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

Constructor Summary

Constructors

Constructor and Description
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

Methods

Modifier and Type	Method and Description
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)