DIA search workflow UI changes

pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs

@@ -221,10 +221,10 @@ public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, r
                         ? Path.Combine(Environment.CurrentDirectory, psi.FileName)
                         : psi.FileName;
                     // ReSharper disable LocalizableElement
-                    sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}", processPath,
+                    sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}\r\nExit code: {4}", processPath,
                         // ReSharper restore LocalizableElement
                         string.Join(" ", proc.StartInfo.Arguments), psi.WorkingDirectory,
-                        stdin != null ? "\r\nStandard input:\r\n" + stdin : "");
+                        stdin != null ? "\r\nStandard input:\r\n" + stdin : "", exit);
                     throw new IOException(sbError.ToString());
                 }
 

pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs

@@ -72,9 +72,10 @@ public BuildPeptideSearchLibraryControl(IModifyDocumentContainer documentContain
             if (_isRunPeptideSearch)
             {
                 panel1.Hide();
-                radioDIA.Text = SkylineResources.BuildPeptideSearchLibraryControl_RunPeptideSearchRadioDIAText_DIA_with_DIA_Umpire;
-                helpTip.SetToolTip(radioDIA, SkylineResources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibraryControl_Library_from_DIA_deconvoluted_to_single_precursor_MS_MS_spectra_and_chromatograms_from_raw_DIA_spectra_of_same_runs);
-                InputFileType = ImportPeptideSearchDlg.InputFile.dda_raw;
+                if (ImportPeptideSearch.IsDIASearch)
+                    InputFileType = ImportPeptideSearchDlg.InputFile.dia_raw;
+                else
+                    InputFileType = ImportPeptideSearchDlg.InputFile.dda_raw;
             }
             else
             {
@@ -115,7 +116,8 @@ public BuildPeptideSearchLibrarySettings(BuildPeptideSearchLibraryControl contro
 
             public BuildPeptideSearchLibrarySettings(IEnumerable<BuildLibraryGridView.File> files, IrtStandard standard,
                 bool includeAmbiguousMatches, bool filterForDocumentPeptides,
-                ImportPeptideSearchDlg.Workflow workFlow, ImportPeptideSearchDlg.InputFile inputFileType, SrmDocument.DOCUMENT_TYPE docType)
+                ImportPeptideSearchDlg.Workflow workFlow,
+                ImportPeptideSearchDlg.InputFile inputFileType, SrmDocument.DOCUMENT_TYPE docType)
             {
                 SearchFileNames = files?.ToArray() ?? Array.Empty<BuildLibraryGridView.File>();
                 Standard = standard;
@@ -669,8 +671,6 @@ public bool PerformDDASearch
             get { return InputFileType != ImportPeptideSearchDlg.InputFile.search_result; }
         }
 
-        public bool DIAConversionNeeded => InputFileType == ImportPeptideSearchDlg.InputFile.dia_raw;
-
         private void OnGridChange(object sender, EventArgs e)
         {
             if (!PerformDDASearch)

pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx

@@ -129,7 +129,7 @@
     <value>6, 42</value>
   </data>
   <data name="radioDIA.Size" type="System.Drawing.Size, System.Drawing">
-    <value>369, 17</value>
+    <value>84, 17</value>
   </data>
   <assembly alias="mscorlib" name="mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" />
   <data name="radioDIA.TabIndex" type="System.Int32, mscorlib">
@@ -468,7 +468,7 @@ like BiblioSpec .blib, EncyclopeDIA .elib, SpectraST .sqt</value>
     <value>gridSearchFiles</value>
   </data>
   <data name="&gt;&gt;gridSearchFiles.Type" xml:space="preserve">
-    <value>pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null</value>
+    <value>pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline-daily, Version=24.1.1.263, Culture=neutral, PublicKeyToken=null</value>
   </data>
   <data name="&gt;&gt;gridSearchFiles.Parent" xml:space="preserve">
     <value>panelPeptideSearch</value>

pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs

@@ -121,7 +121,7 @@ public void InitializeProtocol(Protocol protocol)
 
         public DdaConverterSettings ConverterSettings
         {
-            get { return CurrentProtocol != Protocol.none ? new DdaConverterSettings(this) : null; }
+            get { return DdaConverterSettings.GetSettings(this); }
         }
 
         public class DdaConverterSettings
@@ -130,6 +130,14 @@ public static DdaConverterSettings GetDefault()
             {
                 return new DdaConverterSettings();
             }
+            public static DdaConverterSettings GetSettings(ConverterSettingsControl control)
+            {
+                if (control.CurrentProtocol == Protocol.none)
+                    return null;
+                if (control.CurrentProtocol == Protocol.dia_umpire && !control.UseDiaUmpire)
+                    return null;
+                return new DdaConverterSettings(control);
+            }
 
             public DdaConverterSettings()
             {
@@ -149,7 +157,7 @@ public DdaConverterSettings(ConverterSettingsControl control)
             public Protocol Protocol { get; }
             [Track]
             public DiaUmpire.Config.InstrumentPreset InstrumentPreset { get; }
-            [Track]
+            [Track(defaultValues:typeof(DefaultValuesNullOrEmpty))]
             public IEnumerable<AbstractDdaSearchEngine.Setting> NonDefaultAdditionalSettings { get; }
         }
 
@@ -290,6 +298,12 @@ private void ApplyVisibleAdditionalSettings()
             }
         }
 
+        public bool UseDiaUmpire
+        {
+            get => cbDiaUmpire.Checked;
+            set => cbDiaUmpire.Checked = value;
+        }
+
         public DiaUmpire.Config.InstrumentPreset InstrumentPreset
         {
             get { return (DiaUmpire.Config.InstrumentPreset) cbInstrumentPreset.SelectedIndex; }
@@ -314,14 +328,24 @@ public DiaUmpireDdaConverter GetDiaUmpireConverter()
             return new DiaUmpireDdaConverter(ImportPeptideSearch, _fullScanSettingsControlGetter().IsolationScheme, diaUmpireConfig);
         }
 
-        public MsconvertDdaConverter GetMsconvertConverter()
+        public MsconvertDdaConverter GetDdaConverter()
         {
             return new MsconvertDdaConverter(ImportPeptideSearch);
         }
 
+        public DiaConverter GetDiaConverter()
+        {
+            return new DiaConverter(ImportPeptideSearch);
+        }
+
         public HardklorDdaConverter GetHardklorConverter()
         {
             return new HardklorDdaConverter(ImportPeptideSearch);
         }
+
+        private void cbDiaUmpire_CheckedChanged(object sender, EventArgs e)
+        {
+            diaUmpireSettingsPanel.Enabled = cbDiaUmpire.Checked;
+        }
     }
 }

pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.ja.resx

@@ -196,7 +196,7 @@
     <value>17, 17</value>
   </metadata>
   <data name="cbEstimateBg.ToolTip" xml:space="preserve">
-    <value>推定バックグラウンド信号は、精度を多少犠牲にしてDIA-Umpireプロセスを大幅に高速にします。（EstimageBG）</value>
+	  <value>推定バックグラウンド信号は、精度を多少犠牲にしてDIA-Umpireプロセスを大幅に高速にします。（EstimateBG）</value>
   </data>
   <data name="&gt;&gt;cbEstimateBg.Name" xml:space="preserve">
     <value>cbEstimateBg</value>