Merge remote-tracking branch 'upstream/master'

mzLib/Chemistry/ChemicalFormula.cs

@@ -287,7 +287,7 @@ public void Add(Element element, int count)
             else
             {
                 Elements[element] += count;
-                if (Elements[element] <= 0)
+                if (Elements[element] == 0)
                     Elements.Remove(element);
             }
             formulaString = null;

mzLib/Development/Deconvolution/SinglePeakDeconvolutionTestCase.cs

@@ -0,0 +1,90 @@
+using MassSpectrometry;
+using MzLibUtil;
+using SpectralAveraging;
+using Readers;
+
+namespace Development.Deconvolution
+{
+    /// <summary>
+    /// Contains the expected results from deconvolution a single isotopic peak as well as information on the sample
+    /// </summary>
+    public class SinglePeakDeconvolutionTestCase
+    {
+        /// <summary>
+        /// Instantiate a SinglePeakDeconvolutionTestCase
+        /// </summary>
+        /// <param name="deconvoluter">The object which will be performing the deconvolution when tested</param>
+        /// <param name="sampleInformation">Quick information relevant to the sample, will be visible on test failing. Use this field to allow other to quickly identify which tests are failing</param>
+        /// <param name="spectrumPath">path to the spectrum of interest, current implementation expects the file to </param>
+        /// <param name="scanNumber">One based scan number of spectrum to deconvolute</param>
+        /// <param name="expectedMostAbundantObservedIsotopicMass">Expected mass from deconvolution result</param>
+        /// <param name="expectedIonChargeState">Expected charge state from deconvolution result</param>
+        /// <param name="selectedIonMz">M/z of peak to deconvolute from spectrum</param>
+        /// <param name="precursorPpmMassTolerance">Tolerance which deconvolution results must match expected value</param>
+        public SinglePeakDeconvolutionTestCase(Deconvoluter deconvoluter, string sampleInformation, string spectrumPath, int scanNumber,
+            double expectedMostAbundantObservedIsotopicMass, int expectedIonChargeState, double selectedIonMz, double precursorPpmMassTolerance)
+        {
+            Deconvoluter = deconvoluter;
+            SampleInformation = sampleInformation;
+            ExpectedMostAbundantObservedIsotopicMass = expectedMostAbundantObservedIsotopicMass;
+            ExpectedIonChargeState = expectedIonChargeState;
+            SelectedIonMz = selectedIonMz;
+            DeconvolutionPPmTolerance = new PpmTolerance(precursorPpmMassTolerance);
+            SpectrumToDeconvolute = MsDataFileReader.GetDataFile(spectrumPath)
+                .LoadAllStaticData()
+                .GetAllScansList()
+                .First(p => p.OneBasedScanNumber == scanNumber).MassSpectrum;
+
+            // 8.5 was selected as this is the magic number found in Classic Deconvolution
+            RangeToDeconvolute = new MzRange(selectedIonMz - 8.5, selectedIonMz + 8.5);
+        }
+
+        /// <summary>
+        /// The object which will be performing the deconvolution when tested
+        /// </summary>
+        public Deconvoluter Deconvoluter { get; set; }
+
+        /// <summary>
+        /// Quick information relevant to the sample, will be visible on test failing
+        /// Use this field to allow other to quickly identify which tests are failing
+        /// </summary>
+        public string SampleInformation { get; init; }
+
+        /// <summary>
+        /// Expected mass from deconvolution result
+        /// </summary>
+        public double ExpectedMostAbundantObservedIsotopicMass { get; init; }
+
+        /// <summary>
+        /// Expected charge state from deconvolution result
+        /// </summary>
+        public int ExpectedIonChargeState { get; init; }
+
+        /// <summary>
+        /// M/z of peak to deconvolute from spectrum
+        /// </summary>
+        public double SelectedIonMz { get; init; }
+
+        /// <summary>
+        /// Range within the spectrum to deconvolute
+        /// Currently set to +- 8.5 mz from SelectedIonMz per MetaMorpheus default heuristic
+        /// </summary>
+        public MzRange RangeToDeconvolute { get; init; }
+
+        /// <summary>
+        /// Spectrum to Deconvolute
+        /// </summary>
+        public MzSpectrum SpectrumToDeconvolute { get; init; }
+
+        /// <summary>
+        /// Tolerance which deconvolution results must match expected value
+        /// </summary>
+        public PpmTolerance DeconvolutionPPmTolerance { get; init; }
+
+        public override string ToString()
+        {
+            return $"{Deconvoluter.DeconvolutionType}: {SampleInformation} Charge: {ExpectedIonChargeState}";
+        }
+    }
+}
+