Merge pull request #165 from Alexander-Sol/mzLib566

Alexander-Sol · web-flow · commit ee2a86dcb3ae · 2025-07-25T17:35:46.000-05:00
Update to mzLib 1.0.566, fixed issue when reading in .psmtsv files
diff --git a/CMD/CMD.csproj b/CMD/CMD.csproj
@@ -15,7 +15,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.565" />
+    <PackageReference Include="mzLib" Version="1.0.566" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />
diff --git a/GUI/GUI.csproj b/GUI/GUI.csproj
@@ -16,7 +16,7 @@
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.565" />
+    <PackageReference Include="mzLib" Version="1.0.566" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />
diff --git a/Test/Test.csproj b/Test/Test.csproj
@@ -20,7 +20,7 @@
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.565" />
+    <PackageReference Include="mzLib" Version="1.0.566" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="nunit" Version="4.2.2" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.6.0" />
diff --git a/Util/PsmReader.cs b/Util/PsmReader.cs
@@ -60,18 +60,12 @@ public PsmReader()
             { PsmFileType.PeptideShaker, new string[] { ", " } },
         };
 
-        // TODO: 
-        // try to cast filetype as IQuantifiableResultFile
-        // var readResult as IQuantifiableResultFile
-        // 1. use Parsefiletype extension  to get supported filetype enum
-        // 2. get ResultFile by passing in filePath and enum
-        // try cast resultFile to IQuantResultFile
-        private static List<Identification> TryReadQuantifiableResultFile(string filepath, bool silent, List<SpectraFileInfo> rawfiles)
+        private static List<Identification> TryReadQuantifiableResultFile(string filepath, bool silent, List<SpectraFileInfo> rawfiles, bool usePepQValue)
         {
             try
             {
                 IQuantifiableResultFile quantifiable = FileReader.ReadQuantifiableResultFile(filepath);
-                List<Identification> identifications = quantifiable.MakeIdentifications(rawfiles);
+                List<Identification> identifications = quantifiable.MakeIdentifications(rawfiles, usePepQValue);
                 if (!silent)
                 {
                     Console.WriteLine("Done reading PSMs; found " + identifications.Count);
@@ -89,10 +83,11 @@ private static List<Identification> TryReadQuantifiableResultFile(string filepat
         public List<Identification> ReadPsms(string filepath, bool silent, List<SpectraFileInfo> rawfiles, double qValueThreshold = 0.01, bool usePepQValue = false)
         {
             // check if file path can be read in using readers as QuantifiableResultFile
-            List<Identification> quantifiableIdentifications = TryReadQuantifiableResultFile(filepath, silent, rawfiles);
+            List<Identification> quantifiableIdentifications = TryReadQuantifiableResultFile(filepath, silent, rawfiles, usePepQValue);
             if (quantifiableIdentifications != null)
             {
-                return quantifiableIdentifications;
+                qValueThreshold = Math.Max(qValueThreshold, 0.01);
+                return quantifiableIdentifications.Where(id => id.QValue < qValueThreshold).ToList();
             }
 
             if (_modSequenceToMonoMass == null)
diff --git a/Util/Util.csproj b/Util/Util.csproj
@@ -13,7 +13,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.565" />
+    <PackageReference Include="mzLib" Version="1.0.566" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>

Original file line number	Diff line number	Diff line change
`@@ -60,18 +60,12 @@ public PsmReader()`
`60`	`60`	`{ PsmFileType.PeptideShaker, new string[] { ", " } },`
`61`	`61`	`};`
`62`	`62`
`63`		`- // TODO:`
`64`		`- // try to cast filetype as IQuantifiableResultFile`
`65`		`- // var readResult as IQuantifiableResultFile`
`66`		`- // 1. use Parsefiletype extension to get supported filetype enum`
`67`		`- // 2. get ResultFile by passing in filePath and enum`
`68`		`- // try cast resultFile to IQuantResultFile`
`69`		`- private static List<Identification> TryReadQuantifiableResultFile(string filepath, bool silent, List<SpectraFileInfo> rawfiles)`
	`63`	`+ private static List<Identification> TryReadQuantifiableResultFile(string filepath, bool silent, List<SpectraFileInfo> rawfiles, bool usePepQValue)`
`70`	`64`	`{`
`71`	`65`	`try`
`72`	`66`	`{`
`73`	`67`	`IQuantifiableResultFile quantifiable = FileReader.ReadQuantifiableResultFile(filepath);`
`74`		`- List<Identification> identifications = quantifiable.MakeIdentifications(rawfiles);`
	`68`	`+ List<Identification> identifications = quantifiable.MakeIdentifications(rawfiles, usePepQValue);`
`75`	`69`	`if (!silent)`
`76`	`70`	`{`
`77`	`71`	`Console.WriteLine("Done reading PSMs; found " + identifications.Count);`
`@@ -89,10 +83,11 @@ private static List<Identification> TryReadQuantifiableResultFile(string filepat`
`89`	`83`	`public List<Identification> ReadPsms(string filepath, bool silent, List<SpectraFileInfo> rawfiles, double qValueThreshold = 0.01, bool usePepQValue = false)`
`90`	`84`	`{`
`91`	`85`	`// check if file path can be read in using readers as QuantifiableResultFile`
`92`		`- List<Identification> quantifiableIdentifications = TryReadQuantifiableResultFile(filepath, silent, rawfiles);`
	`86`	`+ List<Identification> quantifiableIdentifications = TryReadQuantifiableResultFile(filepath, silent, rawfiles, usePepQValue);`
`93`	`87`	`if (quantifiableIdentifications != null)`
`94`	`88`	`{`
`95`		`- return quantifiableIdentifications;`
	`89`	`+ qValueThreshold = Math.Max(qValueThreshold, 0.01);`
	`90`	`+ return quantifiableIdentifications.Where(id => id.QValue < qValueThreshold).ToList();`
`96`	`91`	`}`
`97`	`92`
`98`	`93`	`if (_modSequenceToMonoMass == null)`