biojava/biojava — pull request #41 by karlnicholas (2013-08-12 01:43:56+00:00)
Title: Basic Genbank Support

More work on Genbank files, bringing them inline with interfaces. Renamed FastaHeaderParserInterface to SequenceHeaderParserInterface. Changed SequenceParserInterface to use BufferedReader instead of DataInput to provide flexibility for GenbankParser. Updated SequenceFileProxyLoader to BufferedReader. FileProxyProteinSequenceCreator and FileProxyDNASequenceCreator updated to handle generic SequenceCreatorInterface.

Essential files are GenbankSequenceParser, GenbankReader, GenericGenbankHeaderParser, GenbankReaderHelper, GenbankproxySequenceReader.

GenbankproxySequenceReader has the most complete sample code. The basic interfaces don't handle sequence creating and header parsing at the same time, so it has to be done by the user.