java.lang.Object

org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<S>

All Implemented Interfaces:: CharacterStateMatrix<S>

public class BasicCharacterStateMatrix<S> extends Object implements CharacterStateMatrix<S>

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.evoinference.matrix.character.CharacterStateMatrix
CharacterStateMatrix.BinaryStates, CharacterStateMatrix.Format, CharacterStateMatrix.GainLossStates, CharacterStateMatrix.NucleotideStates
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(List<List<S>> states)

BasicCharacterStateMatrix(S[][] states)
Method Summary

Modifier and Type

Method

Description

boolean

containsCharacter(String character)

boolean

containsIdentifier(String identifier)

CharacterStateMatrix<S>

copy()

boolean

equals(Object o)

String

getCharacter(int character_index)

int

getCharacterIndex(String character)

String

getIdentifier(int identifier_index)

int

getIdentifierIndex(String identifier)

int

getNumberOfCharacters()

int

getNumberOfIdentifiers()

S

getState(int identifier_index, int character_index)

S

getState(String identifier, int character_index)

S

getState(String identifier, String character)

boolean

isEmpty()

CharacterStateMatrix<S>

pivot()

void

setCharacter(int character_index, String character)

void

setIdentifier(int identifier_index, String identifier)

void

setState(int identifier_index, int character_index, S state)

void

setState(String identifier, int character_index, S state)

void

setState(String identifier, String character, S state)

void

toWriter(Writer writer)

void

toWriter(Writer writer, CharacterStateMatrix.Format format)

void

writeNexusBinaryChractersBlock(Writer w)

void

writeNexusCharstatelabels(Writer w)

void

writeNexusMatrix(Writer w)

void

writeNexusTaxaBlock(Writer w)

Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- BasicCharacterStateMatrix
  
  public BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters)
- BasicCharacterStateMatrix
  
  public BasicCharacterStateMatrix(int number_of_identifiers, int number_of_characters, S default_state)
- BasicCharacterStateMatrix
  
  public BasicCharacterStateMatrix(List<List<S>> states)
- BasicCharacterStateMatrix
  
  public BasicCharacterStateMatrix(S[][] states)
Method Details
- containsCharacter
  
  public boolean containsCharacter(String character)
  
  Specified by:
  
  containsCharacter in interface CharacterStateMatrix<S>
- containsIdentifier
  
  public boolean containsIdentifier(String identifier)
  
  Specified by:
  
  containsIdentifier in interface CharacterStateMatrix<S>
- copy
  
  public CharacterStateMatrix<S> copy()
  
  Specified by:
  
  copy in interface CharacterStateMatrix<S>
- equals
  
  public boolean equals(Object o)
  
  Overrides:
  
  equals in class Object
- getCharacter
  
  public String getCharacter(int character_index)
  
  Specified by:
  
  getCharacter in interface CharacterStateMatrix<S>
- getCharacterIndex
  
  public int getCharacterIndex(String character)
  
  Specified by:
  
  getCharacterIndex in interface CharacterStateMatrix<S>
- getIdentifier
  
  public String getIdentifier(int identifier_index)
  
  Specified by:
  
  getIdentifier in interface CharacterStateMatrix<S>
- getIdentifierIndex
  
  public int getIdentifierIndex(String identifier)
  
  Specified by:
  
  getIdentifierIndex in interface CharacterStateMatrix<S>
- getNumberOfCharacters
  
  public int getNumberOfCharacters()
  
  Specified by:
  
  getNumberOfCharacters in interface CharacterStateMatrix<S>
- getNumberOfIdentifiers
  
  public int getNumberOfIdentifiers()
  
  Specified by:
  
  getNumberOfIdentifiers in interface CharacterStateMatrix<S>
- getState
  
  public S getState(int identifier_index, int character_index)
  
  Specified by:
  
  getState in interface CharacterStateMatrix<S>
- getState
  
  public S getState(String identifier, int character_index)
  
  Specified by:
  
  getState in interface CharacterStateMatrix<S>
- getState
  
  public S getState(String identifier, String character)
  
  Specified by:
  
  getState in interface CharacterStateMatrix<S>
- isEmpty
  
  public boolean isEmpty()
  
  Specified by:
  
  isEmpty in interface CharacterStateMatrix<S>
- pivot
  
  public CharacterStateMatrix<S> pivot()
  
  Specified by:
  
  pivot in interface CharacterStateMatrix<S>
- setCharacter
  
  public void setCharacter(int character_index, String character)
  
  Specified by:
  
  setCharacter in interface CharacterStateMatrix<S>
- setIdentifier
  
  public void setIdentifier(int identifier_index, String identifier)
  
  Specified by:
  
  setIdentifier in interface CharacterStateMatrix<S>
- setState
  
  public void setState(int identifier_index, int character_index, S state)
  
  Specified by:
  
  setState in interface CharacterStateMatrix<S>
- setState
  
  public void setState(String identifier, int character_index, S state)
  
  Specified by:
  
  setState in interface CharacterStateMatrix<S>
- setState
  
  public void setState(String identifier, String character, S state)
  
  Specified by:
  
  setState in interface CharacterStateMatrix<S>
- toWriter
  
  public void toWriter(Writer writer) throws IOException
  
  Specified by:
  
  toWriter in interface CharacterStateMatrix<S>
  
  Throws:
  
  IOException
- toWriter
  
  public void toWriter(Writer writer, CharacterStateMatrix.Format format) throws IOException
  
  Specified by:
  
  toWriter in interface CharacterStateMatrix<S>
  
  Throws:
  
  IOException
- writeNexusBinaryChractersBlock
  
  public void writeNexusBinaryChractersBlock(Writer w) throws IOException
  
  Throws:
  
  IOException
- writeNexusCharstatelabels
  
  public void writeNexusCharstatelabels(Writer w) throws IOException
  
  Throws:
  
  IOException
- writeNexusMatrix
  
  public void writeNexusMatrix(Writer w) throws IOException
  
  Throws:
  
  IOException
- writeNexusTaxaBlock
  
  public void writeNexusTaxaBlock(Writer w) throws IOException
  
  Throws:
  
  IOException

Class BasicCharacterStateMatrix<S>

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.evoinference.matrix.character.CharacterStateMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

BasicCharacterStateMatrix

BasicCharacterStateMatrix

BasicCharacterStateMatrix

BasicCharacterStateMatrix

Method Details

containsCharacter

containsIdentifier

copy

equals

getCharacter

getCharacterIndex

getIdentifier

getIdentifierIndex

getNumberOfCharacters

getNumberOfIdentifiers

getState

getState

getState

isEmpty

pivot

setCharacter

setIdentifier

setState

setState

setState

toWriter

toWriter

writeNexusBinaryChractersBlock

writeNexusCharstatelabels

writeNexusMatrix

writeNexusTaxaBlock