Package jebl.evolution.align
Class AlignmentTreeBuilderFactory
- java.lang.Object
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- jebl.evolution.align.AlignmentTreeBuilderFactory
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public class AlignmentTreeBuilderFactory extends java.lang.Object
- Version:
- $Id: AlignmentTreeBuilderFactory.java 984 2009-03-06 02:13:55Z richardmoir $
- Author:
- Joseph Heled
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AlignmentTreeBuilderFactory.Result
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Constructor Summary
Constructors Constructor Description AlignmentTreeBuilderFactory()
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Method Summary
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Method Detail
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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 frommethod
- the tree building method to usemodel
- 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.EMPTYuseTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable
- 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
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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 frommethod
- the tree building method to usemodel
- 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
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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 frommethod
- method the tree building method to usealigner
- pairwise aligner which will be used to calculate a pairwise distanceprogressListener
- 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
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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 frommethod
- method the tree building method to usealigner
- pairwise aligner which will be used to calculate a pairwise distanceprogressListener
- must not be null. If you are not interested in progress, pass in ProgressListener.EMPTYmodel
- distance model to use- Returns:
- A tree building result (containing a tree and a distance matrix)
- Throws:
CannotBuildDistanceMatrixException
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build
public static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) throws CannotBuildDistanceMatrixException
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