Uses of Interface
org.biojavax.Namespace

Packages that use Namespace

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio	Classes to represent biological entities and their relationships.
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 Namespace in org.biojavax

Classes in org.biojavax that implement Namespace

Modifier and Type	Class	Description
class	SimpleNamespace	A basic Namespace implemenation.

Methods in org.biojavax that return Namespace

Modifier and Type	Method	Description
static Namespace	RichObjectFactory.getDefaultNamespace()	Returns the default namespace object.

Uses of Namespace in org.biojavax.bio

Methods in org.biojavax.bio that return Namespace

Modifier and Type	Method	Description
Namespace	BioEntry.getNamespace()	Returns the namespace of this bioentry.
Namespace	SimpleBioEntry.getNamespace()	Returns the namespace of this bioentry.

Constructors in org.biojavax.bio with parameters of type Namespace

Constructor	Description
SimpleBioEntry(Namespace ns, String name, String accession, int version)	Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version.

Uses of Namespace in org.biojavax.bio.db.ncbi

Methods in org.biojavax.bio.db.ncbi that return Namespace

Modifier and Type	Method	Description
Namespace	GenbankRichSequenceDB.getNamespace()	Getter for property namespace.
Namespace	GenpeptRichSequenceDB.getNamespace()	Getter for property namespace.

Methods in org.biojavax.bio.db.ncbi with parameters of type Namespace

Modifier and Type	Method	Description
RichSequence	GenbankRichSequenceDB.getRichSequence(String id, Namespace nsp)	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.
void	GenbankRichSequenceDB.setNamespace(Namespace namespace)	Setter for property namespace.
void	GenpeptRichSequenceDB.setNamespace(Namespace namespace)	Setter for property namespace.

Uses of Namespace in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq with parameters of type Namespace

Modifier and Type	Method	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 RichSequenceIterator	RichSequence.IOTools.readEMBL(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)	Read a EMBL file using a custom type of SymbolList.
static RichSequenceIterator	RichSequence.IOTools.readEMBLDNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an EMBL-format stream of DNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readEMBLProtein(BufferedReader br, Namespace ns)	Iterate over the sequences in an EMBL-format stream of Protein sequences.
static RichSequenceIterator	RichSequence.IOTools.readEMBLRNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an EMBL-format stream of RNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readEMBLxml(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)	Read a EMBLxml file using a custom type of SymbolList.
static RichSequenceIterator	RichSequence.IOTools.readEMBLxmlDNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an EMBLxml-format stream of DNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readEMBLxmlProtein(BufferedReader br, Namespace ns)	Iterate over the sequences in an EMBLxml-format stream of Protein sequences.
static RichSequenceIterator	RichSequence.IOTools.readEMBLxmlRNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an EMBLxml-format stream of RNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readFasta(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)	Read a fasta file building a custom type of RichSequence .
static RichSequenceIterator	RichSequence.IOTools.readFasta(BufferedReader br, SymbolTokenization sTok, Namespace ns)	Read a fasta file.
static RichSequenceIterator	RichSequence.IOTools.readFastaDNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an FASTA-format stream of DNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readFastaProtein(BufferedReader br, Namespace ns)	Iterate over the sequences in an FASTA-format stream of Protein sequences.
static RichSequenceIterator	RichSequence.IOTools.readFastaRNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an FASTA-format stream of RNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readFile(File file, RichSequenceBuilderFactory seqFactory, Namespace ns)	Guess which format a file is then attempt to read it.
static RichSequenceIterator	RichSequence.IOTools.readFile(File file, Namespace ns)	Guess which format a file is then attempt to read it.
static RichSequenceIterator	RichSequence.IOTools.readGenbank(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)	Read a GenBank file using a custom type of SymbolList.
static RichSequenceIterator	RichSequence.IOTools.readGenbankDNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an GenBank-format stream of DNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readGenbankProtein(BufferedReader br, Namespace ns)	Iterate over the sequences in an GenBank-format stream of Protein sequences.
static RichSequenceIterator	RichSequence.IOTools.readGenbankRNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an GenBank-format stream of RNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readHashedFastaDNA(BufferedInputStream is, Namespace ns)	Iterate over the sequences in an FASTA-format stream of DNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readINSDseq(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)	Read a INSDseq file using a custom type of SymbolList.
static RichSequenceIterator	RichSequence.IOTools.readINSDseqDNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an INSDseq-format stream of DNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readINSDseqProtein(BufferedReader br, Namespace ns)	Iterate over the sequences in an INSDseq-format stream of Protein sequences.
static RichSequenceIterator	RichSequence.IOTools.readINSDseqRNA(BufferedReader br, Namespace ns)	Iterate over the sequences in an INSDseq-format stream of RNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readStream(BufferedInputStream stream, RichSequenceBuilderFactory seqFactory, Namespace ns)	Guess which format a stream is then attempt to read it.
static RichSequenceIterator	RichSequence.IOTools.readStream(BufferedInputStream stream, Namespace ns)	Guess which format a stream is then attempt to read it.
static RichSequenceIterator	RichSequence.IOTools.readUniProt(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)	Read a UniProt file using a custom type of SymbolList.
static RichSequenceIterator	RichSequence.IOTools.readUniProt(BufferedReader br, Namespace ns)	Iterate over the sequences in an UniProt-format stream of RNA sequences.
static RichSequenceIterator	RichSequence.IOTools.readUniProtXML(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)	Read a UniProt XML file using a custom type of SymbolList.
static RichSequenceIterator	RichSequence.IOTools.readUniProtXML(BufferedReader br, Namespace ns)	Iterate over the sequences in an UniProt XML-format stream of RNA sequences.
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.
static void	RichSequence.IOTools.writeEMBL(OutputStream os, SequenceIterator in, Namespace ns)	Writes sequences from a SequenceIterator to an OutputStream in EMBL Format.
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, SequenceIterator in, Namespace ns)	Writes sequences from a SequenceIterator to an OutputStream in EMBLxml 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, SequenceIterator in, Namespace ns)	Writes Sequences from a SequenceIterator to an OutputStream in Fasta Format.
static void	RichSequence.IOTools.writeFasta(OutputStream os, SequenceIterator in, Namespace ns, FastaHeader header)	Writes Sequences from a SequenceIterator to an OutputStream in Fasta 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.writeFasta(OutputStream os, Sequence seq, Namespace ns, FastaHeader header)	Writes a single Sequence to an OutputStream in Fasta format.
static void	RichSequence.IOTools.writeGenbank(OutputStream os, SequenceIterator in, Namespace ns)	Writes sequences from a SequenceIterator to an OutputStream in GenBank 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, SequenceIterator in, Namespace ns)	Writes sequences from a SequenceIterator to an OutputStream in INSDseq 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, SequenceIterator in, Namespace ns)	Writes sequences from a SequenceIterator to an OutputStream in UniProt 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, SequenceIterator in, Namespace ns)	Writes sequences from a SequenceIterator to an OutputStream in UniProt XML 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 Namespace

