changed around assembly references and added IsoDec to Deconvolution …

…testing environment
smith-chem-wisc · Aug 5, 2024 · ba54e46 · ba54e46
1 parent 097b4bd
commit ba54e46
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Showing 14 changed files with 135 additions and 102 deletions.
diff --git a/...econvolution/StandardDeconvolutionTest.cs → ...nDevelopment/StandardDeconvolutionTest.cs b/...econvolution/StandardDeconvolutionTest.cs → ...nDevelopment/StandardDeconvolutionTest.cs
diff --git a/...tCases/SinglePeakDeconvolutionTestCase.cs → ...tCases/SinglePeakDeconvolutionTestCase.cs b/...tCases/SinglePeakDeconvolutionTestCase.cs → ...tCases/SinglePeakDeconvolutionTestCase.cs
diff --git a/...ion/TestCases/TestDevelopmentTestCases.cs → ...ent/TestCases/TestDevelopmentTestCases.cs b/...ion/TestCases/TestDevelopmentTestCases.cs → ...ent/TestCases/TestDevelopmentTestCases.cs
diff --git a/...ses/WholeSpectrumDeconvolutionTestCase.cs → ...ses/WholeSpectrumDeconvolutionTestCase.cs b/...ses/WholeSpectrumDeconvolutionTestCase.cs → ...ses/WholeSpectrumDeconvolutionTestCase.cs
diff --git a/...on/TestData/Averaged_221110_CytoOnly.mzML → ...nt/TestData/Averaged_221110_CytoOnly.mzML b/...on/TestData/Averaged_221110_CytoOnly.mzML → ...nt/TestData/Averaged_221110_CytoOnly.mzML
diff --git a/...ion/TestData/Averaged_221110_HGHOnly.mzML → ...ent/TestData/Averaged_221110_HGHOnly.mzML b/...ion/TestData/Averaged_221110_HGHOnly.mzML → ...ent/TestData/Averaged_221110_HGHOnly.mzML
diff --git a/...on/TestData/Averaged_221110_UbiqOnly.mzML → ...nt/TestData/Averaged_221110_UbiqOnly.mzML b/...on/TestData/Averaged_221110_UbiqOnly.mzML → ...nt/TestData/Averaged_221110_UbiqOnly.mzML
diff --git a/mzLib/Development/Development.csproj b/mzLib/Development/Development.csproj
@@ -23,13 +23,13 @@
   </ItemGroup>
 
   <ItemGroup>
-    <None Update="Deconvolution\TestData\Averaged_221110_CytoOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_CytoOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
-    <None Update="Deconvolution\TestData\Averaged_221110_HGHOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_HGHOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
-    <None Update="Deconvolution\TestData\Averaged_221110_UbiqOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_UbiqOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
   </ItemGroup>

diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs
@@ -18,7 +18,7 @@ public class IsoDecAlgorithm(DeconvolutionParameters deconParameters)
         private static string _phaseModelPath;
         static IsoDecAlgorithm()
         {
-            _phaseModelPath = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "Deconvolution", "Algorithms", "phase_model.bin");
+            _phaseModelPath = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "Deconvolution", "Algorithms", "IsoDecResources",  "phase_model.bin");
         }
 
         [StructLayout(LayoutKind.Sequential, Pack =1)]
@@ -45,7 +45,7 @@ public struct MatchedPeak
             public int endindex;
         }
 
-        [DllImport("isodeclib.dll", CallingConvention = CallingConvention.Cdecl)]
+        [DllImport("Deconvolution/Algorithms/IsoDecResources/isodeclib.dll", CallingConvention = CallingConvention.Cdecl)]
         public static extern int process_spectrum(float[] mz, float[] intensity, int len, string modelpath, IntPtr matchedpeaks);
 
         public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range)

diff --git a/...ry/Deconvolution/Algorithms/isodeclib.dll → .../Algorithms/IsoDecResources/isodeclib.dll b/...ry/Deconvolution/Algorithms/isodeclib.dll → .../Algorithms/IsoDecResources/isodeclib.dll
diff --git a/...metry/Deconvolution/Algorithms/libmmd.dll → ...ion/Algorithms/IsoDecResources/libmmd.dll b/...metry/Deconvolution/Algorithms/libmmd.dll → ...ion/Algorithms/IsoDecResources/libmmd.dll
diff --git a/.../Deconvolution/Algorithms/phase_model.bin → ...lgorithms/IsoDecResources/phase_model.bin b/.../Deconvolution/Algorithms/phase_model.bin → ...lgorithms/IsoDecResources/phase_model.bin
diff --git a/.../Deconvolution/Algorithms/svml_dispmd.dll → ...lgorithms/IsoDecResources/svml_dispmd.dll b/.../Deconvolution/Algorithms/svml_dispmd.dll → ...lgorithms/IsoDecResources/svml_dispmd.dll
diff --git a/mzLib/MassSpectrometry/MassSpectrometry.csproj b/mzLib/MassSpectrometry/MassSpectrometry.csproj
@@ -10,15 +10,7 @@
     <DebugSymbols>true</DebugSymbols>
   </PropertyGroup>
 
-  <ItemGroup>
-    <None Remove="Deconvolution\Algorithms\phase_model.bin" />
-  </ItemGroup>
 
-  <ItemGroup>
-    <Resource Include="Deconvolution\Algorithms\phase_model.bin">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </Resource>
-  </ItemGroup>
 
   <ItemGroup>
     <PackageReference Include="CsvHelper" Version="32.0.3" />
@@ -30,20 +22,26 @@
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
   </ItemGroup>
 
-  <ItemGroup>
-    <None Update="Deconvolution\Algorithms\isodeclib.dll">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
-    <None Update="Deconvolution\Algorithms\libmmd.dll">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
-    <None Update="Deconvolution\Algorithms\svml_dispmd.dll">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
-  </ItemGroup>
+	<ItemGroup>
+		<None Remove="Deconvolution\Algorithms\isodeclib.dll" />
+		<None Remove="Deconvolution\Algorithms\libmmd.dll" />
+		<None Remove="Deconvolution\Algorithms\phase_model.bin" />
+		<None Remove="Deconvolution\Algorithms\svml_dispmd.dll" />
+	</ItemGroup>
 
-  <ItemGroup>
-    <Folder Include="Deconvolution\Algorithms\Resources\" />
-  </ItemGroup>
+	<ItemGroup>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\isodeclib.dll">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\libmmd.dll">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\phase_model.bin">
+			<CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\svml_dispmd.dll">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+	</ItemGroup>
 
 </Project>