Uses of Interface
org.biojava.bio.seq.Sequence

Packages that use Sequence
org.biojava.bio.dist Probability distributions over Alphabets. 
org.biojava.bio.dp HMM and Dynamic Programming Algorithms. 
org.biojava.bio.gui.sequence Graphical displays of biological sequences and associated annotations. 
org.biojava.bio.gui.sequence.tracklayout Classes for the handling of the layout of a WrappedSequencePanel. 
org.biojava.bio.molbio The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. 
org.biojava.bio.program.das Development client for the Distributed Annotation System. 
org.biojava.bio.program.gff GFF manipulation. 
org.biojava.bio.program.phred Parser for Phred output 
org.biojava.bio.program.ssbind Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. 
org.biojava.bio.program.unigene Objects for representing Unigene clusters. 
org.biojava.bio.program.xff Event-driven parsing system for the Extensible Feature Format (XFF). 
org.biojava.bio.proteomics Utilities to aid in performing various physical analysis of proteins. 
org.biojava.bio.search Interfaces and classes for representing sequence similarity search results. 
org.biojava.bio.seq Classes and interfaces for defining biological sequences and informatics objects. 
org.biojava.bio.seq.db Collections of biological sequence data. 
org.biojava.bio.seq.db.biofetch Client for the OBDA BioFetch protocol. 
org.biojava.bio.seq.db.biosql General purpose Sequence storage in a relational database. 
org.biojava.bio.seq.db.flat Support for OBDA flatfile databases. 
org.biojava.bio.seq.distributed Sequences and SequenceDBs which are composed from data taken from a number of data sources. 
org.biojava.bio.seq.impl Standard in-memory implementations of Sequence and Feature
org.biojava.bio.seq.io Classes and interfaces for processing and producing flat-file representations of sequences. 
org.biojava.bio.seq.io.agave Classes for converting between AGAVE XML and BioJava objects. 
org.biojava.bio.seq.projection Code for projecting Feature objects and systematically altering their properties. 
org.biojava.bio.structure Interfaces and classes for protein structure (PDB). 
org.biojavax.bio.db Interactions between biojavax objects and a DB. 
org.biojavax.bio.seq Rich implementations of Sequences, Locations and Features. 
org.biojavax.bio.seq.io Classes to support the I/O of RichSequence and Bioentry objects. 
 

Uses of Sequence in org.biojava.bio.dist
 

Methods in org.biojava.bio.dist that return Sequence
protected static Sequence DistributionTools.generateOrderNSequence(java.lang.String name, OrderNDistribution d, int length)
          Deprecated. use generateSequence() or generateSymbolList() instead.
static Sequence DistributionTools.generateSequence(java.lang.String name, Distribution d, int length)
          Produces a sequence by randomly sampling the Distribution.
 

Uses of Sequence in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that return Sequence
 Sequence WeightMatrixAnnotator.annotate(Sequence seq)
           
 

Methods in org.biojava.bio.dp with parameters of type Sequence
 Sequence WeightMatrixAnnotator.annotate(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.gui.sequence
 

Methods in org.biojava.bio.gui.sequence that return Sequence
 Sequence PairwiseSequencePanel.getSecondarySequence()
          getSecondarySequence returns the entire secondary Sequence currently being rendered.
 Sequence SequencePanelWrapper.getSequence()
           
 Sequence SequencePoster.getSequence()
          Deprecated.  
 Sequence PairwiseSequencePanel.getSequence()
          getSequence returns the entire Sequence currently being rendered.
 

Methods in org.biojava.bio.gui.sequence with parameters of type Sequence
 void PairwiseSequencePanel.setSecondarySequence(Sequence sequence)
          setSecondarySequence sets the secondary Sequence to be rendered.
 void SequencePanelWrapper.setSequence(Sequence seq)
           
 void SequencePoster.setSequence(Sequence s)
          Deprecated. Set the SymboList to be rendered.
 void PairwiseSequencePanel.setSequence(Sequence sequence)
          setSequence sets the Sequence to be rendered.
 

