org.forester.msa

Class BasicMsa

java.lang.Object

org.forester.msa.BasicMsa

All Implemented Interfaces:

Msa

Direct Known Subclasses:

DeleteableMsa, ResampleableMsa

public class BasicMsa
extends Object
implements Msa

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.msa.Msa

Msa.MSA_FORMAT

Constructor Summary

Constructors

Constructor and Description
BasicMsa(int rows, int columns, MolecularSequence.TYPE type)

Method Summary

Modifier and Type	Method and Description
List<MolecularSequence>	asSequenceList()
static Msa	createInstance(List<MolecularSequence> seqs)
List<Character>	getColumnAt(int col)
String	getIdentifier(int row)
int	getLength()
int	getNumberOfSequences()
char	getResidueAt(int row, int col)
MolecularSequence	getSequence(int row)
MolecularSequence	getSequence(String id)
StringBuffer	getSequenceAsString(int row)
MolecularSequence.TYPE	getType()
boolean	isGapAt(int row, int col)
void	setIdentifier(int row, String id)
void	setResidueAt(int row, int col, char residue)
String	toString()
void	write(Writer w, Msa.MSA_FORMAT format)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BasicMsa

public BasicMsa(int rows,
                int columns,
                MolecularSequence.TYPE type)

Method Detail

asSequenceList

public List<MolecularSequence> asSequenceList()

Specified by:

asSequenceList in interface Msa

getColumnAt

public List<Character> getColumnAt(int col)

Specified by:

getColumnAt in interface Msa

getIdentifier

public String getIdentifier(int row)

Specified by:

getIdentifier in interface Msa

getLength

public int getLength()

Specified by:

getLength in interface Msa

getNumberOfSequences

public int getNumberOfSequences()

Specified by:

getNumberOfSequences in interface Msa

getResidueAt

public char getResidueAt(int row,
                         int col)

Specified by:

getResidueAt in interface Msa

getSequence

public MolecularSequence getSequence(int row)

Specified by:

getSequence in interface Msa

getSequence

public MolecularSequence getSequence(String id)

Specified by:

getSequence in interface Msa

getSequenceAsString

public StringBuffer getSequenceAsString(int row)

Specified by:

getSequenceAsString in interface Msa

getType

public MolecularSequence.TYPE getType()

Specified by:

getType in interface Msa

isGapAt

public boolean isGapAt(int row,
                       int col)

Specified by:

isGapAt in interface Msa

setIdentifier

public void setIdentifier(int row,
                          String id)

Specified by:

setIdentifier in interface Msa

setResidueAt

public void setResidueAt(int row,
                         int col,
                         char residue)

Specified by:

setResidueAt in interface Msa

toString

public String toString()

Overrides:

toString in class Object

write

public void write(Writer w,
                  Msa.MSA_FORMAT format)
           throws IOException

Specified by:

write in interface Msa

Throws:

IOException

createInstance

public static Msa createInstance(List<MolecularSequence> seqs)