[Biojava-l] writeSequence

Keith James kdj@sanger.ac.uk
07 Mar 2001 09:59:05 +0000


I've committed a few files related to writing various file formats
(list below). The code is still incomplete, although everything builds
and writeSequence(sequence, "embl", stream) called on an
EmblLikeFormat instance will dump most of a Sequence to STDOUT as
EMBL format.

What's missing?

* EMBL/Genbank locations (was waiting for fuzzy locations to
  stabilise), boolean qualifiers

* Registration of formats recognised by a particular
  SequenceFormat instance (e.g. EMBL, SwissProt by EmblLikeFormat)

* Error checking; are Symbols correct for the format?

* Setting a default format for particular SequenceFormat instances

* Genbank writeSequence (easy), SwissProt writeSequence (harder)

* Javadoc & DocBook documentation

Classes / interfaces:


  public interface SeqFileFormer extends SeqIOListener

  public abstract class SeqFileFormerFactory

  public class EmblFileFormer implements SeqFileFormer
  (contains private static class Factory extends SeqFileFormerFactory)

  public class SeqIOEventEmitter

  public class SeqFormatTools

Which qualifiers are valid for which feature key, which are mandatory,
quoted, empty etc:



Comments welcome at any stage.



-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA