Class SequenceRelation

    • Field Detail

      • SEQUENCE_RELATION_TYPE_ORTHOLOGY

        public static final java.lang.String SEQUENCE_RELATION_TYPE_ORTHOLOGY
        See Also:
        Constant Field Values
      • SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY

        public static final java.lang.String SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY
        See Also:
        Constant Field Values
      • SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY

        public static final java.lang.String SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY
        See Also:
        Constant Field Values
      • SEQUENCE_RELATION_TYPE_PARALOGY

        public static final java.lang.String SEQUENCE_RELATION_TYPE_PARALOGY
        See Also:
        Constant Field Values
      • SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY

        public static final java.lang.String SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY
        See Also:
        Constant Field Values
      • SEQUENCE_RELATION_TYPE_XENOLOGY

        public static final java.lang.String SEQUENCE_RELATION_TYPE_XENOLOGY
        See Also:
        Constant Field Values
      • SEQUENCE_RELATION_TYPE_UNKNOWN

        public static final java.lang.String SEQUENCE_RELATION_TYPE_UNKNOWN
        See Also:
        Constant Field Values
      • SEQUENCE_RELATION_TYPE_OTHER

        public static final java.lang.String SEQUENCE_RELATION_TYPE_OTHER
        See Also:
        Constant Field Values
    • Constructor Detail

      • SequenceRelation

        public SequenceRelation()
    • Method Detail

      • asText

        public java.lang.StringBuffer asText()
        Specified by:
        asText in interface PhylogenyData
      • copy

        public PhylogenyData copy()
        Description copied from interface: PhylogenyData
        Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.
        Specified by:
        copy in interface PhylogenyData
        Returns:
        a ~deep~ copy of this PhylogenyData
      • getConfidence

        public Confidence getConfidence()
      • getDistance

        public java.lang.Double getDistance()
      • isEqual

        public boolean isEqual​(PhylogenyData data)
        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
      • setConfidence

        public void setConfidence​(Confidence confidence)
      • setDistance

        public void setDistance​(java.lang.Double distance)
      • setRef0

        public void setRef0​(Sequence ref0)
      • setRef1

        public void setRef1​(Sequence ref1)
      • 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