Constructors in org.biojava.bio.gui.sequence with parameters of type Sequence
HeadlessRenderContext(Sequence seq, RangeLocation range, int width)
           
 

Uses of Sequence in org.biojava.bio.gui.sequence.tracklayout
 

Methods in org.biojava.bio.gui.sequence.tracklayout with parameters of type Sequence
 void SimpleTrackLayout.setSequence(Sequence seq)
           
 void UserDefinedTrackLayout.setSequence(Sequence seq)
           
 void TrackLayout.setSequence(Sequence seq)
           
 

Constructors in org.biojava.bio.gui.sequence.tracklayout with parameters of type Sequence
SimpleTrackLayout(Sequence seq, int wrap)
           
 

Uses of Sequence in org.biojava.bio.molbio
 

Methods in org.biojava.bio.molbio that return Sequence
 Sequence RestrictionMapper.annotate(Sequence sequence)
          annotate adds Features which represent restriction sites.
 

Methods in org.biojava.bio.molbio with parameters of type Sequence
 Sequence RestrictionMapper.annotate(Sequence sequence)
          annotate adds Features which represent restriction sites.
 

Uses of Sequence in org.biojava.bio.program.das
 

Methods in org.biojava.bio.program.das that return Sequence
 Sequence DASSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.program.das with parameters of type Sequence
 void DASSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.program.gff
 

Methods in org.biojava.bio.program.gff that return Sequence
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents)
          Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName)
          Annotates a sequence with the features from a GFF entry set.
 

Methods in org.biojava.bio.program.gff with parameters of type Sequence
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents)
          Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName)
          Annotates a sequence with the features from a GFF entry set.
protected  void SequencesAsGFF.doPreProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id)
          Emit any per-sequence header information.
protected  void SequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id)
          Internal method to process an individual Sequence.
static GFFEntrySet GFFTools.gffFromSequence(Sequence seq)
          Creates a GFFEntrySet containing one entry for each feature on a sequence.
 void SequencesAsGFF.processSequence(Sequence seq, GFFDocumentHandler handler)
          Process an individual Sequence, informing handler of any suitable features.
 

Uses of Sequence in org.biojava.bio.program.phred
 

Classes in org.biojava.bio.program.phred that implement Sequence
 class PhredSequence
          PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.
 

Methods in org.biojava.bio.program.phred with parameters of type Sequence
protected  java.lang.String PhredFormat.describeSequence(Sequence seq)
          Return a suitable description line for a Sequence.
 void PhredFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          This method will print symbols to the line width followed by a new line etc.
 void PhredFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 

Uses of Sequence in org.biojava.bio.program.ssbind
 

Methods in org.biojava.bio.program.ssbind that return Sequence
 Sequence SimilarityPairBuilder.getAnnotatedQuerySeq(java.lang.String queryID)
           
 Sequence SimilarityPairBuilder.getAnnotatedSubjectSeq(java.lang.String subjectID)
           
protected  Sequence ViewSequenceFactory.makeQueryViewSequence(java.lang.String queryID)
           
protected  Sequence ViewSequenceFactory.makeSubjectViewSequence(java.lang.String subjectID)
           
 

Uses of Sequence in org.biojava.bio.program.unigene
 

Methods in org.biojava.bio.program.unigene that return Sequence
 Sequence UnigeneCluster.getUnique()
          The unique sequence that is used as a representative for this cluster.
 

