package org.systemsbiology.gaggle.geese.names

Class org.systemsbiology.gaggle.geese.names.NameGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

myGaggleName

java.lang.String myGaggleName

boss

Boss boss

connector

RmiGaggleConnector connector

scrollPane

javax.swing.JScrollPane scrollPane

textArea

javax.swing.JTextArea textArea

controlPanel

javax.swing.JPanel controlPanel

currentDirectory

java.io.File currentDirectory

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

nameSpaceChooser

javax.swing.JComboBox nameSpaceChooser

targetNameSpace

java.lang.String targetNameSpace

species

java.lang.String species

autoBroadcast

boolean autoBroadcast

nameHelper

NewNameHelper nameHelper

translator

Translator translator

dataUri

java.lang.String dataUri

currentInputNames

java.lang.String[] currentInputNames

translatedNames

java.lang.String[] translatedNames

currentInputNetwork

Network currentInputNetwork

translatedNetwork

Network translatedNetwork

currentInputMatrix

DataMatrix currentInputMatrix

translatedMatrix

DataMatrix translatedMatrix

currentClusterName

java.lang.String currentClusterName

currentClusterRowNames

java.lang.String[] currentClusterRowNames

currentClusterColumnNames

java.lang.String[] currentClusterColumnNames

translatedClusterRowNames

java.lang.String[] translatedClusterRowNames

translatedClusterColumnNames

java.lang.String[] translatedClusterColumnNames

Package org.systemsbiology.gaggle.geese.pdfViewer

Class org.systemsbiology.gaggle.geese.pdfViewer.JPanelDemo extends javax.swing.JFrame implements Serializable

Serialized Fields

viewerTitle

java.lang.String viewerTitle

pdfDecoder

PdfDecoder pdfDecoder

the actual JPanel/decoder object

currentFile

java.lang.String currentFile

name of current PDF file

currentPage

int currentPage

current page number (first page is 1)

pageCounter1

javax.swing.JLabel pageCounter1

pageCounter2

javax.swing.JTextField pageCounter2

pageCounter3

javax.swing.JLabel pageCounter3

Package org.systemsbiology.gaggle.geese.regexFilter

Class org.systemsbiology.gaggle.geese.regexFilter.RegexFilterGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

myGaggleName

java.lang.String myGaggleName

regexPattern

java.lang.String regexPattern

boss

Boss boss

connector

RmiGaggleConnector connector

scrollPane

javax.swing.JScrollPane scrollPane

textArea

javax.swing.JTextArea textArea

gooseChooser

javax.swing.JComboBox gooseChooser

autoBroadcast

boolean autoBroadcast

targetGoose

java.lang.String targetGoose

currentSpecies

java.lang.String currentSpecies

filteredNames

java.lang.String[] filteredNames

Package org.systemsbiology.gaggle.geese.sample

Class org.systemsbiology.gaggle.geese.sample.SampleGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

myGaggleName

java.lang.String myGaggleName

activeGooseNames

java.lang.String[] activeGooseNames

boss

Boss boss

connector

RmiGaggleConnector connector

scrollPane

javax.swing.JScrollPane scrollPane

textArea

javax.swing.JTextArea textArea

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

connectButton

javax.swing.JButton connectButton

disconnectButton

javax.swing.JButton disconnectButton

Package org.systemsbiology.gaggle.geese.sequence

Class org.systemsbiology.gaggle.geese.sequence.SequenceGoose extends javax.swing.JFrame implements Serializable

Serialized Fields

myGaggleName

java.lang.String myGaggleName

activeGeeseNames

java.lang.String[] activeGeeseNames

connectButton

javax.swing.JButton connectButton

disconnectButton

javax.swing.JButton disconnectButton

boss

Boss boss

connector

RmiGaggleConnector connector

scrollPane

javax.swing.JScrollPane scrollPane

textArea

javax.swing.JTextArea textArea

gooseChooser

javax.swing.JComboBox gooseChooser

targetGoose

java.lang.String targetGoose

species

java.lang.String species

dataUri

java.lang.String dataUri

fetcher

org.systemsbiology.gaggle.geese.sequence.SequenceFetcher fetcher

sequenceType

java.lang.String sequenceType

autoBroadcast

boolean autoBroadcast

codonTable

CodonTable codonTable

sequencesForBroadcast

java.util.ArrayList<E> sequencesForBroadcast

Package org.systemsbiology.gaggle.util

Class org.systemsbiology.gaggle.util.Index extends java.util.HashMap<java.lang.String,java.util.List<java.lang.String>> implements Serializable

Serialized Fields

caseSensitive

boolean caseSensitive

Class org.systemsbiology.gaggle.util.NewNameHelper extends java.lang.Object implements Serializable

Serialized Fields

uri

java.lang.String uri

rawText

java.lang.String rawText

titles

java.lang.String[] titles

map

java.util.HashMap<K,V> map

canonicalToCommonMap

java.util.HashMap<K,V> canonicalToCommonMap

commonToCanonicalMap

java.util.HashMap<K,V> commonToCanonicalMap

Package org.systemsbiology.gaggle.util.versionTester

Class org.systemsbiology.gaggle.util.versionTester.JavaVersionTester extends javax.swing.JFrame implements Serializable

Serialized Fields

textArea

javax.swing.JTextArea textArea