private DbSpectrum(DbResultsFile resultsFile, double precursorMz, double?matchedPrecursorMz, double retentionTime, byte[] mzBytes, byte[] intensityBytes)
{
PrecursorMz = precursorMz;
MatchedPrecursorMz = matchedPrecursorMz;
ResultsFile = resultsFile;
RetentionTime = retentionTime;
MzBytes = mzBytes;
IntensityBytes = intensityBytes;
}
private DbSpectrum(DbResultsFile resultsFile, double precursorMz, double?matchedPrecursorMz, string documentPeptide, int?documentPrecursorCharge, double retentionTime, byte[] mzBytes, byte[] intensityBytes)
{
PrecursorMz = precursorMz;
MatchedPrecursorMz = matchedPrecursorMz;
DocumentPeptide = documentPeptide;
DocumentPrecursorCharge = documentPrecursorCharge;
ResultsFile = resultsFile;
RetentionTime = retentionTime;
MzBytes = mzBytes;
IntensityBytes = intensityBytes;
}
public DbResultsFile(DbResultsFile other)
: this(other.FilePath)
{
Id = other.Id;
}
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());
}
}
public DbSpectrum(DbResultsFile resultsFile, double precursorMz, double?matchedPrecursorMz, string documentPeptide, int?documentPrecursorCharge, double retentionTime, double[] mzs, double[] intensities)
: this(resultsFile, precursorMz, matchedPrecursorMz, documentPeptide, documentPrecursorCharge, retentionTime, CompressBytes(mzs), CompressBytes(intensities))
{
}
public DbSpectrum(DbResultsFile resultsFile, double precursorMz, double?matchedPrecursorMz, double retentionTime, double[] mzs, double[] intensities)
: this(resultsFile, precursorMz, matchedPrecursorMz, retentionTime, CompressBytes(mzs), CompressBytes(intensities))
{
}