/// <summary>
/// Reads modifications from a sequence with embedded modifications,
/// e.g. AM[16.0]VLC[57.0]
/// This results in some loss of precision, since embedded modifications
/// are only accurate to one decimal place. But this is all that is necessary
/// for further use as spectral libraries for SRM method building.
/// </summary>
/// <param name="refSpectra"></param>
private static void ModsFromModifiedSequence(DbRefSpectra refSpectra)
{
string modSeq = refSpectra.PeptideModSeq;
for (int i = 0, iAa = 0; i < modSeq.Length; i++)
{
char c = modSeq[i];
if (c != '[') // Not L10N
{
iAa++;
}
else
{
int iEnd = modSeq.IndexOf(']', ++i); // Not L10N
double modMass;
if (double.TryParse(modSeq.Substring(i, iEnd - i), out modMass))
{
if (refSpectra.Modifications == null)
{
refSpectra.Modifications = new List <DbModification>();
}
refSpectra.Modifications.Add(new DbModification
{
RefSpectra = refSpectra,
Mass = modMass,
Position = iAa
});
i = iEnd;
iAa++;
}
}
}
}
private static DbRefSpectra MakeRefSpectrum(SpectrumInfo spectrum, string peptideSeq, string modifiedPeptideSeq, double precMz, int precChg)
{
var refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = precMz,
PrecursorCharge = precChg,
PeptideModSeq = modifiedPeptideSeq
};
MakeRefSpectrum(spectrum, refSpectra);
return(refSpectra);
}
private static void SaveRedundantSpectra(ISession sessionRedundant,
IEnumerable <SpectrumKeyTime> redundantSpectraIds,
IDictionary <string, long> dictFiles,
DbRefSpectra refSpectra,
Library library)
{
foreach (var specLiteKey in redundantSpectraIds)
{
if (specLiteKey.Key.RedundantId == 0)
{
continue;
}
// If this source file has already been saved, get its database Id.
// Otherwise, save it.
long spectrumSourceId = GetSpecturmSourceId(sessionRedundant, specLiteKey.FilePath, dictFiles);
// Get peaks for the redundant spectrum
var peaksInfo = library.LoadSpectrum(specLiteKey.Key);
var redundantSpectra = new DbRefSpectraRedundant
{
Id = specLiteKey.Key.RedundantId,
PeptideSeq = refSpectra.PeptideSeq,
PrecursorMZ = refSpectra.PrecursorMZ,
PrecursorCharge = refSpectra.PrecursorCharge,
PeptideModSeq = refSpectra.PeptideModSeq,
NumPeaks = (ushort)peaksInfo.Peaks.Count(),
Copies = refSpectra.Copies,
RetentionTime = specLiteKey.Time.RetentionTime,
IonMobilityValue = specLiteKey.Time.IonMobilityValue.GetValueOrDefault(),
IonMobilityType = specLiteKey.Time.IonMobilityType.GetValueOrDefault(),
IonMobilityHighEnergyDriftTimeOffsetMsec = specLiteKey.Time.IonMobilityHighEnergyDriftTimeOffsetMsec,
FileId = spectrumSourceId
};
var peaks = new DbRefSpectraRedundantPeaks
{
RefSpectra = redundantSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
redundantSpectra.Peaks = peaks;
sessionRedundant.Save(redundantSpectra);
}
sessionRedundant.Flush();
sessionRedundant.Clear();
}
private static void MakeRefSpectrum(SpectrumInfo spectrum, DbRefSpectra refSpectra)
{
short copies = (short)spectrum.SpectrumHeaderInfo.GetRankValue(LibrarySpec.PEP_RANK_COPIES);
var peaksInfo = spectrum.SpectrumPeaksInfo;
refSpectra.Copies = copies;
refSpectra.NumPeaks = (ushort)peaksInfo.Peaks.Length;
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
}
private DbRefSpectra RefSpectrumFromPeaks(SpectrumMzInfo spectrum)
{
var peaksInfo = spectrum.SpectrumPeaks;
var refSpectra = new DbRefSpectra
{
PeptideSeq = FastaSequence.StripModifications(spectrum.Key.Sequence),
PrecursorMZ = spectrum.PrecursorMz,
PrecursorCharge = spectrum.Key.Charge,
PeptideModSeq = spectrum.Key.Sequence,
Copies = 1,
NumPeaks = (ushort)peaksInfo.Peaks.Length
