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

Packages that use Sequence

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
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.fastq	FASTQ and variants sequence format I/O.
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.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.alignment

Methods in org.biojava.bio.alignment with parameters of type Sequence

Modifier and Type	Method	Description
static AlignmentPair	AlignmentPair.align(Sequence query, Sequence subject, AlignmentAlgorithm algorithm)

Constructors in org.biojava.bio.alignment with parameters of type Sequence

Constructor	Description
AlignmentPair(Sequence query, Sequence subject, int queryStart, int queryEnd, int subjectStart, int subjectEnd, SubstitutionMatrix subMatrix)
AlignmentPair(Sequence query, Sequence subject, SubstitutionMatrix subMatrix)

Uses of Sequence in org.biojava.bio.dist

Methods in org.biojava.bio.dist that return Sequence

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
Sequence	WeightMatrixAnnotator.annotate(Sequence seq)

Methods in org.biojava.bio.dp with parameters of type Sequence

Modifier and Type	Method	Description
Sequence	WeightMatrixAnnotator.annotate(Sequence seq)

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

Methods in org.biojava.bio.gui.sequence that return Sequence

Modifier and Type	Method	Description
Sequence	PairwiseSequencePanel.getSecondarySequence()	getSecondarySequence returns the entire secondary Sequence currently being rendered.
Sequence	PairwiseSequencePanel.getSequence()	getSequence returns the entire Sequence currently being rendered.
Sequence	SequencePanelWrapper.getSequence()
Sequence	SequencePoster.getSequence()	Deprecated.

Methods in org.biojava.bio.gui.sequence with parameters of type Sequence

Modifier and Type	Method	Description
void	PairwiseSequencePanel.setSecondarySequence(Sequence sequence)	setSecondarySequence sets the secondary Sequence to be rendered.
void	PairwiseSequencePanel.setSequence(Sequence sequence)	setSequence sets the Sequence to be rendered.
void	SequencePanelWrapper.setSequence(Sequence seq)
void	SequencePoster.setSequence(Sequence s)	Deprecated. Set the SymboList to be rendered.

Constructors in org.biojava.bio.gui.sequence with parameters of type Sequence

Constructor	Description
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

Modifier and Type	Method	Description
void	SimpleTrackLayout.setSequence(Sequence seq)
void	TrackLayout.setSequence(Sequence seq)
void	UserDefinedTrackLayout.setSequence(Sequence seq)

Constructors in org.biojava.bio.gui.sequence.tracklayout with parameters of type Sequence

Constructor	Description
SimpleTrackLayout(Sequence seq, int wrap)

Uses of Sequence in org.biojava.bio.molbio

Methods in org.biojava.bio.molbio that return Sequence

Modifier and Type	Method	Description
Sequence	RestrictionMapper.annotate(Sequence sequence)	annotate adds Features which represent restriction sites.

Methods in org.biojava.bio.molbio with parameters of type Sequence

Modifier and Type	Method	Description
Sequence	RestrictionMapper.annotate(Sequence sequence)	annotate adds Features which represent restriction sites.

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

Methods in org.biojava.bio.program.fastq that return Sequence

Modifier and Type	Method	Description
static Sequence	FastqTools.createDNASequence(Fastq fastq)	Create and return a new DNA Sequence from the specified FASTQ formatted sequence.

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

Methods in org.biojava.bio.program.gff that return Sequence

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
Sequence	Digest.getSequence()

Methods in org.biojava.bio.proteomics with parameters of type Sequence

Modifier and Type	Method	Description
void	Digest.setSequence(Sequence sequence)

Uses of Sequence in org.biojava.bio.search

Methods in org.biojava.bio.search that return Sequence

Modifier and Type	Method	Description
Sequence	SeqSimilaritySearchResult.getQuerySequence()	Returns the query sequence which was used to perform the search.
Sequence	SequenceDBSearchResult.getQuerySequence()	Deprecated.
Sequence	SimpleSeqSimilaritySearchResult.getQuerySequence()

Constructors in org.biojava.bio.search with parameters of type Sequence

Constructor	Description
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

Modifier and Type	Interface	Description
interface	GappedSequence	Extension of GappedSymbolList which also projects features into the gapped coordinate system.

Classes in org.biojava.bio.seq that implement Sequence

Modifier and Type	Class	Description
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

Modifier and Type	Field	Description
Sequence	ComponentFeature.Template.componentSequence

Methods in org.biojava.bio.seq that return Sequence

Modifier and Type	Method	Description
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(String uri, String name)	Create a new Sequence that has no annotation, no features and a zero-length symbol list.
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	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.
Sequence	SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)	Deprecated. Creates a sequence using these parameters.
static Sequence	SequenceTools.createSequence(SymbolList syms, String uri, 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, 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

Modifier and Type	Method	Description
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, 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, 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.
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.

Constructors in org.biojava.bio.seq with parameters of type Sequence

Constructor	Description
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

Modifier and Type	Method	Description
protected Sequence	AnnotatedSequenceDB.doAnnotation(Sequence seq)	Apply the annotation to a sequence.
Sequence	AnnotatedSequenceDB.getSequence(String id)
Sequence	CachingSequenceDB.getSequence(String id)
Sequence	DummySequenceDB.getSequence(String id)
Sequence	GenbankSequenceDB.getSequence(String id)
Sequence	GenpeptSequenceDB.getSequence(String id)
Sequence	HashSequenceDB.getSequence(String id)
Sequence	IndexedSequenceDB.getSequence(String id)
Sequence	SequenceDBLite.getSequence(String id)	Retrieve a single sequence by its id.
Sequence	SubSequenceDB.getSequence(String id)
Sequence	SwissprotSequenceDB.getSequence(String id)
Sequence	ViewingSequenceDB.getSequence(String id)
Sequence	WebSequenceDB.getSequence(String id)	Gets a sequence using its unique ID (eg for GenBank this would be the GI number)

Methods in org.biojava.bio.seq.db with parameters of type Sequence

Modifier and Type	Method	Description
void	AbstractSequenceDB.addSequence(Sequence seq)
void	DummySequenceDB.addSequence(Sequence seq)
void	HashSequenceDB.addSequence(String id, Sequence seq)	Add a sequence under a particular id.
void	HashSequenceDB.addSequence(Sequence seq)
void	SequenceDBLite.addSequence(Sequence seq)	Adds a sequence to the database.
void	WebSequenceDB.addSequence(Sequence seq)	Not supported, You can't add sequences to a WebDB!
String	IDMaker.ByName.calcID(Sequence seq)
String	IDMaker.ByURN.calcID(Sequence seq)
String	IDMaker.calcID(Sequence seq)	Calculate the id for a sequence.
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

Modifier and Type	Method	Description
Sequence	BioFetchSequenceDB.getSequence(String id)

Methods in org.biojava.bio.seq.db.biofetch with parameters of type Sequence

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
Sequence	FlatSequenceDB.getSequence(String id)

Methods in org.biojava.bio.seq.db.flat with parameters of type Sequence

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
Sequence	DistDataSource.getSequence(String id)	Get a Sequence object for an ID.
Sequence	DistributedSequenceDB.getSequence(String id)
Sequence	GFFDataSource.getSequence(String id)
Sequence	SequenceDBDataSource.getSequence(String id)

Methods in org.biojava.bio.seq.distributed with parameters of type Sequence

Modifier and Type	Method	Description
void	DistributedSequenceDB.addSequence(Sequence seq)

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

Classes in org.biojava.bio.seq.impl that implement Sequence

Modifier and Type	Class	Description
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

Modifier and Type	Field	Description
protected Sequence	RevCompSequence.origSeq

Methods in org.biojava.bio.seq.impl that return Sequence

Modifier and Type	Method	Description
Sequence	SimpleSequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)
Sequence	SimpleFeature.getSequence()
Sequence	SubSequence.getSequence()	Return the parent sequence of which this is a partial view

Constructors in org.biojava.bio.seq.impl with parameters of type Sequence

Constructor	Description
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, String name)	Construct a view onto an existing sequence and give it a new name.
ViewSequence(Sequence seq, FeatureRealizer fr)	Construct a view onto a sequence, using a specific FeatureRealizer.

