コード例 #1
0
        public ChromatogramDataProvider(MsDataFileImpl dataFile,
                                        ChromFileInfo fileInfo,
                                        ProgressStatus status,
                                        int startPercent,
                                        int endPercent,
                                        IProgressMonitor loader)
            : base(fileInfo, status, startPercent, endPercent, loader)
        {
            _dataFile = dataFile;

            if (_dataFile.IsThermoFile)
            {
                _readMaxMinutes = 4;
            }

            int len = dataFile.ChromatogramCount;

            _chromIndices = new int[len];

            bool   fixCEOptForShimadzu = dataFile.IsShimadzuFile;
            int    indexPrecursor      = -1;
            double lastPrecursor       = 0;

            for (int i = 0; i < len; i++)
            {
                int    index;
                string id = dataFile.GetChromatogramId(i, out index);

                if (!ChromKey.IsKeyId(id))
                {
                    continue;
                }

                var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
                if (chromKey.Precursor != lastPrecursor)
                {
                    lastPrecursor = chromKey.Precursor;
                    indexPrecursor++;
                }
                var ki = new KeyValuePair <ChromKey, int>(chromKey, index);
                _chromIndices[index] = indexPrecursor;
                _chromIds.Add(ki);
            }

            // Shimadzu can't do the necessary product m/z stepping for itself.
            // So, they provide the CE values in their IDs and we need to adjust
            // product m/z values for them to support CE optimization.
            if (fixCEOptForShimadzu)
            {
                FixCEOptForShimadzu();
            }

            if (_chromIds.Count == 0)
            {
                throw new NoSrmDataException(dataFile.FilePath);
            }

            SetPercentComplete(50);
        }
コード例 #2
0
        public ChromatogramDataProvider(MsDataFileImpl dataFile,
                                        ChromFileInfo fileInfo,
                                        IProgressStatus status,
                                        int startPercent,
                                        int endPercent,
                                        IProgressMonitor loader)
            : base(fileInfo, status, startPercent, endPercent, loader)
        {
            _dataFile = dataFile;

            if (_dataFile.IsThermoFile)
            {
                _readMaxMinutes = 4;
            }

            int len = dataFile.ChromatogramCount;

            _chromIndices = new int[len];

            bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
            int  indexPrecursor      = -1;
            var  lastPrecursor       = SignedMz.ZERO;

            for (int i = 0; i < len; i++)
            {
                int    index;
                string id = dataFile.GetChromatogramId(i, out index);

                if (!ChromKey.IsKeyId(id))
                {
                    continue;
                }

                var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
                if (chromKey.Precursor != lastPrecursor)
                {
                    lastPrecursor = chromKey.Precursor;
                    indexPrecursor++;
                }
                var ki = new ChromKeyProviderIdPair(chromKey, index);
                _chromIndices[index] = indexPrecursor;
                _chromIds.Add(ki);
            }

            // Shimadzu can't do the necessary product m/z stepping for itself.
            // So, they provide the CE values in their IDs and we need to adjust
            // product m/z values for them to support CE optimization.
            if (fixCEOptForShimadzu)
            {
                FixCEOptForShimadzu();
            }

            if (_chromIds.Count == 0)
            {
                throw new NoSrmDataException(FileInfo.FilePath);
            }

            // CONSIDER(kaipot): Some way to support mzML files converted from MIDAS wiff files
            _hasMidasSpectra = (dataFile.IsABFile) && SpectraChromDataProvider.HasSpectrumData(dataFile);

            SetPercentComplete(50);
        }
コード例 #3
0
        public ChromatogramDataProvider(MsDataFileImpl dataFile,
                                        ChromFileInfo fileInfo,
                                        IProgressStatus status,
                                        int startPercent,
                                        int endPercent,
                                        IProgressMonitor loader)
            : base(fileInfo, status, startPercent, endPercent, loader)
        {
            _dataFile = dataFile;
            _globalChromatogramExtractor = new GlobalChromatogramExtractor(dataFile);

            if (_dataFile.IsThermoFile)
            {
                _readMaxMinutes = 4;
            }

            int len = dataFile.ChromatogramCount;

            _chromIndices = new int[len];

            bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
            int  indexPrecursor      = -1;
            var  lastPrecursor       = SignedMz.ZERO;

            for (int i = 0; i < len; i++)
            {
                int    index;
                string id = dataFile.GetChromatogramId(i, out index);

                if (!ChromKey.IsKeyId(id))
                {
                    continue;
                }

                var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
                if (chromKey.Precursor != lastPrecursor)
                {
                    lastPrecursor = chromKey.Precursor;
                    indexPrecursor++;
                }
                if (chromKey.Precursor.IsNegative)
                {
                    _sourceHasNegativePolarityData = true;
                }
                else
                {
                    _sourceHasPositivePolarityData = true;
                }
                var ki = new ChromKeyProviderIdPair(chromKey, index);
                _chromIndices[index] = indexPrecursor;
                _chromIds.Add(ki);
            }

            // Shimadzu can't do the necessary product m/z stepping for itself.
            // So, they provide the CE values in their IDs and we need to adjust
            // product m/z values for them to support CE optimization.
            if (fixCEOptForShimadzu)
            {
                FixCEOptForShimadzu();
            }

            if (_chromIds.Count == 0)
            {
                throw new NoSrmDataException(FileInfo.FilePath);
            }

            // CONSIDER: TIC and BPC are not well defined for SRM and produced chromatograms with over 100,000 points in
            // Agilent CE optimization data. So, keep them off for now.
//            foreach (int globalIndex in _globalChromatogramExtractor.GlobalChromatogramIndexes)
//            {
//                _chromIndices[globalIndex] = globalIndex;
//                _chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromId(_globalChromatogramExtractor.GetChromatogramId(globalIndex, out int indexId), false), globalIndex));
//            }

            foreach (var qcTracePair in _globalChromatogramExtractor.QcTraceByIndex)
            {
                _chromIndices[qcTracePair.Key] = qcTracePair.Key;
                _chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromQcTrace(qcTracePair.Value), qcTracePair.Key));
            }

            // CONSIDER(kaipot): Some way to support mzML files converted from MIDAS wiff files
            _hasMidasSpectra = (dataFile.IsABFile) && SpectraChromDataProvider.HasSpectrumData(dataFile);

            _ionMobilityUnits       = dataFile.IonMobilityUnits;
            _hasIonMobilityCombined = dataFile.HasCombinedIonMobilitySpectra;  // When true, data source provides IMS data in 3-array format, which affects spectrum ID format

            SetPercentComplete(50);
        }