public static void TestVeryCloseExperimentalsModern()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var thePep = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First();
var frags = new List <Product>();
thePep.Fragment(DissociationType.HCD, FragmentationTerminus.Both, frags);
var massArray = frags.Select(p => p.NeutralMass).ToArray();
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1), massArray[4].ToMz(1) + 1e-9 };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 600, 1, null, new CommonParameters()) };
CommonParameters CommonParameters = new CommonParameters(productMassTolerance: new PpmTolerance(5), scoreCutoff: 1, digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: int.MaxValue, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
var indexEngine = new IndexingEngine(new List <Protein> {
prot
}, new List <Modification>(), new List <Modification>(), null, null, null, 1, DecoyType.Reverse,
CommonParameters, null, 30000, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var cse = new ModernSearchEngine(globalPsms, arrayOfSortedMS2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, null, new OpenSearchMode(), 0, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public static void TestVeryCloseExperimentalsModern()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
var thePep = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = thePep.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1), massArray[4].ToMz(1) + 1e-9 };
MzmlMzSpectrum massSpectrum = new MzmlMzSpectrum(mz, intensities, false);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scan = new MzmlScanWithPrecursor(1, massSpectrum, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, 0, null, null, 0, null, DissociationType.Unknown, 1, null, null, "scan=1");
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 600, 1, null) };
CommonParameters CommonParameters = new CommonParameters
{
ProductMassTolerance = new PpmTolerance(5),
DigestionParams = new DigestionParams
{
MaxMissedCleavages = 0,
MinPeptideLength = null,
MaxModificationIsoforms = int.MaxValue,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
},
ConserveMemory = false,
ScoreCutoff = 1
};
var indexEngine = new IndexingEngine(new List <Protein> {
prot
}, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <ProductType> {
ProductType.B, ProductType.Y
}, 1, DecoyType.Reverse, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var cse = new ModernSearchEngine(globalPsms, arrayOfSortedMS2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, new List <ProductType> {
ProductType.B, ProductType.Y
}, 0, CommonParameters, false, new OpenSearchMode(), 0, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}