Release msidal5.3 (#373)

* Update RawDataHandler version * Update Msdial version to 5.3-beta * Update Lbm url * Version up * Fix a bug of chromatogram class * Update target frameworks * Update DisposableCollection * Update version
systemsomicslab · Jun 17, 2024 · 5dac3e8 · 5dac3e8
1 parent 27b6cc5
commit 5dac3e8
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Showing 30 changed files with 38 additions and 36 deletions.
diff --git a/Assemblies/RawDataHandler-Vendor-UnSupported.1.0.8801.99.nupkg b/Assemblies/RawDataHandler-Vendor-UnSupported.1.0.8801.99.nupkg
diff --git a/Assemblies/RawDataHandler-Vendor-UnSupported.1.1.8929.142.nupkg b/Assemblies/RawDataHandler-Vendor-UnSupported.1.1.8929.142.nupkg
diff --git a/src/Common/CommonMVVM/Common/DisposableCollection.cs b/src/Common/CommonMVVM/Common/DisposableCollection.cs
@@ -33,12 +33,12 @@ protected virtual void Dispose(bool disposing) {
                         }
                     }
                     else {
-                        Application.Current.Dispatcher.Invoke(() =>
+                        Application.Current.Dispatcher.InvokeAsync(() =>
                         {
                             foreach (var disposable in this) {
                                 disposable?.Dispose();
                             }
-                        });
+                        }, System.Windows.Threading.DispatcherPriority.Background);
                     }
                 }
 

diff --git a/src/Common/CommonStandard/Algorithm/PeakPick/PeakPick.cs b/src/Common/CommonStandard/Algorithm/PeakPick/PeakPick.cs
@@ -1,6 +1,8 @@
 using CompMs.Common.Algorithm.ChromSmoothing;
 using CompMs.Common.Components;
+#if NETFRAMEWORK || NETSTANDARD
 using CompMs.Common.Extension;
+#endif
 using CompMs.Common.Mathematics.Basic;
 using System;
 using System.Collections.Generic;
@@ -432,7 +434,7 @@ private static ChromatogramGlobalProperty FindChromatogramGlobalProperties(
                 .Select(bin => bin.Max(peak => peak.Intensity) - bin.Min(peak => peak.Intensity))
                 .Where(diff => diff > 0)
                 .ToList();
-            if (amplitudeDiffs.Count >= minNoiseWindowSize) {
+            if (amplitudeDiffs.Count() >= minNoiseWindowSize) {
                 minNoiseLevel = BasicMathematics.Median(amplitudeDiffs);
             }
             var noise = minNoiseLevel * noiseFactor;

diff --git a/src/Common/CommonStandard/CommonStandard.csproj b/src/Common/CommonStandard/CommonStandard.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFrameworks>netstandard2.0;net472</TargetFrameworks>
+    <TargetFrameworks>netstandard2.0;net48;net472;net6.0</TargetFrameworks>
     <AssemblyName>Common</AssemblyName>
     <RootNamespace>CompMs.Common</RootNamespace>
     <Configurations>Debug;Release;Debug vendor unsupported;Release vendor unsupported</Configurations>

diff --git a/src/Common/CommonStandard/Components/Chromatogram.cs b/src/Common/CommonStandard/Components/Chromatogram.cs
@@ -302,7 +302,7 @@ private int SearchRightEdge(int top, int minPoints, double width, ChromXs right)
             int? minRightId = null;
             var minRightInt = _peaks[top].Intensity;
             double rightEdge = _peaks[top].Time + width;
-            for (int i = top + minPoints; i < _peaks.Length - 1; i++) {
+            for (int i = top + minPoints; i < _size - 1; i++) {
                 if (minRightInt < _peaks[i].Intensity || rightEdge < _peaks[i].Time) {
                     break;
                 }

