public void TestFitMinusOneScore(int precursor, string adduct, string commonName, string id, string rawFilePath)
{
var lipid = new Lipid()
{
AdductFull = adduct, CommonName = commonName
};
var lipidTarget = lipid.CreateLipidTarget();
var composition = lipidTarget.Composition;
var compMinus1 = new Composition(composition.C, composition.H - 1, composition.N, composition.O, composition.S, composition.P); //Subtract one hydrogen to make this a minus1 fit score
var lcmsRun = PbfLcMsRun.GetLcMsRun(rawFilePath);
var spectrum = lcmsRun.GetSpectrum(precursor);
var relativeIntensityThreshold = 0.1;
var tolerance = new Tolerance(30, ToleranceUnit.Ppm);
//Get the values to use to calculate pearson correlation
var observedPeaks = LipidUtil.GetAllIsotopePeaks(spectrum, compMinus1, tolerance,
relativeIntensityThreshold);
if (observedPeaks == null)
{
Console.WriteLine("Observed peaks is null for scan " + id);
}
var isotopomerEnvelope = IsoProfilePredictor.GetIsotopomerEnvelop(
compMinus1.C,
compMinus1.H,
compMinus1.N,
compMinus1.O,
compMinus1.S);
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
Console.WriteLine("The theoretical y values are: ");
foreach (var value in isotopomerEnvelope.Envolope)
{
Console.WriteLine(value + ", ");
}
Console.WriteLine("The observed peak intensity x values are: ");
foreach (var value in observedIntensities)
{
Console.WriteLine(value + ", ");
}
}