org.strbio.mol.lib
Class OptimalAAParametersFR

java.lang.Object
  org.strbio.mol.lib.AlignmentParameters
      org.strbio.mol.lib.AlignmentParametersEA
          org.strbio.mol.lib.OptimalAAParametersFR

All Implemented Interfaces:

Description

public class OptimalAAParametersFR
extends AlignmentParametersEA

The optimal fold recognition parameters.

Version:

0.0, 6/28/99

Author:

JMC

Field Summary

Fields inherited from class org.strbio.mol.lib.AlignmentParametersEA

asns1, avgScoreMatch, avgScoreNonMatch, totalZMatch, totalZNonMatch

Fields inherited from class org.strbio.mol.lib.AlignmentParameters

gapModel, scoreList

Constructor Summary

OptimalAAParametersFR()
THESE ARE CURRENTLY THE AA PARAMETERS.

Method Summary

java.lang.String	defaultEAFileFR() Accuracy was parameterized on the TOM data set.
void	setup(Polymer seq, Polymer fold) kludge to set up precalculated phi/psi angles in the fold

Methods inherited from class org.strbio.mol.lib.AlignmentParametersEA

canEstimateAA, canEstimateFR, clearEstAAStats, clearEstFRStats, defaultEAFileAA, estASns1, estASns1SD, estFRAccy, loadEstAAStats, loadEstAAStats, loadEstAAStats, loadEstAAStatsRaw, loadEstAAStatsRaw, loadEstFRStats, loadEstFRStats, loadEstFRStats, loadEstFRStatsRaw, loadEstFRStatsRaw, processAA, processFR, saveEstAAStats, saveEstAAStats, saveEstFRStats, saveEstFRStats

Methods inherited from class org.strbio.mol.lib.AlignmentParameters

addScoreFunction, addScoreFunction, describe, finished, normalizeWeights, setAlignment

Methods inherited from class java.lang.Object

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

Constructor Detail

OptimalAAParametersFR

public OptimalAAParametersFR()

THESE ARE CURRENTLY THE AA PARAMETERS. Optimal parameters are: 70% backbone phi/psi potential, 30% psiblast, affine gap penalty (with overhanging ends penalized).

Method Detail

setup

public void setup(Polymer seq,
                  Polymer fold)

kludge to set up precalculated phi/psi angles in the fold

Overrides:

setup in class AlignmentParameters

defaultEAFileFR

public java.lang.String defaultEAFileFR()

Accuracy was parameterized on the TOM data set.

Overrides:

defaultEAFileFR in class AlignmentParametersEA