};
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
return(refSpectra);
}
public static ICollection <DbRefSpectraPeakAnnotations> Create(DbRefSpectra refSpectra, SpectrumPeaksInfo peaks)
{
List <DbRefSpectraPeakAnnotations> resultList = null;
// Each peak may have more than one annotation
if (peaks.Peaks.Any(p => p.Annotations != null && p.Annotations.Any(a => !SpectrumPeakAnnotation.IsNullOrEmpty(a))))
{
resultList = new List <DbRefSpectraPeakAnnotations>();
var i = 0;
foreach (var peak in peaks.Peaks)
{
if (peak.Annotations != null)
{
foreach (var annotation in peak.Annotations.Where(a => !SpectrumPeakAnnotation.IsNullOrEmpty(a)))
{
var result = new DbRefSpectraPeakAnnotations
{
RefSpectra = refSpectra,
PeakIndex = i,
Name = annotation.Ion.Name,
Formula = annotation.Ion.NeutralFormula,
InchiKey = annotation.Ion.AccessionNumbers.GetInChiKey(),
OtherKeys = annotation.Ion.AccessionNumbers.GetNonInChiKeys(),
Adduct = annotation.Ion.Adduct.ToString(),
Charge = annotation.Ion.Adduct.AdductCharge,
Comment = annotation.Comment,
mzTheoretical = annotation.Ion.MonoisotopicMassMz,
mzObserved = peak.Mz
};
resultList.Add(result);
}
}
i++;
}
}
return(resultList);
}
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));
}
}
}
/// <summary>
/// Minimize any library type to a fully functional BiblioSpec SQLite library.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="library">Existing library to minimize</param>
/// <param name="document">Document for which only used spectra are included in the new library</param>
/// <returns>A new minimized <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary MinimizeLibrary(BiblioSpecLiteSpec librarySpec,
Library library, SrmDocument document)
{
if (!UpdateProgressMessage(string.Format(Resources.BlibDb_MinimizeLibrary_Minimizing_library__0__, library.Name)))
{
return(null);
}
string libAuthority = "unknown.org"; // Not L10N
string libId = library.Name;
// CONSIDER: Use version numbers of the original library?
int libraryRevision = DbLibInfo.INITIAL_LIBRARY_REVISION;
int schemaVersion = 0;
bool saveRetentionTimes = false;
bool saveRedundantLib = false;
var blibLib = library as BiblioSpecLiteLibrary;
if (blibLib != null)
{
string libraryLsid = blibLib.Lsid;
Match matchLsid = REGEX_LSID.Match(libraryLsid);
if (matchLsid.Success)
{
libAuthority = matchLsid.Groups[1].Value;
libId = matchLsid.Groups[2].Value;
}
else
{
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
}
// We will have a RetentionTimes table if schemaVersion if 1 or greater.
saveRetentionTimes = blibLib.SchemaVersion >= 1;
libraryRevision = blibLib.Revision;
schemaVersion = Math.Min(blibLib.SchemaVersion, DbLibInfo.SCHEMA_VERSION_CURRENT);
// If the document has MS1 filtering enabled we will save a minimized version
// of the redundant library, if available.
if (document.Settings.TransitionSettings.FullScan.IsEnabledMs)
{
String redundantLibPath = blibLib.FilePathRedundant;
if (File.Exists(redundantLibPath))
{
string path = BiblioSpecLiteSpec.GetRedundantName(FilePath);
CreateSessionFactory_Redundant(path);
saveRedundantLib = true;
}
}
}
else if (library is BiblioSpecLibrary)
{
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
}
else if (library is XHunterLibrary)
{
libAuthority = XHunterLibrary.DEFAULT_AUTHORITY;
}
else
{
var nistLibrary = library as NistLibrary;
if (nistLibrary != null)
{
libAuthority = NistLibrary.DEFAULT_AUTHORITY;
libId = nistLibrary.Id ?? libId;
}
}
// Use a very specific LSID, since it really only matches this document.
