BasicCharacterStateMatrix
public interface CharacterStateMatrix<S>
Modifier and Type | Interface | 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 |
Modifier and Type | Method | Description |
---|---|---|
boolean |
containsCharacter(java.lang.String character) |
|
boolean |
containsIdentifier(java.lang.String identifier) |
|
CharacterStateMatrix<S> |
copy() |
|
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) |
boolean containsCharacter(java.lang.String character)
boolean containsIdentifier(java.lang.String identifier)
CharacterStateMatrix<S> copy()
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) throws java.io.IOException
java.io.IOException
void toWriter(java.io.Writer writer, CharacterStateMatrix.Format format) throws java.io.IOException
java.io.IOException