Uses of Interface
jebl.evolution.alignments.Alignment
Packages that use Alignment
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
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Uses of Alignment in jebl.evolution.align
Fields in jebl.evolution.align declared as AlignmentMethods in jebl.evolution.align that return AlignmentModifier and TypeMethodDescriptionBartonSternberg.doAlign
(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) BartonSternberg.doAlign
(Alignment a1, Alignment a2, ProgressListener progress) BartonSternberg.doAlign
(Alignment alignment, Sequence sequence, ProgressListener progress) MultipleAligner.doAlign
(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) MultipleAligner.doAlign
(Alignment a1, Alignment a2, ProgressListener progress) MultipleAligner.doAlign
(Alignment alignment, Sequence sequence, ProgressListener progress) Methods in jebl.evolution.align with parameters of type AlignmentModifier and TypeMethodDescriptionAlignmentTreeBuilderFactory.build
(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener) AlignmentTreeBuilderFactory.build
(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) BartonSternberg.doAlign
(Alignment a1, Alignment a2, ProgressListener progress) BartonSternberg.doAlign
(Alignment alignment, Sequence sequence, ProgressListener progress) MultipleAligner.doAlign
(Alignment a1, Alignment a2, ProgressListener progress) MultipleAligner.doAlign
(Alignment alignment, Sequence sequence, ProgressListener progress) -
Uses of Alignment in jebl.evolution.aligners
Methods in jebl.evolution.aligners that return Alignment -
Uses of Alignment in jebl.evolution.alignments
Classes in jebl.evolution.alignments that implement AlignmentModifier and TypeClassDescriptionclass
A basic implementation of the Alignment interface.class
Date: 15/01/2006 Time: 10:13:50class
Date: 17/01/2006 Time: 08:18:32class
Date: 17/01/2006 Time: 08:08:44Methods in jebl.evolution.alignments that return AlignmentMethods in jebl.evolution.alignments with parameters of type AlignmentModifier and TypeMethodDescriptionstatic State[]
ConsensusSequence.constructConsensus
(Alignment source, boolean includeAmbiguities) void
Setup resampled alignment.Constructors in jebl.evolution.alignments with parameters of type AlignmentModifierConstructorDescriptionBootstrappedAlignment
(Alignment srcAlignment) BootstrappedAlignment
(Alignment srcAlignment, long seed) BootstrappedAlignment
(Alignment srcAlignment, 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, Random r) -
Uses of Alignment in jebl.evolution.distances
Constructors in jebl.evolution.distances with parameters of type AlignmentModifierConstructorDescriptionF84DistanceMatrix
(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) -
Uses of Alignment in jebl.evolution.io
Methods in jebl.evolution.io that return types with arguments of type AlignmentModifier and TypeMethodDescriptionAlignmentImporter.importAlignments()
importAlignment.NexusImporter.importAlignments()
Import all alignments in the input from the current position.Methods in jebl.evolution.io with parameters of type AlignmentModifier and TypeMethodDescriptionvoid
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, String name) void
NexusExporter.exportAlignment
(Alignment alignment) exportAlignment.void
PHYLIPExporter.exportAlignment
(Alignment alignment)