From ce17fe1ffef6e6523f7c8484cafb48b13604d79e Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 29 Jul 2024 08:54:00 -0500 Subject: [PATCH 01/12] update csproj --- MetaMorpheus/CMD/CMD.csproj | 2 +- MetaMorpheus/EngineLayer/EngineLayer.csproj | 2 +- MetaMorpheus/GUI/GUI.csproj | 2 +- MetaMorpheus/GuiFunctions/GuiFunctions.csproj | 2 +- MetaMorpheus/TaskLayer/TaskLayer.csproj | 2 +- MetaMorpheus/Test/Test.csproj | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj index f55b7c59b..e06792f4b 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 diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj index 5b15cc792..a4ca65df3 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 diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj index 7586832bf..b45a807c7 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 diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj index 1297f153b..e6e60e11e 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 diff --git a/MetaMorpheus/TaskLayer/TaskLayer.csproj b/MetaMorpheus/TaskLayer/TaskLayer.csproj index f943a6605..e3f13f3f5 100644 --- a/MetaMorpheus/TaskLayer/TaskLayer.csproj +++ b/MetaMorpheus/TaskLayer/TaskLayer.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 Debug;Release full true diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj index c50be0e8b..6af6c596a 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 From 3ce6c53368cdfeba57defdc6b515fff72ee39783 Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 29 Jul 2024 09:22:25 -0500 Subject: [PATCH 02/12] nuget update --- .../Bootstrapper/Bootstrapper.wixproj | 4 +-- MetaMorpheus/CMD/CMD.csproj | 14 +++++++--- MetaMorpheus/EngineLayer/EngineLayer.csproj | 10 +++---- MetaMorpheus/GUI/GUI.csproj | 28 +++++++++---------- MetaMorpheus/GuiFunctions/GuiFunctions.csproj | 4 +-- .../MetaMorpheusSetup.wixproj | 4 +-- MetaMorpheus/TaskLayer/TaskLayer.csproj | 8 +++--- MetaMorpheus/Test/AddCompIonsTest.cs | 2 +- MetaMorpheus/Test/AmbiguityTest.cs | 2 +- MetaMorpheus/Test/AnalysisEngineTest.cs | 2 +- .../Test/AveragingGuiComponentsTest.cs | 2 +- MetaMorpheus/Test/AveragingTests.cs | 2 +- MetaMorpheus/Test/BinGenerationTest.cs | 2 +- MetaMorpheus/Test/CalibrationTests.cs | 2 +- MetaMorpheus/Test/CoIsolationTests.cs | 2 +- MetaMorpheus/Test/CustomAminoAcidsTest.cs | 2 +- MetaMorpheus/Test/CustomFragmentationTest.cs | 2 +- .../Test/DigestionModificationTests.cs | 2 +- MetaMorpheus/Test/EventArgsTest.cs | 2 +- MetaMorpheus/Test/FdrTest.cs | 2 +- MetaMorpheus/Test/GPTMDengineTest.cs | 2 +- MetaMorpheus/Test/GlobalVariablesTest.cs | 2 +- MetaMorpheus/Test/GuiFunctionsTest.cs | 2 +- MetaMorpheus/Test/IndexEngineTest.cs | 2 +- MetaMorpheus/Test/LocalizationTest.cs | 2 +- MetaMorpheus/Test/MatchIonsOfAllCharges.cs | 2 +- .../Test/MetaDraw/FragmentReanalysis.cs | 2 +- .../MetaDraw/MetaDrawSettingsAndViewsTest.cs | 2 +- MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs | 2 +- .../Test/MetaDraw/SpectrumMatchPlotTests.cs | 2 +- MetaMorpheus/Test/ModificationAnalysisTest.cs | 2 +- MetaMorpheus/Test/MsDataFileTest.cs | 2 +- .../Test/MultiProteaseParsimonyTest.cs | 2 +- .../Test/Multiplex_Labeling_TMT_iTRAQ.cs | 2 +- MetaMorpheus/Test/MyEngineTest.cs | 2 +- MetaMorpheus/Test/MyPeptideTest.cs | 2 +- MetaMorpheus/Test/MyTaskTest.cs | 2 +- MetaMorpheus/Test/OutputTest.cs | 2 +- MetaMorpheus/Test/ParameterTest.cs | 2 +- MetaMorpheus/Test/PeptideSpectralMatchTest.cs | 2 +- .../Test/PostSearchAnalysisTaskTests.cs | 2 +- MetaMorpheus/Test/ProteaseTests.cs | 2 +- MetaMorpheus/Test/ProteinGroupTest.cs | 2 +- MetaMorpheus/Test/ProteinLoaderTest.cs | 2 +- MetaMorpheus/Test/PsmTsvWriterTests.cs | 2 +- MetaMorpheus/Test/PsvTsvTest.cs | 2 +- MetaMorpheus/Test/QuantificationTest.cs | 2 +- MetaMorpheus/Test/RetentionTimeTest.cs | 2 +- MetaMorpheus/Test/RobTest.cs | 2 +- MetaMorpheus/Test/SearchEngineTests.cs | 2 +- MetaMorpheus/Test/SearchModesTest.cs | 2 +- MetaMorpheus/Test/SearchTaskTest.cs | 2 +- .../SearchWithPeptidesAddedInParsimony.cs | 2 +- MetaMorpheus/Test/SeqCoverageTest.cs | 2 +- MetaMorpheus/Test/SetUpTests.cs | 2 +- MetaMorpheus/Test/SilacTest.cs | 2 +- MetaMorpheus/Test/SlicedTest.cs | 2 +- .../Test/SpectralLibraryReaderTest.cs | 2 +- MetaMorpheus/Test/SpectralRecoveryTest.cs | 2 +- MetaMorpheus/Test/StefanParsimonyTest.cs | 2 +- MetaMorpheus/Test/Test.csproj | 14 +++++----- MetaMorpheus/Test/TestCmd.cs | 2 +- MetaMorpheus/Test/TestNGlyco.cs | 2 +- MetaMorpheus/Test/TestOGlyco.cs | 2 +- MetaMorpheus/Test/TestPsm.cs | 2 +- MetaMorpheus/Test/TestScanManagement.cs | 2 +- MetaMorpheus/Test/TestToml.cs | 2 +- MetaMorpheus/Test/TestTopDown.cs | 2 +- .../TestNegativeModeDeconvolution.cs | 2 +- MetaMorpheus/Test/VariantSearchTests.cs | 2 +- MetaMorpheus/Test/XLSearchOutputTest.cs | 2 +- MetaMorpheus/Test/XLTest.cs | 2 +- MetaMorpheus/Test/gptmdPrunedBdTests.cs | 2 +- global.json | 2 +- 74 files changed, 112 insertions(+), 106 deletions(-) diff --git a/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj b/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj index f50bbbf4a..044baa25c 100644 --- a/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj +++ b/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj @@ -5,8 +5,8 @@ x64;ARM64 - - + + diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj index e06792f4b..dafe33f0d 100644 --- a/MetaMorpheus/CMD/CMD.csproj +++ b/MetaMorpheus/CMD/CMD.csproj @@ -19,10 +19,16 @@ - - - - + + + all + runtime; build; native; contentfiles; analyzers; buildtransitive + + + + + + diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj index a4ca65df3..27f640c7d 100644 --- a/MetaMorpheus/EngineLayer/EngineLayer.csproj +++ b/MetaMorpheus/EngineLayer/EngineLayer.csproj @@ -17,15 +17,15 @@ - - - + + + - - + + diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj index b45a807c7..97837a870 100644 --- a/MetaMorpheus/GUI/GUI.csproj +++ b/MetaMorpheus/GUI/GUI.csproj @@ -50,28 +50,28 @@ - - - - + + + + - + - - - + + + - - - - + + + + - - + + diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj index e6e60e11e..c729c6b9c 100644 --- a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj +++ b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj @@ -13,10 +13,10 @@ - + - + diff --git a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj index f0c58edcb..303918c12 100644 --- a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj +++ b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj @@ -53,8 +53,8 @@ - - + + diff --git a/MetaMorpheus/TaskLayer/TaskLayer.csproj b/MetaMorpheus/TaskLayer/TaskLayer.csproj index e3f13f3f5..af43b31d2 100644 --- a/MetaMorpheus/TaskLayer/TaskLayer.csproj +++ b/MetaMorpheus/TaskLayer/TaskLayer.csproj @@ -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..7c1a37380 100644 --- a/MetaMorpheus/Test/CustomFragmentationTest.cs +++ b/MetaMorpheus/Test/CustomFragmentationTest.cs @@ -1,7 +1,7 @@ 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; 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 310b011cf..87b70ad30 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..ec39295c0 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; diff --git a/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs b/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs index d28828a8c..ac1cc86f9 100644 --- a/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs +++ b/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs @@ -10,7 +10,7 @@ using GuiFunctions; using MassSpectrometry; using Nett; -using NUnit.Framework; +using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Fragmentation; using Org.BouncyCastle.Bcpg; using pepXML.Generated; diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs index b4cdb076f..866a15ef2 100644 --- a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs +++ b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs @@ -7,7 +7,7 @@ using EngineLayer; using GuiFunctions; using GuiFunctions.ViewModels.Legends; -using NUnit.Framework; +using NUnit.Framework; 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 516b920d7..b83e48622 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 2cea5a6f0..bfe8e089b 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 be7cf4f8d..ea7ff056e 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..bfa926de2 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; diff --git a/MetaMorpheus/Test/ParameterTest.cs b/MetaMorpheus/Test/ParameterTest.cs index 567d7f1cb..beeeed66c 100644 --- a/MetaMorpheus/Test/ParameterTest.cs +++ b/MetaMorpheus/Test/ParameterTest.cs @@ -2,7 +2,7 @@ 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; diff --git a/MetaMorpheus/Test/PeptideSpectralMatchTest.cs b/MetaMorpheus/Test/PeptideSpectralMatchTest.cs index 6d3f3cd5e..48591ebc3 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; diff --git a/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs b/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs index d5ee76ea1..f005cceff 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..719c49a85 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; 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 3e439b4ec..3c58b7ce0 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 9a88b00a9..cddb2bb0b 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 e6b4c04ed..a94af6a18 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 987fb8fc5..bf6106a0e 100644 --- a/MetaMorpheus/Test/SpectralRecoveryTest.cs +++ b/MetaMorpheus/Test/SpectralRecoveryTest.cs @@ -1,7 +1,7 @@ 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; 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 6af6c596a..99b17dc7a 100644 --- a/MetaMorpheus/Test/Test.csproj +++ b/MetaMorpheus/Test/Test.csproj @@ -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 24e3c6612..82fdbd44a 100644 --- a/MetaMorpheus/Test/TestNGlyco.cs +++ b/MetaMorpheus/Test/TestNGlyco.cs @@ -4,7 +4,7 @@ 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; diff --git a/MetaMorpheus/Test/TestOGlyco.cs b/MetaMorpheus/Test/TestOGlyco.cs index fdfbb6f32..af8993ee6 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; diff --git a/MetaMorpheus/Test/TestPsm.cs b/MetaMorpheus/Test/TestPsm.cs index 7a0f63966..87ed8a351 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..34c3c0c90 100644 --- a/MetaMorpheus/Test/XLSearchOutputTest.cs +++ b/MetaMorpheus/Test/XLSearchOutputTest.cs @@ -1,4 +1,4 @@ -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/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" } } From 7964dc8af2862a06a92f206d362d65d682d4fdd9 Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 29 Jul 2024 10:45:47 -0500 Subject: [PATCH 03/12] lets start here --- MetaMorpheus/Bootstrapper/Bootstrapper.wixproj | 2 +- MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj b/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj index 044baa25c..38e08f961 100644 --- a/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj +++ b/MetaMorpheus/Bootstrapper/Bootstrapper.wixproj @@ -1,4 +1,4 @@ - + MetaMorpheusInstaller Bundle diff --git a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj index 303918c12..8285ad14f 100644 --- a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj +++ b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj @@ -1,5 +1,5 @@  - + x64 MetaMorpheusInstaller From 961164bbd0f5c51f3012a6dac2ad85b1c2977910 Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 29 Jul 2024 11:32:01 -0500 Subject: [PATCH 04/12] it ran bro --- MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs | 2 +- MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj | 4 ++-- MetaMorpheus/Test/CustomFragmentationTest.cs | 1 + MetaMorpheus/Test/MatchIonsOfAllCharges.cs | 1 + MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs | 6 ++++-- MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs | 4 +++- MetaMorpheus/Test/OutputTest.cs | 1 + MetaMorpheus/Test/ParameterTest.cs | 1 + MetaMorpheus/Test/PsvTsvTest.cs | 1 + MetaMorpheus/Test/TestNGlyco.cs | 1 + MetaMorpheus/Test/TestOGlyco.cs | 1 + MetaMorpheus/Test/XLSearchOutputTest.cs | 1 + 12 files changed, 18 insertions(+), 6 deletions(-) diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs index 32d02347a..fe92d5333 100644 --- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs +++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs @@ -21,7 +21,7 @@ using System.Windows.Shapes; using Easy.Common.Extensions; using EngineLayer.CrosslinkSearch; -using Org.BouncyCastle.Asn1.X509.Qualified; +//using Org.BouncyCastle.Asn1.X509.Qualified; using Readers; using System.Threading; using Omics.Fragmentation; diff --git a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj index 8285ad14f..25aef3f26 100644 --- a/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj +++ b/MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj @@ -1,5 +1,5 @@  - + x64 MetaMorpheusInstaller @@ -56,7 +56,7 @@ - + diff --git a/MetaMorpheus/Test/CustomFragmentationTest.cs b/MetaMorpheus/Test/CustomFragmentationTest.cs index 7c1a37380..4d4e60cf4 100644 --- a/MetaMorpheus/Test/CustomFragmentationTest.cs +++ b/MetaMorpheus/Test/CustomFragmentationTest.cs @@ -8,6 +8,7 @@ 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/MatchIonsOfAllCharges.cs b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs index ec39295c0..52ad3a44b 100644 --- a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs +++ b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs @@ -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 ac1cc86f9..be54be2d4 100644 --- a/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs +++ b/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs @@ -10,9 +10,11 @@ using GuiFunctions; using MassSpectrometry; using Nett; -using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; +using NUnit.Framework; +using NUnit.Framework.Legacy; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Fragmentation; -using Org.BouncyCastle.Bcpg; +//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 866a15ef2..db0f5d7f7 100644 --- a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs +++ b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs @@ -7,7 +7,9 @@ using EngineLayer; using GuiFunctions; using GuiFunctions.ViewModels.Legends; -using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; +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/OutputTest.cs b/MetaMorpheus/Test/OutputTest.cs index bfa926de2..73981bdd3 100644 --- a/MetaMorpheus/Test/OutputTest.cs +++ b/MetaMorpheus/Test/OutputTest.cs @@ -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 beeeed66c..20d477a94 100644 --- a/MetaMorpheus/Test/ParameterTest.cs +++ b/MetaMorpheus/Test/ParameterTest.cs @@ -8,6 +8,7 @@ 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/PsvTsvTest.cs b/MetaMorpheus/Test/PsvTsvTest.cs index 719c49a85..c4c17e0aa 100644 --- a/MetaMorpheus/Test/PsvTsvTest.cs +++ b/MetaMorpheus/Test/PsvTsvTest.cs @@ -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/TestNGlyco.cs b/MetaMorpheus/Test/TestNGlyco.cs index 82fdbd44a..685a60e93 100644 --- a/MetaMorpheus/Test/TestNGlyco.cs +++ b/MetaMorpheus/Test/TestNGlyco.cs @@ -16,6 +16,7 @@ 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 af8993ee6..ac86df2f7 100644 --- a/MetaMorpheus/Test/TestOGlyco.cs +++ b/MetaMorpheus/Test/TestOGlyco.cs @@ -19,6 +19,7 @@ using MzLibUtil; using Readers; using System.Text; +using NUnit.Framework.Legacy; using Omics.Modifications; namespace Test diff --git a/MetaMorpheus/Test/XLSearchOutputTest.cs b/MetaMorpheus/Test/XLSearchOutputTest.cs index 