diff --git a/Assemblies/RawDataHandler-Vendor-UnSupported.1.0.8801.99.nupkg b/Assemblies/RawDataHandler-Vendor-UnSupported.1.0.8801.99.nupkg deleted file mode 100644 index 5c54e523f..000000000 Binary files a/Assemblies/RawDataHandler-Vendor-UnSupported.1.0.8801.99.nupkg and /dev/null differ diff --git a/Assemblies/RawDataHandler-Vendor-UnSupported.1.1.8929.142.nupkg b/Assemblies/RawDataHandler-Vendor-UnSupported.1.1.8929.142.nupkg new file mode 100644 index 000000000..ad10e9233 Binary files /dev/null and b/Assemblies/RawDataHandler-Vendor-UnSupported.1.1.8929.142.nupkg differ diff --git a/src/Common/CommonMVVM/Common/DisposableCollection.cs b/src/Common/CommonMVVM/Common/DisposableCollection.cs index c596fe13d..2ac116e62 100644 --- 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 index 430e128a9..525e1c7cc 100644 --- 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 index bec94028a..c1d59b2c0 100644 --- a/src/Common/CommonStandard/CommonStandard.csproj +++ b/src/Common/CommonStandard/CommonStandard.csproj @@ -1,7 +1,7 @@  - netstandard2.0;net472 + netstandard2.0;net48;net472;net6.0 Common CompMs.Common Debug;Release;Debug vendor unsupported;Release vendor unsupported diff --git a/src/Common/CommonStandard/Components/Chromatogram.cs b/src/Common/CommonStandard/Components/Chromatogram.cs index 01c452f54..dd54339cc 100644 --- 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 index e33704705..bc6d59e6c 100644 --- 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 index f832c34a0..e97837af0 100644 --- a/src/Common/CommonStandard/Proteomics/Function/PeptideCalc.cs +++ b/src/Common/CommonStandard/Proteomics/Function/PeptideCalc.cs @@ -188,7 +188,7 @@ public static List 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 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 index 74001fb80..941bded44 100644 --- a/src/Common/CommonStandard/Proteomics/Function/ProteinDigestion.cs +++ b/src/Common/CommonStandard/Proteomics/Function/ProteinDigestion.cs @@ -29,7 +29,7 @@ public static List GetDigestedPeptideSequences(List 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 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 index 2734bcd2f..436b8508e 100644 --- a/src/MSDIAL5/MsdialCore/MsdialCore.csproj +++ b/src/MSDIAL5/MsdialCore/MsdialCore.csproj @@ -1,7 +1,7 @@  - netstandard2.0;net48 + netstandard2.0;net48;net6.0 CompMs.MsdialCore Debug;Release;Debug vendor unsupported;Release vendor unsupported 12 @@ -12,10 +12,10 @@ - - - - + + + + diff --git a/src/MSDIAL5/MsdialGuiApp/MsdialGuiApp.csproj b/src/MSDIAL5/MsdialGuiApp/MsdialGuiApp.csproj index 4759e9ebd..2ad1f5e90 100644 --- a/src/MSDIAL5/MsdialGuiApp/MsdialGuiApp.csproj +++ b/src/MSDIAL5/MsdialGuiApp/MsdialGuiApp.csproj @@ -9,7 +9,7 @@ Resources\msdial_icon.ico AnyCPU Debug;Release;Debug vendor unsupported;Release vendor unsupported - http://prime.psc.riken.jp/compms/code/Msp20230908_conventional_converted_dev.lbm2 + https://zenodo.org/records/11399747/files/Msp20230427074147_conventional_converted_dev.lbm2 12 enable diff --git a/src/MSDIAL5/MsdialGuiApp/Properties/Resources.Designer.cs b/src/MSDIAL5/MsdialGuiApp/Properties/Resources.Designer.cs index c8e5189f9..0eacef6d1 100644 --- a/src/MSDIAL5/MsdialGuiApp/Properties/Resources.Designer.cs +++ b/src/MSDIAL5/MsdialGuiApp/Properties/Resources.Designer.cs @@ -88,7 +88,7 @@ public static string VDD_URI { } /// - /// Looks up a localized string similar to 5.3.240328-alpha.5. + /// Looks up a localized string similar to 5.3.240617. /// public static string VERSION { get { diff --git a/src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx b/src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx index 98b3f22f9..cfb57e6f7 100644 --- a/src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx +++ b/src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx @@ -127,6 +127,6 @@ https://api.github.com/repos/systemsomicslab/MsdialWorkbench/releases?per_page=100 - 5.3.240328-alpha.5 + 5.3.240617 \ No newline at end of file diff --git a/src/MSDIAL5/SpectrumViewer/SpectrumViewer.csproj b/src/MSDIAL5/SpectrumViewer/SpectrumViewer.csproj index fa78daba1..ca8603c2d 100644 --- a/src/MSDIAL5/SpectrumViewer/SpectrumViewer.csproj +++ b/src/MSDIAL5/SpectrumViewer/SpectrumViewer.csproj @@ -8,7 +8,7 @@ true CompMs.App.SpectrumViewer SpectrumViewer - net48 + net48;net481 512 {60dc8134-eba5-43b8-bcc9-bb4bc16c2548};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} 4 diff --git a/tests/Common/CommonStandardTests/Algorithm/ChromSmoothing/SmoothingTests.cs b/tests/Common/CommonStandardTests/Algorithm/ChromSmoothing/SmoothingTests.cs index 0d3165f14..6e5b853dc 100644 --- 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 index c9548c916..07f50f9e6 100644 --- a/tests/Common/CommonStandardTests/CommonStandardTests.csproj +++ b/tests/Common/CommonStandardTests/CommonStandardTests.csproj @@ -1,7 +1,7 @@  - net6.0 + net48 false diff --git a/tests/Common/CommonStandardTests/DataStructure/DirectionalLinkedGraphTests.cs b/tests/Common/CommonStandardTests/DataStructure/DirectionalLinkedGraphTests.cs index c8ca75a5d..3bbe79474 100644 --- a/tests/Common/CommonStandardTests/DataStructure/DirectionalLinkedGraphTests.cs +++ b/tests/Common/CommonStandardTests/DataStructure/DirectionalLinkedGraphTests.cs @@ -72,7 +72,7 @@ public void DirectionalLinkedTreeConstructorTest() { class LengthComparer : IEqualityComparer { -#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 index 2fe5003be..92453ddff 100644 --- 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 index 9f467ec17..cad1eb35f 100644 --- 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 index 19c194401..95d2df8b4 100644 --- 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 index 8352c66bd..e36b1ff56 100644 --- 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 index edaa7d01d..697661629 100644 --- 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 index ae130c19b..637574423 100644 --- 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 index 048ecc63e..1f40d4230 100644 --- 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 index 7d13f9348..d4e3fc664 100644 --- 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 index 1804d9e0e..8b02fa9df 100644 --- 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 index 7203d73ef..4797c5a92 100644 --- 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 index 621b2c46b..00f506ec7 100644 --- 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 index 9db6d3741..dead87197 100644 --- 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 index 1bffd4b1c..e078443ee 100644 --- 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;