Merge branch 'master' into Skyline/work/20241006_import_pep_list_order

ProteoWizard · Oct 8, 2024 · 5278882 · 5278882
2 parents 28a2bed + 0f98e37
commit 5278882
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Showing 22 changed files with 108 additions and 42 deletions.
diff --git a/pwiz_tools/Shared/Common/DataBinding/AbstractViewContext.cs b/pwiz_tools/Shared/Common/DataBinding/AbstractViewContext.cs
@@ -498,7 +498,7 @@ protected virtual DataGridViewColumn CreateCustomColumn(PropertyDescriptor prope
             }
             catch (Exception exception)
             {
-                Trace.TraceError(@"Exception constructing column of type {0}:{1}", columnTypeAttribute.ColumnType, exception);
+                Messages.WriteAsyncDebugMessage(@"Exception constructing column of type {0}:{1}", columnTypeAttribute.ColumnType, exception);
                 return null;
             }
         }

diff --git a/pwiz_tools/Shared/Common/DataBinding/Controls/Editor/FilterTab.cs b/pwiz_tools/Shared/Common/DataBinding/Controls/Editor/FilterTab.cs
@@ -18,11 +18,11 @@
  */
 using System;
 using System.Collections.Generic;
-using System.Diagnostics;
 using System.Drawing;
 using System.Linq;
 using System.Windows.Forms;
 using pwiz.Common.Properties;
+using pwiz.Common.SystemUtil;
 
 namespace pwiz.Common.DataBinding.Controls.Editor
 {
@@ -301,7 +301,7 @@ private void DataGridViewFilterOnCellEnter(object sender, DataGridViewCellEventA
 
         private void dataGridViewFilter_DataError(object sender, DataGridViewDataErrorEventArgs e)
         {
-            Trace.TraceError(@"DataGridViewFilterOnDataError:{0}", e.Exception);
+            Messages.WriteAsyncDebugMessage(@"DataGridViewFilterOnDataError:{0}", e.Exception);
         }
 
         protected override void OnLoad(EventArgs e)

diff --git a/pwiz_tools/Shared/Common/DataBinding/Internal/BindingListView.cs b/pwiz_tools/Shared/Common/DataBinding/Internal/BindingListView.cs
@@ -28,6 +28,7 @@
 using pwiz.Common.DataBinding.Clustering;
 using pwiz.Common.DataBinding.Controls;
 using pwiz.Common.DataBinding.Layout;
+using pwiz.Common.SystemUtil;
 
 namespace pwiz.Common.DataBinding.Internal
 {
@@ -533,7 +534,7 @@ public void Dispose()
 
         public void OnUnhandledException(Exception exception)
         {
-            Trace.TraceError(@"BindingListView unhandled exception {0}", exception);
+            Messages.WriteAsyncDebugMessage(@"BindingListView unhandled exception {0}", exception);
             var unhandledExceptionEvent = UnhandledExceptionEvent;
             if (null != unhandledExceptionEvent)
             {

diff --git a/pwiz_tools/Shared/Common/DataBinding/Internal/Pivoter.cs b/pwiz_tools/Shared/Common/DataBinding/Internal/Pivoter.cs
@@ -19,10 +19,10 @@
 
 using System;
 using System.Collections.Generic;
-using System.Diagnostics;
 using System.Linq;
 using System.Threading;
 using pwiz.Common.Collections;
+using pwiz.Common.SystemUtil;
 
 namespace pwiz.Common.DataBinding.Internal
 {
@@ -261,7 +261,7 @@ IDictionary<IList<Tuple<PropertyPath, PivotKey, object>>, List<GroupedRow>> allR
                     }
                     else
                     {
-                        Trace.TraceWarning(@"Unable to pivot on column {0} because it is already pivoted.", pivotColumn.PropertyPath);
+                        Messages.WriteAsyncDebugMessage(@"Unable to pivot on column {0} because it is already pivoted.", pivotColumn.PropertyPath); // N.B. see TraceWarningListener for output details
                     }
                 }
                 var pivotOnKey = PivotKey.GetPivotKey(allPivotKeys, pivotOnKeyValues);

