Ejemplo n.º 1
0
 public SpectrumKeyTime(SpectrumLiteKey key, DbRetentionTimes time, string filePath)
 {
     Key      = key;
     Time     = time;
     FilePath = filePath;
 }
Ejemplo n.º 2
0
 public SpectrumKeyTime(SpectrumLiteKey key, DbRetentionTimes time, string filePath)
 {
     Key = key;
     Time = time;
     FilePath = filePath;
 }
Ejemplo n.º 3
0
        private void BuildRefSpectra(SrmDocument document,
                                     ISession session,
                                     DbRefSpectra refSpectra,
                                     SpectrumInfo[] spectra, // Yes, this could be IEnumerable, but then Resharper throws bogus warnings about possible multiple enumeration
                                     IDictionary <string, long> dictFiles,
                                     ICollection <SpectrumKeyTime> redundantSpectraKeys)
        {
            bool foundBestSpectrum = false;

            foreach (SpectrumInfo spectrum in spectra)
            {
                if (spectrum.IsBest)
                {
                    if (foundBestSpectrum)
                    {
                        throw new InvalidDataException(
                                  string.Format(Resources.BlibDb_BuildRefSpectra_Multiple_reference_spectra_found_for_peptide__0__in_the_library__1__,
                                                refSpectra.PeptideModSeq, FilePath));
                    }

                    foundBestSpectrum = true;

                    MakeRefSpectrum(spectrum, refSpectra);
                }


                // Determine if this spectrum is from a file that is in the document.
                // If it is not, do not save the retention time for this spectrum, and do not
                // add it to the redundant library. However, if this is the reference (best) spectrum
                // we must save its retention time.
                // NOTE: Spectra not used in the results get used for too much now for this to be useful
//                var matchingFile = document.Settings.HasResults
//                    ? document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(spectrum.FilePath))
//                    : null;
//                if (!spectrum.IsBest && matchingFile == null)
//                    continue;

                // If this source file has already been saved, get its database Id.
                // Otherwise, save it.
                long spectrumSourceId = GetSpecturmSourceId(session, spectrum.FilePath, dictFiles);

                // spectrumKey in the SpectrumInfo is an integer for reference(best) spectra,
                // or object of type SpectrumLiteKey for redundant spectra
                object key         = spectrum.SpectrumKey;
                var    specLiteKey = key as SpectrumLiteKey;

                var dbRetentionTimes = new DbRetentionTimes
                {
                    RedundantRefSpectraId = specLiteKey != null ? specLiteKey.RedundantId : 0,
                    RetentionTime         = spectrum.RetentionTime,
                    SpectrumSourceId      = spectrumSourceId,
                    BestSpectrum          = spectrum.IsBest ? 1 : 0,
                    IonMobilityType       = 0,
                    IonMobilityValue      = 0,
                };
                if (null != spectrum.IonMobilityInfo)
                {
                    if (spectrum.IonMobilityInfo.IsCollisionalCrossSection)
                    {
                        dbRetentionTimes.IonMobilityType =
                            (int)BiblioSpecLiteLibrary.IonMobilityType.collisionalCrossSection;
                    }
                    else
                    {
                        dbRetentionTimes.IonMobilityType = (int)BiblioSpecLiteLibrary.IonMobilityType.driftTime;
                    }
                    dbRetentionTimes.IonMobilityValue = spectrum.IonMobilityInfo.Value;
                    dbRetentionTimes.IonMobilityHighEnergyDriftTimeOffsetMsec = spectrum.IonMobilityInfo.HighEnergyDriftTimeOffsetMsec;
                }

                if (refSpectra.RetentionTimes == null)
                {
                    refSpectra.RetentionTimes = new List <DbRetentionTimes>();
                }

                refSpectra.RetentionTimes.Add(dbRetentionTimes);

                if (specLiteKey != null)
                {
                    redundantSpectraKeys.Add(new SpectrumKeyTime(specLiteKey, dbRetentionTimes, spectrum.FilePath));
                }
            }
        }
Ejemplo n.º 4
0
        private void BuildRefSpectra(SrmDocument document,
            ISession session,
            DbRefSpectra refSpectra,
            SpectrumInfo[] spectra, // Yes, this could be IEnumerable, but then Resharper throws bogus warnings about possible multiple enumeration
            IDictionary<string, long> dictFiles,
            ICollection<SpectrumKeyTime> redundantSpectraKeys)
        {
            bool foundBestSpectrum = false;

            foreach(SpectrumInfo spectrum in spectra)
            {
                if(spectrum.IsBest)
                {
                    if(foundBestSpectrum)
                    {
                        throw new InvalidDataException(
                            string.Format(Resources.BlibDb_BuildRefSpectra_Multiple_reference_spectra_found_for_peptide__0__in_the_library__1__,
                                          refSpectra.PeptideModSeq, FilePath));
                    }

                    foundBestSpectrum = true;

                    MakeRefSpectrum(spectrum, refSpectra);
                }

                // Determine if this spectrum is from a file that is in the document.
                // If it is not, do not save the retention time for this spectrum, and do not
                // add it to the redundant library. However, if this is the reference (best) spectrum
                // we must save its retention time.
                // NOTE: Spectra not used in the results get used for too much now for this to be useful
            //                var matchingFile = document.Settings.HasResults
            //                    ? document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(spectrum.FilePath))
            //                    : null;
            //                if (!spectrum.IsBest && matchingFile == null)
            //                    continue;

                // If this source file has already been saved, get its database Id.
                // Otherwise, save it.
                long spectrumSourceId = GetSpecturmSourceId(session, spectrum.FilePath, dictFiles);

                // spectrumKey in the SpectrumInfo is an integer for reference(best) spectra,
                // or object of type SpectrumLiteKey for redundant spectra
                object key = spectrum.SpectrumKey;
                var specLiteKey = key as SpectrumLiteKey;

                var dbRetentionTimes = new DbRetentionTimes
                {
                    RedundantRefSpectraId = specLiteKey != null ? specLiteKey.RedundantId : 0,
                    RetentionTime = spectrum.RetentionTime,
                    SpectrumSourceId = spectrumSourceId,
                    BestSpectrum = spectrum.IsBest ? 1 : 0,
                    IonMobilityType = 0,
                    IonMobilityValue = 0,
                };
                if (null != spectrum.IonMobilityInfo)
                {
                    if (spectrum.IonMobilityInfo.IsCollisionalCrossSection)
                    {
                        dbRetentionTimes.IonMobilityType =
                            (int) BiblioSpecLiteLibrary.IonMobilityType.collisionalCrossSection;
                    }
                    else
                    {
                        dbRetentionTimes.IonMobilityType = (int) BiblioSpecLiteLibrary.IonMobilityType.driftTime;
                    }
                    dbRetentionTimes.IonMobilityValue = spectrum.IonMobilityInfo.Value;
                    dbRetentionTimes.IonMobilityHighEnergyDriftTimeOffsetMsec = spectrum.IonMobilityInfo.HighEnergyDriftTimeOffsetMsec;
                }

                if (refSpectra.RetentionTimes == null)
                    refSpectra.RetentionTimes = new List<DbRetentionTimes>();

                refSpectra.RetentionTimes.Add(dbRetentionTimes);

                if (specLiteKey != null)
                {
                    redundantSpectraKeys.Add(new SpectrumKeyTime(specLiteKey, dbRetentionTimes, spectrum.FilePath));
                }
            }
        }