From ba54e46f0b79cd3cf8a60ff42d3e70b63aa08f67 Mon Sep 17 00:00:00 2001 From: nbollis Date: Mon, 5 Aug 2024 18:29:06 -0500 Subject: [PATCH] changed around assembly references and added IsoDec to Deconvolution testing environment --- .../StandardDeconvolutionTest.cs | 185 +++++++++++------- .../SinglePeakDeconvolutionTestCase.cs | 0 .../TestCases/TestDevelopmentTestCases.cs | 0 .../WholeSpectrumDeconvolutionTestCase.cs | 0 .../TestData/Averaged_221110_CytoOnly.mzML | 0 .../TestData/Averaged_221110_HGHOnly.mzML | 0 .../TestData/Averaged_221110_UbiqOnly.mzML | 0 mzLib/Development/Development.csproj | 6 +- .../Algorithms/IsoDecAlgorithm.cs | 4 +- .../{ => IsoDecResources}/isodeclib.dll | Bin .../{ => IsoDecResources}/libmmd.dll | Bin .../{ => IsoDecResources}/phase_model.bin | Bin .../{ => IsoDecResources}/svml_dispmd.dll | Bin .../MassSpectrometry/MassSpectrometry.csproj | 42 ++-- 14 files changed, 135 insertions(+), 102 deletions(-) rename mzLib/Development/{Deconvolution => DeconvolutionDevelopment}/StandardDeconvolutionTest.cs (55%) rename mzLib/Development/{Deconvolution => DeconvolutionDevelopment}/TestCases/SinglePeakDeconvolutionTestCase.cs (100%) rename mzLib/Development/{Deconvolution => DeconvolutionDevelopment}/TestCases/TestDevelopmentTestCases.cs (100%) rename mzLib/Development/{Deconvolution => DeconvolutionDevelopment}/TestCases/WholeSpectrumDeconvolutionTestCase.cs (100%) rename mzLib/Development/{Deconvolution => DeconvolutionDevelopment}/TestData/Averaged_221110_CytoOnly.mzML (100%) rename mzLib/Development/{Deconvolution => DeconvolutionDevelopment}/TestData/Averaged_221110_HGHOnly.mzML (100%) rename mzLib/Development/{Deconvolution => DeconvolutionDevelopment}/TestData/Averaged_221110_UbiqOnly.mzML (100%) rename mzLib/MassSpectrometry/Deconvolution/Algorithms/{ => IsoDecResources}/isodeclib.dll (100%) rename mzLib/MassSpectrometry/Deconvolution/Algorithms/{ => IsoDecResources}/libmmd.dll (100%) rename mzLib/MassSpectrometry/Deconvolution/Algorithms/{ => IsoDecResources}/phase_model.bin (100%) rename mzLib/MassSpectrometry/Deconvolution/Algorithms/{ => IsoDecResources}/svml_dispmd.dll (100%) diff --git a/mzLib/Development/Deconvolution/StandardDeconvolutionTest.cs b/mzLib/Development/DeconvolutionDevelopment/StandardDeconvolutionTest.cs similarity index 55% rename from mzLib/Development/Deconvolution/StandardDeconvolutionTest.cs rename to mzLib/Development/DeconvolutionDevelopment/StandardDeconvolutionTest.cs index ea02b6dd4..2b73876e1 100644 --- a/mzLib/Development/Deconvolution/StandardDeconvolutionTest.cs +++ b/mzLib/Development/DeconvolutionDevelopment/StandardDeconvolutionTest.cs @@ -14,7 +14,7 @@ namespace Development.Deconvolution /// /// [TestFixture] - [Ignore("Only needed when developing deconvolution methods")] + //[Ignore("Only needed when developing deconvolution methods")] [ExcludeFromCodeCoverage] public class StandardDeconvolutionTest { @@ -38,117 +38,152 @@ static StandardDeconvolutionTest() Loaders.LoadElements(); // define paths to spectra - var ubiquitinPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Deconvolution", "TestData", + var ubiquitinPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DeconvolutionDevelopment", "TestData", "Averaged_221110_UbiqOnly.mzML"); - var hghPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Deconvolution", "TestData", + var hghPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DeconvolutionDevelopment", "TestData", "Averaged_221110_HGHOnly.mzML"); - var cytoPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Deconvolution", "TestData", + var cytoPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DeconvolutionDevelopment", "TestData", "Averaged_221110_CytoOnly.mzML"); // set up deconvoluters to be utilized by test cases - DeconvolutionParameters classicTopDownDeconvolutionParams = new ClassicDeconvolutionParameters(1, 60, 4, 3); - DeconvolutionParameters classicBottomUpDeconvolutionParams = new ClassicDeconvolutionParameters(1, 12, 4, 