search.rb in ms-sequest-0.0.10

- old
+ new

@@ -1,11 +1,9 @@
 
-require 'tap/task'
 require 'ms/sequest/srf'
 require 'ms/mass'
 
-
 # These are for outputting formats used in MS/MS Search engines
 
 module Ms
   module Sequest
     class Srf
@@ -98,38 +96,9 @@
               end
             end
           end
         end
       end
-
-      # Ms::Sequest::Srf::SrfToSearch::task converts to MS formats for DB
-      # searching
-      #
-      # outputs the appropriate file or directory structure for <file>.srf:
-      #     <file>.mgf    # file for mgf
-      #     <file>        # the basename directory for dta
-      class SrfToSearch < Tap::Task
-        config :format, "mgf", :short => 'f' # mgf|dta (default: mgf)
-        def process(srf_file)
-          base = srf_file.sub(/\.srf$/i, '')
-          newfile = 
-            case format
-            when 'dta'
-              base
-            when 'mgf'
-              base << '.' << format
-            end
-          srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false )
-          # options just speed up reading since we don't need .out info anyway
-          case format
-          when 'mgf'
-            srf.to_mgf(newfile)
-          when 'dta'
-            srf.to_dta_files(newfile)
-          end
-        end
-      end
-
 
     end # Srf
   end # Sequest
 end # Ms
 