Uses of Interface
jebl.evolution.sequences.Sequence
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Packages that use Sequence Package Description jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences.jebl.evolution.aligners jebl.evolution.alignments jebl.evolution.io jebl.evolution.sequences -
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Uses of Sequence in jebl.evolution.align
Methods in jebl.evolution.align with parameters of type Sequence Modifier and Type Method Description AlignmentBartonSternberg. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)AlignmentMultipleAligner. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)PairwiseAligner.ResultNeedlemanWunschLinearSpaceAffine. doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)PairwiseAligner.ResultPairwiseAligner. doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)doubleNeedlemanWunschLinearSpaceAffine. getScore(Sequence seq1, Sequence seq2)doublePairwiseAligner. getScore(Sequence seq1, Sequence seq2)Method parameters in jebl.evolution.align with type arguments of type Sequence Modifier and Type Method Description java.lang.String[]BartonSternberg. align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)static AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)static AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener)Will use model F84 for nucleotides and Jukes-Cantor for amino acidstatic AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)AlignmentBartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)AlignmentMultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)static TreeBuilderFactory.DistanceModelSequenceAlignmentsDistanceMatrix. getDefaultDistanceModel(java.util.List<Sequence> seqs)Constructor parameters in jebl.evolution.align with type arguments of type Sequence Constructor Description SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model) -
Uses of Sequence in jebl.evolution.aligners
Method parameters in jebl.evolution.aligners with type arguments of type Sequence Modifier and Type Method Description AlignmentAligner. alignSequences(java.util.Collection<Sequence> sequences) -
Uses of Sequence in jebl.evolution.alignments
Classes in jebl.evolution.alignments that implement Sequence Modifier and Type Class Description classConsensusSequenceMethods in jebl.evolution.alignments that return Sequence Modifier and Type Method Description SequenceBasicAlignment. getSequence(Taxon taxon)SequenceResampledAlignment. getSequence(Taxon taxon)Methods in jebl.evolution.alignments that return types with arguments of type Sequence Modifier and Type Method Description java.util.List<Sequence>Alignment. getSequenceList()java.util.List<Sequence>BasicAlignment. getSequenceList()java.util.List<Sequence>ResampledAlignment. getSequenceList()java.util.Set<Sequence>BasicAlignment. getSequences()java.util.Set<Sequence>ResampledAlignment. getSequences()Methods in jebl.evolution.alignments with parameters of type Sequence Modifier and Type Method Description voidBasicAlignment. addSequence(Sequence sequence)Adds a sequence to this alignmentConstructors in jebl.evolution.alignments with parameters of type Sequence Constructor Description BasicAlignment(Sequence[] sequences)Constructs a basic alignment from an array of sequences.Constructor parameters in jebl.evolution.alignments with type arguments of type Sequence Constructor Description BasicAlignment(java.util.Collection<? extends Sequence> sequences)Constructs a basic alignment from a collection of sequences. -
Uses of Sequence in jebl.evolution.io
Methods in jebl.evolution.io that return types with arguments of type Sequence Modifier and Type Method Description java.util.List<Sequence>FastaImporter. importSequences()java.util.List<Sequence>NexusImporter. importSequences()Import all sequences in the input from the current positionjava.util.List<Sequence>PhylipSequentialImporter. importSequences()importSequences.java.util.List<Sequence>SequenceImporter. importSequences()importSequences.java.util.List<Sequence>NexusImporter. parseCharactersBlock(java.util.List<Taxon> taxonList)Parse the next 'CHARACTERS' block encountered in the input.java.util.List<Sequence>NexusImporter. parseDataBlock(java.util.List<Taxon> taxonList)Parse the next 'DATA' block encountered in the input.Methods in jebl.evolution.io with parameters of type Sequence Modifier and Type Method Description voidImmediateSequenceImporter.Callback. add(Sequence seq)Method parameters in jebl.evolution.io with type arguments of type Sequence Modifier and Type Method Description voidFastaExporter. exportSequences(java.util.Collection<? extends Sequence> sequences)export alignment or set of sequences.voidNexusExporter. exportSequences(java.util.Collection<? extends Sequence> sequences)export alignment.voidSequenceExporter. exportSequences(java.util.Collection<? extends Sequence> sequences)exportSequences. -
