public class GeneSet extends Object
Constructor and Description |
---|
GeneSet() |
GeneSet(GeneSetTerm name) |
GeneSet(GeneSetTerm name,
Collection<Gene> items) |
Modifier and Type | Method and Description |
---|---|
void |
addGene(Gene g)
Add the gene (and its probes)
|
void |
addGenes(Collection<Gene> gs) |
void |
addRedundantGroup(GeneSet redundant) |
void |
clearGenes() |
void |
clearRedundancy() |
void |
clearRedundancy(GeneSet toclear) |
boolean |
equals(Object obj) |
UserDefinedGeneSetManager.GeneSetFileFormat |
getFormat() |
Set<Gene> |
getGenes()
Do not modify this collection directly! Use 'addGene'.
|
String |
getId() |
String |
getName() |
Set<Probe> |
getProbes() |
Set<GeneSet> |
getRedundantGroups()
Can not modify this collection directly; use addRedundantGroup instead.
|
String |
getSourceFile() |
GeneSetTerm |
getTerm() |
int |
hashCode() |
boolean |
hasRedundancy() |
boolean |
isGenes() |
boolean |
isUserDefined() |
void |
setFormat(UserDefinedGeneSetManager.GeneSetFileFormat f) |
void |
setGenes(boolean isGenes) |
void |
setGenes(Collection<Gene> genes) |
void |
setIsGenes(boolean isGenes) |
void |
setRedundantGroups(Set<GeneSet> redundantGroups) |
void |
setSourceFile(String fileName) |
void |
setTerm(GeneSetTerm name) |
void |
setUserDefined(boolean isUserDefined) |
int |
size() |
String |
toString() |
public GeneSet()
public GeneSet(GeneSetTerm name)
name
- public GeneSet(GeneSetTerm name, Collection<Gene> items)
name
- items
- public void addGene(Gene g)
g
- public void addGenes(Collection<Gene> gs)
public void addRedundantGroup(GeneSet redundant)
public void clearGenes()
public void clearRedundancy()
public void clearRedundancy(GeneSet toclear)
public UserDefinedGeneSetManager.GeneSetFileFormat getFormat()
public Set<Gene> getGenes()
public String getId()
public String getName()
public Set<GeneSet> getRedundantGroups()
public String getSourceFile()
public GeneSetTerm getTerm()
public boolean hasRedundancy()
public boolean isGenes()
public boolean isUserDefined()
public void setFormat(UserDefinedGeneSetManager.GeneSetFileFormat f)
public void setGenes(boolean isGenes)
public void setGenes(Collection<Gene> genes)
public void setIsGenes(boolean isGenes)
public void setSourceFile(String fileName)
public void setTerm(GeneSetTerm name)
name
- The name to set.public void setUserDefined(boolean isUserDefined)
public int size()
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