Uses of Interface
jebl.evolution.alignments.Alignment
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Packages that use Alignment Package Description jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences.jebl.evolution.aligners jebl.evolution.alignments jebl.evolution.distances jebl.evolution.io -
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Uses of Alignment in jebl.evolution.align
Fields in jebl.evolution.align declared as Alignment Modifier and Type Field Description Alignment
PairwiseAligner.Result. alignment
Methods in jebl.evolution.align that return Alignment Modifier and Type Method Description Alignment
BartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment
BartonSternberg. doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment
BartonSternberg. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment
MultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment
MultipleAligner. doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment
MultipleAligner. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Methods in jebl.evolution.align with parameters of type Alignment Modifier and Type Method 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)
Alignment
BartonSternberg. doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment
BartonSternberg. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment
MultipleAligner. doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment
MultipleAligner. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
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Uses of Alignment in jebl.evolution.aligners
Methods in jebl.evolution.aligners that return Alignment Modifier and Type Method Description Alignment
Aligner. alignSequences(java.util.Collection<Sequence> sequences)
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Uses of Alignment in jebl.evolution.alignments
Classes in jebl.evolution.alignments that implement Alignment Modifier and Type Class Description class
BasicAlignment
A basic implementation of the Alignment interface.class
BootstrappedAlignment
Date: 15/01/2006 Time: 10:13:50class
JackknifedAlignment
Date: 17/01/2006 Time: 08:18:32class
ResampledAlignment
Date: 17/01/2006 Time: 08:08:44Methods in jebl.evolution.alignments that return Alignment Modifier and Type Method Description Alignment
ConsensusSequence. getSource()
Methods in jebl.evolution.alignments with parameters of type Alignment Modifier and Type Method Description static State[]
ConsensusSequence. constructConsensus(Alignment source, boolean includeAmbiguities)
void
ResampledAlignment. init(Alignment srcAlignment, int[] siteIndices)
Setup resampled alignment.Constructors in jebl.evolution.alignments with parameters of type Alignment Constructor Description BootstrappedAlignment(Alignment srcAlignment)
BootstrappedAlignment(Alignment srcAlignment, long seed)
BootstrappedAlignment(Alignment srcAlignment, java.util.Random r)
ConsensusSequence(Taxon taxon, Alignment source)
Creates a FilteredSequence wrapper to the given source sequence.ConsensusSequence(Taxon taxon, Alignment source, boolean includeAmbiguities)
Creates a FilteredSequence wrapper to the given source sequence.JackknifedAlignment(Alignment srcAlignment, double percent)
JackknifedAlignment(Alignment srcAlignment, double percent, long seed)
JackknifedAlignment(Alignment srcAlignment, double percent, java.util.Random r)
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Uses of Alignment in jebl.evolution.distances
Constructors in jebl.evolution.distances with parameters of type Alignment Constructor Description F84DistanceMatrix(Alignment alignment)
F84DistanceMatrix(Alignment alignment, ProgressListener progress)
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)
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Uses of Alignment in jebl.evolution.io
Methods in jebl.evolution.io that return types with arguments of type Alignment Modifier and Type Method Description java.util.List<Alignment>
AlignmentImporter. importAlignments()
importAlignment.java.util.List<Alignment>
NexusImporter. importAlignments()
Import all alignments in the input from the current position.Methods in jebl.evolution.io with parameters of type Alignment Modifier and Type Method Description void
AlignmentExporter. exportAlignment(Alignment alignment)
export one alignment.void
MEGAExporter. exportAlignment(Alignment alignment)
Deprecated.Files created by this export method won't be importable by MEGA (because they don't have titles).void
MEGAExporter. exportAlignment(Alignment alignment, java.lang.String name)
void
NexusExporter. exportAlignment(Alignment alignment)
exportAlignment.void
PHYLIPExporter. exportAlignment(Alignment alignment)
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