diff --git a/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj b/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj index f50bbbf4a..38e08f961 100644 --- a/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj +++ b/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj @@ -1,12 +1,12 @@ - + MetaMorpheusInstaller Bundle x64;ARM64 - - + + diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj index f55b7c59b..738168802 100644 --- a/MetaMorpheus/CMD/CMD.csproj +++ b/MetaMorpheus/CMD/CMD.csproj @@ -2,7 +2,7 @@ Exe - net6.0 + net8.0 app1.manifest Debug;Release full @@ -19,12 +19,12 @@ - - - - + + + + - + diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj index d59bb2d6a..9ea085e53 100644 --- a/MetaMorpheus/EngineLayer/EngineLayer.csproj +++ b/MetaMorpheus/EngineLayer/EngineLayer.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 Debug;Release 1.0.0.0 full @@ -17,15 +17,15 @@ - - - + + + - + - - + + diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj index 7586832bf..0908127ff 100644 --- a/MetaMorpheus/GUI/GUI.csproj +++ b/MetaMorpheus/GUI/GUI.csproj @@ -2,7 +2,7 @@ WinExe - net6.0-windows + net8.0-windows true false false @@ -50,28 +50,27 @@ - - - - + + + - + - + - - - + + + - - - - + + + + - - + + diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj index 1297f153b..80ad00e5a 100644 --- a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj +++ b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj @@ -1,7 +1,7 @@  - net6.0-windows + net8.0-windows Debug;Release full true @@ -13,10 +13,11 @@ - - + + + - + diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs index 32d02347a..3f953d065 100644 --- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs +++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs @@ -1,7 +1,4 @@ using EngineLayer; -using IO.Mgf; -using IO.MzML; -using IO.ThermoRawFileReader; using iText.IO.Image; using iText.Kernel.Pdf; using MassSpectrometry; @@ -20,8 +17,6 @@ using System.Windows.Media.Imaging; using System.Windows.Shapes; using Easy.Common.Extensions; -using EngineLayer.CrosslinkSearch; -using Org.BouncyCastle.Asn1.X509.Qualified; using Readers; using System.Threading; using Omics.Fragmentation; diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs index 940bd1546..a6e068273 100644 --- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs +++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs @@ -4,19 +4,13 @@ using System.Globalization; using System.IO; using System.Linq; -using System.Reflection; using System.Text; -using System.Windows; -using System.Windows.Media; -using System.Windows.Media.Imaging; using Chemistry; -using Easy.Common.Extensions; using EngineLayer; using iText.IO.Image; using iText.Kernel.Pdf; using iText.Layout; using MassSpectrometry; -using MassSpectrometry.MzSpectra; using mzPlot; using Omics.Fragmentation; using Omics.SpectrumMatch; @@ -24,7 +18,6 @@ using OxyPlot.Annotations; using OxyPlot.Axes; using OxyPlot.Series; -using Canvas = System.Windows.Controls.Canvas; using FontWeights = OxyPlot.FontWeights; using HorizontalAlignment = OxyPlot.HorizontalAlignment; using VerticalAlignment = OxyPlot.VerticalAlignment; diff --git a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj index f0c58edcb..25aef3f26 100644 --- a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj +++ b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj @@ -1,5 +1,5 @@  - + x64 MetaMorpheusInstaller @@ -53,10 +53,10 @@ - - + + - + diff --git a/MetaMorpheus/MetaMorpheusSetup/Product.wxs b/MetaMorpheus/MetaMorpheusSetup/Product.wxs index 4bb106375..fc7b69b92 100644 --- a/MetaMorpheus/MetaMorpheusSetup/Product.wxs +++ b/MetaMorpheus/MetaMorpheusSetup/Product.wxs @@ -24,7 +24,6 @@ - @@ -331,15 +330,6 @@ - - - - - - - - - @@ -412,15 +402,6 @@ - - - - - - - - - diff --git a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs index cbc145fcf..e11ada6df 