Class BasicGoTerm

    • 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

      • 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
      • getName

        public java.lang.String getName()
        Specified by:
        getName 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