Пример #1
0
        /// <summary>
        /// Extract ScanInfo from this RawFile for each scan and add it to the posLayer or negLayer RawFileLayer of this RawFile.
        ///
        /// Only called from InitFromRawFile, which is called only from Init, which is only called from CreateRawFile.
        /// </summary>
        private void InitFromRawFileImpl()
        {
            InfoLists posInfoList = new InfoLists();
            InfoLists negInfoList = new InfoLists();

            for (int scanNum = FirstScanNumber; scanNum <= LastScanNumber; scanNum++)
            {
                if (FirstScanNumber > LastScanNumber)
                {
                    break;
                }
                ScanInfo scanInfo = GetInfoForScanNumber(scanNum);
                if (scanInfo == null)
                {
                    continue;
                }
                if (scanInfo.positiveIonMode)
                {
                    posInfoList.Add(scanInfo, scanNum);
                }
                else
                {
                    negInfoList.Add(scanInfo, scanNum);
                }
            }
            posLayer.SetData(posInfoList, MaximumIntensity);
            negLayer.SetData(negInfoList, MaximumIntensity);
        }
Пример #2
0
        /// <summary>
        /// Take the ScanInfo object and add its contents to the field simLists, ms1Lists, or ms2Lists,
        /// depending on the values of the msLevel and isSim fields of the ScanInfo.
        /// </summary>
        /// <param name="scanInfo">an object containing details about this scan</param>
        /// <param name="scanNum">the unique number of this scan</param>
        public void Add(ScanInfo scanInfo, int scanNum)
        {
            switch (scanInfo.msLevel)
            {
            case MsLevel.Ms1:
                //if (!scanInfo.isSim){
                currentMs2Inds.Clear();
                if (scanInfo.min < ms1Lists.massMin)
                {
                    ms1Lists.massMin = scanInfo.min;
                }
                if (scanInfo.max > ms1Lists.massMax)
                {
                    ms1Lists.massMax = scanInfo.max;
                }
                if (scanInfo.nImsScans > ms1Lists.maxNumIms)
                {
                    ms1Lists.maxNumIms = scanInfo.nImsScans;
                }
                ms1Lists.scans.Add(scanNum);
                ms1Lists.rts.Add(scanInfo.rt);
                ms1Lists.ionInjectionTimes.Add(scanInfo.ionInjectionTime);
                ms1Lists.basepeakIntensities.Add(scanInfo.basepeakIntensity);
                ms1Lists.elapsedTimes.Add(scanInfo.elapsedTime);
                if (scanInfo.hasProfile && !allMassRanges.ContainsKey(scanInfo.min))
                {
                    allMassRanges.Add(scanInfo.min, null);
                }
                else if (!scanInfo.hasProfile && !allMassRanges.ContainsKey(0))
                {
                    allMassRanges.Add(0, null);
                }
                ms1Lists.tics.Add(scanInfo.tic);
                ms1Lists.hasCentroids.Add(scanInfo.hasCentroid);
                ms1Lists.hasProfiles.Add(scanInfo.hasProfile);
                ms1Lists.massAnalyzer.Add(scanInfo.analyzer);
                ms1Lists.minMasses.Add(scanInfo.min);
                ms1Lists.maxMasses.Add(scanInfo.max);
                ms1Lists.resolutions.Add(scanInfo.resolution);
                ms1Lists.intenseCompFactors.Add(scanInfo.intenseCompFactor);
                ms1Lists.emIntenseComp.Add(scanInfo.emIntenseComp);
                ms1Lists.rawOvFtT.Add(scanInfo.rawOvFtT);
                ms1Lists.agcFillList.Add(scanInfo.agcFill);
                ms1Lists.nImsScans.Add(scanInfo.nImsScans);
                ms1Lists.isSim.Add(scanInfo.isSim);
                //}
                break;

