org.strbio.mol.lib
Class FRParameters

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

All Implemented Interfaces:

Description

Direct Known Subclasses:

OptimalFRParameters

public class FRParameters
extends java.lang.Object
implements Description

Fold recognition parameters. This consists of a vector of FRParametersNodes, and a few general parameters.

Version:

1.0, 2/16/00

Author:

JMC

Field Summary

double	bias Bias when computing composite scores
java.util.Vector	methods vector of methods and their weights.
DVector	scoreMatch composite score for each match (weighted sum of scores from all methods)
DVector	scoreNonMatch scores for each non-match
double	weightLength How much to weight the length ratio?

Constructor Summary

FRParameters()
Create an empty list.

Method Summary

void	addMethod(FRParametersNode frpn) add a method to the list of parameters.
boolean	canEstimateFR() will this return valid results for estFR*?
void	clearEstFRStats() remove stats for estimating fold recognition accuracy.
java.lang.String	defaultEAFileFR() get the default file name (in the classpath) for fold recognition parameters.
void	describe(Printf outfile) Describe prints parameters of the components, if they support it
double	estFRAccy(double score) Estimate the accuracy of a given prediction, given the composite score.
void	loadEstFRStats() Load the default accuracy stats from a file in the classpath.
void	loadEstFRStats(java.io.BufferedReader infile) Get the FR accuracy stats out of a file.
void	loadEstFRStats(java.lang.String filename) Get the FR accuracy stats out of a file.
void	loadEstFRStatsRaw(java.io.BufferedReader infile) Get the raw FR accuracy stats out of a file.
void	loadEstFRStatsRaw(java.lang.String filename) Get the raw FR accuracy stats out of a file.
static void	main(java.lang.String[] argv) main processes the old raw EA files and re-saves them in the new format.
FRParametersNode	method(int i) Get the ith method
int	nMethods() how many methods are there?
void	processFR() process the FR stats, for speed in estimation.
void	saveEstFRStats(Printf outfile) Save accuracy stats to a file.
void	saveEstFRStats(java.lang.String filename) Save alignment accuracy stats to a file.

Methods inherited from class java.lang.Object

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

Field Detail

methods

public java.util.Vector methods

vector of methods and their weights.

weightLength

public double weightLength

How much to weight the length ratio?

bias

public double bias

Bias when computing composite scores

scoreMatch

public DVector scoreMatch

composite score for each match (weighted sum of scores from all methods)

scoreNonMatch

public DVector scoreNonMatch

scores for each non-match

Constructor Detail

FRParameters

public FRParameters()

Create an empty list.

Method Detail

defaultEAFileFR

public java.lang.String defaultEAFileFR()

get the default file name (in the classpath) for fold recognition parameters. this should be overridden by subclasses.

estFRAccy

public double estFRAccy(double score)

Estimate the accuracy of a given prediction, given the composite score.

processFR

public void processFR()

process the FR stats, for speed in estimation.

canEstimateFR

public boolean canEstimateFR()

will this return valid results for estFR*?

clearEstFRStats

public void clearEstFRStats()

remove stats for estimating fold recognition accuracy.

saveEstFRStats

public void saveEstFRStats(java.lang.String filename)
                    throws java.io.IOException

Save alignment accuracy stats to a file.

Throws:

java.io.IOException

saveEstFRStats

public void saveEstFRStats(Printf outfile)
                    throws java.io.IOException

Save accuracy stats to a file.

Throws:

java.io.IOException

loadEstFRStats

public void loadEstFRStats(java.io.BufferedReader infile)
                    throws java.io.IOException

Get the FR accuracy stats out of a file.

Throws:

java.io.IOException

loadEstFRStatsRaw

public void loadEstFRStatsRaw(java.io.BufferedReader infile)
                       throws java.io.IOException

Get the raw FR accuracy stats out of a file.

Throws:

java.io.IOException

loadEstFRStats

public void loadEstFRStats(java.lang.String filename)
                    throws java.io.IOException

Get the FR accuracy stats out of a file.

Throws:

java.io.IOException

loadEstFRStatsRaw

public void loadEstFRStatsRaw(java.lang.String filename)
                       throws java.io.IOException

Get the raw FR accuracy stats out of a file.

Throws:

java.io.IOException

loadEstFRStats

public void loadEstFRStats()
                    throws java.io.IOException

Load the default accuracy stats from a file in the classpath.

Throws:

java.io.IOException

addMethod

public void addMethod(FRParametersNode frpn)

add a method to the list of parameters.

nMethods

public int nMethods()

how many methods are there?

method

public FRParametersNode method(int i)

Get the ith method

describe

public void describe(Printf outfile)

Describe prints parameters of the components, if they support it

Specified by:

describe in interface Description

main

public static final void main(java.lang.String[] argv)

main processes the old raw EA files and re-saves them in the new format.