private DefaultMzSpectrum createSpectrum(ChemicalFormula f, double lowerBound, double upperBound, int minCharge)
{
IsotopicDistribution isodist = new IsotopicDistribution(f, 0.1);
IMzSpectrum <MzPeak> massSpectrum1 = new DefaultMzSpectrum(isodist.Masses.ToArray(), isodist.Intensities.ToArray(), false);
massSpectrum1 = massSpectrum1.newSpectrumFilterByNumberOfMostIntense(5);
var chargeToLookAt = minCharge;
var correctedSpectrum = massSpectrum1.newSpectrumApplyFunctionToX(s => s.ToMassToChargeRatio(chargeToLookAt));
List <double> allMasses = new List <double>();
List <double> allIntensitiess = new List <double>();
while (correctedSpectrum.FirstX > lowerBound)
{
foreach (var thisPeak in correctedSpectrum)
{
if (thisPeak.MZ > lowerBound && thisPeak.MZ < upperBound)
{
allMasses.Add(thisPeak.MZ);
allIntensitiess.Add(thisPeak.Intensity);
}
}
chargeToLookAt += 1;
correctedSpectrum = massSpectrum1.newSpectrumApplyFunctionToX(s => s.ToMassToChargeRatio(chargeToLookAt));
}
var allMassesArray = allMasses.ToArray();
var allIntensitiessArray = allIntensitiess.ToArray();
Array.Sort(allMassesArray, allIntensitiessArray);
return(new DefaultMzSpectrum(allMassesArray, allIntensitiessArray, false));
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
ChemicalFormulaModification carbamidomethylationOfCMod = new ChemicalFormulaModification("H3C2NO", "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
DefaultMzSpectrum MS1 = createSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
DefaultMzSpectrum MS2 = createMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
MsDataScan <IMzSpectrum <MzPeak> >[] Scans = new MsDataScan <IMzSpectrum <MzPeak> > [2];
Scans[0] = new MsDataScan <IMzSpectrum <MzPeak> >(1, MS1.newSpectrumApplyFunctionToX(b => b + 0.000001 * b + 0.000001), "spectrum 1", 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "FTMS first spectrum", MZAnalyzerType.Unknown, 1, MS1.SumOfAllY);
Scans[1] = new MsDataScan <IMzSpectrum <MzPeak> >(2, MS2.newSpectrumApplyFunctionToX(b => b + 0.00001 * b + 0.00001), "spectrum 2", 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "FTMS second spectrum", MZAnalyzerType.Unknown, 1, MS2.SumOfAllY, "spectrum 1", 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 0.141146966879759, 1134.26091302033);
var myMsDataFile = new FakeMsDataFile(@"myFakeFile.mzML", Scans);
MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(myMsDataFile, Path.Combine(Path.GetDirectoryName(myMsDataFile.FilePath), Path.GetFileNameWithoutExtension(myMsDataFile.FilePath)) + ".mzML");
Mzml okay = new Mzml(@"myFakeFile.mzML");
okay.Open();
okay.GetScan(2);
Assert.AreEqual(1, okay.GetSpectrumNumber(1));
Assert.AreEqual(2, okay.GetSpectrumNumber(2));
}
