Uses of Interface
org.biojava.bio.seq.Sequence
Packages that use Sequence
Package
Description
Classes to generate and describe sequence alignments.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical displays of biological sequences and associated annotations.
Classes for the handling of the layout of a WrappedSequencePanel.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
FASTQ and variants sequence format I/O.
GFF manipulation.
Parser for Phred output
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Objects for representing Unigene clusters.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utilities to aid in performing various physical analysis of proteins.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
Standard in-memory implementations of
Sequence and
Feature.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Code for projecting Feature objects and systematically altering their
properties.
Interactions between biojavax objects and a DB.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of Sequence in org.biojava.bio.alignment
Methods in org.biojava.bio.alignment with parameters of type SequenceModifier and TypeMethodDescriptionstatic AlignmentPairAlignmentPair.align(Sequence query, Sequence subject, AlignmentAlgorithm algorithm) Constructors in org.biojava.bio.alignment with parameters of type SequenceModifierConstructorDescriptionAlignmentPair(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 SequenceModifier and TypeMethodDescriptionprotected static final SequenceDistributionTools.generateOrderNSequence(String name, OrderNDistribution d, int length) Deprecated.use generateSequence() or generateSymbolList() instead.static final SequenceDistributionTools.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 SequenceMethods in org.biojava.bio.dp with parameters of type Sequence -
Uses of Sequence in org.biojava.bio.gui.sequence
Methods in org.biojava.bio.gui.sequence that return SequenceModifier and TypeMethodDescriptionPairwiseSequencePanel.getSecondarySequence()getSecondarySequencereturns the entire secondarySequencecurrently being rendered.PairwiseSequencePanel.getSequence()getSequencereturns the entireSequencecurrently being rendered.SequencePanelWrapper.getSequence()SequencePoster.getSequence()Deprecated.Methods in org.biojava.bio.gui.sequence with parameters of type SequenceModifier and TypeMethodDescriptionvoidPairwiseSequencePanel.setSecondarySequence(Sequence sequence) setSecondarySequencesets the secondarySequenceto be rendered.voidPairwiseSequencePanel.setSequence(Sequence sequence) setSequencesets theSequenceto be rendered.voidSequencePanelWrapper.setSequence(Sequence seq) voidSequencePoster.setSequence(Sequence s) Deprecated.Set the SymboList to be rendered.Constructors in org.biojava.bio.gui.sequence with parameters of type SequenceModifierConstructorDescriptionHeadlessRenderContext(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 SequenceModifier and TypeMethodDescriptionvoidSimpleTrackLayout.setSequence(Sequence seq) voidTrackLayout.setSequence(Sequence seq) voidUserDefinedTrackLayout.setSequence(Sequence seq) Constructors in org.biojava.bio.gui.sequence.tracklayout with parameters of type Sequence -
Uses of Sequence in org.biojava.bio.molbio
Methods in org.biojava.bio.molbio that return SequenceModifier and TypeMethodDescriptionannotateaddsFeatures which represent restriction sites.Methods in org.biojava.bio.molbio with parameters of type Sequence -
Uses of Sequence in org.biojava.bio.program.fastq
Methods in org.biojava.bio.program.fastq that return SequenceModifier and TypeMethodDescriptionstatic SequenceFastqTools.createDNASequence(Fastq fastq) Create and return a new DNASequencefrom the specified FASTQ formatted sequence. -
Uses of Sequence in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff that return SequenceModifier and TypeMethodDescriptionstatic SequenceGFFTools.annotateSequence(Sequence seq, GFFEntrySet ents) Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.static SequenceGFFTools.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 SequenceModifier and TypeMethodDescriptionstatic SequenceGFFTools.annotateSequence(Sequence seq, GFFEntrySet ents) Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.static SequenceGFFTools.annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName) Annotates a sequence with the features from a GFF entry set.protected voidSequencesAsGFF.doPreProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) Emit any per-sequence header information.protected voidSequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) Internal method to process an individual Sequence.static GFFEntrySetGFFTools.gffFromSequence(Sequence seq) Creates a GFFEntrySet containing one entry for each feature on a sequence.voidSequencesAsGFF.