Class BranchData

    • Constructor Detail

      • BranchData

        public BranchData()
    • Method Detail

      • addConfidence

        public void addConfidence​(Confidence confidence)
      • 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​(int index)
      • getConfidences

        public java.util.List<Confidence> getConfidences()
      • getNumberOfConfidences

        public int getNumberOfConfidences()
      • 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
      • isHasBranchColor

        public boolean isHasBranchColor()
      • isHasBranchWidth

        public boolean isHasBranchWidth()
      • isHasConfidences

        public boolean isHasConfidences()
      • setBranchColor

        public void setBranchColor​(BranchColor branch_color)
      • setBranchWidth

        public void setBranchWidth​(BranchWidth branch_width)
      • 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