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

Packages that use RichSequenceFormat

Package	Description
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Uses of RichSequenceFormat in org.biojavax.bio.seq.io

Classes in org.biojavax.bio.seq.io that implement RichSequenceFormat

Modifier and Type	Class and Description
class	EMBLFormat Format reader for EMBL files.
class	EMBLxmlFormat Format reader for EMBLxml files.
class	FastaFormat Format object representing FASTA files.
class	GenbankFormat Format reader for GenBank files.
class	INSDseqFormat Format reader for INSDseq files.
static class	RichSequenceFormat.BasicFormat Provides a basic format with simple things like line-widths precoded.
static class	RichSequenceFormat.HeaderlessFormat Provides the basic implementation required for simple header/footer-less files such as Genbank.
class	UniProtFormat Format reader for UniProt files.
class	UniProtXMLFormat Format reader for UniProtXML files.

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

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.
RichStreamWriter(OutputStream os, RichSequenceFormat format) Generate a new RichStreamWriter to the stream os and using format.