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 SequenceModifier and TypeClassDescriptionclassPhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.Methods in org.biojava.bio.program.phred with parameters of type SequenceModifier and TypeMethodDescriptionprotected StringPhredFormat.describeSequence(Sequence seq) Return a suitable description line for a Sequence.voidPhredFormat.writeSequence(Sequence seq, PrintStream os) This method will print symbols to the line width followed by a new line etc.voidPhredFormat.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 SequenceModifier and TypeMethodDescriptionSimilarityPairBuilder.getAnnotatedQuerySeq(String queryID) SimilarityPairBuilder.getAnnotatedSubjectSeq(String subjectID) protected SequenceViewSequenceFactory.makeQueryViewSequence(String queryID) protected SequenceViewSequenceFactory.makeSubjectViewSequence(String subjectID) -
Uses of Sequence in org.biojava.bio.program.unigene
Methods in org.biojava.bio.program.unigene that return Sequence -
Uses of Sequence in org.biojava.bio.program.xff
Methods in org.biojava.bio.program.xff that return SequenceModifier and TypeMethodDescriptionstatic Sequencestatic SequenceXFFTools.readXFF(File xffFile, String seqID, FiniteAlphabet alpha) Methods in org.biojava.bio.program.xff with parameters of type SequenceModifier and TypeMethodDescriptionstatic voidXFFTools.annotateXFF(File xffFile, Sequence sequence) static voidXFFTools.annotateXFF(File xffFile, Sequence sequence, Annotation ann) -
Uses of Sequence in org.biojava.bio.proteomics
Methods in org.biojava.bio.proteomics that return SequenceMethods in org.biojava.bio.proteomics with parameters of type Sequence -
Uses of Sequence in org.biojava.bio.search
Methods in org.biojava.bio.search that return SequenceModifier and TypeMethodDescriptionSeqSimilaritySearchResult.getQuerySequence()Returns the query sequence which was used to perform the search.SequenceDBSearchResult.getQuerySequence()Deprecated.SimpleSeqSimilaritySearchResult.getQuerySequence()Constructors in org.biojava.bio.search with parameters of type SequenceModifierConstructorDescriptionSequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Deprecated.Creates a newSequenceDBSearchResult.SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Creates a newSimpleSeqSimilaritySearchResult. -
Uses of Sequence in org.biojava.bio.seq
Subinterfaces of Sequence in org.biojava.bio.seqModifier and TypeInterfaceDescriptioninterfaceExtension of GappedSymbolList which also projects features into the gapped coordinate system.Classes in org.biojava.bio.seq that implement SequenceModifier and TypeClassDescriptionclassA circular view onto another Sequence object.classA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.classA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.Fields in org.biojava.bio.seq declared as SequenceMethods in org.biojava.bio.seq that return SequenceModifier and TypeMethodDescriptionReturn an annotated version of a sequence.static SequenceDNATools.createDNASequence(String dna, String name) Return a new DNA Sequence for dna.static SequenceSequenceTools.createDummy(String uri, String name) Create a new Sequence that has no annotation, no features and a zero-length symbol list.static SequenceSequenceTools.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 SequenceNucleotideTools.createNucleotideSequence(String nucleotide, String name) Return a new Nucleotide Sequence for nucleotide.static SequenceProteinTools.createProteinSequence(String protein, String name) Return a new PROTEIN Sequence for protein.static SequenceRNATools.createRNASequence(String rna, String name) Return a new RNA Sequence for rna.SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation) Deprecated.Creates a sequence using these parameters.static SequenceSequenceTools.createSequence(SymbolList syms, String uri, String name, Annotation ann) ComponentFeature.getComponentSequence()Get the sequence object which provides a component of this feature's parent sequence.Feature.getSequence()Return theSequenceobject to which this feature is (ultimately) attached.static SequenceSequenceTools.maskSequence(Sequence seq, RangeLocation loc) Mask of a sequence.SequenceIterator.nextSequence()Returns the next sequence in the iterator.static SequenceSequenceTools.reverseComplement(Sequence seq) Reverse-complement a sequence, and flip all of its features.static SequenceSequenceTools.subSequence(Sequence seq, int start, int end) Extract a sub-sequence from a sequence.static SequenceSequenceTools.subSequence(Sequence seq, int start, int end, String name) Extract a sub-sequence from a sequence.static SequenceSequenceTools.