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Packages that use Sequence | |
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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.das | Development client for the Distributed Annotation System. |
org.biojava.bio.program.gff | GFF manipulation. |
org.biojava.bio.program.phred | Parser for Phred output |
org.biojava.bio.program.ssbind | Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. |
org.biojava.bio.program.unigene | Objects for representing Unigene clusters. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins. |
org.biojava.bio.search | Interfaces and classes for representing sequence similarity search results. |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.db | Collections of biological sequence data. |
org.biojava.bio.seq.db.biofetch | Client for the OBDA BioFetch protocol. |
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.seq.db.flat | Support for OBDA flatfile databases. |
org.biojava.bio.seq.distributed | Sequences and SequenceDBs which are composed from data taken from a number of data sources. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
org.biojava.bio.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences. |
org.biojava.bio.seq.io.agave | Classes for converting between AGAVE XML and BioJava objects. |
org.biojava.bio.seq.projection | Code for projecting Feature objects and systematically altering their properties. |
org.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 |
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Methods in org.biojava.bio.alignment with parameters of type Sequence | |
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Alignment |
NeedlemanWunsch.getAlignment(Sequence query,
Sequence target)
This method is good if one wants to reuse the alignment calculated by this class in another BioJava class. |
abstract Alignment |
SequenceAlignment.getAlignment(Sequence query,
Sequence subject)
This method also performs a sequence alignment of the two given sequences but it returns an Alignment object instead of the score. |
double |
SmithWaterman.pairwiseAlignment(Sequence query,
Sequence subject)
Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment. |
double |
NeedlemanWunsch.pairwiseAlignment(Sequence query,
Sequence subject)
Global pairwise sequence alginment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm. |
abstract double |
SequenceAlignment.pairwiseAlignment(Sequence query,
Sequence subject)
Performs a pairwise sequence alignment of the two given sequences. |
Uses of Sequence in org.biojava.bio.dist |
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Methods in org.biojava.bio.dist that return Sequence | |
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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 |
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Methods in org.biojava.bio.dp that return Sequence | |
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Sequence |
WeightMatrixAnnotator.annotate(Sequence seq)
|
Methods in org.biojava.bio.dp with parameters of type Sequence | |
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Sequence |
WeightMatrixAnnotator.annotate(Sequence seq)
|
Uses of Sequence in org.biojava.bio.gui.sequence |
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Methods in org.biojava.bio.gui.sequence that return Sequence | |
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Sequence |
PairwiseSequencePanel.getSecondarySequence()
getSecondarySequence returns the entire secondary
Sequence currently being rendered. |
Sequence |
PairwiseSequencePanel.getSequence()
getSequence returns the entire
Sequence currently being rendered. |
Sequence |
SequencePoster.getSequence()
Deprecated. |
Sequence |
SequencePanelWrapper.getSequence()
|
Methods in org.biojava.bio.gui.sequence with parameters of type Sequence | |
---|---|
void |
PairwiseSequencePanel.setSecondarySequence(Sequence sequence)
setSecondarySequence sets the secondary
Sequence to be rendered. |
void |
PairwiseSequencePanel.setSequence(Sequence sequence)
setSequence sets the Sequence
to be rendered. |
void |
SequencePoster.setSequence(Sequence s)
Deprecated. Set the SymboList to be rendered. |
void |
SequencePanelWrapper.setSequence(Sequence seq)
|
Constructors in org.biojava.bio.gui.sequence with parameters of type Sequence | |
---|---|
HeadlessRenderContext(Sequence seq,
RangeLocation range,
int width)
|
Uses of Sequence in org.biojava.bio.gui.sequence.tracklayout |
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Methods in org.biojava.bio.gui.sequence.tracklayout with parameters of type Sequence | |
