A B C D E F G H I J K L M N O P Q R S T U V W X 

A

AboutBox - Class in ubic.erminej.gui
Displays 'about' information for the software.
AboutBox(Frame) - Constructor for class ubic.erminej.gui.AboutBox
 
AbstractGeneSetPvalGenerator - Class in ubic.erminej.analysis
Base implementation of pvalue generator
AbstractGeneSetPvalGenerator(SettingsHolder, GeneAnnotations, Map<Gene, Double>, StatusViewer) - Constructor for class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
AbstractLongTask - Class in ubic.erminej.analysis
 
AbstractLongTask() - Constructor for class ubic.erminej.analysis.AbstractLongTask
 
AbstractResamplingGeneSetScore - Class in ubic.erminej.analysis
 
AbstractResamplingGeneSetScore() - Constructor for class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
accept(File) - Method in class ubic.erminej.gui.file.DataFileFilter
 
accept(File) - Method in class ubic.erminej.gui.file.ImageFileFilter
 
accept(File) - Method in class ubic.erminej.gui.file.XMLFileFilter
 
actionButton - Variable in class ubic.erminej.gui.AppDialog
 
actionButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.AppDialog
 
actionButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.file.DataDirectoryDialog
 
actionButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.StartupPanel
 
addActionListener(ActionListener) - Method in class ubic.erminej.gui.StartupPanel
 
addAnnotation(Gene, Collection<GeneSetTerm>) - Method in class ubic.erminej.data.GeneAnnotations
 
addDependentPanel(GeneSetPanel) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
addedGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
addedGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
addedGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
addedNewGeneSet(GeneSet) - Method in class ubic.erminej.gui.MainFrame
 
addExactNormalProbabilityComputer(int, double, double) - Method in class ubic.erminej.data.Histogram
 
addGene(Gene) - Method in class ubic.erminej.data.GeneSet
Add the gene (and its probes)
addGene(Gene) - Method in class ubic.erminej.data.Probe
 
addGenes(Collection<Gene>) - Method in class ubic.erminej.data.GeneSet
 
addGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.Gene
Updates membership (for probes too).
addGeneSet(GeneSet) - Method in class ubic.erminej.data.GeneAnnotations
 
addGeneSet(GeneSetTerm, Collection<Gene>) - Method in class ubic.erminej.data.GeneAnnotations
 
addGeneSet(GeneSetTerm, Collection<Gene>, String) - Method in class ubic.erminej.data.GeneAnnotations
Add a user-defined gene set.
addHelp(String) - Method in class ubic.erminej.gui.AppDialog
 
addHelp(String) - Method in class ubic.erminej.gui.util.WizardStep
 
addMain(JPanel) - Method in class ubic.erminej.gui.AppDialog
 
addMain(JPanel) - Method in class ubic.erminej.gui.util.WizardStep
 
addProbe(Probe) - Method in class ubic.erminej.data.Gene
 
addProbe(Probe) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
addProbes(Collection<Probe>) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
addRedundantGroup(GeneSet) - Method in class ubic.erminej.data.GeneSet
 
addRun() - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
addRun() - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
addRun() - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
addRun() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
addStep(WizardStep) - Method in class ubic.erminej.gui.util.Wizard
 
addStep(WizardStep, boolean) - Method in class ubic.erminej.gui.util.Wizard
 
addToGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.Probe
 
addVarPanel(SettingsHolder.Method, SettingsHolder.GeneScoreMethod) - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep5
 
adjustScores(Map<Gene, Double>, boolean, boolean) - Method in class ubic.erminej.data.Multifunctionality
Given a set of scores for genes, adjust them to correct for multifunctionality, using a regression approach.
ALERT_UPDATE_FREQUENCY - Static variable in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
ALWAYS_USE_EMPIRICAL - Static variable in class ubic.erminej.SettingsHolder
 
ANALYSIS_SETTINGS - Static variable in class ubic.erminej.Settings
Settings that we need to write to analysis results files.
AnalysisWizard - Class in ubic.erminej.gui.analysis
 
AnalysisWizard(MainFrame, GeneAnnotations) - Constructor for class ubic.erminej.gui.analysis.AnalysisWizard
 
AnalysisWizardStep1 - Class in ubic.erminej.gui.analysis
Choose the method for the analysis.
AnalysisWizardStep1(AnalysisWizard, Settings) - Constructor for class ubic.erminej.gui.analysis.AnalysisWizardStep1
 
AnalysisWizardStep2 - Class in ubic.erminej.gui.analysis
Set the inputs for the analysis - score file, raw data file.
AnalysisWizardStep2(AnalysisWizard, Settings) - Constructor for class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
AnalysisWizardStep3 - Class in ubic.erminej.gui.analysis
Choose the aspects to use.
AnalysisWizardStep3(AnalysisWizard, Settings) - Constructor for class ubic.erminej.gui.analysis.AnalysisWizardStep3
 
AnalysisWizardStep4 - Class in ubic.erminej.gui.analysis
Generic settings common to all methods (range of gene set sizes, replicate probe handling)
AnalysisWizardStep4(AnalysisWizard, Settings) - Constructor for class ubic.erminej.gui.analysis.AnalysisWizardStep4
 
AnalysisWizardStep5 - Class in ubic.erminej.gui.analysis
The last step of the analysis wizard, picking method-specific settings.
AnalysisWizardStep5(AnalysisWizard, Settings) - Constructor for class ubic.erminej.gui.analysis.AnalysisWizardStep5
 
analyze() - Method in class ubic.erminej.classScoreCMD
 
Analyzer - Class in ubic.erminej
 
Analyzer(SettingsHolder, StatusViewer, GeneAnnotations) - Constructor for class ubic.erminej.Analyzer
 
Analyzer(SettingsHolder, StatusViewer, GeneAnnotations, String) - Constructor for class ubic.erminej.Analyzer
For loading an analysis from a file.
ANNOT_FILE - Static variable in class ubic.erminej.SettingsHolder
 
ANNOT_FORMAT - Static variable in class ubic.erminej.SettingsHolder
 
AnnotationFileFetcher - Class in ubic.erminej.data
Assistance in getting gene annotation files.
AnnotationFileFetcher(SettingsHolder) - Constructor for class ubic.erminej.data.AnnotationFileFetcher
 
AnnotationListFrame - Class in ubic.erminej.gui.file
Shows list of available annotation files for download.
AnnotationListFrame(List<ArrayDesignValueObject>) - Constructor for class ubic.erminej.gui.file.AnnotationListFrame
 
AppDialog - Class in ubic.erminej.gui
 
AppDialog() - Constructor for class ubic.erminej.gui.AppDialog
 
AppDialog(JFrame, int, int) - Constructor for class ubic.erminej.gui.AppDialog
 
averagePrecision(Collection<Gene>) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
 

B

backButton - Variable in class ubic.erminej.gui.util.Wizard
 
backButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
backButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizard
 
backButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.util.Wizard
Define what happens when the 'back' button is pressed
benjaminihochberg() - Method in class ubic.erminej.analysis.MultipleTestCorrector
Benjamini-Hochberg correction of pvalues.
BIG_IS_BETTER - Static variable in class ubic.erminej.SettingsHolder
 
bonferroni() - Method in class ubic.erminej.analysis.MultipleTestCorrector
Bonferroni correction of class pvalues.
BottomPanel - Variable in class ubic.erminej.gui.util.Wizard
 
BottomPanelWrap - Variable in class ubic.erminej.gui.util.Wizard
 

C

calcNumOfBins() - Method in class ubic.erminej.data.Histogram
 
callingframe - Variable in class ubic.erminej.gui.AppDialog
 
callingFrame - Variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
callingframe - Variable in class ubic.erminej.gui.util.Wizard
 
cancelButton - Variable in class ubic.erminej.gui.AppDialog
 
cancelButton - Variable in class ubic.erminej.gui.util.Wizard
 
cancelButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
cancelButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.AppDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.file.DataDirectoryDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizard
 
cancelButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.util.Wizard
Define what happens when the 'cancel' button is pressed.
centerContainer(Container) - Static method in class ubic.erminej.gui.util.GuiUtil
Center a frame on the screen.
checkAspect(GeneSetTerm, boolean) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
checkAspectAndRedundancy(GeneSetTerm) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
If GO data isn't initialized, this returns true.
chooseBackgroundColorForPvalue(double) - Static method in class ubic.erminej.gui.util.Colors
 
chooseChildLocation(Container, Container) - Static method in class ubic.erminej.gui.util.GuiUtil
 
chooseColorForMultifunctionalityEffect(GeneSetResult) - Static method in class ubic.erminej.gui.util.Colors
 
CLASS_FILE - Static variable in class ubic.erminej.SettingsHolder
 
CLASS_SCORE_METHOD - Static variable in class ubic.erminej.SettingsHolder
 
classMaxSize - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
classMinSize - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
classPval(GeneSetTerm) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
classPval(GeneSetTerm) - Method in class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
Get results for one class, based on class id.
classPval(Collection<Gene>, GeneSetTerm) - Method in class ubic.erminej.analysis.OraPvalGenerator
Get results for one class, based on class id.
classPvalGeneratorRaw() - Method in class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
Same thing as classPval, but returns a more raw map of genesets to scores (pvalues) (see below) instead of adding them to the results object.
classPvalue(GeneSetTerm) - Method in class ubic.erminej.analysis.ExperimentScoreQuickPvalGenerator
This is stripped-down version of classPvalue.
classScoreCMD - Class in ubic.erminej
Run ermineJ from the command line (or fire up the GUI).
classScoreCMD() - Constructor for class ubic.erminej.classScoreCMD
 
ClassScoreSimple - Class in ubic.erminej
Simple API to run ermineJ analyses, using Strings as the initial representations.
ClassScoreSimple(List<String>, List<String>, List<Collection<String>>) - Constructor for class ubic.erminej.ClassScoreSimple
Note that these Lists must all be in the same order with respect to the probes.
clear() - Method in class ubic.erminej.gui.util.StatusJlabel
 
clearGenes() - Method in class ubic.erminej.data.GeneSet
 
clearRedundancy() - Method in class ubic.erminej.data.GeneSet
 
clearRedundancy(GeneSet) - Method in class ubic.erminej.data.GeneSet
 
clearStatus() - Method in class ubic.erminej.gui.util.Wizard
Make the status bar empty.
closeWindow_actionPerformed(WindowEvent) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
COLORS - Static variable in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
Colors - Class in ubic.erminej.gui.util
 
Colors() - Constructor for class ubic.erminej.gui.util.Colors
 
compareTo(GeneSetResult) - Method in class ubic.erminej.data.EmptyGeneSetResult
 
compareTo(Gene) - Method in class ubic.erminej.data.Gene
 
compareTo(GeneSetResult) - Method in class ubic.erminej.data.GeneSetResult
Default comparator for this class: sorts by the pvalue.
compareTo(GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerm
 
compareTo(MatrixPoint) - Method in class ubic.erminej.gui.table.MatrixPoint
 
compareTo(JLinkLabel) - Method in class ubic.erminej.gui.util.JLinkLabel
 
computeCounts() - Method in class ubic.erminej.analysis.OraPvalGenerator
Calculate numOverThreshold and numUnderThreshold for hypergeometric distribution.
computeQuantiles(SettingsHolder, GeneScores) - Static method in class ubic.erminej.analysis.ScoreQuantiles
 
computeRawScore(double[], Collection<Gene>) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
Basic method to calculate the raw score for a gene set, given an array of the gene scores for items in the class.
config - Variable in class ubic.erminej.SettingsHolder
 
configure() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
configurePopup(MouseEvent) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
Configure the base popup common to any compoment showing gene sets.
configurePopupListener() - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
containsRow(Probe) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
convert(JSONValue) - Method in class ubic.erminej.data.AnnotationFileFetcher
 
CorrelationPvalGenerator - Class in ubic.erminej.analysis
 
CorrelationPvalGenerator(SettingsHolder, GeneAnnotations, DoubleMatrix<Probe, String>, Histogram, StatusViewer) - Constructor for class ubic.erminej.analysis.CorrelationPvalGenerator
 
correlationWithGeneMultifunctionality(List<Gene>) - Method in class ubic.erminej.data.Multifunctionality
 
correlationWithGoTermMultifunctionality(List<GeneSetTerm>) - Method in class ubic.erminej.data.Multifunctionality
 
createDetailsTable() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
currentlySelectedGeneSet - Variable in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
CUSTOM_GENE_SET_DIRECTORY_PROPERTY - Static variable in class ubic.erminej.SettingsHolder
 
CUSTOM_GENESET_FILES - Static variable in class ubic.erminej.SettingsHolder
 

D

DATA_COL - Static variable in class ubic.erminej.SettingsHolder
 
DATA_DIRECTORY - Static variable in class ubic.erminej.SettingsHolder
 
DataDirectoryDialog - Class in ubic.erminej.gui.file
 
DataDirectoryDialog(Settings) - Constructor for class ubic.erminej.gui.file.DataDirectoryDialog
 
