## 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(String name, OrderNDistribution d, int length)` Deprecated. use generateSequence() or generateSymbolList() instead.
`static Sequence` `DistributionTools.generateSequence(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` `SequencePoster.getSequence()` Deprecated.
`Sequence` `SequencePanelWrapper.getSequence()`
`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` `SequencePoster.setSequence(Sequence s)` Deprecated. Set the SymboList to be rendered.
`void` `SequencePanelWrapper.setSequence(Sequence seq)`
`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` `UserDefinedTrackLayout.setSequence(Sequence seq)`
`void` `TrackLayout.setSequence(Sequence seq)`
`void` `SimpleTrackLayout.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 `Feature`s which represent restriction sites.

Methods in org.biojava.bio.molbio with parameters of type Sequence
`Sequence` `RestrictionMapper.annotate(Sequence sequence)` `annotate` adds `Feature`s 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(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, String id)` Emit any per-sequence header information.
`protected void` `SequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, 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 String` `PhredFormat.describeSequence(Sequence seq)` Return a suitable description line for a Sequence.
`void` `PhredFormat.writeSequence(Sequence seq, PrintStream os)` This method will print symbols to the line width followed by a new line etc.
`void` `PhredFormat.writeSequence(Sequence seq, String format, 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(String queryID)`
`Sequence` `SimilarityPairBuilder.getAnnotatedSubjectSeq(String subjectID)`
`protected Sequence` `ViewSequenceFactory.makeQueryViewSequence(String queryID)`
`protected Sequence` `ViewSequenceFactory.makeSubjectViewSequence(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(File xffFile, String seqID)`
`static Sequence` `XFFTools.readXFF(File xffFile, String seqID, FiniteAlphabet alpha)`

Methods in org.biojava.bio.program.xff with parameters of type Sequence
`static void` `XFFTools.annotateXFF(File xffFile, Sequence sequence)`
`static void` `XFFTools.annotateXFF(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` `SequenceDBSearchResult.getQuerySequence()` Deprecated.
`Sequence` `SeqSimilaritySearchResult.getQuerySequence()` Returns the query sequence which was used to perform the search.

Constructors in org.biojava.bio.search with parameters of type Sequence
`SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation)` Deprecated. Creates a new `SequenceDBSearchResult`.
`SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, 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(String dna, String name)` Return a new DNA Sequence for dna.
`static Sequence` `SequenceTools.createDummy(Alphabet alpha, int length, Symbol sym, String uri, String name)` Create a new Sequence that contains a single symbol repeated over and over.
`static Sequence` `SequenceTools.createDummy(String uri, String name)` Create a new Sequence that has no annotation, no features and a zero-length symbol list.
`static Sequence` `NucleotideTools.createNucleotideSequence(String nucleotide, String name)` Return a new Nucleotide Sequence for nucleotide.
`static Sequence` `ProteinTools.createProteinSequence(String protein, String name)` Return a new PROTEIN Sequence for protein.
`static Sequence` `RNATools.createRNASequence(String rna, String name)` Return a new RNA Sequence for rna.
`static Sequence` `SequenceTools.createSequence(SymbolList syms, String uri, String name, Annotation ann)`
`Sequence` `SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)` Deprecated. Creates a sequence using these parameters.
`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, String name)` Extract a sub-sequence from a sequence.
`static Sequence` `SequenceTools.subSequence(Sequence seq, int start, int end, 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` `SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)`
`Feature` `FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)` Install a feature on the specified sequence.
`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, String name)` Extract a sub-sequence from a sequence.
`static Sequence` `SequenceTools.subSequence(Sequence seq, int start, int end, 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, 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` `WebSequenceDB.getSequence(String id)` Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
`Sequence` `ViewingSequenceDB.getSequence(String id)`
`Sequence` `SwissprotSequenceDB.getSequence(String id)`
`Sequence` `SubSequenceDB.getSequence(String id)`
`Sequence` `SequenceDBLite.getSequence(String id)` Retrieve a single sequence by its id.
`Sequence` `IndexedSequenceDB.getSequence(String id)`
`Sequence` `HashSequenceDB.getSequence(String id)`
`Sequence` `GenpeptSequenceDB.getSequence(String id)`
`Sequence` `GenbankSequenceDB.getSequence(String id)`
`Sequence` `DummySequenceDB.getSequence(String id)`
`Sequence` `CachingSequenceDB.getSequence(String id)`
`Sequence` `AnnotatedSequenceDB.getSequence(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` `SequenceDBLite.addSequence(Sequence seq)` Adds a sequence to the database.
`void` `HashSequenceDB.addSequence(Sequence seq)`
`void` `DummySequenceDB.addSequence(Sequence seq)`
`void` `AbstractSequenceDB.addSequence(Sequence seq)`
`void` `HashSequenceDB.addSequence(String id, Sequence seq)` Add a sequence under a particular id.
`String` `IDMaker.calcID(Sequence seq)` Calculate the id for a sequence.
`String` `IDMaker.ByURN.calcID(Sequence seq)`
`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(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(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(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` `SequenceDBDataSource.getSequence(String id)`
`Sequence` `GFFDataSource.getSequence(String id)`
`Sequence` `DistributedSequenceDB.getSequence(String id)`
`Sequence` `DistDataSource.getSequence(String id)` Get a Sequence object for an 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, String uri, 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, String urn, 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, 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, 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` `SmartSequenceBuilder.makeSequence()`
`Sequence` `SimpleSequenceBuilder.makeSequence()`
`Sequence` `SimpleAssemblyBuilder.makeSequence()`
`Sequence` `SequenceDBSequenceBuilder.makeSequence()` create the sequence
`Sequence` `SequenceBuilderFilter.makeSequence()`
`Sequence` `SequenceBuilderBase.makeSequence()`
`Sequence` `SequenceBuilder.makeSequence()` Return the Sequence object which has been constructed by this builder.
`Sequence` `StreamReader.nextSequence()` Pull the next sequence out of the stream.

