Package org.forester.evoinference.matrix.character

Class BasicCharacterStateMatrix<S>

java.lang.Object

org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<S>

All Implemented Interfaces:

CharacterStateMatrix<S>

public class BasicCharacterStateMatrix<S>
extends java.lang.Object
implements CharacterStateMatrix<S>

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.evoinference.matrix.character.CharacterStateMatrix

CharacterStateMatrix.BinaryStates, CharacterStateMatrix.Format, CharacterStateMatrix.GainLossStates, CharacterStateMatrix.NucleotideStates

Constructor Summary

Constructors

Constructor	Description
BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters)
BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters, S default_state)
BasicCharacterStateMatrix(java.util.List<java.util.List<S>> states)
BasicCharacterStateMatrix(S[][] states)

Method Summary

Modifier and Type	Method	Description
boolean	containsCharacter(java.lang.String character)
boolean	containsIdentifier(java.lang.String identifier)
CharacterStateMatrix<S>	copy()
boolean	equals(java.lang.Object o)
java.lang.String	getCharacter(int character_index)
int	getCharacterIndex(java.lang.String character)
java.lang.String	getIdentifier(int identifier_index)
int	getIdentifierIndex(java.lang.String identifier)
int	getNumberOfCharacters()
int	getNumberOfIdentifiers()
S	getState(int identifier_index, int character_index)
S	getState(java.lang.String identifier, int character_index)
S	getState(java.lang.String identifier, java.lang.String character)
boolean	isEmpty()
CharacterStateMatrix<S>	pivot()
void	setCharacter(int character_index, java.lang.String character)
void	setIdentifier(int identifier_index, java.lang.String identifier)
void	setState(int identifier_index, int character_index, S state)
void	setState(java.lang.String identifier, int character_index, S state)
void	setState(java.lang.String identifier, java.lang.String character, S state)
void	toWriter(java.io.Writer writer)
void	toWriter(java.io.Writer writer, CharacterStateMatrix.Format format)
void	writeNexusBinaryChractersBlock(java.io.Writer w)
void	writeNexusCharstatelabels(java.io.Writer w)
void	writeNexusMatrix(java.io.Writer w)
void	writeNexusTaxaBlock(java.io.Writer w)

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BasicCharacterStateMatrix

public BasicCharacterStateMatrix(int number_of_identifiers,
                                 int number_of_characters)

BasicCharacterStateMatrix

public BasicCharacterStateMatrix(int number_of_identifiers,
                                 int number_of_characters,
                                 S default_state)

BasicCharacterStateMatrix

public BasicCharacterStateMatrix(java.util.List<java.util.List<S>> states)

BasicCharacterStateMatrix

public BasicCharacterStateMatrix(S[][] states)

Method Detail

containsCharacter

public boolean containsCharacter(java.lang.String character)

Specified by:

containsCharacter in interface CharacterStateMatrix<S>

containsIdentifier

public boolean containsIdentifier(java.lang.String identifier)

Specified by:

containsIdentifier in interface CharacterStateMatrix<S>

copy

public CharacterStateMatrix<S> copy()

Specified by:

copy in interface CharacterStateMatrix<S>

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

getCharacter

public java.lang.String getCharacter(int character_index)

Specified by:

getCharacter in interface CharacterStateMatrix<S>

getCharacterIndex

public int getCharacterIndex(java.lang.String character)

Specified by:

getCharacterIndex in interface CharacterStateMatrix<S>

getIdentifier

public java.lang.String getIdentifier(int identifier_index)

Specified by:

getIdentifier in interface CharacterStateMatrix<S>

getIdentifierIndex

public int getIdentifierIndex(java.lang.String identifier)

Specified by:

getIdentifierIndex in interface CharacterStateMatrix<S>

getNumberOfCharacters

public int getNumberOfCharacters()

Specified by:

getNumberOfCharacters in interface CharacterStateMatrix<S>

getNumberOfIdentifiers

public int getNumberOfIdentifiers()

Specified by:

getNumberOfIdentifiers in interface CharacterStateMatrix<S>

getState

public S getState(int identifier_index,
                  int character_index)

Specified by:

getState in interface CharacterStateMatrix<S>

getState

public S getState(java.lang.String identifier,
                  int character_index)

Specified by:

getState in interface CharacterStateMatrix<S>

getState

public S getState(java.lang.String identifier,
                  java.lang.String character)

Specified by:

getState in interface CharacterStateMatrix<S>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface CharacterStateMatrix<S>

pivot

public CharacterStateMatrix<S> pivot()

Specified by:

pivot in interface CharacterStateMatrix<S>

setCharacter

public void setCharacter(int character_index,
                         java.lang.String character)

Specified by:

setCharacter in interface CharacterStateMatrix<S>

setIdentifier

public void setIdentifier(int identifier_index,
                          java.lang.String identifier)

Specified by:

setIdentifier in interface CharacterStateMatrix<S>

setState

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

Specified by:

setState in interface CharacterStateMatrix<S>

setState

public void setState(java.lang.String identifier,
                     int character_index,
                     S state)

Specified by:

setState in interface CharacterStateMatrix<S>

setState

public void setState(java.lang.String identifier,
                     java.lang.String character,
                     S state)

Specified by:

setState in interface CharacterStateMatrix<S>

toWriter

public void toWriter(java.io.Writer writer)
              throws java.io.IOException

Specified by:

toWriter in interface CharacterStateMatrix<S>

Throws:

java.io.IOException

toWriter

public void toWriter(java.io.Writer writer,
                     CharacterStateMatrix.Format format)
              throws java.io.IOException

Specified by:

toWriter in interface CharacterStateMatrix<S>

Throws:

java.io.IOException

writeNexusBinaryChractersBlock

public void writeNexusBinaryChractersBlock(java.io.Writer w)
                                    throws java.io.IOException

Throws:

java.io.IOException

writeNexusCharstatelabels

public void writeNexusCharstatelabels(java.io.Writer w)
                               throws java.io.IOException

Throws:

java.io.IOException

writeNexusMatrix

public void writeNexusMatrix(java.io.Writer w)
                      throws java.io.IOException

Throws:

java.io.IOException

writeNexusTaxaBlock

public void writeNexusTaxaBlock(java.io.Writer w)
                         throws java.io.IOException

Throws:

java.io.IOException