Package jebl.evolution.align
Class SequenceAlignmentsDistanceMatrix
java.lang.Object
jebl.evolution.distances.BasicDistanceMatrix
jebl.evolution.align.SequenceAlignmentsDistanceMatrix
- All Implemented Interfaces:
DistanceMatrix
Builds a distance matrix by performing a series of pairwise alignments between the
specified sequences (unlike the methods in jebl.evolution.distances, which
extract the pairwise distances from a multiple sequence alignment).
- Version:
- $Id: SequenceAlignmentsDistanceMatrix.java 1057 2010-05-24 03:20:46Z matt_kearse $
- Author:
- Joseph Heled
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Constructor Summary
ConstructorsConstructorDescriptionSequenceAlignmentsDistanceMatrix
(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress) SequenceAlignmentsDistanceMatrix
(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model) -
Method Summary
Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix
getDistance, getDistance, getDistances, getSize, getSubmatrix, getTaxa
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Constructor Details
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SequenceAlignmentsDistanceMatrix
public SequenceAlignmentsDistanceMatrix(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress) throws CannotBuildDistanceMatrixException -
SequenceAlignmentsDistanceMatrix
public SequenceAlignmentsDistanceMatrix(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model) throws CannotBuildDistanceMatrixException
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Method Details
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getDefaultDistanceModel
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