string libLsid = string.Format("urn:lsid:{0}:spectral_libary:bibliospec:nr:minimal:{1}:{2}:{3}.{4}", // Not L10N
libAuthority, libId, Guid.NewGuid(), libraryRevision, schemaVersion);
var dictLibrary = new Dictionary <LibKey, BiblioLiteSpectrumInfo>();
// Hash table to store the database IDs of any source files in the library
// Source file information is available only in Bibliospec libraries, schema version >= 1
var dictFiles = new Dictionary <string, long>();
var dictFilesRedundant = new Dictionary <string, long>();
ISession redundantSession = null;
ITransaction redundantTransaction = null;
int redundantSpectraCount = 0;
try
{
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
var settings = document.Settings;
int peptideCount = document.PeptideCount;
int savedCount = 0;
foreach (var nodePep in document.Peptides)
{
var mods = nodePep.ExplicitMods;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
// Only get library info from precursors that use the desired library
if (!nodeGroup.HasLibInfo || !Equals(nodeGroup.LibInfo.LibraryName, library.Name))
{
continue;
}
TransitionGroup group = nodeGroup.TransitionGroup;
string peptideSeq = group.Peptide.Sequence;
int precursorCharge = group.PrecursorCharge;
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
var calcPre = settings.GetPrecursorCalc(labelType, mods);
var peptideModSeq = calcPre.GetModifiedSequence(peptideSeq, false);
var libKey = new LibKey(peptideModSeq, precursorCharge);
if (dictLibrary.ContainsKey(libKey))
{
continue;
}
// saveRetentionTimes will be false unless this is a BiblioSpec(schemaVersion >=1) library.
if (!saveRetentionTimes)
{
// get the best spectra
foreach (var spectrumInfo in library.GetSpectra(libKey, labelType, LibraryRedundancy.best))
{
DbRefSpectra refSpectra = MakeRefSpectrum(spectrumInfo,
peptideSeq,
peptideModSeq,
nodeGroup.PrecursorMz,
precursorCharge);
session.Save(refSpectra);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey, refSpectra.Copies,
refSpectra.NumPeaks,
(int)(refSpectra.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
}
session.Flush();
session.Clear();
}
// This is a BiblioSpec(schemaVersion >=1) library.
else
{
// get all the spectra, including the redundant ones if this library has any
var spectra = library.GetSpectra(libKey, labelType, LibraryRedundancy.all_redundant).ToArray();
// Avoid saving to the RefSpectra table for isotope label types that have no spectra
if (spectra.Length == 0)
{
continue;
}
DbRefSpectra refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = nodeGroup.PrecursorMz,
PrecursorCharge = precursorCharge,
PeptideModSeq = peptideModSeq
};
// Get all the information for this reference spectrum.
// For BiblioSpec (schema ver >= 1), this can include retention time information
// for this spectrum as well as any redundant spectra for the peptide.
// Ids of spectra in the redundant library, where available, are also returned.
var redundantSpectraKeys = new List <SpectrumKeyTime>();
BuildRefSpectra(document, session, refSpectra, spectra, dictFiles, redundantSpectraKeys);
session.Save(refSpectra);
session.Flush();
session.Clear();
// TODO(nicksh): preserve retention time information.
var retentionTimesByFileId = default(IndexedRetentionTimes);
var driftTimesByFileId = default(IndexedIonMobilities);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey,
refSpectra.Copies,
refSpectra.NumPeaks,
(int)(refSpectra.Id ?? 0),
retentionTimesByFileId,
driftTimesByFileId));
// Save entries in the redundant library.
if (saveRedundantLib && redundantSpectraKeys.Count > 0)
{
if (redundantSession == null)
{
redundantSession = OpenWriteSession_Redundant();
redundantTransaction = redundantSession.BeginTransaction();
}
SaveRedundantSpectra(redundantSession, redundantSpectraKeys, dictFilesRedundant, refSpectra, library);
redundantSpectraCount += redundantSpectraKeys.Count;
}
}
}
savedCount++;
if (!UpdateProgress(peptideCount, savedCount))
{
return(null);
}
}
// Simulate ctime(d), which is what BlibBuild uses.
