[BioRuby-cvs] bioruby/lib/bio/shell demo.rb,1.2,1.3

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell
In directory dev.open-bio.org:/tmp/cvs-serv9643

Modified Files:
	demo.rb 
Log Message:
* follow the change of some bioruby shell commands


Index: demo.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/demo.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** demo.rb	26 Mar 2006 00:38:10 -0000	1.2
--- demo.rb	24 Dec 2006 08:40:43 -0000	1.3
***************
*** 25,29 ****
  
      def initialize
!       @bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
      end
  
--- 25,29 ----
  
      def initialize
!       @bind = Bio::Shell.cache[:binding]
      end
  
***************
*** 39,44 ****
      end
  
      def mito
!       run(%q[entry = ent("data/kumamushi.gb")], "Load kumamushi gene from GenBank database entry ...", false) &&
        run(%q[disp entry], "Check the contents ...", false) &&
        run(%q[kuma = flatparse(entry)], "Parse the database entry ...", true) &&
--- 39,47 ----
      end
  
+     def aldh2
+     end
+ 
      def mito
!       run(%q[entry = getent("data/kumamushi.gb")], "Load kumamushi gene from GenBank database entry ...", false) &&
        run(%q[disp entry], "Check the contents ...", false) &&
        run(%q[kuma = flatparse(entry)], "Parse the database entry ...", true) &&
***************
*** 62,66 ****
  
      def sequence
!       run(%q[dna = seq("atgc" * 100)], "Generating DNA sequence ...", true) &&
        run(%q[doublehelix dna], "Double helix representation", false) &&
        run(%q[protein = dna.translate], "Translate DNA into Protein ...", true) &&
--- 65,69 ----
  
      def sequence
!       run(%q[dna = getseq("atgc" * 100)], "Generating DNA sequence ...", true) &&
        run(%q[doublehelix dna], "Double helix representation", false) &&
        run(%q[protein = dna.translate], "Translate DNA into Protein ...", true) &&
***************
*** 71,75 ****
  
      def entry
!       run(%q[kuma = obj("gb:AF237819")], "Obtain an entry from GenBank database", false) &&
        run(%q[kuma.definition], "Definition of the entry", true) &&
        run(%q[kuma.naseq], "Sequence of the entry", true) &&
--- 74,78 ----
  
      def entry
!       run(%q[kuma = getobj("gb:AF237819")], "Obtain an entry from GenBank database", false) &&
        run(%q[kuma.definition], "Definition of the entry", true) &&
        run(%q[kuma.naseq], "Sequence of the entry", true) &&
***************
*** 82,91 ****
        run(%q[pwd], "Show current working directory ...", false) &&
        run(%q[dir], "Show directory contents ...", false) &&
!       run(%q[dir "session"], "Show directory contents ...", false) &&
        true
      end
  
      def pdb
!       run(%q[ent_1bl8 = ent("pdb:1bl8")], "Retrieving PDB entry 1BL8 ...", false) &&
        run(%q[head ent_1bl8], "Head part of the entry ...", false) &&
        run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) &&
--- 85,94 ----
        run(%q[pwd], "Show current working directory ...", false) &&
        run(%q[dir], "Show directory contents ...", false) &&
!       run(%q[dir "shell/session"], "Show directory contents ...", false) &&
        true
      end
  
      def pdb
!       run(%q[ent_1bl8 = getent("pdb:1bl8")], "Retrieving PDB entry 1BL8 ...", false) &&
        run(%q[head ent_1bl8], "Head part of the entry ...", false) &&
        run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) &&