org.forester.msa
Class BasicMsa

java.lang.Object
  org.forester.msa.BasicMsa

All Implemented Interfaces:

Msa

Direct Known Subclasses:

ResampleableMsa

public class BasicMsa
extends java.lang.Object
implements Msa

Constructor Summary

BasicMsa(int rows, int columns, Sequence.TYPE type)

Method Summary

static Msa	createInstance(java.util.List<Sequence> seqs)
java.util.List<java.lang.Character>	getColumnAt(int col)
java.lang.Object	getIdentifier(int row)
int	getLength()
int	getNumberOfSequences()
char	getResidueAt(int row, int col)
java.lang.StringBuffer	getSequenceAsString(int row)
Sequence.TYPE	getType()
void	setIdentifier(int row, java.lang.Object id)
void	setResidueAt(int row, int col, char residue)
java.lang.String	toString()
void	write(java.io.Writer w)

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,
                Sequence.TYPE type)

Method Detail

getIdentifier

public java.lang.Object 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

getSequenceAsString

public java.lang.StringBuffer getSequenceAsString(int row)

Specified by:

getSequenceAsString in interface Msa

getType

public Sequence.TYPE getType()

Specified by:

getType in interface Msa

setIdentifier

public void setIdentifier(int row,
                          java.lang.Object 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 java.lang.String toString()

Overrides:

toString in class java.lang.Object

write

public void write(java.io.Writer w)
           throws java.io.IOException

Specified by:

write in interface Msa

Throws:

java.io.IOException

createInstance

public static Msa createInstance(java.util.List<Sequence> seqs)

getColumnAt

public java.util.List<java.lang.Character> getColumnAt(int col)

Specified by:

getColumnAt in interface Msa