[BioRuby-cvs] bioruby/lib/bio/db/genbank format_genbank.rb, 1.1.2.3, 1.1.2.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory dev.open-bio.org:/tmp/cvs-serv13124/lib/bio/db/genbank

Modified Files:
      Tag: BRANCH-biohackathon2008
	format_genbank.rb 
Log Message:
simplify sequence formatting routine


Index: format_genbank.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/Attic/format_genbank.rb,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** format_genbank.rb	7 May 2008 12:28:56 -0000	1.1.2.3
--- format_genbank.rb	28 May 2008 13:26:33 -0000	1.1.2.4
***************
*** 102,111 ****
  
      # formats sequence lines as GenBank
!     def each_genbank_seqline(str) #:yields: counter, seqline
        i = 1
!       a = str.scan(/.{1,60}/) do |s|
!         yield i, s.gsub(/(.{1,10})/, " \\1")
          i += 60
        end
      end
  
--- 102,114 ----
  
      # formats sequence lines as GenBank
!     def seq_format_genbank(str)
        i = 1
!       result = str.gsub(/.{1,60}/) do |s|
!         s = s.gsub(/.{1,10}/, ' \0')
!         y = sprintf("%9d%s\n", i, s)
          i += 60
+         y
        end
+       result
      end
  
***************
*** 129,135 ****
  <%= format_features_genbank(features || [])
   %>ORIGIN
! <% each_genbank_seqline(seq) do |i, s|
!  %><%= sprintf('%9d', i) %><%= s %>
! <% end %>//
  __END_OF_TEMPLATE__
  
--- 132,137 ----
  <%= format_features_genbank(features || [])
   %>ORIGIN
! <%= seq_format_genbank(seq)
!  %>//
  __END_OF_TEMPLATE__