lib/ms/sequest/srf/search.rb in ms-sequest-0.1.2 vs lib/ms/sequest/srf/search.rb in ms-sequest-0.2.1

@@ -2,11 +2,11 @@
 require 'ms/sequest/srf'
 require 'ms/mass'
 
 # These are for outputting formats used in MS/MS Search engines
 
-module Ms
+module MS
   module Sequest
     class Srf
       module Search
         # Writes an MGF file to given filename or base_name + '.mgf' if no
         # filename given.
@@ -19,11 +19,11 @@
           filename =
             if filename ; filename
             else
               base_name + '.mgf'
             end
-          h_plus = Ms::Mass::MASCOT_H_PLUS
+          h_plus = MS::Mass::H_PLUS
           File.open(filename, 'wb') do |out|
             dta_files.zip(index) do |dta, i_ar|
               chrg = dta.charge
               out.print "BEGIN IONS\n"
               out.print "TITLE=#{[base_name, *i_ar].push('dta').join('.')}\n"
@@ -102,15 +102,15 @@
 
       include Search
 
     end # Srf
   end # Sequest
-end # Ms
+end # MS
 
 
 require 'optparse'
-module Ms::Sequest::Srf::Search
+module MS::Sequest::Srf::Search
   def self.commandline(argv, progname=$0)
     opt = {
       :format => 'mgf'
     }
     opts = OptionParser.new do |op|
@@ -143,10 +143,10 @@
             base
           when 'mgf'
             base << '.' << format
           end
         end
-      srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )
+      srf = MS::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )
       # options just speed up reading since we don't need .out info anyway
       case format
       when 'mgf'
         srf.to_mgf(newfile)
       when 'dta'