no.uio.labmed.biojava.alignment
Class SimpleAligner

java.lang.Object
  |
  +--no.uio.labmed.biojava.alignment.AbstractAligner
        |
        +--no.uio.labmed.biojava.alignment.SimpleAligner
All Implemented Interfaces:
AlignerInterface

public class SimpleAligner
extends AbstractAligner

Implementation of the Needleman-Wunsch and Smith-Waterman algorithm for sequence alignment.


Constructor Summary
SimpleAligner()
           
SimpleAligner(ScoreInterface _score)
           
 
Method Summary
 float align(org.biojava.bio.symbol.SymbolList a, org.biojava.bio.symbol.SymbolList b)
           
 void setLocalAlignment(boolean flag)
           
 void setPenalties(float gapOpen, float gapExt)
           
 void setRememberMatrix(boolean flag)
           
 void setScore(ScoreInterface _score)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SimpleAligner

public SimpleAligner()

SimpleAligner

public SimpleAligner(ScoreInterface _score)
Method Detail

align

public float align(org.biojava.bio.symbol.SymbolList a,
                   org.biojava.bio.symbol.SymbolList b)
Specified by:
align in interface AlignerInterface
Specified by:
align in class AbstractAligner

setScore

public void setScore(ScoreInterface _score)

setPenalties

public void setPenalties(float gapOpen,
                         float gapExt)

setLocalAlignment

public void setLocalAlignment(boolean flag)

setRememberMatrix

public void setRememberMatrix(boolean flag)