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

Version:

$Id: SubstScoreMatrix.java 360 2006-06-22 07:42:48Z pepster $

Author:

Alexei Drummond

Field Summary

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

score

Constructor Summary

Constructors

Constructor and Description
SubstScoreMatrix(RateMatrix rateMatrix)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getAlphabet()
java.lang.String	getName()

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

duplicate, forMatrix, getMatrixString, getScore, includeAdditionalCharacters, includeGaps, toString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SubstScoreMatrix

public SubstScoreMatrix(RateMatrix rateMatrix)

Method Detail

getName

public java.lang.String getName()

Returns:

human readable name

getAlphabet

public java.lang.String getAlphabet()

Returns:

a string containing the valid characters for this score matrix.