Fix for MzLib PR #939 failed integration tests

Author: pcruzparri

MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs

@@ -384,21 +384,13 @@ public static void MetaDraw_SearchTaskTest()
             // test that the stationary sequence annotation was drawn
             string modifiedBaseSeq = psm.BaseSeq.Substring(MetaDrawSettings.FirstAAonScreenIndex, MetaDrawSettings.NumberOfAAOnScreen);
             string fullSequence = psm.BaseSeq;
-            Dictionary<int, List<string>> modDictionary = PsmFromTsv.ParseModifications(psm.FullSequence);
+            Dictionary<int, string> modDictionary = PsmFromTsv.ParseModifications(psm.FullSequence);
             foreach (var mod in modDictionary.OrderByDescending(p => p.Key))
             {
                 // if modification is within the visible region
                 if (mod.Key >= MetaDrawSettings.FirstAAonScreenIndex && mod.Key < (MetaDrawSettings.FirstAAonScreenIndex + MetaDrawSettings.NumberOfAAOnScreen))
                 {
-                    // account for multiple modifications on the same amino acid
-                    for (int i = mod.Value.Count - 1; i > -1; i--)
-                    {
-                        fullSequence = fullSequence.Insert(mod.Key - MetaDrawSettings.FirstAAonScreenIndex, "[" + mod.Value[i] + "]");
-                        if (i >= 1)
-                        {
-                            fullSequence = fullSequence.Insert(mod.Key, "|");
-                        }
-                    }
+                    fullSequence = fullSequence.Insert(mod.Key - MetaDrawSettings.FirstAAonScreenIndex, "[" + mod.Value + "]");
                 }
             }
             List<MatchedFragmentIon> matchedIons = psm.MatchedIons.Where(p => p.NeutralTheoreticalProduct.ResiduePosition > MetaDrawSettings.FirstAAonScreenIndex &&
@@ -432,15 +424,7 @@ public static void MetaDraw_SearchTaskTest()
                 // if modification is within the visible region
                 if (mod.Key >= MetaDrawSettings.FirstAAonScreenIndex && mod.Key < (MetaDrawSettings.FirstAAonScreenIndex + MetaDrawSettings.NumberOfAAOnScreen))
                 {
-                    // account for multiple modifications on the same amino acid
-                    for (int i = mod.Value.Count - 1; i > -1; i--)
-                    {
-                        fullSequence = fullSequence.Insert(mod.Key - MetaDrawSettings.FirstAAonScreenIndex, "[" + mod.Value[i] + "]");
-                        if (i >= 1)
-                        {
-                            fullSequence = fullSequence.Insert(mod.Key, "|");
-                        }
-                    }
+                    fullSequence = fullSequence.Insert(mod.Key - MetaDrawSettings.FirstAAonScreenIndex, "[" + mod.Value + "]");
                 }
             }
             matchedIons = modPsm.MatchedIons.Where(p => p.NeutralTheoreticalProduct.ResiduePosition > MetaDrawSettings.FirstAAonScreenIndex &&

MetaMorpheus/Test/PsvTsvTest.cs

@@ -174,20 +174,8 @@ public static void TestParseModification()
             modDict = PsmFromTsv.ParseModifications(twoMods.FullSequence);
             Assert.That(modDict.Count == 2);
             Assert.That(modDict.ContainsKey(0) && modDict.ContainsKey(104));
-            Assert.That(modDict[0].Count == 1);
             Assert.That(modDict[0].Contains("UniProt:N-acetylserine on S"));
-            Assert.That(modDict[104].Count == 1);
             Assert.That(modDict[104].Contains("UniProt:N5-methylglutamine on Q"));
-
-
-            // psm with two mods on the same amino acid
-            string fullSeq = "[Common Fixed:Carbamidomethyl on C]|[UniProt:N-acetylserine on S]KPRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFK";
-            modDict = PsmFromTsv.ParseModifications(fullSeq);
-            Assert.That(modDict.Count == 1);
-            Assert.That(modDict.ContainsKey(0));
-            Assert.That(modDict[0].Count == 2);
-            Assert.That(modDict[0].Contains("Common Fixed:Carbamidomethyl on C"));
-            Assert.That(modDict[0].Contains("UniProt:N-acetylserine on S"));
         }
 
         [Test]