Package 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
- Version:
- $Id: NucleotideScores.java 916 2008-05-26 03:33:27Z matt_kearse $
- Author:
- Richard Moir, Alexei Drummond
-
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionNucleotideScores
(float match, float misMatch) NucleotideScores
(float match, float misMatch, float ambiguousMatch) 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, boolean useWeightedAmbigousMatches) NucleotideScores
(NucleotideScores scores) NucleotideScores
(Scores scores, double percentmatches) -
Method Summary
Methods inherited from class jebl.evolution.align.scores.Scores
duplicate, forMatrix, getMatrixString, getScore, includeAdditionalCharacters, includeGaps
-
Field Details
-
IUB
-
CLUSTALW
-
-
Constructor Details
-
NucleotideScores
-
NucleotideScores
public NucleotideScores(float match, float misMatch) - Parameters:
match
- match scoremisMatch
- mismatch score
-
NucleotideScores
public NucleotideScores(float match, float misMatch, float ambiguousMatch) -
NucleotideScores
-
NucleotideScores
public NucleotideScores(String name, float match, float mismatchTransition, float mismatchTransversion) -
NucleotideScores
public NucleotideScores(String name, float match, float mismatchTransition, float mismatchTransversion, float ambiguousMatch, boolean useWeightedAmbigousMatches) -
NucleotideScores
-
-
Method Details