org.forester.development
Class BasicMsa

java.lang.Object
  extended by org.forester.development.BasicMsa
All Implemented Interfaces:
Msa

public class BasicMsa
extends Object
implements Msa


Constructor Summary
BasicMsa()
           
 
Method Summary
 void addSequence(Sequence sequence, boolean check_for_equal_length)
           
 Msa copy()
           
 Msa createSubAlignment(int[] sequences, int[] positions)
           
 int[] findSequence(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(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)