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

Description

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

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

Modifier and Type

Method

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 Details
- 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 Details
- 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

Class BasicGoTerm

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

BasicGoTerm

BasicGoTerm

Method Details

asSimpleText

asText

compareTo

copy

equals

getAltIds

getComment

getDefinition

getGoId

getGoNameSpace

getGoRelationships

getGoSubsets

getGoXRefs

getName

getSuperGoIds

hashCode

isEqual

isObsolete

setComment

setDefinition

setGoSubsets

toNHX

toPhyloXML

toString