public void WriteMzmlTest() { var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR"); OldSchoolChemicalFormulaModification carbamidomethylationOfCMod = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H3C2NO"), "carbamidomethylation of C", ModificationSites.C); peptide.AddModification(carbamidomethylationOfCMod); MzmlMzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1); MzmlMzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500); IMzmlScan[] Scans = new IMzmlScan[2]; Scans[0] = new MzmlScan(1, MS1, 1, true, Polarity.Positive, 1.0, new MzRange(300, 2000), " first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, "scan=1"); Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, true, Polarity.Positive, 2.0, new MzRange(100, 1500), " second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 1134.26091302033, 1, "scan=2"); var myMsDataFile = new FakeMsDataFile(Scans); var oldFirstValue = myMsDataFile.GetOneBasedScan(1).MassSpectrum.FirstX; var secondScan = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>; Assert.AreEqual(1, secondScan.IsolationRange.Maximum - secondScan.IsolationRange.Minimum); MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, "argh.mzML", false); Mzml okay = Mzml.LoadAllStaticData(@"argh.mzML"); okay.GetOneBasedScan(2); Assert.AreEqual(1, okay.GetClosestOneBasedSpectrumNumber(1)); Assert.AreEqual(2, okay.GetClosestOneBasedSpectrumNumber(2)); var newFirstValue = okay.GetOneBasedScan(1).MassSpectrum.FirstX; Assert.AreEqual(oldFirstValue.Value, newFirstValue.Value, 1e-9); var secondScan2 = okay.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>; Assert.AreEqual(1, secondScan2.IsolationRange.Maximum - secondScan2.IsolationRange.Minimum); secondScan2.MassSpectrum.ReplaceXbyApplyingFunction((a) => 44); Assert.AreEqual(44, secondScan2.MassSpectrum.LastX); }
public void LoadMzmlTest() { Mzml a = Mzml.LoadAllStaticData(@"tiny.pwiz.1.1.mzML"); var ya = a.GetOneBasedScan(1).MassSpectrum; Assert.AreEqual(15, ya.Size); var ya2 = a.GetOneBasedScan(2).MassSpectrum; Assert.AreEqual(10, ya2.Size); var ya3 = a.GetOneBasedScan(3).MassSpectrum; Assert.AreEqual(0, ya3.Size); var ya4 = a.GetOneBasedScan(4).MassSpectrum; Assert.AreEqual(15, ya4.Size); IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > ok = a; Assert.AreEqual(1, ok.GetClosestOneBasedSpectrumNumber(5)); }
public void LoadMzmlFromConvertedMGFTest() { Mzml a = Mzml.LoadAllStaticData(@"tester.mzML"); var ya = a.GetOneBasedScan(1).MassSpectrum; Assert.AreEqual(192, ya.Size); var ya2 = a.GetOneBasedScan(3).MassSpectrum; Assert.AreEqual(165, ya2.Size); var ya3 = a.GetOneBasedScan(5).MassSpectrum; Assert.AreEqual(551, ya3.Size); var ya4 = a.GetOneBasedScan(975).MassSpectrum; Assert.AreEqual(190, ya4.Size); MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "CreateFileFromConvertedMGF.mzML", false); Mzml b = Mzml.LoadAllStaticData(@"CreateFileFromConvertedMGF.mzML"); MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(b, "CreateFileFromConvertedMGF2.mzML", false); }
public static void LoadCompressedMzml() { ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.RAW"); Mzml b = Mzml.LoadAllStaticData(@"smallCentroid.mzML"); Assert.AreEqual(a.NumSpectra, b.NumSpectra); Assert.AreEqual(a.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, 1e-8); Assert.IsTrue(Math.Abs((a.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8); Assert.AreEqual(a.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY, 1e-8); Assert.IsTrue(Math.Abs((a.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8); Assert.AreEqual(a.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, 1e-8); Assert.IsTrue(Math.Abs((a.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8); }