Uses of Sequence in jebl.evolution.sequences
Classes in jebl.evolution.sequences that implement Sequence Modifier and Type Class Description classBasicSequenceA default implementation of the Sequence interface.classCanonicalSequenceA default implementation of the Sequence interface that converts sequence characters to States such that calling getString() will always return uppercase residues with nucleotide U residues converted to TclassCodonSequenceA codon implementation of the Sequence interface.classFilteredSequenceclassGaplessSequenceclassTranslatedSequenceMethods in jebl.evolution.sequences that return Sequence Modifier and Type Method Description static SequenceSequence. appendSequences(Sequence sequence1, Sequence sequence2)Append two sequences together to create a new sequence object.SequenceSequences. getSequence(Taxon taxon)static SequenceSequence. getSubSequence(Sequence sequence, int from, int to)Returns a sub-sequence for states from, to (inclusive).static SequenceSequenceTester. getTestSequence1()static SequenceSequenceTester. getTestSequence2()static SequenceSequence. replaceStates(Sequence sequence, java.util.List<State> searchStates, State replaceState)Searchers and replaces a sequence of any states givenstatic SequenceSequence. stripGaps(Sequence sequence)Strips a sequence of gapsstatic SequenceSequence. stripStates(Sequence sequence, java.util.List<State> stripStates)Strips a sequence of any states givenstatic SequenceUtils. translate(Sequence sequence, GeneticCode geneticCode)static SequenceUtils. translate(Sequence sequence, GeneticCode geneticCode, int readingFrame)static SequenceSequence. trimSequence(Sequence sequence, java.util.List<State> trimStates)Methods in jebl.evolution.sequences that return types with arguments of type Sequence Modifier and Type Method Description java.util.Set<Sequence>Sequences. getSequences()Methods in jebl.evolution.sequences with parameters of type Sequence Modifier and Type Method Description static SequenceSequence. appendSequences(Sequence sequence1, Sequence sequence2)Append two sequences together to create a new sequence object.static intUtils. getGaplessLocation(Sequence sequence, int gappedLocation)Gets the site location index for this sequence excluding any gaps.static intUtils. getGappedLocation(Sequence sequence, int gaplessLocation)Gets the site location index for this sequence that corresponds to a location given excluding all gaps.static intSequence. getStateCount(Sequence sequence, State state)Counts the number of occurances of a statestatic intUtils. getStopCodonCount(Sequence sequence)Counts the number of stop codons in an amino acid sequencestatic SequenceSequence. getSubSequence(Sequence sequence, int from, int to)Returns a sub-sequence for states from, to (inclusive).static SequenceSequence. replaceStates(Sequence sequence, java.util.List<State> searchStates, State replaceState)Searchers and replaces a sequence of any states givenstatic SequenceSequence. stripGaps(Sequence sequence)Strips a sequence of gapsstatic SequenceSequence. stripStates(Sequence sequence, java.util.List<State> stripStates)Strips a sequence of any states givenstatic SequenceUtils. translate(Sequence sequence, GeneticCode geneticCode)static SequenceUtils. translate(Sequence sequence, GeneticCode geneticCode, int readingFrame)static SequenceSequence. trimSequence(Sequence sequence, java.util.List<State> trimStates)Constructors in jebl.evolution.sequences with parameters of type Sequence Constructor Description FilteredSequence(Sequence source)Creates a FilteredSequence wrapper to the given source sequence.GaplessSequence(Sequence source)TranslatedSequence(Sequence source, GeneticCode geneticCode)Create a TranslatedSequence from a source codon or nucleotide sequenceTranslatedSequence(Sequence source, GeneticCode geneticCode, int frame)Create a TranslatedSequence from a source codon or nucleotide sequence
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