Uses of Interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory (BioJava-1.5-beta API)

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

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

Packages that use RichSequenceBuilderFactory
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 RichSequenceBuilderFactory in org.biojavax.bio.db.ncbi

Methods in org.biojavax.bio.db.ncbi that return RichSequenceBuilderFactory
`RichSequenceBuilderFactory` | `GenbankRichSequenceDB.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.

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.

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES