Uses of Interface org.biojavax.Namespace (BioJava-1.5-beta API)

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## Uses of Interface
org.biojavax.Namespace

Packages that use Namespace
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 |
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
`class` | `SimpleNamespace` A basic Namespace implemenation.

Methods in org.biojavax that return Namespace
`static Namespace` | `RichObjectFactory.getDefaultNamespace()` Returns the default namespace object.

Uses of Namespace in org.biojavax.bio

Methods in org.biojavax.bio that return Namespace
`Namespace` | `SimpleBioEntry.getNamespace()` Returns the namespace of this bioentry.
`Namespace` | `BioEntry.getNamespace()` Returns the namespace of this bioentry.

Constructors in org.biojavax.bio with parameters of type Namespace
`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
`Namespace` | `GenbankRichSequenceDB.getNamespace()` Getter for property namespace.

Methods in org.biojavax.bio.db.ncbi with parameters of type Namespace
`RichSequence` | `GenbankRichSequenceDB.getRichSequence(String id, Namespace nsp)` Given the appropriate Genbank ID, return the matching RichSequence object.
`void` | `GenbankRichSequenceDB.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
`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, Namespace ns)` Read a fasta file.
`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.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, Namespace ns)` Guess which format a file is then attempt to read it.
`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.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.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, Namespace ns)` Guess which format a stream is then attempt to read it.
`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.readUniProt(BufferedReader br, Namespace ns)` Iterate over the sequences in an UniProt-format stream of RNA sequences.
`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.readUniProtXML(BufferedReader br, Namespace ns)` Iterate over the sequences in an UniProt XML-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 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 `Sequence`s 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.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
`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
`static RichLocation` | `GenbankLocationParser.parseLocation(Namespace featureNS, String featureAccession, String locationString)` Parses a location.
`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` | `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` | `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` | `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` | `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. If namespace is null, then the namespace of the sequence in the fasta is used.
`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` | `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. If namespace is null, then the namespace of the sequence in the fasta is used.
`void` | `SimpleRichSequenceBuilder.setNamespace(Namespace namespace)` Call back method so the event emitter can tell the listener the namespace of the record being read.
`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` | `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, String format, Namespace ns)` As per `EMBLFormat.writeSequence(Sequence, Namespace)`, except that it also takes a format parameter.
`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
`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.

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