net.sourceforge.cilib.bioinf.sequencealignment
Class Similarity

java.lang.Object
  net.sourceforge.cilib.bioinf.sequencealignment.Similarity

All Implemented Interfaces:

ScoringMethod

public class Similarity
extends Object
implements ScoringMethod

SIMILARITY SCORING FUNCTION Score all possible pairwise combinations in column Requires (N * (N-1))/2 comparisons for N sequences Total score = sum of score for each column SoP routine has been optimized for speed. SHOULD BE USED WITHOUT ADDED GAP PENALTY METHOD (weight2 = 0) BECAUSE IT ALREADY HAS A GAP PENALTY OR SET THE GAP_PENALTY TO 0 and use a gap penalty method

Author:

fzablocki

Constructor Summary

Similarity()

Method Summary

double	getScore(ArrayList<String> alignment)
void	setGapPenalty(int gapPenalty)
void	setMatch(int match)
void	setMismatch(int mismatch)
void	setVerbose(boolean verbose)
void	setWeight(boolean weight)

Methods inherited from class java.lang.Object

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

Constructor Detail

Similarity

public Similarity()

Method Detail

setWeight

public void setWeight(boolean weight)

setVerbose

public void setVerbose(boolean verbose)

setMatch

public void setMatch(int match)

setMismatch

public void setMismatch(int mismatch)

setGapPenalty

public void setGapPenalty(int gapPenalty)

getScore

public double getScore(ArrayList<String> alignment)

Specified by:

getScore in interface ScoringMethod