Package jebl.evolution.align.scores
Class NucleotideScores
- java.lang.Object
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- jebl.evolution.align.scores.Scores
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- jebl.evolution.align.scores.NucleotideScores
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- All Implemented Interfaces:
ScoreMatrix
- Direct Known Subclasses:
Hamming
,JukesCantor
public class NucleotideScores extends Scores
- Version:
- $Id: NucleotideScores.java 916 2008-05-26 03:33:27Z matt_kearse $
- Author:
- Richard Moir, Alexei Drummond
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Field Summary
Fields Modifier and Type Field Description static NucleotideScores
CLUSTALW
static NucleotideScores
IUB
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Constructor Summary
Constructors Constructor Description NucleotideScores(float match, float misMatch)
NucleotideScores(float match, float misMatch, float ambiguousMatch)
NucleotideScores(java.lang.String name, float match, float misMatch)
NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion)
NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion, float ambiguousMatch, boolean useWeightedAmbigousMatches)
NucleotideScores(NucleotideScores scores)
NucleotideScores(Scores scores, double percentmatches)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getAlphabet()
java.lang.String
getName()
java.lang.String
toString()
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Methods inherited from class jebl.evolution.align.scores.Scores
duplicate, forMatrix, getMatrixString, getScore, includeAdditionalCharacters, includeGaps
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Field Detail
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IUB
public static final NucleotideScores IUB
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CLUSTALW
public static final NucleotideScores CLUSTALW
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Constructor Detail
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NucleotideScores
public NucleotideScores(NucleotideScores scores)
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NucleotideScores
public NucleotideScores(float match, float misMatch)
- Parameters:
match
- match scoremisMatch
- mismatch score
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NucleotideScores
public NucleotideScores(float match, float misMatch, float ambiguousMatch)
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NucleotideScores
public NucleotideScores(java.lang.String name, float match, float misMatch)
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NucleotideScores
public NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion)
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NucleotideScores
public NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion, float ambiguousMatch, boolean useWeightedAmbigousMatches)
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NucleotideScores
public NucleotideScores(Scores scores, double percentmatches)
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