java.lang.Comparable<GoTerm>
, GoTerm
, PhylogenyData
public class BasicGoTerm extends java.lang.Object implements GoTerm
Constructor | Description |
---|---|
BasicGoTerm(java.lang.String id,
java.lang.String name,
java.lang.String namespace,
boolean is_obsolete) |
|
BasicGoTerm(GoId id,
java.lang.String name,
GoNameSpace namespace,
boolean is_obsolete) |
Modifier and Type | Method | Description |
---|---|---|
java.lang.StringBuffer |
asSimpleText() |
|
java.lang.StringBuffer |
asText() |
|
int |
compareTo(GoTerm go_term) |
Compares based on GO id.
|
PhylogenyData |
copy() |
Makes a shallow copy.
|
boolean |
equals(java.lang.Object o) |
Return true if both GO id and namespace are equal.
|
java.util.List<GoId> |
getAltIds() |
|
java.lang.String |
getComment() |
|
java.lang.String |
getDefinition() |
|
GoId |
getGoId() |
|
GoNameSpace |
getGoNameSpace() |
|
java.util.List<GoRelationship> |
getGoRelationships() |
|
java.util.List<GoSubset> |
getGoSubsets() |
|
java.util.List<GoXRef> |
getGoXRefs() |
|
java.lang.String |
getName() |
|
java.util.List<GoId> |
getSuperGoIds() |
|
int |
hashCode() |
Hashcode is based on hashcode of GO id.
|
boolean |
isEqual(PhylogenyData go_term) |
Compares this PhylogenyData to PhylogenyData data.
|
boolean |
isObsolete() |
|
void |
setComment(java.lang.String comment) |
|
void |
setDefinition(java.lang.String definition) |
|
void |
setGoSubsets(java.util.List<GoSubset> go_subsets) |
|
java.lang.StringBuffer |
toNHX() |
|
void |
toPhyloXML(java.io.Writer writer,
int level,
java.lang.String indentation) |
Writes a phyloXML representation of this phylogeny data.
|
java.lang.String |
toString() |
public BasicGoTerm(GoId id, java.lang.String name, GoNameSpace namespace, boolean is_obsolete)
public BasicGoTerm(java.lang.String id, java.lang.String name, java.lang.String namespace, boolean is_obsolete)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public int compareTo(GoTerm go_term)
compareTo
in interface java.lang.Comparable<GoTerm>
public PhylogenyData copy()
copy
in interface PhylogenyData
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public java.lang.String getComment()
getComment
in interface GoTerm
public java.lang.String getDefinition()
getDefinition
in interface GoTerm
public GoNameSpace getGoNameSpace()
getGoNameSpace
in interface GoTerm
public java.util.List<GoRelationship> getGoRelationships()
getGoRelationships
in interface GoTerm
public java.util.List<GoSubset> getGoSubsets()
getGoSubsets
in interface GoTerm
public java.util.List<GoXRef> getGoXRefs()
getGoXRefs
in interface GoTerm
public java.util.List<GoId> getSuperGoIds()
getSuperGoIds
in interface GoTerm
public int hashCode()
hashCode
in class java.lang.Object
public boolean isEqual(PhylogenyData go_term)
PhylogenyData
isEqual
in interface PhylogenyData
public boolean isObsolete()
isObsolete
in interface GoTerm
public void setComment(java.lang.String comment)
public void setDefinition(java.lang.String definition)
public void setGoSubsets(java.util.List<GoSubset> go_subsets)
public java.lang.StringBuffer toNHX()
toNHX
in interface PhylogenyData
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
java.io.IOException
public java.lang.String toString()
toString
in class java.lang.Object