DataDirectoryDialog(MainFrame) - Constructor for class ubic.erminej.gui.file.DataDirectoryDialog
 
DataFileFilter - Class in ubic.erminej.gui.file
 
DataFileFilter() - Constructor for class ubic.erminej.gui.file.DataFileFilter
 
DataIOUtils - Class in ubic.erminej.data
 
DataIOUtils() - Constructor for class ubic.erminej.data.DataIOUtils
 
dataPreviewScoresActionPerformed() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
DEFAULT_CUSTOM_GENE_SET_DIR_NAME - Static variable in class ubic.erminej.SettingsHolder
 
DEFAULT_FILTER_NONSPECIFIC - Static variable in class ubic.erminej.data.GeneAnnotations
Whether to filter out probes that hit more than one gene
DEFAULT_GENE_URL_BASE - Static variable in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
DEFAULT_USER_DATA_DIR_NAME - Static variable in class ubic.erminej.SettingsHolder
 
defaults - Static variable in class ubic.erminej.SettingsHolder
 
DELETED - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
deleteGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
Remove a gene set (class) from all the maps that reference it.
deleteSubClone(GeneAnnotations) - Method in class ubic.erminej.data.GeneAnnotations
Remove a no-longer-needed subclone.
deleteUserGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
 
deleteUserGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.UserDefinedGeneSetManager
Delete a user-defined gene set from disk and from the annotations in memory.
deleteUserGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
deleteUserGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
deleteUserGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
DetailsOutputDataFileChooser - Class in ubic.erminej.gui.geneset.details
Customized file browser.
DetailsOutputDataFileChooser(boolean, boolean, String) - Constructor for class ubic.erminej.gui.geneset.details.DetailsOutputDataFileChooser
 
DetailsOutputImageFileChooser - Class in ubic.erminej.gui.geneset.details
 
DetailsOutputImageFileChooser(boolean, boolean, String) - Constructor for class ubic.erminej.gui.geneset.details.DetailsOutputImageFileChooser
Creates a new instance of JDetailsFileChooser
disableMenusForLoad() - Method in class ubic.erminej.gui.MainFrame
 
DO_LOG - Static variable in class ubic.erminej.SettingsHolder
 
doAnalysis() - Method in class ubic.erminej.Analyzer
 

E

EmptyGeneSetResult - Class in ubic.erminej.data
Placeholder for sets that were not used.
EmptyGeneSetResult(GeneSetTerm) - Constructor for class ubic.erminej.data.EmptyGeneSetResult
 
END_OF_SETTINGS_SEPARATOR - Static variable in class ubic.erminej.ResultsPrinter
 
enrichmentForMultifunctionality(Collection<Gene>) - Method in class ubic.erminej.data.Multifunctionality
This is like correlationWithGeneMultifunctionality(List), but without an order list to start with, and intended for cases where the number of genes is smaller than the total number of genes.
enrichmentForMultifunctionalityPvalue(Collection<Gene>) - Method in class ubic.erminej.data.Multifunctionality
 
equals(Object) - Method in class ubic.erminej.data.Gene
 
equals(Object) - Method in class ubic.erminej.data.GeneSet
 
equals(Object) - Method in class ubic.erminej.data.GeneSetResult
 
equals(Object) - Method in class ubic.erminej.data.GeneSetTerm
 
equals(Object) - Method in class ubic.erminej.data.Probe
 
ErmineJGui - Class in ubic.erminej
Main for GUI
ErmineJGui(Settings) - Constructor for class ubic.erminej.ErmineJGui
 
error(String) - Static method in class ubic.erminej.gui.util.GuiUtil
 
error(String, Throwable) - Static method in class ubic.erminej.gui.util.GuiUtil
 
expandAll(boolean) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
expandNode(TreePath, boolean) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
Fully expand or collapse a node.
expandToGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
ExperimentScoreQuickPvalGenerator - Class in ubic.erminej.analysis
Does the same thing as GeneSetResamplingPvalGeneratorbut is stripped-down for using during resampling.
ExperimentScoreQuickPvalGenerator(SettingsHolder, GeneAnnotations, Map<Gene, Double>, StatusViewer) - Constructor for class ubic.erminej.analysis.ExperimentScoreQuickPvalGenerator
 

F

FDR_THRESHOLD_FOR_FILTER - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
fetchList() - Method in class ubic.erminej.data.AnnotationFileFetcher
Get the list of available annotations
fileBrowsePanel(Container, ActionListener) - Static method in class ubic.erminej.gui.util.GuiUtil
Build a standardized file browse field+button.
filter(boolean) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
filter() - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
filter(Collection<GeneSetTerm>) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
filter(boolean) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
filter(boolean) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
filter(Collection<GeneSetTerm>) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
filter(Collection<GeneSetTerm>) - Method in class ubic.erminej.gui.MainFrame
 
FILTER_NONSPECIFIC - Static variable in class ubic.erminej.SettingsHolder
 
filterByUserGeneSets(boolean) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
FilteredGeneSetTreeModel - Class in ubic.erminej.gui.geneset.tree
Deals with showing filtered views of the gene set tree.
FilteredGeneSetTreeModel(GeneAnnotations, TreeModel) - Constructor for class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
find() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1A
 
find(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
findGene(String) - Method in class ubic.erminej.data.GeneAnnotations
Case insensitive
findGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
 
findGeneSet(String) - Method in class ubic.erminej.data.GeneAnnotations
 
findGeneSetInTree(GeneSetTerm) - Method in class ubic.erminej.gui.MainFrame
 
findInTree(ActionEvent) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
findProbe(String) - Method in class ubic.erminej.data.GeneAnnotations
Case insensitive
findProbes(String) - Method in class ubic.erminej.data.GeneAnnotations
Create a selected probes list based on a search string.
findSetsByGene(String) - Method in class ubic.erminej.data.GeneAnnotations
Identify gene sets that contain a particular gene or probe.
findSetsByName(String) - Method in class ubic.erminej.data.GeneAnnotations
 
findTerm(String) - Method in class ubic.erminej.data.GeneAnnotations
 
finishButton - Variable in class ubic.erminej.gui.util.Wizard
 
finishEditing(ActionEvent) - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
finishEditing(ActionEvent) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizard
 
finishEditing(ActionEvent) - Method in class ubic.erminej.gui.util.Wizard
Define what happens when the 'finish' button is pressed.
firePropertyChange(String, Object, Object) - Method in class ubic.erminej.gui.table.JMatrixCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class ubic.erminej.gui.table.JMatrixCellRenderer
 
firePropertyChange(String, Object, Object) - Method in class ubic.erminej.gui.table.JVerticalHeaderRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class ubic.erminej.gui.table.JVerticalHeaderRenderer
 
fireResultsChanged() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
fireTableDataChanged() - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 

G

GEMMA_GENE_SEARCH_URL_BASE - Static variable in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
GEMMA_URL_BASE - Static variable in class ubic.erminej.SettingsHolder
 
Gene - Class in ubic.erminej.data
Represents a Gene entity.
Gene(String) - Constructor for class ubic.erminej.data.Gene
 
Gene(String, String) - Constructor for class ubic.erminej.data.Gene
 
GENE_COUNT_COLUMN_INDEX - Static variable in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
GENE_REP_TREATMENT - Static variable in class ubic.erminej.SettingsHolder
 
GENE_SCORE_THRESHOLD_KEY - Static variable in class ubic.erminej.SettingsHolder
 
GENE_SCORE_THRESHOLD_LEGACY_KEY - Static variable in class ubic.erminej.SettingsHolder
 
GENE_SET_RESAMPLING_SCORE_METHOD - Static variable in class ubic.erminej.SettingsHolder
 
GENE_URL_BASE - Static variable in class ubic.erminej.SettingsHolder
 
GeneAnnotationParser - Class in ubic.erminej.data
Reads tab-delimited file to create maps of probes to classes, classes to probes, probes to genes, genes to probes.
GeneAnnotationParser(GeneSetTerms) - Constructor for class ubic.erminej.data.GeneAnnotationParser
 
GeneAnnotationParser(GeneSetTerms, StatusViewer) - Constructor for class ubic.erminej.data.GeneAnnotationParser
 
GeneAnnotationParser.Format - Enum in ubic.erminej.data
 
GeneAnnotations - Class in ubic.erminej.data
Maintains gene annotations.
GeneAnnotations(Collection<Gene>, GeneSetTerms, SettingsHolder, StatusViewer) - Constructor for class ubic.erminej.data.GeneAnnotations
 
GeneAnnotations(GeneAnnotations, Collection<Probe>) - Constructor for class ubic.erminej.data.GeneAnnotations
Create a read-only new annotation set based on an existing one, for selected probes, removing probes with no annotations.
GeneAnnotations(GeneAnnotations, Collection<Probe>, boolean) - Constructor for class ubic.erminej.data.GeneAnnotations
Create a read-only new annotation set based on an existing one, for selected probes, optionally removing unannotated probes.
GeneAnnotations(List<Gene>, List<Collection<GeneSetTerm>>, StatusViewer) - Constructor for class ubic.erminej.data.GeneAnnotations
Constructor designed for use when a file is not the immediate input of the data.
GeneAnnotations(List<String>, List<String>, List<Collection<String>>) - Constructor for class ubic.erminej.data.GeneAnnotations
 
geneAnnots - Variable in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
geneData - Variable in class ubic.erminej.classScoreCMD
 
geneData - Variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
generateGeneSetResults() - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
Compute the results for all the gene sets under consideration.
generateGeneSetResults() - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
generateGeneSetResults() - Method in class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
 
generateGeneSetResults(boolean) - Method in class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
 
generateGeneSetResults() - Method in class ubic.erminej.analysis.OraPvalGenerator
 
generateGeneSetResults() - Method in class ubic.erminej.analysis.RocPvalGenerator
 
generateGeneSetResults(boolean) - Method in class ubic.erminej.analysis.RocPvalGenerator
 
generateNulldistribution(StatusViewer, long) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
Generate a null distribution, using a selected random seed.
generateNullDistribution(StatusViewer) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
Used for methods which require randomly sampling classes to generate a null distribution of scores based on gene-by-gene scores.
generateNullDistribution(StatusViewer) - Method in interface ubic.erminej.analysis.NullDistributionGenerator
 
generateNulldistribution(StatusViewer, long) - Method in class ubic.erminej.analysis.ResamplingCorrelationGeneSetScore
Generate a null distribution, using a selected random seed.
generateNullDistribution(StatusViewer) - Method in class ubic.erminej.analysis.ResamplingCorrelationGeneSetScore
Build background distributions of within-gene set mean correlations.
generateResultColumnHeadingTooltip(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
Create the text shown when user hovers mouse over the heading of a result column
generator - Variable in class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
 
GeneScores - Class in ubic.erminej.data
Parse and store probe->score associations.
GeneScores(Collection<String>, Settings, StatusViewer, GeneAnnotations, String) - Constructor for class ubic.erminej.data.GeneScores
Constructor for the case when we are just taking in a hit list.
GeneScores(GeneScores, GeneAnnotations) - Constructor for class ubic.erminej.data.GeneScores
Create a copy of source that contains only the probes given.
GeneScores(InputStream, SettingsHolder, StatusViewer, GeneAnnotations) - Constructor for class ubic.erminej.data.GeneScores
 
GeneScores(List<String>, List<Double>, GeneAnnotations, SettingsHolder) - Constructor for class ubic.erminej.data.GeneScores
Constructor designed for use when input is not a file.
GeneScores(String, SettingsHolder, StatusViewer, GeneAnnotations) - Constructor for class ubic.erminej.data.GeneScores
 
geneScoreThreshold - Variable in class ubic.erminej.analysis.OraPvalGenerator
 
GeneSet - Class in ubic.erminej.data
A group of genes, such as those defined by GO annotations or KEGG pathways.
GeneSet() - Constructor for class ubic.erminej.data.GeneSet
 
GeneSet(GeneSetTerm) - Constructor for class ubic.erminej.data.GeneSet
 
GeneSet(GeneSetTerm, Collection<Gene>) - Constructor for class ubic.erminej.data.GeneSet
 
GeneSetDetails - Class in ubic.erminej.data
Combination of scores and data for a gene set, for visualization
GeneSetDetails(GeneSetTerm, GeneAnnotations, StatusViewer) - Constructor for class ubic.erminej.data.GeneSetDetails
Show without any results.
GeneSetDetails(GeneSetTerm, GeneSetResult, GeneAnnotations, Settings, GeneScores, StatusViewer) - Constructor for class ubic.erminej.data.GeneSetDetails
The data matrix will be read in based on the settings, or can be changed later.
GeneSetDetailsFrame - Class in ubic.erminej.gui.geneset.details
 
GeneSetDetailsFrame(GeneSetDetails, StatusViewer) - Constructor for class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
GeneSetDetailsImageWriter - Class in ubic.erminej.data
Methods for writing a GeneSetDetails heatmap to a image file
GeneSetDetailsImageWriter() - Constructor for class ubic.erminej.data.GeneSetDetailsImageWriter
 
