Ejemplo n.º 1
0
        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);
        }
Ejemplo n.º 2
0
        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);
        }
Ejemplo n.º 3
0
        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);
        }
Ejemplo n.º 4
0
        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
        }
Ejemplo n.º 5
0
        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());
        }
Ejemplo n.º 6
0
 internal virtual void AddTheoreticalLabelledIsotopicProfile(IsotopicProfile theorLabelledIso)
 {
     throw new NotImplementedException();
 }
Ejemplo n.º 7
0
 internal virtual void AddLabelledIso(IsotopicProfile labelledIso)
 {
     throw new NotImplementedException();
 }
Ejemplo n.º 8
0
 public abstract double GetRatio(double[] xvals, double[] yvals,
                                 DeconTools.Backend.Core.IsotopicProfile iso1, DeconTools.Backend.Core.IsotopicProfile iso2,
                                 double backgroundIntensity);
Ejemplo n.º 9
0
 protected TargetedResultBase(TargetBase target)
 {
     Target               = target;
     IsotopicProfile      = new IsotopicProfile();
     ChromPeakQualityList = new List <ChromPeakQualityData>();
 }
Ejemplo n.º 10
0
 internal override void AddTheoreticalLabelledIsotopicProfile(IsotopicProfile theorLabelledIso)
 {
     this.TheorIsotopicProfileLabeled = theorLabelledIso;
 }
Ejemplo n.º 11
0
 internal override void AddLabelledIso(IsotopicProfile labelledIso)
 {
     this.IsotopicProfileLabeled = labelledIso;
 }