100644 --- a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs +++ b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs @@ -621,6 +621,42 @@ protected List LoadProteins(string taskId, List dbFilenameLi { Warn("Warning: " + emptyProteinEntries + " empty protein entries ignored"); } + + Status("Done loading proteins", new List { taskId }); + + if (!proteinList.Any(p => p.IsDecoy)) + { + return proteinList; + } + + // Sanitize the decoys + + HashSet targetPeptideSequences = new(); + foreach(var protein in proteinList.Where(p => !p.IsDecoy)) + { + // When thinking about decoy collisions, we can ignore modifications + foreach(var peptide in protein.Digest(commonParameters.DigestionParams, new List(), new List())) + { + targetPeptideSequences.Add(peptide.BaseSequence); + } + } + // Now, we iterate through the decoys and scramble the sequences that correspond to target peptides + for(int i = 0; i < proteinList.Count; i++) + { + if(proteinList[i].IsDecoy) + { + var peptidesToReplace = proteinList[i] + .Digest(commonParameters.DigestionParams, new List(), new List()) + .Select(p => p.BaseSequence) + .Where(targetPeptideSequences.Contains) + .ToList(); + if(peptidesToReplace.Any()) + { + proteinList[i] = Protein.ScrambleDecoyProteinSequence(proteinList[i], commonParameters.DigestionParams, forbiddenSequences: targetPeptideSequences, peptidesToReplace); + } + } + } + return proteinList; } diff --git a/MetaMorpheus/TaskLayer/TaskLayer.csproj b/MetaMorpheus/TaskLayer/TaskLayer.csproj index f943a6605..6efa31fb1 100644 --- a/MetaMorpheus/TaskLayer/TaskLayer.csproj +++ b/MetaMorpheus/TaskLayer/TaskLayer.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 Debug;Release full true @@ -17,12 +17,12 @@ - - - + + + - - + + diff --git a/MetaMorpheus/Test/AddCompIonsTest.cs b/MetaMorpheus/Test/AddCompIonsTest.cs index ab21114fd..8b75190bb 100644 --- a/MetaMorpheus/Test/AddCompIonsTest.cs +++ b/MetaMorpheus/Test/AddCompIonsTest.cs @@ -5,7 +5,7 @@ using EngineLayer.ModernSearch; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/AmbiguityTest.cs b/MetaMorpheus/Test/AmbiguityTest.cs index eb9be37fc..f483560ef 100644 --- a/MetaMorpheus/Test/AmbiguityTest.cs +++ b/MetaMorpheus/Test/AmbiguityTest.cs @@ -2,7 +2,7 @@ using EngineLayer; using EngineLayer.ClassicSearch; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/AnalysisEngineTest.cs b/MetaMorpheus/Test/AnalysisEngineTest.cs index 548cedb1e..29ee6db0a 100644 --- a/MetaMorpheus/Test/AnalysisEngineTest.cs +++ b/MetaMorpheus/Test/AnalysisEngineTest.cs @@ -3,7 +3,7 @@ using EngineLayer.HistogramAnalysis; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/AveragingGuiComponentsTest.cs b/MetaMorpheus/Test/AveragingGuiComponentsTest.cs index 9013d9c59..09e07e48d 100644 --- a/MetaMorpheus/Test/AveragingGuiComponentsTest.cs +++ b/MetaMorpheus/Test/AveragingGuiComponentsTest.cs @@ -5,7 +5,7 @@ using System.Text; using System.Threading.Tasks; using GuiFunctions; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using SpectralAveraging; namespace Test diff --git a/MetaMorpheus/Test/AveragingTests.cs b/MetaMorpheus/Test/AveragingTests.cs index a42558d08..8c416abde 100644 --- a/MetaMorpheus/Test/AveragingTests.cs +++ b/MetaMorpheus/Test/AveragingTests.cs @@ -7,7 +7,7 @@ using FlashLFQ; using GuiFunctions; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Readers; using SpectralAveraging; using TaskLayer; diff --git a/MetaMorpheus/Test/BinGenerationTest.cs b/MetaMorpheus/Test/BinGenerationTest.cs index 703f9c9a7..36cc3a0f8 100644 --- a/MetaMorpheus/Test/BinGenerationTest.cs +++ b/MetaMorpheus/Test/BinGenerationTest.