[BioRuby-cvs] bioruby/lib/bio/shell/plugin seq.rb,1.13,1.14

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv9842/bio/shell/plugin

Modified Files:
	seq.rb 
Log Message:
* seqstat method is adapted to the change of Bio::Sequence#translate
* codon_usage_table method is integrated to codontable method (in plugin/codon.rb)


Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** seq.rb	28 Nov 2005 02:06:47 -0000	1.13
--- seq.rb	28 Nov 2005 07:13:55 -0000	1.14
***************
*** 79,83 ****
        rep << "3'->5' sequence   : #{rev.fold(70,20).strip}#{dot}\n"
        [ 1, 2, 3, -1, -2, -3 ].each do |frame|
!         pep = fwd.translate(frame).fold(70,20).strip
          rep << "Translation  #{frame.to_s.rjust(2)}   : #{pep}#{dot}\n"
        end
--- 79,83 ----
        rep << "3'->5' sequence   : #{rev.fold(70,20).strip}#{dot}\n"
        [ 1, 2, 3, -1, -2, -3 ].each do |frame|
!         pep = seq.subseq(1, max+2).translate(frame).fold(70,20).strip
          rep << "Translation  #{frame.to_s.rjust(2)}   : #{pep}#{dot}\n"
        end
***************
*** 99,106 ****
          hash[codon] = percent
        end
!       #--
!       #*TODO* how to hide this method
!       #++
!       rep << codon_usage_table(1, hash).output
  
        begin
--- 99,103 ----
          hash[codon] = percent
        end
!       rep << codontable(1, hash).output #*TODO* how to hide?
  
        begin