3); + List topDownDeconvolutionParametersToTest = + [ + new ClassicDeconvolutionParameters(1, 60, 4, 3), + new IsoDecDeconvolutionParameters() + ]; - // Add Individual peak test cases - List singlePeakDeconvolutionTestCases = new() + List bottomUpDeconvolutionParametersToTest = + [ + new ClassicDeconvolutionParameters(1, 12, 4, 3), + new IsoDecDeconvolutionParameters() + ]; + + + + // Add Individual peak test cases for top down + List singlePeakDeconvolutionTestCases = new(); + foreach (var deconParams in topDownDeconvolutionParametersToTest) { // uniquitin, direct injection - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10038.4, 8, 1254.8, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10039.41, 9, 1115.49, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10041.4, 10, 1004.14, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10041.46, 11, 912.86, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10043.4, 12, 836.95, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10043.41, 13, 772.57, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10044.44, 14, 717.46, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10045.5, 15, 669.70, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", - ubiquitinPath, 1, 10045.44, 16, 627.84, 20), + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10038.4, 8, 1254.8, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10039.41, 9, 1115.49, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10041.4, 10, 1004.14, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10041.46, 11, 912.86, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10043.4, 12, 836.95, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10043.41, 13, 772.57, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10044.44, 14, 717.46, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10045.5, 15, 669.70, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection PolyUbiquitin, Averaged", + ubiquitinPath, 1, 10045.44, 16, 627.84, 20)); // hgh, direct injection - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22139.41, 11, 2012.29, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22139.41, 11, 2012.29, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22136.28, 12, 1844.69, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22136.28, 12, 1844.69, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22137.31, 13, 1702.87, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22137.31, 13, 1702.87, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22139.32, 14, 1581.38, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22139.32, 14, 1581.38, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22139.25, 15, 1475.95, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22139.25, 15, 1475.95, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injectio Human Growth Hormone, Averaged", - hghPath, 1, 22140.32, 16, 1383.77, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22140.32, 16, 1383.77, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22141.31, 17, 1302.43, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22141.31, 17, 1302.43, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22142.34, 18, 1230.13, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, + hghPath, 1, 22142.34, 18, 1230.13, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", - hghPath, 1, 22143.36, 19, 1165.44, 20), + hghPath, 1, 22143.36, 19, 1165.44, 20)); // cytochrome c, direct injection - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12367.44, 9, 1374.16, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12367.4, 10, 1236.74, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12368.4, 11, 1124.40, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12370.44, 12, 1030.87, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12371.45, 13, 951.65, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12373.48, 14, 883.82, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12373.5, 15, 