String version
Histogram hist
org.jfree.chart.ChartPanel jChartPanel
int inSize
double rawScore
GeneAnnotations geneData
List<E> results
Settings settings
int currentResultSet
Analyzer athread
StatusViewer statusMessenger
GeneSetTablePanel tablePanel
GeneSetTreePanel treePanel
JMenu analysisMenu
JMenu diagnosticsMenu
JMenu classMenu
JMenu fileMenu
JMenu helpMenu
JMenu runViewMenu
JTabbedPane tabs
JProgressBar progressBar
JMenuItem defineClassMenuItem
JMenuItem cancelAnalysisMenuItem
JMenuItem loadAnalysisMenuItem
JMenuItem modClassMenuItem
JMenuItem runAnalysisMenuItem
JMenuItem saveAnalysisMenuItem
JPanel statusBarPanel
JButton actionButton
JTextField classFileTextField
JTextField annotFileTextField
JComboBox<E> annotFormat
JTextField projectFileTextField
Settings settings
JButton locateAnnotsButton
StatusViewer statusMessenger
int step
SettingsHolder.Method analysisType
SettingsHolder.GeneScoreMethod geneScoreMethod
Settings settings
GeneAnnotations geneAnnots
AnalysisWizardStep1 step1
AnalysisWizardStep2 step2
AnalysisWizardStep3 step3
AnalysisWizardStep4 step4
AnalysisWizardStep5 step5
int maxSteps
AnalysisWizard wiz
Settings settings
JRadioButton oraButton
JRadioButton resampButton
JRadioButton corrButton
JRadioButton prButton
JRadioButton rocButton
AnalysisWizard wiz
Settings settings
JFileChooser chooser
JTextField rawFileTextField
JTextField scoreFileTextField
JTextField scoreColTextField
JPanel quickPickPanel
JTextField dataColTextField
JButton scoreFileBrowseButton
AtomicBoolean ready
Settings settings
JCheckBox biologicalProcessButton
JCheckBox molecularFunctionButton
JCheckBox cellularComponentButton
JCheckBox userDefinedButton
ActionListener countNumGroupsListener
Settings settings
JTextField jTextFieldMaxClassSize
JTextField jTextFieldMinClassSize
JRadioButton jRadioButtonBestReplicates
JRadioButton jRadioButtonMeanReplicates
KeyListener countNumGroupsKeyListener
boolean enableMultifuncCheckbox
boolean bigIsBetter
JPanel corrPanel
boolean doFullEmpirical
boolean doLog
boolean doMfCorr
String extraHelp
String help
JRadioButton jRadioButtonMean
JRadioButton jRadioButtonMedian
AtomicInteger numIterations
JPanel oraPanel
AtomicReference<V> oraThreshold
JPanel prPanel
JPanel resampPanel
JPanel rocPanel
Settings settings
JPanel step5Panel
int currentScoreColumn
String currentScoreFile
StatusViewer statusMessenger
JFileChooser chooser
JButton loadBrowseButton
Settings settings
JTextField dataDir
JPanel loadPanel
JLabel annotLabel
JPanel centerPanel
MainFrame callingFrame
GeneAnnotations geneData
StatusViewer messenger
Settings settings
Collection<E> dependentPanels
Point popupPoint
GeneSetTerm selectedItem
int width
int height
boolean includeAnnotations
boolean includeLabels
boolean includeScalebar
int matrixColumnWidth
JTable table
JScrollPane tableScrollPane
JToolBar toolBar
JRadioButtonMenuItem blackbodyColormapMenuItem
DetailsOutputDataFileChooser fileChooser
JMenu fileMenu
JRadioButtonMenuItem greenredColormapMenuItem
DetailsOutputImageFileChooser imageChooser
JLabel m_cellWidthLabel
JSlider m_cellWidthSlider
JLabel m_colorRangeLabel
JSlider m_colorRangeSlider
JGradientBar colorScaleBar
JCheckBoxMenuItem m_normalizeMenuItem
JMenuItem saveDataMenuItem
JMenuBar menuBar
