org.strbio.mol.lib
Class OptimalAAParameters

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

All Implemented Interfaces:

Description

public class OptimalAAParameters
extends AlignmentParametersEA

The optimal alignment parameters for maximizing alignment accuracy.

Version:

1.0, 6/25/99

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

OptimalAAParameters()
Optimal parameters are: 70% backbone phi/psi potential, 30% psiblast, affine gap penalty of 3.955210, 0.124641 (with overhanging ends penalized).

Method Summary

java.lang.String	defaultEAFileAA() 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, defaultEAFileFR, 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

OptimalAAParameters

public OptimalAAParameters()

Optimal parameters are: 70% backbone phi/psi potential, 30% psiblast, affine gap penalty of 3.955210, 0.124641 (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

defaultEAFileAA

public java.lang.String defaultEAFileAA()

Accuracy was parameterized on the TOM data set.

Overrides:

defaultEAFileAA in class AlignmentParametersEA