Field Detail

• COUNT_DEFAULT

  public static final int COUNT_DEFAULT

  See Also:

  Constant Field Values

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)

• asSimpleText

  public java.lang.StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• 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