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

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

Modifier and Type	Field	Description
protected Sequence	SequenceBuilderBase.seq

Methods in org.biojava.bio.seq.io that return Sequence

Modifier and Type	Method	Description
Sequence	SequenceBuilder.makeSequence()	Return the Sequence object which has been constructed by this builder.
Sequence	SequenceBuilderBase.makeSequence()
Sequence	SequenceBuilderFilter.makeSequence()
Sequence	SequenceDBSequenceBuilder.makeSequence()	create the sequence
Sequence	SimpleAssemblyBuilder.makeSequence()
Sequence	SimpleSequenceBuilder.makeSequence()
Sequence	SmartSequenceBuilder.makeSequence()
Sequence	StreamReader.nextSequence()	Pull the next sequence out of the stream.

Methods in org.biojava.bio.seq.io with parameters of type Sequence

Modifier and Type	Method	Description
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	EmblLikeFormat.writeSequence(Sequence seq, PrintStream os)	Deprecated.
void	EmblLikeFormat.writeSequence(Sequence seq, String format, PrintStream os)	Deprecated. use 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	FastaFormat.writeSequence(Sequence seq, String format, PrintStream os)	Deprecated. use writeSequence(Sequence seq, PrintStream os)
void	GAMEFormat.writeSequence(Sequence seq, PrintStream os)
void	GAMEFormat.writeSequence(Sequence seq, String format, PrintStream os)
void	GenbankFormat.writeSequence(Sequence seq, PrintStream os)	Deprecated.
void	GenbankFormat.writeSequence(Sequence seq, String format, PrintStream os)	Deprecated. use writeSequence(Sequence seq, PrintStream os)
void	SequenceFormat.writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	SequenceFormat.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

Modifier and Type	Field	Description
protected Sequence	AGAVEBioSeqHandler.sequence
protected Sequence	AGAVEContigHandler.sequence

Methods in org.biojava.bio.seq.io.agave with parameters of type Sequence

Modifier and Type	Method	Description
protected void	StAXFeatureHandler.addFeatureToSequence(Sequence seq)
void	AGAVECallbackItf.reportSequence(Sequence sequence)
void	AGAVEChromosomeCallbackItf.reportSequence(Sequence sequence)
void	AGAVEChromosomeHandler.reportSequence(Sequence sequence)
void	AGAVEContigCallbackItf.reportSequence(Sequence sequence)
void	AGAVEContigHandler.reportSequence(Sequence sequence)
void	AGAVEHandler.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

Modifier and Type	Method	Description
Sequence	ProjectedFeature.getSequence()
Sequence	ProjectionContext.getSequence(Feature projFeat)	Get the sequence for a feature.
Sequence	ReparentContext.getSequence(Feature f)

Uses of Sequence in org.biojavax.bio.db

Methods in org.biojavax.bio.db that return Sequence

Modifier and Type	Method	Description
Sequence	AbstractRichSequenceDB.getSequence(String id)

Methods in org.biojavax.bio.db with parameters of type Sequence

Modifier and Type	Method	Description
void	AbstractRichSequenceDB.addSequence(Sequence seq)

Uses of Sequence in org.biojavax.bio.seq

Subinterfaces of Sequence in org.biojavax.bio.seq

Modifier and Type	Interface	Description
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

Modifier and Type	Class	Description
class	SimpleRichSequence	A simple implementation of RichSequence.
class	ThinRichSequence	A simple implementation of RichSequence.

Methods in org.biojavax.bio.seq that return Sequence

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Constructor	Description
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

Modifier and Type	Method	Description
Sequence	RichSequenceBuilder.makeSequence()	Return the Sequence object which has been constructed by this builder.
Sequence	SimpleRichSequenceBuilder.makeSequence()	Return the Sequence object which has been constructed by this builder.
Sequence	HashedFastaIterator.nextSequence()
Sequence	RichStreamReader.nextSequence()	Returns the next sequence in the iterator.

Methods in org.biojavax.bio.seq.io with parameters of type Sequence

Modifier and Type	Method	Description
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, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified 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	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	EMBLxmlFormat.writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	EMBLxmlFormat.writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.
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, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	FastaFormat.writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.
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	GenbankFormat.writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	GenbankFormat.writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.
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	INSDseqFormat.writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	INSDseqFormat.writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.
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	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	UniProtFormat.writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	UniProtFormat.writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.
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	UniProtXMLFormat.writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	UniProtXMLFormat.writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.
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.