Uses of Sequence in org.biojava.bio.program.xff
 

Methods in org.biojava.bio.program.xff that return Sequence
static Sequence XFFTools.readXFF(java.io.File xffFile, java.lang.String seqID)
           
static Sequence XFFTools.readXFF(java.io.File xffFile, java.lang.String seqID, FiniteAlphabet alpha)
           
 

Methods in org.biojava.bio.program.xff with parameters of type Sequence
static void XFFTools.annotateXFF(java.io.File xffFile, Sequence sequence)
           
static void XFFTools.annotateXFF(java.io.File xffFile, Sequence sequence, Annotation ann)
           
 

Uses of Sequence in org.biojava.bio.proteomics
 

Methods in org.biojava.bio.proteomics that return Sequence
 Sequence Digest.getSequence()
           
 

Methods in org.biojava.bio.proteomics with parameters of type Sequence
 void Digest.setSequence(Sequence sequence)
           
 

Uses of Sequence in org.biojava.bio.search
 

Methods in org.biojava.bio.search that return Sequence
 Sequence SimpleSeqSimilaritySearchResult.getQuerySequence()
           
 Sequence SeqSimilaritySearchResult.getQuerySequence()
          Returns the query sequence which was used to perform the search.
 Sequence SequenceDBSearchResult.getQuerySequence()
          Deprecated.  
 

Constructors in org.biojava.bio.search with parameters of type Sequence
SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
          Deprecated. Creates a new SequenceDBSearchResult.
SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
          Creates a new SimpleSeqSimilaritySearchResult.
 

Uses of Sequence in org.biojava.bio.seq
 

Subinterfaces of Sequence in org.biojava.bio.seq
 interface GappedSequence
          Extension of GappedSymbolList which also projects features into the gapped coordinate system.
 

Classes in org.biojava.bio.seq that implement Sequence
 class CircularView
           A circular view onto another Sequence object.
 class NewSimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 class SimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 

Fields in org.biojava.bio.seq declared as Sequence
 Sequence ComponentFeature.Template.componentSequence
           
 

Methods in org.biojava.bio.seq that return Sequence
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
static Sequence DNATools.createDNASequence(java.lang.String dna, java.lang.String name)
          Return a new DNA Sequence for dna.
static Sequence SequenceTools.createDummy(Alphabet alpha, int length, Symbol sym, java.lang.String uri, java.lang.String name)
          Create a new Sequence that contains a single symbol repeated over and over.
static Sequence SequenceTools.createDummy(java.lang.String uri, java.lang.String name)
          Create a new Sequence that has no annotation, no features and a zero-length symbol list.
static Sequence NucleotideTools.createNucleotideSequence(java.lang.String nucleotide, java.lang.String name)
          Return a new Nucleotide Sequence for nucleotide.
static Sequence ProteinTools.createProteinSequence(java.lang.String protein, java.lang.String name)
          Return a new PROTEIN Sequence for protein.
static Sequence RNATools.createRNASequence(java.lang.String rna, java.lang.String name)
          Return a new RNA Sequence for rna.
 Sequence SequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)
          Deprecated. Creates a sequence using these parameters.
static Sequence SequenceTools.createSequence(SymbolList syms, java.lang.String uri, java.lang.String name, Annotation ann)
           
 Sequence ComponentFeature.getComponentSequence()
          Get the sequence object which provides a component of this feature's parent sequence.
 Sequence Feature.getSequence()
          Return the Sequence object to which this feature is (ultimately) attached.
static Sequence SequenceTools.maskSequence(Sequence seq, RangeLocation loc)
          Mask of a sequence.
 Sequence SequenceIterator.nextSequence()
          Returns the next sequence in the iterator.
static Sequence SequenceTools.reverseComplement(Sequence seq)
          Reverse-complement a sequence, and flip all of its features.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end)
          Extract a sub-sequence from a sequence.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end, java.lang.String name)
          Extract a sub-sequence from a sequence.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end, java.lang.String name, StrandedFeature.Strand strand)
          Extract a sub-sequence from a sequence.
 

