/// <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));
}
/// <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);
}
/// <summary>
/// Make a BiblioSpec SQLite library from a list of spectra and their intensities.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="listSpectra">List of existing spectra, by LibKey</param>
/// <param name="libraryName">Name of the library to be created</param>
/// <param name="progressMonitor">Progress monitor to display progress in creating library</param>
/// <returns>A library of type <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary CreateLibraryFromSpectra(BiblioSpecLiteSpec librarySpec,
List <SpectrumMzInfo> listSpectra,
string libraryName,
IProgressMonitor progressMonitor)
{
const string libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
const int majorVer = 1;
const int minorVer = 0;
string libId = libraryName;
// 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(), majorVer, minorVer);
var dictLibrary = new Dictionary <LibKey, BiblioLiteSpectrumInfo>();
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
int progressPercent = 0;
int i = 0;
var status = new ProgressStatus(Resources.BlibDb_CreateLibraryFromSpectra_Creating_spectral_library_for_imported_transition_list);
foreach (var spectrum in listSpectra)
{
++i;
var dbRefSpectrum = RefSpectrumFromPeaks(spectrum);
session.Save(dbRefSpectrum);
dictLibrary.Add(spectrum.Key,
new BiblioLiteSpectrumInfo(spectrum.Key, dbRefSpectrum.Copies,
dbRefSpectrum.NumPeaks,
(int)(dbRefSpectrum.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
{
return(null);
}
int progressNew = (i * 100 / listSpectra.Count);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
}
session.Flush();
session.Clear();
// 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 = majorVer,
MinorVersion = minorVer
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
}
var libraryEntries = dictLibrary.Values.ToArray();
return(new BiblioSpecLiteLibrary(librarySpec, libLsid, majorVer, minorVer,
libraryEntries, FileStreamManager.Default));
}
/// <summary>
/// Make a BiblioSpec SQLite library from a list of spectra and their intensities.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="listSpectra">List of existing spectra, by LibKey</param>
/// <param name="libraryName">Name of the library to be created</param>
/// <param name="progressMonitor">Progress monitor to display progress in creating library</param>
/// <returns>A library of type <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary CreateLibraryFromSpectra(BiblioSpecLiteSpec librarySpec,
List<SpectrumMzInfo> listSpectra,
string libraryName,
IProgressMonitor progressMonitor)
{
const string libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
const int majorVer = 1;
const int minorVer = 0;
string libId = libraryName;
// 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(), majorVer, minorVer);
var dictLibrary = new Dictionary<LibKey, BiblioLiteSpectrumInfo>();
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
int progressPercent = 0;
int i = 0;
var status = new ProgressStatus(Resources.BlibDb_CreateLibraryFromSpectra_Creating_spectral_library_for_imported_transition_list);
foreach (var spectrum in listSpectra)
{
++i;
var dbRefSpectrum = RefSpectrumFromPeaks(spectrum);
session.Save(dbRefSpectrum);
dictLibrary.Add(spectrum.Key,
new BiblioLiteSpectrumInfo(spectrum.Key, dbRefSpectrum.Copies,
dbRefSpectrum.NumPeaks,
(int)(dbRefSpectrum.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
return null;
int progressNew = (i * 100 / listSpectra.Count);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
}
session.Flush();
session.Clear();
// 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 = majorVer,
MinorVersion = minorVer
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
}
var libraryEntries = dictLibrary.Values.ToArray();
return new BiblioSpecLiteLibrary(librarySpec, libLsid, majorVer, minorVer,
libraryEntries, FileStreamManager.Default);
}
