Interface CharacterStateMatrix<S>
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- All Known Implementing Classes:
BasicCharacterStateMatrix
public interface CharacterStateMatrix<S>
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Nested Class Summary
Nested Classes 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
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Method Summary
All Methods Instance Methods Abstract Methods 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)
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Method Detail
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containsCharacter
boolean containsCharacter(java.lang.String character)
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containsIdentifier
boolean containsIdentifier(java.lang.String identifier)
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copy
CharacterStateMatrix<S> copy()
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getCharacter
java.lang.String getCharacter(int character_index)
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getCharacterIndex
int getCharacterIndex(java.lang.String character)
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getIdentifier
java.lang.String getIdentifier(int identifier_index)
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getIdentifierIndex
int getIdentifierIndex(java.lang.String identifier)
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getNumberOfCharacters
int getNumberOfCharacters()
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getNumberOfIdentifiers
int getNumberOfIdentifiers()
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getState
S getState(int identifier_index, int character_index)
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getState
S getState(java.lang.String identifier, int character_index)
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getState
S getState(java.lang.String identifier, java.lang.String character)
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isEmpty
boolean isEmpty()
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pivot
CharacterStateMatrix<S> pivot()
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setCharacter
void setCharacter(int character_index, java.lang.String character)
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setIdentifier
void setIdentifier(int identifier_index, java.lang.String identifier)
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setState
void setState(int identifier_index, int character_index, S state)
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setState
void setState(java.lang.String identifier, int character_index, S state)
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setState
void setState(java.lang.String identifier, java.lang.String character, S state)
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toWriter
void toWriter(java.io.Writer writer) throws java.io.IOException
- Throws:
java.io.IOException
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toWriter
void toWriter(java.io.Writer writer, CharacterStateMatrix.Format format) throws java.io.IOException
- Throws:
java.io.IOException
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