net.sourceforge.cilib.bioinf.sequencealignment
Class BLOSUM62SoP
java.lang.Object
net.sourceforge.cilib.bioinf.sequencealignment.BLOSUM62SoP
- All Implemented Interfaces:
- ScoringMethod
public class BLOSUM62SoP
- extends Object
- implements ScoringMethod
This class implements the Sum Of Pairs scoring function that uses the BLOSUM62 substitutions matrices
that give scores for proteins in a biologically meaningful manner.
SoP routine has been optimized for speed.
- Author:
- Fabien Zablocki
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BLOSUM62SoP
public BLOSUM62SoP()
setVerbose
public void setVerbose(boolean verbose)
setWeight
public void setWeight(boolean weight)
getScore
public double getScore(ArrayList<String> alignment)
- Specified by:
getScore
in interface ScoringMethod
Copyright © 2009 CIRG. All Rights Reserved.