edited FileNameToFilePath method in MSFraggerPsm to account for MSFra…

…gger file name additions and wrote tests

mzLib/FlashLFQ/ResultsReading/IdentificationAdapter.cs

@@ -28,6 +28,7 @@ public static List<Identification> MakeIdentifications(IQuantifiableResultFile q
                 SpectraFileInfo file = null;
                 if (allFiles.TryGetValue(record.FileName, out var fileInfo))
                 {
+                    // placeholder values for SpectraFileInfo that will be edited later
                     file = new SpectraFileInfo(record.FileName, "", 1, 1, 1);
                 }
                 else

mzLib/Readers/ExternalResults/IndividualResultRecords/MsFraggerPsm.cs

@@ -95,7 +95,17 @@ public class MsFraggerPsm : IQuantifiableRecord
         public double NextScore { get; set; }
 
         [Name("PeptideProphet Probability")]
-        public double PeptideProphetProbability { get; set; }
+        [CsvHelper.Configuration.Attributes.Optional]
+        private double? _peptideProphetProbability;
+
+        /// <summary>
+        /// New MsFragger output renames the header "PeptideProphet Probability" as just "Probability".
+        /// Headers are mutually exclusive, will not both occur in the same file. 
+        /// As such, both instances need to be accounted for seperately as optional fields. 
+        /// </summary>
+        [Name("Probability")]
+        [CsvHelper.Configuration.Attributes.Optional]
+        private double? _probability;
 
         [Name("Number of Enzymatic Termini")]
         public int NumberOfEnzymaticTermini { get; set; }
@@ -158,6 +168,11 @@ public class MsFraggerPsm : IQuantifiableRecord
         [Ignore]
         public int OneBasedScanNumber => _oneBasedScanNumber ??= int.Parse(Spectrum.Split('.')[1]);
 
+        /// <summary>
+        /// Ensures Probabilty is asscociated either the Probability or PeptideProphet Probability header or 0
+        /// </summary>
+        [Ignore] public double PeptideProphetProbability => _probability ?? _peptideProphetProbability ?? 0;
+
         #endregion
 
         #region IQuantifiableRecord Implementation

mzLib/Readers/ExternalResults/ResultFiles/MsFraggerPsmFile.cs

@@ -56,11 +56,10 @@ public Dictionary<string, string> FileNametoFilePath (List<string> fullFilePath)
 
             foreach(var fileName in rawFileNames)
             {
-                string shortFileName = Path.GetFileNameWithoutExtension(fileName);
-                if (shortFileName.Contains("."))
-                {
-                    shortFileName = Path.GetFileNameWithoutExtension(shortFileName);
-                }
+                string shortFileName = Path.GetFileName(fileName);
+                // MSFragger results append the raw file with "interact-" and replace .raw with .pep.xml
+                // In order to correctly match the file names, these changes must be removed
+                shortFileName = shortFileName.Replace("interact-", "").Replace(".pep.xml", "");
 
                 foreach(var file in fullFilePath)
                 {

mzLib/Test/FileReadingTests/ExternalFileTypes/SmallCalibratibleYeastFragger_psm.tsv