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void |
UserDefinedTrackLayout.setSequence(Sequence seq)
|
void |
SimpleTrackLayout.setSequence(Sequence seq)
|
void |
TrackLayout.setSequence(Sequence seq)
|
Constructors in org.biojava.bio.gui.sequence.tracklayout with parameters of type Sequence | |
---|---|
SimpleTrackLayout(Sequence seq,
int wrap)
|
Uses of Sequence in org.biojava.bio.molbio |
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Methods in org.biojava.bio.molbio that return Sequence | |
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Sequence |
RestrictionMapper.annotate(Sequence sequence)
annotate adds Feature s which
represent restriction sites. |
Methods in org.biojava.bio.molbio with parameters of type Sequence | |
---|---|
Sequence |
RestrictionMapper.annotate(Sequence sequence)
annotate adds Feature s which
represent restriction sites. |
Uses of Sequence in org.biojava.bio.program.das |
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Methods in org.biojava.bio.program.das that return Sequence | |
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Sequence |
DASSequenceDB.getSequence(String id)
|
Methods in org.biojava.bio.program.das with parameters of type Sequence | |
---|---|
void |
DASSequenceDB.addSequence(Sequence seq)
|
Uses of Sequence in org.biojava.bio.program.gff |
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Methods in org.biojava.bio.program.gff that return Sequence | |
---|---|
static Sequence |
GFFTools.annotateSequence(Sequence seq,
GFFEntrySet ents)
Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence. |
static Sequence |
GFFTools.annotateSequence(Sequence seq,
GFFEntrySet ents,
boolean checkSeqName)
Annotates a sequence with the features from a GFF entry set. |
Methods in org.biojava.bio.program.gff with parameters of type Sequence | |
---|---|
static Sequence |
GFFTools.annotateSequence(Sequence seq,
GFFEntrySet ents)
Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence. |
static Sequence |
GFFTools.annotateSequence(Sequence seq,
GFFEntrySet ents,
boolean checkSeqName)
Annotates a sequence with the features from a GFF entry set. |
protected void |
SequencesAsGFF.doPreProcessSequence(Sequence seq,
GFFDocumentHandler handler,
String id)
Emit any per-sequence header information. |
protected void |
SequencesAsGFF.doProcessSequence(Sequence seq,
GFFDocumentHandler handler,
String id)
Internal method to process an individual Sequence. |
static GFFEntrySet |
GFFTools.gffFromSequence(Sequence seq)
Creates a GFFEntrySet containing one entry for each feature on a sequence. |
void |
SequencesAsGFF.processSequence(Sequence seq,
GFFDocumentHandler handler)
Process an individual Sequence, informing handler of any suitable features. |
Uses of Sequence in org.biojava.bio.program.phred |
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Classes in org.biojava.bio.program.phred that implement Sequence | |
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class |
PhredSequence
PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores. |
Methods in org.biojava.bio.program.phred with parameters of type Sequence | |
---|---|
protected String |
PhredFormat.describeSequence(Sequence seq)
Return a suitable description line for a Sequence. |
void |
PhredFormat.writeSequence(Sequence seq,
PrintStream os)
This method will print symbols to the line width followed by a new line etc. |
void |
PhredFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
Deprecated. use writeSequence(Sequence seq, PrintStream os) |
Uses of Sequence in org.biojava.bio.program.ssbind |
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Methods in org.biojava.bio.program.ssbind that return Sequence | |
---|---|
Sequence |
SimilarityPairBuilder.getAnnotatedQuerySeq(String queryID)
|
Sequence |
SimilarityPairBuilder.getAnnotatedSubjectSeq(String subjectID)
|
protected Sequence |
ViewSequenceFactory.makeQueryViewSequence(String queryID)
|
protected Sequence |
ViewSequenceFactory.makeSubjectViewSequence(String subjectID)
|
Uses of Sequence in org.biojava.bio.program.unigene |
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Methods in org.biojava.bio.program.unigene that return Sequence | |
---|---|
Sequence |
UnigeneCluster.getUnique()
The unique sequence that is used as a representative for this cluster. |
Uses of Sequence in org.biojava.bio.program.xff |
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Methods in org.biojava.bio.program.xff that return Sequence | |
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static Sequence |
XFFTools.readXFF(File xffFile,
