org.strbio.mol.lib
Class ScoreBlosum62

java.lang.Object
  org.strbio.mol.lib.ScoreBlosum62

All Implemented Interfaces:

ScoreFunction

public class ScoreBlosum62
extends java.lang.Object
implements ScoreFunction

A scoring function that uses the default Blosum62 matrix

  Version 1.0, 1/28/99 - original version
  

Version:

1.0, 1/28/99

Author:

JMC

Constructor Summary

ScoreBlosum62()

Method Summary

double	score(Monomer a, Monomer b) This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad.
double	score(Residue a, Residue b)

Methods inherited from class java.lang.Object

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

Constructor Detail

ScoreBlosum62

public ScoreBlosum62()

Method Detail

score

public double score(Residue a,
                    Residue b)

score

public double score(Monomer a,
                    Monomer b)

Description copied from interface: ScoreFunction

This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad. If this is not the case, be sure to comment it as such! If monomer order matters to your scoring function, the first monomer should be from the sequence (unknown structure), and the second monomer should be from the fold (known structure).

Specified by:

score in interface ScoreFunction