Interface CharacterStateMatrix<S>
-
- All Known Implementing Classes:
BasicCharacterStateMatrix
public interface CharacterStateMatrix<S>
-
-
Nested Class Summary
Nested Classes Modifier and Type Interface Description static classCharacterStateMatrix.BinaryStatesIt is crucial that the order ABSENT, UNKNOWN, PRESENT not be changes since this determines the sort order.static classCharacterStateMatrix.Formatstatic classCharacterStateMatrix.GainLossStatesstatic classCharacterStateMatrix.NucleotideStates
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description booleancontainsCharacter(java.lang.String character)booleancontainsIdentifier(java.lang.String identifier)CharacterStateMatrix<S>copy()java.lang.StringgetCharacter(int character_index)intgetCharacterIndex(java.lang.String character)java.lang.StringgetIdentifier(int identifier_index)intgetIdentifierIndex(java.lang.String identifier)intgetNumberOfCharacters()intgetNumberOfIdentifiers()SgetState(int identifier_index, int character_index)SgetState(java.lang.String identifier, int character_index)SgetState(java.lang.String identifier, java.lang.String character)booleanisEmpty()CharacterStateMatrix<S>pivot()voidsetCharacter(int character_index, java.lang.String character)voidsetIdentifier(int identifier_index, java.lang.String identifier)voidsetState(int identifier_index, int character_index, S state)voidsetState(java.lang.String identifier, int character_index, S state)voidsetState(java.lang.String identifier, java.lang.String character, S state)voidtoWriter(java.io.Writer writer)voidtoWriter(java.io.Writer writer, CharacterStateMatrix.Format format)
-
-
-
Method Detail
-
containsCharacter
boolean containsCharacter(java.lang.String character)
-
containsIdentifier
boolean containsIdentifier(java.lang.String identifier)
-
copy
CharacterStateMatrix<S> copy()
-
getCharacter
java.lang.String getCharacter(int character_index)
-
getCharacterIndex
int getCharacterIndex(java.lang.String character)
-
getIdentifier
java.lang.String getIdentifier(int identifier_index)
-
getIdentifierIndex
int getIdentifierIndex(java.lang.String identifier)
-
getNumberOfCharacters
int getNumberOfCharacters()
-
getNumberOfIdentifiers
int getNumberOfIdentifiers()
-
getState
S getState(int identifier_index, int character_index)
-
getState
S getState(java.lang.String identifier, int character_index)
-
getState
S getState(java.lang.String identifier, java.lang.String character)
-
isEmpty
boolean isEmpty()
-
pivot
CharacterStateMatrix<S> pivot()
-
setCharacter
void setCharacter(int character_index, java.lang.String character)
-
setIdentifier
void setIdentifier(int identifier_index, java.lang.String identifier)
-
setState
void setState(int identifier_index, int character_index, S state)
-
setState
void setState(java.lang.String identifier, int character_index, S state)
-
setState
void setState(java.lang.String identifier, java.lang.String character, S state)
-
toWriter
void toWriter(java.io.Writer writer) throws java.io.IOException- Throws:
java.io.IOException
-
toWriter
void toWriter(java.io.Writer writer, CharacterStateMatrix.Format format) throws java.io.IOException- Throws:
java.io.IOException
-
-