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/MetaMorpheus/Test/CalibrationTests.cs b/MetaMorpheus/Test/CalibrationTests.cs index 76165bd78..a69900d1f 100644 --- a/MetaMorpheus/Test/CalibrationTests.cs +++ b/MetaMorpheus/Test/CalibrationTests.cs @@ -3,7 +3,7 @@ using EngineLayer.Calibration; using FlashLFQ; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Collections.Generic; using System.ComponentModel; diff --git a/MetaMorpheus/Test/CoIsolationTests.cs b/MetaMorpheus/Test/CoIsolationTests.cs index 0c4748ca9..972bbbf7d 100644 --- a/MetaMorpheus/Test/CoIsolationTests.cs +++ b/MetaMorpheus/Test/CoIsolationTests.cs @@ -3,7 +3,7 @@ using EngineLayer.ClassicSearch; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/CustomAminoAcidsTest.cs b/MetaMorpheus/Test/CustomAminoAcidsTest.cs index fe4e0b306..66b4d0add 100644 --- a/MetaMorpheus/Test/CustomAminoAcidsTest.cs +++ b/MetaMorpheus/Test/CustomAminoAcidsTest.cs @@ -1,7 +1,7 @@ using Chemistry; using Proteomics.AminoAcidPolymer; using System.IO; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using EngineLayer; using System.Collections.Generic; diff --git a/MetaMorpheus/Test/CustomFragmentationTest.cs b/MetaMorpheus/Test/CustomFragmentationTest.cs index aa08ee440..4d4e60cf4 100644 --- a/MetaMorpheus/Test/CustomFragmentationTest.cs +++ b/MetaMorpheus/Test/CustomFragmentationTest.cs @@ -1,13 +1,14 @@ using EngineLayer; using MzLibUtil; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Fragmentation; using System.Collections.Generic; using System.Diagnostics.CodeAnalysis; using System.IO; using System.Linq; using MassSpectrometry; +using NUnit.Framework.Legacy; using Omics.Fragmentation.Peptide; using TaskLayer; using UsefulProteomicsDatabases; diff --git a/MetaMorpheus/Test/DigestionModificationTests.cs b/MetaMorpheus/Test/DigestionModificationTests.cs index a3884b357..001d05d78 100644 --- a/MetaMorpheus/Test/DigestionModificationTests.cs +++ b/MetaMorpheus/Test/DigestionModificationTests.cs @@ -1,5 +1,5 @@ using EngineLayer; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/MetaMorpheus/Test/EventArgsTest.cs b/MetaMorpheus/Test/EventArgsTest.cs index 9a489d430..bd028252e 100644 --- a/MetaMorpheus/Test/EventArgsTest.cs +++ b/MetaMorpheus/Test/EventArgsTest.cs @@ -3,7 +3,7 @@ using EngineLayer.Localization; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/FdrTest.cs b/MetaMorpheus/Test/FdrTest.cs index 12643d0e8..645d7dd60 100644 --- a/MetaMorpheus/Test/FdrTest.cs +++ b/MetaMorpheus/Test/FdrTest.cs @@ -6,7 +6,7 @@ using EngineLayer.ModernSearch; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/GPTMDengineTest.cs b/MetaMorpheus/Test/GPTMDengineTest.cs index 622d1f25f..a06db8496 100644 --- a/MetaMorpheus/Test/GPTMDengineTest.cs +++ b/MetaMorpheus/Test/GPTMDengineTest.cs @@ -3,7 +3,7 @@ using EngineLayer.Gptmd; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/GlobalVariablesTest.cs b/MetaMorpheus/Test/GlobalVariablesTest.cs index 0865e6b79..749c0212e 100644 --- a/MetaMorpheus/Test/GlobalVariablesTest.cs +++ b/MetaMorpheus/Test/GlobalVariablesTest.cs @@ -1,5 +1,5 @@ using EngineLayer; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Collections.Generic; using System.IO; diff --git a/MetaMorpheus/Test/GuiFunctionsTest.cs b/MetaMorpheus/Test/GuiFunctionsTest.cs index b7bc613f5..139bd705a 100644 --- a/MetaMorpheus/Test/GuiFunctionsTest.cs +++ b/MetaMorpheus/Test/GuiFunctionsTest.cs @@ -1,5 +1,5 @@ using GuiFunctions.Databases; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using System; using System.Collections.Generic; diff --git a/MetaMorpheus/Test/IndexEngineTest.cs b/MetaMorpheus/Test/IndexEngineTest.cs index 1cdf6e962..c60fd14ba 100644 --- a/MetaMorpheus/Test/IndexEngineTest.cs +++ b/MetaMorpheus/Test/IndexEngineTest.cs @@ -1,7 +1,7 @@ using EngineLayer; using EngineLayer.Indexing; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/LocalizationTest.cs b/MetaMorpheus/Test/LocalizationTest.cs index 4df8a6c79..f2fb765ee 100644 --- a/MetaMorpheus/Test/LocalizationTest.cs +++ b/MetaMorpheus/Test/LocalizationTest.cs @@ -3,7 +3,7 @@ using EngineLayer.Localization; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs index 