[Biojava-l] Feature table refinements

[Keith James]

A summary of recent changes:

 Added FuzzyPointLocation and updated read/write code for Embl/Genbank
 (this is still experimental).

 Features are now properly sorted in the table i.e. 'source'
 feature(s) first, rather than strictly numerical order. See
 the Comparator 'ByEmblOrderComparator' in interface Feature.

 Qualifier types (i.e. Annotation keys) within a Feature are sorted by
 naturalOrder when written to the table.

 There is a field in interface Feature to be used as a key in a
 Feature's Annotation to identify that the various flatfile writers
 should not dump this information to the file:

 public static final String PROPERTY_DATA_KEY = "internal_data";


 SeqFormatTools.formatLocationBlock() now writes canonical EMBL style
 locations like join(complement(...),complement(...)) instead of the
 alternative complement(join(...,...) which Artemis accepts.

 SeqFormatTools contains only static methods. A few new ones have been
 added to write EMBL-style String representations of the various
 Locations. The Locations themselves are not EMBL-centric, so their
 own toString() methods are not suitable for this.

Keith

-- 

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