824.90, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12374.56, 16, 773.41, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12374.47, 17, 727.91, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12376.44, 18, 687.58, 20), - new SinglePeakDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", - cytoPath, 1, 12360.6, 20, 619.03, 20) - }; + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12367.44, 9, 1374.16, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12367.4, 10, 1236.74, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12368.4, 11, 1124.40, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12370.44, 12, 1030.87, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12371.45, 13, 951.65, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12373.48, 14, 883.82, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12373.5, 15, 824.90, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12374.56, 16, 773.41, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12374.47, 17, 727.91, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12376.44, 18, 687.58, 20)); + singlePeakDeconvolutionTestCases.Add(new SinglePeakDeconvolutionTestCase(deconParams, + "Direct Injection Cytochrome C, Averaged", + cytoPath, 1, 12360.6, 20, 619.03, 20)); + } _singlePeakTestCases = singlePeakDeconvolutionTestCases; - // Add whole spectrum test cases - List wholeSpectrumDeconvolutionTestCases = new() + // Add whole spectrum test cases for top down + List wholeSpectrumDeconvolutionTestCases = new(); + foreach (var deconParams in topDownDeconvolutionParametersToTest) { - new WholeSpectrumDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection PolyUbiquitin, Averaged", + wholeSpectrumDeconvolutionTestCases.Add(new WholeSpectrumDeconvolutionTestCase(deconParams, "Direct Injection PolyUbiquitin, Averaged", ubiquitinPath, 1, 20, new[] { 10038.4, 10039.41, 10041.4, 10041.46, 10043.4, 10043.41, 10044.44, 10045.5, 10045.44, }, new[] { 8, 9, 10, 11, 12, 13, 14, 15, 16 }, - new[] { 1254.8, 1115.49, 1004.14, 912.86, 836.95, 772.57, 717.46, 669.70, 627.84 }), + new[] { 1254.8, 1115.49, 1004.14, 912.86, 836.95, 772.57, 717.46, 669.70, 627.84 })); - new WholeSpectrumDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Human Growth Hormone, Averaged", + wholeSpectrumDeconvolutionTestCases.Add(new WholeSpectrumDeconvolutionTestCase(deconParams, "Direct Injection Human Growth Hormone, Averaged", hghPath, 1, 20, new []{22139.41, 22136.28, 22137.31, 22139.32, 22139.25, 22140.32, 22141.31, 22142.34, 22143.36}, new []{11, 12, 13, 14, 15, 16, 17, 18, 19}, - new []{2012.29, 1844.69, 1702.87, 1581.38, 1475.95, 1383.77, 1302.43, 1230.13, 1165.44}), + new []{2012.29, 1844.69, 1702.87, 1581.38, 1475.95, 1383.77, 1302.43, 1230.13, 1165.44})); - new WholeSpectrumDeconvolutionTestCase(classicTopDownDeconvolutionParams, "Direct Injection Cytochrome C, Averaged", + wholeSpectrumDeconvolutionTestCases.Add(new WholeSpectrumDeconvolutionTestCase(deconParams, "Direct Injection Cytochrome C, Averaged", cytoPath, 1, 20, new []{12367.44, 12367.4, 12368.4, 12370.44, 12371.45, 12373.48, 12373.5, 12374.56, 12374.47, 12376.44, 12360.6}, new []{9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20}, - new []{1374.16, 1236.74, 1124.40, 1030.87, 951.65, 883.82, 824.90, 773.41, 727.91, 687.58, 619.03}), + new []{1374.16, 1236.74, 1124.40, 1030.87, 951.65, 883.82, 824.90, 773.41, 727.91, 687.58, 619.03})); }; _wholeSpectrumDeconvolutionTestCases = wholeSpectrumDeconvolutionTestCases; + + // TODO: Add cases for bottom up deconvolution } #endregion diff --git a/mzLib/Development/Deconvolution/TestCases/SinglePeakDeconvolutionTestCase.cs b/mzLib/Development/DeconvolutionDevelopment/TestCases/SinglePeakDeconvolutionTestCase.cs similarity index 100% rename from mzLib/Development/Deconvolution/TestCases/SinglePeakDeconvolutionTestCase.cs rename to mzLib/Development/DeconvolutionDevelopment/TestCases/SinglePeakDeconvolutionTestCase.cs diff --git