org.forester.evoinference.matrix.character

Interface CharacterStateMatrix<S>

All Known Implementing Classes:

BasicCharacterStateMatrix

public interface CharacterStateMatrix<S>

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
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

Modifier and Type	Method and Description
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