org.forester.development

Class BasicMsa

java.lang.Object

org.forester.development.BasicMsa

All Implemented Interfaces:

Msa

public class BasicMsa
extends java.lang.Object
implements Msa

Constructor Summary

Constructors

Constructor and Description
BasicMsa()

Method Summary

Methods

Modifier and Type	Method and Description
void	addSequence(Sequence sequence, boolean check_for_equal_length)
Msa	copy()
Msa	createSubAlignment(int[] sequences, int[] positions)
int[]	findSequence(java.lang.String name, boolean case_sensitive, boolean partial_match)
int	getLength()
int	getNumberOfSequences()
char	getResidueAt(int col, int row)
Sequence	getSequence(int i)
boolean	isAppearsAligned()
boolean	isEmpty()
void	removeSequence(int i)

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicMsa

public BasicMsa()

Method Detail

addSequence

public void addSequence(Sequence sequence,
               boolean check_for_equal_length)

copy

public Msa copy()

createSubAlignment

public Msa createSubAlignment(int[] sequences,
                     int[] positions)

findSequence

public int[] findSequence(java.lang.String name,
                 boolean case_sensitive,
                 boolean partial_match)

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

getSequence

public Sequence getSequence(int i)

Specified by:

getSequence in interface Msa

isAppearsAligned

public boolean isAppearsAligned()

isEmpty

public boolean isEmpty()

removeSequence

public void removeSequence(int i)