org.forester.phylogenyinference
Interface CharacterStateMatrix<S>

All Known Implementing Classes:
BasicCharacterStateMatrix

public interface CharacterStateMatrix<S>


Nested Class Summary
static class CharacterStateMatrix.BinaryStates
          It is crucial that the order ABSENT, UNKNOWN, PRESENT not be changes since this determines the sort order.
static class CharacterStateMatrix.Format
           
static class CharacterStateMatrix.GainLossStates
           
static class CharacterStateMatrix.NucleotideStates
           
 
Method Summary
 boolean containsCharacter(String character)
           
 boolean containsIdentifier(String identifier)
           
 CharacterStateMatrix<S> copy()
           
 String getCharacter(int character_index)
           
 int getCharacterIndex(String character)
           
 String getIdentifier(int identifier_index)
           
 int getIdentifierIndex(String identifier)
           
 int getNumberOfCharacters()
           
 int getNumberOfIdentifiers()
           
 S getState(int identifier_index, int character_index)
           
 S getState(String identifier, int character_index)
           
 S getState(String identifier, String character)
           
 boolean isEmpty()
           
 CharacterStateMatrix<S> pivot()
           
 void setCharacter(int character_index, String character)
           
 void setIdentifier(int identifier_index, String identifier)
           
 void setState(int identifier_index, int character_index, S state)
           
 void setState(String identifier, int character_index, S state)
           
 void setState(String identifier, String character, S state)
           
 void toWriter(Writer writer)
           
 void toWriter(Writer writer, CharacterStateMatrix.Format format)
           
 

Method Detail

containsCharacter

boolean containsCharacter(String character)

containsIdentifier

boolean containsIdentifier(String identifier)

copy

CharacterStateMatrix<S> copy()

getCharacter

String getCharacter(int character_index)

getCharacterIndex

int getCharacterIndex(String character)

getIdentifier

String getIdentifier(int identifier_index)

getIdentifierIndex

int getIdentifierIndex(String identifier)

getNumberOfCharacters

int getNumberOfCharacters()

getNumberOfIdentifiers

int getNumberOfIdentifiers()

getState

S getState(int identifier_index,
           int character_index)

getState

S getState(String identifier,
           int character_index)

getState

S getState(String identifier,
           String character)

isEmpty

boolean isEmpty()

pivot

CharacterStateMatrix<S> pivot()

setCharacter

void setCharacter(int character_index,
                  String character)

setIdentifier

void setIdentifier(int identifier_index,
                   String identifier)

setState

void setState(int identifier_index,
              int character_index,
              S state)

setState

void setState(String identifier,
              int character_index,
              S state)

setState

void setState(String identifier,
              String character,
              S state)

toWriter

void toWriter(Writer writer)
              throws IOException
Throws:
IOException

toWriter

void toWriter(Writer writer,
              CharacterStateMatrix.Format format)
              throws IOException
Throws:
IOException