Changeset 4504

Timestamp:

Jun 18, 2013, 1:19:17 PM (10 years ago)

Author:

Fredrik Levander

Message:

Refs #809. Setting modification mass difference if absent.

File:

• trunk/api/core/src/org/proteios/core/Modification.java (modified) (1 diff)

trunk/api/core/src/org/proteios/core/Modification.java

@@ -296 +296 @@
     modMap.put("Deamidation", "MOD:00400");
     modMap.put("Pyro_glu", "MOD:00420");
-    modMap.put("Pyro-glu", "MOD:00040");    
+    modMap.put("Pyro-glu", "MOD:00040");
     mod.setCvId(modMap.get(mod.getName()));
-    mod.setPosition(mod.getPosition()+1);
+    if (mod.getMonoisotopicDeltaMass() == 0d && modMap.containsKey(mod
+      .getName()))
+    {
+      Map<String, Double> modMassMap = new HashMap<String, Double>();
+      modMassMap.put("Carbamidomethyl", 57.021464);
+      modMassMap.put("Phospho", 79.966331);
+      modMassMap.put("Oxidation", 15.994915);
+      modMassMap.put("Acetyl", 42.010565);
+      modMassMap.put("Deamidation", 0.984016);
+      modMassMap.put("Pyro_glu", -18.010565);
+      modMassMap.put("Pyro-glu", -17.026549);
+      mod.setMonoisotopicDeltaMass(modMassMap.get(mod.getName()));
+    }
+    mod.setPosition(mod.getPosition() + 1);
   }
 }