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 AlignmentPair
AlignmentPair.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 Sequence
DistributionTools.generateOrderNSequence
(String name, OrderNDistribution d, int length) Deprecated.use generateSequence() or generateSymbolList() instead.static final 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 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()
getSecondarySequence
returns the entire secondarySequence
currently being rendered.PairwiseSequencePanel.getSequence()
getSequence
returns the entireSequence
currently being rendered.SequencePanelWrapper.getSequence()
SequencePoster.getSequence()
Deprecated.Methods in org.biojava.bio.gui.sequence with parameters of type SequenceModifier and TypeMethodDescriptionvoid
PairwiseSequencePanel.setSecondarySequence
(Sequence sequence) setSecondarySequence
sets the secondarySequence
to be rendered.void
PairwiseSequencePanel.setSequence
(Sequence sequence) setSequence
sets theSequence
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 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 TypeMethodDescriptionvoid
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 -
Uses of Sequence in org.biojava.bio.molbio
Methods in org.biojava.bio.molbio that return SequenceModifier and TypeMethodDescriptionannotate
addsFeature
s 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 Sequence
FastqTools.createDNASequence
(Fastq fastq) Create and return a new DNASequence
from 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 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 SequenceModifier and TypeMethodDescriptionstatic 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 SequenceModifier and TypeClassDescriptionclass
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 SequenceModifier and TypeMethodDescriptionprotected 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 SequenceModifier and TypeMethodDescriptionSimilarityPairBuilder.getAnnotatedQuerySeq
(String queryID) 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 -
Uses of Sequence in org.biojava.bio.program.xff
Methods in org.biojava.bio.program.xff that return SequenceModifier and TypeMethodDescriptionstatic Sequence
static Sequence
XFFTools.readXFF
(File xffFile, String seqID, FiniteAlphabet alpha) Methods in org.biojava.bio.program.xff with parameters of type SequenceModifier and TypeMethodDescriptionstatic 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 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 TypeInterfaceDescriptioninterface
Extension of GappedSymbolList which also projects features into the gapped coordinate system.Classes in org.biojava.bio.seq that implement SequenceModifier and TypeClassDescriptionclass
A circular view onto another Sequence object.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A 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 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.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) ComponentFeature.getComponentSequence()
Get the sequence object which provides a component of this feature's parent sequence.Feature.getSequence()
Return theSequence
object to which this feature is (ultimately) attached.static Sequence
SequenceTools.maskSequence
(Sequence seq, RangeLocation loc) Mask of a 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 SequenceModifier and TypeMethodDescriptionstatic void
SequenceTools.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 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.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 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
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
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 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 Sequence
AnnotatedSequenceDB.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 TypeMethodDescriptionvoid
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!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 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 TypeMethodDescriptionvoid
FlatSequenceDB.addSequence
(Sequence sequence) addSequence
always throws aChangeVetoException
as 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 class
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.class
A reverse complement view ontoSequence
interface.class
Simple implementation of GappedSequence.class
A basic implementation of theSequence
interface.class
View a sub-section of a given sequence object, including all the features intersecting that region.class
A 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 aSimpleFeature
on 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 String
FastaFormat.describeSequence
(Sequence seq) Deprecated.Return a suitable description line for a Sequence.void
SeqIOEventEmitter.getSeqIOEvents
(Sequence seq, SeqIOListener listener) Deprecated.getSeqIOEvents
scans aSequence
object and sends events describing its data to theSeqIOListener
.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 aSequence
orRichSequence
to aPrintStream
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 SequenceModifier and TypeFieldDescriptionprotected Sequence
AGAVEBioSeqHandler.sequence
protected Sequence
AGAVEContigHandler.sequence
Methods in org.biojava.bio.seq.io.agave with parameters of type SequenceModifier and TypeMethodDescriptionprotected 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
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 SequenceModifier and TypeMethodDescriptionProjectedFeature.getSequence()
ProjectionContext.getSequence
(Feature projFeat) Get the sequence for a feature.final Sequence
ReparentContext.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 TypeInterfaceDescriptioninterface
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement SequenceModifier and TypeClassDescriptionclass
A simple implementation of RichSequence.class
A simple implementation of RichSequence.Methods in org.biojavax.bio.seq that return SequenceModifier and TypeMethodDescriptionSimpleRichFeature.getSequence()
Return theSequence
object 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 RichSequence
Boldly attempts to convert aSequence
into aRichSequence
.static void
RichSequence.IOTools.writeEMBL
(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequence
to anOutputStream
in EMBL format.static void
RichSequence.IOTools.writeEMBLxml
(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequence
to anOutputStream
in EMBLxml format.static void
RichSequence.IOTools.writeFasta
(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequence
to anOutputStream
in Fasta format.static void
RichSequence.IOTools.writeFasta
(OutputStream os, Sequence seq, Namespace ns, FastaHeader header) Writes a singleSequence
to anOutputStream
in Fasta format.static void
RichSequence.IOTools.writeGenbank
(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequence
to anOutputStream
in GenBank format.static void
RichSequence.IOTools.writeINSDseq
(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequence
to anOutputStream
in INSDseq format.static void
RichSequence.IOTools.writeUniProt
(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequence
to anOutputStream
in UniProt format.static void
RichSequence.IOTools.writeUniProtXML
(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequence
to anOutputStream
in 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 TypeMethodDescriptionvoid
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 specifiedPrintStream
, using the specified format.void
EMBLFormat.writeSequence
(Sequence seq, String format, Namespace ns) As perEMBLFormat.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 specifiedPrintStream
, 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 specifiedPrintStream
, 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 specifiedPrintStream
, 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 specifiedPrintStream
, 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 specifiedPrintStream
, 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 specifiedPrintStream
, 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.