GeneSetDetailsTableModel - Class in ubic.erminej.gui.geneset.details
Our table model for one gene set.
GeneSetDetailsTableModel(MatrixDisplay<Probe, String>, GeneSetDetails, SettingsHolder) - Constructor for class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
geneSetExists(String) - Method in class ubic.erminej.data.GeneAnnotations
Returns true if the class is in the classToProbe map
GeneSetMapTools - Class in ubic.erminej.data
Utility methods
GeneSetMapTools() - Constructor for class ubic.erminej.data.GeneSetMapTools
 
geneSetMeanCorrel(DenseDoubleMatrix<String, String>) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
Note that we don't worry about replicates here - it would slow things down too much.
geneSetMeanCorrel(int[]) - Method in class ubic.erminej.analysis.ResamplingCorrelationGeneSetScore
Compute the average correlation for a set of vectors.
GeneSetPanel - Class in ubic.erminej.gui.geneset
A generic class to support the display of lists or trees Gene Sets and analysis results.
GeneSetPanel(Settings, MainFrame) - Constructor for class ubic.erminej.gui.geneset.GeneSetPanel
 
GeneSetPanelPopupMenu - Class in ubic.erminej.gui.geneset
Pop-up menu to display when user is browsing the table or tree.
GeneSetPanelPopupMenu(GeneSetTerm) - Constructor for class ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
 
GeneSetPvalRun - Class in ubic.erminej.analysis
Class that does all the work in doing gene set scoring.
GeneSetPvalRun(SettingsHolder, GeneAnnotations, StatusViewer) - Constructor for class ubic.erminej.analysis.GeneSetPvalRun
Do a new analysis.
GeneSetPvalRun(SettingsHolder, GeneAnnotations, StatusViewer, Map<GeneSetTerm, GeneSetResult>, String) - Constructor for class ubic.erminej.analysis.GeneSetPvalRun
Use this when we are loading in existing results from a file.
GeneSetPvalRun(SettingsHolder, GeneScores) - Constructor for class ubic.erminej.analysis.GeneSetPvalRun
Do a new analysis, starting from the bare essentials (correlation method not available) (simple API)
GeneSetRankingContextWindow - Class in ubic.erminej.gui.geneset.details
Show ROC and Precision-recall curves -- things that show the gene set in the context of the full ranking.
GeneSetRankingContextWindow(GeneSetDetails) - Constructor for class ubic.erminej.gui.geneset.details.GeneSetRankingContextWindow
 
GeneSetResamplingBackgroundDistributionGenerator - Class in ubic.erminej.analysis
Calculates a background distribution for class scores derived from randomly selected individual gene scores.
GeneSetResamplingBackgroundDistributionGenerator(SettingsHolder, Map<Gene, Double>) - Constructor for class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
 
GeneSetResamplingPvalGenerator - Class in ubic.erminej.analysis
Generates gene set p values using the resampling-based 'experiment score' method of Pavlidis et al.
GeneSetResamplingPvalGenerator(SettingsHolder, GeneAnnotations, Map<Gene, Double>, StatusViewer) - Constructor for class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
 
GeneSetResamplingPvalGenerator(GeneSetResamplingPvalGenerator, Map<Gene, Double>) - Constructor for class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
Clone a generator; don't recompute the background.
GeneSetResult - Class in ubic.erminej.data
Data structure to store class scoring information about a class.
GeneSetResult() - Constructor for class ubic.erminej.data.GeneSetResult
 
GeneSetResult(GeneSetTerm, int, int, double, double, double, SettingsHolder) - Constructor for class ubic.erminej.data.GeneSetResult
 
GeneSetResult(GeneSetTerm, int, int, SettingsHolder) - Constructor for class ubic.erminej.data.GeneSetResult
 
GeneSetTableModel - Class in ubic.erminej.gui.geneset.table
Model for displaying list of gene sets and results in the main frame.
GeneSetTableModel(GeneAnnotations, List<GeneSetPvalRun>) - Constructor for class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
GeneSetTablePanel - Class in ubic.erminej.gui.geneset.table
A table that lists the Gene Sets with their scores, and allows user interaction.
GeneSetTablePanel(MainFrame, Settings) - Constructor for class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
geneSetTerm - Variable in class ubic.erminej.data.GeneSetResult
 
GeneSetTerm - Class in ubic.erminej.data
Represents a GO term (most commonly) or other way of grouping genes.
GeneSetTerm(String) - Constructor for class ubic.erminej.data.GeneSetTerm
 
GeneSetTerm(String, String) - Constructor for class ubic.erminej.data.GeneSetTerm
 
GeneSetTerm(String, String, String) - Constructor for class ubic.erminej.data.GeneSetTerm
 
GeneSetTerms - Class in ubic.erminej.data
Maintain information on GeneSetTerms (including but not limited GO terms).
GeneSetTerms(InputStream) - Constructor for class ubic.erminej.data.GeneSetTerms
 
GeneSetTerms(String, Settings) - Constructor for class ubic.erminej.data.GeneSetTerms
 
GeneSetTerms(String, boolean) - Constructor for class ubic.erminej.data.GeneSetTerms
 
GeneSetTerms(Collection<GeneSetTerm>) - Constructor for class ubic.erminej.data.GeneSetTerms
Create based only on 'user defined', without reading in GO.
GeneSetTerms(InputStream, boolean) - Constructor for class ubic.erminej.data.GeneSetTerms
 
GeneSetTreeNode - Class in ubic.erminej.gui.geneset.tree
 
GeneSetTreeNode(DirectedGraphNode<String, GeneSetTerm>) - Constructor for class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
 
GeneSetTreePanel - Class in ubic.erminej.gui.geneset.tree
A Tree display that shows Gene Sets and their scores, and allows uer interaction.
GeneSetTreePanel(MainFrame, Settings) - Constructor for class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
GeneSetWizard - Class in ubic.erminej.gui.geneset.edit
For creating or editing gene sets.
GeneSetWizard(MainFrame, GeneAnnotations, boolean) - Constructor for class ubic.erminej.gui.geneset.edit.GeneSetWizard
Use this constructor to let the user choose which gene set to look at or to make a new one.
GeneSetWizard(MainFrame, GeneAnnotations, GeneSetTerm) - Constructor for class ubic.erminej.gui.geneset.edit.GeneSetWizard
Use this constructor when you know the gene set to be looked at, and the user doesn't have to selected it from the list (modify a gene set).
GeneSetWizardStep1 - Class in ubic.erminej.gui.geneset.edit
Choose where the user is getting the information for the new gene set: either a file, or manual entry.
GeneSetWizardStep1(GeneSetWizard, SettingsHolder) - Constructor for class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1
 
GeneSetWizardStep1A - Class in ubic.erminej.gui.geneset.edit
Step to choose a gene set to modify from the a list.
GeneSetWizardStep1A(GeneSetWizard, GeneAnnotations) - Constructor for class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1A
Only show the user's sets
GeneSetWizardStep1A(GeneSetWizard, GeneAnnotations, Collection<GeneSet>) - Constructor for class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1A
 
GeneSetWizardStep2 - Class in ubic.erminej.gui.geneset.edit
Step to add/remove probes/genes from a gene set.
GeneSetWizardStep2(GeneSetWizard, GeneAnnotations) - Constructor for class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
 
GeneSetWizardStep3 - Class in ubic.erminej.gui.geneset.edit
Get ID and description.
GeneSetWizardStep3(GeneSetWizard) - Constructor for class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
geneToScoreMap - Variable in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
GeneUrlDialog - Class in ubic.erminej.gui.geneset.details
 
GeneUrlDialog(SettingsHolder) - Constructor for class ubic.erminej.gui.geneset.details.GeneUrlDialog
 
get(String) - Method in class ubic.erminej.data.GeneSetTerms
Note that it is probably preferable to use findTerm from GeneAnnotations; this is used while setting that up.
get_range() - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
getActiveProbes() - Method in class ubic.erminej.data.Gene
 
getAllChildren(GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerms
 
getAllParents(GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerms
 
getAllTerms() - Method in class ubic.erminej.data.GeneAnnotations
Get all gene sets, including ones that might be empty or redundant.
getAlwaysUseEmpirical() - Method in class ubic.erminej.SettingsHolder
 
getAnalysisType() - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
getAnnotFile() - Method in class ubic.erminej.SettingsHolder
 
getAnnotFormat() - Method in class ubic.erminej.Settings
 
getAnnotFormat() - Method in class ubic.erminej.SettingsHolder
 
getAspect() - Method in class ubic.erminej.data.GeneSetTerm
 
getBigIsBetter() - Method in class ubic.erminej.SettingsHolder
 
getBins() - Method in class ubic.erminej.data.Histogram
 
getBinSize() - Method in class ubic.erminej.data.Histogram
 
getCacheHits() - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
getChild(Object, int) - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
getChildCount(Object) - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
getChildren(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
 
getChildren(GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerms
 
getClassFile() - Method in class ubic.erminej.SettingsHolder
Returns setting values.
getClassID() - Method in class ubic.erminej.data.GeneSetDetails
 
getClassIndex(int, int) - Method in class ubic.erminej.data.Histogram
 
getClassScoreMethod() - Method in class ubic.erminej.Settings
 
getClassScoreMethod() - Method in class ubic.erminej.SettingsHolder
 
getClassScoreMethodName() - Method in class ubic.erminej.SettingsHolder
A human-readable version of the name
getColumnClass(int) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
getColumnClass(int) - Method in class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
 
getColumnClass(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
getColumnCount() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
getColumnCount() - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
getColumnCount() - Method in class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
 
getColumnCount() - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
getColumnIndexForRun(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
getColumnName(int) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
getColumnName(int) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
getColumnName(int) - Method in class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
 
getColumnName(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
getConfig() - Method in class ubic.erminej.Settings
 
getConfig() - Method in class ubic.erminej.SettingsHolder
 
getCorrectedPvalue() - Method in class ubic.erminej.data.EmptyGeneSetResult
 
getCorrectedPvalue() - Method in class ubic.erminej.data.GeneSetResult
 
getCurrentlySelectedGeneSet() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
getCurrentMatrixDisplayRowOrder() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
Creates new row keys for the JMatrixDisplay object (m_matrixDisplay).
getCurrentResultSet() - Method in class ubic.erminej.gui.MainFrame
 
getCurrentResultSetIndex() - Method in class ubic.erminej.gui.MainFrame
 
getCustomGeneSetDirectory() - Method in class ubic.erminej.SettingsHolder
 
getCustomGeneSetFiles() - Method in class ubic.erminej.SettingsHolder
 
getData() - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
getDataCol() - Method in class ubic.erminej.SettingsHolder
 
getDataDirectory() - Method in class ubic.erminej.SettingsHolder
 
getDataFileName() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
getDataMatrix() - Method in class ubic.erminej.data.GeneSetDetails
 
getDataStartColumn() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
getDefaultGeneUrl() - Method in class ubic.erminej.SettingsHolder
 
getDefaultSettingsValue(String) - Method in class ubic.erminej.SettingsHolder
 
getDefaultUserClassesDirPath() - Static method in class ubic.erminej.SettingsHolder
 
getDefaultUserDataDirPath() - Static method in class ubic.erminej.SettingsHolder
 
getDefinition() - Method in class ubic.erminej.data.GeneSetTerm
 
getDescription() - Method in class ubic.erminej.data.Probe
 
getDescription() - Method in class ubic.erminej.gui.file.DataFileFilter
 
getDescription() - Method in class ubic.erminej.gui.file.ImageFileFilter
 
getDescription() - Method in class ubic.erminej.gui.file.XMLFileFilter
 
getDoLog() - Method in class ubic.erminej.SettingsHolder
 
getFilterNonSpecific() - Method in class ubic.erminej.SettingsHolder
 
getFormat() - Method in class ubic.erminej.data.GeneSet
 
getGemmaID() - Method in class ubic.erminej.data.Gene
 
getGene() - Method in class ubic.erminej.data.Probe
 
getGeneAnnots() - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
getGeneCount() - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
getGeneData() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getGeneData() - Method in class ubic.erminej.data.GeneSetDetails
 
getGeneMultifunctionalityQuantiles() - Method in class ubic.erminej.data.Multifunctionality
Get QuantileBin1D, which can tell you the quantile for a given value, or the expected value for a given quantile.
getGeneRepTreatment() - Method in class ubic.erminej.Settings
 
getGeneRepTreatment() - Method in class ubic.erminej.SettingsHolder
 
getGenes() - Method in class ubic.erminej.data.GeneAnnotations
Return all genes, including those that are 'inactive'.
getGenes() - Method in class ubic.erminej.data.GeneSet
Do not modify this collection directly! Use 'addGene'.
getGenes() - Method in class ubic.erminej.data.Probe
 
getGenesAboveThreshold() - Method in class ubic.erminej.analysis.OraPvalGenerator
 
getGeneScoreColumnName() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getGeneScoreFileDirectory() - Method in class ubic.erminej.SettingsHolder
 
