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 AlignmentPairwiseAligner.Result. alignmentMethods in jebl.evolution.align that return Alignment Modifier and Type Method Description AlignmentBartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)AlignmentBartonSternberg. doAlign(Alignment a1, Alignment a2, ProgressListener progress)AlignmentBartonSternberg. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)AlignmentMultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)AlignmentMultipleAligner. doAlign(Alignment a1, Alignment a2, ProgressListener progress)AlignmentMultipleAligner. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)Methods in jebl.evolution.align with parameters of type Alignment Modifier and Type Method Description static AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener)static AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)AlignmentBartonSternberg. doAlign(Alignment a1, Alignment a2, ProgressListener progress)AlignmentBartonSternberg. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)AlignmentMultipleAligner. doAlign(Alignment a1, Alignment a2, ProgressListener progress)AlignmentMultipleAligner. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress) -
Uses of Alignment in jebl.evolution.aligners
Methods in jebl.evolution.aligners that return Alignment Modifier and Type Method Description AlignmentAligner. alignSequences(java.util.Collection<Sequence> sequences) -
Uses of Alignment in jebl.evolution.alignments
Classes in jebl.evolution.alignments that implement Alignment Modifier and Type Class Description classBasicAlignmentA basic implementation of the Alignment interface.classBootstrappedAlignmentDate: 15/01/2006 Time: 10:13:50classJackknifedAlignmentDate: 17/01/2006 Time: 08:18:32classResampledAlignmentDate: 17/01/2006 Time: 08:08:44Methods in jebl.evolution.alignments that return Alignment Modifier and Type Method Description AlignmentConsensusSequence. getSource()Methods in jebl.evolution.alignments with parameters of type Alignment Modifier and Type Method Description static State[]ConsensusSequence. constructConsensus(Alignment source, boolean includeAmbiguities)voidResampledAlignment. 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) -
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) -
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 voidAlignmentExporter. 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, java.lang.String name)voidNexusExporter. exportAlignment(Alignment alignment)exportAlignment.voidPHYLIPExporter. exportAlignment(Alignment alignment)
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