NewAnalysisPanel analysisPanel
ProcessingPanel processingPanel
ResultsPanel resultsPanel
boolean modManagerOpened
javax.swing.JTabbedPane tabbedPanel
java.awt.Dimension preferredLayoutSize
java.awt.Frame publicParent
java.lang.String input
javax.swing.JButton jButton1
javax.swing.JButton jButton2
javax.swing.JLabel jLabel1
javax.swing.JTextField jTextField1
BiggerLabel titleLabel
javax.swing.JButton okButton
boolean success
peridot.AnalysisData expression
int thresholdMin
int thresholdMax
int threshold
java.lang.String roundingMode
java.lang.String[] roundingModes
java.io.File expressionFile
java.io.File conditionsFile
java.util.SortedMap<K,V> conditions
boolean changedConditions
java.util.HashMap<K,V> conditionPanels
javax.swing.JButton addNewConditionButton
java.awt.Frame parent
boolean loadedFromPrevious
peridot.Archiver.Spreadsheet.Info info
javax.swing.JPanel adjustPanel
javax.swing.JPanel bottomButtonsPanel
javax.swing.JButton cancelButton
javax.swing.JPanel conditionsPane
javax.swing.JScrollPane conditionsScrollPane
javax.swing.JButton createButton
javax.swing.JTextField expressionPathField
javax.swing.JLabel geneExpressionLabel
javax.swing.JTextField idAndConditionsField
javax.swing.JLabel idAndConditionsLabel
javax.swing.JLabel jLabel1
javax.swing.JPanel labelsPanel
javax.swing.JPanel pathsPanel
javax.swing.JSeparator jSeparator1
javax.swing.JSeparator jSeparator2
javax.swing.JSeparator jSeparator3
javax.swing.JButton selectConditionsFileButton
javax.swing.JButton selectExpressionFileButton
javax.swing.JPanel setFilesPanel
javax.swing.JPanel roundingPanel
javax.swing.JLabel roundingModesLabel
javax.swing.JComboBox<E> roundingModesComboBox
javax.swing.JPanel thresholdPanel
javax.swing.JLabel thresholdLabel
javax.swing.JSlider thresholdSlider
javax.swing.JPanel leftPanel
javax.swing.JPanel rightPanel
BiggerLabel boxPlotTitle
Label boxPlotSubtitle
javax.swing.JLabel boxPlot
javax.swing.JTabbedPane tabsPanel
javax.swing.JScrollPane scrollPanel
javax.swing.JPanel textPanel
javax.swing.JTextArea textArea
peridot.Output buffer
java.lang.Thread updater
java.util.concurrent.atomic.AtomicBoolean stopFlag
java.util.concurrent.atomic.AtomicBoolean newTextFlag
ViewResultsPanel results
ParametersPanel parametersPanel
javax.swing.JButton jButton1
peridot.Archiver.Spreadsheet table
java.io.File file
java.lang.String separator
boolean cancel
boolean loadingInfo
CheckBox headerOnFirstLine
CheckBox labelsOnFirstColumn
RadioButton tab
RadioButton space
RadioButton comma
RadioButton semicolon
RadioButton custom
javax.swing.JTextField customSep
javax.swing.ButtonGroup sepOptions
Table dataTable
javax.swing.JScrollPane scroller
BiggerLabel titleLabel
BigButton okButton
Panel upperPanel
Panel middlePanel
Panel checkBoxesPanel
Panel sepOptionsPanel
Panel bottomPanel
java.lang.Class<T> type
java.awt.Dimension dialogSize
java.awt.Dimension buttonSize
javax.swing.tree.TreeNode[] selected
java.lang.String name
boolean mandatory
java.lang.String defaultToolTip
java.lang.String invalidNameToolTip
javax.swing.JLabel descriptionLabel
javax.swing.JTextField nameField
javax.swing.JCheckBox mandatoryCheckBox
javax.swing.JButton addButton
peridot.script.RModule script
java.lang.String info
Panel generalInfoPanel
Label scriptNameLabel
Label fileNameLabel
Button openFileButton
Label max2CondLabel
Label needsReplicatesLabel
Panel resultsPanel
Label resultsLabel
javax.swing.JScrollPane resultsScroller
javax.swing.JList<E> resultsList
Panel inputPanel
Label inputLabel
javax.swing.JScrollPane inputScroller
javax.swing.JList<E> inputList
Panel paramsPanel
Label paramsLabel
javax.swing.JScrollPane paramsScroller
javax.swing.JList<E> paramsList
Panel packagesPanel
Label packagesLabel
javax.swing.JScrollPane packagesScroller
javax.swing.JList<E> packagesList
javax.swing.JTextArea infoArea
javax.swing.JScrollPane infoScroller
java.awt.Dimension dialogSize