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 SequenceModifier and TypeMethodDescriptionstatic voidSequenceTools.addAllFeatures(Sequence seq, FeatureHolder fh) Add features to a sequence that contain the same information as all those in a feature holder.Return an annotated version of a sequence.static GappedSequenceSequenceTools.gappedView(Sequence seq) Create a new gapped sequence for a sequence.static SequenceSequenceTools.maskSequence(Sequence seq, RangeLocation loc) Mask of a sequence.FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template) Install a feature on the specified sequence.SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp) static SequenceSequenceTools.reverseComplement(Sequence seq) Reverse-complement a sequence, and flip all of its features.static SequenceSequenceTools.subSequence(Sequence seq, int start, int end) Extract a sub-sequence from a sequence.static SequenceSequenceTools.subSequence(Sequence seq, int start, int end, String name) Extract a sub-sequence from a sequence.static SequenceSequenceTools.subSequence(Sequence seq, int start, int end, String name, StrandedFeature.Strand strand) Extract a sub-sequence from a sequence.static ViewSequenceCreate 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 ViewSequenceCreate 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 ViewSequenceSequenceTools.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 SequenceModifierConstructorDescriptionCircularView(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 SequenceModifier and TypeMethodDescriptionprotected SequenceAnnotatedSequenceDB.doAnnotation(Sequence seq) Apply the annotation to a sequence.AnnotatedSequenceDB.getSequence(String id) CachingSequenceDB.getSequence(String id) DummySequenceDB.getSequence(String id) GenbankSequenceDB.getSequence(String id) GenpeptSequenceDB.getSequence(String id) HashSequenceDB.getSequence(String id) IndexedSequenceDB.getSequence(String id) SequenceDBLite.getSequence(String id) Retrieve a single sequence by its id.SubSequenceDB.getSequence(String id) SwissprotSequenceDB.getSequence(String id) ViewingSequenceDB.getSequence(String id) 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 SequenceModifier and TypeMethodDescriptionvoidAbstractSequenceDB.addSequence(Sequence seq) voidDummySequenceDB.addSequence(Sequence seq) voidHashSequenceDB.addSequence(String id, Sequence seq) Add a sequence under a particular id.voidHashSequenceDB.addSequence(Sequence seq) voidSequenceDBLite.addSequence(Sequence seq) Adds a sequence to the database.voidWebSequenceDB.addSequence(Sequence seq) Not supported, You can't add sequences to a WebDB!Calculate the id for a sequence.protected SequenceAnnotatedSequenceDB.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 SequenceMethods in org.biojava.bio.seq.db.biofetch with parameters of type Sequence -
Uses of Sequence in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql that return SequenceModifier and TypeMethodDescriptionBioSQLSequenceDB.getSequence(int bioentry_id) Deprecated.BioSQLSequenceDB.getSequence(String id) Deprecated.Methods in org.biojava.bio.seq.db.biosql with parameters of type Sequence -
Uses of Sequence in org.biojava.bio.seq.db.flat
Methods in org.biojava.bio.seq.db.flat that return SequenceMethods in org.biojava.bio.seq.db.flat with parameters of type SequenceModifier and TypeMethodDescriptionvoidFlatSequenceDB.addSequence(Sequence sequence) addSequencealways throws aChangeVetoExceptionas this implementation is immutable. -
Uses of Sequence in org.biojava.bio.seq.distributed
Methods in org.biojava.bio.seq.distributed that return SequenceModifier and TypeMethodDescriptionDistDataSource.getSequence(String id) Get a Sequence object for an ID.DistributedSequenceDB.getSequence(String id) GFFDataSource.getSequence(String id) SequenceDBDataSource.getSequence(String id) Methods in org.biojava.bio.seq.distributed with parameters of type Sequence -
Uses of Sequence in org.biojava.bio.seq.impl
