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);
}