diff --git a/src/Common/CommonStandard/Proteomics/DataObj/Peptide.cs b/src/Common/CommonStandard/Proteomics/DataObj/Peptide.cs
@@ -33,7 +33,7 @@ public string Sequence {
         [IgnoreMember]
         public string ModifiedSequence { get => SequenceObj.IsEmptyOrNull() ? string.Empty : String.Join("", SequenceObj.Select(n => n.Code())); }
         [Key(2)]
-        public Range Position { get; set; }
+        public CompMs.Common.DataObj.Range Position { get; set; }
         [Key(3)]
         public double ExactMass { get; set; }
         [IgnoreMember]

diff --git a/src/Common/CommonStandard/Proteomics/Function/PeptideCalc.cs b/src/Common/CommonStandard/Proteomics/Function/PeptideCalc.cs
@@ -188,7 +188,7 @@ public static List<Peptide> Sequence2PeptidesByVariableModifications(Peptide pep
             foreach (var result in results) {
                 var nPep = new Peptide() {
                     DatabaseOrigin = peptide.DatabaseOrigin, DatabaseOriginID = peptide.DatabaseOriginID, SequenceObj = result,
-                    Position = new Range(peptide.Position.Start, peptide.Position.End), IsProteinCterminal = peptide.IsProteinCterminal, IsProteinNterminal = peptide.IsProteinNterminal
+                    Position = new CompMs.Common.DataObj.Range(peptide.Position.Start, peptide.Position.End), IsProteinCterminal = peptide.IsProteinCterminal, IsProteinNterminal = peptide.IsProteinNterminal
                 };
                 //nPep.SequenceObj = result;
                 var formula = CalculatePeptideFormula(result);
@@ -273,7 +273,7 @@ public static List<Peptide> Sequence2FastPeptidesByVariableModifications(
                         DatabaseOrigin = peptide.DatabaseOrigin, 
                         DatabaseOriginID = peptide.DatabaseOriginID,
                         SequenceObj = result,
-                        Position = new Range(peptide.Position.Start, peptide.Position.End), 
+                        Position = new CompMs.Common.DataObj.Range(peptide.Position.Start, peptide.Position.End), 
                         IsProteinCterminal = peptide.IsProteinCterminal, 
                         IsProteinNterminal = peptide.IsProteinNterminal
                     };

diff --git a/src/Common/CommonStandard/Proteomics/Function/ProteinDigestion.cs b/src/Common/CommonStandard/Proteomics/Function/ProteinDigestion.cs
@@ -29,7 +29,7 @@ public static List<Peptide> GetDigestedPeptideSequences(List<AminoAcid> proteinS
 
                 if (cleavagesites.Contains(twoletterAAs)) {
                     end = i;
-                    var peptide = new Peptide() { DatabaseOrigin = database, DatabaseOriginID = databaseID, SequenceObj = proteinSeqObj.GetRange(start, end - start + 1), Position = new Range(start, end) };
+                    var peptide = new Peptide() { DatabaseOrigin = database, DatabaseOriginID = databaseID, SequenceObj = proteinSeqObj.GetRange(start, end - start + 1), Position = new CompMs.Common.DataObj.Range(start, end) };
                     peptide.IsProteinNterminal = start == 0 ? true : false;
                     peptide.IsProteinCterminal = end == proteinSeqObj.Count - 1 ? true : false;
                     peptides.Add(peptide);
@@ -57,7 +57,7 @@ public static List<Peptide> GetDigestedPeptideSequences(string proteinSequence,
                     start = peptides[j].Position.Start;
                     end = peptides[j + i].Position.End;
 
