mzlib update to 504 which removes zero intensity peaks (#2102)

smith-chem-wisc · Nov 11, 2021 · 0a8df46 · 0a8df46
1 parent f7b7bde
commit 0a8df46
Show file tree

Hide file tree

Showing 9 changed files with 7 additions and 1,210 deletions.
diff --git a/CMD/CMD.csproj b/CMD/CMD.csproj
@@ -23,7 +23,7 @@
     <PackageReference Include="Microsoft.ML" Version="1.3.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="1.3.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.500" />
+    <PackageReference Include="mzLib" Version="1.0.504" />
     <PackageReference Include="Nett" Version="0.13.0" />
   </ItemGroup>
 

diff --git a/EngineLayer/EngineLayer.csproj b/EngineLayer/EngineLayer.csproj
@@ -20,7 +20,7 @@
     <PackageReference Include="Microsoft.ML" Version="1.3.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="1.3.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.500" />
+    <PackageReference Include="mzLib" Version="1.0.504" />
     <PackageReference Include="NETStandard.Library" Version="2.0.3" />
     <PackageReference Include="Nett" Version="0.13.0" />
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />

diff --git a/GUI/GUI.csproj b/GUI/GUI.csproj
@@ -55,7 +55,7 @@
     <PackageReference Include="Microsoft.ML.DataView" Version="1.3.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="1.3.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.500" />
+    <PackageReference Include="mzLib" Version="1.0.504" />
     <PackageReference Include="Nett" Version="0.13.0" />
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OxyPlot.Core" Version="2.0.0" />

diff --git a/GuiFunctions/GuiFunctions.csproj b/GuiFunctions/GuiFunctions.csproj
@@ -14,7 +14,7 @@
 
   <ItemGroup>
     <PackageReference Include="itext7" Version="7.1.13" />
-    <PackageReference Include="mzLib" Version="1.0.500" />
+    <PackageReference Include="mzLib" Version="1.0.504" />
     <PackageReference Include="OxyPlot.Wpf" Version="2.0.0" />
   </ItemGroup>
 

diff --git a/TaskLayer/TaskLayer.csproj b/TaskLayer/TaskLayer.csproj
@@ -20,7 +20,7 @@
     <PackageReference Include="Microsoft.ML" Version="1.3.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="1.3.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.500" />
+    <PackageReference Include="mzLib" Version="1.0.504" />
     <PackageReference Include="NetSerializer" Version="4.1.1" />
     <PackageReference Include="Nett" Version="0.13.0" />
   </ItemGroup>

diff --git a/Test/CalibrationTests.cs b/Test/CalibrationTests.cs
@@ -1,4 +1,5 @@
 using EngineLayer;
+using EngineLayer.Calibration;
 using FlashLFQ;
 using MassSpectrometry;
 using NUnit.Framework;
@@ -68,33 +69,6 @@ public static void ExperimentalDesignCalibrationTest(string nonCalibratedFile)
             Directory.Delete(unitTestFolder, true);
         }
 
-        [Test]
-        public static void CalibrationZeroIntensityTest()
-        {
-            //check that peaks with zero intensity don't crash the program
-
-            // set up directories
-            string unitTestFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"ExperimentalDesignCalibrationTest");
-            string outputFolder = Path.Combine(unitTestFolder, @"TaskOutput");
-            Directory.CreateDirectory(unitTestFolder);
-            Directory.CreateDirectory(outputFolder);
-
-            // set up original spectra file (input to calibration)
-            string nonCalibratedFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\withZeros.mzML");
-            MyFileManager myFileManager = new MyFileManager(false);
-
-            MsDataFile myMsDataFile = myFileManager.LoadFile(nonCalibratedFilePath,  new CommonParameters());
-            Assert.IsTrue(myMsDataFile.GetAllScansList().Any(x => x.MassSpectrum.YArray.Contains(0)));
-
-
-            // protein db
-            string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\zero.fasta.gz");
-
-            // run calibration
-            CalibrationTask calibrationTask = new CalibrationTask();
-            calibrationTask.RunTask(outputFolder, new List<DbForTask> { new DbForTask(myDatabase, false) }, new List<string> { nonCalibratedFilePath }, "test");
-        }
-
         [Test]
         public static void CalibrationTestLowRes()
         {

diff --git a/Test/Test.csproj b/Test/Test.csproj
@@ -18,7 +18,7 @@
   <ItemGroup>
     <PackageReference Include="Microsoft.ML" Version="1.3.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="1.3.1" />
-    <PackageReference Include="mzLib" Version="1.0.500" />
+    <PackageReference Include="mzLib" Version="1.0.504" />
     <PackageReference Include="NUnit" Version="3.12.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="3.16.1" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.5.0" />
@@ -235,18 +235,12 @@
     <None Update="TestData\VariantCrossTest.psmtsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
-    <None Update="TestData\withZeros.mzML">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
     <None Update="TestData\XCorrSearchTest_AllPSMs.psmtsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
     <None Update="TestData\XCorrUnitTest.tsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
-    <None Update="TestData\zero.fasta.gz">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
     <None Update="testFileParams.toml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>

diff --git a/Test/TestData/withZeros.mzML b/Test/TestData/withZeros.mzML
diff --git a/Test/TestData/zero.fasta.gz b/Test/TestData/zero.fasta.gz