Uses of Interface
org.biojavax.bio.seq.io.RichSequenceFormat
Packages that use RichSequenceFormat
Package
Description
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of RichSequenceFormat in org.biojavax.bio.seq.io
Classes in org.biojavax.bio.seq.io that implement RichSequenceFormatModifier and TypeClassDescriptionclassFormat reader for EMBL files.classFormat reader for EMBLxml files.classFormat object representing FASTA files.classFormat reader for GenBank files.classFormat reader for INSDseq files.static classProvides a basic format with simple things like line-widths precoded.static classProvides the basic implementation required for simple header/footer-less files such as Genbank.classFormat reader for UniProt files.classFormat reader for UniProtXML files.Constructors in org.biojavax.bio.seq.io with parameters of type RichSequenceFormatModifierConstructorDescriptionRichStreamReader(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.