- 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
-
- 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
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The minimum gene set size to be considered.
- setMtc(SettingsHolder.MultiTestCorrMethod) - Method in class ubic.erminej.Settings
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- setMultifunctionalityCorrectedRankDelta(Integer) - Method in class ubic.erminej.data.GeneSetResult
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Set how much this result changes in rank when multifunctionality correction is applied.
- setMultifunctionalityRank(Double) - Method in class ubic.erminej.data.GeneSetResult
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- setName(String) - Method in class ubic.erminej.analysis.GeneSetPvalRun
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- setName(String) - Method in class ubic.erminej.data.GeneSetTerm
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- setNcbiId(Integer) - Method in class ubic.erminej.data.Gene
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- setNcbiTaxonId(Integer) - Method in class ubic.erminej.data.Gene
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- setNumRuns(int) - Method in class ubic.erminej.data.Histogram
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- setOutputFile(String) - Method in class ubic.erminej.Settings
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Mostly used for testing
- setPoint(Point) - Method in class ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
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- setPrefFile(String) - Method in class ubic.erminej.Settings
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- setProbes(Collection<Probe>) - Method in class ubic.erminej.data.Gene
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- setProbes(Collection<Probe>) - Method in class ubic.erminej.gui.geneset.ProbeTableModel
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- setProperty(String, Object) - Method in class ubic.erminej.Settings
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Set an arbitrary property.
- setPValue(double) - Method in class ubic.erminej.data.GeneSetResult
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- setQuantile(int) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
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- setQuantile(int) - Method in class ubic.erminej.Settings
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- setRandomSeed(long) - Method in class ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
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- setRandomSeed(long) - Method in interface ubic.erminej.analysis.NullDistributionGenerator
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- setRandomSeed(long) - Method in class ubic.erminej.analysis.ResamplingCorrelationGeneSetScore
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- setRank(int) - Method in class ubic.erminej.data.GeneSetResult
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Where 1 is the best.
- setRawFile(String) - Method in class ubic.erminej.SettingsHolder
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- setRedundantGroups(Set<GeneSet>) - Method in class ubic.erminej.data.GeneSet
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- setRelativeRank(double) - Method in class ubic.erminej.data.GeneSetResult
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Where 0 is the best and 1 is the worst.
- setResults(GeneSetPvalRun) - Method in class ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
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- setSaveAllGenesInOutput(boolean) - Method in class ubic.erminej.Settings
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- setSavedToFile(boolean) - Method in class ubic.erminej.analysis.GeneSetPvalRun
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- setScore(double) - Method in class ubic.erminej.data.GeneSetResult
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- setScoreCol(int) - Method in class ubic.erminej.Settings
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Which column of the input score file has the scores.
- setScoreFile(String) - Method in class ubic.erminej.SettingsHolder
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- setSelectedCustomGeneSets(Collection<GeneSetTerm>) - Method in class ubic.erminej.Settings
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- setSelectedItem(GeneSetTerm) - Method in class ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
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- setSizes(int, int) - Method in class ubic.erminej.data.GeneSetResult
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- setSourceFile(String) - Method in class ubic.erminej.data.GeneSet
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- setStale(boolean) - Method in class ubic.erminej.data.Multifunctionality
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- setStartingSet(GeneSet) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
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- setStartingSet(Collection<Gene>) - Method in class ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
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- setTerm(GeneSetTerm) - Method in class ubic.erminej.data.GeneSet
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- setTester(boolean) - Method in class ubic.erminej.Settings
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- setTests(int) - Method in class ubic.erminej.analysis.CorrelationPvalGenerator
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- setText(String) - Method in class ubic.erminej.gui.util.ScrollingTextAreaDialog
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- settings - Variable in class ubic.erminej.analysis.AbstractGeneSetPvalGenerator
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- settings - Variable in class ubic.erminej.classScoreCMD
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- settings - Variable in class ubic.erminej.gui.geneset.GeneSetPanel
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- Settings - Class in ubic.erminej
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Basically a wrapper around a Commons Configuration object.
- Settings() - Constructor for class ubic.erminej.Settings
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Create the settings, reading them from a file to be determined by the constructor.
- Settings(boolean) - Constructor for class ubic.erminej.Settings
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- Settings(SettingsHolder) - Constructor for class ubic.erminej.Settings
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Creates settings object from a copy.
- Settings(String) - Constructor for class ubic.erminej.Settings
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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
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Autosave will not be set.
- SettingsHolder - Class in ubic.erminej
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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
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- SettingsHolder() - Constructor for class ubic.erminej.SettingsHolder
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- SettingsHolder.GeneScoreMethod - Enum in ubic.erminej
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For the gene set resampling method, how are scores computed for the group?
- SettingsHolder.Method - Enum in ubic.erminej
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Which gene set scoring method to use.
