[BioRuby-cvs] bioruby/lib/bio/io ensembl.rb, 1.2, 1.3 fetch.rb, 1.8, 1.9

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv5347/lib/bio/io

Modified Files:
	ensembl.rb fetch.rb 
Log Message:
* Changes due to the refactoring of Bio::Command.


Index: ensembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ensembl.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ensembl.rb	27 Apr 2006 05:38:50 -0000	1.2
--- ensembl.rb	14 Jul 2006 14:28:44 -0000	1.3
***************
*** 215,219 ****
  
          result = nil      
!         Bio::Command::NetTools.net_http_start(@uri.host, @uri.port) {|http|
            result, = http.post(@path, data)
          }
--- 215,219 ----
  
          result = nil      
!         Bio::Command.start_http(@uri.host, @uri.port) {|http|
            result, = http.post(@path, data)
          }

Index: fetch.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fetch.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** fetch.rb	8 May 2006 14:29:58 -0000	1.8
--- fetch.rb	14 Jul 2006 14:28:44 -0000	1.9
***************
*** 107,111 ****
        query = query.join('&')
    
!       Bio::Command::NetTools.read_uri(@url + '?' + URI.escape(query))
      end
    
--- 107,111 ----
        query = query.join('&')
    
!       Bio::Command.read_uri(@url + '?' + URI.escape(query))
      end
    
***************
*** 142,146 ****
        query = "info=dbs"
  
!       Bio::Command::NetTools.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
      end
    
--- 142,146 ----
        query = "info=dbs"
  
!       Bio::Command.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
      end
    
***************
*** 159,163 ****
          query = "info=formats;db=#{database}"
  
!         Bio::Command::NetTools.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
        end
      end
--- 159,163 ----
          query = "info=formats;db=#{database}"
  
!         Bio::Command.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
        end
      end
***************
*** 173,177 ****
        query = "info=maxids"
  
!       Bio::Command::NetTools.read_uri(@url + '?' + URI.escape(query)).to_i
      end
    
--- 173,177 ----
        query = "info=maxids"
  
!       Bio::Command.read_uri(@url + '?' + URI.escape(query)).to_i
      end