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

Packages that use RichSequenceBuilderFactory
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
 RichSequenceBuilderFactory GenbankRichSequenceDB.getFactory()
          Getter for property factory.
 RichSequenceBuilderFactory GenpeptRichSequenceDB.getFactory()
          Getter for property factory.
 

Methods in org.biojavax.bio.db.ncbi with parameters of type RichSequenceBuilderFactory
 void 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 RichSequenceBuilderFactory
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
 class SimpleRichSequenceBuilderFactory
          Generates RichSequenceBuilder objects.
 

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