Merge pull request #174 from smith-chem-wisc/StefanBranch

uhuh

Author: stefanks

MetaMorpheusGUI/MainWindow.xaml.cs

@@ -178,7 +178,7 @@ private void LoadSearchModesFromFile()
         {
             searchModeObservableCollection.Add(new SinglePpmAroundZeroSearchMode(5));
             searchModeObservableCollection.Add(new SingleAbsoluteAroundZeroSearchMode(0.05));
-            searchModeObservableCollection.Add(new DotSearchMode(new double[] { 0, 1.003 }, new Tolerance(ToleranceUnit.PPM, 5)));
+            searchModeObservableCollection.Add(new DotSearchMode(new double[] { 0, 1.003, 2.006, 3.009 }, new Tolerance(ToleranceUnit.PPM, 5)));
             searchModeObservableCollection.Add(new IntervalSearchMode(new List<DoubleRange>() { new DoubleRange(-2.1, 2.1) }));
             searchModeObservableCollection.Add(new OpenSearchMode());
         }

MetaMorpheusGUI/SearchTaskWindow.xaml.cs

@@ -158,29 +158,36 @@ private void addNewAllowedPrecursorMassDiffsButton_Click(object sender, RoutedEv
             // Format: name, "interval", intervals
             // Format: name, "dot", num, "ppm" or "da", dots
 
-            var split = newAllowedPrecursorMassDiffsTextBox.Text.Split(' ');
-
-            switch (split[1])
+            try
             {
-                case "dot":
-                    ToleranceUnit tu = ToleranceUnit.PPM;
-                    if (split[3].Equals("ppm"))
-                        tu = ToleranceUnit.PPM;
-                    else if (split[3].Equals("da"))
-                        tu = ToleranceUnit.Absolute;
-                    else
+                var split = newAllowedPrecursorMassDiffsTextBox.Text.Split(' ');
+
+                switch (split[1])
+                {
+                    case "dot":
+                        ToleranceUnit tu = ToleranceUnit.PPM;
+                        if (split[3].Equals("ppm"))
+                            tu = ToleranceUnit.PPM;
+                        else if (split[3].Equals("da"))
+                            tu = ToleranceUnit.Absolute;
+                        else
+                            break;
+                        DotSearchMode dsm = new DotSearchMode(split[0], Array.ConvertAll(split[4].Split(','), Double.Parse), new Tolerance(tu, double.Parse(split[2], CultureInfo.InvariantCulture)));
+                        SearchModes.Add(new SearchModeFoSearch(dsm));
+                        allowedPrecursorMassDiffsDataGrid.Items.Refresh();
+                        break;
+
+                    case "interval":
+                        IEnumerable<DoubleRange> doubleRanges = Array.ConvertAll(split[2].Split(','), b => new DoubleRange(double.Parse(b.Trim(new char[] { '[', ']' }).Split(';')[0], CultureInfo.InvariantCulture), double.Parse(b.Trim(new char[] { '[', ']' }).Split(';')[1], CultureInfo.InvariantCulture)));
+                        IntervalSearchMode ism = new IntervalSearchMode(split[0], doubleRanges);
+                        SearchModes.Add(new SearchModeFoSearch(ism));
+                        allowedPrecursorMassDiffsDataGrid.Items.Refresh();
                         break;
-                    DotSearchMode dsm = new DotSearchMode(split[0], Array.ConvertAll(split[4].Split(','), Double.Parse), new Tolerance(tu, double.Parse(split[2], CultureInfo.InvariantCulture)));
-                    SearchModes.Add(new SearchModeFoSearch(dsm));
-                    allowedPrecursorMassDiffsDataGrid.Items.Refresh();
-                    break;
-
-                case "interval":
-                    IEnumerable<DoubleRange> doubleRanges = Array.ConvertAll(split[2].Split(','), b => new DoubleRange(double.Parse(b.Trim(new char[] { '[', ']' }).Split('-')[0], CultureInfo.InvariantCulture), double.Parse(b.Trim(new char[] { '[', ']' }).Split('-')[1], CultureInfo.InvariantCulture)));
-                    IntervalSearchMode ism = new IntervalSearchMode(split[0], doubleRanges);
-                    SearchModes.Add(new SearchModeFoSearch(ism));
-                    allowedPrecursorMassDiffsDataGrid.Items.Refresh();
-                    break;
+                }
+            }
+            catch (Exception)
+            {
+                MessageBox.Show("Examples:" + Environment.NewLine + "name dot 5 ppm 0,1.003,2.006" + Environment.NewLine + "name interval [-4;-3],[-0.5;0.5],[101;102]", "Error parsing search mode text box", MessageBoxButton.OK, MessageBoxImage.Warning);
             }
         }
 

OldInternalLogic/OldInternalLogic.csproj

@@ -121,9 +121,6 @@
     <Content Include="f.txt">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </Content>
-    <Content Include="help.txt">
-      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
-    </Content>
     <Content Include="glyco.txt">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </Content>

OldInternalLogic/combos.txt

@@ -1,14 +1,15 @@
-79.966331 21.981943
-15.994915 31.989829
-42.010565 0.984016
-14.015650 28.031300
-15.994915 21.981943
-31.989829 0.984016
-15.994915 15.994915
-14.015650 14.015650
-0.984016 21.981943
-15.994915 0.984016
--17.02655 15.994915
--17.026549 0.984016
-21.981943 21.981943
+79.966331 21.981943
+15.994915 31.989829
+42.010565 0.984016
+14.015650 28.031300
+15.994915 21.981943
+31.989829 0.984016
+15.994915 15.994915
+14.015650 14.015650
+0.984016 21.981943
+0.984016 0.984016
+15.994915 0.984016
+-17.02655 15.994915
+-17.026549 0.984016
+21.981943 21.981943
 14.015650 0.984016