org.strbio.mol.lib
Class FRParametersNode

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

All Implemented Interfaces:

Description

public class FRParametersNode
extends java.lang.Object
implements Description

Fold recognition parameters. This consists of a set of parameters to do an alignment, followed by a set of parameters for evaluating the score for the resulting alignment. Finally, 4 weights are given to measure the relative contributions of these results to the overall FR scheme.

Version:

1.0, 2/16/00

Author:

JMC

Field Summary

AlignmentParameters	creationAP Alignment parameters used to create the alignment.
AlignmentParameters	evaluationAP Alignment parameters used to evaluate the alignment.
double	weightAverage How much to weight the average (gapped) score of the alignments?
double	weightCoverage How much to weight the alignment coverage of the alignments?
double	weightTotal How much to weight the total score of the alignments?
double	weightZScore How much to weight the Z score (of the total score) of the alignments?

Constructor Summary

FRParametersNode()
Create an empty node.

Method Summary

void	describe(Printf outfile) Describe prints parameters of the components, if they support it

Methods inherited from class java.lang.Object

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

Field Detail

creationAP

public AlignmentParameters creationAP

Alignment parameters used to create the alignment. If null, the existing alignment will be used.

evaluationAP

public AlignmentParameters evaluationAP

Alignment parameters used to evaluate the alignment. If null, the creationAP will be used. Both cannot be null.

weightAverage

public double weightAverage

How much to weight the average (gapped) score of the alignments?

weightTotal

public double weightTotal

How much to weight the total score of the alignments?

weightZScore

public double weightZScore

How much to weight the Z score (of the total score) of the alignments?

weightCoverage

public double weightCoverage

How much to weight the alignment coverage of the alignments?

Constructor Detail

FRParametersNode

public FRParametersNode()

Create an empty node.

Method Detail

describe

public void describe(Printf outfile)

Describe prints parameters of the components, if they support it

Specified by:

describe in interface Description