getGeneScoreMethod() - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
getGeneScores() - Method in class ubic.erminej.data.GeneScores
Note that these will already be log-transformed, if that was requested by the user.
getGeneScoreThreshold() - Method in class ubic.erminej.analysis.OraPvalGenerator
 
getGeneScoreThreshold() - Method in class ubic.erminej.Settings
 
getGeneScoreThreshold() - Method in class ubic.erminej.SettingsHolder
Value used for ORA
getGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneSetGenes(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneSetGraph() - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneSetId() - Method in class ubic.erminej.data.GeneSetResult
 
getGeneSetId() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
getGeneSetName() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
getGeneSetProbes(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneSetPvalue(String) - Method in class ubic.erminej.ClassScoreSimple
Gene the resulting gene set pvalue for a given id.
getGeneSetResamplingScoreMethod() - Method in class ubic.erminej.Settings
 
getGeneSetResamplingScoreMethod() - Method in class ubic.erminej.SettingsHolder
 
getGeneSets() - Method in class ubic.erminej.data.Gene
 
getGeneSets() - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneSets(Collection<GeneSetTerm>) - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneSets() - Method in class ubic.erminej.data.GeneSetTerms
 
getGeneSets() - Method in class ubic.erminej.data.Probe
 
getGeneSetScores(GeneSetTerm) - Method in class ubic.erminej.data.GeneScores
Get the gene scores for just the genes in the set indicated.
getGeneSetTerms() - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneSetTermsHolder() - Method in class ubic.erminej.data.GeneAnnotations
 
getGeneToScoreMap() - Method in class ubic.erminej.data.GeneScores
Note that these values will already be log tranformed if that was requested.
getGeneToScoreMap(boolean) - Method in class ubic.erminej.data.GeneScores
 
getGeneUrlBase() - Method in class ubic.erminej.SettingsHolder
 
getGoldStandardFile() - Method in class ubic.erminej.SettingsHolder
Mostly used for testing
getGONameMap() - Method in class ubic.erminej.data.GOParser
Get a simple Map that contains keys that are the GO ids, values are the names.
getGOTermMultifunctionality(GeneSetTerm) - Method in class ubic.erminej.data.Multifunctionality
 
getGOTermMultifunctionalityPvalue(GeneSetTerm) - Method in class ubic.erminej.data.Multifunctionality
 
getGOTermMultifunctionalityRank(GeneSetTerm) - Method in class ubic.erminej.data.Multifunctionality
 
getGraph() - Method in class ubic.erminej.data.GeneSetTerms
 
getGraph() - Method in class ubic.erminej.data.GOParser
Get the graph that was created.
getHeaderToolTip(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
getHelpUrl() - Method in class ubic.erminej.SettingsHolder
 
getHist() - Method in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
getHist() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getHistMax() - Method in class ubic.erminej.data.Histogram
 
getHistMin() - Method in class ubic.erminej.data.Histogram
 
getHistogram(int) - Method in class ubic.erminej.data.Histogram
 
getId() - Method in class ubic.erminej.data.GeneSet
 
getId() - Method in class ubic.erminej.data.GeneSetTerm
 
getInputMethod() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1
 
getIterations() - Method in class ubic.erminej.SettingsHolder
 
getLatestResults() - Method in class ubic.erminej.Analyzer
Blocks until results are returned.
getLeaves() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
getLoadFile() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1
 
getLogFile() - Method in class ubic.erminej.Settings
Determine where to put the log file.
getMaxClassSize() - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
getMaxClassSize() - Method in class ubic.erminej.SettingsHolder
 
getMessenger() - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
getMfCorrectedFdr() - Method in class ubic.erminej.data.GeneSetResult
 
getMfCorrectedPvalue() - Method in class ubic.erminej.data.GeneSetResult
 
getMinClassSize() - Method in class ubic.erminej.SettingsHolder
 
getMinGeneSetSize() - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
getMinGeneSetSize() - Method in class ubic.erminej.data.Histogram
 
getMinimumGeneSetSize() - Method in class ubic.erminej.data.GeneAnnotations
 
getMostMultifunctional(Collection<Gene>) - Method in class ubic.erminej.data.Multifunctionality
Convenience method.
getMtc() - Method in class ubic.erminej.SettingsHolder
 
getMultifunctionality() - Method in class ubic.erminej.data.GeneAnnotations
 
getMultifunctionalityCorrectedRankDelta() - Method in class ubic.erminej.data.GeneSetResult
 
getMultifunctionalityCorrelation() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getMultifunctionalityEnrichment() - Method in class ubic.erminej.analysis.GeneSetPvalRun
For ORA only.
getMultifunctionalityEnrichmentPvalue() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getMultifunctionalityRank() - Method in class ubic.erminej.data.GeneSetResult
 
getMultifunctionalityRank(Gene) - Method in class ubic.erminej.data.Multifunctionality
 
getMultifunctionalityScore(Gene) - Method in class ubic.erminej.data.Multifunctionality
 
getName() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getName() - Method in class ubic.erminej.data.Gene
 
getName() - Method in class ubic.erminej.data.GeneSet
 
getName() - Method in class ubic.erminej.data.GeneSetTerm
 
getName() - Method in class ubic.erminej.data.Probe
 
getNcbiId() - Method in class ubic.erminej.data.Gene
 
getNcbiTaxonId() - Method in class ubic.erminej.data.Gene
 
getNumAboveThreshold() - Method in class ubic.erminej.analysis.GeneSetPvalRun
ORA-only.
getNumBins() - Method in class ubic.erminej.data.Histogram
 
getNumGenes() - Method in class ubic.erminej.data.GeneSetResult
 
getNumGenes() - Method in class ubic.erminej.data.Multifunctionality
How many genes have multifunctionality scores.
getNumGenesOverThreshold() - Method in class ubic.erminej.analysis.OraPvalGenerator
Always for the genes.
getNumGenesUnderThreshold() - Method in class ubic.erminej.analysis.OraPvalGenerator
Always for genes.
getNumGenesUsed() - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
getNumGenesUsed() - Method in class ubic.erminej.data.GeneScores
 
getNumGoTerms(Gene) - Method in class ubic.erminej.data.Multifunctionality
 
getNumHistograms() - Method in class ubic.erminej.data.Histogram
 
getNumProbes() - Method in class ubic.erminej.data.GeneSetResult
 
getNumProbesUsed() - Method in class ubic.erminej.data.GeneScores
 
getNumResultSets() - Method in class ubic.erminej.gui.MainFrame
 
getNumRuns() - Method in class ubic.erminej.data.Histogram
 
getOriginalGeneData() - Method in class ubic.erminej.gui.MainFrame
Get the original, "fresh" gene annotation data.
getOwner() - Method in class ubic.erminej.gui.util.WizardStep
 
getParents(GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerms
 
getPoint() - Method in class ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
 
getPreferredSize() - Method in class ubic.erminej.gui.table.JVerticalHeaderRenderer
 
getProbability(int, int, boolean) - Method in class ubic.erminej.data.Histogram
 
getProbeAtRow(int) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
getProbeCount() - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
getProbes() - Method in class ubic.erminej.data.Gene
 
getProbes() - Method in class ubic.erminej.data.GeneAnnotations
 
getProbes() - Method in class ubic.erminej.data.GeneSet
 
getProbes() - Method in class ubic.erminej.data.GeneSetDetails
 
getProbes() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
Get the results of the user's picking.
getProbes() - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
getProbeScores() - Method in class ubic.erminej.data.GeneScores
Note that these values will already be log-transformed if that was requested.
getProbeScores() - Method in class ubic.erminej.data.GeneSetDetails
Just for the probes in this set.
getProbeToScoreMap() - Method in class ubic.erminej.data.GeneScores
Note that these values will already be log-transformed if that was requested
getProjectFileName() - Method in class ubic.erminej.gui.StartupPanel
 
getProperty(String) - Method in class ubic.erminej.SettingsHolder
 
getPrunedGeneAnnotations() - Method in class ubic.erminej.data.GeneScores
 
getPvalue() - Method in class ubic.erminej.data.EmptyGeneSetResult
 
getPvalue() - Method in class ubic.erminej.data.GeneSetResult
 
getQuantile() - Method in class ubic.erminej.SettingsHolder
 
getRank() - Method in class ubic.erminej.data.GeneSetResult
Low numbers are better ranks.
getRankedGenes() - Method in class ubic.erminej.data.GeneScores
 
getRawDataFileDirectory() - Method in class ubic.erminej.SettingsHolder
 
getRawDataFileName() - Method in class ubic.erminej.SettingsHolder
 
getRawGeneMultifunctionalityRank(Gene) - Method in class ubic.erminej.data.Multifunctionality
 
getRedundantGroups() - Method in class ubic.erminej.data.GeneSet
Can not modify this collection directly; use addRedundantGroup instead.
getRelativeRank() - Method in class ubic.erminej.data.GeneSetResult
 
getResults() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getResultSet(int) - Method in class ubic.erminej.gui.MainFrame
 
getResultSets() - Method in class ubic.erminej.gui.MainFrame
 
getRowCount() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
getRowCount() - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
getRowCount() - Method in class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
 
getRowCount() - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
getRowCount() - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
getRunIndex(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
getRunName(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
getRunSettings() - Method in class ubic.erminej.data.GeneSetDetails
 
getRunViewMenu() - Method in class ubic.erminej.gui.MainFrame
 
getSaveAllGenesInOutput() - Method in class ubic.erminej.SettingsHolder
 
getSaveFileName() - Method in class ubic.erminej.classScoreCMD
 
getScore() - Method in class ubic.erminej.data.GeneSetResult
 
getScoreCol() - Method in class ubic.erminej.SettingsHolder
 
getScoreColumnName() - Method in class ubic.erminej.data.GeneScores
Might not be available.
getScoreFile() - Method in class ubic.erminej.SettingsHolder
 
getSelected() - Method in class ubic.erminej.gui.file.AnnotationListFrame
 
getSelectedCustomGeneSets() - Method in class ubic.erminej.SettingsHolder
 
getSelectedGeneSet() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1A
 
getSelectedItem() - Method in class ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
 
getSelectedRunNum() - Method in class ubic.erminej.gui.SaveAnalysisDialog
 
getSettings() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
getSettings() - Method in class ubic.erminej.classScoreCMD
 
getSettings() - Method in class ubic.erminej.data.GeneAnnotations
 
getSettings() - Method in class ubic.erminej.data.GeneSetDetails
 
getSettings() - Method in class ubic.erminej.data.GeneSetResult
 
getSettings() - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
getSettings() - Method in class ubic.erminej.gui.MainFrame
 
getSettingsHolder() - Method in class ubic.erminej.Settings
 
getSimilarities(String, Map<String, Collection<String>>) - Static method in class ubic.erminej.data.GeneSetMapTools
 
getSortedClasses(Map<GeneSetTerm, GeneSetResult>) - Static method in class ubic.erminej.analysis.GeneSetPvalRun
 
getSortedClasses(Map<GeneSetTerm, GeneSetResult>, boolean) - Static method in class ubic.erminej.analysis.GeneSetPvalRun
 
getSourceFile() - Method in class ubic.erminej.data.GeneSet
 
getSourceGeneScores() - Method in class ubic.erminej.data.GeneSetDetails
The full set of GeneScores from which this was derived.
getStartColumn() - Method in class ubic.erminej.gui.geneset.details.JGeneScoreFileChooser
 
getStartColumn() - Method in class ubic.erminej.gui.geneset.details.JRawFileChooser
The column number where the data to import starts.
getStatusField() - Method in class ubic.erminej.gui.util.Wizard
 
getStatusMessenger() - Method in class ubic.erminej.classScoreCMD
 
getStatusMessenger() - Method in class ubic.erminej.gui.MainFrame
 
getStringProperty(String) - Method in class ubic.erminej.SettingsHolder
 
getSymbol() - Method in class ubic.erminej.data.Gene
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class ubic.erminej.gui.table.JBarGraphCellRenderer
This method is called each time a cell in a column using this renderer needs to be rendered.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class ubic.erminej.gui.table.JMatrixCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class ubic.erminej.gui.table.JVerticalHeaderRenderer
This method is called each time a column header using this renderer needs to be rendered.
getTablePanel() - Method in class ubic.erminej.gui.MainFrame
 
getTerm() - Method in class ubic.erminej.data.GeneSet
 
getTerm() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
 
getTerms() - Method in class ubic.erminej.data.GeneSetTerms
 
getTests() - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
getTitle() - Method in class ubic.erminej.data.GeneSetDetails
 
getTreeModel() - Method in class ubic.erminej.data.GeneSetTerms
 
getTreePanel() - Method in class ubic.erminej.gui.MainFrame
 
getUrl() - Method in class ubic.erminej.gui.geneset.details.GeneUrlDialog
Get the url that was set.
getURL() - Method in class ubic.erminej.gui.util.JLinkLabel
 
getUseBiologicalProcess() - Method in class ubic.erminej.SettingsHolder
 
getUseCellularComponent() - Method in class ubic.erminej.SettingsHolder
 
getUseLog() - Method in class ubic.erminej.SettingsHolder
 
getUseMolecularFunction() - Method in class ubic.erminej.SettingsHolder
 
getUserDefinedGeneSets() - Method in class ubic.erminej.data.GeneAnnotations
 
getUserDefinedTerms() - Method in class ubic.erminej.data.GeneAnnotations
Get the gene sets that are user-defined.
getUserGeneSetDirectory() - Method in class ubic.erminej.SettingsHolder
Get the path to the directory where custom gene sets are stored (default should be like ${HOME}/ermineJ.data/genesets).
getUseUserDefined() - Method in class ubic.erminej.SettingsHolder
 
getValue(int, double, boolean) - Method in class ubic.erminej.data.Histogram
 
getValue() - Method in class ubic.erminej.gui.table.MatrixPoint
 
getValueAt(int, int) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
 
getValueAt(int, int) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
getValueAt(int, int) - Method in class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
 
getValueAt(int, int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
getValueMap(String) - Method in class ubic.erminej.data.GeneScores
 
goChild - Static variable in class ubic.erminej.gui.util.Colors
 
goData - Variable in class ubic.erminej.classScoreCMD
 
GOLD_STANDARD_FILE - Static variable in class ubic.erminej.SettingsHolder
 
goParent - Static variable in class ubic.erminej.gui.util.Colors
 
GOParser - Class in ubic.erminej.data
Read in the GO XML file provided by the Gene Ontology Consortium.
GOParser(InputStream) - Constructor for class ubic.erminej.data.GOParser
 
