jebl.evolution.align
Class AlignmentTreeBuilderFactory

java.lang.Object
  extended by jebl.evolution.align.AlignmentTreeBuilderFactory

public class AlignmentTreeBuilderFactory
extends java.lang.Object

Version:
$Id: AlignmentTreeBuilderFactory.java 984 2009-03-06 02:13:55Z richardmoir $
Author:
Joseph Heled

Nested Class Summary
static class AlignmentTreeBuilderFactory.Result
           
 
Constructor Summary
AlignmentTreeBuilderFactory()
           
 
Method Summary
static AlignmentTreeBuilderFactory.Result build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener)
           
static AlignmentTreeBuilderFactory.Result build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener)
          Will use model F84 for nucleotides and Jukes-Cantor for amino acid
static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AlignmentTreeBuilderFactory

public AlignmentTreeBuilderFactory()
Method Detail

build

public static AlignmentTreeBuilderFactory.Result build(Alignment alignment,
                                                       TreeBuilderFactory.Method method,
                                                       TreeBuilderFactory.DistanceModel model,
                                                       ProgressListener progressListener,
                                                       boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
                                                throws CannotBuildDistanceMatrixException
Parameters:
alignment - Alignment to calculate distance matrix from
method - the tree building method to use
model - substitution model for distance matrix: JukesCantor, TamuraNei, HKY or F84.
progressListener - must not be null. If you are not interested in progress, pass in ProgressListener.EMPTY
useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable - If the alignment contains pairs of sequences that are not overlapping it is not possible to build a tree from the alignment. If this parameter is false, then CannotBuildDistanceMatrixException will be thrown. If this parameter is true, then twice the maximum distance between all other pairs will be used non-overlapping pairs.
Returns:
A tree building result (containing a tree and a distance matrix)
Throws:
CannotBuildDistanceMatrixException - only if useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable is false

build

public static AlignmentTreeBuilderFactory.Result build(Alignment alignment,
                                                       TreeBuilderFactory.Method method,
                                                       TreeBuilderFactory.DistanceModel model,
                                                       ProgressListener progressListener)
                                                throws CannotBuildDistanceMatrixException
Parameters:
alignment - Alignment to calculate distance matrix from
method - the tree building method to use
model - substitution model for distance matrix: JukesCantor, TamuraNei, HKY or F84.
progressListener - must not be null. If you are not interested in progress, pass in ProgressListener.EMPTY
Returns:
A tree building result (containing a tree and a distance matrix)
Throws:
CannotBuildDistanceMatrixException

build

public static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs,
                                                       TreeBuilderFactory.Method method,
                                                       PairwiseAligner aligner,
                                                       ProgressListener progressListener)
                                                throws CannotBuildDistanceMatrixException
Will use model F84 for nucleotides and Jukes-Cantor for amino acid

Parameters:
seqs - Sequences to build distance matrix from
method - method the tree building method to use
aligner - pairwise aligner which will be used to calculate a pairwise distance
progressListener - must not be null. If you are not interested in progress, pass in ProgressListener.EMPTY
Returns:
A tree building result (containing a tree and a distance matrix)
Throws:
CannotBuildDistanceMatrixException

build

public static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs,
                                                       TreeBuilderFactory.Method method,
                                                       PairwiseAligner aligner,
                                                       ProgressListener progressListener,
                                                       TreeBuilderFactory.DistanceModel model)
                                                throws CannotBuildDistanceMatrixException
Parameters:
seqs - Sequences to build distance matrix from
method - method the tree building method to use
aligner - pairwise aligner which will be used to calculate a pairwise distance
progressListener - must not be null. If you are not interested in progress, pass in ProgressListener.EMPTY
model - distance model to use
Returns:
A tree building result (containing a tree and a distance matrix)
Throws:
CannotBuildDistanceMatrixException

build

public static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs,
                                                       TreeBuilderFactory.Method method,
                                                       MultipleAligner aligner,
                                                       ProgressListener progress,
                                                       boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
                                                throws CannotBuildDistanceMatrixException
Throws:
CannotBuildDistanceMatrixException


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