Uses of Interface
jebl.evolution.sequences.Sequence

Packages that use Sequence

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
jebl.evolution.sequences

Uses of Sequence in jebl.evolution.align

Methods in jebl.evolution.align with parameters of type Sequence

Alignment	BartonSternberg.doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment	MultipleAligner.doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
PairwiseAligner.Result	NeedlemanWunschLinearSpaceAffine.doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)
PairwiseAligner.Result	PairwiseAligner.doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)
double	NeedlemanWunschLinearSpaceAffine.getScore(Sequence seq1, Sequence seq2)
double	PairwiseAligner.getScore(Sequence seq1, Sequence seq2)

Method parameters in jebl.evolution.align with type arguments of type Sequence

String[]	BartonSternberg.align(List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMIsmatchCosts)
static AlignmentTreeBuilderFactory.Result	AlignmentTreeBuilderFactory.build(List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress)
static AlignmentTreeBuilderFactory.Result	AlignmentTreeBuilderFactory.build(List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progress)
Alignment	BartonSternberg.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment	MultipleAligner.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)

Constructor parameters in jebl.evolution.align with type arguments of type Sequence

SequenceAlignmentsDistanceMatrix(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)

Uses of Sequence in jebl.evolution.aligners

Method parameters in jebl.evolution.aligners with type arguments of type Sequence

Alignment

Aligner.alignSequences(Collection<Sequence> sequences)

Uses of Sequence in jebl.evolution.alignments

Classes in jebl.evolution.alignments that implement Sequence

class

ConsensusSequence

Methods in jebl.evolution.alignments that return Sequence

Sequence	BasicAlignment.getSequence(Taxon taxon)
Sequence	ResampledAlignment.getSequence(Taxon taxon)

Methods in jebl.evolution.alignments that return types with arguments of type Sequence

List<Sequence>	Alignment.getSequenceList()
List<Sequence>	BasicAlignment.getSequenceList()
List<Sequence>	ResampledAlignment.getSequenceList()
Set<Sequence>	BasicAlignment.getSequences()
Set<Sequence>	ResampledAlignment.getSequences()

Methods in jebl.evolution.alignments with parameters of type Sequence

void	BasicAlignment.addSequence(Sequence sequence) Adds a sequence to this alignment

Constructors in jebl.evolution.alignments with parameters of type Sequence

BasicAlignment(Sequence[] sequences)
Constructs a basic alignment from an array of sequences.

Constructor parameters in jebl.evolution.alignments with type arguments of type Sequence

BasicAlignment(Collection<? extends Sequence> sequences)
Constructs a basic alignment from a collection of sequences.

Uses of Sequence in jebl.evolution.distances

Method parameters in jebl.evolution.distances with type arguments of type Sequence

protected static double[]	ModelBasedDistanceMatrix.getFrequencies(List<Sequence> sequences) As a side effect, this method sets freqR and freqY if called on nucleotide sequences.
protected static double[]	ModelBasedDistanceMatrix.getFrequenciesSafe(List<Sequence> sequences) As a side effect, this method sets freqR and freqY if called on nucleotide sequences.

Uses of Sequence in jebl.evolution.io

Methods in jebl.evolution.io that return types with arguments of type Sequence

List<Sequence>	FastaImporter.importSequences()
List<Sequence>	NexusImporter.importSequences() importSequences.
List<Sequence>	PhylipSequentialImporter.importSequences() importSequences.
List<Sequence>	SequenceImporter.importSequences() importSequences.
List<Sequence>	NexusImporter.parseCharactersBlock(List<Taxon> taxonList) Parses a 'CHARACTERS' block.
List<Sequence>	NexusImporter.parseDataBlock(List<Taxon> taxonList) Parses a 'DATA' block.

Methods in jebl.evolution.io with parameters of type Sequence

void	ImmediateSequenceImporter.Callback.add(Sequence seq)

Method parameters in jebl.evolution.io with type arguments of type Sequence

void	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 Sequence

class	BasicSequence A default implementation of the Sequence interface.
class	FilteredSequence
class	GaplessSequence
class	TranslatedSequence

Methods in jebl.evolution.sequences that return Sequence

Sequence	Sequences.getSequence(Taxon taxon)
static Sequence	SequenceTester.getTestSequence1()
static Sequence	SequenceTester.getTestSequence2()

Methods in jebl.evolution.sequences that return types with arguments of type Sequence

Set<Sequence>

Sequences.getSequences()

Methods in jebl.evolution.sequences with parameters of type Sequence

protected abstract State[]	FilteredSequence.filterSequence(Sequence source)
protected State[]	GaplessSequence.filterSequence(Sequence source)
protected State[]	TranslatedSequence.filterSequence(Sequence source)
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.

Constructors in jebl.evolution.sequences with parameters of type Sequence

FilteredSequence(Sequence source)
Creates a FilteredSequence wrapper to the given source sequence.

GaplessSequence(Sequence source)

TranslatedSequence(Sequence source, GeneticCode geneticCode)