JMenu optionsMenu
JMenuItem saveImageMenuItem
JMenuItem setGeneUrlBaseMenuItem
JMenuItem switchDataFileMenuItem
JMenuItem switchGeneScoreFileMenuItem
JMenu viewMenu
JPanel jPanelStatus
JLabel jLabelStatus
StatusViewer statusMessenger
JMatrixCellRenderer matrixCellRenderer
JVerticalHeaderRenderer verticalHeaderRenderer
Settings settings
GeneSetDetails geneSetDetails
int matrixColumnCount
MatrixDisplay<R,C> matrixDisplay
boolean normalizeSavedData
boolean normalizeSavedImage
GeneSetDetailsTableModel tableModel
SettingsHolder runSettings
Color[] colorMap
boolean normalizeMatrixView
MatrixDisplay<R,C> matrixDisplay
List<E> probeIDs
Map<K,V> scoresForProbesInSet
Map<K,V> scoreRanks
GeneAnnotations geneData
SettingsHolder settings
Map<K,V> linkLabels
String[] tableColumnNames
String urlbase
QuantileBin1D scoreQuantiles
QuantileBin1D mfQuantiles
Map<K,V> multifuncForProbesInSet
Map<K,V> multifuncForGenesInSet
Map<K,V> mfGeneRanks
GeneAnnotations geneData
GeneScores geneScores
GeneSetTerm geneSetTerm
JPanel mainPanel
Dimension dlgSize
JPanel bottomPanel
JButton cancelButton
JButton setButton
JPanel centerPanel
JTextField urlTextField
JLabel jLabelStatus
JPanel jPanelStatus
JPanel BottomPanelWrap
StatusViewer statusMessenger
SettingsHolder settings
ubic.erminej.gui.geneset.details.JGeneScoreFileChooser.JScoreChooserOptions m_options
JTextField scoreColTextField
ubic.erminej.gui.geneset.details.JRawFileChooser.JRawFileChooserOptions m_options
JTextField dataColTextField
SettingsHolder settings
GeneAnnotations geneData
GeneSetWizardStep1 step1
GeneSetWizardStep1A step1A
GeneSetWizardStep2 step2
GeneSetWizardStep3 step3
int step
boolean makingNewGeneSet
boolean nostep1
GeneSet oldGeneSet
StatusViewer messenger
Collection<E> loadedGenes
JButton browseButton
JTextField classFile
JFileChooser chooser
int inputMethod
GeneAnnotations geneData
JTable oldClassTable
JTextField searchTextField
GeneSet selectedGeneSet
GeneAnnotations geneData
JTable probeTable
JTable newClassTable
ProbeTableModel ncTableModel
JTextField searchTextField
ProbeTableModel sourceProbeModel
JLabel jLabel2
JTextField classIDTF
JTextArea classDescTA
GeneSetTableModel model
List<E> resultToolTips
JTable table
TableRowSorter<M extends TableModel> sorter
boolean filterBySize
boolean filterBySignificance
GeneSetPvalRun results
GeneAnnotations annots
Collection<E> selectedTerms
JTree goTree
GeneSetTerm currentlySelectedGeneSet
ubic.erminej.gui.geneset.tree.GeneSetTreeNodeRenderer rend
TreeModel geneSetTreeModel
FilteredGeneSetTreeModel filteredTreeModel
TreePath currentlySelectedTreePath
Collection<E> currentSelectedSets
AtomicBoolean expansionCancel
List<E> m_values
boolean m_isSelected
boolean m_isBarGraph
DecimalFormat m_regular
double maxValue
Color[] colors
MatrixDisplay<R,C> m_matrixDisplay
String m_columnName
int PREFERRED_HEIGHT
int MAX_TEXT_LENGTH
Double value
String url
JTextArea ta
JPanel mainPanel
JPanel BottomPanel
JPanel BottomPanelWrap
JLabel jLabelStatus
JPanel jPanelStatus
JButton nextButton
JButton backButton
JButton cancelButton
JButton finishButton
JFrame callingframe
List<E> steps
StatusViewer statusMessenger
Wizard owner
Copyright © 2002-2013 UBC Centre for High-Throughput Biology. All Rights Reserved.