jebl.evolution.align
Class SequenceAlignmentsDistanceMatrix

java.lang.Object
  extended by jebl.evolution.distances.BasicDistanceMatrix
      extended by 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

Constructor Summary
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)
           
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model)
           
 
Method Summary
static TreeBuilderFactory.DistanceModel getDefaultDistanceModel(java.util.List<Sequence> seqs)
           
 
Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix
getDistance, getDistance, getDistances, getSize, getSubmatrix, getTaxa
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

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
Method Detail

getDefaultDistanceModel

public static TreeBuilderFactory.DistanceModel getDefaultDistanceModel(java.util.List<Sequence> seqs)


http://code.google.com/p/jebl2/