public class AlignmentTreeBuilderFactory
extends java.lang.Object
Modifier and Type | Class | Description |
---|---|---|
static class |
AlignmentTreeBuilderFactory.Result |
Constructor | Description |
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AlignmentTreeBuilderFactory() |
public static AlignmentTreeBuilderFactory.Result build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) throws CannotBuildDistanceMatrixException
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.CannotBuildDistanceMatrixException
- only if useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable is falsepublic static AlignmentTreeBuilderFactory.Result build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener) throws CannotBuildDistanceMatrixException
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.EMPTYCannotBuildDistanceMatrixException
public static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener) throws CannotBuildDistanceMatrixException
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.EMPTYCannotBuildDistanceMatrixException
public static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model) throws CannotBuildDistanceMatrixException
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 useCannotBuildDistanceMatrixException
public static AlignmentTreeBuilderFactory.Result build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) throws CannotBuildDistanceMatrixException
http://code.google.com/p/jebl2/