string createTime = string.Format("{0:ddd MMM dd HH:mm:ss yyyy}", DateTime.Now); // Not L10N? different date/time format in different countries
DbLibInfo libInfo = new DbLibInfo
{
LibLSID = libLsid,
CreateTime = createTime,
NumSpecs = dictLibrary.Count,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
if (redundantTransaction != null)
{
var scoreType = new DbScoreTypes {
Id = 0, ScoreType = "UNKNOWN"
}; // Not L10N
redundantSession.Save(scoreType);
libInfo = new DbLibInfo
{
LibLSID = libLsid.Replace(":nr:", ":redundant:"), // Not L10N
CreateTime = createTime,
NumSpecs = redundantSpectraCount,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
redundantSession.Save(libInfo);
redundantSession.Flush();
redundantSession.Clear();
redundantTransaction.Commit();
}
}
}
finally
{
if (redundantTransaction != null)
{
redundantTransaction.Dispose();
}
if (redundantSession != null)
{
redundantSession.Dispose();
}
}
var libraryEntries = dictLibrary.Values.ToArray();
return(new BiblioSpecLiteLibrary(librarySpec, libLsid, libraryRevision, schemaVersion,
libraryEntries, FileStreamManager.Default));
}
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 DbRefSpectra RefSpectrumFromPeaks(SpectrumMzInfo spectrum)
{
var peaksInfo = spectrum.SpectrumPeaks;
var refSpectra = new DbRefSpectra
{
PeptideSeq = FastaSequence.StripModifications(spectrum.Key.Sequence),
PrecursorMZ = spectrum.PrecursorMz,
PrecursorCharge = spectrum.Key.Charge,
PeptideModSeq = spectrum.Key.Sequence,
Copies = 1,
NumPeaks = (ushort)peaksInfo.Peaks.Length
};
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
return refSpectra;
}
private static void SaveRedundantSpectra(ISession sessionRedundant,
IEnumerable<SpectrumKeyTime> redundantSpectraIds,
IDictionary<string, long> dictFiles,
DbRefSpectra refSpectra,
Library library)
{
foreach (var specLiteKey in redundantSpectraIds)
{
if (specLiteKey.Key.RedundantId == 0)
{
continue;
}
// If this source file has already been saved, get its database Id.
// Otherwise, save it.
long spectrumSourceId = GetSpecturmSourceId(sessionRedundant, specLiteKey.FilePath, dictFiles);
// Get peaks for the redundant spectrum
var peaksInfo = library.LoadSpectrum(specLiteKey.Key);
var redundantSpectra = new DbRefSpectraRedundant
{
Id = specLiteKey.Key.RedundantId,
PeptideSeq = refSpectra.PeptideSeq,
PrecursorMZ = refSpectra.PrecursorMZ,
PrecursorCharge = refSpectra.PrecursorCharge,
PeptideModSeq = refSpectra.PeptideModSeq,
NumPeaks = (ushort) peaksInfo.Peaks.Count(),
Copies = refSpectra.Copies,
RetentionTime = specLiteKey.Time.RetentionTime,
IonMobilityValue = specLiteKey.Time.IonMobilityValue.GetValueOrDefault(),
IonMobilityType = specLiteKey.Time.IonMobilityType.GetValueOrDefault(),
IonMobilityHighEnergyDriftTimeOffsetMsec = specLiteKey.Time.IonMobilityHighEnergyDriftTimeOffsetMsec,
FileId = spectrumSourceId
};
var peaks = new DbRefSpectraRedundantPeaks
{
RefSpectra = redundantSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
redundantSpectra.Peaks = peaks;
sessionRedundant.Save(redundantSpectra);
}
sessionRedundant.Flush();
sessionRedundant.Clear();
}
/// <summary>
/// Reads modifications from a sequence with embedded modifications,
/// e.g. AM[16.0]VLC[57.0]
/// This results in some loss of precision, since embedded modifications
/// are only accurate to one decimal place. But this is all that is necessary
/// for further use as spectral libraries for SRM method building.
