public IsotopicProfile CloneIsotopicProfile()
{
var iso = new IsotopicProfile();
iso.AverageMass = AverageMass;
iso.ChargeState = ChargeState;
iso.IntensityMostAbundant = IntensityMostAbundant;
iso.IntensityMostAbundantTheor = IntensityMostAbundantTheor;
iso.MonoIsotopicMass = MonoIsotopicMass;
iso.MonoIsotopicPeakIndex = MonoIsotopicPeakIndex;
iso.MonoPeakMZ = MonoPeakMZ;
iso.MonoPlusTwoAbundance = MonoPlusTwoAbundance;
iso.MostAbundantIsotopeMass = MostAbundantIsotopeMass;
iso.IsSaturated = IsSaturated;
iso.OriginalIntensity = OriginalIntensity;
iso.Peaklist = new List <MSPeak>();
foreach (var mspeak in Peaklist)
{
var peak = new MSPeak(mspeak.XValue, mspeak.Height, mspeak.Width, mspeak.SignalToNoise);
iso.Peaklist.Add(peak);
}
iso.Score = Score;
iso.ScoreCountBasis = ScoreCountBasis;
return(iso);
}
public override double GetRatio(double[] xvals, double[] yvals,
DeconTools.Backend.Core.IsotopicProfile iso1, DeconTools.Backend.Core.IsotopicProfile iso2,
double backgroundIntensity)
{
double returnVal = -1;
returnVal = GetRatioBasedOnAreaUnderPeaks(xvals, yvals, iso1, iso2, backgroundIntensity);
return(returnVal);
}
public double GetRatioBasedOnMostIntensePeak(DeconTools.Backend.Core.IsotopicProfile iso1, DeconTools.Backend.Core.IsotopicProfile iso2)
{
double returnVal = -1;
if (iso1 == null || iso2 == null)
{
return(returnVal);
}
double iso1MaxIntens = iso1.getMostIntensePeak().Height;
double iso2MaxIntens = iso2.getMostIntensePeak().Height;
return(returnVal);
}
public double GetRatioBasedOnAreaUnderPeaks(double[] xvals, double[] yvals,
DeconTools.Backend.Core.IsotopicProfile iso1, DeconTools.Backend.Core.IsotopicProfile iso2,
double backgroundIntensity)
{
double returnRatio = -1;
//define starting m/z value based on peak m/z and width
var leftMostMZ = iso1.Peaklist[0].XValue - 1; // 4σ = peak width at base; '-1' ensures we are starting outside the peak.
//find starting point (use binary search)
var indexOfStartingPoint = Utilities.MathUtils.BinarySearchWithTolerance(xvals, leftMostMZ, 0, xvals.Length - 1, 0.1);
if (indexOfStartingPoint == -1)
{
indexOfStartingPoint = 0;
}
var area1 = IsotopicProfileUtilities.CalculateAreaOfProfile(iso1, xvals, yvals, backgroundIntensity, ref indexOfStartingPoint);
var area2 = IsotopicProfileUtilities.CalculateAreaOfProfile(iso2, xvals, yvals, backgroundIntensity, ref indexOfStartingPoint);
if (area1 < 0)
{
area1 = 0;
}
if (area2 > 0)
{
returnRatio = area1 / area2;
}
else
{
returnRatio = 9999; // this will indicate the problem of the second isotope having a 0 or negative area.
}
return(returnRatio);
//iterate over peaks from isotopic profile 1
//iterate over raw m/z values.
//If within peak m/z range, calculate area (trapazoid)
//repeat the above with isotopic profile 2
}
protected string buildBasicConsoleInfo()
{
var sb = new StringBuilder();
sb.Append("****** Match ******\n");
sb.Append("NET = \t" + Target.NormalizedElutionTime.ToString("0.000") + "\n");
sb.Append("ChromPeak ScanNum = " + ChromPeakSelected.XValue.ToString(CultureInfo.InvariantCulture) + "\n");
sb.Append("ChromPeak NETVal = " + ChromPeakSelected.NETValue.ToString("0.000") + "\n");
sb.Append("ScanSet = { ");
foreach (var scanNum in ScanSet.IndexValues)
{
sb.Append(scanNum);
sb.Append(", ");
}
sb.Append("} \n");
if (IsotopicProfile?.Peaklist != null && IsotopicProfile.Peaklist.Count > 0)
{
sb.Append("Observed MZ and intensity = " + IsotopicProfile.getMonoPeak().XValue + "\t" + IsotopicProfile.getMonoPeak().Height + "\n");
}
sb.Append("FitScore = " + Score.ToString("0.0000") + "\n");
return(sb.ToString());
}
internal virtual void AddTheoreticalLabelledIsotopicProfile(IsotopicProfile theorLabelledIso)
{
throw new NotImplementedException();
}
internal virtual void AddLabelledIso(IsotopicProfile labelledIso)
{
throw new NotImplementedException();
}
public abstract double GetRatio(double[] xvals, double[] yvals,
DeconTools.Backend.Core.IsotopicProfile iso1, DeconTools.Backend.Core.IsotopicProfile iso2,
double backgroundIntensity);
protected TargetedResultBase(TargetBase target)
{
Target = target;
IsotopicProfile = new IsotopicProfile();
ChromPeakQualityList = new List <ChromPeakQualityData>();
}
internal override void AddTheoreticalLabelledIsotopicProfile(IsotopicProfile theorLabelledIso)
{
this.TheorIsotopicProfileLabeled = theorLabelledIso;
}
internal override void AddLabelledIso(IsotopicProfile labelledIso)
{
this.IsotopicProfileLabeled = labelledIso;
}