GOParser(InputStream, boolean) - Constructor for class ubic.erminej.data.GOParser
 
GREY1 - Static variable in class ubic.erminej.gui.util.Colors
 
GREY2 - Static variable in class ubic.erminej.gui.util.Colors
 
GREY3 - Static variable in class ubic.erminej.gui.util.Colors
 
GREY4 - Static variable in class ubic.erminej.gui.util.Colors
 
GREY5 - Static variable in class ubic.erminej.gui.util.Colors
 
GuiUtil - Class in ubic.erminej.gui.util
Little oft-used functions.
GuiUtil() - Constructor for class ubic.erminej.gui.util.GuiUtil
 

H

hasAnnots() - Method in class ubic.erminej.data.Probe
 
hasBeenSavedToFile() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
hasGene(Gene) - Method in class ubic.erminej.data.GeneAnnotations
 
hasGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
 
hashCode() - Method in class ubic.erminej.data.Gene
 
hashCode() - Method in class ubic.erminej.data.GeneSet
 
hashCode() - Method in class ubic.erminej.data.GeneSetResult
 
hashCode() - Method in class ubic.erminej.data.GeneSetTerm
 
hashCode() - Method in class ubic.erminej.data.Probe
 
hasProbe(Probe) - Method in class ubic.erminej.data.GeneAnnotations
 
hasRedundancy(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
Check if a group has any redundancies.
hasRedundancy() - Method in class ubic.erminej.data.GeneSet
 
hasSelectedChild() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
If it's included in a filtered set.
hasSignificantChild() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
 
hasUsableAspect(GeneSetTerm, boolean) - Method in class ubic.erminej.data.GeneAnnotations
 
HEADER - Static variable in class ubic.erminej.Settings
Header for the config file.
helpButton - Variable in class ubic.erminej.gui.AppDialog
 
helpButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.AppDialog
 
helpButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.file.DataDirectoryDialog
 
HelpHelper - Class in ubic.erminej.gui
Makes it easier to add help access wherever we want To use this, you can do the following, for example for a menu item.
HelpHelper() - Constructor for class ubic.erminej.gui.HelpHelper
 
helpLocateAnnotations() - Method in class ubic.erminej.gui.StartupPanel
 
hideEmpty - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
hideInsignificant - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
hideNonCustom - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
hist - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
hist - Variable in class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
 
Histogram - Class in ubic.erminej.data
Stores distributions for geneSets ( a series of histograms).
Histogram(int, int, int, double, double) - Constructor for class ubic.erminej.data.Histogram
 
histogramMax - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
histogramMin - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 

I

ifInterruptedStop() - Method in class ubic.erminej.analysis.AbstractLongTask
 
ignoreSimilar(double, GeneAnnotations, StatusViewer, int, int, double) - Static method in class ubic.erminej.data.GeneSetMapTools
Remove classes which are too similar to some other class.
ImageFileFilter - Class in ubic.erminej.gui.file
 
ImageFileFilter() - Constructor for class ubic.erminej.gui.file.ImageFileFilter
 
includeAnnotations() - Method in class ubic.erminej.gui.geneset.details.DetailsOutputDataFileChooser
 
includeLabels() - Method in class ubic.erminej.gui.geneset.details.DetailsOutputImageFileChooser
 
INIT_COLUMNS - Static variable in class ubic.erminej.gui.geneset.table.GeneSetTableModel
The number of columns that are always there, before runs are listed.
initHelp(AbstractButton, SettingsHolder) - Method in class ubic.erminej.gui.HelpHelper
Initializes JavaHelp by creating HelpSet and HelpBroker objects and attaching an action listener an AbstractButton
initialize() - Method in class ubic.erminej.classScoreCMD
 
initialize(GeneAnnotations) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
initialize(GeneAnnotations) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
Called after data files are read in.
initializeAllData() - Method in class ubic.erminej.gui.MainFrame
Reinitialize everything
insert(MutableTreeNode, int) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
 
IS_TESTER - Static variable in class ubic.erminej.SettingsHolder
 
isAspect() - Method in class ubic.erminej.data.GeneSetTerm
 
isAutoSaving() - Method in class ubic.erminej.Settings
 
isFilterBySignificance() - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
isFilterBySize() - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
isFinishedNormally() - Method in class ubic.erminej.Analyzer
 
isGenes() - Method in class ubic.erminej.data.GeneSet
 
isLeaf(GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerms
 
isNegativeLog10Transformed() - Method in class ubic.erminej.data.GeneScores
 
isParent(GeneSetTerm, GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerms
 
isReadOnly() - Method in class ubic.erminej.data.GeneAnnotations
Test whether this was constructed 'subcloning' style.
isReady() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep1
 
isReady() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
isReady() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep3
 
isReady() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep4
 
isReady() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep5
 
isReady() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1
 
isReady() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1A
 
isReady() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
 
isReady() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
isReady() - Method in class ubic.erminej.gui.util.WizardStep
 
isSaveAllGenes() - Method in class ubic.erminej.classScoreCMD
 
isSaveAllGenes() - Method in class ubic.erminej.gui.SaveAnalysisDialog
 
isStale() - Method in class ubic.erminej.data.Multifunctionality
 
isStop() - Method in class ubic.erminej.Analyzer
 
isTester() - Method in class ubic.erminej.SettingsHolder
 
isUseCommandLineInterface() - Method in class ubic.erminej.classScoreCMD
 
isUserDefined() - Method in class ubic.erminej.data.GeneSet
 
isUserDefined() - Method in class ubic.erminej.data.GeneSetTerm
 
isWasError() - Method in class ubic.erminej.Analyzer
 
ITERATIONS - Static variable in class ubic.erminej.SettingsHolder
 

J

JBarGraphCellRenderer - Class in ubic.erminej.gui.table
Renders the "pvalue bars" in the details views.
JBarGraphCellRenderer() - Constructor for class ubic.erminej.gui.table.JBarGraphCellRenderer
 
JBarGraphCellRenderer(double, Color[]) - Constructor for class ubic.erminej.gui.table.JBarGraphCellRenderer
 
jbInit() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep1
 
jbInit() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
jbInit() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep3
 
jbInit() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep4
 
jbInit() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep5
 
jbInit() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1
 
jbInit() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep1A
 
jbInit() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
 
jbInit() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
jbInit() - Method in class ubic.erminej.gui.util.WizardStep
 
JGeneScoreFileChooser - Class in ubic.erminej.gui.geneset.details
Warning: this is basically the same as JRawFileChooser.
JGeneScoreFileChooser(String, int) - Constructor for class ubic.erminej.gui.geneset.details.JGeneScoreFileChooser
 
JHistViewer - Class in ubic.erminej.gui
 
JHistViewer(Histogram, int, double) - Constructor for class ubic.erminej.gui.JHistViewer
This is the default constructor
jlabel - Variable in class ubic.erminej.gui.util.StatusJlabel
 
jLabelStatus - Variable in class ubic.erminej.gui.util.Wizard
 
JLinkLabel - Class in ubic.erminej.gui.util
 
JLinkLabel(String, String) - Constructor for class ubic.erminej.gui.util.JLinkLabel
 
JMatrixCellRenderer - Class in ubic.erminej.gui.table
For rendering heatmaps in tables.
JMatrixCellRenderer(MatrixDisplay<Probe, String>) - Constructor for class ubic.erminej.gui.table.JMatrixCellRenderer
 
jPanelStatus - Variable in class ubic.erminej.gui.util.Wizard
 
JRawFileChooser - Class in ubic.erminej.gui.geneset.details
Similar to JGeneScoreFileChooser
JRawFileChooser(String, int) - Constructor for class ubic.erminej.gui.geneset.details.JRawFileChooser
 
JVerticalHeaderRenderer - Class in ubic.erminej.gui.table
Create text going up vertically for the headings.
JVerticalHeaderRenderer() - Constructor for class ubic.erminej.gui.table.JVerticalHeaderRenderer
 

K

keyPressed(KeyEvent) - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
keyReleased(KeyEvent) - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
keyTyped(KeyEvent) - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 

L

LIGHTBLUE1 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTBLUE2 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTBLUE3 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTBLUE4 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTBLUE5 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTGREEN1 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTGREEN2 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTGREEN3 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTGREEN4 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTGREEN5 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTRED1 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTRED2 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTRED3 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTRED4 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTRED5 - Static variable in class ubic.erminej.gui.util.Colors
 
LIGHTYELLOW - Static variable in class ubic.erminej.gui.util.Colors
 
LINE_WIDTH - Static variable in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
load(GeneAnnotations, String, StatusViewer) - Static method in class ubic.erminej.ResultsFileReader
 
loadAnalysis() - Method in class ubic.erminej.Analyzer
Load from a file, which can contain more than one set.
loadAnalysis() - Method in class ubic.erminej.gui.MainFrame
 
loadAnalysis(String) - Method in class ubic.erminej.gui.MainFrame
 
loadDataMatrix(String) - Method in class ubic.erminej.data.GeneSetDetails
Update or set the data matrix source.
loadPlainGeneList(String) - Method in class ubic.erminej.data.GeneAnnotations
 
loadPlainGeneList(String) - Method in class ubic.erminej.data.UserDefinedGeneSetManager
Read in a list of genes or probe ids from a file.
loadProject() - Method in class ubic.erminej.gui.MainFrame
 
loadUserDefined() - Method in class ubic.erminej.SettingsHolder
 
loadUserGeneSetFile(InputStream) - Method in class ubic.erminej.data.UserDefinedGeneSetManager
For testing only -- does NOT set the file name since we don't know it.
log - Static variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
log - Static variable in class ubic.erminej.analysis.MultipleTestCorrector
 
log - Static variable in class ubic.erminej.Analyzer
 
log - Static variable in class ubic.erminej.data.GeneSetDetails
 
log - Static variable in class ubic.erminej.data.GeneSetMapTools
 
log - Static variable in class ubic.erminej.data.GeneSetTerms
 
log - Static variable in class ubic.erminej.data.Histogram
 
log - Static variable in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
log - Static variable in class ubic.erminej.gui.util.GuiUtil
 
log - Static variable in class ubic.erminej.gui.util.WizardStep
 

M

m_isBarGraph - Variable in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
m_isSelected - Variable in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
m_noFocusBorder - Static variable in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
m_selectionBackground - Static variable in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
m_values - Variable in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
main(String[]) - Static method in class ubic.erminej.classScoreCMD
 
main(String[]) - Static method in class ubic.erminej.ErmineJGui
 
main(String[]) - Static method in class ubic.erminej.gui.analysis.AnalysisWizardStep1
 
main(String[]) - Static method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
main(String[]) - Static method in class ubic.erminej.gui.analysis.AnalysisWizardStep3
 
main(String[]) - Static method in class ubic.erminej.gui.file.AnnotationListFrame
 
main(String[]) - Static method in class ubic.erminej.gui.StartupPanel
 
MainFrame - Class in ubic.erminej.gui
The main ErmineJ application GUI frame.
MainFrame() - Constructor for class ubic.erminej.gui.MainFrame
 
MainFrame(Settings) - Constructor for class ubic.erminej.gui.MainFrame
 
mainPanel - Variable in class ubic.erminej.gui.util.Wizard
 
makeMouseListener() - Method in class ubic.erminej.gui.util.JLinkLabel
If this is to be used outside of a JTable rendering context, you should call this method.
matrixDisplay - Variable in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
MatrixPoint - Class in ubic.erminej.gui.table
 