Constructor	Description
SimpleRichSequence(Namespace ns, String name, String accession, int version, SymbolList symList, Double seqversion)	Creates a new instance of SimpleRichSequence.
ThinRichSequence(Namespace ns, String name, String accession, int version, Alphabet alpha, Double seqversion)	Creates a new instance of ThinRichSequence.

Uses of Namespace in org.biojavax.bio.seq.io

Methods in org.biojavax.bio.seq.io with parameters of type Namespace

Modifier and Type	Method	Description
static RichLocation	GenbankLocationParser.parseLocation(Namespace featureNS, String featureAccession, String locationString)	Parses a location.
void	FastaFormat.processHeader(String line, RichSeqIOListener rsiol, Namespace ns)	Parse the Header information from the Fasta Description line
boolean	EMBLFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	EMBLxmlFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	FastaFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	GenbankFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	INSDseqFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	RichSequenceFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener listener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	UniProtFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	UniProtXMLFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
void	DebuggingRichSeqIOListener.setNamespace(Namespace namespace)
void	RichSeqIOAdapter.setNamespace(Namespace namespace)
void	RichSeqIOListener.setNamespace(Namespace namespace)	Call back method so the event emitter can tell the listener the namespace of the record being read.
void	SimpleRichSequenceBuilder.setNamespace(Namespace namespace)	Call back method so the event emitter can tell the listener the namespace of the record being read.
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, 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, 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.
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, 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, 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, Namespace ns)	Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
void	RichStreamWriter.writeStream(SequenceIterator ss, Namespace ns)	Write each of the sequences in ss to the stream in the given format.

Constructors in org.biojavax.bio.seq.io with parameters of type Namespace

Constructor	Description
HashedFastaIterator(BufferedInputStream is, Alphabet alpha, Namespace ns)
RichStreamReader(BufferedReader reader, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns)	Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.
RichStreamReader(InputStream is, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns)	Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.