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Packages that use Sequence | |
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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 |
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Methods in jebl.evolution.align with parameters of type Sequence | |
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Alignment |
MultipleAligner.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress)
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Alignment |
BartonSternberg.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress)
|
PairwiseAligner.Result |
NeedlemanWunschLinearSpaceAffine.doAlignment(Sequence seq1,
Sequence seq2,
ProgressListener progress)
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PairwiseAligner.Result |
PairwiseAligner.doAlignment(Sequence seq1,
Sequence seq2,
ProgressListener progress)
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double |
NeedlemanWunschLinearSpaceAffine.getScore(Sequence seq1,
Sequence seq2)
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double |
PairwiseAligner.getScore(Sequence seq1,
Sequence seq2)
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Method parameters in jebl.evolution.align with type arguments of type Sequence | |
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java.lang.String[] |
BartonSternberg.align(java.util.List<Sequence> sourceSequences,
ProgressListener progress,
boolean refineOnly,
boolean estimateMatchMismatchCosts)
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static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
MultipleAligner aligner,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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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 acid |
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
PairwiseAligner aligner,
ProgressListener progressListener,
TreeBuilderFactory.DistanceModel model)
|
Alignment |
MultipleAligner.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress)
|
Alignment |
BartonSternberg.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress)
|
static TreeBuilderFactory.DistanceModel |
SequenceAlignmentsDistanceMatrix.getDefaultDistanceModel(java.util.List<Sequence> seqs)
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Constructor parameters in jebl.evolution.align with type arguments of type Sequence | |
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SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress)
|
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SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress,
TreeBuilderFactory.DistanceModel model)
|
Uses of Sequence in jebl.evolution.aligners |
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Method parameters in jebl.evolution.aligners with type arguments of type Sequence | |
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Alignment |
Aligner.alignSequences(java.util.Collection<Sequence> sequences)
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Uses of Sequence in jebl.evolution.alignments |
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Classes in jebl.evolution.alignments that implement Sequence | |
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class |
ConsensusSequence
|
Methods in jebl.evolution.alignments that return Sequence | |
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Sequence |
BasicAlignment.getSequence(Taxon taxon)
|
Sequence |
ResampledAlignment.getSequence(Taxon taxon)
|
Methods in jebl.evolution.alignments that return types with arguments of type Sequence | |
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java.util.List<Sequence> |
Alignment.getSequenceList()
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java.util.List<Sequence> |
BasicAlignment.getSequenceList()
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java.util.List<Sequence> |
ResampledAlignment.getSequenceList()
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java.util.Set<Sequence> |
BasicAlignment.getSequences()
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java.util.Set<Sequence> |
ResampledAlignment.getSequences()
|
Methods in jebl.evolution.alignments with parameters of type Sequence | |
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void |
BasicAlignment.addSequence(Sequence sequence)
Adds a sequence to this alignment |
Constructors in jebl.evolution.alignments with parameters of type Sequence | |
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BasicAlignment(Sequence[] sequences)
Constructs a basic alignment from an array of sequences. |
Constructor parameters in jebl.evolution.alignments with type arguments of type Sequence | |
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BasicAlignment(java.util.Collection<? extends Sequence> sequences)
Constructs a basic alignment from a collection of sequences. |
Uses of Sequence in jebl.evolution.io |
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Methods in jebl.evolution.io that return types with arguments of type Sequence | |
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java.util.List<Sequence> |
PhylipSequentialImporter.importSequences()
importSequences. |
java.util.List<Sequence> |
NexusImporter.importSequences()
Import all sequences in the input from the current position |
java.util.List<Sequence> |
SequenceImporter.importSequences()
importSequences. |
java.util.List<Sequence> |
FastaImporter.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 | |
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void |
ImmediateSequenceImporter.Callback.add(Sequence seq)
|
Method parameters in jebl.evolution.io with type arguments of type Sequence | |
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void |
FastaExporter.exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment or set of sequences. |
void |
SequenceExporter.exportSequences(java.util.Collection<? extends Sequence> sequences)
exportSequences. |
void |
NexusExporter.exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment. |
Uses of Sequence in jebl.evolution.sequences |
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Classes in jebl.evolution.sequences that implement Sequence | |
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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 T |
class |
FilteredSequence
|
class |
GaplessSequence
|
class |
TranslatedSequence
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Methods in jebl.evolution.sequences that return Sequence | |
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Sequence |
Sequences.getSequence(Taxon taxon)
|
static Sequence |
SequenceTester.getTestSequence1()
|
static Sequence |
SequenceTester.getTestSequence2()
|
static Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode)
Translates a given Sequence to a corresponding Sequence under the given genetic code. |
Methods in jebl.evolution.sequences that return types with arguments of type Sequence | |
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java.util.Set<Sequence> |
Sequences.getSequences()
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Methods in jebl.evolution.sequences with parameters of type Sequence | |
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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 Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode)
Translates a given Sequence to a corresponding Sequence under the given genetic code. |
Constructors in jebl.evolution.sequences with parameters of type Sequence | |
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FilteredSequence(Sequence source)
Creates a FilteredSequence wrapper to the given source sequence. |
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GaplessSequence(Sequence source)
|
|
TranslatedSequence(Sequence source,
GeneticCode geneticCode)
|
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