org.forester.phylogenyinference
Class BasicCharacterStateMatrix<S>

java.lang.Object
  extended by org.forester.phylogenyinference.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.phylogenyinference.CharacterStateMatrix
CharacterStateMatrix.BinaryStates, CharacterStateMatrix.Format, CharacterStateMatrix.GainLossStates, CharacterStateMatrix.NucleotideStates
 
Constructor Summary
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
 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 Detail

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 Detail

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