Methods in org.biojava.bio.seq.io with parameters of type Sequence
`protected 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(OutputStream os, Sequence seq)` Deprecated. Writes a single Sequence to an OutputStream in EMBL format.
`static void` `SeqIOTools.writeFasta(OutputStream os, Sequence seq)` Deprecated. Writes a single Sequence to an OutputStream in Fasta format.
`static void` `SeqIOTools.writeGenbank(OutputStream os, Sequence seq)` Deprecated. Writes a single Sequence to an OutputStream in Genbank format.
`static void` `SeqIOTools.writeGenpept(OutputStream os, Sequence seq)` Deprecated. Writes a single Sequence to an OutputStream in Genpept format.
`void` `SequenceFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `GenbankFormat.writeSequence(Sequence seq, PrintStream os)` Deprecated.
`void` `GAMEFormat.writeSequence(Sequence seq, PrintStream os)`
`void` `FastaFormat.writeSequence(Sequence seq, PrintStream os)` Deprecated. Writes a `Sequence` or `RichSequence` to a `PrintStream` in FASTA format.
`void` `EmblLikeFormat.writeSequence(Sequence seq, PrintStream os)` Deprecated.
`void` `SequenceFormat.writeSequence(Sequence seq, String format, PrintStream os)` Deprecated. use writeSequence(Sequence seq, PrintStream os)
`void` `GenbankFormat.writeSequence(Sequence seq, String format, PrintStream os)` Deprecated. use writeSequence(Sequence seq, PrintStream os)
`void` `GAMEFormat.writeSequence(Sequence seq, String format, PrintStream os)`
`void` `FastaFormat.writeSequence(Sequence seq, String format, PrintStream os)` Deprecated. use writeSequence(Sequence seq, PrintStream os)
`void` `EmblLikeFormat.writeSequence(Sequence seq, String format, PrintStream os)` Deprecated. use writeSequence(Sequence seq, PrintStream os)
`static void` `SeqIOTools.writeSwissprot(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` `AGAVEContigHandler.sequence`
`protected Sequence` `AGAVEBioSeqHandler.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` `AGAVEContigHandler.reportSequence(Sequence sequence)`
`void` `AGAVEContigCallbackItf.reportSequence(Sequence sequence)`
`void` `AGAVEChromosomeHandler.reportSequence(Sequence sequence)`
`void` `AGAVEChromosomeCallbackItf.reportSequence(Sequence sequence)`
`void` `AGAVECallbackItf.reportSequence(Sequence sequence)`
`protected void` `AgaveWriter.write(Sequence seq)` Writing Sequence.
`void` `AgaveWriter.writeSequence(Sequence seq, 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` `ReparentContext.getSequence(Feature f)`
`Sequence` `ProjectionContext.getSequence(Feature projFeat)` Get the sequence for a feature.

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(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(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in EMBL format.
`static void` `RichSequence.IOTools.writeEMBLxml(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in EMBLxml format.
`static void` `RichSequence.IOTools.writeFasta(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in Fasta format.
`static void` `RichSequence.IOTools.writeFasta(OutputStream os, Sequence seq, Namespace ns, FastaHeader header)` Writes a single `Sequence` to an `OutputStream` in Fasta format.
`static void` `RichSequence.IOTools.writeGenbank(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in GenBank format.
`static void` `RichSequence.IOTools.writeINSDseq(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in INSDseq format.
`static void` `RichSequence.IOTools.writeUniProt(OutputStream os, Sequence seq, Namespace ns)` Writes a single `Sequence` to an `OutputStream` in UniProt format.
`static void` `RichSequence.IOTools.writeUniProtXML(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. Implementations of this for a RichSequenceBuilder should delegate to makeRichSequence() and return only RichSequence objects.
`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` `UniProtXMLFormat.writeSequence(Sequence seq, Namespace ns)` Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is null, then the sequence's own namespace is used.
`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. Namespace is ignored as UniProt has no concept of it.
`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. Namespace is ignored as INSDseq has no concept of it.
`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. Namespace is ignored as Genbank has no concept of it.
`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. If namespace is null, then the sequence's own namespace is used.
`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. Namespace is ignored as EMBLxml has no concept of it.
`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. Namespace is ignored as EMBL has no concept of it.
`void` `UniProtXMLFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `UniProtFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `INSDseqFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `GenbankFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `FastaFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `EMBLxmlFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `EMBLFormat.writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `EMBLFormat.writeSequence(Sequence seq, String format, Namespace ns)` As per `EMBLFormat.writeSequence(Sequence, Namespace)`, except that it also takes a format parameter.
`void` `UniProtXMLFormat.writeSequence(Sequence seq, String format, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
`void` `UniProtFormat.writeSequence(Sequence seq, String format, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
`void` `INSDseqFormat.writeSequence(Sequence seq, String format, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
`void` `GenbankFormat.writeSequence(Sequence seq, String format, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
`void` `FastaFormat.writeSequence(Sequence seq, String format, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
`void` `EMBLxmlFormat.writeSequence(Sequence seq, String format, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
`void` `EMBLFormat.writeSequence(Sequence seq, String format, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.