MatrixPoint(int, int, double) - Constructor for class ubic.erminej.gui.table.MatrixPoint
 
MatrixPreviewer - Class in ubic.erminej.gui.util
Uses a dialog box (FIXME: this could just extend JDialog)
MatrixPreviewer() - Constructor for class ubic.erminej.gui.util.MatrixPreviewer
 
MAX_CLASS_SIZE - Static variable in class ubic.erminej.SettingsHolder
 
MAX_DEFINITION_LENGTH - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
MAX_GENES_FOR_DETAIL_VIEWING - Static variable in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
maybeEnableSomeMenus() - Method in class ubic.erminej.gui.MainFrame
 
messenger - Variable in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
messenger - Variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
MIN_CLASS_SIZE - Static variable in class ubic.erminej.SettingsHolder
 
model - Variable in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
modMenuItem_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
mouseButton_actionPerformed(MouseEvent) - Method in class ubic.erminej.gui.AppDialog
 
mouseReleased(MouseEvent) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
MTC_CONFIG_NAME - Static variable in class ubic.erminej.SettingsHolder
 
MULTIFUNC_COLUMN_INDEX - Static variable in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
MultiFuncDiagWindow - Class in ubic.erminej.gui.analysis
Visualizations of multifunctionality statistics across all the gene sets.
MultiFuncDiagWindow(MainFrame) - Constructor for class ubic.erminej.gui.analysis.MultiFuncDiagWindow
 
Multifunctionality - Class in ubic.erminej.data
Implementation of multifunctionality computations as described in Gillis and Pavlidis (2011) PLoS ONE 6:2:e17258.
Multifunctionality(GeneAnnotations, StatusViewer) - Constructor for class ubic.erminej.data.Multifunctionality
Construct Multifunctionality information based on the state of the GO annotations -- this accounts only for the probes in the annotations.
multipleTestCorrect(List<GeneSetTerm>, Map<GeneSetTerm, GeneSetResult>) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
Perform multiple test correction during the multifunctionality correction.
MultipleTestCorrector - Class in ubic.erminej.analysis
Perform multiple test correction on class scores.
MultipleTestCorrector(SettingsHolder, List<GeneSetTerm>, GeneAnnotations, GeneScores, Map<GeneSetTerm, GeneSetResult>, StatusViewer) - Constructor for class ubic.erminej.analysis.MultipleTestCorrector
 

N

nextButton - Variable in class ubic.erminej.gui.util.Wizard
 
nextButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
nextButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizard
 
nextButton_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.util.Wizard
Define what happens when the 'next' button is pressed
NO_ASPECT_AVAILABLE - Static variable in class ubic.erminej.data.GeneSetTerms
Name for aspect when none is defined.
NO_NAME_AVAILABLE - Static variable in class ubic.erminej.data.GeneSetTerm
 
NOACTION - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
NORMAL_APPROX_SAMPLE_FREQUENCY - Static variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
Check for fit to a normal distribution every n trials.
normalized() - Method in class ubic.erminej.gui.geneset.details.DetailsOutputDataFileChooser
 
normalized() - Method in class ubic.erminej.gui.geneset.details.DetailsOutputImageFileChooser
 
NullDistributionGenerator - Interface in ubic.erminej.analysis
 
numActiveGeneSets() - Method in class ubic.erminej.data.GeneAnnotations
Count how many gene sets will be analyzed given the user's current settings (min and max size and aspects)
numActiveGeneSets(int, int) - Method in class ubic.erminej.data.GeneAnnotations
Count how many gene sets will be analyzed given the user's current selected aspects and the provided minimum and maximum sizes.
numAnnotatedGenes() - Method in class ubic.erminej.data.GeneAnnotations
Compute how many genes have Gene set annotations.
numClasses - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
numGenes() - Method in class ubic.erminej.data.GeneAnnotations
How many genes are currently available
numGenesAboveThreshold(double) - Method in class ubic.erminej.data.GeneScores
 
numGeneSets() - Method in class ubic.erminej.data.GeneAnnotations
Get the number of gene sets currently available.
numGenesInGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
Get the number of genes in a gene set, identified by id.
numGenesInSet(GeneSetTerm) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
numGenesUsed - Variable in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
numProbes() - Method in class ubic.erminej.data.GeneAnnotations
 
numProbesForGene(Gene) - Method in class ubic.erminej.data.GeneAnnotations
Get how many probes point to the same gene.
numProbesInGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.GeneAnnotations
Get the number of probes in a gene set, identified by id.
numProbesInSet(GeneSetTerm) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
numRuns - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 

O

openUrl() - Method in class ubic.erminej.gui.util.JLinkLabel
 
openUrlForGeneSet(String, GeneSetTerm) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
Forms a url like url + term.getId().
OraPvalGenerator - Class in ubic.erminej.analysis
Compute gene set scores based on over-representation analysis (ORA).
OraPvalGenerator(SettingsHolder, GeneScores, GeneAnnotations, StatusViewer) - Constructor for class ubic.erminej.analysis.OraPvalGenerator
 
OUTPUT_FILE - Static variable in class ubic.erminej.SettingsHolder
 

P

padogWeights() - Method in class ubic.erminej.data.Multifunctionality
 
paintBackground(Graphics) - Method in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
paintComponent(Graphics) - Method in class ubic.erminej.gui.table.JBarGraphCellRenderer
 
paintComponent(Graphics) - Method in class ubic.erminej.gui.table.JVerticalHeaderRenderer
 
pickAnnotation() - Method in class ubic.erminej.data.AnnotationFileFetcher
Show a list of available annotation files.
PINK - Static variable in class ubic.erminej.gui.util.Colors
 
plotHistogram(String, JFreeChart) - Static method in class ubic.erminej.gui.analysis.Plotting
 
Plotting - Class in ubic.erminej.gui.analysis
Utilities for generating plots in a consistent way.
Plotting() - Constructor for class ubic.erminej.gui.analysis.Plotting
 
populateRanks(Map<GeneSetTerm, GeneSetResult>) - Static method in class ubic.erminej.analysis.GeneSetPvalRun
Fill in the ranks
popupRespondAndGetGeneSet(MouseEvent) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
popupRespondAndGetGeneSet(MouseEvent) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
popupRespondAndGetGeneSet(MouseEvent) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
PREFERENCES_FILE_NAME - Static variable in class ubic.erminej.SettingsHolder
 
previewMatrix(Window, List<Object[]>, Object[]) - Static method in class ubic.erminej.gui.util.MatrixPreviewer
 
previewMatrix(Window, String, Integer) - Static method in class ubic.erminej.gui.util.MatrixPreviewer
 
previewMatrix(Window, StringMatrix<String, String>) - Static method in class ubic.erminej.gui.util.MatrixPreviewer
 
previewScoresActionPerformed() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
Show a preview of the dat
print(Writer) - Method in class ubic.erminej.data.GeneAnnotations
Print out the gene annotations in the same format we got them in, but if the gene sets have been modified, this will be reflected.
print(Writer) - Method in class ubic.erminej.data.GeneSetResult
 
print(Writer, String) - Method in class ubic.erminej.data.GeneSetResult
The format is:
print(Writer) - Method in class ubic.erminej.data.Histogram
Prints the histogram to stdout.
printHeadings(Writer) - Method in class ubic.erminej.data.GeneSetResult
 
printHeadings(Writer, String) - Method in class ubic.erminej.data.GeneSetResult
 
printHelp(String) - Method in class ubic.erminej.classScoreCMD
 
Probe - Class in ubic.erminej.data
Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.
Probe(String) - Constructor for class ubic.erminej.data.Probe
 
Probe(String, String) - Constructor for class ubic.erminej.data.Probe
 
Probe(String, String, Collection<Gene>) - Constructor for class ubic.erminej.data.Probe
 
ProbeTableModel - Class in ubic.erminej.gui.geneset
Simple tabular representation of probes.
ProbeTableModel(Collection<Probe>) - Constructor for class ubic.erminej.gui.geneset.ProbeTableModel
 
ProbeTableModel(GeneAnnotations) - Constructor for class ubic.erminej.gui.geneset.ProbeTableModel
 
processCommandLine(String, String[]) - Method in class ubic.erminej.classScoreCMD
 

Q

QUANTILE_CONFIG_NAME - Static variable in class ubic.erminej.SettingsHolder
 

R

rankLargeScoresBest() - Method in class ubic.erminej.data.GeneScores
 
ranksOfGenesInSet(Collection<Gene>) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
RAW_FILE_CONFIG_NAME - Static variable in class ubic.erminej.SettingsHolder
 
read(InputStream, GeneAnnotationParser.Format, SettingsHolder) - Method in class ubic.erminej.data.GeneAnnotationParser
 
read(String, GeneAnnotationParser.Format, Settings) - Method in class ubic.erminej.data.GeneAnnotationParser
 
readAffyCsv(InputStream, Set<String>, SettingsHolder) - Method in class ubic.erminej.data.GeneAnnotationParser
Parse affy formatted files (CSV or tabbed should be okay)
readAgilent(InputStream, Set<String>, SettingsHolder) - Method in class ubic.erminej.data.GeneAnnotationParser
 
readDataMatrixForAnalysis(GeneAnnotations, SettingsHolder) - Static method in class ubic.erminej.data.DataIOUtils
 
readDefault(InputStream, Collection<Gene>, SettingsHolder, boolean) - Method in class ubic.erminej.data.GeneAnnotationParser
Main default reading method.
readDefault(String, Collection<Gene>, SettingsHolder, boolean) - Method in class ubic.erminej.data.GeneAnnotationParser
 
refreshView() - Method in class ubic.erminej.gui.geneset.GeneSetPanel
Updating, reapplying filters
refreshView() - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
Revalidate, refilter and (resort? NO) the table.
refreshView() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
Force to repaint, reapply filters.
removeActionListener(ActionListener) - Method in class ubic.erminej.gui.StartupPanel
 
removeAspect(GeneAnnotations, GeneSetTerms, StatusViewer, String) - Static method in class ubic.erminej.data.GeneSetMapTools
 
removeBySize(GeneAnnotations, StatusViewer, int, int) - Static method in class ubic.erminej.data.GeneSetMapTools
Remove gene sets that don't meet certain criteria.
removedGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
Update the view to reflect changes
removedGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
removedGeneSet(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
removeGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.Gene
 
removeGeneSet(GeneSetTerm) - Method in class ubic.erminej.data.Probe
 
removeProbe(Probe) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
removeProbes(Collection<Probe>) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
removeResults() - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
removeRun(GeneSetPvalRun) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
Do any extra cleanup after a run has been deleted.
removeRun(GeneSetPvalRun) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
removeRun(GeneSetPvalRun) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
removeRun(int) - Method in class ubic.erminej.gui.MainFrame
Remove a run from the list of results that are currently loaded.
removeRunData(int) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
removeRunPopupMenu_actionPerformed(ActionEvent) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
removeUserDefined(GeneSetTerm) - Method in class ubic.erminej.data.GeneSetTerms
 
removeVarPanel(SettingsHolder.Method) - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep5
 
renameRun(int, String) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
renameRun(int, String) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
ResamplingCorrelationGeneSetScore - Class in ubic.erminej.analysis
 
ResamplingCorrelationGeneSetScore(SettingsHolder, DoubleMatrix<Probe, String>) - Constructor for class ubic.erminej.analysis.ResamplingCorrelationGeneSetScore
 
reset() - Method in class ubic.erminej.data.GeneSetTerm
 
resetSignificanceFilters() - Method in class ubic.erminej.gui.MainFrame
 
resetView() - Method in class ubic.erminej.gui.geneset.GeneSetPanel
Restore view
resetView() - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
resetView() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
RESOURCE_LOCATION - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
RESOURCE_LOCATION - Static variable in class ubic.erminej.gui.MainFrame
 
RESTORED - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
ResultsFileReader - Class in ubic.erminej
Load results from a file.
ResultsFileReader() - Constructor for class ubic.erminej.ResultsFileReader
 
ResultsPrinter - Class in ubic.erminej
 
ResultsPrinter() - Constructor for class ubic.erminej.ResultsPrinter
 
resultToolTips - Variable in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
revalidate() - Method in class ubic.erminej.gui.table.JMatrixCellRenderer
 
revalidate() - Method in class ubic.erminej.gui.table.JVerticalHeaderRenderer
 
RocPvalGenerator - Class in ubic.erminej.analysis
Compute gene set p values based on the receiver operating characteristic (ROC).
RocPvalGenerator(SettingsHolder, GeneAnnotations, Map<Gene, Double>, StatusViewer) - Constructor for class ubic.erminej.analysis.RocPvalGenerator
 
run() - Method in class ubic.erminej.Analyzer
 
run(String[]) - Method in class ubic.erminej.classScoreCMD
 
run(List<Double>) - Method in class ubic.erminej.ClassScoreSimple
Run an analysis using the current configuration.
RUN_INDICATOR - Static variable in class ubic.erminej.ResultsPrinter
 
