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.io   
jebl.evolution.sequences   
 

Uses of Sequence in jebl.evolution.align
 

Methods in jebl.evolution.align with parameters of type Sequence
 Alignment MultipleAligner.doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
           
 Alignment BartonSternberg.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
 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 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)
           
 

Constructor parameters in jebl.evolution.align with type arguments of type Sequence
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
 Alignment Aligner.alignSequences(java.util.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
 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
 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(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
 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
 void ImmediateSequenceImporter.Callback.add(Sequence seq)
           
 

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

Classes in jebl.evolution.sequences that implement Sequence
 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
           
 

Methods in jebl.evolution.sequences that return Sequence
 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
 java.util.Set<Sequence> Sequences.getSequences()
           
 

Methods in jebl.evolution.sequences with parameters of type Sequence
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
FilteredSequence(Sequence source)
          Creates a FilteredSequence wrapper to the given source sequence.
GaplessSequence(Sequence source)
           
TranslatedSequence(Sequence source, GeneticCode geneticCode)
           
 



http://code.google.com/p/jebl2/