/// </summary>
/// <param name="refSpectra"></param>
private static void ModsFromModifiedSequence(DbRefSpectra refSpectra)
{
string modSeq = refSpectra.PeptideModSeq;
for (int i = 0, iAa = 0; i < modSeq.Length; i++)
{
char c = modSeq[i];
if (c != '[') // Not L10N
iAa++;
else
{
int iEnd = modSeq.IndexOf(']', ++i); // Not L10N
double modMass;
if (double.TryParse(modSeq.Substring(i, iEnd - i), out modMass))
{
if (refSpectra.Modifications == null)
refSpectra.Modifications = new List<DbModification>();
refSpectra.Modifications.Add(new DbModification
{
RefSpectra = refSpectra,
Mass = modMass,
Position = iAa
});
i = iEnd;
iAa++;
}
}
}
}
private static void MakeRefSpectrum(SpectrumInfo spectrum, DbRefSpectra refSpectra)
{
short copies = (short)spectrum.SpectrumHeaderInfo.GetRankValue(LibrarySpec.PEP_RANK_COPIES);
var peaksInfo = spectrum.SpectrumPeaksInfo;
refSpectra.Copies = copies;
refSpectra.NumPeaks = (ushort) peaksInfo.Peaks.Length;
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
}
private static DbRefSpectra MakeRefSpectrum(SpectrumInfo spectrum, string peptideSeq, string modifiedPeptideSeq, double precMz, int precChg)
{
var refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = precMz,
PrecursorCharge = precChg,
PeptideModSeq = modifiedPeptideSeq
};
MakeRefSpectrum(spectrum, refSpectra);
return refSpectra;
}
/// <summary>
/// Minimize any library type to a fully functional BiblioSpec SQLite library.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="library">Existing library to minimize</param>
/// <param name="document">Document for which only used spectra are included in the new library</param>
/// <returns>A new minimized <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary MinimizeLibrary(BiblioSpecLiteSpec librarySpec,
Library library, SrmDocument document)
{
if (!UpdateProgressMessage(string.Format(Resources.BlibDb_MinimizeLibrary_Minimizing_library__0__, library.Name)))
return null;
string libAuthority = "unknown.org"; // Not L10N
string libId = library.Name;
// CONSIDER: Use version numbers of the original library?
int libraryRevision = DbLibInfo.INITIAL_LIBRARY_REVISION;
int schemaVersion = 0;
bool saveRetentionTimes = false;
bool saveRedundantLib = false;
var blibLib = library as BiblioSpecLiteLibrary;
if (blibLib != null)
{
string libraryLsid = blibLib.Lsid;
Match matchLsid = REGEX_LSID.Match(libraryLsid);
if (matchLsid.Success)
{
libAuthority = matchLsid.Groups[1].Value;
libId = matchLsid.Groups[2].Value;
}
else
{
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
}
// We will have a RetentionTimes table if schemaVersion if 1 or greater.
saveRetentionTimes = blibLib.SchemaVersion >= 1;
libraryRevision = blibLib.Revision;
schemaVersion = Math.Min(blibLib.SchemaVersion, DbLibInfo.SCHEMA_VERSION_CURRENT);
// If the document has MS1 filtering enabled we will save a minimized version
// of the redundant library, if available.
if(document.Settings.TransitionSettings.FullScan.IsEnabledMs)
{
String redundantLibPath = blibLib.FilePathRedundant;
if(File.Exists(redundantLibPath))
{
string path = BiblioSpecLiteSpec.GetRedundantName(FilePath);
CreateSessionFactory_Redundant(path);
saveRedundantLib = true;
}
}
}
else if (library is BiblioSpecLibrary)
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
else if (library is XHunterLibrary)
libAuthority = XHunterLibrary.DEFAULT_AUTHORITY;
else
{
var nistLibrary = library as NistLibrary;
if (nistLibrary != null)
{
libAuthority = NistLibrary.DEFAULT_AUTHORITY;
libId = nistLibrary.Id ?? libId;
}
}
// Use a very specific LSID, since it really only matches this document.
string libLsid = string.Format("urn:lsid:{0}:spectral_libary:bibliospec:nr:minimal:{1}:{2}:{3}.{4}", // Not L10N
libAuthority, libId, Guid.NewGuid(), libraryRevision, schemaVersion);
var dictLibrary = new Dictionary<LibKey, BiblioLiteSpectrumInfo>();
// Hash table to store the database IDs of any source files in the library
// Source file information is available only in Bibliospec libraries, schema version >= 1
var dictFiles = new Dictionary<string, long>();
var dictFilesRedundant = new Dictionary<string, long>();
ISession redundantSession = null;
ITransaction redundantTransaction = null;
int redundantSpectraCount = 0;
try
{
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
var settings = document.Settings;
int peptideCount = document.PeptideCount;
int savedCount = 0;
foreach (var nodePep in document.Peptides)
{
var mods = nodePep.ExplicitMods;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
// Only get library info from precursors that use the desired library
if (!nodeGroup.HasLibInfo || !Equals(nodeGroup.LibInfo.LibraryName, library.Name))
continue;
TransitionGroup group = nodeGroup.TransitionGroup;
string peptideSeq = group.Peptide.Sequence;
int precursorCharge = group.PrecursorCharge;
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
var calcPre = settings.GetPrecursorCalc(labelType, mods);
var peptideModSeq = calcPre.GetModifiedSequence(peptideSeq, false);
var libKey = new LibKey(peptideModSeq, precursorCharge);
if (dictLibrary.ContainsKey(libKey))
continue;
// saveRetentionTimes will be false unless this is a BiblioSpec(schemaVersion >=1) library.
