diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs index 8a45c88f6..07e5a3308 100644 --- a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs +++ b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs @@ -21,7 +21,6 @@ public class FdrAnalysisEngine : MetaMorpheusEngine /// public static bool QvalueThresholdOverride // property { - get { return qvalueThresholdOverride; } // get method set { qvalueThresholdOverride = value; } // set method } public FdrAnalysisEngine(List psms, int massDiffAcceptorNumNotches, CommonParameters commonParameters, @@ -209,6 +208,7 @@ public void CalculateQValue(List psms, bool peptideLevelCalculati } else { + //we don't want to apply the QValueThreshod if(psms.Count < PsmCountThresholdForInvertedQvalue) { diff --git a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs index 52ad3a44b..e0609e38a 100644 --- a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs +++ b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs @@ -20,6 +20,7 @@ using Omics.Modifications; using Omics.SpectrumMatch; using static System.Net.WebRequestMethods; +using EngineLayer.FdrAnalysis; namespace Test { @@ -425,7 +426,7 @@ public static void TestLibraryUpdate() string rawCopy = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\UpdateLibrary\rawCopy.mzML"); System.IO.File.Copy(raw1, rawCopy); - + FdrAnalysisEngine.QvalueThresholdOverride = true; EverythingRunnerEngine UpdateLibrary = new(new List<(string, MetaMorpheusTask)> { ("UpdateSpectraFileOutput", task) }, new List { raw1, raw2 }, new List { new DbForTask(lib, false), new DbForTask( db1,false), new DbForTask(db2, false) }, thisTaskOutputFolder); UpdateLibrary.Run(); @@ -452,6 +453,7 @@ public static void TestLibraryUpdate() updatedLib.CloseConnections(); Directory.Delete(thisTaskOutputFolder, true); + FdrAnalysisEngine.QvalueThresholdOverride = false; } [Test] diff --git a/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs b/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs index 11f99296b..913f16411 100644 --- a/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs +++ b/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs @@ -71,6 +71,7 @@ public static void AllResultsAndResultsTxtContainsCorrectValues_QValue_BottomUp( Assert.AreEqual("All target PSMs with q-value <= 0.01: " + TaGe_SA_A549_3_snip_2ExpectedPsms, singleFileResults[5]); Assert.AreEqual("All target peptides with q-value <= 0.01: " + TaGe_SA_A549_3_snip_2ExpectedPeptides, singleFileResults[6]); Assert.AreEqual("All target protein groups with q-value <= 0.01 (1% FDR): 166", singleFileResults[7]); + FdrAnalysisEngine.QvalueThresholdOverride = false; } [Test] @@ -103,6 +104,7 @@ public static void AllResultsAndResultsTxtContainsCorrectValues_PepQValue_Bottom Assert.AreEqual("TaGe_SA_A549_3_snip_2 - Target PSMs with pep q-value <= 0.01: 192", results[13]); Assert.AreEqual("TaGe_SA_A549_3_snip_2 - Target peptides with pep q-value <= 0.01: 155", results[14]); Assert.AreEqual("TaGe_SA_A549_3_snip_2 - Target protein groups within 1 % FDR: 141", results[15]); + FdrAnalysisEngine.QvalueThresholdOverride = false; } /// @@ -112,7 +114,6 @@ public static void AllResultsAndResultsTxtContainsCorrectValues_PepQValue_Bottom [TestCaseSource(nameof(GetTestCases))] public static void AllResultTxtContainsCorrectNumberOfResultLines(EverythingRunnerEngineTestCases testCaseIdentifier) { - FdrAnalysisEngine.QvalueThresholdOverride = true; var testCase = EverythingRunnerEngineTestCase.GetTestCase(testCaseIdentifier); int expectedIndividualFileLines = testCase.DataFileList.Count == 1 || !testCase.WriteIndividualResults @@ -158,7 +159,6 @@ public static void AllResultTxtContainsCorrectNumberOfResultLines(EverythingRunn [TestCaseSource(nameof(GetTestCases))] public static void CorrectFilesAreWrittenWithCorrectName(EverythingRunnerEngineTestCases testCaseIdentifier) { - FdrAnalysisEngine.QvalueThresholdOverride = true; var testCase = EverythingRunnerEngineTestCase.GetTestCase(testCaseIdentifier); var psmFiles = Directory.GetFiles(testCase.OutputDirectory, "*PSMs.psmtsv", SearchOption.AllDirectories); var pepXmlFiles = Directory.GetFiles(testCase.OutputDirectory, "*.pep.xml", SearchOption.AllDirectories); diff --git a/MetaMorpheus/Test/ProteinGroupTest.cs b/MetaMorpheus/Test/ProteinGroupTest.cs index 8df95e4e7..71fb93b8b 100644 --- a/MetaMorpheus/Test/ProteinGroupTest.cs +++ b/MetaMorpheus/Test/ProteinGroupTest.cs @@ -14,6 +14,7 @@ using Omics.Digestion; using Omics.Modifications; using UsefulProteomicsDatabases; +using EngineLayer.FdrAnalysis; namespace Test { @@ -206,6 +207,8 @@ public static void TestModificationInfoListInProteinGroupsOutput() string mzmlName = @"TestData\PrunedDbSpectra.mzml"; string fastaName = @"TestData\DbForPrunedDb.fasta"; string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPrunedGeneration"); + + FdrAnalysisEngine.QvalueThresholdOverride = false; var engine = new EverythingRunnerEngine(taskList, new List { mzmlName }, new List { new DbForTask(fastaName, false) }, outputFolder); engine.Run(); string final = Path.Combine(MySetUpClass.outputFolder, "task2", "DbForPrunedDbGPTMDproteinPruned.xml"); diff --git a/MetaMorpheus/Test/QuantificationTest.cs b/MetaMorpheus/Test/QuantificationTest.cs index b004ec459..c99fb0677 100644 --- a/MetaMorpheus/Test/QuantificationTest.cs +++ b/MetaMorpheus/Test/QuantificationTest.cs @@ -15,6 +15,7 @@ using System.Text; using Omics.Modifications; using TaskLayer; +using EngineLayer.FdrAnalysis; namespace Test { @@ -224,6 +225,7 @@ public static void TestProteinQuantFileHeaders(bool hasDefinedExperimentalDesign } // run the search/quantification + FdrAnalysisEngine.QvalueThresholdOverride = false; SearchTask task = new SearchTask(); task.RunTask(unitTestFolder, new List { new DbForTask(dbName, false) }, fileInfos.Select(p => p.FullFilePathWithExtension).ToList(), ""); diff --git a/MetaMorpheus/Test/SearchEngineTests.cs b/MetaMorpheus/Test/SearchEngineTests.cs index fd21766af..5e1a5590d 100644 --- a/MetaMorpheus/Test/SearchEngineTests.cs +++ b/MetaMorpheus/Test/SearchEngineTests.cs @@ -111,8 +111,8 @@ public static void TestSearchEngineResultsPsmFromTsv() Assert.AreEqual("K", psm.PreviousAminoAcid); Assert.AreEqual("P46013", psm.ProteinAccession); Assert.AreEqual("Proliferation marker protein Ki-67", psm.ProteinName); - Assert.That(0.0, Is.EqualTo(psm.QValue).Within(1E-04)); - Assert.That(0.0, Is.EqualTo(psm.QValueNotch).Within(1E-04)); + Assert.That(0, Is.EqualTo(psm.QValue).Within(1E-04)); + Assert.That(0, Is.EqualTo(psm.QValueNotch).Within(1E-04)); Assert.AreEqual(45.59512, psm.RetentionTime); Assert.AreEqual(662.486, psm.Score); Assert.AreEqual("[2742 to 2761]", psm.StartAndEndResiduesInProtein); diff --git a/MetaMorpheus/Test/TestToml.cs b/MetaMorpheus/Test/TestToml.cs index 2f375d329..b7ba84996 100644 --- a/MetaMorpheus/Test/TestToml.cs +++ b/MetaMorpheus/Test/TestToml.cs @@ -1,11 +1,8 @@ -using Chemistry; -using EngineLayer; -using EngineLayer.ClassicSearch; +using EngineLayer; using MassSpectrometry; using MzLibUtil; using Nett; using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert; -using Proteomics; using Proteomics.ProteolyticDigestion; using System.Collections.Generic; using System.IO; @@ -14,7 +11,6 @@ using Omics.Fragmentation; using SpectralAveraging; using TaskLayer; -using UsefulProteomicsDatabases; using EngineLayer.FdrAnalysis; namespace Test