[BioRuby-cvs] bioruby/lib/bio/appl blast.rb, 1.29, 1.30 fasta.rb, 1.20, 1.21 hmmer.rb, 1.5, 1.6

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv5268/lib/bio/appl

Modified Files:
	blast.rb fasta.rb hmmer.rb 
Log Message:
* Changes due to the refactoring of Bio::Command.
* Changed to use Bio::Command.new_http instead of Net::HTTP.new.


Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** blast.rb	16 May 2006 09:50:13 -0000	1.29
--- blast.rb	14 Jul 2006 14:26:39 -0000	1.30
***************
*** 83,88 ****
      autoload :Bl2seq,       'bio/appl/bl2seq/report'
  
-     include Bio::Command::Tools
- 
      # This is a shortcut for Bio::Blast.new:
      #  Bio::Blast.local(program, database, options)
--- 83,86 ----
***************
*** 227,231 ****
      def option
        # backward compatibility
!       make_command_line(@options)
      end
  
--- 225,229 ----
      def option
        # backward compatibility
!       Bio::Command.make_command_line(@options)
      end
  
***************
*** 254,258 ****
        report = nil
  
!       @output = call_command_local(cmd, query)
        report = parse_result(@output)
  
--- 252,256 ----
        report = nil
  
!       @output = Bio::Command.query_command(cmd, query)
        report = parse_result(@output)
  
***************
*** 278,282 ****
          'dbname'         => @db,
          'sequence'       => CGI.escape(query),
!         'other_param'    => CGI.escape(make_command_line_unix(opt)),
          'matrix'         => matrix,
          'filter'         => filter,
--- 276,280 ----
          'dbname'         => @db,
          'sequence'       => CGI.escape(query),
!         'other_param'    => CGI.escape(Bio::Command.make_command_line_unix(opt)),
          'matrix'         => matrix,
          'filter'         => filter,
***************
*** 295,299 ****
  
        begin
!         http = Net::HTTP.new(host)
          http.open_timeout = 300
          http.read_timeout = 600
--- 293,297 ----
  
        begin
!         http = Bio::Command.new_http(host)
          http.open_timeout = 300
          http.read_timeout = 600

Index: fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/fasta.rb,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** fasta.rb	26 Sep 2005 13:00:04 -0000	1.20
--- fasta.rb	14 Jul 2006 14:26:39 -0000	1.21
***************
*** 33,38 ****
      #autoload :?????,  'bio/appl/fasta/format6'
  
-     include Bio::Command::Tools
- 
      def initialize(program, db, opt = [], server = 'local')
        @format	= 10
--- 33,36 ----
***************
*** 60,64 ****
      def option
        # backward compatibility
!       make_command_line(@options)
      end
  
--- 58,62 ----
      def option
        # backward compatibility
!       Bio::Command.make_command_line(@options)
      end
  
***************
*** 115,119 ****
        report = nil
  
!       @output = call_command_local(cmd, query)
        report = parse_result(@output)
  
--- 113,117 ----
        report = nil
  
!       @output = Bio::Command.query_command(cmd, query)
        report = parse_result(@output)
  
***************
*** 132,136 ****
          'dbname'	=> @db,
          'sequence'	=> CGI.escape(query),
!         'other_param'	=> CGI.escape(make_command_line_unix(@options)),
          'ktup_value'	=> @ktup,
          'matrix'	=> @matrix,
--- 130,134 ----
          'dbname'	=> @db,
          'sequence'	=> CGI.escape(query),
!         'other_param'	=> CGI.escape(Bio::Command.make_command_line_unix(@options)),
          'ktup_value'	=> @ktup,
          'matrix'	=> @matrix,
***************
*** 146,150 ****
  
        begin
!         http = Net::HTTP.new(host)
          http.open_timeout = 300
          http.read_timeout = 600
--- 144,148 ----
  
        begin
!         http = Bio::Command.new_http(host)
          http.open_timeout = 300
          http.read_timeout = 600

Index: hmmer.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/hmmer.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** hmmer.rb	2 Feb 2006 17:08:36 -0000	1.5
--- hmmer.rb	14 Jul 2006 14:26:39 -0000	1.6
***************
*** 73,78 ****
    autoload :Report, 'bio/appl/hmmer/report'
  
-   include Bio::Command::Tools
- 
    # Prgrams name. (hmmsearch or hmmpfam).
    attr_accessor :program
--- 73,76 ----
***************
*** 113,117 ****
    # backward compatibility.
    def option
!     make_command_line(@options)
    end
  
--- 111,115 ----
    # backward compatibility.
    def option
!     Bio::Command.make_command_line(@options)
    end
  
***************
*** 132,136 ****
      report = nil
      
!     @output = call_command_local(cmd, nil)
      report = parse_result(@output)
        
--- 130,134 ----
      report = nil
      
!     @output = Bio::Command.query_command(cmd, nil)
      report = parse_result(@output)