Package jebl.evolution.align
Class SequenceAlignmentsDistanceMatrix
- java.lang.Object
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- jebl.evolution.distances.BasicDistanceMatrix
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- jebl.evolution.align.SequenceAlignmentsDistanceMatrix
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- All Implemented Interfaces:
DistanceMatrix
public class SequenceAlignmentsDistanceMatrix extends BasicDistanceMatrix
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
Constructors Constructor Description SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model)
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static TreeBuilderFactory.DistanceModel
getDefaultDistanceModel(java.util.List<Sequence> seqs)
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Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix
getDistance, getDistance, getDistances, getSize, getSubmatrix, getTaxa
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Constructor Detail
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SequenceAlignmentsDistanceMatrix
public SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress) throws CannotBuildDistanceMatrixException
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SequenceAlignmentsDistanceMatrix
public SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model) throws CannotBuildDistanceMatrixException
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Method Detail
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getDefaultDistanceModel
public static TreeBuilderFactory.DistanceModel getDefaultDistanceModel(java.util.List<Sequence> seqs)
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