String seqID)
|
static Sequence |
XFFTools.readXFF(File xffFile,
String seqID,
FiniteAlphabet alpha)
|
Methods in org.biojava.bio.program.xff with parameters of type Sequence | |
---|---|
static void |
XFFTools.annotateXFF(File xffFile,
Sequence sequence)
|
static void |
XFFTools.annotateXFF(File xffFile,
Sequence sequence,
Annotation ann)
|
Uses of Sequence in org.biojava.bio.proteomics |
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Methods in org.biojava.bio.proteomics that return Sequence | |
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Sequence |
Digest.getSequence()
|
Methods in org.biojava.bio.proteomics with parameters of type Sequence | |
---|---|
void |
Digest.setSequence(Sequence sequence)
|
Uses of Sequence in org.biojava.bio.search |
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Methods in org.biojava.bio.search that return Sequence | |
---|---|
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 | |
---|---|
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 |
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Subinterfaces of Sequence in org.biojava.bio.seq | |
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interface |
GappedSequence
Extension of GappedSymbolList which also projects features into the gapped coordinate system. |
Classes in org.biojava.bio.seq that implement Sequence | |
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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 | |
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Sequence |
ComponentFeature.Template.componentSequence
|
Methods in org.biojava.bio.seq that return Sequence | |
---|---|
Sequence |
SequenceAnnotator.annotate(Sequence seq)
Return an annotated version of a sequence. |
static Sequence |
DNATools.createDNASequence(String dna,
String name)
Return a new DNA Sequence for dna. |
static Sequence |
SequenceTools.createDummy(Alphabet alpha,
int length,
Symbol sym,
String uri,
String name)
Create a new Sequence that contains a single symbol repeated over and over. |
static Sequence |
SequenceTools.createDummy(String uri,
String name)
Create a new Sequence that has no annotation, no features and a zero-length symbol list. |
static Sequence |
NucleotideTools.createNucleotideSequence(String nucleotide,
String name)
Return a new Nucleotide Sequence for nucleotide. |
static Sequence |
ProteinTools.createProteinSequence(String protein,
String name)
Return a new PROTEIN Sequence for protein. |
static Sequence |
RNATools.createRNASequence(String rna,
String name)
Return a new RNA Sequence for rna. |
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 | |
---|---|
static void |
SequenceTools.addAllFeatures(Sequence seq,
FeatureHolder fh)
Add features to a sequence that contain the same information as all those in a feature holder. |
Sequence |
SequenceAnnotator.annotate(Sequence seq)
Return an annotated version of a sequence. |
static GappedSequence |
SequenceTools.gappedView(Sequence seq)
Create a new gapped sequence for a sequence. |
static Sequence |
SequenceTools.maskSequence(Sequence seq,
RangeLocation loc)
Mask of a sequence. |
Feature |
SimpleFeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template temp)
|
Feature |
FeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template template)
Install a feature on the specified sequence. |
static Sequence |
SequenceTools.reverseComplement(Sequence seq)
Reverse-complement a sequence, and flip all of its features. |
static Sequence |
SequenceTools.subSequence(Sequence seq,
int start,
int end)
Extract a sub-sequence from a sequence. |
static Sequence |
SequenceTools.subSequence(Sequence seq,
int start,
int end,
String name)
Extract a sub-sequence from a sequence. |
static Sequence |
SequenceTools.subSequence(Sequence seq,
int start,
int end,
String name,
StrandedFeature.Strand strand)
Extract a sub-sequence from a sequence. |
static ViewSequence |
SequenceTools.view(Sequence seq)
Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. |
static ViewSequence |
SequenceTools.view(Sequence seq,
FeatureRealizer fr)
Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features. |
static ViewSequence |
SequenceTools.view(Sequence seq,
String name)
Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. |
Constructors in org.biojava.bio.seq with parameters of type Sequence | |
---|---|
CircularView(Sequence seq)
|
|
CircularView(Sequence seq,
FeatureRealizer fr)
|
Uses of Sequence in org.biojava.bio.seq.db |
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Methods in org.biojava.bio.seq.db that return Sequence | |
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protected Sequence |
