Uses of Class
jebl.evolution.distances.CannotBuildDistanceMatrixException

Packages that use CannotBuildDistanceMatrixException
jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences. 
jebl.evolution.distances   
 

Uses of CannotBuildDistanceMatrixException in jebl.evolution.align
 

Methods in jebl.evolution.align that throw CannotBuildDistanceMatrixException
 java.lang.String[] BartonSternberg.align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)
           
static AlignmentTreeBuilderFactory.Result AlignmentTreeBuilderFactory.build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener)
           
static AlignmentTreeBuilderFactory.Result AlignmentTreeBuilderFactory.build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
static AlignmentTreeBuilderFactory.Result AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
static AlignmentTreeBuilderFactory.Result AlignmentTreeBuilderFactory.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 AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)
           
 

Constructors in jebl.evolution.align that throw CannotBuildDistanceMatrixException
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)
           
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model)
           
 

Uses of CannotBuildDistanceMatrixException in jebl.evolution.distances
 

Constructors in jebl.evolution.distances that throw CannotBuildDistanceMatrixException
HKYDistanceMatrix(Alignment alignment, ProgressListener progress)
           
HKYDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress)
           
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress)
           
TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
 



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