@@ -0,0 +1,6 @@
+Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins
+SmallCalibratibleYeast.00002.00002.2	E:\MadeleineH\YeastProteomeMSFragger\1\interact-SmallCalibratibleYeast.pep.xml	RGNVCGDAK	RGNVCGDAK	NVSVKEIR.RGNVCGDAK.NDPPKGCA	R	N	9	2	1443.6643	975.4455	975.4455	488.7300	488.7300	975.4556	488.7351	-0.0101	0.00047835460000	25.7810	11.6900	0.9997	2	1	320	328	1.81151584E8	5C(57.0215)		0.00	true	sp|P02994|EF1A_YEAST	P02994	EF1A_YEAST	TEF1	Elongation factor 1-alpha		
+SmallCalibratibleYeast.00004.00004.2	E:\MadeleineH\YeastProteomeMSFragger\1\interact-SmallCalibratibleYeast.pep.xml	EKAEAEAEK		GIREKRAR.EKAEAEAEK.KK	R	K	9	2	1444.1241	1003.4855	1003.4855	502.7500	502.7500	1003.4821	502.7483	0.0033	0.02974116000000	18.6380	12.6310	0.9269	2	1	189	197	3.6544424E7			0.00	false	sp|P40212|RL13B_YEAST	P40212	RL13B_YEAST	RPL13B	Large ribosomal subunit protein eL13B	RPL13A	sp|Q12690|RL13A_YEAST
+SmallCalibratibleYeast.00008.00008.2	E:\MadeleineH\YeastProteomeMSFragger\1\interact-SmallCalibratibleYeast.pep.xml	KITSNQR		FNVPIDGK.KITSNQR.IVAAIPTI	K	I	7	2	1446.0237	845.4655	845.4655	423.7400	423.7400	845.4719	423.7432	-0.0064	0.13056640000000	17.5940	12.5170	0.9646	2	1	33	39	2.5555878E7			0.00	true	sp|P00560|PGK_YEAST	P00560	PGK_YEAST	PGK1	Phosphoglycerate kinase		
+SmallCalibratibleYeast.00009.00009.2	E:\MadeleineH\YeastProteomeMSFragger\1\interact-SmallCalibratibleYeast.pep.xml	GIDHTSK		.GIDHTSK.QHKRSGHR	M	Q	7	2	1446.2545	756.3855	756.3855	379.2000	379.2000	756.3766	379.1956	0.0089	0.01669167000000	17.6100	9.8270	0.9965	2	0	2	8	6.739196E7			0.00	false	sp|P0CX49|RL18A_YEAST	P0CX49	RL18A_YEAST	RPL18A	Large ribosomal subunit protein eL18A	RPL18B	sp|P0CX50|RL18B_YEAST
+SmallCalibratibleYeast.00010.00010.2	E:\MadeleineH\YeastProteomeMSFragger\1\interact-SmallCalibratibleYeast.pep.xml	EKAEAEAEK		GIREKRAR.EKAEAEAEK.KK	R	K	9	2	1446.4789	1003.4855	1003.4855	502.7500	502.7500	1003.4821	502.7483	0.0033	0.02315876000000	18.5780	12.4510	0.9875	2	1	189	197	3.6544424E7			0.00	false	sp|P40212|RL13B_YEAST	P40212	RL13B_YEAST	RPL13B	Large ribosomal subunit protein eL13B	RPL13A	sp|Q12690|RL13A_YEAST

mzLib/Test/Test.csproj

@@ -318,6 +318,12 @@
     <None Update="FileReadingTests\ExternalFileTypes\MsPathFinderT_TargetResults_IcTarget.tsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="FileReadingTests\ExternalFileTypes\psm.tsv">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="FileReadingTests\ExternalFileTypes\SmallCalibratibleYeastFragger_psm.tsv">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="FileReadingTests\ExternalFileTypes\ToppicProteoformSingle_TopPICv1.5.3_proteoform_single.tsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>

mzLib/TestFlashLFQ/TestIdentificationAdapter.cs

@@ -84,5 +84,23 @@ public void TestFileNametoFilePath(string path)
             Assert.AreEqual(output, fullFilePath1);
             Assert.That(!allFiles.ContainsValue(fullFilePath2));
         }
+
+        [Test]
+        [TestCase(@"FileReadingTests\ExternalFileTypes\SmallCalibratibleYeastFragger_psm.tsv")]
+        public void TestFileNametoFilePathLocalPath(string path)
+        {
+            string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, path);
+            MsFraggerPsmFile file = new MsFraggerPsmFile(filePath);
+            string fileName = file.First().FileName;
+
+            List<string> fullFilePath = new List<string>();
+            string rawFilePath = @"DataFiles\SmallCalibratibleYeast.mzml";
+            fullFilePath.Add(rawFilePath);
+
+            Dictionary<string, string> allFiles = file.FileNametoFilePath(fullFilePath);
+
+            Assert.That(allFiles.TryGetValue(fileName, out var output));
+            Assert.AreEqual(output, rawFilePath);
+        }
     }
 }