Package org.forester.phylogeny.data

Class BinaryCharacters

java.lang.Object
org.forester.phylogeny.data.BinaryCharacters
All Implemented Interfaces:
PhylogenyData
public class BinaryCharacters extends Object implements PhylogenyData

  • Field Details

  • Constructor Details

  • Method Details

    • addGainedCharacter

      public void addGainedCharacter(String binary_character)

    • addLostCharacter

      public void addLostCharacter(String binary_character)

    • addPresentCharacter

      public void addPresentCharacter(String binary_character)

    • asSimpleText

      public StringBuffer asSimpleText()
      Specified by:
      asSimpleText in interface PhylogenyData

    • asText

      public 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 SortedSet<String> getGainedCharacters()

    • getGainedCharactersAsStringArray

      public String[] getGainedCharactersAsStringArray()

    • getGainedCharactersAsStringBuffer

      public StringBuffer getGainedCharactersAsStringBuffer()

    • getGainedCount

      public int getGainedCount()

    • getLostCharacters

      public SortedSet<String> getLostCharacters()

    • getLostCharactersAsStringArray

      public String[] getLostCharactersAsStringArray()

    • getLostCharactersAsStringBuffer

      public StringBuffer getLostCharactersAsStringBuffer()

    • getLostCount

      public int getLostCount()

    • getPresentCharacters

      public SortedSet<String> getPresentCharacters()

    • getPresentCharactersAsStringArray

      public String[] getPresentCharactersAsStringArray()

    • getPresentCharactersAsStringBuffer

      public StringBuffer getPresentCharactersAsStringBuffer()

    • getPresentCount

      public int getPresentCount()

    • getType

      public 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(String type)

    • toNHX

      public StringBuffer toNHX()
      Specified by:
      toNHX in interface PhylogenyData

    • toPhyloXML

      public void toPhyloXML(Writer writer, int level, String indentation) throws IOException
      Description copied from interface: PhylogenyData
      Writes a phyloXML representation of this phylogeny data.
      Specified by:
      toPhyloXML in interface PhylogenyData
      Throws:
      IOException

    • toString

      public String toString()
      Overrides:
      toString in class Object