java.awt.Dimension availableSize
java.awt.Dimension defaultPanelSize
java.awt.Dimension scrollerSize
int componentPanelHeight
int componentPanelWidth
java.lang.String selectedScript
java.awt.Dimension dialogSize
java.awt.Dimension containerSize
java.awt.Dimension scrollerSize
java.awt.Dimension buttonSize
java.awt.Dimension buttonContainerSize
int wGap
int hGap
Panel modulesContainer
Panel buttonsContainer
Panel analysisModListContainer
Panel postAnalysisModListContainer
BigLabel analysisModLabel
BigLabel postAnalysisModLabel
BigButton addButton
BigButton editButton
BigButton detailsButton
BigButton deleteButton
BigButton importButton
BigButton exportButton
peridot.script.RModule script
java.lang.String info
java.io.File scriptFile
java.io.File scriptInTemp
java.lang.String name
boolean max2Conditions
boolean needsReplicates
java.util.Map<K,V> requiredParameters
java.util.Set<E> requiredExternalFiles
java.util.Set<E> requiredPackages
java.util.Set<E> results
java.util.Set<E> mandatory
java.util.Set<E> requiredScripts
boolean canHandleFloatValues
java.lang.Class<T> scriptType
java.lang.String originalScript
boolean editing
boolean changedScript
boolean editedScript
Panel scriptNamePanel
Panel fileNamePanel
Panel generalInfoPanel
Panel resultsPanel
Panel inputsPanel
Panel buttonsPanel
Panel paramsPanel
javax.swing.JScrollPane resultsScroller
javax.swing.JScrollPane infoScroller
javax.swing.JScrollPane inputsScroller
javax.swing.JScrollPane paramsScroller
Label scriptNameLabel
Label fileNameLabel
Label resultsLabel
Label paramsLabel
Label inputsLabel
javax.swing.JTextField scriptNameField
javax.swing.JTextField fileNameField
javax.swing.JTextField newResultField
javax.swing.JTextArea infoArea
CheckBox max2CondOption
CheckBox needsReplicatesOption
javax.swing.DefaultListModel<E> resultsListModel
javax.swing.DefaultListModel<E> inputsListModel
javax.swing.DefaultListModel<E> paramsListModel
javax.swing.JList<E> resultsList
javax.swing.JList<E> inputsList
javax.swing.JList<E> paramsList
javax.swing.JButton selectScriptFileButton
javax.swing.JButton addNewResultButton
javax.swing.JButton eraseResultButton
javax.swing.JButton eraseInputButton
javax.swing.JButton addNewInputButton
javax.swing.JButton eraseParamButton
javax.swing.JButton addNewParamButton
javax.swing.JButton createButton
javax.swing.JButton cancelButton
java.awt.Dimension dialogSize
java.awt.Dimension availableSize
java.awt.Dimension componentPanelSize
java.awt.Dimension scrollerSize
int componentPanelHeight
int componentPanelWidth
int buttonPanelHeight
Panel packagesPanel
Label packagesLabel
javax.swing.JScrollPane packagesScroller
javax.swing.JList<E> packagesList
javax.swing.DefaultListModel<E> packagesListModel
javax.swing.JButton addPackageButton
javax.swing.JButton rmPackageButton
java.lang.String name
java.lang.String version
boolean successful
peridot.script.r.Package newPackage
javax.swing.JButton okButton
javax.swing.JButton cancelButton
javax.swing.JLabel instructionsLabel
javax.swing.JLabel versionInstructionsLabel
javax.swing.JTextField nameTextField
javax.swing.JTextField versionTextField
java.lang.String name
java.lang.String type
boolean successful
RadioButton[] paramOptions
javax.swing.ButtonGroup optionsGroup
Panel optionsPanel
javax.swing.JButton okButton
javax.swing.JButton cancelButton
javax.swing.JLabel instructionsLabel
javax.swing.JTextField nameTextField
javafx.embed.swing.JFXPanel jfxPanel
boolean onStart
java.lang.Runnable onEnd
javax.swing.JList<E> contents
javax.swing.JLabel conditionNameLabel
javax.swing.JButton editNameButton
java.awt.Dimension defaultSize
java.awt.Dimension contentsSize
java.awt.Dimension contentsMinSize
java.awt.Dimension internalPanelMax
java.awt.Dimension internalPanelMin
peridot.AnalysisData expression
java.awt.Frame parentFrame
java.util.TreeSet<E> selectedScripts
java.util.TreeSet<E> availableScripts