AnnotatedSequenceDB.doAnnotation(Sequence seq)
Apply the annotation to a sequence. |
Sequence |
HashSequenceDB.getSequence(String id)
|
Sequence |
WebSequenceDB.getSequence(String id)
Gets a sequence using its unique ID (eg for GenBank this would be the GI number) |
Sequence |
SwissprotSequenceDB.getSequence(String id)
|
Sequence |
ViewingSequenceDB.getSequence(String id)
|
Sequence |
CachingSequenceDB.getSequence(String id)
|
Sequence |
GenbankSequenceDB.getSequence(String id)
|
Sequence |
IndexedSequenceDB.getSequence(String id)
|
Sequence |
AnnotatedSequenceDB.getSequence(String id)
|
Sequence |
SequenceDBLite.getSequence(String id)
Retrieve a single sequence by its id. |
Sequence |
SubSequenceDB.getSequence(String id)
|
Sequence |
GenpeptSequenceDB.getSequence(String id)
|
Sequence |
DummySequenceDB.getSequence(String id)
|
Methods in org.biojava.bio.seq.db with parameters of type Sequence | |
---|---|
void |
HashSequenceDB.addSequence(Sequence seq)
|
void |
WebSequenceDB.addSequence(Sequence seq)
Not supported, You can't add sequences to a WebDB! |
void |
AbstractSequenceDB.addSequence(Sequence seq)
|
void |
SequenceDBLite.addSequence(Sequence seq)
Adds a sequence to the database. |
void |
DummySequenceDB.addSequence(Sequence seq)
|
void |
HashSequenceDB.addSequence(String id,
Sequence seq)
Add a sequence under a particular id. |
String |
IDMaker.calcID(Sequence seq)
Calculate the id for a sequence. |
String |
IDMaker.ByURN.calcID(Sequence seq)
|
String |
IDMaker.ByName.calcID(Sequence seq)
|
protected Sequence |
AnnotatedSequenceDB.doAnnotation(Sequence seq)
Apply the annotation to a sequence. |
Uses of Sequence in org.biojava.bio.seq.db.biofetch |
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Methods in org.biojava.bio.seq.db.biofetch that return Sequence | |
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Sequence |
BioFetchSequenceDB.getSequence(String id)
|
Methods in org.biojava.bio.seq.db.biofetch with parameters of type Sequence | |
---|---|
void |
BioFetchSequenceDB.addSequence(Sequence seq)
|
Uses of Sequence in org.biojava.bio.seq.db.biosql |
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Methods in org.biojava.bio.seq.db.biosql that return Sequence | |
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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 | |
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void |
BioSQLSequenceDB.addSequence(Sequence seq)
Deprecated. |
Uses of Sequence in org.biojava.bio.seq.db.flat |
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Methods in org.biojava.bio.seq.db.flat that return Sequence | |
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Sequence |
FlatSequenceDB.getSequence(String id)
|
Methods in org.biojava.bio.seq.db.flat with parameters of type Sequence | |
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void |
FlatSequenceDB.addSequence(Sequence sequence)
addSequence always throws a
ChangeVetoException as this implementation is
immutable. |
Uses of Sequence in org.biojava.bio.seq.distributed |
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Methods in org.biojava.bio.seq.distributed that return Sequence | |
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Sequence |
SequenceDBDataSource.getSequence(String id)
|
Sequence |
DistDataSource.getSequence(String id)
Get a Sequence object for an ID. |
Sequence |
GFFDataSource.getSequence(String id)
|
Sequence |
DistributedSequenceDB.getSequence(String id)
|
Methods in org.biojava.bio.seq.distributed with parameters of type Sequence | |
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void |
DistributedSequenceDB.addSequence(Sequence seq)
|
Uses of Sequence in org.biojava.bio.seq.impl |
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Classes in org.biojava.bio.seq.impl that implement Sequence | |
---|---|
class |
DummySequence
A Sequence implementation that has a name and URI but no features, and a zero length symbol list. |
class |
RevCompSequence
A reverse complement view onto Sequence interface. |
class |
SimpleGappedSequence
Simple implementation of GappedSequence. |
class |
SimpleSequence
A basic implementation of the Sequence interface. |
class |
SubSequence
View a sub-section of a given sequence object, including all the features intersecting that region. |
class |
ViewSequence
A view onto another Sequence object. |
Fields in org.biojava.bio.seq.impl declared as Sequence | |
---|---|
protected Sequence |
RevCompSequence.origSeq
|
Methods in org.biojava.bio.seq.impl that return Sequence | |
---|---|
Sequence |