diff --git a/pwiz_tools/Shared/Common/Graph/CurveDataHandler.cs b/pwiz_tools/Shared/Common/Graph/CurveDataHandler.cs
@@ -18,8 +18,8 @@
  */
 using System;
 using System.Collections.Generic;
-using System.Diagnostics;
 using System.Linq;
+using pwiz.Common.SystemUtil;
 using ZedGraph;
 
 namespace pwiz.Common.Graph
@@ -232,7 +232,7 @@ protected virtual Func<PointPair, double> ValueOfPointFuncForAxis(DataFrameBuild
             {
                 return point => point.Y;
             }
-            Trace.TraceError(@"Could not determine type of axis {0}", axis);
+            Messages.WriteAsyncDebugMessage(@"Could not determine type of axis {0}", axis);
             return null;
         }
 

diff --git a/pwiz_tools/Shared/CommonUtil/CommonUtil.csproj b/pwiz_tools/Shared/CommonUtil/CommonUtil.csproj
@@ -170,6 +170,7 @@
       <SubType>Form</SubType>
     </Compile>
     <Compile Include="SystemUtil\CommonTextUtil.cs" />
+    <Compile Include="SystemUtil\Messages.cs" />
     <Compile Include="SystemUtil\FileSize.cs" />
     <Compile Include="SystemUtil\FileSizeFormatProvider.cs" />
     <Compile Include="SystemUtil\IFormView.cs" />
@@ -270,20 +271,20 @@
       <LastGenOutput>Resources.Designer.cs</LastGenOutput>
       <SubType>Designer</SubType>
     </EmbeddedResource>
-	<EmbeddedResource Include="CommonResources\GeneralTerms.ja.resx">
+    <EmbeddedResource Include="CommonResources\GeneralTerms.ja.resx">
       <DependentUpon>GeneralTerms.resx</DependentUpon>
       <SubType>Designer</SubType>
     </EmbeddedResource>
     <EmbeddedResource Include="CommonResources\GeneralTerms.zh-CHS.resx">
       <DependentUpon>GeneralTerms.resx</DependentUpon>
       <SubType>Designer</SubType>
     </EmbeddedResource>
-	<EmbeddedResource Include="CommonResources\GeneralTerms.resx">
+    <EmbeddedResource Include="CommonResources\GeneralTerms.resx">
       <Generator>ResXFileCodeGenerator</Generator>
       <LastGenOutput>GeneralTerms.Designer.cs</LastGenOutput>
       <SubType>Designer</SubType>
     </EmbeddedResource>
-	<EmbeddedResource Include="CommonResources\Images.ja.resx">
+    <EmbeddedResource Include="CommonResources\Images.ja.resx">
       <DependentUpon>Images.resx</DependentUpon>
       <SubType>Designer</SubType>
     </EmbeddedResource>

diff --git a/pwiz_tools/Shared/CommonUtil/SystemUtil/Caching/Receiver.cs b/pwiz_tools/Shared/CommonUtil/SystemUtil/Caching/Receiver.cs
@@ -17,7 +17,6 @@
  * limitations under the License.
  */
 using System;
-using System.Diagnostics;
 using System.Windows.Forms;
 
 namespace pwiz.Common.SystemUtil.Caching
@@ -135,7 +134,7 @@ public void Dispose()
                 _workOrder = null;
                 if (OwnerControl != null)
                 {
-                    Trace.TraceInformation("CalculatedValueListener destroyed: {0}", Producer.ValueType);
+                    Messages.WriteAsyncDebugMessage("CalculatedValueListener destroyed: {0}", Producer.ValueType); // N.B. see TraceWarningListener for output details
                     OwnerControl.HandleDestroyed -= OwnerControlHandleDestroyed;
                     OwnerControl = null;
                 }

diff --git a/pwiz_tools/Shared/CommonUtil/SystemUtil/CommonActionUtil.cs b/pwiz_tools/Shared/CommonUtil/SystemUtil/CommonActionUtil.cs
@@ -17,7 +17,6 @@
  * limitations under the License.
  */
 using System;
-using System.Diagnostics;
 using System.Threading;
 using System.Windows.Forms;
 