Classes in org.biojava.bio.seq.impl that implement SequenceModifier and TypeClassDescriptionfinal classA Sequence implementation that has a name and URI but no features, and a zero length symbol list.classA reverse complement view ontoSequenceinterface.classSimple implementation of GappedSequence.classA basic implementation of theSequenceinterface.classView a sub-section of a given sequence object, including all the features intersecting that region.classA view onto another Sequence object.Fields in org.biojava.bio.seq.impl declared as SequenceMethods in org.biojava.bio.seq.impl that return SequenceModifier and TypeMethodDescriptionSimpleSequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation) SimpleFeature.getSequence()SubSequence.getSequence()Return the parent sequence of which this is a partial viewConstructors in org.biojava.bio.seq.impl with parameters of type SequenceModifierConstructorDescriptionRevCompSequence(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 aSimpleFeatureon the given sequence.SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template) 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 newSimpleRestrictionSite.SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template) Creates a newSimpleSimilarityPairFeature.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 SequenceMethods in org.biojava.bio.seq.io that return SequenceModifier and TypeMethodDescriptionSequenceBuilder.makeSequence()Return the Sequence object which has been constructed by this builder.SequenceBuilderBase.makeSequence()SequenceBuilderFilter.makeSequence()SequenceDBSequenceBuilder.makeSequence()create the sequenceSimpleAssemblyBuilder.makeSequence()SimpleSequenceBuilder.makeSequence()SmartSequenceBuilder.makeSequence()StreamReader.nextSequence()Pull the next sequence out of the stream.Methods in org.biojava.bio.seq.io with parameters of type SequenceModifier and TypeMethodDescriptionprotected StringFastaFormat.describeSequence(Sequence seq) Deprecated.Return a suitable description line for a Sequence.voidSeqIOEventEmitter.getSeqIOEvents(Sequence seq, SeqIOListener listener) Deprecated.getSeqIOEventsscans aSequenceobject and sends events describing its data to theSeqIOListener.static voidSeqIOTools.writeEmbl(OutputStream os, Sequence seq) Deprecated.Writes a single Sequence to an OutputStream in EMBL format.static voidSeqIOTools.writeFasta(OutputStream os, Sequence seq) Deprecated.Writes a single Sequence to an OutputStream in Fasta format.static voidSeqIOTools.writeGenbank(OutputStream os, Sequence seq) Deprecated.Writes a single Sequence to an OutputStream in Genbank format.static voidSeqIOTools.writeGenpept(OutputStream os, Sequence seq) Deprecated.Writes a single Sequence to an OutputStream in Genpept format.voidEmblLikeFormat.writeSequence(Sequence seq, PrintStream os) Deprecated.voidEmblLikeFormat.writeSequence(Sequence seq, String format, PrintStream os) Deprecated.use writeSequence(Sequence seq, PrintStream os)voidFastaFormat.writeSequence(Sequence seq, PrintStream os) Deprecated.Writes aSequenceorRichSequenceto aPrintStreamin FASTA format.voidFastaFormat.writeSequence(Sequence seq, String format, PrintStream os) Deprecated.use writeSequence(Sequence seq, PrintStream os)voidGAMEFormat.writeSequence(Sequence seq, PrintStream os) voidGAMEFormat.writeSequence(Sequence seq, String format, PrintStream os) voidGenbankFormat.writeSequence(Sequence seq, PrintStream os) Deprecated.voidGenbankFormat.writeSequence(Sequence seq, String format, PrintStream os) Deprecated.use writeSequence(Sequence seq, PrintStream os)voidSequenceFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidSequenceFormat.writeSequence(Sequence seq, String format, PrintStream os) Deprecated.use writeSequence(Sequence seq, PrintStream os)static voidSeqIOTools.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 SequenceModifier and TypeFieldDescriptionprotected SequenceAGAVEBioSeqHandler.sequenceprotected SequenceAGAVEContigHandler.sequenceMethods in org.biojava.bio.seq.io.agave with parameters of type SequenceModifier and TypeMethodDescriptionprotected voidStAXFeatureHandler.addFeatureToSequence(Sequence seq) voidAGAVECallbackItf.reportSequence(Sequence sequence) voidAGAVEChromosomeCallbackItf.reportSequence(Sequence sequence) voidAGAVEChromosomeHandler.reportSequence(Sequence sequence) voidAGAVEContigCallbackItf.reportSequence(Sequence sequence) voidAGAVEContigHandler.reportSequence(Sequence sequence) voidAGAVEHandler.reportSequence(Sequence sequence) protected voidWriting Sequence.voidAgaveWriter.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 SequenceModifier and TypeMethodDescriptionProjectedFeature.getSequence()ProjectionContext.getSequence(Feature projFeat) Get the sequence for a feature.final SequenceReparentContext.getSequence(Feature f) -
Uses of Sequence in org.biojavax.bio.db
Methods in org.biojavax.bio.db that return SequenceMethods in org.biojavax.bio.db with parameters of type Sequence -
Uses of Sequence in org.biojavax.bio.seq