Methods in org.biojava.bio.seq with parameters of type Sequence
static void SequenceTools.addAllFeatures(Sequence seq, FeatureHolder fh)
          Add features to a sequence that contain the same information as all those in a feature holder.
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
static GappedSequence SequenceTools.gappedView(Sequence seq)
          Create a new gapped sequence for a sequence.
static Sequence SequenceTools.maskSequence(Sequence seq, RangeLocation loc)
          Mask of a sequence.
 Feature FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)
          Install a feature on the specified sequence.
 Feature SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)
           
static Sequence SequenceTools.reverseComplement(Sequence seq)
          Reverse-complement a sequence, and flip all of its features.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end)
          Extract a sub-sequence from a sequence.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end, java.lang.String name)
          Extract a sub-sequence from a sequence.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end, java.lang.String name, StrandedFeature.Strand strand)
          Extract a sub-sequence from a sequence.
static ViewSequence SequenceTools.view(Sequence seq)
          Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
static ViewSequence SequenceTools.view(Sequence seq, FeatureRealizer fr)
          Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features.
static ViewSequence SequenceTools.view(Sequence seq, java.lang.String name)
          Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
 

Constructors in org.biojava.bio.seq with parameters of type Sequence
CircularView(Sequence seq)
           
CircularView(Sequence seq, FeatureRealizer fr)
           
 

Uses of Sequence in org.biojava.bio.seq.db
 

Methods in org.biojava.bio.seq.db that return Sequence
protected  Sequence AnnotatedSequenceDB.doAnnotation(Sequence seq)
          Apply the annotation to a sequence.
 Sequence GenbankSequenceDB.getSequence(java.lang.String id)
           
 Sequence CachingSequenceDB.getSequence(java.lang.String id)
           
 Sequence ViewingSequenceDB.getSequence(java.lang.String id)
           
 Sequence GenpeptSequenceDB.getSequence(java.lang.String id)
           
 Sequence WebSequenceDB.getSequence(java.lang.String id)
          Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
 Sequence SubSequenceDB.getSequence(java.lang.String id)
           
 Sequence HashSequenceDB.getSequence(java.lang.String id)
           
 Sequence IndexedSequenceDB.getSequence(java.lang.String id)
           
 Sequence AnnotatedSequenceDB.getSequence(java.lang.String id)
           
 Sequence DummySequenceDB.getSequence(java.lang.String id)
           
 Sequence SequenceDBLite.getSequence(java.lang.String id)
          Retrieve a single sequence by its id.
 Sequence SwissprotSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.db with parameters of type Sequence
 void WebSequenceDB.addSequence(Sequence seq)
          Not supported, You can't add sequences to a WebDB!
 void HashSequenceDB.addSequence(Sequence seq)
           
 void AbstractSequenceDB.addSequence(Sequence seq)
           
 void DummySequenceDB.addSequence(Sequence seq)
           
 void SequenceDBLite.addSequence(Sequence seq)
          Adds a sequence to the database.
 void HashSequenceDB.addSequence(java.lang.String id, Sequence seq)
          Add a sequence under a particular id.
 java.lang.String IDMaker.calcID(Sequence seq)
          Calculate the id for a sequence.
 java.lang.String IDMaker.ByURN.calcID(Sequence seq)
           
 java.lang.String IDMaker.ByName.calcID(Sequence seq)
           
protected  Sequence AnnotatedSequenceDB.doAnnotation(Sequence seq)
          Apply the annotation to a sequence.
 

Uses of Sequence in org.biojava.bio.seq.db.biofetch
 

Methods in org.biojava.bio.seq.db.biofetch that return Sequence
 Sequence BioFetchSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.db.biofetch with parameters of type Sequence
 void BioFetchSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.seq.db.biosql
 

Methods in org.biojava.bio.seq.db.biosql that return Sequence
 Sequence BioSQLSequenceDB.getSequence(int bioentry_id)
          Deprecated.  
 Sequence BioSQLSequenceDB.getSequence(java.lang.String id)
          Deprecated.  
 