a/mzLib/Development/Deconvolution/TestCases/TestDevelopmentTestCases.cs b/mzLib/Development/DeconvolutionDevelopment/TestCases/TestDevelopmentTestCases.cs similarity index 100% rename from mzLib/Development/Deconvolution/TestCases/TestDevelopmentTestCases.cs rename to mzLib/Development/DeconvolutionDevelopment/TestCases/TestDevelopmentTestCases.cs diff --git a/mzLib/Development/Deconvolution/TestCases/WholeSpectrumDeconvolutionTestCase.cs b/mzLib/Development/DeconvolutionDevelopment/TestCases/WholeSpectrumDeconvolutionTestCase.cs similarity index 100% rename from mzLib/Development/Deconvolution/TestCases/WholeSpectrumDeconvolutionTestCase.cs rename to mzLib/Development/DeconvolutionDevelopment/TestCases/WholeSpectrumDeconvolutionTestCase.cs diff --git a/mzLib/Development/Deconvolution/TestData/Averaged_221110_CytoOnly.mzML b/mzLib/Development/DeconvolutionDevelopment/TestData/Averaged_221110_CytoOnly.mzML similarity index 100% rename from mzLib/Development/Deconvolution/TestData/Averaged_221110_CytoOnly.mzML rename to mzLib/Development/DeconvolutionDevelopment/TestData/Averaged_221110_CytoOnly.mzML diff --git a/mzLib/Development/Deconvolution/TestData/Averaged_221110_HGHOnly.mzML b/mzLib/Development/DeconvolutionDevelopment/TestData/Averaged_221110_HGHOnly.mzML similarity index 100% rename from mzLib/Development/Deconvolution/TestData/Averaged_221110_HGHOnly.mzML rename to mzLib/Development/DeconvolutionDevelopment/TestData/Averaged_221110_HGHOnly.mzML diff --git a/mzLib/Development/Deconvolution/TestData/Averaged_221110_UbiqOnly.mzML b/mzLib/Development/DeconvolutionDevelopment/TestData/Averaged_221110_UbiqOnly.mzML similarity index 100% rename from mzLib/Development/Deconvolution/TestData/Averaged_221110_UbiqOnly.mzML rename to mzLib/Development/DeconvolutionDevelopment/TestData/Averaged_221110_UbiqOnly.mzML diff --git a/mzLib/Development/Development.csproj b/mzLib/Development/Development.csproj index 0f0eaf199..cd65a3163 100644 --- a/mzLib/Development/Development.csproj +++ b/mzLib/Development/Development.csproj @@ -23,13 +23,13 @@ - + PreserveNewest - + PreserveNewest - + PreserveNewest diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs index 9b1ff3715..8cf6f5e4d 100644 --- 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 Deconvolute(MzSpectrum spectrum, MzRange range) diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/isodeclib.dll b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/isodeclib.dll similarity index 100% rename from mzLib/MassSpectrometry/Deconvolution/Algorithms/isodeclib.dll rename to mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/isodeclib.dll diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/libmmd.dll b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/libmmd.dll similarity index 100% rename from mzLib/MassSpectrometry/Deconvolution/Algorithms/libmmd.dll rename to mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/libmmd.dll diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/phase_model.bin b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/phase_model.bin similarity index 100% rename from mzLib/MassSpectrometry/Deconvolution/Algorithms/phase_model.bin rename to mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/phase_model.bin diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/svml_dispmd.dll b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/svml_dispmd.dll similarity index 100% rename from mzLib/MassSpectrometry/Deconvolution/Algorithms/svml_dispmd.dll rename to mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecResources/svml_dispmd.dll diff --git a/mzLib/MassSpectrometry/MassSpectrometry.csproj b/mzLib/MassSpectrometry/MassSpectrometry.csproj index f618774c1..01a16f805 100644 --- a/mzLib/MassSpectrometry/MassSpectrometry.csproj +++ b/mzLib/MassSpectrometry/MassSpectrometry.csproj @@ -10,15 +10,7 @@ true - - - - - - Always - - @@ -30,20 +22,26 @@ - - - Always - - - Always - - - Always - - + + + + + + - - - + + + Always + + + Always + + + Always + + + Always + +