Subinterfaces of Sequence in org.biojavax.bio.seqModifier and TypeInterfaceDescriptioninterfaceA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement SequenceModifier and TypeClassDescriptionclassA simple implementation of RichSequence.classA simple implementation of RichSequence.Methods in org.biojavax.bio.seq that return SequenceModifier and TypeMethodDescriptionSimpleRichFeature.getSequence()Return theSequenceobject to which this feature is (ultimately) attached.RichSequence.IOTools.SingleRichSeqIterator.nextSequence()Returns the next sequence in the iterator.Methods in org.biojavax.bio.seq with parameters of type SequenceModifier and TypeMethodDescriptionstatic RichSequenceBoldly attempts to convert aSequenceinto aRichSequence.static voidRichSequence.IOTools.writeEMBL(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin EMBL format.static voidRichSequence.IOTools.writeEMBLxml(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin EMBLxml format.static voidRichSequence.IOTools.writeFasta(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin Fasta format.static voidRichSequence.IOTools.writeFasta(OutputStream os, Sequence seq, Namespace ns, FastaHeader header) Writes a singleSequenceto anOutputStreamin Fasta format.static voidRichSequence.IOTools.writeGenbank(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin GenBank format.static voidRichSequence.IOTools.writeINSDseq(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin INSDseq format.static voidRichSequence.IOTools.writeUniProt(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin UniProt format.static voidRichSequence.IOTools.writeUniProtXML(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin UniProt XML format.Constructors in org.biojavax.bio.seq with parameters of type SequenceModifierConstructorDescriptionCreates an iterator over a single sequence. -
Uses of Sequence in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that return SequenceModifier and TypeMethodDescriptionRichSequenceBuilder.makeSequence()Return the Sequence object which has been constructed by this builder.SimpleRichSequenceBuilder.makeSequence()Return the Sequence object which has been constructed by this builder.HashedFastaIterator.nextSequence()RichStreamReader.nextSequence()Returns the next sequence in the iterator.Methods in org.biojavax.bio.seq.io with parameters of type SequenceModifier and TypeMethodDescriptionvoidEMBLFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidEMBLFormat.writeSequence(Sequence seq, String format, PrintStream os) writeSequencewrites a sequence to the specifiedPrintStream, using the specified format.voidEMBLFormat.writeSequence(Sequence seq, String format, Namespace ns) As perEMBLFormat.writeSequence(Sequence, Namespace), except that it also takes a format parameter.voidEMBLFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidEMBLxmlFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidEMBLxmlFormat.writeSequence(Sequence seq, String format, PrintStream os) writeSequencewrites a sequence to the specifiedPrintStream, using the specified format.voidEMBLxmlFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidFastaFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidFastaFormat.writeSequence(Sequence seq, String format, PrintStream os) writeSequencewrites a sequence to the specifiedPrintStream, using the specified format.voidFastaFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidGenbankFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidGenbankFormat.writeSequence(Sequence seq, String format, PrintStream os) writeSequencewrites a sequence to the specifiedPrintStream, using the specified format.voidGenbankFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidINSDseqFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidINSDseqFormat.writeSequence(Sequence seq, String format, PrintStream os) writeSequencewrites a sequence to the specifiedPrintStream, using the specified format.voidINSDseqFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidRichSequenceFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidUniProtFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidUniProtFormat.writeSequence(Sequence seq, String format, PrintStream os) writeSequencewrites a sequence to the specifiedPrintStream, using the specified format.voidUniProtFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidUniProtXMLFormat.writeSequence(Sequence seq, PrintStream os) writeSequencewrites a sequence to the specified PrintStream, using the default format.voidUniProtXMLFormat.writeSequence(Sequence seq, String format, PrintStream os) writeSequencewrites a sequence to the specifiedPrintStream, using the specified format.voidUniProtXMLFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.