34c3c0c90..98a685013 100644 --- a/MetaMorpheus/Test/XLSearchOutputTest.cs +++ b/MetaMorpheus/Test/XLSearchOutputTest.cs @@ -4,6 +4,7 @@ using TaskLayer; using EngineLayer; using System.Linq; +using NUnit.Framework.Legacy; using Omics.Fragmentation; namespace Test From 38f67790433ce1d6b9040432fa05e07a488a0fb2 Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 29 Jul 2024 11:54:14 -0500 Subject: [PATCH 05/12] fsad --- MetaMorpheus/CMD/CMD.csproj | 6 ------ MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs | 5 ----- MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs | 1 - 3 files changed, 12 deletions(-) diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj index dafe33f0d..f5b93d6ee 100644 --- a/MetaMorpheus/CMD/CMD.csproj +++ b/MetaMorpheus/CMD/CMD.csproj @@ -20,12 +20,6 @@ - - all - runtime; build; native; contentfiles; analyzers; buildtransitive - - - diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs index fe92d5333..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/Test/MetaDraw/FragmentReanalysis.cs b/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs index be54be2d4..e91eeca48 100644 --- a/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs +++ b/MetaMorpheus/Test/MetaDraw/FragmentReanalysis.cs @@ -14,7 +14,6 @@ using NUnit.Framework.Legacy; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Omics.Fragmentation; -//using Org.BouncyCastle.Bcpg; using pepXML.Generated; using Readers; using TaskLayer; From b89012d5c2487b2f727d043c0f4ad8ec97a5a814 Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 29 Jul 2024 13:24:28 -0500 Subject: [PATCH 06/12] remove ostensibly unused dlls --- MetaMorpheus/GUI/GUI.csproj | 1 - MetaMorpheus/MetaMorpheusSetup/Product.wxs | 19 ------------------- 2 files changed, 20 deletions(-) diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj index 97837a870..847b8abad 100644 --- a/MetaMorpheus/GUI/GUI.csproj +++ b/MetaMorpheus/GUI/GUI.csproj @@ -50,7 +50,6 @@ - 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 @@ - - - - - - - - - From 82449d5d5ac857f1cbd0bb401438778afed64a8e Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 29 Jul 2024 13:47:15 -0500 Subject: [PATCH 07/12] bouncy castle linked to itext for writing pdf --- MetaMorpheus/GuiFunctions/GuiFunctions.csproj | 1 + .../MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs | 7 ------- 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj index c729c6b9c..5fdce1bcc 100644 --- a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj +++ b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj @@ -14,6 +14,7 @@ + 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; From be7295dfac91221533ed6dee64a9262e27d584c7 Mon Sep 17 00:00:00 2001 From: trishorts Date: Tue, 30 Jul 2024 11:32:37 -0500 Subject: [PATCH 08/12] unused using --- MetaMorpheus/Test/TestNGlyco.cs | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/MetaMorpheus/Test/TestNGlyco.cs b/MetaMorpheus/Test/TestNGlyco.cs index 685a60e93..22c93d57e 100644 --- a/MetaMorpheus/Test/TestNGlyco.cs +++ b/MetaMorpheus/Test/TestNGlyco.cs @@ -1,8 +1,5 @@ -using Chemistry; -using EngineLayer; -using EngineLayer.CrosslinkSearch; +using EngineLayer; using EngineLayer.GlycoSearch; -using EngineLayer.Indexing; using MassSpectrometry; using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; @@ -13,7 +10,6 @@ using System.IO; using System.Linq; using TaskLayer; -using UsefulProteomicsDatabases; using MzLibUtil; using Nett; using NUnit.Framework.Legacy; From e2bee662088975e661ee8f1ebede19977f1a07f6 Mon Sep 17 00:00:00 2001 From: trishorts Date: Tue, 30 Jul 2024 11:35:47 -0500 Subject: [PATCH 09/12] more unused usings --- MetaMorpheus/Test/TestOGlyco.cs | 5 ----- 1 file changed, 5 deletions(-) diff --git a/MetaMorpheus/Test/TestOGlyco.cs b/MetaMorpheus/Test/TestOGlyco.cs index ac86df2f7..39e014bce 100644 --- a/MetaMorpheus/Test/TestOGlyco.cs +++ b/MetaMorpheus/Test/TestOGlyco.cs @@ -13,12 +13,7 @@ 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; From 068d54143225e430088e9d56b4569d74ca9f1c0a Mon Sep 17 00:00:00 2001 From: trishorts Date: Tue, 30 Jul 2024 12:57:46 -0500 Subject: [PATCH 10/12] close spectrum library connection --- MetaMorpheus/Test/SpectralRecoveryTest.cs | 2 ++ 1 file changed, 2 insertions(+) diff --git a/MetaMorpheus/Test/SpectralRecoveryTest.cs b/MetaMorpheus/Test/SpectralRecoveryTest.cs index bf6106a0e..e863abe99 100644 --- a/MetaMorpheus/Test/SpectralRecoveryTest.cs +++ b/MetaMorpheus/Test/SpectralRecoveryTest.cs @@ -8,6 +8,7 @@ using System.Collections.Generic; using System.IO; using System.Linq; +using System.Security.Cryptography; using System.Text; using Omics.Modifications; using TaskLayer; @@ -267,6 +268,7 @@ 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(); } [Test] From 493f50bcf545a67e46bf972359aceb3acc22e262 Mon Sep 17 00:00:00 2001 From: Alex Date: Thu, 1 Aug 2024 23:17:38 -0500 Subject: [PATCH 11/12] added decoy sanitizing to MetaMorpheus task. Not sure why tests are breaking --- MetaMorpheus/CMD/CMD.csproj | 2 +- MetaMorpheus/EngineLayer/EngineLayer.csproj | 2 +- MetaMorpheus/GUI/GUI.csproj | 2 +- MetaMorpheus/GuiFunctions/GuiFunctions.csproj | 2 +- MetaMorpheus/TaskLayer/MetaMorpheusTask.cs | 35 +++++++++++++++++++ MetaMorpheus/TaskLayer/TaskLayer.csproj | 2 +- MetaMorpheus/Test/Test.csproj | 2 +- 7 files changed, 41 insertions(+), 6 deletions(-) diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj index f5b93d6ee..738168802 100644 --- a/MetaMorpheus/CMD/CMD.csproj +++ b/MetaMorpheus/CMD/CMD.csproj @@ -24,7 +24,7 @@ - + diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj index 27f640c7d..1092e029c 100644 --- a/MetaMorpheus/EngineLayer/EngineLayer.csproj +++ b/MetaMorpheus/EngineLayer/EngineLayer.csproj @@ -21,7 +21,7 @@ - + diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj index 847b8abad..0908127ff 100644 --- a/MetaMorpheus/GUI/GUI.csproj +++ b/MetaMorpheus/GUI/GUI.csproj @@ -54,7 +54,7 @@ - + diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj index 5fdce1bcc..80ad00e5a 100644 --- a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj +++ b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj @@ -15,7 +15,7 @@ - + diff --git a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs index cbc70c44b..fc7a30b09 100644 --- a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs +++ b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs @@ -620,6 +620,41 @@ 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 af43b31d2..6efa31fb1 100644 --- a/MetaMorpheus/TaskLayer/TaskLayer.csproj +++ b/MetaMorpheus/TaskLayer/TaskLayer.csproj @@ -21,7 +21,7 @@ - + diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj index 99b17dc7a..5b4cabb4b 100644 --- a/MetaMorpheus/Test/Test.csproj +++ b/MetaMorpheus/Test/Test.csproj @@ -23,7 +23,7 @@ - + From 8a4492ad2a0ce9a0c96674de2a99bb3c1637384c Mon Sep 17 00:00:00 2001 From: Alex Date: Thu, 1 Aug 2024 23:34:23 -0500 Subject: [PATCH 12/12] idk --- MetaMorpheus/TaskLayer/MetaMorpheusTask.cs | 1 + MetaMorpheus/Test/PeptideSpectralMatchTest.cs | 9 +++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs index fc7a30b09..7de92a6dc 100644 --- a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs +++ b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs @@ -629,6 +629,7 @@ protected List LoadProteins(string taskId, List dbFilenameLi } // Sanitize the decoys + HashSet targetPeptideSequences = new(); foreach(var protein in proteinList.Where(p => !p.IsDecoy)) { diff --git a/MetaMorpheus/Test/PeptideSpectralMatchTest.cs b/MetaMorpheus/Test/PeptideSpectralMatchTest.cs index 48591ebc3..a5f097ed5 100644 --- a/MetaMorpheus/Test/PeptideSpectralMatchTest.cs +++ b/MetaMorpheus/Test/PeptideSpectralMatchTest.cs @@ -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());