Class BinaryCharacters

    • Constructor Detail

      • BinaryCharacters

        public BinaryCharacters()
      • BinaryCharacters

        public BinaryCharacters​(java.util.SortedSet<java.lang.String> present_characters,
                                java.util.SortedSet<java.lang.String> gained_characters,
                                java.util.SortedSet<java.lang.String> lost_characters,
                                java.lang.String type)
      • BinaryCharacters

        public BinaryCharacters​(java.util.SortedSet<java.lang.String> present_characters,
                                java.util.SortedSet<java.lang.String> gained_characters,
                                java.util.SortedSet<java.lang.String> lost_characters,
                                java.lang.String type,
                                int present_count,
                                int gained_count,
                                int lost_count)
    • Method Detail

      • addGainedCharacter

        public void addGainedCharacter​(java.lang.String binary_character)
      • addLostCharacter

        public void addLostCharacter​(java.lang.String binary_character)
      • addPresentCharacter

        public void addPresentCharacter​(java.lang.String binary_character)
      • 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
      • getGainedCharacters

        public java.util.SortedSet<java.lang.String> getGainedCharacters()
      • getGainedCharactersAsStringArray

        public java.lang.String[] getGainedCharactersAsStringArray()
      • getGainedCharactersAsStringBuffer

        public java.lang.StringBuffer getGainedCharactersAsStringBuffer()
      • getGainedCount

        public int getGainedCount()
      • getLostCharacters

        public java.util.SortedSet<java.lang.String> getLostCharacters()
      • getLostCharactersAsStringArray

        public java.lang.String[] getLostCharactersAsStringArray()
      • getLostCharactersAsStringBuffer

        public java.lang.StringBuffer getLostCharactersAsStringBuffer()
      • getLostCount

        public int getLostCount()
      • getPresentCharacters

        public java.util.SortedSet<java.lang.String> getPresentCharacters()
      • getPresentCharactersAsStringArray

        public java.lang.String[] getPresentCharactersAsStringArray()
      • getPresentCharactersAsStringBuffer

        public java.lang.StringBuffer getPresentCharactersAsStringBuffer()
      • getPresentCount

        public int getPresentCount()
      • getType

        public java.lang.String getType()
      • 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
      • setType

        public void setType​(java.lang.String type)
      • 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