jebl.evolution.align.scores
Class AminoAcidScores

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

All Implemented Interfaces:

ScoreMatrix

Direct Known Subclasses:

Blosum45, Blosum50, Blosum55, Blosum60, Blosum62, Blosum65, Blosum70, Blosum75, Blosum80, Blosum85, Blosum90, Pam100, Pam110, Pam120, Pam130, Pam140, Pam150, Pam160, Pam170, Pam180, Pam190, Pam200, Pam210, Pam220, Pam230, Pam240, Pam250

public class AminoAcidScores
extends Scores

Author:

Alexei Drummond

Field Summary

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

score

Constructor Summary

AminoAcidScores()

AminoAcidScores(float m, float n)

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

AminoAcidScores

public AminoAcidScores()

AminoAcidScores

public AminoAcidScores(float m,
                       float n)

Method Detail

getName

public String getName()

Returns:

human readable name

getAlphabet

public final String getAlphabet()

Returns:

a string containing the valid characters for this score matrix.