Uses of Interface
org.biojavax.Namespace
Packages that use Namespace
Package
Description
The Biojava extensions packages, classes that extend the core biojava
functionality
Classes to represent biological entities and their relationships.
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 Namespace in org.biojavax
Classes in org.biojavax that implement NamespaceMethods in org.biojavax that return NamespaceModifier and TypeMethodDescriptionstatic NamespaceRichObjectFactory.getDefaultNamespace()Returns the default namespace object. -
Uses of Namespace in org.biojavax.bio
Methods in org.biojavax.bio that return NamespaceModifier and TypeMethodDescriptionBioEntry.getNamespace()Returns the namespace of this bioentry.SimpleBioEntry.getNamespace()Returns the namespace of this bioentry.Constructors in org.biojavax.bio with parameters of type NamespaceModifierConstructorDescriptionSimpleBioEntry(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 NamespaceModifier and TypeMethodDescriptionGenbankRichSequenceDB.getNamespace()Getter for property namespace.GenpeptRichSequenceDB.getNamespace()Getter for property namespace.Methods in org.biojavax.bio.db.ncbi with parameters of type NamespaceModifier and TypeMethodDescriptionGenbankRichSequenceDB.getRichSequence(String id, Namespace nsp) 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.voidGenbankRichSequenceDB.setNamespace(Namespace namespace) Setter for property namespace.voidGenpeptRichSequenceDB.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 NamespaceModifier and TypeMethodDescriptionstatic RichSequenceRichSequence.Tools.createRichSequence(Namespace ns, String name, String seqString, Alphabet alpha) Create a new RichSequence in the specified namespace.static RichSequenceRichSequence.Tools.createRichSequence(Namespace ns, String name, SymbolList syms) Create a new RichSequence in the specified namespace.static RichSequenceIteratorRichSequence.IOTools.readEMBL(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBL file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readEMBLDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLxml(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBLxml file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readEMBLxmlDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLxmlProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLxmlRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readFasta(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a fasta file building a custom type ofRichSequence.static RichSequenceIteratorRichSequence.IOTools.readFasta(BufferedReader br, SymbolTokenization sTok, Namespace ns) Read a fasta file.static RichSequenceIteratorRichSequence.IOTools.readFastaDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readFastaProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readFastaRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readFile(File file, RichSequenceBuilderFactory seqFactory, Namespace ns) Guess which format a file is then attempt to read it.static RichSequenceIteratorGuess which format a file is then attempt to read it.static RichSequenceIteratorRichSequence.IOTools.readGenbank(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a GenBank file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readGenbankDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readGenbankProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readGenbankRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readHashedFastaDNA(BufferedInputStream is, Namespace ns) Iterate over the sequences in an FASTA-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readINSDseq(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a INSDseq file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readINSDseqDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readINSDseqProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readINSDseqRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readStream(BufferedInputStream stream, RichSequenceBuilderFactory seqFactory, Namespace ns) Guess which format a stream is then attempt to read it.static RichSequenceIteratorRichSequence.IOTools.readStream(BufferedInputStream stream, Namespace ns) Guess which format a stream is then attempt to read it.static RichSequenceIteratorRichSequence.IOTools.readUniProt(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readUniProt(BufferedReader br, Namespace ns) Iterate over the sequences in an UniProt-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readUniProtXML(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt XML file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readUniProtXML(BufferedReader br, Namespace ns) Iterate over the sequences in an UniProt XML-format stream of RNA sequences.static RichSequenceRichSequence.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 voidRichSequence.IOTools.writeEMBL(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIteratorto anOutputStreamin EMBL Format.static voidRichSequence.IOTools.writeEMBL(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin EMBL format.static voidRichSequence.IOTools.writeEMBLxml(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIteratorto anOutputStreamin EMBLxml Format.static voidRichSequence.IOTools.writeEMBLxml(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin EMBLxml format.static voidRichSequence.IOTools.writeFasta(OutputStream os, SequenceIterator in, Namespace ns) WritesSequences from aSequenceIteratorto anOutputStreamin Fasta Format.static voidRichSequence.IOTools.writeFasta(OutputStream os, SequenceIterator in, Namespace ns, FastaHeader header) WritesSequences from aSequenceIteratorto anOutputStreamin Fasta Format.static voidRichSequence.IOTools.writeFasta(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin Fasta format.static voidRichSequence.IOTools.writeFasta(OutputStream os, Sequence seq, Namespace ns, FastaHeader header) Writes a singleSequenceto anOutputStreamin Fasta format.static voidRichSequence.IOTools.writeGenbank(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIteratorto anOutputStreamin GenBank Format.static voidRichSequence.IOTools.writeGenbank(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin GenBank format.static voidRichSequence.IOTools.writeINSDseq(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIteratorto anOutputStreamin INSDseq Format.static voidRichSequence.IOTools.writeINSDseq(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin INSDseq format.static voidRichSequence.IOTools.writeUniProt(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIteratorto anOutputStreamin UniProt Format.static voidRichSequence.IOTools.writeUniProt(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin UniProt format.static voidRichSequence.IOTools.writeUniProtXML(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIteratorto anOutputStreamin UniProt XML Format.static voidRichSequence.IOTools.writeUniProtXML(OutputStream os, Sequence seq, Namespace ns) Writes a singleSequenceto anOutputStreamin UniProt XML format.Constructors in org.biojavax.bio.seq with parameters of type NamespaceModifierConstructorDescriptionSimpleRichSequence(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 NamespaceModifier and TypeMethodDescriptionstatic RichLocationGenbankLocationParser.parseLocation(Namespace featureNS, String featureAccession, String locationString) Parses a location.voidFastaFormat.processHeader(String line, RichSeqIOListener rsiol, Namespace ns) Parse the Header information from the Fasta Description linebooleanEMBLFormat.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.booleanEMBLxmlFormat.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.booleanFastaFormat.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.booleanGenbankFormat.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.booleanINSDseqFormat.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.booleanRichSequenceFormat.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.booleanUniProtFormat.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.booleanUniProtXMLFormat.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.voidDebuggingRichSeqIOListener.setNamespace(Namespace namespace) voidRichSeqIOAdapter.setNamespace(Namespace namespace) voidRichSeqIOListener.setNamespace(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.voidSimpleRichSequenceBuilder.setNamespace(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.voidEMBLFormat.writeSequence(Sequence seq, String format, Namespace ns) As perEMBLFormat.writeSequence(Sequence, Namespace), except that it also takes a format parameter.voidEMBLFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidEMBLxmlFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidFastaFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidGenbankFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidINSDseqFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidRichSequenceFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidUniProtFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidUniProtXMLFormat.writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.voidRichStreamWriter.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 NamespaceModifierConstructorDescriptionHashedFastaIterator(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.