-                    var peptide = new Peptide() { DatabaseOrigin = database, DatabaseOriginID = databaseID, SequenceObj = proteinSeqObj.GetRange(start, end - start + 1), Position = new Range(start, end) };
+                    var peptide = new Peptide() { DatabaseOrigin = database, DatabaseOriginID = databaseID, SequenceObj = proteinSeqObj.GetRange(start, end - start + 1), Position = new CompMs.Common.DataObj.Range(start, end) };
                     peptide.IsProteinNterminal = start == 0 ? true : false;
                     peptide.IsProteinCterminal = end == proteinSequence.Length - 1 ? true : false;
                     peptide.MissedCleavages = i;

diff --git a/src/MSDIAL5/MsdialCore/MsdialCore.csproj b/src/MSDIAL5/MsdialCore/MsdialCore.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFrameworks>netstandard2.0;net48</TargetFrameworks>
+    <TargetFrameworks>netstandard2.0;net48;net6.0</TargetFrameworks>
     <RootNamespace>CompMs.MsdialCore</RootNamespace>
     <Configurations>Debug;Release;Debug vendor unsupported;Release vendor unsupported</Configurations>
     <LangVersion>12</LangVersion>
@@ -12,10 +12,10 @@
     <PackageReference Include="Accord" Version="3.8.0" />
     <PackageReference Include="Accord.Math" Version="3.8.0" />
     <PackageReference Include="Accord.Statistics" Version="3.8.0" />
-	  <PackageReference Include="RawDataHandler" Version="1.0.*" Condition="'$(Configuration)'=='Release'" />
-	  <PackageReference Include="RawDataHandler" Version="1.0.*-*" Condition="'$(Configuration)'=='Debug'" />
-	  <PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*-*" Condition="'$(Configuration)'=='Debug vendor unsupported'" />
-	  <PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*" Condition="'$(Configuration)'=='Release vendor unsupported'" />
+	  <PackageReference Include="RawDataHandler" Version="1.1.*" Condition="'$(Configuration)'=='Release'" />
+	  <PackageReference Include="RawDataHandler" Version="1.1.*-*" Condition="'$(Configuration)'=='Debug'" />
+	  <PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.1.*-*" Condition="'$(Configuration)'=='Debug vendor unsupported'" />
+	  <PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.1.*" Condition="'$(Configuration)'=='Release vendor unsupported'" />
 	  <PackageReference Include="System.Data.SQLite.Core" Version="1.0.112.2" />
     <PackageReference Include="System.IO.Compression" Version="4.3.0" />
   </ItemGroup>

diff --git a/src/MSDIAL5/MsdialGuiApp/MsdialGuiApp.csproj b/src/MSDIAL5/MsdialGuiApp/MsdialGuiApp.csproj
@@ -9,7 +9,7 @@
 		<ApplicationIcon>Resources\msdial_icon.ico</ApplicationIcon>
 		<PlatformTarget>AnyCPU</PlatformTarget>
 		<Configurations>Debug;Release;Debug vendor unsupported;Release vendor unsupported</Configurations>
-		<Lbm2Url>http://prime.psc.riken.jp/compms/code/Msp20230908_conventional_converted_dev.lbm2</Lbm2Url>
+		<Lbm2Url>https://zenodo.org/records/11399747/files/Msp20230427074147_conventional_converted_dev.lbm2</Lbm2Url>
     <LangVersion>12</LangVersion>
     <Nullable>enable</Nullable>
 	</PropertyGroup>

diff --git a/src/MSDIAL5/MsdialGuiApp/Properties/Resources.Designer.cs b/src/MSDIAL5/MsdialGuiApp/Properties/Resources.Designer.cs
diff --git a/src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx b/src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx
@@ -127,6 +127,6 @@
     <value>https://api.github.com/repos/systemsomicslab/MsdialWorkbench/releases?per_page=100</value>
   </data>
   <data name="VERSION" xml:space="preserve">
-    <value>5.3.240328-alpha.5</value>
+    <value>5.3.240617</value>
   </data>
 </root>
diff --git a/src/MSDIAL5/SpectrumViewer/SpectrumViewer.csproj b/src/MSDIAL5/SpectrumViewer/SpectrumViewer.csproj
@@ -8,7 +8,7 @@
     <UseWindowsForms>true</UseWindowsForms>
     <RootNamespace>CompMs.App.SpectrumViewer</RootNamespace>
     <AssemblyName>SpectrumViewer</AssemblyName>
-    <TargetFramework>net48</TargetFramework>
+    <TargetFrameworks>net48;net481</TargetFrameworks>
     <FileAlignment>512</FileAlignment>
     <ProjectTypeGuids>{60dc8134-eba5-43b8-bcc9-bb4bc16c2548};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}</ProjectTypeGuids>
     <WarningLevel>4</WarningLevel>

