Uses of Interface
org.biojavax.bio.seq.RichSequence
Packages that use RichSequence
Package
Description
This package contains the interfaces that need to be implemented by discrete alignment services.
This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services
through the WWW.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of RichSequence in org.biojavax.bio.alignment
Methods in org.biojavax.bio.alignment with parameters of type RichSequenceModifier and TypeMethodDescriptionRemotePairwiseAlignmentService.sendAlignmentRequest
(RichSequence rs, RemotePairwiseAlignmentProperties rpa) Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object -
Uses of RichSequence in org.biojavax.bio.alignment.blast
Methods in org.biojavax.bio.alignment.blast with parameters of type RichSequenceModifier and TypeMethodDescriptionRemoteQBlastService.sendAlignmentRequest
(RichSequence rs, RemotePairwiseAlignmentProperties rpa) This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence. -
Uses of RichSequence in org.biojavax.bio.db
Methods in org.biojavax.bio.db that return RichSequenceModifier and TypeMethodDescriptionHashRichSequenceDB.getRichSequence
(String id) RichSequenceDBLite.getRichSequence
(String id) Retrieve a single RichSequence by its id.Methods in org.biojavax.bio.db with parameters of type RichSequenceModifier and TypeMethodDescriptionvoid
AbstractRichSequenceDB.addRichSequence
(RichSequence seq) protected void
HashRichSequenceDB.addRichSequence
(String id, RichSequence seq) void
HashRichSequenceDB.addRichSequence
(RichSequence seq) Add a sequence.void
RichSequenceDBLite.addRichSequence
(RichSequence seq) Adds a sequence to the database. -
Uses of RichSequence in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql that return RichSequenceModifier and TypeMethodDescriptionBioSQLRichSequenceDB.fullyLoadRichSequence
(RichSequence id) BioSQLRichSequenceDB.getRichSequence
(String id) Methods in org.biojavax.bio.db.biosql with parameters of type RichSequenceModifier and TypeMethodDescriptionvoid
BioSQLRichSequenceDB.addRichSequence
(RichSequence seq) void
BioSQLRichSequenceHandler.edit
(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.BioSQLRichSequenceDB.fullyLoadRichSequence
(RichSequence id) BioSQLRichSequenceHandler.iterator
(RichSequence seq) An Iterator over all Symbols in this SymbolList.BioSQLRichSequenceHandler.seqString
(RichSequence seq) Stringify this Sequences.BioSQLRichSequenceHandler.subList
(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.BioSQLRichSequenceHandler.subStr
(RichSequence seq, int start, int end) Return a region of this sequence as a String.BioSQLRichSequenceHandler.symbolAt
(RichSequence seq, int index) Return the symbol at index, counting from 1.BioSQLRichSequenceHandler.toList
(RichSequence seq) Returns a List of symbols. -
Uses of RichSequence in org.biojavax.bio.db.ncbi
Methods in org.biojavax.bio.db.ncbi that return RichSequenceModifier and TypeMethodDescriptionGenbankRichSequenceDB.getRichSequence
(String id) Given the appropriate Genbank ID, return the matching RichSequence object.GenbankRichSequenceDB.getRichSequence
(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.GenpeptRichSequenceDB.getRichSequence
(String id) Given the appropriate Genbank ID, return the matching RichSequence object.GenpeptRichSequenceDB.getRichSequence
(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object. -
Uses of RichSequence in org.biojavax.bio.seq
Classes in org.biojavax.bio.seq that implement RichSequenceModifier and TypeClassDescriptionclass
A simple implementation of RichSequence.class
A simple implementation of RichSequence.Methods in org.biojavax.bio.seq that return RichSequenceModifier and TypeMethodDescriptionstatic RichSequence
RichSequence.Tools.createRichSequence
(String namespace, String name, String seqString, Alphabet alpha) Create a new RichSequence in the specified namespace.static RichSequence
RichSequence.Tools.createRichSequence
(String name, String seqString, Alphabet alpha) Create a new RichSequence in the default namespace.static RichSequence
RichSequence.Tools.createRichSequence
(String name, SymbolList syms) Create a new RichSequence in the default namespace.static RichSequence
RichSequence.Tools.createRichSequence
(Namespace ns, String name, String seqString, Alphabet alpha) Create a new RichSequence in the specified namespace.static RichSequence
RichSequence.Tools.createRichSequence
(Namespace ns, String name, SymbolList syms) Create a new RichSequence in the specified namespace.static RichSequence
Boldly attempts to convert aSequence
into aRichSequence
.RichSequence.IOTools.SingleRichSeqIterator.nextRichSequence()
RichSequenceIterator.nextRichSequence()
static RichSequence
RichSequence.Tools.subSequence
(RichSequence s, int from, int to, Namespace newNamespace, String newName, String newAccession, String newIdentifier, int newVersion, Double seqVersion) Creates a new sequence from a subregion of another sequence.Methods in org.biojavax.bio.seq with parameters of type RichSequenceModifier and TypeMethodDescriptionvoid
DummyRichSequenceHandler.edit
(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.void
RichSequenceHandler.edit
(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.DummyRichSequenceHandler.iterator
(RichSequence seq) An Iterator over all Symbols in this SymbolList.RichSequenceHandler.iterator
(RichSequence seq) An Iterator over all Symbols in this SymbolList.DummyRichSequenceHandler.seqString
(RichSequence seq) Stringify this Sequences.RichSequenceHandler.seqString
(RichSequence seq) Stringify this Sequences.DummyRichSequenceHandler.subList
(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.RichSequenceHandler.subList
(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.static RichSequence
RichSequence.Tools.subSequence
(RichSequence s, int from, int to, Namespace newNamespace, String newName, String newAccession, String newIdentifier, int newVersion, Double seqVersion) Creates a new sequence from a subregion of another sequence.DummyRichSequenceHandler.subStr
(RichSequence seq, int start, int end) Return a region of this sequence as a String.RichSequenceHandler.subStr
(RichSequence seq, int start, int end) Return a region of this sequence as a String.DummyRichSequenceHandler.symbolAt
(RichSequence seq, int index) Return the symbol at index, counting from 1.RichSequenceHandler.symbolAt
(RichSequence seq, int index) Return the symbol at index, counting from 1.DummyRichSequenceHandler.toList
(RichSequence seq) Returns a List of symbols.RichSequenceHandler.toList
(RichSequence seq) Returns a List of symbols. -
Uses of RichSequence in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that return RichSequenceModifier and TypeMethodDescriptionRichSequenceBuilder.makeRichSequence()
Build a RichSequence.SimpleRichSequenceBuilder.makeRichSequence()
Build a RichSequence.HashedFastaIterator.nextRichSequence()
RichStreamReader.nextRichSequence()