public SpectrumKeyTime(SpectrumLiteKey key, DbRetentionTimes time, string filePath)
{
Key = key;
Time = time;
FilePath = filePath;
}
public SpectrumKeyTime(SpectrumLiteKey key, DbRetentionTimes time, string filePath)
{
Key = key;
Time = time;
FilePath = filePath;
}
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));
}
}
}
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));
}
}
}
