lib/ms/in_silico/spectrum.rb in ms-in_silico-0.1.0 vs lib/ms/in_silico/spectrum.rb in ms-in_silico-0.2.0

@@ -110,10 +110,13 @@
         
         # Scans the sequence to produce a ladder of masses and a
         # hash of (residue, locations) pairs which indicate the
         # indicies at which the residue occurs in sequence. The
         # ladder corresponds to the M values described above.
+        # Characters in the sequence that do not add mass, such
+        # as whitespace, are skipped and do not add an entry to
+        # the ladder.
         #  
         # Returns [ladder, {residue => locations}].
         #
         # ==== Inputs
         # sequence:: a string
@@ -130,13 +133,17 @@
           residues_to_locate.each_byte {|byte| locations[byte] = []}
 
           mass = 0
           ladder = []
           sequence.each_byte do |byte|
-            mass += masses_by_byte[byte]
-            location = locations[byte]
-
-            location << ladder.length if location
+            # check a mass is added... if not (as for whitespace) 
+            # then skip to the next byte
+            next if (mass == (mass += masses_by_byte[byte]))
+            
+            if location = locations[byte]
+              location << ladder.length
+            end
+            
             ladder << mass
           end
 
           hash = {}
           0.upto(residues_to_locate.length-1) do |index|
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