Merge pull request #194 from smith-chem-wisc/StefanBranch

Stefan branch

Author: stefanks

EngineLayer/PsmWithMultiplePossiblePeptides.cs

@@ -140,7 +140,7 @@ internal static string TabSeparatedHeader
                 sb.Append("MissedCleavages" + '\t');
                 sb.Append("PeptideMonoisotopicMass" + '\t');
                 sb.Append("MassDiff (Da)" + '\t');
-                sb.Append("Decoy/Contaminant");
+                sb.Append("Decoy/Contaminant/Target");
                 return sb.ToString();
             }
         }
@@ -165,7 +165,12 @@ public override string ToString()
             sb.Append(MissedCleavages.ToString(CultureInfo.InvariantCulture) + '\t');
             sb.Append(PeptideMonoisotopicMass.ToString("F5", CultureInfo.InvariantCulture) + '\t');
             sb.Append((ScanPrecursorMass - PeptideMonoisotopicMass).ToString("F5", CultureInfo.InvariantCulture) + '\t');
-            sb.Append("" + (IsDecoy ? "D" : " ") + (IsContaminant ? "C" : " "));
+            if (IsDecoy)
+                sb.Append("D");
+            else if (IsContaminant)
+                sb.Append("C");
+            else
+                sb.Append("T");
 
             return sb.ToString();
         }

GUI/MainWindow.xaml.cs

@@ -359,7 +359,7 @@ private void tasksDataGrid_MouseDoubleClick(object sender, MouseButtonEventArgs
                 switch (ok.TaskType)
                 {
                     case MyTask.Search:
-                        var searchDialog = new SearchTaskWindow(ok as SearchTask, modListObservableCollection, searchModeObservableCollection);
+                        var searchDialog = new SearchTaskWindow(ok as SearchTask, modListObservableCollection);
                         searchDialog.ShowDialog();
                         break;
 

GUI/SearchTaskWindow.xaml.cs

@@ -4,6 +4,7 @@
 using System.Collections.Generic;
 using System.Collections.ObjectModel;
 using System.Globalization;
+using System.IO;
 using System.Linq;
 using System.Windows;
 using System.Windows.Controls;
@@ -40,10 +41,10 @@ public SearchTaskWindow(IEnumerable<ModList> modList, IEnumerable<SearchMode> se
             this.saveButton.Content = "Add the Search Task";
         }
 
-        public SearchTaskWindow(SearchTask task, IEnumerable<ModList> modList, IEnumerable<SearchMode> searchModes)
+        public SearchTaskWindow(SearchTask task, IEnumerable<ModList> modList)
         {
             InitializeComponent();
-            PopulateChoices(modList, searchModes);
+            PopulateChoices(modList, task.SearchModes.Select(b => b.SearchMode));
 
             TheTask = task;
             UpdateFieldsFromTask(TheTask);
@@ -65,7 +66,7 @@ private void Row_DoubleClick(object sender, MouseButtonEventArgs e)
             var hm = ye.Content as TextBlock;
             if (hm != null && !string.IsNullOrEmpty(hm.Text))
             {
-                System.Diagnostics.Process.Start(hm.Text);
+                System.Diagnostics.Process.Start(Path.Combine(@"Mods", hm.Text));
             }
         }