jebl.evolution.align
Class SequenceAlignmentsDistanceMatrix
java.lang.Object
jebl.evolution.distances.BasicDistanceMatrix
jebl.evolution.align.SequenceAlignmentsDistanceMatrix
- 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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SequenceAlignmentsDistanceMatrix
public SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress)
throws CannotBuildDistanceMatrixException
- Throws:
CannotBuildDistanceMatrixException
SequenceAlignmentsDistanceMatrix
public SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress,
TreeBuilderFactory.DistanceModel model)
throws CannotBuildDistanceMatrixException
- Throws:
CannotBuildDistanceMatrixException
getDefaultDistanceModel
public static TreeBuilderFactory.DistanceModel getDefaultDistanceModel(java.util.List<Sequence> seqs)
http://code.google.com/p/jebl2/