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);
}
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);
}
public static void AddSpectra(MidasLibSpec libSpec, MsDataFilePath[] resultsFiles, SrmDocument doc, ILoadMonitor monitor, out List <MsDataFilePath> failedFiles)
{
// Get spectra from results files
var newSpectra = new List <DbSpectrum>();
var progress = new ProgressStatus(string.Empty).ChangeMessage(Resources.MidasLibrary_AddSpectra_Reading_MIDAS_spectra);
const int percentResultsFiles = 80;
failedFiles = new List <MsDataFilePath>();
for (var i = 0; i < resultsFiles.Length; i++)
{
var resultsFile = resultsFiles[i];
try
{
monitor.UpdateProgress(progress.ChangePercentComplete(i * percentResultsFiles / resultsFiles.Length));
var filePath = resultsFile.GetFilePath();
if (File.Exists(filePath))
{
var sampleIndex = resultsFile.GetSampleIndex();
using (var msd = new MsDataFileImpl(filePath, sampleIndex == -1 ? 0 : sampleIndex, resultsFile.GetLockMassParameters(), requireVendorCentroidedMS2: true))
{
if (ChromatogramDataProvider.HasChromatogramData(msd) && SpectraChromDataProvider.HasSpectrumData(msd))
{
var chromPrecursors = ReadChromPrecursorsFromMsd(msd, monitor).ToList();
newSpectra.AddRange(ReadDbSpectraFromMsd(msd, monitor));
MatchSpectraToChrom(newSpectra, chromPrecursors, monitor);
}
}
MatchSpectraToPeptides(newSpectra, doc, monitor);
}
else
{
failedFiles.Add(resultsFile);
}
}
catch (Exception x)
{
monitor.UpdateProgress(progress.ChangeErrorException(x));
failedFiles.Add(resultsFile);
}
if (monitor.IsCanceled)
{
monitor.UpdateProgress(progress.Cancel());
return;
}
}
if (!newSpectra.Any())
{
monitor.UpdateProgress(progress.Complete());
return;
}
progress = progress.ChangePercentComplete(percentResultsFiles);
monitor.UpdateProgress(progress);
// Add spectra to library
var midasLib = !File.Exists(libSpec.FilePath) ? Create(libSpec) : Load(libSpec, monitor);
if (midasLib == null)
{
monitor.UpdateProgress(progress.ChangeErrorException(new Exception(Resources.MidasLibrary_AddSpectra_Error_loading_MIDAS_library_for_adding_spectra_)));
return;
}
progress = progress.ChangeMessage(Resources.MidasLibrary_AddSpectra_Adding_spectra_to_MIDAS_library);
monitor.UpdateProgress(progress);
var results = new Dictionary <string, DbResultsFile>();
if (midasLib._spectra != null)
{
foreach (var kvp in midasLib._spectra)
{
results[kvp.Key.FilePath] = kvp.Key;
}
}
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(libSpec.FilePath, typeof(MidasLibrary), false))
using (var session = new SessionWithLock(sessionFactory.OpenSession(), new ReaderWriterLock(), true))
using (var transaction = session.BeginTransaction())
{
for (var i = 0; i < newSpectra.Count; i++)
{
if (monitor.IsCanceled)
{
transaction.Rollback();
monitor.UpdateProgress(progress.Cancel());
return;
}
var spectrum = newSpectra[i];
monitor.UpdateProgress(progress.ChangePercentComplete(percentResultsFiles + (int)(100.0 * i / newSpectra.Count)));
DbResultsFile resultsFile;
if (!results.TryGetValue(spectrum.ResultsFile.FilePath, out resultsFile))
{
resultsFile = new DbResultsFile(spectrum.ResultsFile)
{
Id = null
};
results[spectrum.ResultsFile.FilePath] = resultsFile;
session.SaveOrUpdate(resultsFile);
}
else if (midasLib._spectra != null)
{
List <DbSpectrum> existingSpectra;
if (midasLib._spectra.TryGetValue(resultsFile, out existingSpectra) &&
existingSpectra.Any(x => Equals(x.ResultsFile.FilePath, spectrum.ResultsFile.FilePath) &&
Equals(x.PrecursorMz, spectrum.PrecursorMz) &&
Equals(x.RetentionTime, spectrum.RetentionTime)))
{
// This spectrum already exists in the library
continue;
}
}
var spectrumNewDisconnected = new DbSpectrum(spectrum)
{
Id = null, ResultsFile = resultsFile
};
session.SaveOrUpdate(spectrumNewDisconnected);
}
transaction.Commit();
monitor.UpdateProgress(progress.Complete());
}
}
