Package | Description |
---|---|
ubic.erminej.data | |
ubic.erminej.gui | |
ubic.erminej.gui.geneset | |
ubic.erminej.gui.geneset.edit |
Modifier and Type | Method and Description |
---|---|
GeneSet |
GeneAnnotations.addGeneSet(GeneSetTerm geneSetId,
Collection<Gene> gs,
String sourceFile)
Add a user-defined gene set.
|
GeneSet |
GeneAnnotations.findGeneSet(GeneSetTerm term) |
GeneSet |
GeneAnnotations.findGeneSet(String name) |
GeneSet |
GeneAnnotations.getGeneSet(GeneSetTerm classid) |
Modifier and Type | Method and Description |
---|---|
Set<GeneSet> |
GeneAnnotations.getGeneSets() |
Collection<GeneSet> |
GeneAnnotations.getGeneSets(Collection<GeneSetTerm> terms) |
Set<GeneSet> |
GeneSet.getRedundantGroups()
Can not modify this collection directly; use addRedundantGroup instead.
|
Set<GeneSet> |
GeneAnnotations.getUserDefinedGeneSets() |
protected Collection<GeneSet> |
UserDefinedGeneSetManager.loadUserGeneSetFile(InputStream is)
For testing only -- does NOT set the file name since we don't know it.
|
Modifier and Type | Method and Description |
---|---|
void |
GeneAnnotations.addGeneSet(GeneSet set) |
void |
GeneSet.addRedundantGroup(GeneSet redundant) |
void |
GeneSet.clearRedundancy(GeneSet toclear) |
void |
UserDefinedGeneSetManager.saveGeneSet(GeneSet setToSave)
Write a gene set to disk, in the directory set in the preferences.
|
void |
GeneAnnotations.saveGeneSet(GeneSet toSave)
Save changes to a user-defined gene set.
|
Modifier and Type | Method and Description |
---|---|
void |
GeneSet.setRedundantGroups(Set<GeneSet> redundantGroups) |
Modifier and Type | Method and Description |
---|---|
void |
MainFrame.addedNewGeneSet(GeneSet newGeneSet) |
Constructor and Description |
---|
SimpleGeneSetListTableModel(Collection<GeneSet> geneSets)
Offer up only the given gene sets
|
Modifier and Type | Method and Description |
---|---|
GeneSet |
GeneSetWizardStep1A.getSelectedGeneSet() |
Modifier and Type | Method and Description |
---|---|
protected void |
GeneSetWizardStep2.setStartingSet(GeneSet original) |
Constructor and Description |
---|
GeneSetWizardStep1A(GeneSetWizard wiz,
GeneAnnotations geneData,
Collection<GeneSet> geneSets) |
Copyright © 2002-2013 UBC Centre for High-Throughput Biology. All Rights Reserved.