internal static void PrintResults(SpectrumComparisonResult evaluationTests)
{
Console.WriteLine("Theoretical / Experimental match evaluation-----");
Console.WriteLine("ACount {0} :: {1}", evaluationTests.ACount.Count, PrintSequence(evaluationTests.ACount));
Console.WriteLine("BCount {0} :: {1}", evaluationTests.BCount.Count, PrintSequence(evaluationTests.BCount));
Console.WriteLine("CCount {0} :: {1}", evaluationTests.CCount.Count, PrintSequence(evaluationTests.CCount));
Console.WriteLine("XCount {0} :: {1}", evaluationTests.XCount.Count, PrintSequence(evaluationTests.XCount));
Console.WriteLine("YCount {0} :: {1}", evaluationTests.YCount.Count, PrintSequence(evaluationTests.YCount));
Console.WriteLine("ZCount {0} :: {1}", evaluationTests.ZCount.Count, PrintSequence(evaluationTests.ZCount));
Console.WriteLine("GoldenAX {0}", evaluationTests.ComplementaryPairsAX);
Console.WriteLine("GoldenBY {0}", evaluationTests.ComplementaryPairsBY);
Console.WriteLine("GoldenCZ {0}", evaluationTests.ComplementaryPairsCZ);
Console.WriteLine("SignalPercentage {0}", evaluationTests.SignalPercentage);
Console.WriteLine("------------------------------------------------");
}
public static SpectrumComparisonResult Do(List <TheTests> theTests, List <PredictedIon> theoretical, MSFull experimentalTmp, double ppm, int cleanedPeptideSequenceLength, double relativeIntensityThreshold)
{
SpectrumComparisonResult scr = new SpectrumComparisonResult();
//Make sure we dont screw up the original spectrum
MSFull experimental = PatternTools.ObjectCopier.Clone(experimentalTmp);
double maxIntensity = experimental.MSData.Max(a => a.Intensity);
experimental.MSData.RemoveAll(a => a.Intensity / maxIntensity < relativeIntensityThreshold);
bool allTests = false;
if (theTests.Contains(TheTests.AllTests))
{
allTests = true;
}
//Just to make sure
foreach (PredictedIon p in theoretical)
{
p.Matched = false;
}
//Before all find all matched theoretical and experimental
List <Ion> matchedIons = new List <Ion>(100);
foreach (PredictedIon pi in theoretical)
{
List <Ion> theIons = experimental.MSData.FindAll(a => PatternTools.pTools.PPM(a.MZ, pi.MZ) < ppm);
if (theIons.Count > 0)
{
matchedIons.AddRange(theIons);
pi.Matched = true;
}
}
matchedIons = matchedIons.Distinct().ToList();
if (theTests.Contains(TheTests.SignalPercentage) || allTests)
{
scr.SignalPercentage = Math.Round(matchedIons.Sum(a => a.Intensity) / experimental.TotalIonIntensity, 6);
}
if (theTests.Contains(TheTests.ACount) || allTests)
{
scr.ACount = SequentialScore(theoretical, IonSeries.A);
}
if (theTests.Contains(TheTests.BCount) || allTests)
{
scr.BCount = SequentialScore(theoretical, IonSeries.B);
}
if (theTests.Contains(TheTests.CCount) || allTests)
{
scr.CCount = SequentialScore(theoretical, IonSeries.C);
}
if (theTests.Contains(TheTests.XCount) || allTests)
{
scr.XCount = SequentialScore(theoretical, IonSeries.X);
}
if (theTests.Contains(TheTests.YCount) || allTests)
{
scr.YCount = SequentialScore(theoretical, IonSeries.Y);
}
if (theTests.Contains(TheTests.ZCount) || allTests)
{
scr.ZCount = SequentialScore(theoretical, IonSeries.Z);
}
if (theTests.Contains(TheTests.ComplementaryPairsAX) || allTests)
{
scr.ComplementaryPairsAX = CountComplementaryPairs(scr.ACount, scr.XCount, cleanedPeptideSequenceLength);
}
if (theTests.Contains(TheTests.ComplementaryPairsBY) || allTests)
{
scr.ComplementaryPairsBY = CountComplementaryPairs(scr.BCount, scr.YCount, cleanedPeptideSequenceLength);
}
if (theTests.Contains(TheTests.ComplementaryPairsCZ) || allTests)
{
scr.ComplementaryPairsCZ = CountComplementaryPairs(scr.CCount, scr.ZCount, cleanedPeptideSequenceLength);
}
return(scr);
}