SimpleSequenceFactory.createSequence(SymbolList symList,
String uri,
String name,
Annotation annotation)
|
Sequence |
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 | |
---|---|
RevCompSequence(Sequence seq)
URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these. |
|
RevCompSequence(Sequence seq,
String urn,
String name,
Annotation annotation)
|
|
SimpleFeature(Sequence sourceSeq,
FeatureHolder parent,
Feature.Template template)
Create a SimpleFeature on the given sequence. |
|
SimpleFramedFeature(Sequence sourceSeq,
FeatureHolder parent,
FramedFeature.Template template)
|
|
SimpleGappedSequence(Sequence seq)
|
|
SimpleHomologyFeature(Sequence sourceSeq,
FeatureHolder parent,
HomologyFeature.Template template)
|
|
SimpleRemoteFeature(Sequence sourceSeq,
FeatureHolder parent,
RemoteFeature.Template template)
|
|
SimpleRestrictionSite(Sequence sourceSeq,
FeatureHolder parent,
RestrictionSite.Template template)
Creates a new SimpleRestrictionSite . |
|
SimpleSimilarityPairFeature(Sequence sourceSeq,
FeatureHolder parent,
SimilarityPairFeature.Template template)
Creates a new SimpleSimilarityPairFeature . |
|
SimpleStrandedFeature(Sequence sourceSeq,
FeatureHolder parent,
StrandedFeature.Template template)
|
|
SubSequence(Sequence seq,
int start,
int end)
Construct a new SubSequence of the specified sequence. |
|
SubSequence(Sequence seq,
int start,
int end,
String name)
Construct a new SubSequence of the specified sequence. |
|
ViewSequence(Sequence seq)
Construct a view onto an existing sequence which takes on that sequence's name. |
|
ViewSequence(Sequence seq,
FeatureRealizer fr)
Construct a view onto a sequence, using a specific FeatureRealizer. |
|
ViewSequence(Sequence seq,
String name)
Construct a view onto an existing sequence and give it a new name. |
Uses of Sequence in org.biojava.bio.seq.io |
---|
Fields in org.biojava.bio.seq.io declared as Sequence | |
---|---|
protected Sequence |
SequenceBuilderBase.seq
|
Methods in org.biojava.bio.seq.io that return Sequence | |
---|---|
Sequence |
SequenceBuilderFilter.makeSequence()
|
Sequence |
SequenceBuilderBase.makeSequence()
|
Sequence |
SmartSequenceBuilder.makeSequence()
|
Sequence |
SimpleSequenceBuilder.makeSequence()
|
Sequence |
SequenceBuilder.makeSequence()
Return the Sequence object which has been constructed by this builder. |
Sequence |
SimpleAssemblyBuilder.makeSequence()
|
Sequence |
SequenceDBSequenceBuilder.makeSequence()
create the sequence |
Sequence |
StreamReader.nextSequence()
Pull the next sequence out of the stream. |
Methods in org.biojava.bio.seq.io with parameters of type Sequence | |
---|---|
protected 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 |
GenbankFormat.writeSequence(Sequence seq,
PrintStream os)
Deprecated. |
void |
SequenceFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
EmblLikeFormat.writeSequence(Sequence seq,
PrintStream os)
Deprecated. |
void |
GAMEFormat.writeSequence(Sequence seq,
PrintStream os)
|
void |
FastaFormat.writeSequence(Sequence seq,
PrintStream os)
Deprecated. Writes a Sequence or RichSequence to a
PrintStream in FASTA format. |
void |
GenbankFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
Deprecated. use writeSequence(Sequence seq, PrintStream os) |
void |
SequenceFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
Deprecated. use writeSequence(Sequence seq, PrintStream os) |
void |
EmblLikeFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
Deprecated. use writeSequence(Sequence seq, PrintStream os) |
void |
GAMEFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
|
void |
FastaFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
Deprecated. use writeSequence(Sequence seq, PrintStream os) |
static void |
SeqIOTools.writeSwissprot(OutputStream os,
Sequence seq)
Deprecated. Writes a single Sequence to an OutputStream in SwissProt format. |
Uses of Sequence in org.biojava.bio.seq.io.agave |
---|
Fields in org.biojava.bio.seq.io.agave declared as Sequence | |
---|---|
protected Sequence |
AGAVEBioSeqHandler.sequence
|
protected Sequence |
AGAVEContigHandler.sequence
|
Methods in org.biojava.bio.seq.io.agave with parameters of type Sequence | |
---|---|
protected void |
StAXFeatureHandler.addFeatureToSequence(Sequence seq)
|
void |
AGAVEContigCallbackItf.reportSequence(Sequence sequence)
|
void |
AGAVECallbackItf.reportSequence(Sequence sequence)
|
void |
AGAVEChromosomeCallbackItf.reportSequence(Sequence sequence)
|
void |
AGAVEHandler.reportSequence(Sequence sequence)
|
void |
AGAVEChromosomeHandler.reportSequence(Sequence sequence)
|
void |
AGAVEContigHandler.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 |