RUN_NAME_FIELD_PATTERN - Static variable in class ubic.erminej.ResultsPrinter
 

S

SAVE_ALL_GENES_IN_OUTPUT - Static variable in class ubic.erminej.SettingsHolder
 
saveAnalysisAction() - Method in class ubic.erminej.gui.MainFrame
 
SaveAnalysisDialog - Class in ubic.erminej.gui
Choose the run and whether the gene symbols should be included in the output.
SaveAnalysisDialog(MainFrame, Settings, int) - Constructor for class ubic.erminej.gui.SaveAnalysisDialog
 
saveData(String, boolean, boolean, boolean) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
fixme - this should not be in the gui.
saveGeneSet(GeneSet) - Method in class ubic.erminej.data.GeneAnnotations
Save changes to a user-defined gene set.
saveGeneSet(GeneSet) - Method in class ubic.erminej.data.UserDefinedGeneSetManager
Write a gene set to disk, in the directory set in the preferences.
saveImage(String, boolean) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
saveProject() - Method in class ubic.erminej.gui.MainFrame
 
saveValues() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep1
 
saveValues() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
saveValues() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep3
 
saveValues() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep4
 
saveValues() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep5
Save the values to the configuration.
SCORE_COL - Static variable in class ubic.erminej.SettingsHolder
 
SCORE_FILE - Static variable in class ubic.erminej.SettingsHolder
 
ScoreQuantiles - Class in ubic.erminej.analysis
 
ScoreQuantiles() - Constructor for class ubic.erminej.analysis.ScoreQuantiles
 
scoreToPval(int, double) - Method in class ubic.erminej.analysis.GeneSetResamplingPvalGenerator
Convert a raw score into a pvalue, based on background distribution
ScrollingTextAreaDialog - Class in ubic.erminej.gui.util
 
ScrollingTextAreaDialog(Frame, String, boolean) - Constructor for class ubic.erminej.gui.util.ScrollingTextAreaDialog
 
searchButton_actionPerformed_adapter() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
do a search.
SELECTED_CUSTOM_GENESETS - Static variable in class ubic.erminej.SettingsHolder
 
selectUserDefined() - Method in class ubic.erminej.data.GeneAnnotations
Make the selection the user-defined sets only.
set_class_max_size(int) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
set_class_min_size(int) - Method in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
set_range(double) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
setActionButtonText(String) - Method in class ubic.erminej.gui.AppDialog
 
setActionPerformed() - Method in class ubic.erminej.gui.geneset.details.GeneUrlDialog
This is the business
setActiveProbes(Collection<Probe>) - Method in class ubic.erminej.data.Gene
 
setAlwaysUseEmpirical(boolean) - Method in class ubic.erminej.Settings
 
setAnalysisType(SettingsHolder.Method) - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
setAnnotFile(String) - Method in class ubic.erminej.Settings
 
setAnnotFormat(GeneAnnotationParser.Format) - Method in class ubic.erminej.Settings
 
setAspect(String) - Method in class ubic.erminej.data.GeneSetTerm
 
setBigGeneScoreIsBetter(boolean) - Method in class ubic.erminej.ClassScoreSimple
Indicate that in the original gene scores, whether big values are better.
setBigIsBetter(boolean) - Method in class ubic.erminej.Settings
 
setCacheHits(int) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
setCancelButtonText(String) - Method in class ubic.erminej.gui.AppDialog
 
setCaretPosition(int) - Method in class ubic.erminej.gui.util.ScrollingTextAreaDialog
 
setChartTitleFont(JFreeChart) - Static method in class ubic.erminej.gui.analysis.Plotting
 
setClassFile(String) - Method in class ubic.erminej.Settings
 
setClassMaxSize(int) - Method in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
setClassScoreMethod(int) - Method in class ubic.erminej.ClassScoreSimple
Set the type of anlaysis to run.
setClassScoreMethod(SettingsHolder.Method) - Method in class ubic.erminej.Settings
 
setCorrectedPvalue(double) - Method in class ubic.erminej.data.GeneSetResult
 
setCurrentResultSet(GeneSetPvalRun) - Method in class ubic.erminej.gui.MainFrame
 
setCurrentResultSetIndex(int) - Method in class ubic.erminej.gui.MainFrame
 
setCustomGeneSetDirectory(String) - Method in class ubic.erminej.Settings
 
setCustomGeneSetFiles(Collection<String>) - Method in class ubic.erminej.SettingsHolder
 
setDataCol(int) - Method in class ubic.erminej.Settings
 
setDataDirectory(String) - Method in class ubic.erminej.Settings
 
setDataMatrix(DoubleMatrix<Probe, String>) - Method in class ubic.erminej.data.GeneSetDetails
You only need to use this if you want to replace the matrix.
setDefinition(String) - Method in class ubic.erminej.data.GeneSetTerm
 
setDescription(String) - Method in class ubic.erminej.gui.file.ImageFileFilter
 
setDescText(String) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
setDoLog(boolean) - Method in class ubic.erminej.Settings
 
setEditable(boolean) - Method in class ubic.erminej.gui.util.ScrollingTextAreaDialog
 
setFilterBySignificance(boolean) - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
setFilterBySize(boolean) - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
setFilterEmpty(boolean) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
setFilterEmptyResults(boolean) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
setFilterNonSpecific(boolean) - Method in class ubic.erminej.data.GeneAnnotationParser
 
setFilterNonSpecific(boolean) - Method in class ubic.erminej.Settings
 
setFilterNonUsers(boolean) - Method in class ubic.erminej.gui.geneset.table.GeneSetTableModel
 
setFilterSelectedTerms(Collection<GeneSetTerm>) - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
setFinishDisabled() - Method in class ubic.erminej.gui.util.Wizard
Disable the "finish" button, indicating the user has some steps to do yet.
setFinishEnabled() - Method in class ubic.erminej.gui.util.Wizard
Enable the "finish" button, indicating the user can get out of the wizard at this stage.
setFormat(UserDefinedGeneSetManager.GeneSetFileFormat) - Method in class ubic.erminej.data.GeneSet
 
setGemmaId(Long) - Method in class ubic.erminej.data.Gene
 
setGene(Gene) - Method in class ubic.erminej.data.Probe
Assumes we only have one gene per probe.
setGeneReplicateTreatment(int) - Method in class ubic.erminej.ClassScoreSimple
How to handle situations when more than one probe corresponds to the same gene.
setGeneRepTreatment(SettingsHolder.MultiProbeHandling) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
setGeneRepTreatment(SettingsHolder.MultiProbeHandling) - Method in class ubic.erminej.Settings
 
setGenes(boolean) - Method in class ubic.erminej.data.GeneSet
 
setGenes(Collection<Gene>) - Method in class ubic.erminej.data.GeneSet
 
setGenes(Collection<Gene>) - Method in class ubic.erminej.data.Probe
 
setGeneScoreMethod(SettingsHolder.GeneScoreMethod) - Method in class ubic.erminej.gui.analysis.AnalysisWizard
 
setGeneScores(GeneScores) - Method in class ubic.erminej.data.GeneSetDetails
Switch out the gene scores.
setGeneScoreSummaryMethod(int) - Method in class ubic.erminej.ClassScoreSimple
Set the method to be used to summarize gene sets during resampling analysis.
setGeneScoreThreshold(double) - Method in class ubic.erminej.ClassScoreSimple
Set the threshold to use for ORA analysis.
setGeneScoreThreshold(double) - Method in class ubic.erminej.Settings
Only applies to ORA
setGeneSetResamplingScoreMethod(SettingsHolder.GeneScoreMethod) - Method in class ubic.erminej.Settings
Set the method used to compute how values are combined (GSR method only).
setGeneSets(Collection<GeneSetTerm>) - Method in class ubic.erminej.data.Gene
 
setGeneSets(Collection<GeneSetTerm>) - Method in class ubic.erminej.data.Probe
 
setGeneUrlBase(String) - Method in class ubic.erminej.Settings
 
setGoldStandardFile(String) - Method in class ubic.erminej.Settings
Mostly used for testing
setHasSelectedChild(boolean) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
 
setHasSignificantChild(boolean) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
 
setHelpButtonText(String) - Method in class ubic.erminej.gui.AppDialog
 
setHideInsignificant(boolean) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
Has no effect unless you call filter() afterwards
setHistogram(Histogram) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
setHistogramRange() - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
Figure out the limits that should be used for the histogram.
setIdFieldEnabled(boolean) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
setIdText(String) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
 
setIsGenes(boolean) - Method in class ubic.erminej.data.GeneSet
 
setIterations(int) - Method in class ubic.erminej.ClassScoreSimple
The number of iterations to be used during resampling.
setIterations(int) - Method in class ubic.erminej.Settings
 
setLabel(String, ImageIcon) - Method in class ubic.erminej.gui.util.StatusJlabel
 
setLoadUserDefined(boolean) - Method in class ubic.erminej.SettingsHolder
 
setLogTransformGeneScores(boolean) - Method in class ubic.erminej.ClassScoreSimple
Set to true if your inputs are p-values.
setMaxClassSize(int) - Method in class ubic.erminej.Settings
 
setMaxGeneSetSize(int) - Method in class ubic.erminej.ClassScoreSimple
The maximum gene set size to be considered.
setMessenger(StatusViewer) - Method in class ubic.erminej.data.GeneAnnotations
 
setMessenger(StatusViewer) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
setMfCorrectedFdr(double) - Method in class ubic.erminej.data.GeneSetResult
 
setMfCorrectedPvalue(double) - Method in class ubic.erminej.data.GeneSetResult
 
setMinClassSize(int) - Method in class ubic.erminej.Settings
 
setMinGeneSetSize(int) - Method in class ubic.erminej.ClassScoreSimple
The minimum gene set size to be considered.
setMtc(SettingsHolder.MultiTestCorrMethod) - Method in class ubic.erminej.Settings
 
setMultifunctionalityCorrectedRankDelta(Integer) - Method in class ubic.erminej.data.GeneSetResult
Set how much this result changes in rank when multifunctionality correction is applied.
setMultifunctionalityRank(Double) - Method in class ubic.erminej.data.GeneSetResult
 
setName(String) - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
setName(String) - Method in class ubic.erminej.data.GeneSetTerm
 
setNcbiId(Integer) - Method in class ubic.erminej.data.Gene
 
setNcbiTaxonId(Integer) - Method in class ubic.erminej.data.Gene
 
setNumRuns(int) - Method in class ubic.erminej.data.Histogram
 
setOutputFile(String) - Method in class ubic.erminej.Settings
Mostly used for testing
setPoint(Point) - Method in class ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
 
setPrefFile(String) - Method in class ubic.erminej.Settings
 
setProbes(Collection<Probe>) - Method in class ubic.erminej.data.Gene
 
setProbes(Collection<Probe>) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
 
setProperty(String, Object) - Method in class ubic.erminej.Settings
Set an arbitrary property.
setPValue(double) - Method in class ubic.erminej.data.GeneSetResult
 
setQuantile(int) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
 
setQuantile(int) - Method in class ubic.erminej.Settings
 
setRandomSeed(long) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
 
setRandomSeed(long) - Method in interface ubic.erminej.analysis.NullDistributionGenerator
 
setRandomSeed(long) - Method in class ubic.erminej.analysis.ResamplingCorrelationGeneSetScore
 
setRank(int) - Method in class ubic.erminej.data.GeneSetResult
Where 1 is the best.
setRawFile(String) - Method in class ubic.erminej.SettingsHolder
 
setRedundantGroups(Set<GeneSet>) - Method in class ubic.erminej.data.GeneSet
 
setRelativeRank(double) - Method in class ubic.erminej.data.GeneSetResult
Where 0 is the best and 1 is the worst.
setResults(GeneSetPvalRun) - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
 
setSaveAllGenesInOutput(boolean) - Method in class ubic.erminej.Settings
 
setSavedToFile(boolean) - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
setScore(double) - Method in class ubic.erminej.data.GeneSetResult
 
setScoreCol(int) - Method in class ubic.erminej.Settings
Which column of the input score file has the scores.
setScoreFile(String) - Method in class ubic.erminej.SettingsHolder
 
setSelectedCustomGeneSets(Collection<GeneSetTerm>) - Method in class ubic.erminej.Settings
 
setSelectedItem(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
 
setSizes(int, int) - Method in class ubic.erminej.data.GeneSetResult
 
setSourceFile(String) - Method in class ubic.erminej.data.GeneSet
 
setStale(boolean) - Method in class ubic.erminej.data.Multifunctionality
 
setStartingSet(GeneSet) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
 
setStartingSet(Collection<Gene>) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
 
setTerm(GeneSetTerm) - Method in class ubic.erminej.data.GeneSet
 
setTester(boolean) - Method in class ubic.erminej.Settings
 
setTests(int) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
 
setText(String) - Method in class ubic.erminej.gui.util.ScrollingTextAreaDialog
 
settings - Variable in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
 
settings - Variable in class ubic.erminej.classScoreCMD
 
settings - Variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
Settings - Class in ubic.erminej
Basically a wrapper around a Commons Configuration object.
Settings() - Constructor for class ubic.erminej.Settings
Create the settings, reading them from a file to be determined by the constructor.
Settings(boolean) - Constructor for class ubic.erminej.Settings
 
