Uses of Interface
org.biojavax.bio.seq.RichSequence

Packages that use RichSequence

Package	Description
org.biojavax.bio.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojavax.bio.alignment.blast	This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services through the WWW.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.
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 RichSequence in org.biojavax.bio.alignment

Methods in org.biojavax.bio.alignment with parameters of type RichSequence

Modifier and Type	Method and Description
String	RemotePairwiseAlignmentService.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 RichSequence

Modifier and Type	Method and Description
String	RemoteQBlastService.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 RichSequence

Modifier and Type	Method and Description
RichSequence	RichSequenceDBLite.getRichSequence(String id) Retrieve a single RichSequence by its id.
RichSequence	HashRichSequenceDB.getRichSequence(String id)

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

Modifier and Type	Method and Description
void	RichSequenceDBLite.addRichSequence(RichSequence seq) Adds a sequence to the database.
void	HashRichSequenceDB.addRichSequence(RichSequence seq) Add a sequence.
void	AbstractRichSequenceDB.addRichSequence(RichSequence seq)
protected void	HashRichSequenceDB.addRichSequence(String id, RichSequence seq)

Uses of RichSequence in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql that return RichSequence

Modifier and Type	Method and Description
RichSequence	BioSQLRichSequenceDB.fullyLoadRichSequence(RichSequence id)
RichSequence	BioSQLRichSequenceDB.getRichSequence(String id)

Methods in org.biojavax.bio.db.biosql with parameters of type RichSequence

Modifier and Type	Method and Description
void	BioSQLRichSequenceDB.addRichSequence(RichSequence seq)
void	BioSQLRichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.
RichSequence	BioSQLRichSequenceDB.fullyLoadRichSequence(RichSequence id)
Iterator	BioSQLRichSequenceHandler.iterator(RichSequence seq) An Iterator over all Symbols in this SymbolList.
String	BioSQLRichSequenceHandler.seqString(RichSequence seq) Stringify this Sequences.
SymbolList	BioSQLRichSequenceHandler.subList(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.
String	BioSQLRichSequenceHandler.subStr(RichSequence seq, int start, int end) Return a region of this sequence as a String.
Symbol	BioSQLRichSequenceHandler.symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.
List	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 RichSequence

Modifier and Type	Method and Description
RichSequence	GenpeptRichSequenceDB.getRichSequence(String id) Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenbankRichSequenceDB.getRichSequence(String id) Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenpeptRichSequenceDB.getRichSequence(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenbankRichSequenceDB.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 RichSequence

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

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

Modifier and Type	Method and Description
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	RichSequence.Tools.createRichSequence(String name, String seqString, Alphabet alpha) Create a new RichSequence in the default namespace.
static 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, SymbolList syms) Create a new RichSequence in the default namespace.
static RichSequence	RichSequence.Tools.enrich(Sequence s) Boldly attempts to convert a Sequence into a RichSequence.
RichSequence	RichSequenceIterator.nextRichSequence()
RichSequence	RichSequence.IOTools.SingleRichSeqIterator.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 RichSequence

Modifier and Type	Method and Description
void	RichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.
void	DummyRichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.
Iterator<Symbol>	RichSequenceHandler.iterator(RichSequence seq) An Iterator over all Symbols in this SymbolList.
Iterator<Symbol>	DummyRichSequenceHandler.iterator(RichSequence seq) An Iterator over all Symbols in this SymbolList.
String	RichSequenceHandler.seqString(RichSequence seq) Stringify this Sequences.
String	DummyRichSequenceHandler.seqString(RichSequence seq) Stringify this Sequences.
SymbolList	RichSequenceHandler.subList(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.
SymbolList	DummyRichSequenceHandler.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.
String	RichSequenceHandler.subStr(RichSequence seq, int start, int end) Return a region of this sequence as a String.
String	DummyRichSequenceHandler.subStr(RichSequence seq, int start, int end) Return a region of this sequence as a String.
Symbol	RichSequenceHandler.symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.
Symbol	DummyRichSequenceHandler.symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.
List<Symbol>	RichSequenceHandler.toList(RichSequence seq) Returns a List of symbols.
List<Symbol>	DummyRichSequenceHandler.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 RichSequence

Modifier and Type	Method and Description
RichSequence	SimpleRichSequenceBuilder.makeRichSequence() Build a RichSequence.
RichSequence	RichSequenceBuilder.makeRichSequence() Build a RichSequence.
RichSequence	RichStreamReader.nextRichSequence()
RichSequence	HashedFastaIterator.nextRichSequence()