Uses of Interface
jebl.evolution.sequences.Sequence
-
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 -
-
Uses of Sequence in jebl.evolution.align
Methods in jebl.evolution.align with parameters of type Sequence Modifier and Type Method Description 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 Modifier and Type Method Description java.lang.String[]
BartonSternberg. align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. 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.Result
AlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)
Alignment
BartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment
MultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
static TreeBuilderFactory.DistanceModel
SequenceAlignmentsDistanceMatrix. 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 Alignment
Aligner. 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 class
ConsensusSequence
Methods in jebl.evolution.alignments that return Sequence Modifier and Type Method Description Sequence
BasicAlignment. getSequence(Taxon taxon)
Sequence
ResampledAlignment. 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 void
BasicAlignment. 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 void
ImmediateSequenceImporter.Callback. add(Sequence seq)
void
FastaExporter. exportSequence(Sequence sequence)
export a sequence.Method parameters in jebl.evolution.io with type arguments of type Sequence Modifier and Type Method Description void
FastaExporter. exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment or set of sequences.void
NexusExporter. exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment.void
SequenceExporter. 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 class
BasicSequence
A default implementation of the Sequence interface.class
CanonicalSequence
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
CodonSequence
A codon implementation of the Sequence interface.class
FilteredSequence
class
GaplessSequence
class
TranslatedSequence
Methods in jebl.evolution.sequences that return Sequence Modifier and Type Method Description static Sequence
Sequence. appendSequences(Sequence sequence1, Sequence sequence2)
Append two sequences together to create a new sequence object.Sequence
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, java.util.List<State> searchStates, State replaceState)
Searchers and replaces a sequence of any states givenstatic Sequence
Sequence. stripGaps(Sequence sequence)
Strips a sequence of gapsstatic Sequence
Sequence. stripStates(Sequence sequence, java.util.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, 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 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, java.util.List<State> searchStates, State replaceState)
Searchers and replaces a sequence of any states givenstatic Sequence
Sequence. stripGaps(Sequence sequence)
Strips a sequence of gapsstatic Sequence
Sequence. stripStates(Sequence sequence, java.util.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, 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
-