0ea6dcdc6..52ad3a44b 100644 --- a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs +++ b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs @@ -5,7 +5,7 @@ using EngineLayer.ClassicSearch; using IO.MzML; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; @@ -15,6 +15,7 @@ using MassSpectrometry; using Nett; using EngineLayer.Gptmd; +using NUnit.Framework.Legacy; using Omics.Digestion; using Omics.Modifications; using Omics.SpectrumMatch; diff --git a/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs b/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs index d28828a8c..e91eeca48 100644 --- a/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs +++ b/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs @@ -11,8 +11,9 @@ using MassSpectrometry; using Nett; using NUnit.Framework; +using NUnit.Framework.Legacy; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Fragmentation; -using Org.BouncyCastle.Bcpg; using pepXML.Generated; using Readers; using TaskLayer; diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs index 35bd816e8..c9ebd9b9e 100644 --- a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs +++ b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs @@ -8,6 +8,8 @@ using GuiFunctions; using GuiFunctions.ViewModels.Legends; using NUnit.Framework; +using NUnit.Framework.Legacy; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using OxyPlot; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs index 3c591066f..29c5b3686 100644 --- a/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs +++ b/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs @@ -14,7 +14,7 @@ using EngineLayer; using GuiFunctions; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using OxyPlot.Series; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs index f7f4e3232..2331545c0 100644 --- a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs +++ b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs @@ -8,7 +8,7 @@ using System.Windows.Controls; using EngineLayer; using GuiFunctions; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using OxyPlot; using OxyPlot.Annotations; using Omics.Fragmentation; diff --git a/MetaMorpheus/Test/ModificationAnalysisTest.cs b/MetaMorpheus/Test/ModificationAnalysisTest.cs index c184f94fe..a3d3d590c 100644 --- a/MetaMorpheus/Test/ModificationAnalysisTest.cs +++ b/MetaMorpheus/Test/ModificationAnalysisTest.cs @@ -2,7 +2,7 @@ using EngineLayer.FdrAnalysis; using EngineLayer.ModificationAnalysis; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/MsDataFileTest.cs b/MetaMorpheus/Test/MsDataFileTest.cs index af380cad1..48c72fb04 100644 --- a/MetaMorpheus/Test/MsDataFileTest.cs +++ b/MetaMorpheus/Test/MsDataFileTest.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Collections.Generic; using System.IO; diff --git a/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs b/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs index 10a95401d..d44d3226c 100644 --- a/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs +++ b/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs @@ -1,7 +1,7 @@ using EngineLayer; using EngineLayer.FdrAnalysis; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/Multiplex_Labeling_TMT_iTRAQ.cs b/MetaMorpheus/Test/Multiplex_Labeling_TMT_iTRAQ.cs index 20682d7b3..338c6b34e 100644 --- a/MetaMorpheus/Test/Multiplex_Labeling_TMT_iTRAQ.cs +++ b/MetaMorpheus/Test/Multiplex_Labeling_TMT_iTRAQ.cs @@ -2,7 +2,7 @@ using EngineLayer; using IO.MzML; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/MyEngineTest.cs b/MetaMorpheus/Test/MyEngineTest.cs index 3c2030942..b8c31d273 100644 --- a/MetaMorpheus/Test/MyEngineTest.cs +++ b/MetaMorpheus/Test/MyEngineTest.cs @@ -1,5 +1,5 @@ using EngineLayer; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.Collections.Generic; using System.Text; diff --git a/MetaMorpheus/Test/MyPeptideTest.cs