Exemple #1
0
        private void SetIsotopeDistributionToZero(PeakData peakData, ThrashV1Peak peak, double zeroingStartMz,
                                                  double zeroingStopMz, double monoMw, int chargeState, bool clearSpectrum, HornTransformResults record,
                                                  bool debug = false)
        {
            var peakIndices = new List <int>();

            peakIndices.Add(peak.PeakIndex);
            var mzDelta = record.DeltaMz;

            if (debug)
            {
                Console.Error.WriteLine("Clearing peak data for " + peak.Mz + " Delta = " + mzDelta);
                Console.Error.WriteLine("Zeroing range = " + zeroingStartMz + " to " + zeroingStopMz);
            }

            double maxMz = 0;

            if (IsO16O18Data)
            {
                maxMz = (monoMw + 3.5) / chargeState + ChargeCarrierMass;
            }

            var numUnprocessedPeaks = peakData.GetNumUnprocessedPeaks();

            if (numUnprocessedPeaks == 0)
            {
                record.IsotopePeakIndices.Add(peak.PeakIndex);
                return;
            }

            if (clearSpectrum)
            {
                if (debug)
                {
                    Console.Error.WriteLine("Deleting main peak :" + peak.Mz);
                }
                SetPeakToZero(peak.DataIndex, ref peakData.IntensityList, ref peakData.MzList, debug);
            }

            peakData.RemovePeaks(peak.Mz - peak.FWHM, peak.Mz + peak.FWHM, debug);

            if (1 / (peak.FWHM * chargeState) < 3) // gord:  ??
            {
                record.IsotopePeakIndices.Add(peak.PeakIndex);
                peakData.RemovePeaks(zeroingStartMz, zeroingStopMz, debug);
                return;
            }

            // Delete isotopes of mzs higher than mz of starting isotope
            for (var peakMz = peak.Mz + 1.003 / chargeState;
                 (!IsO16O18Data || peakMz <= maxMz) && peakMz <= zeroingStopMz + 2 * peak.FWHM;
                 peakMz += 1.003 / chargeState)
            {
                if (debug)
                {
                    Console.Error.WriteLine("\tFinding next peak top from " + (peakMz - 2 * peak.FWHM) + " to " +
                                            (peakMz + 2 * peak.FWHM) + " pk = " + peakMz + " FWHM = " + peak.FWHM);
                }
                ThrashV1Peak nextPeak;
                peakData.GetPeakFromAll(peakMz - 2 * peak.FWHM, peakMz + 2 * peak.FWHM, out nextPeak);

                if (nextPeak.Mz.Equals(0))
                {
                    if (debug)
                    {
                        Console.Error.WriteLine("\t\tNo peak found.");
                    }
                    break;
                }
                if (debug)
                {
                    Console.Error.WriteLine("\t\tFound peak to delete =" + nextPeak.Mz);
                }

                // Before assuming that the next peak is indeed an isotope, we must check for the height of this
                // isotope. If the height is greater than expected by a factor of 3, lets not delete it.
                peakIndices.Add(nextPeak.PeakIndex);
                SetPeakToZero(nextPeak.DataIndex, ref peakData.IntensityList, ref peakData.MzList, debug);

                peakData.RemovePeaks(nextPeak.Mz - peak.FWHM, nextPeak.Mz + peak.FWHM, debug);
                peakMz = nextPeak.Mz;
            }

            // Delete isotopes of mzs lower than mz of starting isotope
            // TODO: Use the delta m/z to make sure to remove 1- peaks from the unprocessed list, but not from the list of peaks?
            for (var peakMz = peak.Mz - 1.003 / chargeState;
                 peakMz > zeroingStartMz - 2 * peak.FWHM;
                 peakMz -= 1.003 / chargeState)
            {
                if (debug)
                {
                    Console.Error.WriteLine("\tFinding previous peak top from " + (peakMz - 2 * peak.FWHM) + " to " +
                                            (peakMz + 2 * peak.FWHM) + " pk = " + peakMz + " FWHM = " + peak.FWHM);
                }
                ThrashV1Peak nextPeak;
                peakData.GetPeakFromAll(peakMz - 2 * peak.FWHM, peakMz + 2 * peak.FWHM, out nextPeak);
                if (nextPeak.Mz.Equals(0))
                {
                    if (debug)
                    {
                        Console.Error.WriteLine("\t\tNo peak found.");
                    }
                    break;
                }
                if (debug)
                {
                    Console.Error.WriteLine("\t\tFound peak to delete =" + nextPeak.Mz);
                }
                peakIndices.Add(nextPeak.PeakIndex);
                SetPeakToZero(nextPeak.DataIndex, ref peakData.IntensityList, ref peakData.MzList, debug);
                peakData.RemovePeaks(nextPeak.Mz - peak.FWHM, nextPeak.Mz + peak.FWHM, debug);
                peakMz = nextPeak.Mz;
            }

            if (debug)
            {
                Console.Error.WriteLine("Done Clearing peak data for " + peak.Mz);
            }

            peakIndices.Sort();
            // now insert into array.
            var numPeaksObserved       = peakIndices.Count;
            var numIsotopesObserved    = 0;
            var lastIsotopeNumObserved = int.MinValue;

            for (var i = 0; i < numPeaksObserved; i++)
            {
                var currentIndex = peakIndices[i];
                var currentPeak  = new ThrashV1Peak(peakData.PeakTops[currentIndex]);
                var isotopeNum   = (int)(Math.Abs((currentPeak.Mz - peak.Mz) * chargeState / 1.003) + 0.5);
                if (currentPeak.Mz < peak.Mz)
                {
                    isotopeNum = -1 * isotopeNum;
                }
                if (isotopeNum > lastIsotopeNumObserved)
                {
                    lastIsotopeNumObserved = isotopeNum;
                    numIsotopesObserved++;
                    if (numIsotopesObserved > MaxIsotopes)
                    {
                        break;
                    }
                    record.IsotopePeakIndices.Add(peakIndices[i]);
                }
                else
                {
                    record.IsotopePeakIndices[numIsotopesObserved - 1] = peakIndices[i];
                }
            }
            if (debug)
            {
                Console.Error.WriteLine("Copied " + record.NumIsotopesObserved + " isotope peak indices into record ");
            }
        }