Uses of Interface
org.biojavax.bio.seq.io.RichSequenceBuilderFactory

Packages that use RichSequenceBuilderFactory

Package	Description
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 RichSequenceBuilderFactory in org.biojavax.bio.db.ncbi

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

Modifier and Type	Method and Description
RichSequenceBuilderFactory	GenpeptRichSequenceDB.getFactory() Getter for property factory.
RichSequenceBuilderFactory	GenbankRichSequenceDB.getFactory() Getter for property factory.

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

Modifier and Type	Method and Description
void	GenpeptRichSequenceDB.setFactory(RichSequenceBuilderFactory factory) Setter for property factory.
void	GenbankRichSequenceDB.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 RichSequenceBuilderFactory

Modifier and Type	Method and Description
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.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 of RichSequence .
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 RichSequenceBuilderFactory

Modifier and Type	Class and Description
class	SimpleRichSequenceBuilderFactory Generates RichSequenceBuilder objects.

Fields in org.biojavax.bio.seq.io declared as RichSequenceBuilderFactory

Modifier and Type	Field and Description
static RichSequenceBuilderFactory	RichSequenceBuilderFactory.FACTORY Accessor for the default factory.
static RichSequenceBuilderFactory	RichSequenceBuilderFactory.PACKED Accessor for a factory that produces builders that compress the SymbolList of a RichSequence.
static RichSequenceBuilderFactory	RichSequenceBuilderFactory.THRESHOLD Accessor for a factory that produces builders that compress the SymbolList of a RichSequence when the length of the SymbolList exceeds THRESHOLD.

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

Constructor and Description
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.