b/MetaMorpheus/Test/MyPeptideTest.cs index 4d82c08a8..73250b0e3 100644 --- a/MetaMorpheus/Test/MyPeptideTest.cs +++ b/MetaMorpheus/Test/MyPeptideTest.cs @@ -5,7 +5,7 @@ using EngineLayer.ModernSearch; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/MyTaskTest.cs b/MetaMorpheus/Test/MyTaskTest.cs index c62e3c84b..981ebd34f 100644 --- a/MetaMorpheus/Test/MyTaskTest.cs +++ b/MetaMorpheus/Test/MyTaskTest.cs @@ -2,7 +2,7 @@ using MassSpectrometry; using MzLibUtil; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/MetaMorpheus/Test/OutputTest.cs b/MetaMorpheus/Test/OutputTest.cs index 0ab40e7ff..73981bdd3 100644 --- a/MetaMorpheus/Test/OutputTest.cs +++ b/MetaMorpheus/Test/OutputTest.cs @@ -3,7 +3,7 @@ using MassSpectrometry; using MzLibUtil; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; @@ -11,6 +11,7 @@ using System.IO; using System.IO.Compression; using System.Linq; +using NUnit.Framework.Legacy; using Readers; using TaskLayer; using UsefulProteomicsDatabases; diff --git a/MetaMorpheus/Test/ParameterTest.cs b/MetaMorpheus/Test/ParameterTest.cs index 567d7f1cb..20d477a94 100644 --- a/MetaMorpheus/Test/ParameterTest.cs +++ b/MetaMorpheus/Test/ParameterTest.cs @@ -2,12 +2,13 @@ using MassSpectrometry; using MzLibUtil; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; +using NUnit.Framework.Legacy; using Omics.Digestion; using Omics.Fragmentation.Peptide; using TaskLayer; diff --git a/MetaMorpheus/Test/PeptideSpectralMatchTest.cs b/MetaMorpheus/Test/PeptideSpectralMatchTest.cs index 6d3f3cd5e..a5f097ed5 100644 --- a/MetaMorpheus/Test/PeptideSpectralMatchTest.cs +++ b/MetaMorpheus/Test/PeptideSpectralMatchTest.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics.ProteolyticDigestion; using Proteomics; using System; @@ -33,11 +33,11 @@ public static void GetAminoAcidCoverageTest() int missedCleavages = 0; CleavageSpecificity cleavageSpecificity = CleavageSpecificity.Full; string peptideDescription = null; - int? pairedTargetDecoyHash = null; + string pairedTargetDecoySequence = null; PeptideWithSetModifications pwsmNoBaseSequence = new(sequence, allKnownMods, numFixedMods, digestionParams, myProtein, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, cleavageSpecificity, - peptideDescription, pairedTargetDecoyHash); + peptideDescription, pairedTargetDecoySequence); PeptideSpectralMatch psmNoBaseSequenceNoMFI = new(pwsmNoBaseSequence, 0, 10, 0, ms2ScanOneMzTen, commonParams, new List()); psmNoBaseSequenceNoMFI.ResolveAllAmbiguities(); @@ -52,9 +52,10 @@ public static void GetAminoAcidCoverageTest() sequence = "PEPTIDE"; oneBasedEndResidueInProtein = Math.Max(sequence.Length, 0); myProtein = new Protein(sequence, "ACCESSION"); - PeptideWithSetModifications pwsmBaseSequence = new(sequence, allKnownMods, numFixedMods, digestionParams, myProtein, + var test = new PeptideWithSetModifications(sequence, allKnownMods); + PeptideWithSetModifications pwsmBaseSequence = new PeptideWithSetModifications(sequence, allKnownMods, numFixedMods, digestionParams, myProtein, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, cleavageSpecificity, - peptideDescription, pairedTargetDecoyHash); + peptideDescription, pairedTargetDecoySequence); PeptideSpectralMatch psmBaseSequenceNoMFI = new(pwsmBaseSequence, 0, 10, 0, ms2ScanOneMzTen, commonParams, new List()); diff --git a/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs b/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs index fb6fec18c..ea33d0753 100644 --- a/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs +++ b/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs @@ -1,7 +1,7 @@ using System.Collections.Generic; using System.IO; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using TaskLayer; namespace Test diff --git a/MetaMorpheus/Test/ProteaseTests.cs b/MetaMorpheus/Test/ProteaseTests.cs index 682124464..e573e4a39 100644 --- a/MetaMorpheus/Test/ProteaseTests.cs +++ b/MetaMorpheus/Test/ProteaseTests.cs @@ -6,7 +6,7 @@ using System.Threading.Tasks; using EngineLayer; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using TaskLayer; diff --git a/MetaMorpheus/Test/ProteinGroupTest.cs b/MetaMorpheus/Test/ProteinGroupTest.cs index 8d92eb2b8..8df95e4e7 100644 --- a/MetaMorpheus/Test/ProteinGroupTest.cs +++ b/MetaMorpheus/Test/ProteinGroupTest.cs @@ -1,5 +1,5 @@ using EngineLayer; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using System.Collections.Generic; using System.Linq; diff --git a/MetaMorpheus/Test/ProteinLoaderTest.cs b/MetaMorpheus/Test/ProteinLoaderTest.cs index 3b5fe63fa..0b0fc0e2f 100644 --- a/MetaMorpheus/Test/ProteinLoaderTest.cs +++ b/MetaMorpheus/Test/ProteinLoaderTest.cs @@ -1,5 +1,5 @@ using EngineLayer; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.Collections.Generic; using System.IO; using TaskLayer; diff --git a/MetaMorpheus/Test/PsmTsvWriterTests.cs b/MetaMorpheus/Test/PsmTsvWriterTests.cs index 4b973ac5f..7ef38fea1 100644 --- a/MetaMorpheus/Test/PsmTsvWriterTests.cs +++ b/MetaMorpheus/Test/PsmTsvWriterTests.cs @@ -1,7 +1,7 @@ using Chemistry; using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/PsvTsvTest.cs b/MetaMorpheus/Test/PsvTsvTest.cs index 8e9daac6c..c4c17e0aa 100644 --- a/MetaMorpheus/Test/PsvTsvTest.cs +++ b/MetaMorpheus/Test/PsvTsvTest.cs @@ -1,7 +1,7 @@ using EngineLayer; using GuiFunctions; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Digestion; using Omics.Fragmentation; using Omics.Modifications; @@ -12,6 +12,7 @@ using System.IO; using System.Linq; using System.Text.RegularExpressions; +using NUnit.Framework.Legacy; namespace Test { diff --git a/MetaMorpheus/Test/QuantificationTest.cs b/MetaMorpheus/Test/QuantificationTest.cs index 4df793fd9..b004ec459 100644 --- a/MetaMorpheus/Test/QuantificationTest.cs +++ b/MetaMorpheus/Test/QuantificationTest.cs @@ -3,7 +3,7 @@ using FlashLFQ; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/RetentionTimeTest.cs b/MetaMorpheus/Test/RetentionTimeTest.cs index 72102952c..006f9a760 100644 --- a/MetaMorpheus/Test/RetentionTimeTest.cs +++ b/MetaMorpheus/Test/RetentionTimeTest.cs @@ -1,4 +1,4 @@ -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using Proteomics.RetentionTimePrediction; diff --git a/MetaMorpheus/Test/RobTest.cs b/MetaMorpheus/Test/RobTest.cs index 1b87dcd13..11f01df6a 100644 --- a/MetaMorpheus/Test/RobTest.cs +++ b/MetaMorpheus/Test/RobTest.cs @@ -2,7 +2,7 @@ using EngineLayer; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/SearchEngineTests.cs b/MetaMorpheus/Test/SearchEngineTests.cs index f0e444f8b..9053a1bb1 100644 --- a/MetaMorpheus/Test/SearchEngineTests.cs +++ b/MetaMorpheus/Test/SearchEngineTests.cs @@ -7,7 +7,7 @@ using MassSpectrometry; using MzLibUtil; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.AminoAcidPolymer; using Omics.Fragmentation; diff --git a/MetaMorpheus/Test/SearchModesTest.cs b/MetaMorpheus/Test/SearchModesTest.cs index 9abe07631..6e5e815f1 100644 --- a/MetaMorpheus/Test/SearchModesTest.cs +++ b/MetaMorpheus/Test/SearchModesTest.cs @@ -1,6 +1,6 @@ using EngineLayer; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Collections.Generic; using System.Linq; diff --git a/MetaMorpheus/Test/SearchTaskTest.cs b/MetaMorpheus/Test/SearchTaskTest.cs index 32e03d4e5..51943247c 100644 --- a/MetaMorpheus/Test/SearchTaskTest.cs +++ b/MetaMorpheus/Test/SearchTaskTest.cs @@ -1,7 +1,7 @@ using EngineLayer; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/SearchWithPeptidesAddedInParsimony.cs b/MetaMorpheus/Test/SearchWithPeptidesAddedInParsimony.cs index e7c44fe94..64fa0d220 100644 --- a/MetaMorpheus/Test/SearchWithPeptidesAddedInParsimony.cs +++ b/MetaMorpheus/Test/SearchWithPeptidesAddedInParsimony.