Class BasicCharacterStateMatrix<S>
- java.lang.Object
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- org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<S>
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- All Implemented Interfaces:
CharacterStateMatrix<S>
public class BasicCharacterStateMatrix<S> extends java.lang.Object implements CharacterStateMatrix<S>
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.forester.evoinference.matrix.character.CharacterStateMatrix
CharacterStateMatrix.BinaryStates, CharacterStateMatrix.Format, CharacterStateMatrix.GainLossStates, CharacterStateMatrix.NucleotideStates
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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)
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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Constructor Detail
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BasicCharacterStateMatrix
public BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters)
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BasicCharacterStateMatrix
public BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters, S default_state)
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BasicCharacterStateMatrix
public BasicCharacterStateMatrix(java.util.List<java.util.List<S>> states)
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BasicCharacterStateMatrix
public BasicCharacterStateMatrix(S[][] states)
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Method Detail
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containsCharacter
public boolean containsCharacter(java.lang.String character)
- Specified by:
containsCharacter
in interfaceCharacterStateMatrix<S>
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containsIdentifier
public boolean containsIdentifier(java.lang.String identifier)
- Specified by:
containsIdentifier
in interfaceCharacterStateMatrix<S>
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copy
public CharacterStateMatrix<S> copy()
- Specified by:
copy
in interfaceCharacterStateMatrix<S>
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equals
public boolean equals(java.lang.Object o)
- Overrides:
equals
in classjava.lang.Object
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getCharacter
public java.lang.String getCharacter(int character_index)
- Specified by:
getCharacter
in interfaceCharacterStateMatrix<S>
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getCharacterIndex
public int getCharacterIndex(java.lang.String character)
- Specified by:
getCharacterIndex
in interfaceCharacterStateMatrix<S>
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getIdentifier
public java.lang.String getIdentifier(int identifier_index)
- Specified by:
getIdentifier
in interfaceCharacterStateMatrix<S>
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getIdentifierIndex
public int getIdentifierIndex(java.lang.String identifier)
- Specified by:
getIdentifierIndex
in interfaceCharacterStateMatrix<S>
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getNumberOfCharacters
public int getNumberOfCharacters()
- Specified by:
getNumberOfCharacters
in interfaceCharacterStateMatrix<S>
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getNumberOfIdentifiers
public int getNumberOfIdentifiers()
- Specified by:
getNumberOfIdentifiers
in interfaceCharacterStateMatrix<S>
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getState
public S getState(int identifier_index, int character_index)
- Specified by:
getState
in interfaceCharacterStateMatrix<S>
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getState
public S getState(java.lang.String identifier, int character_index)
- Specified by:
getState
in interfaceCharacterStateMatrix<S>
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getState
public S getState(java.lang.String identifier, java.lang.String character)
- Specified by:
getState
in interfaceCharacterStateMatrix<S>
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isEmpty
public boolean isEmpty()
- Specified by:
isEmpty
in interfaceCharacterStateMatrix<S>
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pivot
public CharacterStateMatrix<S> pivot()
- Specified by:
pivot
in interfaceCharacterStateMatrix<S>
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setCharacter
public void setCharacter(int character_index, java.lang.String character)
- Specified by:
setCharacter
in interfaceCharacterStateMatrix<S>
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setIdentifier
public void setIdentifier(int identifier_index, java.lang.String identifier)
- Specified by:
setIdentifier
in interfaceCharacterStateMatrix<S>
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setState
public void setState(int identifier_index, int character_index, S state)
- Specified by:
setState
in interfaceCharacterStateMatrix<S>
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setState
public void setState(java.lang.String identifier, int character_index, S state)
- Specified by:
setState
in interfaceCharacterStateMatrix<S>
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setState
public void setState(java.lang.String identifier, java.lang.String character, S state)
- Specified by:
setState
in interfaceCharacterStateMatrix<S>
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toWriter
public void toWriter(java.io.Writer writer) throws java.io.IOException
- Specified by:
toWriter
in interfaceCharacterStateMatrix<S>
- Throws:
java.io.IOException
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toWriter
public void toWriter(java.io.Writer writer, CharacterStateMatrix.Format format) throws java.io.IOException
- Specified by:
toWriter
in interfaceCharacterStateMatrix<S>
- Throws:
java.io.IOException
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writeNexusBinaryChractersBlock
public void writeNexusBinaryChractersBlock(java.io.Writer w) throws java.io.IOException
- Throws:
java.io.IOException
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writeNexusCharstatelabels
public void writeNexusCharstatelabels(java.io.Writer w) throws java.io.IOException
- Throws:
java.io.IOException
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writeNexusMatrix
public void writeNexusMatrix(java.io.Writer w) throws java.io.IOException
- Throws:
java.io.IOException
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writeNexusTaxaBlock
public void writeNexusTaxaBlock(java.io.Writer w) throws java.io.IOException
- Throws:
java.io.IOException
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