Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.trees |
Modifier and Type | Method and Description |
---|---|
static TreeBuilderFactory.DistanceModel |
SequenceAlignmentsDistanceMatrix.getDefaultDistanceModel(java.util.List<Sequence> seqs) |
Modifier and Type | Method and Description |
---|---|
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,
PairwiseAligner aligner,
ProgressListener progressListener,
TreeBuilderFactory.DistanceModel model) |
Constructor and Description |
---|
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress,
TreeBuilderFactory.DistanceModel model) |
Modifier and Type | Method and Description |
---|---|
static TreeBuilderFactory.DistanceModel |
TreeBuilderFactory.DistanceModel.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static TreeBuilderFactory.DistanceModel[] |
TreeBuilderFactory.DistanceModel.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
http://code.google.com/p/jebl2/