SequenceAlignmentsDistanceMatrix (JEBL2 lib API)

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	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

All Methods Static Methods Concrete Methods
Modifier and Type Method 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

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static TreeBuilderFactory.DistanceModel`	`getDefaultDistanceModel(java.util.List<Sequence> seqs)`

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)

Class SequenceAlignmentsDistanceMatrix

Constructor Summary

Method Summary

Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix

Methods inherited from class java.lang.Object

Constructor Detail

SequenceAlignmentsDistanceMatrix

SequenceAlignmentsDistanceMatrix

Method Detail

getDefaultDistanceModel