if (!saveRetentionTimes)
{
// get the best spectra
foreach (var spectrumInfo in library.GetSpectra(libKey, labelType, LibraryRedundancy.best))
{
DbRefSpectra refSpectra = MakeRefSpectrum(spectrumInfo,
peptideSeq,
peptideModSeq,
nodeGroup.PrecursorMz,
precursorCharge);
session.Save(refSpectra);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey, refSpectra.Copies,
refSpectra.NumPeaks,
(int) (refSpectra.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
}
session.Flush();
session.Clear();
}
// This is a BiblioSpec(schemaVersion >=1) library.
else
{
// get all the spectra, including the redundant ones if this library has any
var spectra = library.GetSpectra(libKey, labelType, LibraryRedundancy.all_redundant).ToArray();
// Avoid saving to the RefSpectra table for isotope label types that have no spectra
if (spectra.Length == 0)
continue;
DbRefSpectra refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = nodeGroup.PrecursorMz,
PrecursorCharge = precursorCharge,
PeptideModSeq = peptideModSeq
};
// Get all the information for this reference spectrum.
// For BiblioSpec (schema ver >= 1), this can include retention time information
// for this spectrum as well as any redundant spectra for the peptide.
// Ids of spectra in the redundant library, where available, are also returned.
var redundantSpectraKeys = new List<SpectrumKeyTime>();
BuildRefSpectra(document, session, refSpectra, spectra, dictFiles, redundantSpectraKeys);
session.Save(refSpectra);
session.Flush();
session.Clear();
// TODO(nicksh): preserve retention time information.
var retentionTimesByFileId = default(IndexedRetentionTimes);
var driftTimesByFileId = default(IndexedIonMobilities);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey,
refSpectra.Copies,
refSpectra.NumPeaks,
(int) (refSpectra.Id ?? 0),
retentionTimesByFileId,
driftTimesByFileId));
// Save entries in the redundant library.
if (saveRedundantLib && redundantSpectraKeys.Count > 0)
{
if (redundantSession == null)
{
redundantSession = OpenWriteSession_Redundant();
redundantTransaction = redundantSession.BeginTransaction();
}
SaveRedundantSpectra(redundantSession, redundantSpectraKeys, dictFilesRedundant, refSpectra, library);
redundantSpectraCount += redundantSpectraKeys.Count;
}
}
}
savedCount++;
if (!UpdateProgress(peptideCount, savedCount))
return null;
}
// Simulate ctime(d), which is what BlibBuild uses.
string createTime = string.Format("{0:ddd MMM dd HH:mm:ss yyyy}", DateTime.Now); // Not L10N? different date/time format in different countries
DbLibInfo libInfo = new DbLibInfo
{
LibLSID = libLsid,
CreateTime = createTime,
NumSpecs = dictLibrary.Count,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
if (redundantTransaction != null)
{
var scoreType = new DbScoreTypes {Id = 0, ScoreType = "UNKNOWN"}; // Not L10N
redundantSession.Save(scoreType);
libInfo = new DbLibInfo
{
LibLSID = libLsid.Replace(":nr:", ":redundant:"), // Not L10N
CreateTime = createTime,
NumSpecs = redundantSpectraCount,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
redundantSession.Save(libInfo);
redundantSession.Flush();
redundantSession.Clear();
redundantTransaction.Commit();
}
}
}
finally
{
if(redundantTransaction != null)
{
redundantTransaction.Dispose();
}
if (redundantSession != null)
{
redundantSession.Dispose();
}
}
var libraryEntries = dictLibrary.Values.ToArray();
return new BiblioSpecLiteLibrary(librarySpec, libLsid, libraryRevision, schemaVersion,
libraryEntries, FileStreamManager.Default);
}