            case MsLevel.Ms2:
                if (scanInfo.min < ms2Lists.massMin)
                {
                    ms2Lists.massMin = scanInfo.min;
                }
                if (scanInfo.max > ms2Lists.massMax)
                {
                    ms2Lists.massMax = scanInfo.max;
                }
                if (scanInfo.nImsScans > ms2Lists.maxNumIms)
                {
                    ms2Lists.maxNumIms = scanInfo.nImsScans;
                }
                currentMs2Inds.Add(ms2Lists.scansList.Count);
                ms2Lists.scansList.Add(scanNum);
                ms2Lists.prevMs1IndexList.Add(ms1Lists.scans.Count - 1);
                ms2Lists.mzList.Add(scanInfo.ms2ParentMz);
                ms2Lists.fragmentTypeList.Add(scanInfo.ms2FragType);
                ms2Lists.rtList.Add(scanInfo.rt);
                ms2Lists.ionInjectionTimesList.Add(scanInfo.ionInjectionTime);
                ms2Lists.basepeakIntensityList.Add(scanInfo.basepeakIntensity);
                ms2Lists.elapsedTimesList.Add(scanInfo.elapsedTime);
                ms2Lists.energiesList.Add(scanInfo.energy);
                ms2Lists.summationsList.Add(scanInfo.summations);
                ms2Lists.monoisotopicMzList.Add(scanInfo.ms2MonoMz);
                ms2Lists.ticList.Add(scanInfo.tic);
                ms2Lists.hasCentroidList.Add(scanInfo.hasCentroid);
                ms2Lists.hasProfileList.Add(scanInfo.hasProfile);
                ms2Lists.analyzerList.Add(scanInfo.analyzer);
                ms2Lists.minMassList.Add(scanInfo.min);
                ms2Lists.maxMassList.Add(scanInfo.max);
                ms2Lists.isolationMzMinList.Add(scanInfo.ms2IsolationMin);
                ms2Lists.isolationMzMaxList.Add(scanInfo.ms2IsolationMax);
                ms2Lists.resolutionList.Add(scanInfo.resolution);
                ms2Lists.intenseCompFactor.Add(scanInfo.intenseCompFactor);
                ms2Lists.emIntenseComp.Add(scanInfo.emIntenseComp);
                ms2Lists.rawOvFtT.Add(scanInfo.rawOvFtT);
                ms2Lists.agcFillList.Add(scanInfo.agcFill);
                ms2Lists.nImsScans.Add(scanInfo.nImsScans);
                break;

            case MsLevel.Ms3:
                if (scanInfo.min < ms3Lists.massMin)
                {
                    ms3Lists.massMin = scanInfo.min;
                }
                if (scanInfo.max > ms3Lists.massMax)
                {
                    ms3Lists.massMax = scanInfo.max;
                }
                if (scanInfo.nImsScans > ms3Lists.maxNumIms)
                {
                    ms3Lists.maxNumIms = scanInfo.nImsScans;
                }
                ms3Lists.scansList.Add(scanNum);
                ms3Lists.prevMs2IndexList.Add(GetPrecursorMs2(currentMs2Inds, scanInfo.ms2ParentMz));
                //ms3Lists.ms3PrevMs2IndexList.Add(ms2Lists.ms2ScansList.Count - 1);
                ms3Lists.mz1List.Add(scanInfo.ms2ParentMz);
                ms3Lists.mz2List.Add(scanInfo.ms3ParentMz);
                ms3Lists.fragmentTypeList.Add(scanInfo.ms2FragType);
                ms3Lists.rtList.Add(scanInfo.rt);
                ms3Lists.ionInjectionTimesList.Add(scanInfo.ionInjectionTime);
                ms3Lists.basepeakIntensityList.Add(scanInfo.basepeakIntensity);
                ms3Lists.elapsedTimesList.Add(scanInfo.elapsedTime);
                ms3Lists.energiesList.Add(scanInfo.energy);
                ms3Lists.summationsList.Add(scanInfo.summations);
                ms3Lists.monoisotopicMzList.Add(scanInfo.ms2MonoMz);
                ms3Lists.ticList.Add(scanInfo.tic);
                ms3Lists.hasCentroidList.Add(scanInfo.hasCentroid);
                ms3Lists.hasProfileList.Add(scanInfo.hasProfile);
                ms3Lists.analyzerList.Add(scanInfo.analyzer);
                ms3Lists.minMassList.Add(scanInfo.min);
                ms3Lists.maxMassList.Add(scanInfo.max);
                ms3Lists.isolationMzMinList.Add(scanInfo.ms2IsolationMin);
                ms3Lists.isolationMzMaxList.Add(scanInfo.ms2IsolationMax);
                ms3Lists.resolutionList.Add(scanInfo.resolution);
                ms3Lists.intenseCompFactor.Add(scanInfo.intenseCompFactor);
                ms3Lists.emIntenseComp.Add(scanInfo.emIntenseComp);
                ms3Lists.rawOvFtT.Add(scanInfo.rawOvFtT);
                ms3Lists.agcFillList.Add(scanInfo.agcFill);
                ms3Lists.nImsScans.Add(scanInfo.nImsScans);
                break;

            default:
                throw new Exception("Invalid MS level.");
            }
        }