bioworks.rb in mspire-0.1.7

- old
+ new

@@ -13,16 +13,19 @@
 module SpecIDXML; end
 
 class SpecID::Bioworks
   # Regular expressions
   @@bioworksinfo_re = /<bioworksinfo>(.*)<\/bioworksinfo>/o
+  @@modifications_re = /<modifications>(.*)<\/modifications>/o
   @@protein_re = /<protein>/o
   @@origfilename_re = /<origfilename>(.*)<\/origfilename>/o
   @@origfilepath_re = /<origfilepath>(.*)<\/origfilepath>/o
 
 
   attr_accessor :prots, :version, :global_filename, :origfilename, :origfilepath
+  # a string of modifications e.g., "(M* +15.99491) (S@ +14.9322) "
+  attr_accessor :modifications
   attr_writer :peps
 
   def hi_prob_best ; false end
 
   # -> prints to file filename1.sqt, filename2.sqt
@@ -194,10 +197,11 @@
     @origfilepath = get_regex_val(fh, @@origfilepath_re)
     if @origfilename
       @global_filename = @origfilename.gsub(File.extname(@origfilename), "")
     end
     @version = get_regex_val(fh, @@bioworksinfo_re)
+    @modifications = get_regex_val(fh, @@modifications_re)
     @prots = get_prots(fh, self)
     fh.close
   end
 
   def get_prots(fh, bioworks)
@@ -454,10 +458,10 @@
       (first_scan, last_scan) = first_scan
     else
       first_scan = first_scan[0]
       last_scan = first_scan
     end
-    return base_name, first_scan, last_scan
+    [base_name, first_scan, last_scan]
   end
 
   def file=(arg)
     ## Set these vals by index:
     #puts "AERRG: #{arg}"