Uses of Interface
jebl.evolution.alignments.Alignment
Packages that use Alignment
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
-
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 TypeClassDescriptionclassA basic implementation of the Alignment interface.classDate: 15/01/2006 Time: 10:13:50classDate: 17/01/2006 Time: 08:18:32classDate: 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) voidSetup 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 TypeMethodDescriptionvoidAlignmentExporter.exportAlignment(Alignment alignment) export one alignment.voidMEGAExporter.exportAlignment(Alignment alignment) Deprecated.Files created by this export method won't be importable by MEGA (because they don't have titles).voidMEGAExporter.exportAlignment(Alignment alignment, String name) voidNexusExporter.exportAlignment(Alignment alignment) exportAlignment.voidPHYLIPExporter.exportAlignment(Alignment alignment)