Package | Description |
---|---|
ubic.erminej | |
ubic.erminej.analysis | |
ubic.erminej.data | |
ubic.erminej.gui | |
ubic.erminej.gui.analysis | |
ubic.erminej.gui.geneset.details | |
ubic.erminej.gui.geneset.edit |
Modifier and Type | Class and Description |
---|---|
class |
Settings
Basically a wrapper around a Commons Configuration object.
|
Modifier and Type | Method and Description |
---|---|
SettingsHolder |
classScoreCMD.getSettings() |
SettingsHolder |
Settings.getSettingsHolder() |
Modifier and Type | Method and Description |
---|---|
static void |
ResultsPrinter.write(String path,
SettingsHolder masterSettings,
Collection<GeneSetPvalRun> runsToSave)
Used for saving "projects".
|
static void |
Settings.writeAnalysisSettings(SettingsHolder settings,
String fileName)
Write a configuration to the given file - but just settings relevant to analysis (not window locations, for
example).
|
static void |
Settings.writeAnalysisSettings(SettingsHolder settings,
Writer out)
Write a configuration to the given output - but just settings relevant to analysis (not window locations, for
example).
|
Constructor and Description |
---|
Analyzer(SettingsHolder settings,
StatusViewer messenger,
GeneAnnotations geneAnnots) |
Analyzer(SettingsHolder settings,
StatusViewer messenger,
GeneAnnotations geneAnnots,
String loadFile)
For loading an analysis from a file.
|
Settings(SettingsHolder settingsToCopy)
Creates settings object from a copy.
|
Modifier and Type | Field and Description |
---|---|
protected SettingsHolder |
AbstractGeneSetPvalGenerator.settings |
Modifier and Type | Method and Description |
---|---|
SettingsHolder |
GeneSetPvalRun.getSettings() |
Modifier and Type | Method and Description |
---|---|
static QuantileBin1D |
ScoreQuantiles.computeQuantiles(SettingsHolder settings,
GeneScores geneScores) |
Modifier and Type | Method and Description |
---|---|
SettingsHolder |
GeneSetDetails.getRunSettings() |
SettingsHolder |
GeneAnnotations.getSettings() |
SettingsHolder |
GeneSetResult.getSettings() |
Modifier and Type | Method and Description |
---|---|
GeneAnnotations |
GeneAnnotationParser.read(InputStream i,
GeneAnnotationParser.Format format,
SettingsHolder settings) |
protected GeneAnnotations |
GeneAnnotationParser.readAffyCsv(InputStream bis,
Set<String> activeGenes,
SettingsHolder settings)
Parse affy formatted files (CSV or tabbed should be okay)
|
protected GeneAnnotations |
GeneAnnotationParser.readAgilent(InputStream bis,
Set<String> activeGenes,
SettingsHolder settings) |
static DoubleMatrix<Probe,String> |
DataIOUtils.readDataMatrixForAnalysis(GeneAnnotations geneAnnots,
SettingsHolder settings) |
GeneAnnotations |
GeneAnnotationParser.readDefault(InputStream bis,
Collection<Gene> activeGenes,
SettingsHolder settings,
boolean simple)
Main default reading method.
|
GeneAnnotations |
GeneAnnotationParser.readDefault(String fileName,
Collection<Gene> genes,
SettingsHolder settings,
boolean simple) |
Constructor and Description |
---|
AnnotationFileFetcher(SettingsHolder settingsHolder) |
GeneAnnotations(Collection<Gene> genes,
GeneSetTerms geneSetTerms,
SettingsHolder settings,
StatusViewer messenger) |
GeneScores(InputStream is,
SettingsHolder settings,
StatusViewer m,
GeneAnnotations geneAnnotations) |
GeneScores(List<String> probes,
List<Double> scores,
GeneAnnotations geneAnnots,
SettingsHolder settings)
Constructor designed for use when input is not a file.
|
GeneScores(String filename,
SettingsHolder settings,
StatusViewer messenger,
GeneAnnotations geneAnnots) |
GeneSetResult(GeneSetTerm id,
int numProbes,
int numGenes,
double score,
double pvalue,
double correctedPvalue,
SettingsHolder settings) |
GeneSetResult(GeneSetTerm id,
int numProbes,
int numGenes,
SettingsHolder settings) |
UserDefinedGeneSetManager(GeneAnnotations annots,
SettingsHolder settings,
StatusViewer messenger) |
Modifier and Type | Method and Description |
---|---|
boolean |
HelpHelper.initHelp(AbstractButton c,
SettingsHolder settings)
Initializes JavaHelp by creating HelpSet and HelpBroker objects and attaching an action listener an
AbstractButton
|
void |
MainFrame.startAnalysis(SettingsHolder runSettings) |
Modifier and Type | Method and Description |
---|---|
SettingsHolder |
AnalysisWizard.getSettings() |
Constructor and Description |
---|
GeneSetDetailsTableModel(MatrixDisplay<Probe,String> matrixDisplay,
GeneSetDetails geneSetDetails,
SettingsHolder settings) |
GeneUrlDialog(SettingsHolder settings) |
Constructor and Description |
---|
GeneSetWizardStep1(GeneSetWizard wiz,
SettingsHolder settings) |
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