Package jebl.evolution.align
Class BartonSternberg
java.lang.Object
jebl.evolution.align.BartonSternberg
- All Implemented Interfaces:
MultipleAligner
- Version:
- $Id: BartonSternberg.java 1025 2009-10-23 01:29:48Z matt_kearse $ Implements the BartonSternberg multiple sequence alignment algorithm. Note: this is not yet complete, it does not create an initial ordering in which to add sequences to the profile. Also, after creating the profile, it just removes and adds each sequence back into the profile a fixed number of times(currently two).
- Author:
- Matt Kearse
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Constructor Summary
ConstructorsConstructorDescriptionBartonSternberg
(Scores scores, float gapOpen, float gapExtend, int refinementIterations, boolean freeGapsAtEnds, boolean fastGuide) -
Method Summary
Modifier and TypeMethodDescriptionfinal String[]
align
(List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts) doAlign
(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) doAlign
(Alignment a1, Alignment a2, ProgressListener progress) doAlign
(Alignment alignment, Sequence sequence, ProgressListener progress) double
getScore()
static void
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Constructor Details
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BartonSternberg
public BartonSternberg(Scores scores, float gapOpen, float gapExtend, int refinementIterations, boolean freeGapsAtEnds, boolean fastGuide)
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Method Details
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getEstimatedScores
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align
public final String[] align(List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts) throws CannotBuildDistanceMatrixException - Parameters:
sourceSequences
-progress
-refineOnly
- if specified, then the input sequences are assumed to be aligned already, and this function will only refine the alignment.- Throws:
CannotBuildDistanceMatrixException
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main
- Throws:
IOException
ImportException
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doAlign
- Specified by:
doAlign
in interfaceMultipleAligner
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doAlign
- Specified by:
doAlign
in interfaceMultipleAligner
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doAlign
- Specified by:
doAlign
in interfaceMultipleAligner
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getScore
public double getScore()
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