Skip to content

Commit de98bc6

Browse files
Alexander-SolAlexander-Sol
committed
Update to most recent mzLib
1 parent 380428b commit de98bc6

File tree

8 files changed

+22
-13
lines changed

8 files changed

+22
-13
lines changed

‎CMD/CMD.csproj

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@
1515
<ItemGroup>
1616
<PackageReference Include="CommandLineParser" Version="2.7.82" />
1717
<PackageReference Include="MathNet.Numerics" Version="5.0.0" />
18-
<PackageReference Include="mzLib" Version="1.0.564" />
18+
<PackageReference Include="mzLib" Version="1.0.565" />
1919
<PackageReference Include="NetSerializer" Version="4.1.2" />
2020
<PackageReference Include="Nett" Version="0.15.0" />
2121
<PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />

‎GUI/GUI.csproj

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
1616
</PropertyGroup>
1717
<ItemGroup>
1818
<PackageReference Include="MathNet.Numerics" Version="5.0.0" />
19-
<PackageReference Include="mzLib" Version="1.0.564" />
19+
<PackageReference Include="mzLib" Version="1.0.565" />
2020
<PackageReference Include="NetSerializer" Version="4.1.2" />
2121
<PackageReference Include="Nett" Version="0.15.0" />
2222
<PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />

‎Test/SampleFiles/ExperimentalDesign.tsv

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
FileName Condition Biorep Fraction Techrep
2+
SmallCalibratible_Yeast Default 1 1 1

‎Test/SampleFiles/MetaMorpheus/ExperimentalDesign.tsv

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
FileName Condition Biorep Fraction Techrep
2+
SmallCalibratible_Yeast Default 1 1 1

‎Test/SampleFiles/percolatorMzml.mzML renamed to ‎Test/SampleFiles/Percolator/percolatorMzml.mzML

File renamed without changes.

‎Test/Test.cs

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -23,17 +23,19 @@ internal class Test
2323
[TestCase("Morpheus", "SmallCalibratible_Yeast.PSMs.tsv")]
2424
[TestCase("MaxQuant", "msms.txt")]
2525
[TestCase("PeptideShaker", "Default PSM Report.tabular")]
26-
[TestCase("Percolator", "percolatorTestData.txt", "percolatorMzml.mzML")]
26+
[TestCase("Percolator", "percolatorTestData.txt", "Percolator\\percolatorMzml.mzML")]
2727
[TestCase("Generic", "AllPSMs.tsv")]
2828
[TestCase("MsFragger", "Fragger_v4p3_psm.tsv")]
2929
public static void TestOutputs(string search, string psmFilename, string mzmlFileName = "SmallCalibratible_Yeast.mzML")
3030
{
31-
var myDirectory = Path.Combine(TestContext.CurrentContext.TestDirectory, "SampleFiles");
32-
var pathOfIdentificationFile = Path.Combine(myDirectory, search, psmFilename);
33-
var pathOfMzml = Path.Combine(myDirectory, mzmlFileName);
31+
var defaultDirectory = Path.Combine(TestContext.CurrentContext.TestDirectory, "SampleFiles");
32+
var pathOfIdentificationFile = Path.Combine(defaultDirectory, search, psmFilename);
33+
var pathOfMzml = Path.Combine(defaultDirectory, mzmlFileName);
3434
Assert.That(File.Exists(pathOfIdentificationFile));
3535
Assert.That(File.Exists(pathOfMzml));
3636

37+
var myDirectory = Path.GetDirectoryName(pathOfMzml);
38+
3739
string[] myargs = new string[]
3840
{
3941
"--rep",
@@ -46,15 +48,15 @@ public static void TestOutputs(string search, string psmFilename, string mzmlFil
4648

4749
CMD.FlashLfqExecutable.Main(myargs);
4850

49-
string peaksPath = Path.Combine(myDirectory, search, "QuantifiedPeaks.tsv");
51+
string peaksPath = Path.Combine(defaultDirectory, search, "QuantifiedPeaks.tsv");
5052
Assert.That(File.Exists(peaksPath));
5153
File.Delete(peaksPath);
5254

53-
string peptidesPath = Path.Combine(myDirectory, search, "QuantifiedPeptides.tsv");
55+
string peptidesPath = Path.Combine(defaultDirectory, search, "QuantifiedPeptides.tsv");
5456
Assert.That(File.Exists(peptidesPath));
5557
File.Delete(peptidesPath);
5658

57-
string proteinsPath = Path.Combine(myDirectory, search, "QuantifiedProteins.tsv");
59+
string proteinsPath = Path.Combine(defaultDirectory, search, "QuantifiedProteins.tsv");
5860
Assert.That(File.Exists(proteinsPath));
5961
File.Delete(proteinsPath);
6062
}

‎Test/Test.csproj

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@
2020
</ItemGroup>
2121
<ItemGroup>
2222
<PackageReference Include="MathNet.Numerics" Version="5.0.0" />
23-
<PackageReference Include="mzLib" Version="1.0.564" />
23+
<PackageReference Include="mzLib" Version="1.0.565" />
2424
<PackageReference Include="NetSerializer" Version="4.1.2" />
2525
<PackageReference Include="nunit" Version="4.2.2" />
2626
<PackageReference Include="NUnit3TestAdapter" Version="4.6.0" />
@@ -31,6 +31,9 @@
3131
<ProjectReference Include="..\Util\Util.csproj" />
3232
</ItemGroup>
3333
<ItemGroup>
34+
<None Update="SampleFiles\ExperimentalDesign.tsv">
35+
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
36+
</None>
3437
<None Update="SampleFiles\Generic\NewGenericInput.tsv">
3538
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
3639
</None>
@@ -46,8 +49,8 @@
4649
<None Update="SampleFiles\Parallel\20100614_Velos1_TaGe_SA_Jurkat_4.mzML">
4750
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
4851
</None>
49-
<None Update="SampleFiles\ExperimentalDesign.tsv">
50-
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
52+
<None Update="SampleFiles\MetaMorpheus\ExperimentalDesign.tsv">
53+
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
5154
</None>
5255
<None Update="SampleFiles\Generic\AllPSMs.tsv">
5356
<CopyToOutputDirectory>Always</CopyToOutputDirectory>

‎Util/Util.csproj

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
<ItemGroup>
1414
<PackageReference Include="CommandLineParser" Version="2.7.82" />
1515
<PackageReference Include="MathNet.Numerics" Version="5.0.0" />
16-
<PackageReference Include="mzLib" Version="1.0.564" />
16+
<PackageReference Include="mzLib" Version="1.0.565" />
1717
<PackageReference Include="NetSerializer" Version="4.1.2" />
1818
<PackageReference Include="Nett" Version="0.15.0" />
1919
</ItemGroup>

0 commit comments

Comments
 (0)