Merge pull request #170 from smith-chem-wisc/StefanBranch

oh oby

Author: stefanks

InternalLogic/IndexEngine.cs

@@ -56,6 +56,7 @@ public override string ToString()
             sb.AppendLine("Number of fixed mods: " + fixedModifications.Count);
             sb.AppendLine("Number of variable mods: " + variableModifications.Count);
             sb.AppendLine("Number of localizeable mods: " + localizeableModifications.Count);
+            sb.AppendLine("lp: " + string.Join(",", lp));
             sb.Append("protease: " + protease);
             return sb.ToString();
         }

InternalLogicWithFileIO/GPTMDTask/GPTMDTask.cs

@@ -44,6 +44,7 @@ public GptmdTask(ObservableCollection<ModList> modList)
             listOfModListsForGPTMD[1].Variable = true;
             listOfModListsForGPTMD[2].Localize = true;
             listOfModListsForGPTMD[3].Gptmd = true;
+            listOfModListsForGPTMD[4].Gptmd = true;
             precursorMassTolerance = new Tolerance(ToleranceUnit.PPM, 10);
             TaskType = MyTask.Gptmd;
             Tol = 0.003;

MetaMorpheusGUI/MainWindow.xaml.cs

@@ -50,6 +50,7 @@ public MainWindow()
             modListObservableCollection.Add(new ModList("v.txt"));
             modListObservableCollection.Add(new ModList("ptmlist.txt"));
             modListObservableCollection.Add(new ModList("m.txt"));
+            modListObservableCollection.Add(new ModList("glyco.txt"));
             modListObservableCollection.Add(new ModList("r.txt"));
             modListObservableCollection.Add(new ModList("s.txt"));
 

OldInternalLogic/OldInternalLogic.csproj

@@ -116,6 +116,9 @@
     <Content Include="help.txt">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </Content>
+    <Content Include="glyco.txt">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </Content>
     <Content Include="m.txt">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </Content>

OldInternalLogic/glyco.txt

@@ -0,0 +1,73 @@
+Glycans
+ID   HexNAc
+FT   MOD_RES
+TG   Asparagine
+PP   Anywhere.
+SL   Labile
+MM   203.079373
+CF   C8 O5 N1 H14
+//
+ID   HexNAc
+FT   MOD_RES
+TG   Serine
+PP   Anywhere.
+SL   Labile
+MM   203.079373
+CF   C8 O5 N1 H14
+//
+ID   HexNAc
+FT   MOD_RES
+TG   Threonine
+PP   Anywhere.
+SL   Labile
+MM   203.079373
+CF   C8 O5 N1 H14
+//
+ID   Hexose
+FT   MOD_RES
+TG   Asparagine
+PP   Anywhere.
+SL   Labile
+MM   162.052824
+CF   C6 O5 H10
+//
+ID   Hexose
+FT   MOD_RES
+TG   Serine
+PP   Anywhere.
+SL   Labile
+MM   162.052824
+CF   C6 O5 H10
+//
+ID   Hexose
+FT   MOD_RES
+TG   Threonine
+PP   Anywhere.
+SL   Labile
+MM   162.052824
+CF   C6 O5 H10
+//
+ID   Fucose
+FT   MOD_RES
+TG   Asparagine
+PP   Anywhere.
+SL   Labile
+MM   146.057909
+CF   C6 H10 O4
+//
+ID   Fucose
+FT   MOD_RES
+TG   Serine
+PP   Anywhere.
+SL   Labile
+MM   146.057909
+CF   C6 H10 O4
+//
+ID   Fucose
+FT   MOD_RES
+TG   Threonine
+PP   Anywhere.
+SL   Labile
+MM   146.057909
+CF   C6 H10 O4
+//

OldInternalLogic/m.txt

@@ -526,54 +526,6 @@ SL   Sticky
 MM   156.10111
 CF   C6 H12 N1 4O
 //
-ID   HexNAc
-FT   MOD_RES
-TG   Asparagine
-PP   Anywhere.
-SL   Labile
-MM   203.079373
-CF   C8 O5 N1 H14
-//
-ID   HexNAc
-FT   MOD_RES
-TG   Serine
-PP   Anywhere.
-SL   Labile
-MM   203.079373
-CF   C8 O5 N1 H14
-//
-ID   HexNAc
-FT   MOD_RES
-TG   Threonine
-PP   Anywhere.
-SL   Labile
-MM   203.079373
-CF   C8 O5 N1 H14
-//
-ID   Hexose
-FT   MOD_RES
-TG   Asparagine
-PP   Anywhere.
-SL   Labile
-MM   162.052824
-CF   C6 O5 H10
-//
-ID   Hexose
-FT   MOD_RES
-TG   Serine
-PP   Anywhere.
-SL   Labile
-MM   162.052824
-CF   C6 O5 H10
-//
-ID   Hexose
-FT   MOD_RES
-TG   Threonine
-PP   Anywhere.
-SL   Labile
-MM   162.052824
-CF   C6 O5 H10
-//
 ID   Farnesylation
 FT   MOD_RES
 TG   Cysteine

Test/MyTaskTest.cs

@@ -26,17 +26,20 @@ public static void TestEverythingRunner()
             ModList modlist2 = new ModList("v.txt");
             ModList modlist3 = new ModList("ptmlist.txt");
             ModList modlist4 = new ModList("m.txt");
+            ModList modlist5 = new ModList("glyco.txt");
             ObservableCollection<ModList> modList = new ObservableCollection<ModList> { modlist1, modlist2, modlist3 };
             CalibrationTask task1 = new CalibrationTask(modList);
-            GptmdTask task2 = new GptmdTask(new ObservableCollection<ModList> { modlist1, modlist2, modlist3, modlist4 });
+            GptmdTask task2 = new GptmdTask(new ObservableCollection<ModList> { modlist1, modlist2, modlist3, modlist4, modlist5 });
 
             IEnumerable<SearchMode> allSms = new List<SearchMode> { new SinglePpmAroundZeroSearchMode(5) };
 
-            SearchTask task3 = new SearchTask(new ObservableCollection<ModList> { modlist1, modlist2, modlist3, modlist4 }, allSms);
+            SearchTask task3 = new SearchTask(new ObservableCollection<ModList> { modlist1, modlist2, modlist3, modlist4, modlist5 }, allSms);
             task3.ListOfModListsForSearch[3].Localize = true;
+            task3.ListOfModListsForSearch[4].Localize = true;
 
-            SearchTask task4 = new SearchTask(new ObservableCollection<ModList> { modlist1, modlist2, modlist3, modlist4 }, allSms);
+            SearchTask task4 = new SearchTask(new ObservableCollection<ModList> { modlist1, modlist2, modlist3, modlist4, modlist5 }, allSms);
             task4.ListOfModListsForSearch[3].Localize = true;
+            task4.ListOfModListsForSearch[4].Localize = true;
             task4.ClassicSearch = false;
             List<MyTaskEngine> taskList = new List<MyTaskEngine> { task1, task2, task3, task4 };