@@ -53,7 +52,7 @@ public static void HandleException(Exception exception)
             {
                 return;
             }
-            Trace.TraceWarning(@"Unhandled Exception: {0}", exception);
+            Messages.WriteAsyncDebugMessage(@"Unhandled Exception: {0}", exception); // N.B. see TraceWarningListener for output details
         }
 
         public static bool SafeBeginInvoke(Control control, Action action)

diff --git a/pwiz_tools/Shared/CommonUtil/SystemUtil/Messages.cs b/pwiz_tools/Shared/CommonUtil/SystemUtil/Messages.cs
@@ -0,0 +1,45 @@
+/*
+ * Original author: Brian Pratt <bspratt .at. proteinms . net>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2024 University of Washington - Seattle, WA
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+using System.Diagnostics;
+
+namespace pwiz.Common.SystemUtil
+{
+    /// <summary>
+    /// Provides a mechanism for showing non-blocking messages.
+    ///
+    /// Really just a wrapper for Trace, which we don't want to call
+    /// directly as it looks too much like leftover debug code.
+    ///
+    /// </summary>
+    public static class Messages
+    {
+        public static void WriteAsyncDebugMessage(string message, params object[] args)
+        {
+            Trace.TraceInformation(message, args);
+        }
+
+        public static void WriteAsyncUserMessage(string message, params object[] args)
+        {
+            // For Skyline UI, the TraceWarningListener class causes these messages to appear in the
+            // Immediate Window, for commandline they appear in the console.
+            Trace.TraceWarning(message, args);  
+        }
+    }
+}
diff --git a/pwiz_tools/Shared/ProteomeDb/API/ProteinMatcher.cs b/pwiz_tools/Shared/ProteomeDb/API/ProteinMatcher.cs
@@ -18,13 +18,14 @@
  */
 using System;
 using System.Collections.Generic;
-using System.Diagnostics;
 using System.Linq;
 using System.Threading;
 using NHibernate;
 using pwiz.ProteomeDatabase.DataModel;
 using pwiz.ProteomeDatabase.Util;
 using pwiz.Common.Collections;
+using pwiz.Common.SystemUtil;
+
 namespace pwiz.ProteomeDatabase.API
 {
     /// <summary>
@@ -252,7 +253,7 @@ private void ExecuteBackground()
                 {
                     return;
                 }
-                Trace.TraceError(@"Unhandled exception: {0}", exception);
+                Messages.WriteAsyncDebugMessage(@"Unhandled exception: {0}", exception);
             }
         }
 

diff --git a/pwiz_tools/Shared/zedgraph/ZedGraph/ZedGraphControl.cs b/pwiz_tools/Shared/zedgraph/ZedGraph/ZedGraphControl.cs
@@ -622,7 +622,7 @@ protected override void OnPaint( PaintEventArgs e )
                 }
                 catch (Exception exception)
                 {
-                    Trace.TraceWarning(@"Error when painting a zedGraph:{0}", exception);
+                    Trace.TraceInformation(@"Error when painting a zedGraph:{0}", exception); // N.B. see TraceWarningListener for output details
                 }
 			}
 

diff --git a/pwiz_tools/Skyline/Alerts/ReportShutdownDlg.cs b/pwiz_tools/Skyline/Alerts/ReportShutdownDlg.cs
@@ -18,12 +18,12 @@
  */
 
 using System;
-using System.Diagnostics;
 using System.IO;
 using System.Linq;
 using System.Reflection;
 using System.Text;
 using System.Windows.Forms;
+using pwiz.Common.SystemUtil;
 using pwiz.Skyline.Util;
 using pwiz.Skyline.Util.Extensions;
 