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/MetaMorpheus/Test/SeqCoverageTest.cs b/MetaMorpheus/Test/SeqCoverageTest.cs index 81d7bda7c..6605f3d27 100644 --- a/MetaMorpheus/Test/SeqCoverageTest.cs +++ b/MetaMorpheus/Test/SeqCoverageTest.cs @@ -1,6 +1,6 @@ using System; using EngineLayer; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/SetUpTests.cs b/MetaMorpheus/Test/SetUpTests.cs index aa40c1f4d..3115c3dc7 100644 --- a/MetaMorpheus/Test/SetUpTests.cs +++ b/MetaMorpheus/Test/SetUpTests.cs @@ -1,6 +1,6 @@ // Copyright 2016 Stefan Solntsev using EngineLayer; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.IO; using TaskLayer; diff --git a/MetaMorpheus/Test/SilacTest.cs b/MetaMorpheus/Test/SilacTest.cs index a46cbf186..b4a315c77 100644 --- a/MetaMorpheus/Test/SilacTest.cs +++ b/MetaMorpheus/Test/SilacTest.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.AminoAcidPolymer; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/SlicedTest.cs b/MetaMorpheus/Test/SlicedTest.cs index b59c8392f..7a056f57e 100644 --- a/MetaMorpheus/Test/SlicedTest.cs +++ b/MetaMorpheus/Test/SlicedTest.cs @@ -1,5 +1,5 @@ using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Collections.Generic; using System.IO; diff --git a/MetaMorpheus/Test/SpectralLibraryReaderTest.cs b/MetaMorpheus/Test/SpectralLibraryReaderTest.cs index 25244e2c4..2fc4b87e3 100644 --- a/MetaMorpheus/Test/SpectralLibraryReaderTest.cs +++ b/MetaMorpheus/Test/SpectralLibraryReaderTest.cs @@ -1,4 +1,4 @@ -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.IO; using System; using System.Linq; diff --git a/MetaMorpheus/Test/SpectralRecoveryTest.cs b/MetaMorpheus/Test/SpectralRecoveryTest.cs index da8b65bb0..40c519ec4 100644 --- a/MetaMorpheus/Test/SpectralRecoveryTest.cs +++ b/MetaMorpheus/Test/SpectralRecoveryTest.cs @@ -1,13 +1,14 @@ using EngineLayer; using EngineLayer.ClassicSearch; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; using System.Linq; +using System.Security.Cryptography; using System.Text; using Omics.Modifications; using TaskLayer; @@ -276,6 +277,7 @@ public static void MiniClassicSearchEngineTest() Assert.AreEqual(allPsmsArray[5].BaseSequence, peptideSpectralMatches[0].BaseSequence); Assert.That(peptideSpectralMatches[0].SpectralAngle, Is.EqualTo(allPsmsArray[5].SpectralAngle).Within(0.01)); } + sl.CloseConnections(); } diff --git a/MetaMorpheus/Test/StefanParsimonyTest.cs b/MetaMorpheus/Test/StefanParsimonyTest.cs index 7fb4ea560..5de2ad29c 100644 --- a/MetaMorpheus/Test/StefanParsimonyTest.cs +++ b/MetaMorpheus/Test/StefanParsimonyTest.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj index 2725c3e1c..1282df5e9 100644 --- a/MetaMorpheus/Test/Test.csproj +++ b/MetaMorpheus/Test/Test.csproj @@ -1,7 +1,7 @@  - net6.0-windows + net8.0-windows false Debug;Release full @@ -16,17 +16,17 @@ - + runtime; build; native; contentfiles; analyzers; buildtransitive all - - - - - - - + + + + + + + diff --git a/MetaMorpheus/Test/TestCmd.cs b/MetaMorpheus/Test/TestCmd.cs index 6180ae6d1..5c86f99c4 100644 --- a/MetaMorpheus/Test/TestCmd.cs +++ b/MetaMorpheus/Test/TestCmd.cs @@ -1,4 +1,4 @@ -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Diagnostics; using System.IO; diff --git a/MetaMorpheus/Test/TestNGlyco.cs b/MetaMorpheus/Test/TestNGlyco.cs index 9bff1f531..67fe9158d 100644 --- a/MetaMorpheus/Test/TestNGlyco.cs +++ b/MetaMorpheus/Test/TestNGlyco.cs @@ -1,10 +1,7 @@ -using Chemistry; -using EngineLayer; -using EngineLayer.CrosslinkSearch; +using EngineLayer; using EngineLayer.GlycoSearch; -using EngineLayer.Indexing; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; @@ -13,9 +10,9 @@ using System.IO; using System.Linq; using TaskLayer; -using UsefulProteomicsDatabases; using MzLibUtil; using Nett; +using NUnit.Framework.Legacy; using Omics.Modifications; namespace Test diff --git a/MetaMorpheus/Test/TestOGlyco.cs b/MetaMorpheus/Test/TestOGlyco.cs index 7d8ded90a..37ccb8bca 100644 --- a/MetaMorpheus/Test/TestOGlyco.cs +++ b/MetaMorpheus/Test/TestOGlyco.