[BioRuby-cvs] bioruby/lib/bio/shell/plugin keggapi.rb,1.10,1.11

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory dev.open-bio.org:/tmp/cvs-serv9893

Modified Files:
	keggapi.rb 
Log Message:
* Bio::Shell::Private module is nolonger extended to Bio::Shell


Index: keggapi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/keggapi.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** keggapi.rb	9 Feb 2006 20:48:53 -0000	1.10
--- keggapi.rb	24 Dec 2006 08:49:12 -0000	1.11
***************
*** 12,19 ****
  
    module Private
      def keggapi_definition2tab(list)
        ary = []
        list.each do |entry|
!         ary << "#{entry.entry_id}:\t#{entry.definition}"
        end
        return ary
--- 12,22 ----
  
    module Private
+ 
+     module_function
+ 
      def keggapi_definition2tab(list)
        ary = []
        list.each do |entry|
!         ary << "#{entry.entry_id}\t#{entry.definition}"
        end
        return ary
***************
*** 50,53 ****
--- 53,57 ----
        yield result
      else
+       puts result
        return result
      end
***************
*** 56,59 ****
--- 60,64 ----
    def btit(str)
      result = keggapi.btit(str)
+     puts result
      return result
    end
***************
*** 61,64 ****
--- 66,70 ----
    def bconv(str)
      result = keggapi.bconv(str)
+     puts result
      return result
    end
***************
*** 68,72 ****
    def keggdbs
      list = keggapi.list_databases
!     result = Bio::Shell.keggapi_definition2tab(list).join("\n")
      puts result
      return list.map {|x| x.entry_id}
--- 74,78 ----
    def keggdbs
      list = keggapi.list_databases
!     result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
      puts result
      return list.map {|x| x.entry_id}
***************
*** 75,79 ****
    def keggorgs
      list = keggapi.list_organisms
!     result = Bio::Shell.keggapi_definition2tab(list).sort.join("\n")
      puts result
      return list.map {|x| x.entry_id}
--- 81,85 ----
    def keggorgs
      list = keggapi.list_organisms
!     result = Bio::Shell::Private.keggapi_definition2tab(list).sort.join("\n")
      puts result
      return list.map {|x| x.entry_id}
***************
*** 82,90 ****
    def keggpathways(org = "map")
      list = keggapi.list_pathways(org)
!     result = Bio::Shell.keggapi_definition2tab(list).join("\n")
      puts result
      return list.map {|x| x.entry_id}
    end
  
    def kegggenomeseq(org)
      result = ""
--- 88,97 ----
    def keggpathways(org = "map")
      list = keggapi.list_pathways(org)
!     result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
      puts result
      return list.map {|x| x.entry_id}
    end
  
+   # use KEGG DAS insetad
    def kegggenomeseq(org)
      result = ""