org.strbio.mol.lib
Class ScoreJDB10

java.lang.Object
  org.strbio.mol.lib.ScoreJDB10

All Implemented Interfaces:

ScoreFunction

public class ScoreJDB10
extends java.lang.Object
implements ScoreFunction

A scoring function that uses JDB's 10% ID matrix.

  Version 1.0, 5/18/99 - original version
  

Version:

1.0, 5/188/99

Author:

JMC

Field Summary

java.lang.String

defaultTable the default table comes from Tom Defay's "easy table"

Constructor Summary

ScoreJDB10()
If no filename is specified, use the default table.

ScoreJDB10(java.lang.String filename)

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

Field Detail

defaultTable

public final java.lang.String defaultTable

the default table comes from Tom Defay's "easy table"

See Also:

Constant Field Values

Constructor Detail

ScoreJDB10

public ScoreJDB10(java.lang.String filename)
           throws java.io.IOException

Throws:

java.io.IOException

ScoreJDB10

public ScoreJDB10()

If no filename is specified, use the default table. Can't call the other constructor due to stupid Java syntax.

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