@@ -75,7 +75,7 @@ public static void SaveExceptionFile(Exception exception, bool forced = false)
 
             if (!forced)
             {
-                Trace.TraceError(exceptionInfo);
+                Messages.WriteAsyncDebugMessage(exceptionInfo);
                 Console.WriteLine(exceptionInfo);
             }
 

diff --git a/pwiz_tools/Skyline/Model/Databinding/ReportSpecConverter.cs b/pwiz_tools/Skyline/Model/Databinding/ReportSpecConverter.cs
@@ -19,10 +19,10 @@
 using System;
 using System.Collections.Generic;
 using System.ComponentModel;
-using System.Diagnostics;
 using System.Linq;
 using System.Reflection;
 using pwiz.Common.DataBinding;
+using pwiz.Common.SystemUtil;
 using pwiz.Skyline.Model.DocSettings;
 using pwiz.Skyline.Model.Hibernate;
 
@@ -270,7 +270,7 @@ private ColumnSpec ConvertReportColumn(ReportColumn reportColumn)
                     oldCaption = null;
                     if (null == propertyPath)
                     {
-                        Trace.TraceWarning(@"Unable to parse ratio property {0}", part);
+                        Messages.WriteAsyncDebugMessage(@"Unable to parse ratio property {0}", part);
                         propertyPath = PropertyPath.Root.Property(part);
                     }
                 }
@@ -283,7 +283,7 @@ private ColumnSpec ConvertReportColumn(ReportColumn reportColumn)
                     PropertyInfo property = component.GetProperty(part);
                     if (null == property)
                     {
-                        Trace.TraceWarning(@"Could not find property {0}", part);
+                        Messages.WriteAsyncDebugMessage(@"Could not find property {0}", part);
                         continue;
                     }
                     propertyPath = PropertyPath.Root.Property(part);

diff --git a/pwiz_tools/Skyline/Model/DocSettings/TransitionSettings.cs b/pwiz_tools/Skyline/Model/DocSettings/TransitionSettings.cs
@@ -1180,6 +1180,7 @@ public bool Equals(TransitionFilter obj)
                    ArrayUtil.EqualsDeep(obj._peptideProductCharges, _peptideProductCharges) &&
                    ArrayUtil.EqualsDeep(obj._peptideIonTypes, _peptideIonTypes) &&
                    ArrayUtil.EqualsDeep(obj._smallMoleculePrecursorAdducts, _smallMoleculePrecursorAdducts) &&
+                   ArrayUtil.EqualsDeep(obj._smallMoleculeFragmentAdducts, _smallMoleculeFragmentAdducts) &&
                    ArrayUtil.EqualsDeep(obj._smallMoleculeIonTypes, _smallMoleculeIonTypes) &&
                    Equals(obj.FragmentRangeFirst, FragmentRangeFirst) &&
                    Equals(obj.FragmentRangeLast, FragmentRangeLast) &&
@@ -1205,6 +1206,7 @@ public override int GetHashCode()
                 result = (result * 397) ^ _peptideProductCharges.GetHashCodeDeep();
                 result = (result * 397) ^ _peptideIonTypes.GetHashCodeDeep();
                 result = (result * 397) ^ _smallMoleculePrecursorAdducts.GetHashCodeDeep();
+                result = (result * 397) ^ _smallMoleculeFragmentAdducts.GetHashCodeDeep();
                 result = (result * 397) ^ _smallMoleculeIonTypes.GetHashCodeDeep();
                 result = (result * 397) ^ FragmentRangeFirst.GetHashCode();
                 result = (result*397) ^ FragmentRangeLast.GetHashCode();

diff --git a/pwiz_tools/Skyline/Model/Lib/ChromLib/ChromatogramLibrary.cs b/pwiz_tools/Skyline/Model/Lib/ChromLib/ChromatogramLibrary.cs
@@ -18,7 +18,6 @@
  */
 using System;
 using System.Collections.Generic;
-using System.Diagnostics;
 using System.Globalization;
 using System.IO;
 using System.Linq;
@@ -571,7 +570,7 @@ private bool LoadLibraryFromDatabase(ILoadMonitor loader)
             }
             catch (Exception e)
             {
-                Trace.TraceWarning(ChromLibResources.ChromatogramLibrary_LoadLibraryFromDatabase_Error_loading_chromatogram_library__0_, e);
+                Messages.WriteAsyncUserMessage(ChromLibResources.ChromatogramLibrary_LoadLibraryFromDatabase_Error_loading_chromatogram_library__0_, e);
                 return false;
             }
         }
@@ -692,7 +691,7 @@ private bool LoadFromCache(ILoadMonitor loadMonitor, ProgressStatus status)
             }
             catch (Exception exception)
             {
-                Trace.TraceWarning(ChromLibResources.ChromatogramLibrary_LoadFromCache_Exception_reading_cache__0_, exception);
+                Messages.WriteAsyncUserMessage(ChromLibResources.ChromatogramLibrary_LoadFromCache_Exception_reading_cache__0_, exception);
                 return false;
             }
         }