Settings(SettingsHolder) - Constructor for class ubic.erminej.Settings
Creates settings object from a copy.
Settings(String) - Constructor for class ubic.erminej.Settings
Create a Settings object from the header of a results file or from a regular configuration file - autosave will not be set so they cannot be changed.
Settings(URL) - Constructor for class ubic.erminej.Settings
Autosave will not be set.
SettingsHolder - Class in ubic.erminej
Holds settings for retrieval but doesn't allow changing them (with a couple of exceptions) or saving them.
SettingsHolder(PropertiesConfiguration) - Constructor for class ubic.erminej.SettingsHolder
 
SettingsHolder() - Constructor for class ubic.erminej.SettingsHolder
 
SettingsHolder.GeneScoreMethod - Enum in ubic.erminej
For the gene set resampling method, how are scores computed for the group?
SettingsHolder.Method - Enum in ubic.erminej
Which gene set scoring method to use.
SettingsHolder.MultiProbeHandling - Enum in ubic.erminej
What to do when there are multiple values for a gene.
SettingsHolder.MultiTestCorrMethod - Enum in ubic.erminej
How to correct for multiple tests.
setUpHeaderPopupMenus() - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
for the table heading
setUseBiologicalProcess(boolean) - Method in class ubic.erminej.Settings
 
setUseCellularComponent(boolean) - Method in class ubic.erminej.Settings
 
setUseMolecularFunction(boolean) - Method in class ubic.erminej.Settings
 
setUseMultifunctionalityCorrection(boolean) - Method in class ubic.erminej.Settings
 
setUseNormalApprox(boolean) - Method in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
setUserDefined(boolean) - Method in class ubic.erminej.data.GeneSet
 
setUserDefined(boolean) - Method in class ubic.erminej.data.GeneSetTerm
 
setUserGeneSetDirectory(String) - Method in class ubic.erminej.Settings
 
setUseSpeedUp(boolean) - Method in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
If you set this to true, when large class sizes are analyzed, not every size is measured directly.
setUseUserDefined(boolean) - Method in class ubic.erminej.SettingsHolder
 
setValues() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep1
 
showDetailsForGeneSet(GeneSetTerm, GeneSetPvalRun) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
Create the popup window with the visualization for a specific gene set and results.
showDialog() - Method in class ubic.erminej.gui.AppDialog
 
showError(String) - Method in class ubic.erminej.gui.util.StatusJlabel
 
showError(String, Throwable) - Method in class ubic.erminej.gui.util.StatusJlabel
 
showError(Throwable) - Method in class ubic.erminej.gui.util.StatusJlabel
 
showError(String) - Method in class ubic.erminej.gui.util.Wizard
Print an error message to the status bar.
showError(String) - Method in class ubic.erminej.gui.util.WizardStep
Print an error message to the status bar.
showLogs() - Method in class ubic.erminej.gui.MainFrame
 
showPopupMenu(MouseEvent) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
 
showPopupMenu(MouseEvent) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
showPopupMenu(MouseEvent) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
 
showProgress(String) - Method in class ubic.erminej.gui.util.StatusJlabel
 
showStatus(String, boolean) - Method in class ubic.erminej.gui.util.StatusJlabel
 
showStatus(String) - Method in class ubic.erminej.gui.util.StatusJlabel
 
showStatus(String) - Method in class ubic.erminej.gui.util.Wizard
Print a message to the status bar.
showStatus(String) - Method in class ubic.erminej.gui.util.WizardStep
Print a message to the status bar.
showUserMenuItemActionPerformed(boolean) - Method in class ubic.erminej.gui.MainFrame
 
showWarning(String) - Method in class ubic.erminej.gui.util.StatusJlabel
 
showWizard() - Method in class ubic.erminej.gui.util.Wizard
 
SimpleGeneSetListTableModel - Class in ubic.erminej.gui.geneset
Simplified table model for listing gene sets (e.g.
SimpleGeneSetListTableModel(Collection<GeneSet>) - Constructor for class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
Offer up only the given gene sets
SimpleGeneSetListTableModel(GeneAnnotations) - Constructor for class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
Offer up all gene sets.
size() - Method in class ubic.erminej.data.GeneSet
 
SPEDUPSIZEEXTRASTEP - Static variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
SPEEDUPSIZECUT - Static variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
The size we use to start skipping sizes for resampling.
startAnalysis(SettingsHolder) - Method in class ubic.erminej.gui.MainFrame
 
StartupPanel - Class in ubic.erminej.gui
Panel shown on initial startup of the application.
StartupPanel(Settings, StatusViewer) - Constructor for class ubic.erminej.gui.StartupPanel
 
StatusJlabel - Class in ubic.erminej.gui.util
 
StatusJlabel(JLabel) - Constructor for class ubic.erminej.gui.util.StatusJlabel
 
statusMessenger - Variable in class ubic.erminej.classScoreCMD
 
stopRunning(boolean) - Method in class ubic.erminej.Analyzer
 
subClone(Collection<Probe>) - Method in class ubic.erminej.data.GeneAnnotations
Create a new annotation set based on an existing one, for selected probes, removing probes with no annotations.
switchAnnotations() - Method in class ubic.erminej.gui.MainFrame
 
switchGeneScoreFile() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
Keep the same gene set, but change the scores.
switchGeneScoreFile() - Method in class ubic.erminej.gui.MainFrame
 
switchRawDataFile() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
switchRawDataFile(boolean) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
 
switchRawDataFile() - Method in class ubic.erminej.gui.MainFrame
 

T

table - Variable in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
 
testDir(String) - Static method in class ubic.erminej.gui.util.GuiUtil
 
testFile(String) - Static method in class ubic.erminej.gui.util.GuiUtil
 
tocdf() - Method in class ubic.erminej.data.Histogram
Convert raw histograms to CDFs.
TOLERANCE - Static variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
Used to control interations.
toString() - Method in class ubic.erminej.analysis.GeneSetPvalRun
 
toString() - Method in class ubic.erminej.data.Gene
 
toString() - Method in class ubic.erminej.data.GeneScores
 
toString() - Method in class ubic.erminej.data.GeneSet
 
toString() - Method in class ubic.erminej.data.GeneSetTerm
 
toString() - Method in class ubic.erminej.data.Histogram
 
toString() - Method in class ubic.erminej.data.Probe
 
toString() - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreeNode
 
toString() - Method in class ubic.erminej.gui.util.JLinkLabel
 
toString() - Method in class ubic.erminej.Settings
 
toTableModel() - Method in class ubic.erminej.data.GeneAnnotations
 

U

ubic.erminej - package ubic.erminej
 
ubic.erminej.analysis - package ubic.erminej.analysis
 
ubic.erminej.data - package ubic.erminej.data
 
ubic.erminej.gui - package ubic.erminej.gui
 
ubic.erminej.gui.analysis - package ubic.erminej.gui.analysis
 
ubic.erminej.gui.file - package ubic.erminej.gui.file
 
ubic.erminej.gui.geneset - package ubic.erminej.gui.geneset
 
ubic.erminej.gui.geneset.details - package ubic.erminej.gui.geneset.details
 
ubic.erminej.gui.geneset.edit - package ubic.erminej.gui.geneset.edit
 
ubic.erminej.gui.geneset.table - package ubic.erminej.gui.geneset.table
 
ubic.erminej.gui.geneset.tree - package ubic.erminej.gui.geneset.tree
 
ubic.erminej.gui.table - package ubic.erminej.gui.table
 
ubic.erminej.gui.util - package ubic.erminej.gui.util
 
update(int, double) - Method in class ubic.erminej.data.Histogram
Update the count for one bin.
update() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep5
Resync with the settings.
updateCountLabel() - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
 
updateNumGeneSetsActive() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep3
 
updateNumGeneSetsActive() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep4
 
updateRunViewMenu() - Method in class ubic.erminej.gui.MainFrame
 
updateView() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep2
 
upperTail() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep5
 
upperTail() - Method in class ubic.erminej.SettingsHolder
Determine whether we should be using the upper tails of our histograms.
url - Variable in class ubic.erminej.gui.util.JLinkLabel
 
USE_BIOL_PROC - Static variable in class ubic.erminej.SettingsHolder
 
USE_CELL_COMP - Static variable in class ubic.erminej.SettingsHolder
 
USE_MOL_FUNC - Static variable in class ubic.erminej.SettingsHolder
 
USE_MULTIFUNCTIONALITY_CORRECTION - Static variable in class ubic.erminej.SettingsHolder
 
USE_USER_DEFINED_GROUPS - Static variable in class ubic.erminej.SettingsHolder
 
useMultifunctionalityCorrection() - Method in class ubic.erminej.SettingsHolder
 
useNormalApprox - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 
USER_DEFINED - Static variable in class ubic.erminej.data.GeneSetTerms
Name for root of tree representing user-defined gene sets.
USER_NODE_COLOR - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
USER_NODE_TEXT_COLOR - Static variable in class ubic.erminej.gui.geneset.GeneSetPanel
 
UserDefinedGeneSetManager - Class in ubic.erminej.data
This is designed to work as a singleton in the scope of a running ErmineJ instance.
UserDefinedGeneSetManager(GeneAnnotations, SettingsHolder, StatusViewer) - Constructor for class ubic.erminej.data.UserDefinedGeneSetManager
 
UserDefinedGeneSetManager.GeneSetFileFormat - Enum in ubic.erminej.data
 
USERGUI_DEFAULT_PROPERTIES - Static variable in class ubic.erminej.Settings
Part of the distribution, where defaults can be read from.
USERGUI_PROPERTIES - Static variable in class ubic.erminej.Settings
Filename for settings.
useSpeedUp - Variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
 

V

validate() - Method in class ubic.erminej.gui.table.JMatrixCellRenderer
 
validate() - Method in class ubic.erminej.gui.table.JVerticalHeaderRenderer
 
valueOf(String) - Static method in enum ubic.erminej.data.GeneAnnotationParser.Format
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.erminej.data.UserDefinedGeneSetManager.GeneSetFileFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.erminej.SettingsHolder.GeneScoreMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.erminej.SettingsHolder.Method
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.erminej.SettingsHolder.MultiProbeHandling
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.erminej.SettingsHolder.MultiTestCorrMethod
Returns the enum constant of this type with the specified name.
values() - Static method in enum ubic.erminej.data.GeneAnnotationParser.Format
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.erminej.data.UserDefinedGeneSetManager.GeneSetFileFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.erminej.SettingsHolder.GeneScoreMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.erminej.SettingsHolder.Method
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.erminej.SettingsHolder.MultiProbeHandling
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.erminej.SettingsHolder.MultiTestCorrMethod
Returns an array containing the constants of this enum type, in the order they are declared.
viewContext() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
Pop up a chart showing ROC and PR curves for this gene set in the full ranking.

W

wasCancelled() - Method in class ubic.erminej.gui.SaveAnalysisDialog
 
westfallyoung() - Method in class ubic.erminej.analysis.MultipleTestCorrector
Run WY with a default number of trials.
westfallyoung(int) - Method in class ubic.erminej.analysis.MultipleTestCorrector
Westfall-Young pvalue correction.
Wizard - Class in ubic.erminej.gui.util
Simple "wizard" implementation.
Wizard(JFrame, int, int) - Constructor for class ubic.erminej.gui.util.Wizard
 
WizardStep - Class in ubic.erminej.gui.util
 
WizardStep(Wizard) - Constructor for class ubic.erminej.gui.util.WizardStep
 
write(File) - Method in class ubic.erminej.data.GeneScores
Write the gene scores to a file.
write(String, GeneSetPvalRun, boolean) - Static method in class ubic.erminej.ResultsPrinter
 
write(String, SettingsHolder, Collection<GeneSetPvalRun>) - Static method in class ubic.erminej.ResultsPrinter
Used for saving "projects".
writeAnalysisSettings(SettingsHolder, String) - Static method in class ubic.erminej.Settings
Write a configuration to the given file - but just settings relevant to analysis (not window locations, for example).
writeAnalysisSettings(SettingsHolder, Writer) - Static method in class ubic.erminej.Settings
Write a configuration to the given output - but just settings relevant to analysis (not window locations, for example).
writeAnalysisSettings(String) - Method in class ubic.erminej.Settings
Intended to be used for saving results to the header of an output file.
writePng(GeneSetDetails, String, Color[], boolean, boolean, boolean) - Static method in class ubic.erminej.data.GeneSetDetailsImageWriter
 
writePrefs() - Method in class ubic.erminej.gui.MainFrame
 
writePrefs() - Method in class ubic.erminej.Settings
Save the preferences to disk, if necessary, to the DEFAULT location (e.g.

X

XMLFileFilter - Class in ubic.erminej.gui.file
 
XMLFileFilter() - Constructor for class ubic.erminej.gui.file.XMLFileFilter
 
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