org.forester.go

Class BasicGoTerm

java.lang.Object

org.forester.go.BasicGoTerm

All Implemented Interfaces:

Comparable<GoTerm>, GoTerm, PhylogenyData

public class BasicGoTerm
extends Object
implements GoTerm

Constructor Summary

Constructors

Constructor and Description
BasicGoTerm(GoId id, String name, GoNameSpace namespace, boolean is_obsolete)
BasicGoTerm(String id, String name, String namespace, boolean is_obsolete)

Method Summary

Modifier and Type	Method and Description
StringBuffer	asSimpleText()
StringBuffer	asText()
int	compareTo(GoTerm go_term) Compares based on GO id.
PhylogenyData	copy() Makes a shallow copy.
boolean	equals(Object o) Return true if both GO id and namespace are equal.
List<GoId>	getAltIds()
String	getComment()
String	getDefinition()
GoId	getGoId()
GoNameSpace	getGoNameSpace()
List<GoRelationship>	getGoRelationships()
List<GoSubset>	getGoSubsets()
List<GoXRef>	getGoXRefs()
String	getName()
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(String comment)
void	setDefinition(String definition)
void	setGoSubsets(List<GoSubset> go_subsets)
StringBuffer	toNHX()
void	toPhyloXML(Writer writer, int level, String indentation) Writes a phyloXML representation of this phylogeny data.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BasicGoTerm

public BasicGoTerm(GoId id,
                   String name,
                   GoNameSpace namespace,
                   boolean is_obsolete)

BasicGoTerm

public BasicGoTerm(String id,
                   String name,
                   String namespace,
                   boolean is_obsolete)

Method Detail

asSimpleText

public StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public StringBuffer asText()

Specified by:

asText in interface PhylogenyData

compareTo

public int compareTo(GoTerm go_term)

Compares based on GO id.

Specified by:

compareTo in interface Comparable<GoTerm>

copy

public PhylogenyData copy()

Makes a shallow copy.

Specified by:

copy in interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

equals

public boolean equals(Object o)

Return true if both GO id and namespace are equal.

Overrides:

equals in class Object

getAltIds

public List<GoId> getAltIds()

Specified by:

getAltIds in interface GoTerm

getComment

public String getComment()

Specified by:

getComment in interface GoTerm

getDefinition

public String getDefinition()

Specified by:

getDefinition in interface GoTerm

getGoId

public GoId getGoId()

Specified by:

getGoId in interface GoTerm

getGoNameSpace

public GoNameSpace getGoNameSpace()

Specified by:

getGoNameSpace in interface GoTerm

getGoRelationships

public List<GoRelationship> getGoRelationships()

Specified by:

getGoRelationships in interface GoTerm

getGoSubsets

public List<GoSubset> getGoSubsets()

Specified by:

getGoSubsets in interface GoTerm

getGoXRefs

public List<GoXRef> getGoXRefs()

Specified by:

getGoXRefs in interface GoTerm

getName

public String getName()

Specified by:

getName in interface GoTerm

getSuperGoIds

public List<GoId> getSuperGoIds()

Specified by:

getSuperGoIds in interface GoTerm

hashCode

public int hashCode()

Hashcode is based on hashcode of GO id.

Overrides:

hashCode in class Object

isEqual

public boolean isEqual(PhylogenyData go_term)

Description copied from interface: PhylogenyData

Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.

Specified by:

isEqual in interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

isObsolete

public boolean isObsolete()

Specified by:

isObsolete in interface GoTerm

setComment

public void setComment(String comment)

setDefinition

public void setDefinition(String definition)

setGoSubsets

public void setGoSubsets(List<GoSubset> go_subsets)

toNHX

public StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(Writer writer,
                       int level,
                       String indentation)
                throws IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object