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 TypeClassDescriptionclass
Format reader for EMBL files.class
Format reader for EMBLxml files.class
Format object representing FASTA files.class
Format reader for GenBank files.class
Format reader for INSDseq files.static class
Provides a basic format with simple things like line-widths precoded.static class
Provides the basic implementation required for simple header/footer-less files such as Genbank.class
Format reader for UniProt files.class
Format 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.