public class UserDefinedGeneSetManager extends Object
Modifier and Type | Class and Description |
---|---|
static class |
UserDefinedGeneSetManager.GeneSetFileFormat |
Constructor and Description |
---|
UserDefinedGeneSetManager(GeneAnnotations annots,
SettingsHolder settings,
StatusViewer messenger) |
Modifier and Type | Method and Description |
---|---|
boolean |
deleteUserGeneSet(GeneSetTerm termToDelete)
Delete a user-defined gene set from disk and from the annotations in memory.
|
Collection<Gene> |
loadPlainGeneList(String fileName)
Read in a list of genes or probe ids from a file.
|
protected Collection<GeneSet> |
loadUserGeneSetFile(InputStream is)
For testing only -- does NOT set the file name since we don't know it.
|
void |
saveGeneSet(GeneSet setToSave)
Write a gene set to disk, in the directory set in the preferences.
|
public UserDefinedGeneSetManager(GeneAnnotations annots, SettingsHolder settings, StatusViewer messenger)
public boolean deleteUserGeneSet(GeneSetTerm termToDelete)
ngs
- public Collection<Gene> loadPlainGeneList(String fileName) throws IOException
fileName
- IOException
public void saveGeneSet(GeneSet setToSave) throws IOException
type
- IOException
protected Collection<GeneSet> loadUserGeneSetFile(InputStream is) throws IOException
is
- IOException
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