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Methods in org.biojava.bio.seq.projection that return Sequence | |
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Sequence |
ProjectedFeature.getSequence()
|
Sequence |
ReparentContext.getSequence(Feature f)
|
Sequence |
ProjectionContext.getSequence(Feature projFeat)
Get the sequence for a feature. |
Uses of Sequence in org.biojavax.bio.db |
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Methods in org.biojavax.bio.db that return Sequence | |
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Sequence |
AbstractRichSequenceDB.getSequence(String id)
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Methods in org.biojavax.bio.db with parameters of type Sequence | |
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void |
AbstractRichSequenceDB.addSequence(Sequence seq)
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Uses of Sequence in org.biojavax.bio.seq |
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Subinterfaces of Sequence in org.biojavax.bio.seq | |
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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 | |
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class |
SimpleRichSequence
A simple implementation of RichSequence. |
class |
ThinRichSequence
A simple implementation of RichSequence. |
Methods in org.biojavax.bio.seq that return Sequence | |
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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 | |
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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.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 | |
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RichSequence.IOTools.SingleRichSeqIterator(Sequence seq)
Creates an iterator over a single sequence. |
Uses of Sequence in org.biojavax.bio.seq.io |
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Methods in org.biojavax.bio.seq.io that return Sequence | |
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Sequence |
RichSequenceBuilder.makeSequence()
Return the Sequence object which has been constructed by this builder. Implementations of this for a RichSequenceBuilder should delegate to makeRichSequence() and return only RichSequence objects. |
Sequence |
SimpleRichSequenceBuilder.makeSequence()
Return the Sequence object which has been constructed by this builder. |
Sequence |
RichStreamReader.nextSequence()
Returns the next sequence in the iterator. |
Methods in org.biojavax.bio.seq.io with parameters of type Sequence | |
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void |
EMBLFormat.writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as EMBL has no concept of it. |
void |
GenbankFormat.writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as Genbank has no concept of it. |
void |
INSDseqFormat.writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as INSDseq has no concept of it. |
void |
UniProtFormat.writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as UniProt has no concept of it. |
void |
EMBLxmlFormat.writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as EMBLxml has no concept of it. |
void |
UniProtXMLFormat.writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is null, then the sequence's own namespace is used. |
void |
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 |
FastaFormat.writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is null, then the sequence's own namespace is used. |
void |
EMBLFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
GenbankFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
INSDseqFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
UniProtFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
EMBLxmlFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
UniProtXMLFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
FastaFormat.writeSequence(Sequence seq,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
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,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
void |
GenbankFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
void |
INSDseqFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
void |
UniProtFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
void |
EMBLxmlFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
void |
UniProtXMLFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
void |
FastaFormat.writeSequence(Sequence seq,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
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