Methods in org.biojava.bio.seq.db.biosql with parameters of type Sequence
 void BioSQLSequenceDB.addSequence(Sequence seq)
          Deprecated.  
 

Uses of Sequence in org.biojava.bio.seq.db.flat
 

Methods in org.biojava.bio.seq.db.flat that return Sequence
 Sequence FlatSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.db.flat with parameters of type Sequence
 void FlatSequenceDB.addSequence(Sequence sequence)
          addSequence always throws a ChangeVetoException as this implementation is immutable.
 

Uses of Sequence in org.biojava.bio.seq.distributed
 

Methods in org.biojava.bio.seq.distributed that return Sequence
 Sequence DistDataSource.getSequence(java.lang.String id)
          Get a Sequence object for an ID.
 Sequence SequenceDBDataSource.getSequence(java.lang.String id)
           
 Sequence GFFDataSource.getSequence(java.lang.String id)
           
 Sequence DistributedSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.distributed with parameters of type Sequence
 void DistributedSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.seq.impl
 

Classes in org.biojava.bio.seq.impl that implement Sequence
 class DummySequence
          A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
 class RevCompSequence
          A reverse complement view onto Sequence interface.
 class SimpleGappedSequence
          Simple implementation of GappedSequence.
 class SimpleSequence
          A basic implementation of the Sequence interface.
 class SubSequence
          View a sub-section of a given sequence object, including all the features intersecting that region.
 class ViewSequence
          A view onto another Sequence object.
 

Fields in org.biojava.bio.seq.impl declared as Sequence
protected  Sequence RevCompSequence.origSeq
           
 

Methods in org.biojava.bio.seq.impl that return Sequence
 Sequence SimpleSequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)
           
 Sequence SubSequence.getSequence()
          Return the parent sequence of which this is a partial view
 Sequence SimpleFeature.getSequence()
           
 

Constructors in org.biojava.bio.seq.impl with parameters of type Sequence
RevCompSequence(Sequence seq)
          URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these.
RevCompSequence(Sequence seq, java.lang.String urn, java.lang.String name, Annotation annotation)
           
SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)
          Create a SimpleFeature on the given sequence.
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template)
           
SimpleGappedSequence(Sequence seq)
           
SimpleHomologyFeature(Sequence sourceSeq, FeatureHolder parent, HomologyFeature.Template template)
           
SimpleRemoteFeature(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template)
           
SimpleRestrictionSite(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template)
          Creates a new SimpleRestrictionSite.
SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template)
          Creates a new SimpleSimilarityPairFeature.
SimpleStrandedFeature(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template)
           
SubSequence(Sequence seq, int start, int end)
          Construct a new SubSequence of the specified sequence.
SubSequence(Sequence seq, int start, int end, java.lang.String name)
          Construct a new SubSequence of the specified sequence.
ViewSequence(Sequence seq)
          Construct a view onto an existing sequence which takes on that sequence's name.
ViewSequence(Sequence seq, FeatureRealizer fr)
          Construct a view onto a sequence, using a specific FeatureRealizer.
ViewSequence(Sequence seq, java.lang.String name)
          Construct a view onto an existing sequence and give it a new name.
 

Uses of Sequence in org.biojava.bio.seq.io
 

Fields in org.biojava.bio.seq.io declared as Sequence
protected  Sequence SequenceBuilderBase.seq
           
 

Methods in org.biojava.bio.seq.io that return Sequence
 Sequence SimpleAssemblyBuilder.makeSequence()
           
 Sequence SimpleSequenceBuilder.makeSequence()
           
 Sequence SequenceBuilderBase.makeSequence()
           
 Sequence SequenceBuilder.makeSequence()
          Return the Sequence object which has been constructed by this builder.
 Sequence SmartSequenceBuilder.makeSequence()
           
 Sequence SequenceBuilderFilter.makeSequence()
           
 Sequence SequenceDBSequenceBuilder.makeSequence()
          create the sequence
 Sequence StreamReader.nextSequence()
          Pull the next sequence out of the stream.
 

