[BioRuby-cvs] bioruby/lib/bio/appl blast.rb,1.26,1.27

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory pub.open-bio.org:/tmp/cvs-serv29928/lib/bio/appl

Modified Files:
	blast.rb 
Log Message:
* Removed TAB.


Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** blast.rb	26 Sep 2005 13:00:04 -0000	1.26
--- blast.rb	18 Dec 2005 17:28:55 -0000	1.27
***************
*** 40,53 ****
  
      def initialize(program, db, opt = [], server = 'local')
!       @program	= program
!       @db	= db
!       @server	= server
  
        @blastall = 'blastall'
!       @matrix	= nil
!       @filter	= nil
  
!       @output	= ''
!       @parser	= nil
  
        begin
--- 40,53 ----
  
      def initialize(program, db, opt = [], server = 'local')
!       @program  = program
!       @db       = db
!       @server   = server
  
        @blastall = 'blastall'
!       @matrix   = nil
!       @filter   = nil
  
!       @output   = ''
!       @parser   = nil
  
        begin
***************
*** 64,72 ****
          end
        end
!       @options	= [ *a ]
      end
      attr_accessor :program, :db, :options, :server, :blastall, :matrix, :filter
      attr_reader :output, :format
!     attr_writer :parser		# to change :xmlparser, :rexml, :tab
  
      def self.local(program, db, option = '')
--- 64,72 ----
          end
        end
!       @options = [ *a ]
      end
      attr_accessor :program, :db, :options, :server, :blastall, :matrix, :filter
      attr_reader :output, :format
!     attr_writer :parser  # to change :xmlparser, :rexml, :tab
  
      def self.local(program, db, option = '')
***************
*** 97,102 ****
        ary = []
        input.each("</BlastOutput>\n") do |xml|
!         xml.sub!(/[^<]*(<?)/, '\1')		# skip before <?xml> tag
!         next if xml.empty?			# skip trailing no hits
          if block_given?
            yield Report.new(xml, parser)
--- 97,102 ----
        ary = []
        input.each("</BlastOutput>\n") do |xml|
!         xml.sub!(/[^<]*(<?)/, '\1') # skip before <?xml> tag
!         next if xml.empty?          # skip trailing no hits
          if block_given?
            yield Report.new(xml, parser)
***************
*** 146,158 ****
  
        form = {
!         'style'		=> 'raw',
!         'prog'		=> @program,
!         'dbname'	=> @db,
!         'sequence'	=> CGI.escape(query),
!         'other_param'	=> CGI.escape(make_command_line_unix(opt)),
!         'matrix'	=> matrix,
!         'filter'	=> filter,
!         'V_value'	=> 500,		# default value for GenomeNet
!         'B_value'	=> 250,		# default value for GenomeNet
          'alignment_view' => 0,
        }
--- 146,158 ----
  
        form = {
!         'style'          => 'raw',
!         'prog'           => @program,
!         'dbname'         => @db,
!         'sequence'       => CGI.escape(query),
!         'other_param'    => CGI.escape(make_command_line_unix(opt)),
!         'matrix'         => matrix,
!         'filter'         => filter,
!         'V_value'        => 500, # default value for GenomeNet
!         'B_value'        => 250, # default value for GenomeNet
          'alignment_view' => 0,
        }