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);
}
