jebl.evolution.align.scores
Class NucleotideScores

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

All Implemented Interfaces:

ScoreMatrix

Direct Known Subclasses:

Hamming, JukesCantor

public class NucleotideScores
extends Scores

Author:

Richard Moir, Alexei Drummond

Field Summary

static NucleotideScores	CLUSTALW
static NucleotideScores	IUB

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

score

Constructor Summary

protected	NucleotideScores()
	NucleotideScores(float match, float misMatch)
	NucleotideScores(float match, float misMatch, float ambiguousMatch)
	NucleotideScores(NucleotideScores scores)
	NucleotideScores(Scores scores, double percentmatches)
	NucleotideScores(String name, float match, float misMatch)
	NucleotideScores(String name, float match, float mismatchTransition, float mismatchTransversion)
	NucleotideScores(String name, float match, float mismatchTransition, float mismatchTransversion, float ambiguousMatch)

Method Summary

String	getAlphabet()
String	getName()
String	toString()

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

buildScores, duplicate, getExtraResidues, getScore, includeAdditionalCharacters, includeGaps

Methods inherited from class java.lang.Object

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

Field Detail

IUB

public static final NucleotideScores IUB

CLUSTALW

public static final NucleotideScores CLUSTALW

Constructor Detail

NucleotideScores

protected NucleotideScores()

NucleotideScores

public NucleotideScores(NucleotideScores scores)

NucleotideScores

public NucleotideScores(float match,
                        float misMatch)

Parameters:

match - match score

misMatch - mismatch score

NucleotideScores

public NucleotideScores(float match,
                        float misMatch,
                        float ambiguousMatch)

NucleotideScores

public NucleotideScores(String name,
                        float match,
                        float misMatch)

NucleotideScores

public NucleotideScores(String name,
                        float match,
                        float mismatchTransition,
                        float mismatchTransversion)

NucleotideScores

public NucleotideScores(String name,
                        float match,
                        float mismatchTransition,
                        float mismatchTransversion,
                        float ambiguousMatch)

NucleotideScores

public NucleotideScores(Scores scores,
                        double percentmatches)

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.

toString

public String toString()

Overrides:

toString in class Scores