CharacterStateMatrix<S>
public class BasicCharacterStateMatrix<S> extends java.lang.Object implements CharacterStateMatrix<S>
CharacterStateMatrix.BinaryStates, CharacterStateMatrix.Format, CharacterStateMatrix.GainLossStates, CharacterStateMatrix.NucleotideStates
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) |
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) |
public BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters)
public BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters, S default_state)
public BasicCharacterStateMatrix(java.util.List<java.util.List<S>> states)
public BasicCharacterStateMatrix(S[][] states)
public boolean containsCharacter(java.lang.String character)
containsCharacter
in interface CharacterStateMatrix<S>
public boolean containsIdentifier(java.lang.String identifier)
containsIdentifier
in interface CharacterStateMatrix<S>
public CharacterStateMatrix<S> copy()
copy
in interface CharacterStateMatrix<S>
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public java.lang.String getCharacter(int character_index)
getCharacter
in interface CharacterStateMatrix<S>
public int getCharacterIndex(java.lang.String character)
getCharacterIndex
in interface CharacterStateMatrix<S>
public java.lang.String getIdentifier(int identifier_index)
getIdentifier
in interface CharacterStateMatrix<S>
public int getIdentifierIndex(java.lang.String identifier)
getIdentifierIndex
in interface CharacterStateMatrix<S>
public int getNumberOfCharacters()
getNumberOfCharacters
in interface CharacterStateMatrix<S>
public int getNumberOfIdentifiers()
getNumberOfIdentifiers
in interface CharacterStateMatrix<S>
public S getState(int identifier_index, int character_index)
getState
in interface CharacterStateMatrix<S>
public S getState(java.lang.String identifier, int character_index)
getState
in interface CharacterStateMatrix<S>
public S getState(java.lang.String identifier, java.lang.String character)
getState
in interface CharacterStateMatrix<S>
public boolean isEmpty()
isEmpty
in interface CharacterStateMatrix<S>
public CharacterStateMatrix<S> pivot()
pivot
in interface CharacterStateMatrix<S>
public void setCharacter(int character_index, java.lang.String character)
setCharacter
in interface CharacterStateMatrix<S>
public void setIdentifier(int identifier_index, java.lang.String identifier)
setIdentifier
in interface CharacterStateMatrix<S>
public void setState(int identifier_index, int character_index, S state)
setState
in interface CharacterStateMatrix<S>
public void setState(java.lang.String identifier, int character_index, S state)
setState
in interface CharacterStateMatrix<S>
public void setState(java.lang.String identifier, java.lang.String character, S state)
setState
in interface CharacterStateMatrix<S>
public void toWriter(java.io.Writer writer) throws java.io.IOException
toWriter
in interface CharacterStateMatrix<S>
java.io.IOException
public void toWriter(java.io.Writer writer, CharacterStateMatrix.Format format) throws java.io.IOException
toWriter
in interface CharacterStateMatrix<S>
java.io.IOException
public void writeNexusBinaryChractersBlock(java.io.Writer w) throws java.io.IOException
java.io.IOException
public void writeNexusCharstatelabels(java.io.Writer w) throws java.io.IOException
java.io.IOException
public void writeNexusMatrix(java.io.Writer w) throws java.io.IOException
java.io.IOException
public void writeNexusTaxaBlock(java.io.Writer w) throws java.io.IOException
java.io.IOException