[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.6,0.58.2.7

[Jan Aerts]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.6
retrieving revision 0.58.2.7
diff -C2 -d -r0.58.2.6 -r0.58.2.7
*** sequence.rb	15 Feb 2008 05:29:50 -0000	0.58.2.6
--- sequence.rb	20 Feb 2008 09:56:22 -0000	0.58.2.7
***************
*** 371,375 ****
      return [@primary_accession, @secondary_accessions].flatten
    end
!   
  end # Sequence
  
--- 371,375 ----
      return [@primary_accession, @secondary_accessions].flatten
    end
! 
  end # Sequence