Methods in org.biojava.bio.seq.io with parameters of type Sequence
protected  java.lang.String FastaFormat.describeSequence(Sequence seq)
          Deprecated. Return a suitable description line for a Sequence.
 void SeqIOEventEmitter.getSeqIOEvents(Sequence seq, SeqIOListener listener)
          Deprecated. getSeqIOEvents scans a Sequence object and sends events describing its data to the SeqIOListener.
static void SeqIOTools.writeEmbl(java.io.OutputStream os, Sequence seq)
          Deprecated. Writes a single Sequence to an OutputStream in EMBL format.
static void SeqIOTools.writeFasta(java.io.OutputStream os, Sequence seq)
          Deprecated. Writes a single Sequence to an OutputStream in Fasta format.
static void SeqIOTools.writeGenbank(java.io.OutputStream os, Sequence seq)
          Deprecated. Writes a single Sequence to an OutputStream in Genbank format.
static void SeqIOTools.writeGenpept(java.io.OutputStream os, Sequence seq)
          Deprecated. Writes a single Sequence to an OutputStream in Genpept format.
 void FastaFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          Deprecated. Writes a Sequence or RichSequence to a PrintStream in FASTA format.
 void SequenceFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void GenbankFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          Deprecated.  
 void GAMEFormat.writeSequence(Sequence seq, java.io.PrintStream os)
           
 void EmblLikeFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          Deprecated.  
 void FastaFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 void SequenceFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 void GenbankFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 void GAMEFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
           
 void EmblLikeFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
static void SeqIOTools.writeSwissprot(java.io.OutputStream os, Sequence seq)
          Deprecated. Writes a single Sequence to an OutputStream in SwissProt format.
 

Uses of Sequence in org.biojava.bio.seq.io.agave
 

Fields in org.biojava.bio.seq.io.agave declared as Sequence
protected  Sequence AGAVEBioSeqHandler.sequence
           
protected  Sequence AGAVEContigHandler.sequence
           
 

Methods in org.biojava.bio.seq.io.agave with parameters of type Sequence
protected  void StAXFeatureHandler.addFeatureToSequence(Sequence seq)
           
 void AGAVEHandler.reportSequence(Sequence sequence)
           
 void AGAVECallbackItf.reportSequence(Sequence sequence)
           
 void AGAVEChromosomeCallbackItf.reportSequence(Sequence sequence)
           
 void AGAVEContigHandler.reportSequence(Sequence sequence)
           
 void AGAVEContigCallbackItf.reportSequence(Sequence sequence)
           
 void AGAVEChromosomeHandler.reportSequence(Sequence sequence)
           
protected  void AgaveWriter.write(Sequence seq)
          Writing Sequence.
 void AgaveWriter.writeSequence(Sequence seq, java.io.PrintStream os)
          Write sequence into AGAVE XML format.
 

Uses of Sequence in org.biojava.bio.seq.projection
 

Methods in org.biojava.bio.seq.projection that return Sequence
 Sequence ProjectedFeature.getSequence()
           
 Sequence ProjectionContext.getSequence(Feature projFeat)
          Get the sequence for a feature.
 Sequence ReparentContext.getSequence(Feature f)
           
 

Uses of Sequence in org.biojava.bio.structure
 

Methods in org.biojava.bio.structure that return Sequence
 Sequence ChainImpl.getBJSequence()
          Convert the SEQRES groups of a Chain to a Biojava Sequence object.
 Sequence Chain.getBJSequence()
          Convert the SEQRES groups of a Chain to a Biojava Sequence object.
 

