public static void DifferentAnalyzersTest() { IMzmlScan[] scans = new IMzmlScan[2]; double[] intensities1 = new double[] { 1 }; double[] mz1 = new double[] { 50 }; MzmlMzSpectrum massSpec1 = new MzmlMzSpectrum(mz1, intensities1, false); scans[0] = new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1"); double[] intensities2 = new double[] { 1 }; double[] mz2 = new double[] { 30 }; MzmlMzSpectrum massSpec2 = new MzmlMzSpectrum(mz2, intensities2, false); scans[1] = new MzmlScanWithPrecursor(2, massSpec2, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.IonTrap3D, massSpec2.SumOfAllY, 50, null, null, 50, 1, DissociationType.CID, 1, null, null, "2"); FakeMsDataFile f = new FakeMsDataFile(scans); MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML"), false); Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML")); Assert.AreEqual(MZAnalyzerType.Orbitrap, ok.First().MzAnalyzer); Assert.AreEqual(MZAnalyzerType.IonTrap3D, ok.Last().MzAnalyzer); }
public void LoadMzmlAnotherTest() { Mzml a = Mzml.LoadAllStaticData(@"small.pwiz.1.1.mzML"); Assert.AreEqual(19914, a.First().MassSpectrum.Size); //a = new Mzml(@"small.pwiz.1.1.mzML", 400); //a.Open(); //Assert.AreEqual(400, a.First().MassSpectrum.Size); //var cool = a.GetOneBasedScan(6) as MzmlScanWithPrecursor; //Assert.AreEqual(1, cool.IsolationWidth); //a.Close(); }
public static void LoadThermoTest2() { ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw"); Assert.AreEqual(360, a.NumSpectra); Assert.GreaterOrEqual(1000, a.GetOneBasedScan(1).MassSpectrum.Extract(0, 500).Last().X); Assert.AreEqual(2, a.GetOneBasedScan(1).MassSpectrum.FilterByY(5e6, double.MaxValue).Count()); var ye = a.GetOneBasedScan(1).MassSpectrum.CopyTo2DArray(); Assert.AreEqual(77561752, a.GetOneBasedScan(1).TotalIonCurrent); Assert.AreEqual(144, a.GetClosestOneBasedSpectrumNumber(2)); var newSpectrum = new ThermoSpectrum(a.GetOneBasedScan(51).MassSpectrum); Assert.AreEqual(1120, a.GetOneBasedScan(1).MassSpectrum.Size); var newDeconvolution = a.GetOneBasedScan(1).MassSpectrum.Deconvolute(new MzRange(double.MinValue, double.MaxValue), 1, 10, 1, 4).ToList(); Assert.IsTrue(newDeconvolution.Any(b => Math.Abs(b.peaks.First().mz.ToMass(b.charge) - 523.257) < 0.001)); MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML"), false); var sdafaf = a.Deconvolute(null, null, 1, 30, 10, 3, 10, b => true).OrderByDescending(b => b.NumPeaks).First(); Assert.IsTrue(Math.Abs(262.64 - sdafaf.Mass.ToMz(2)) <= 0.01); using (ThermoDynamicData dynamicThermo = ThermoDynamicData.InitiateDynamicConnection(@"05-13-16_cali_MS_60K-res_MS.raw")) { Assert.AreEqual(136, dynamicThermo.GetClosestOneBasedSpectrumNumber(1.89)); dynamicThermo.ClearCachedScans(); } Mzml readCovertedMzmlFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML")); Assert.AreEqual(a.First().Polarity, readCovertedMzmlFile.First().Polarity); }