Uses of Interface
org.biojavax.bio.seq.io.RichSequenceBuilderFactory
Packages that use RichSequenceBuilderFactory
Package
Description
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 RichSequenceBuilderFactory in org.biojavax.bio.db.ncbi
Methods in org.biojavax.bio.db.ncbi that return RichSequenceBuilderFactoryModifier and TypeMethodDescriptionGenbankRichSequenceDB.getFactory()
Getter for property factory.GenpeptRichSequenceDB.getFactory()
Getter for property factory.Methods in org.biojavax.bio.db.ncbi with parameters of type RichSequenceBuilderFactoryModifier and TypeMethodDescriptionvoid
GenbankRichSequenceDB.setFactory
(RichSequenceBuilderFactory factory) Setter for property factory.void
GenpeptRichSequenceDB.setFactory
(RichSequenceBuilderFactory factory) Setter for property factory. -
Uses of RichSequenceBuilderFactory in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq with parameters of type RichSequenceBuilderFactoryModifier and TypeMethodDescriptionstatic 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.readEMBLxml
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBLxml file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readFasta
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a fasta file building a custom type ofRichSequence
.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.readINSDseq
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a INSDseq file using a custom type of SymbolList.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, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readUniProtXML
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt XML file using a custom type of SymbolList. -
Uses of RichSequenceBuilderFactory in org.biojavax.bio.seq.io
Classes in org.biojavax.bio.seq.io that implement RichSequenceBuilderFactoryModifier and TypeClassDescriptionclass
Generates RichSequenceBuilder objects.Fields in org.biojavax.bio.seq.io declared as RichSequenceBuilderFactoryModifier and TypeFieldDescriptionstatic final RichSequenceBuilderFactory
RichSequenceBuilderFactory.FACTORY
Accessor for the default factory.static final RichSequenceBuilderFactory
RichSequenceBuilderFactory.PACKED
Accessor for a factory that produces builders that compress theSymbolList
of aRichSequence
.static final RichSequenceBuilderFactory
RichSequenceBuilderFactory.THRESHOLD
Accessor for a factory that produces builders that compress theSymbolList
of aRichSequence
when the length of theSymbolList
exceedsTHRESHOLD
.Constructors in org.biojavax.bio.seq.io with parameters of type RichSequenceBuilderFactoryModifierConstructorDescriptionRichStreamReader
(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.