org.forester.development
Class BasicMsa
java.lang.Object
org.forester.development.BasicMsa
- All Implemented Interfaces:
- Msa
public class BasicMsa
- extends Object
- implements Msa
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BasicMsa
public BasicMsa()
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)