jebl.evolution.align.scores
Class SubstScoreMatrix

java.lang.Object
  jebl.evolution.align.scores.Scores
      jebl.evolution.align.scores.SubstScoreMatrix

All Implemented Interfaces:

ScoreMatrix

public class SubstScoreMatrix
extends Scores

Author:

Alexei Drummond

Field Summary

Fields inherited from class jebl.evolution.align.scores.Scores

score

Constructor Summary

SubstScoreMatrix(RateMatrix rateMatrix)

Method Summary

String	getAlphabet()
String	getName()

Methods inherited from class jebl.evolution.align.scores.Scores

buildScores, duplicate, getExtraResidues, getScore, includeAdditionalCharacters, includeGaps, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

SubstScoreMatrix

public SubstScoreMatrix(RateMatrix rateMatrix)

Method Detail

getName

public String getName()

Returns:

human readable name

getAlphabet

public String getAlphabet()

Returns:

a string containing the valid characters for this score matrix.