- SettingsHolder.MultiProbeHandling - Enum in ubic.erminej
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What to do when there are multiple values for a gene.
- SettingsHolder.MultiTestCorrMethod - Enum in ubic.erminej
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How to correct for multiple tests.
- setUpHeaderPopupMenus() - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
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for the table heading
- setUseBiologicalProcess(boolean) - Method in class ubic.erminej.Settings
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- setUseCellularComponent(boolean) - Method in class ubic.erminej.Settings
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- setUseMolecularFunction(boolean) - Method in class ubic.erminej.Settings
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- setUseMultifunctionalityCorrection(boolean) - Method in class ubic.erminej.Settings
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- setUseNormalApprox(boolean) - Method in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
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- setUserDefined(boolean) - Method in class ubic.erminej.data.GeneSet
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- setUserDefined(boolean) - Method in class ubic.erminej.data.GeneSetTerm
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- setUserGeneSetDirectory(String) - Method in class ubic.erminej.Settings
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- setUseSpeedUp(boolean) - Method in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
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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
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- setValues() - Method in class ubic.erminej.gui.analysis.AnalysisWizardStep1
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- showDetailsForGeneSet(GeneSetTerm, GeneSetPvalRun) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
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Create the popup window with the visualization for a specific gene set and results.
- showDialog() - Method in class ubic.erminej.gui.AppDialog
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- showError(String) - Method in class ubic.erminej.gui.util.StatusJlabel
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- showError(String, Throwable) - Method in class ubic.erminej.gui.util.StatusJlabel
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- showError(Throwable) - Method in class ubic.erminej.gui.util.StatusJlabel
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- showError(String) - Method in class ubic.erminej.gui.util.Wizard
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Print an error message to the status bar.
- showError(String) - Method in class ubic.erminej.gui.util.WizardStep
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Print an error message to the status bar.
- showLogs() - Method in class ubic.erminej.gui.MainFrame
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- showPopupMenu(MouseEvent) - Method in class ubic.erminej.gui.geneset.GeneSetPanel
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- showPopupMenu(MouseEvent) - Method in class ubic.erminej.gui.geneset.table.GeneSetTablePanel
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- showPopupMenu(MouseEvent) - Method in class ubic.erminej.gui.geneset.tree.GeneSetTreePanel
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- showProgress(String) - Method in class ubic.erminej.gui.util.StatusJlabel
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- showStatus(String, boolean) - Method in class ubic.erminej.gui.util.StatusJlabel
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- showStatus(String) - Method in class ubic.erminej.gui.util.StatusJlabel
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- showStatus(String) - Method in class ubic.erminej.gui.util.Wizard
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Print a message to the status bar.
- showStatus(String) - Method in class ubic.erminej.gui.util.WizardStep
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Print a message to the status bar.
- showUserMenuItemActionPerformed(boolean) - Method in class ubic.erminej.gui.MainFrame
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- showWarning(String) - Method in class ubic.erminej.gui.util.StatusJlabel
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- showWizard() - Method in class ubic.erminej.gui.util.Wizard
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- SimpleGeneSetListTableModel - Class in ubic.erminej.gui.geneset
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Simplified table model for listing gene sets (e.g.
- SimpleGeneSetListTableModel(Collection<GeneSet>) - Constructor for class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
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Offer up only the given gene sets
- SimpleGeneSetListTableModel(GeneAnnotations) - Constructor for class ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
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Offer up all gene sets.
- size() - Method in class ubic.erminej.data.GeneSet
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- SPEDUPSIZEEXTRASTEP - Static variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
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- SPEEDUPSIZECUT - Static variable in class ubic.erminej.analysis.AbstractResamplingGeneSetScore
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The size we use to start skipping sizes for resampling.
- startAnalysis(SettingsHolder) - Method in class ubic.erminej.gui.MainFrame
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- StartupPanel - Class in ubic.erminej.gui
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Panel shown on initial startup of the application.
- StartupPanel(Settings, StatusViewer) - Constructor for class ubic.erminej.gui.StartupPanel
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- StatusJlabel - Class in ubic.erminej.gui.util
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- StatusJlabel(JLabel) - Constructor for class ubic.erminej.gui.util.StatusJlabel
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- statusMessenger - Variable in class ubic.erminej.classScoreCMD
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- stopRunning(boolean) - Method in class ubic.erminej.Analyzer
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- subClone(Collection<Probe>) - Method in class ubic.erminej.data.GeneAnnotations
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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
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- switchGeneScoreFile() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
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Keep the same gene set, but change the scores.
- switchGeneScoreFile() - Method in class ubic.erminej.gui.MainFrame
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- switchRawDataFile() - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
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- switchRawDataFile(boolean) - Method in class ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
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- switchRawDataFile() - Method in class ubic.erminej.gui.MainFrame
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