org.forester.development

Class SimpleMutableMsa

java.lang.Object

org.forester.development.SimpleMutableMsa

All Implemented Interfaces:

Msa

public class SimpleMutableMsa
extends java.lang.Object
implements Msa

Constructor Summary

Constructors

Constructor and Description
SimpleMutableMsa(java.lang.String[] names, java.lang.String[] seqs)

Method Summary

Methods

Modifier and Type	Method and Description
void	deleteResidueAt(int col, int row)
double	getGapScore()
int	getLength()
int	getNumberOfSequences()
char	getResidueAt(int col, int row)
double	getScore()
Sequence	getSequence(int i)
void	insertResidueAt(int col, int row)

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleMutableMsa

public SimpleMutableMsa(java.lang.String[] names,
                java.lang.String[] seqs)

Method Detail

deleteResidueAt

public void deleteResidueAt(int col,
                   int row)

getGapScore

public double getGapScore()

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 col,
                int row)

Specified by:

getResidueAt in interface Msa

getScore

public double getScore()

getSequence

public Sequence getSequence(int i)

Specified by:

getSequence in interface Msa

insertResidueAt

public void insertResidueAt(int col,
                   int row)