org.strbio.mol.lib
Class ScoreList

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

All Implemented Interfaces:

Description

public class ScoreList
extends java.lang.Object
implements Description

A scoring function return a identity matrix; this is set up so that a sampling of all calls to score() over a large set of sequences and folds will average 0.0 with a standard deviation of 1.0.

  Version 1.3, 1/11/00 - added setAlignment
  Version 1.2, 7/1/99 - added describe
  Version 1.1, 4/3/98 - added setup, finished functions
  Version 1.0, 4/1/98 - original version
  

Version:

1.3, 1/11/00

Author:

JMC

Field Summary

ScoreFunction	func This encapsulates an object that implements ScoreFunction.
ScoreList	next The next in the list, or null if there are no more scoring functions.

Constructor Summary

ScoreList()
make an empty ScoreList node.

ScoreList(ScoreFunction sf)
make a ScoreList node with a ScoreFunction.

ScoreList(ScoreFunction sf, double w)
make a ScoreList node with a ScoreFunction and a weight.

Method Summary

void	describe(Printf outfile) Tell scoring functions to describe themselves, if possible.
void	finished(Polymer p) Tell scoring functions you're finished with a given protein, for all scoring functions that implement ScoreSetup.
void	finished(Polymer seq, Polymer fold) Tell scoring functions you're finished with a given protein pair, for all scoring functions that implement ScoreSetup2.
void	normalizeWeights() make the absolute value of all the weights in this list (starting at this) add up to one.
void	setAlignment(Alignment al) Set up scoring functions with a given Alignment functions that implement AlignmentDependent
void	setup(Polymer p) Set up scoring functions for a given protein, for all scoring functions that implement ScoreSetup.
void	setup(Polymer seq, Polymer fold) Set up scoring functions for a given protein pair, for all scoring functions that implement ScoreSetup2.
double	totalScore(Monomer a, Monomer b) return the total score for a monomer pair, from all scoring functions at this point on.

Methods inherited from class java.lang.Object

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

Field Detail

func

public ScoreFunction func

This encapsulates an object that implements ScoreFunction.

next

public ScoreList next

The next in the list, or null if there are no more scoring functions.

Constructor Detail

ScoreList

public ScoreList()

make an empty ScoreList node.

ScoreList

public ScoreList(ScoreFunction sf)

make a ScoreList node with a ScoreFunction.

ScoreList

public ScoreList(ScoreFunction sf,
                 double w)

make a ScoreList node with a ScoreFunction and a weight.

Method Detail

totalScore

public double totalScore(Monomer a,
                         Monomer b)

return the total score for a monomer pair, from all scoring functions at this point on. Should be called on the first member in a list.

normalizeWeights

public void normalizeWeights()

make the absolute value of all the weights in this list (starting at this) add up to one. Absolute value is important because some scoring functions may need to be reversed. This should be called on the first member in a list. Does nothing if all weights are zero.

setup

public void setup(Polymer p)

Set up scoring functions for a given protein, for all scoring functions that implement ScoreSetup.

See Also:

ScoreSetup

setAlignment

public void setAlignment(Alignment al)

Set up scoring functions with a given Alignment functions that implement AlignmentDependent

See Also:

AlignmentDependent

finished

public void finished(Polymer p)

Tell scoring functions you're finished with a given protein, for all scoring functions that implement ScoreSetup.

See Also:

ScoreSetup

setup

public void setup(Polymer seq,
                  Polymer fold)

Set up scoring functions for a given protein pair, for all scoring functions that implement ScoreSetup2.

See Also:

ScoreSetup2

finished

public void finished(Polymer seq,
                     Polymer fold)

Tell scoring functions you're finished with a given protein pair, for all scoring functions that implement ScoreSetup2.

See Also:

ScoreSetup2

describe

public void describe(Printf outfile)

Tell scoring functions to describe themselves, if possible.

Specified by:

describe in interface Description