# Uses of Class
jebl.evolution.distances.CannotBuildDistanceMatrixException

Packages that use CannotBuildDistanceMatrixException
Package
Description
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
Modifier and Type
Method
Description
`final String[]`
BartonSternberg.`align(List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)`
`static AlignmentTreeBuilderFactory.Result`
AlignmentTreeBuilderFactory.`build(List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)`
`static AlignmentTreeBuilderFactory.Result`
AlignmentTreeBuilderFactory.`build(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(List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)`
`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)`
Constructors in jebl.evolution.align that throw CannotBuildDistanceMatrixException
Modifier
Constructor
Description
``
`SequenceAlignmentsDistanceMatrix(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)`
``
`SequenceAlignmentsDistanceMatrix(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
Modifier
Constructor
Description
``
`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)`