[BioRuby-cvs] bioruby/lib/bio/shell/plugin seq.rb,1.3,1.4

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv10873/lib/bio/shell/plugin

Modified Files:
	seq.rb 
Log Message:
* Changed way to print output (puts -> display).
* Now returns the pretty DNA sequence in String.


Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** seq.rb	23 Sep 2005 15:51:59 -0000	1.3
--- seq.rb	28 Oct 2005 02:08:10 -0000	1.4
***************
*** 100,104 ****
--- 100,108 ----
    end
  
+   # Reterns and displays a DNA sequence pretty printing 
+   # in B-type double helix.
+   # Argument ``seq'' required at least 16 bases length.
    def double_helix(seq)
+     str = ''
      m = [[5, 0], [4, 2], [3, 3], [2, 4], 
           [1, 4], [0, 3], [0, 2], [1, 0]]
***************
*** 106,116 ****
        m.each_with_index do |mij, x|
          base = subseq[x, 1]
!         puts ' ' * mij[0] + base + '-' * mij[1] + base.complement
        end
        m.reverse.each_with_index do |mij, x|
          base = subseq[x + 8, 1]
!         puts ' ' * mij[0] + base.complement + '-' * mij[1] + base
        end
      end
    end
  
--- 110,122 ----
        m.each_with_index do |mij, x|
          base = subseq[x, 1]
!         str << ' ' * mij[0] + base + '-' * mij[1] + base.complement + "\n"
        end
        m.reverse.each_with_index do |mij, x|
          base = subseq[x + 8, 1]
!         str << ' ' * mij[0] + base.complement + '-' * mij[1] + base + "\n"
        end
      end
+     display(str)
+     return str
    end