diff --git a/tests/Common/CommonStandardTests/Algorithm/ChromSmoothing/SmoothingTests.cs b/tests/Common/CommonStandardTests/Algorithm/ChromSmoothing/SmoothingTests.cs
@@ -1,5 +1,5 @@
 using CompMs.Common.Components;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using Microsoft.VisualStudio.TestTools.UnitTesting;

diff --git a/tests/Common/CommonStandardTests/CommonStandardTests.csproj b/tests/Common/CommonStandardTests/CommonStandardTests.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFrameworks>net48</TargetFrameworks>
 
     <IsPackable>false</IsPackable>
 

diff --git a/tests/Common/CommonStandardTests/DataStructure/DirectionalLinkedGraphTests.cs b/tests/Common/CommonStandardTests/DataStructure/DirectionalLinkedGraphTests.cs
@@ -72,7 +72,7 @@ public void DirectionalLinkedTreeConstructorTest() {
 
         class LengthComparer : IEqualityComparer<string>
         {
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
             public bool Equals(string x, string y) {
 #else
             public bool Equals([AllowNull] string x, [AllowNull] string y) {
@@ -82,7 +82,7 @@ public bool Equals([AllowNull] string x, [AllowNull] string y) {
                 return x.Length == y.Length;
             }
 
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
             public int GetHashCode(string obj) {
 #else
             public int GetHashCode([DisallowNull] string obj) {

diff --git a/tests/Common/CommonStandardTests/Lipidomics/CeramidesSpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/CeramidesSpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.Parser;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/EtherPCSpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/EtherPCSpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.FormulaGenerator.DataObj;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/EtherPESpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/EtherPESpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.Parser;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/HexCerSpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/HexCerSpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.Parser;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/LPXSpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/LPXSpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.Parser;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/OadSpectrumPeakGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/OadSpectrumPeakGeneratorTests.cs
@@ -1,7 +1,7 @@
 using CompMs.Common.Components;
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.Parser;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/Omega3nChainGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/Omega3nChainGeneratorTests.cs
@@ -1,4 +1,4 @@
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using Microsoft.VisualStudio.TestTools.UnitTesting;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/OtherLipidSpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/OtherLipidSpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.Parser;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/PCSpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/PCSpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.FormulaGenerator.DataObj;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/PXSpectrumGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/PXSpectrumGeneratorTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using CompMs.Common.Parser;

diff --git a/tests/Common/CommonStandardTests/Lipidomics/SpectrumPeakGeneratorTests.cs b/tests/Common/CommonStandardTests/Lipidomics/SpectrumPeakGeneratorTests.cs
@@ -1,7 +1,7 @@
 using CompMs.Common.Components;
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Enum;
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using Microsoft.VisualStudio.TestTools.UnitTesting;

diff --git a/tests/Common/CommonStandardTests/Parser/TextLibraryParserTests.cs b/tests/Common/CommonStandardTests/Parser/TextLibraryParserTests.cs
@@ -1,6 +1,6 @@
 using CompMs.Common.DataObj.Property;
 using CompMs.Common.Algorithm.IsotopeCalc;
-#if  NETSTANDARD
+#if  NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using Microsoft.VisualStudio.TestTools.UnitTesting;

diff --git a/tests/Common/CommonStandardTests/Utility/SearchCollectionTest.cs b/tests/Common/CommonStandardTests/Utility/SearchCollectionTest.cs
@@ -1,4 +1,4 @@
-#if NETSTANDARD
+#if NETSTANDARD || NETFRAMEWORK
 using CompMs.Common.Extension;
 #endif
 using Microsoft.VisualStudio.TestTools.UnitTesting;