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Omics.Fragmentation; using Proteomics.ProteolyticDigestion; @@ -13,12 +13,8 @@ using Nett; using EngineLayer.GlycoSearch; using FlashLFQ; -using NUnit.Framework.Internal; using SpectralAveraging; -using Chemistry; -using MzLibUtil; -using Readers; -using System.Text; +using NUnit.Framework.Legacy; using Omics.Modifications; using ThermoFisher.CommonCore.BackgroundSubtraction; using Easy.Common.Extensions; diff --git a/MetaMorpheus/Test/TestPsm.cs b/MetaMorpheus/Test/TestPsm.cs index 77b521eb5..5500fd414 100644 --- a/MetaMorpheus/Test/TestPsm.cs +++ b/MetaMorpheus/Test/TestPsm.cs @@ -4,7 +4,7 @@ using EngineLayer.Localization; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/MetaMorpheus/Test/TestScanManagement.cs b/MetaMorpheus/Test/TestScanManagement.cs index 537fc658c..18a60e1fa 100644 --- a/MetaMorpheus/Test/TestScanManagement.cs +++ b/MetaMorpheus/Test/TestScanManagement.cs @@ -1,7 +1,7 @@ using EngineLayer; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.Collections.Generic; using System.Linq; using TaskLayer; diff --git a/MetaMorpheus/Test/TestToml.cs b/MetaMorpheus/Test/TestToml.cs index f17690598..ed848c8d0 100644 --- a/MetaMorpheus/Test/TestToml.cs +++ b/MetaMorpheus/Test/TestToml.cs @@ -4,7 +4,7 @@ using MassSpectrometry; using MzLibUtil; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System.Collections.Generic; diff --git a/MetaMorpheus/Test/TestTopDown.cs b/MetaMorpheus/Test/TestTopDown.cs index c76f95057..8d83d978a 100644 --- a/MetaMorpheus/Test/TestTopDown.cs +++ b/MetaMorpheus/Test/TestTopDown.cs @@ -7,7 +7,7 @@ using EngineLayer.ModernSearch; using IO.MzML; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Modifications; using Proteomics; using Proteomics.ProteolyticDigestion; diff --git a/MetaMorpheus/Test/Transcriptomics/TestNegativeModeDeconvolution.cs b/MetaMorpheus/Test/Transcriptomics/TestNegativeModeDeconvolution.cs index f99d0c644..e91f0432e 100644 --- a/MetaMorpheus/Test/Transcriptomics/TestNegativeModeDeconvolution.cs +++ b/MetaMorpheus/Test/Transcriptomics/TestNegativeModeDeconvolution.cs @@ -1,7 +1,7 @@ using EngineLayer; using MassSpectrometry; using MzLibUtil; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Readers; using System; using System.Collections.Generic; diff --git a/MetaMorpheus/Test/VariantSearchTests.cs b/MetaMorpheus/Test/VariantSearchTests.cs index d13602de4..8cc06df6a 100644 --- a/MetaMorpheus/Test/VariantSearchTests.cs +++ b/MetaMorpheus/Test/VariantSearchTests.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/MetaMorpheus/Test/XLSearchOutputTest.cs b/MetaMorpheus/Test/XLSearchOutputTest.cs index 7a1406887..98a685013 100644 --- a/MetaMorpheus/Test/XLSearchOutputTest.cs +++ b/MetaMorpheus/Test/XLSearchOutputTest.cs @@ -1,9 +1,10 @@ -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.Collections.Generic; using System.IO; using TaskLayer; using EngineLayer; using System.Linq; +using NUnit.Framework.Legacy; using Omics.Fragmentation; namespace Test diff --git a/MetaMorpheus/Test/XLTest.cs b/MetaMorpheus/Test/XLTest.cs index b30e5f40e..229189c3b 100644 --- a/MetaMorpheus/Test/XLTest.cs +++ b/MetaMorpheus/Test/XLTest.cs @@ -6,7 +6,7 @@ using MassSpectrometry; using MzLibUtil; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.AminoAcidPolymer; using Omics.Fragmentation; diff --git a/MetaMorpheus/Test/gptmdPrunedBdTests.cs b/MetaMorpheus/Test/gptmdPrunedBdTests.cs index 1267d3909..e7c23ff38 100644 --- a/MetaMorpheus/Test/gptmdPrunedBdTests.cs +++ b/MetaMorpheus/Test/gptmdPrunedBdTests.cs @@ -1,6 +1,6 @@ using EngineLayer; using MassSpectrometry; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/global.json b/global.json index 989bcd0dd..0650fccd4 100644 --- a/global.json +++ b/global.json @@ -1,6 +1,6 @@ { "sdk": { - "version": "6.0.402", + "version": "8.0.204", "rollForward": "latestFeature" } }