Uses of Sequence in org.biojavax.bio.db
 

Methods in org.biojavax.bio.db that return Sequence
 Sequence AbstractRichSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojavax.bio.db with parameters of type Sequence
 void AbstractRichSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojavax.bio.seq
 

Subinterfaces of Sequence in org.biojavax.bio.seq
 interface RichSequence
          A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
 

Classes in org.biojavax.bio.seq that implement Sequence
 class SimpleRichSequence
          A simple implementation of RichSequence.
 class ThinRichSequence
          A simple implementation of RichSequence.
 

Methods in org.biojavax.bio.seq that return Sequence
 Sequence SimpleRichFeature.getSequence()
          Return the Sequence object to which this feature is (ultimately) attached.
 Sequence RichSequence.IOTools.SingleRichSeqIterator.nextSequence()
          Returns the next sequence in the iterator.
 

Methods in org.biojavax.bio.seq with parameters of type Sequence
static RichSequence RichSequence.Tools.enrich(Sequence s)
          Boldly attempts to convert a Sequence into a RichSequence.
static void RichSequence.IOTools.writeEMBL(java.io.OutputStream os, Sequence seq, Namespace ns)
          Writes a single Sequence to an OutputStream in EMBL format.
static void RichSequence.IOTools.writeEMBLxml(java.io.OutputStream os, Sequence seq, Namespace ns)
          Writes a single Sequence to an OutputStream in EMBLxml format.
static void RichSequence.IOTools.writeFasta(java.io.OutputStream os, Sequence seq, Namespace ns)
          Writes a single Sequence to an OutputStream in Fasta format.
static void RichSequence.IOTools.writeFasta(java.io.OutputStream os, Sequence seq, Namespace ns, FastaHeader header)
          Writes a single Sequence to an OutputStream in Fasta format.
static void RichSequence.IOTools.writeGenbank(java.io.OutputStream os, Sequence seq, Namespace ns)
          Writes a single Sequence to an OutputStream in GenBank format.
static void RichSequence.IOTools.writeINSDseq(java.io.OutputStream os, Sequence seq, Namespace ns)
          Writes a single Sequence to an OutputStream in INSDseq format.
static void RichSequence.IOTools.writeUniProt(java.io.OutputStream os, Sequence seq, Namespace ns)
          Writes a single Sequence to an OutputStream in UniProt format.
static void RichSequence.IOTools.writeUniProtXML(java.io.OutputStream os, Sequence seq, Namespace ns)
          Writes a single Sequence to an OutputStream in UniProt XML format.
 

Constructors in org.biojavax.bio.seq with parameters of type Sequence
RichSequence.IOTools.SingleRichSeqIterator(Sequence seq)
          Creates an iterator over a single sequence.
 

Uses of Sequence in org.biojavax.bio.seq.io
 

Methods in org.biojavax.bio.seq.io that return Sequence
 Sequence SimpleRichSequenceBuilder.makeSequence()
          Return the Sequence object which has been constructed by this builder.
 Sequence RichSequenceBuilder.makeSequence()
          Return the Sequence object which has been constructed by this builder.
 Sequence RichStreamReader.nextSequence()
          Returns the next sequence in the iterator.
 Sequence HashedFastaIterator.nextSequence()
           
 

Methods in org.biojavax.bio.seq.io with parameters of type Sequence
 void EMBLxmlFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void FastaFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void UniProtXMLFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void EMBLFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void UniProtFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void GenbankFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void RichSequenceFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void INSDseqFormat.writeSequence(Sequence seq, Namespace ns)
          Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
 void EMBLxmlFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void FastaFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void UniProtXMLFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void EMBLFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void UniProtFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void GenbankFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void INSDseqFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void EMBLFormat.writeSequence(Sequence seq, java.lang.String format, Namespace ns)
          As per EMBLFormat.writeSequence(Sequence, Namespace), except that it also takes a format parameter.
 void EMBLxmlFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the specified format.
 void FastaFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the specified format.
 void UniProtXMLFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the specified format.
 void EMBLFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the specified format.
 void UniProtFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the specified format.
 void GenbankFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the specified format.
 void INSDseqFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the specified format.