Modifier and Type | Field and Description |
---|---|
protected GeneAnnotations |
classScoreCMD.geneData |
Modifier and Type | Method and Description |
---|---|
static Collection<GeneSetPvalRun> |
ResultsFileReader.load(GeneAnnotations geneAnnots,
String filename,
StatusViewer messenger) |
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.
|
Modifier and Type | Field and Description |
---|---|
protected GeneAnnotations |
AbstractGeneSetPvalGenerator.geneAnnots |
Modifier and Type | Method and Description |
---|---|
GeneAnnotations |
GeneSetPvalRun.getGeneData() |
Modifier and Type | Method and Description |
---|---|
GeneAnnotations |
GeneSetDetails.getGeneData() |
GeneAnnotations |
GeneScores.getPrunedGeneAnnotations() |
GeneAnnotations |
GeneAnnotationParser.read(InputStream i,
GeneAnnotationParser.Format format,
SettingsHolder settings) |
GeneAnnotations |
GeneAnnotationParser.read(String fileName,
GeneAnnotationParser.Format format,
Settings 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) |
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) |
GeneAnnotations |
GeneAnnotations.subClone(Collection<Probe> probesToRetain)
Create a new annotation set based on an existing one, for selected probes, removing probes with no annotations.
|
Modifier and Type | Method and Description |
---|---|
void |
GeneAnnotations.deleteSubClone(GeneAnnotations a)
Remove a no-longer-needed subclone.
|
static void |
GeneSetMapTools.ignoreSimilar(double fractionSameThreshold,
GeneAnnotations ga,
StatusViewer messenger,
int maxClassSize,
int minClassSize,
double bigClassPenalty)
Remove classes which are too similar to some other class.
|
static DoubleMatrix<Probe,String> |
DataIOUtils.readDataMatrixForAnalysis(GeneAnnotations geneAnnots,
SettingsHolder settings) |
static void |
GeneSetMapTools.removeAspect(GeneAnnotations ga,
GeneSetTerms gon,
StatusViewer messenger,
String aspect) |
static void |
GeneSetMapTools.removeBySize(GeneAnnotations ga,
StatusViewer messenger,
int minClassSize,
int maxClassSize)
Remove gene sets that don't meet certain criteria.
|
Constructor and Description |
---|
GeneAnnotations(GeneAnnotations start,
Collection<Probe> probes)
Create a read-only new annotation set based on an existing one, for selected probes, removing
probes with no annotations.
|
GeneAnnotations(GeneAnnotations start,
Collection<Probe> probes,
boolean pruneUnannotated)
Create a read-only new annotation set based on an existing one, for selected probes, optionally
removing unannotated probes.
|
GeneScores(Collection<String> identifiers,
Settings settings,
StatusViewer m,
GeneAnnotations geneAnnotations,
String outputFileName)
Constructor for the case when we are just taking in a hit list.
|
GeneScores(GeneScores source,
GeneAnnotations geneAnnots)
Create a copy of source that contains only the probes given.
|
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) |
GeneSetDetails(GeneSetTerm classID,
GeneAnnotations geneData,
StatusViewer callerStatusViewer)
Show without any results.
|
GeneSetDetails(GeneSetTerm classID,
GeneSetResult result,
GeneAnnotations geneData,
Settings settings,
GeneScores geneScores,
StatusViewer statusViewer)
The data matrix will be read in based on the settings, or can be changed later.
|
Multifunctionality(GeneAnnotations go,
StatusViewer m)
Construct Multifunctionality information based on the state of the GO annotations -- this accounts only for the
probes in the annotations.
|
UserDefinedGeneSetManager(GeneAnnotations annots,
SettingsHolder settings,
StatusViewer messenger) |
Modifier and Type | Method and Description |
---|---|
GeneAnnotations |
MainFrame.getOriginalGeneData()
Get the original, "fresh" gene annotation data.
|
Modifier and Type | Method and Description |
---|---|
GeneAnnotations |
AnalysisWizard.getGeneAnnots() |
Constructor and Description |
---|
AnalysisWizard(MainFrame callingframe,
GeneAnnotations geneAnnots) |
Modifier and Type | Field and Description |
---|---|
protected GeneAnnotations |
GeneSetPanel.geneData |
Constructor and Description |
---|
ProbeTableModel(GeneAnnotations geneData) |
SimpleGeneSetListTableModel(GeneAnnotations geneDat)
Offer up all gene sets.
|
Constructor and Description |
---|
GeneSetWizard(MainFrame callingframe,
GeneAnnotations geneData,
boolean makingNew)
Use this constructor to let the user choose which gene set to look at or to make a new one.
|
GeneSetWizard(MainFrame callingframe,
GeneAnnotations geneData,
GeneSetTerm geneSetId)
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).
|
GeneSetWizardStep1A(GeneSetWizard wiz,
GeneAnnotations geneData)
Only show the user's sets
|
GeneSetWizardStep1A(GeneSetWizard wiz,
GeneAnnotations geneData,
Collection<GeneSet> geneSets) |
GeneSetWizardStep2(GeneSetWizard wiz,
GeneAnnotations geneData) |
Modifier and Type | Method and Description |
---|---|
void |
GeneSetTablePanel.initialize(GeneAnnotations initialGoData) |
Constructor and Description |
---|
GeneSetTableModel(GeneAnnotations geneData,
List<GeneSetPvalRun> results) |
Modifier and Type | Method and Description |
---|---|
void |
GeneSetTreePanel.initialize(GeneAnnotations gd)
Called after data files are read in.
|
Constructor and Description |
---|
FilteredGeneSetTreeModel(GeneAnnotations annots,
TreeModel toWrap) |
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