org.strbio.mol.lib
Class ScorePSIBlast

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

All Implemented Interfaces:

Description, ScoreFunction, ScoreSetup

public class ScorePSIBlast
extends java.lang.Object
implements ScoreFunction, ScoreSetup, Description

A scoring function that uses PSI-BLAST matrices.

  Version 1.1, 6/7/99 - moved to org.strbio.mol.lib
  Version 1.0, 1/28/99 - original version
  

Version:

1.1, 6/7/99

Author:

JMC

Constructor Summary

ScorePSIBlast()

Method Summary

void	describe(Printf outfile) This should print info about the object to an output file.
void	finished(Polymer p) This function is called when you are done using the function on a polymer.
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(ProfResPSI a, ProfResPSI b)
void	setup(Polymer p) This function is to set up the scoring function for use on a polymer.

Methods inherited from class java.lang.Object

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

Constructor Detail

ScorePSIBlast

public ScorePSIBlast()

Method Detail

score

public double score(ProfResPSI a,
                    ProfResPSI 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

setup

public void setup(Polymer p)

Description copied from interface: ScoreSetup

This function is to set up the scoring function for use on a polymer.

Specified by:

setup in interface ScoreSetup

finished

public void finished(Polymer p)

Description copied from interface: ScoreSetup

This function is called when you are done using the function on a polymer.

Specified by:

finished in interface ScoreSetup

describe

public void describe(Printf outfile)

Description copied from interface: Description

This should print info about the object to an output file.

Specified by:

describe in interface Description