Uses of Interface
jebl.evolution.sequences.Sequence
Packages that use Sequence
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
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Uses of Sequence in jebl.evolution.align
Methods in jebl.evolution.align with parameters of type SequenceModifier and TypeMethodDescriptionBartonSternberg.doAlign
(Alignment alignment, Sequence sequence, ProgressListener progress) MultipleAligner.doAlign
(Alignment alignment, Sequence sequence, ProgressListener progress) NeedlemanWunschLinearSpaceAffine.doAlignment
(Sequence seq1, Sequence seq2, ProgressListener progress) PairwiseAligner.doAlignment
(Sequence seq1, Sequence seq2, ProgressListener progress) double
double
Method parameters in jebl.evolution.align with type arguments of type SequenceModifier and TypeMethodDescriptionfinal String[]
BartonSternberg.align
(List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts) AlignmentTreeBuilderFactory.build
(List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) AlignmentTreeBuilderFactory.build
(List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener) Will use model F84 for nucleotides and Jukes-Cantor for amino acidAlignmentTreeBuilderFactory.build
(List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model) BartonSternberg.doAlign
(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) MultipleAligner.doAlign
(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) SequenceAlignmentsDistanceMatrix.getDefaultDistanceModel
(List<Sequence> seqs) Constructor parameters in jebl.evolution.align with type arguments of type SequenceModifierConstructorDescriptionSequenceAlignmentsDistanceMatrix
(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress) SequenceAlignmentsDistanceMatrix
(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 -
Uses of Sequence in jebl.evolution.alignments
Classes in jebl.evolution.alignments that implement SequenceMethods in jebl.evolution.alignments that return SequenceModifier and TypeMethodDescriptionBasicAlignment.getSequence
(Taxon taxon) ResampledAlignment.getSequence
(Taxon taxon) Methods in jebl.evolution.alignments that return types with arguments of type SequenceModifier and TypeMethodDescriptionAlignment.getSequenceList()
BasicAlignment.getSequenceList()
ResampledAlignment.getSequenceList()
BasicAlignment.getSequences()
ResampledAlignment.getSequences()
Methods in jebl.evolution.alignments with parameters of type SequenceModifier and TypeMethodDescriptionvoid
BasicAlignment.addSequence
(Sequence sequence) Adds a sequence to this alignmentConstructors in jebl.evolution.alignments with parameters of type SequenceModifierConstructorDescriptionBasicAlignment
(Sequence[] sequences) Constructs a basic alignment from an array of sequences.Constructor parameters in jebl.evolution.alignments with type arguments of type SequenceModifierConstructorDescriptionBasicAlignment
(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 SequenceModifier and TypeMethodDescriptionFastaImporter.importSequences()
NexusImporter.importSequences()
Import all sequences in the input from the current positionPhylipSequentialImporter.importSequences()
importSequences.SequenceImporter.importSequences()
importSequences.NexusImporter.parseCharactersBlock
(List<Taxon> taxonList) Parse the next 'CHARACTERS' block encountered in the input.NexusImporter.parseDataBlock
(List<Taxon> taxonList) Parse the next 'DATA' block encountered in the input.Methods in jebl.evolution.io with parameters of type SequenceModifier and TypeMethodDescriptionvoid
void
FastaExporter.exportSequence
(Sequence sequence) export a sequence.Method parameters in jebl.evolution.io with type arguments of type SequenceModifier and TypeMethodDescriptionvoid
FastaExporter.exportSequences
(Collection<? extends Sequence> sequences) export alignment or set of sequences.void
NexusExporter.exportSequences
(Collection<? extends Sequence> sequences) export alignment.void
SequenceExporter.exportSequences
(Collection<? extends Sequence> sequences) exportSequences. -
Uses of Sequence in jebl.evolution.sequences
Classes in jebl.evolution.sequences that implement SequenceModifier and TypeClassDescriptionclass
A default implementation of the Sequence interface.class
A 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 Tclass
A codon implementation of the Sequence interface.class
class
class
Methods in jebl.evolution.sequences that return SequenceModifier and TypeMethodDescriptionstatic Sequence
Sequence.appendSequences
(Sequence sequence1, Sequence sequence2) Append two sequences together to create a new sequence object.Sequences.getSequence
(Taxon taxon) static Sequence
Sequence.getSubSequence
(Sequence sequence, int from, int to) Returns a sub-sequence for states from, to (inclusive).static Sequence
SequenceTester.getTestSequence1()
static Sequence
SequenceTester.getTestSequence2()
static Sequence
Sequence.replaceStates
(Sequence sequence, List<State> searchStates, State replaceState) Searchers and replaces a sequence of any states givenstatic Sequence
Strips a sequence of gapsstatic Sequence
Sequence.stripStates
(Sequence sequence, List<State> stripStates) Strips a sequence of any states givenstatic Sequence
Utils.translate
(Sequence sequence, GeneticCode geneticCode) static Sequence
Utils.translate
(Sequence sequence, GeneticCode geneticCode, int readingFrame) static Sequence
Sequence.trimSequence
(Sequence sequence, List<State> trimStates) Methods in jebl.evolution.sequences that return types with arguments of type SequenceMethods in jebl.evolution.sequences with parameters of type SequenceModifier and TypeMethodDescriptionstatic Sequence
Sequence.appendSequences
(Sequence sequence1, Sequence sequence2) Append two sequences together to create a new sequence object.static int
Utils.getGaplessLocation
(Sequence sequence, int gappedLocation) Gets the site location index for this sequence excluding any gaps.static int
Utils.getGappedLocation
(Sequence sequence, int gaplessLocation) Gets the site location index for this sequence that corresponds to a location given excluding all gaps.static int
Sequence.getStateCount
(Sequence sequence, State state) Counts the number of occurances of a statestatic int
Utils.getStopCodonCount
(Sequence sequence) Counts the number of stop codons in an amino acid sequencestatic Sequence
Sequence.getSubSequence
(Sequence sequence, int from, int to) Returns a sub-sequence for states from, to (inclusive).static Sequence
Sequence.replaceStates
(Sequence sequence, List<State> searchStates, State replaceState) Searchers and replaces a sequence of any states givenstatic Sequence
Strips a sequence of gapsstatic Sequence
Sequence.stripStates
(Sequence sequence, List<State> stripStates) Strips a sequence of any states givenstatic Sequence
Utils.translate
(Sequence sequence, GeneticCode geneticCode) static Sequence
Utils.translate
(Sequence sequence, GeneticCode geneticCode, int readingFrame) static Sequence
Sequence.trimSequence
(Sequence sequence, List<State> trimStates) Constructors in jebl.evolution.sequences with parameters of type SequenceModifierConstructorDescriptionFilteredSequence
(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