//[Test]
public static void TestGetCombinedMs2Scans()
{
var myMsDataFile = new TestDataFile(5);
bool DoPrecursorDeconvolution = true;
bool UseProvidedPrecursorInfo = true;
double DeconvolutionIntensityRatio = 4;
int DeconvolutionMaxAssumedChargeState = 10;
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Write prime code to combine MS2MS3
Dictionary <int, double> listOfScanPrecusor = new Dictionary <int, double>();
List <IMzmlScan> ListOfSortedMsScans = new List <IMzmlScan>();
List <Ms2ScanWithSpecificMass> test = new List <Ms2ScanWithSpecificMass>();
foreach (var ms2scan in myMsDataFile.OfType <IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > >())
{
if (ms2scan.MsnOrder == 2 && !listOfScanPrecusor.Contains(new KeyValuePair <int, double>(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ)))
{
if (ms2scan.OneBasedPrecursorScanNumber.HasValue)
{
listOfScanPrecusor.Add(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ);
List <int> currentScanMS2OneBasedScanNumber = new List <int>();
currentScanMS2OneBasedScanNumber.Add(ms2scan.OneBasedScanNumber);
var mz2 = ms2scan.MassSpectrum.XArray.ToList();
var intensities2 = ms2scan.MassSpectrum.YArray.ToList();
for (int i = 1; i < 7; i++)
{
if (ms2scan.OneBasedScanNumber + i <= myMsDataFile.NumSpectra)
{
var x = myMsDataFile.GetOneBasedScan(ms2scan.OneBasedScanNumber + i) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
//var x = myMsDataFile.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().ElementAt(i);
if (x.MsnOrder == 2 && x.SelectedIonMZ == ms2scan.SelectedIonMZ)
{
currentScanMS2OneBasedScanNumber.Add(x.OneBasedScanNumber);
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
if (x.MsnOrder == 3 && currentScanMS2OneBasedScanNumber.Contains(x.OneBasedPrecursorScanNumber.Value))
{
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
}
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.ToArray(), intensities2.ToArray(), false);
ListOfSortedMsScans.Add(new MzmlScanWithPrecursor(ms2scan.OneBasedScanNumber, MassSpectrum2, ms2scan.MsnOrder, ms2scan.IsCentroid, Polarity.Positive, ms2scan.RetentionTime,
ms2scan.ScanWindowRange, ms2scan.ScanFilter, ms2scan.MzAnalyzer, ms2scan.TotalIonCurrent, ms2scan.SelectedIonMZ, ms2scan.SelectedIonChargeStateGuess, ms2scan.SelectedIonIntensity, ms2scan.IsolationMz, null, ms2scan.DissociationType, ms2scan.OneBasedPrecursorScanNumber, ms2scan.SelectedIonMonoisotopicGuessMz, ms2scan.InjectionTime, ""));
}
}
}
foreach (var ms2scan in ListOfSortedMsScans.OfType <IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > >())
{
test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, ""));
}
var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
//Using function to combine MS2MS3
//var listOfSortedms2Scans2 = MetaMorpheusTask.GetCombinedMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Assert.AreEqual(5, myMsDataFile.NumSpectra);
//Assert.AreEqual(1, listOfSortedms2Scans2.Count());
}