diff --git a/pwiz_tools/Skyline/Model/Lib/EncylopeDiaLibrary.cs b/pwiz_tools/Skyline/Model/Lib/EncylopeDiaLibrary.cs
@@ -21,7 +21,6 @@
 using System.Data;
 using System.Data.Common;
 using System.Data.SQLite;
-using System.Diagnostics;
 using System.IO;
 using System.Linq;
 using System.Text;
@@ -466,7 +465,7 @@ private bool LoadFromCache(ILoadMonitor loader)
             }
             catch (Exception exception)
             {
-                Trace.TraceWarning(@"Exception loading cache: {0}", exception);
+                Messages.WriteAsyncDebugMessage(@"Exception loading cache: {0}", exception);
                 return false;
             }
         }

diff --git a/pwiz_tools/Skyline/Model/Results/PeptideChromData.cs b/pwiz_tools/Skyline/Model/Results/PeptideChromData.cs
@@ -19,11 +19,11 @@
 using System;
 using System.Collections.Generic;
 using System.Collections.ObjectModel;
-using System.Diagnostics;
 using System.Drawing;
 using System.Linq;
 using pwiz.Common.Collections;
 using pwiz.Common.PeakFinding;
+using pwiz.Common.SystemUtil;
 using pwiz.Skyline.Model.DocSettings;
 using pwiz.Skyline.Model.Results.Scoring;
 using pwiz.Skyline.Util;
@@ -959,11 +959,11 @@ public bool FilterByRetentionTime()
                         string precursorText = GetTextForNode(NodePep, dataSet.NodeGroup, null);
                         if (dataSet.MinRawTime > dataSet.MaxRawTime)
                         {
-                            Trace.TraceWarning(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_empty_chromatograms_for__0_, precursorText);
+                            Messages.WriteAsyncUserMessage(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_empty_chromatograms_for__0_, precursorText);
                         }
                         else
                         {
-                            Trace.TraceWarning(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_chromatograms_for___0___because_the_explicit_retention_time__1__is_not_between__2__and__3_,
+                            Messages.WriteAsyncUserMessage(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_chromatograms_for___0___because_the_explicit_retention_time__1__is_not_between__2__and__3_,
                                 precursorText, explicitRT, dataSet.MinRawTime, dataSet.MaxRawTime);
                         }
                         DataSets.RemoveAt(i);
@@ -978,11 +978,11 @@ public bool FilterByRetentionTime()
                                 string transitionText = GetTextForNode(NodePep, dataSet.NodeGroup, chrom.DocNode);
                                 if (!chrom.Times.Any())
                                 {
-                                    Trace.TraceWarning(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_empty_chromatograms_for__0_, transitionText);
+                                    Messages.WriteAsyncUserMessage(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_empty_chromatograms_for__0_, transitionText);
                                 }
                                 else
                                 {
-                                    Trace.TraceWarning(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_chromatograms_for___0___because_the_explicit_retention_time__1__is_not_between__2__and__3_,
+                                    Messages.WriteAsyncUserMessage(ResultsResources.PeptideChromDataSets_FilterByRetentionTime_Discarding_chromatograms_for___0___because_the_explicit_retention_time__1__is_not_between__2__and__3_,
                                         transitionText, explicitRT, chrom.Times.First(), chrom.Times.Last());
                                 }
                                 dataSet.Chromatograms.RemoveAt(j);