java.util.TreeSet<E> availablePackages
java.util.TreeMap<K,V> specificParameters
java.util.Map<K,V> scriptCheckboxes
ParametersPanel parametersPanel
NewExpressionDialog expressionGUI
int sleepBetweenComponents
int sleepBetweenChecks
int nPostAnalysisModules
int nAnalysisModules
javax.swing.JButton createButton
javax.swing.JPanel createContainer
javax.swing.JButton defineButton
javax.swing.JPanel defineExpressionContainer
javax.swing.JLabel expressionDescriptionLabel
javax.swing.JLabel multiConditionsLabel
javax.swing.JLabel needsReplicatesLabel
javax.swing.JLabel geneExprLabel1
javax.swing.JButton defineGeneListButton
javax.swing.JPanel defineGeneListContainer
javax.swing.JLabel geneListDescriptionLabel
javax.swing.JLabel geneListLabel
boolean modulesAlwaysVisible
javax.swing.JPanel leftSide
javax.swing.JPanel modulesContainer
javax.swing.JLabel modulesLabel
javax.swing.JPanel modulesLeftSide
javax.swing.JPanel modulesRightSide
javax.swing.JSeparator modulesSeparator
javax.swing.JLabel othersPackages
javax.swing.JLabel packagesLabel1
javax.swing.JPanel packagesPanel
javax.swing.JPanel parametersContainer
javax.swing.JLabel parametersLabel
javax.swing.JPanel rightSide
javax.swing.JPanel scriptsPanel
javax.swing.JSeparator separator1
javax.swing.JSeparator separator2
javax.swing.JSeparator separator3
java.util.TreeMap<K,V> editModuleParamsButtons
java.util.TreeMap<K,V> moduleDetailButtons
peridot.AnalysisParameters params
java.util.Map<K,V> paramPanels
java.util.Map<K,V> paramCheckboxes
java.util.Map<K,V> paramLabels
java.util.Map<K,V> paramFields
java.util.Map<K,V> defaultValues
boolean defaultValueButtons
javax.swing.ImageIcon failIcon
javax.swing.ImageIcon failIconBig
javax.swing.ImageIcon clearIcon
javax.swing.ImageIcon clearIconBig
javax.swing.ImageIcon stopIcon
javax.swing.ImageIcon stopAllIconBig
javax.swing.ImageIcon loaderIcon
javax.swing.JFrame parent
java.util.concurrent.ConcurrentHashMap<K,V> outputDialogs
java.util.Set<E> scripts
java.util.concurrent.ConcurrentHashMap<K,V> scriptMonitor
java.lang.Thread scriptsStatusWatcher
java.lang.Runnable statusWatcher
java.util.concurrent.atomic.AtomicBoolean isProcessing
peridot.script.Task task
javax.swing.JButton abortAllButton
javax.swing.JLabel finalResultDescription
javax.swing.JSeparator jSeparator1
javax.swing.JSeparator jSeparator2
javax.swing.JScrollPane otherResultsScroller
javax.swing.JLabel othersLabel
javax.swing.JPanel packagesBarsPanel
javax.swing.JLabel packagesLabel
javax.swing.JScrollPane packagesScroller
javax.swing.JPanel scriptsBarsPanel
java.lang.String noGenesFoundStr
javax.swing.JFrame parent
java.util.HashMap<K,V> analysisModules
java.util.HashMap<K,V> postAnalysisModules
java.io.File vennDiagramDir
javax.swing.JPanel bottomPanel
javax.swing.JSeparator bottomSeparator
javax.swing.JPanel innerUpperPanel
javax.swing.JPanel middlePanel
javax.swing.JButton openSaveFolderFileChooser
javax.swing.JPanel packListArea
javax.swing.JPanel postAnalysisPanel
javax.swing.JTextField saveFolderInputField
javax.swing.JLabel saveInLabel
javax.swing.JButton saveResultsButton
javax.swing.JLabel successfulOthersLabel
javax.swing.JLabel topLabel
javax.swing.JSeparator topSeparator
javax.swing.JPanel upperPanel
javax.swing.JButton viewResultsButton
javax.swing.JPanel consensusPanel
javax.swing.JPanel individualPanel
java.awt.Dimension smallButtonSize
javax.swing.JLabel nameLabel
javax.swing.JLabel successLabel
javax.swing.JLabel waitingLabel
javax.swing.JLabel failLabel
javax.swing.JButton stopButton
javax.swing.JButton outputButton
java.util.concurrent.atomic.AtomicBoolean stoppable
peridot.script.ScriptExec scriptExec
ScriptProgressMonitorPanel.IconState iconState
ScriptOutputDialog outputDialog
java.util.HashMap<K,V> resultViewers
java.lang.String scriptName
java.io.File resultsDir
boolean analysisModule
javax.swing.JTabbedPane tabsPanel