Constructor Detail

• BasicGoTerm

  public BasicGoTerm​(GoId id,
                     java.lang.String name,
                     GoNameSpace namespace,
                     boolean is_obsolete)

• BasicGoTerm

  public BasicGoTerm​(java.lang.String id,
                     java.lang.String name,
                     java.lang.String namespace,
                     boolean is_obsolete)

Method Detail

• asSimpleText

  public java.lang.StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• asText

  public java.lang.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 java.lang.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​(java.lang.Object o)

  Return true if both GO id and namespace are equal.

  Overrides:

  equals in class java.lang.Object

• getAltIds

  public java.util.List<GoId> getAltIds()

  Specified by:

  getAltIds in interface GoTerm

• getComment

  public java.lang.String getComment()

  Specified by:

  getComment in interface GoTerm

• getDefinition

  public java.lang.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 java.util.List<GoRelationship> getGoRelationships()

  Specified by:

  getGoRelationships in interface GoTerm

• getGoSubsets

  public java.util.List<GoSubset> getGoSubsets()

  Specified by:

  getGoSubsets in interface GoTerm

• getGoXRefs

  public java.util.List<GoXRef> getGoXRefs()

  Specified by:

  getGoXRefs in interface GoTerm

• getName

  public java.lang.String getName()

  Specified by:

  getName in interface GoTerm

• getSuperGoIds

  public java.util.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 java.lang.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​(java.lang.String comment)

• setDefinition

  public void setDefinition​(java.lang.String definition)

• setGoSubsets

  public void setGoSubsets​(java.util.List<GoSubset> go_subsets)

• toNHX

  public java.lang.StringBuffer toNHX()

  Specified by:

  toNHX in interface PhylogenyData

• toPhyloXML

  public void toPhyloXML​(java.io.Writer writer,
                         int level,
                         java.lang.String indentation)
                  throws java.io.IOException

  Description copied from interface: PhylogenyData
  Writes a phyloXML representation of this phylogeny data.

  Specified by:

  toPhyloXML in interface PhylogenyData

  Throws:

  java.io.IOException

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object