protein_group.rb in ms-ident-0.1.1

- old
+ new

@@ -26,11 +26,16 @@
       # id) then any object will work.  If they are Struct objects, you might
       # consider redefining the #hash method to be object_id for performance and
       # accuracy.
       #
       # returns an array of ProteinGroup objects, each set with :peptide_hits
-      def self.peptide_hits_to_protein_groups(peptide_hits, &sort_by)
+      #
+      # If update_peptide_hits is true, then each peptide_hit is linked to the array
+      # of protein_groups it is associated with using :protein_groups.  A
+      # symbol can also be passed in, and that method will be called instead.
+      def self.peptide_hits_to_protein_groups(peptide_hits, update_peptide_hits=false, &sort_by)
+        update_peptide_hits = 'protein_groups='.to_sym if (update_peptide_hits==true)
         sort_by ||= PRIORITIZE_PROTEINS
         # note to self: I wrote this in 2011, so I think I know what I'm doing now
         protein_to_peptides = Hash.new {|h,k| h[k] = Set.new }
         peptide_hits.each do |peptide_hit|
           peptide_hit.proteins.each do |protein|
@@ -61,9 +66,12 @@
               accounted_for.add(peptide_hit)
             end
           end
           group.peptide_hits = peptide_set if has_an_unaccounted_peptide
           has_an_unaccounted_peptide
+        end
+        if update_peptide_hits
+          greedy_first.each {|pg, pephits| pephits.each {|hit| hit.send(update_peptide_hits, pg) } } 
         end
         greedy_first.map(&:first)
       end
 
     end