public Chromatogram(DbChromatogram dbChromatogram)
: this()
{
MzMin = dbChromatogram.MzMin;
MzMax = dbChromatogram.MzMax;
ChromatogramPoints = ImmutableList.ValueOf(dbChromatogram.ChromatogramPoints);
}
private void SaveChromatograms(ICollection <AnalysisChromatograms> analyses, MsDataFile msDataFile)
{
using (ISession session = workspace.OpenWriteSession())
{
ITransaction transaction = session.BeginTransaction();
foreach (AnalysisChromatograms analysis in analyses)
{
var dbPeptideAnalysis = session.Get <DbPeptideFileAnalysis>(analysis.PeptideFileAnalysis.Id);
if (dbPeptideAnalysis == null)
{
continue;
}
dbPeptideAnalysis.Times = analysis.Times.ToArray();
dbPeptideAnalysis.ScanIndexes = analysis.ScanIndexes.ToArray();
dbPeptideAnalysis.HasChromatograms = true;
session.Update(dbPeptideAnalysis);
var dbChromatogramDict = dbPeptideAnalysis.GetChromatogramDict();
foreach (Chromatogram chromatogram in analysis.Chromatograms)
{
DbChromatogram dbChromatogram;
if (!dbChromatogramDict.TryGetValue(chromatogram.MzKey, out dbChromatogram))
{
dbChromatogram = new DbChromatogram
{
PeptideFileAnalysis = dbPeptideAnalysis,
MzKey = chromatogram.MzKey,
};
}
dbChromatogram.IntensitiesBytes = ArrayConverter.ToBytes(chromatogram.Intensities.ToArray());
dbChromatogram.PeakMzsBytes = ArrayConverter.ToBytes(chromatogram.PeakMzs.ToArray());
dbChromatogram.Mz = chromatogram.Mz;
session.SaveOrUpdate(dbChromatogram);
}
}
if (msDataFile != null)
{
msDataFile.MsDataFileData.Save(session);
}
transaction.Commit();
}
foreach (var analysis in analyses)
{
Debug.Assert(_activePeptideFileAnalysisIds.Contains(analysis.PeptideFileAnalysis.Id.Value));
analysis.PeptideFileAnalysis.HasChromatograms = true;
}
}
private void SaveChromatograms(ChromatogramTask chromatogramTask, ICollection<AnalysisChromatograms> analyses, bool finished)
{
if (analyses.Count == 0)
{
return;
}
if (!IsRunning())
{
return;
}
_workspace.RunOnEventQueue(() =>
{
if (
chromatogramTask.Workspace.CompareSettings(_workspace)
.HasChromatogramMassChange)
{
return;
}
foreach (var analysisChromatograms in analyses)
{
PeptideAnalysis peptideAnalysis;
_workspace.PeptideAnalyses.TryGetValue(
analysisChromatograms.PeptideAnalysisId, out peptideAnalysis);
if (peptideAnalysis == null ||
0 == peptideAnalysis.GetChromatogramRefCount())
{
continue;
}
var peptideFileAnalysis =
peptideAnalysis.GetFileAnalysis(
analysisChromatograms.PeptideFileAnalysisId);
if (peptideFileAnalysis == null)
{
continue;
}
peptideFileAnalysis.SetChromatograms(analysisChromatograms);
}
});
if (!chromatogramTask.CanSave())
{
return;
}
using (_session = _workspace.OpenWriteSession())
{
// TODO(nicksh)
// if (chromatogramTask.WorkspaceChange.MassVersion != _workspace.SavedWorkspaceChange.MassVersion)
// {
// return;
// }
_session.BeginTransaction();
foreach (AnalysisChromatograms analysis in analyses)
{
if (!IsRunning())
{
return;
}
var dbPeptideFileAnalysis = _session.Get<DbPeptideFileAnalysis>(analysis.PeptideFileAnalysisId);
if (dbPeptideFileAnalysis == null)
{
continue;
}
if (analysis.MinCharge != dbPeptideFileAnalysis.PeptideAnalysis.MinCharge
|| analysis.MaxCharge != dbPeptideFileAnalysis.PeptideAnalysis.MaxCharge)
{
continue;
}
foreach (DbChromatogramSet dbChromatogramSet in _session.CreateCriteria(typeof(DbChromatogramSet))
.Add(Restrictions.Eq("PeptideFileAnalysis", dbPeptideFileAnalysis)).List())
{
foreach (DbChromatogram dbChromatogram in _session.CreateCriteria(typeof(DbChromatogram))
.Add(Restrictions.Eq("ChromatogramSet", dbChromatogramSet)).List())
{
_session.Delete(dbChromatogram);
}
_session.Delete(dbChromatogramSet);
}
dbPeptideFileAnalysis.ChromatogramSet = null;
_session.Update(dbPeptideFileAnalysis);
_session.Flush();
dbPeptideFileAnalysis.ChromatogramSet = new DbChromatogramSet
{
PeptideFileAnalysis = dbPeptideFileAnalysis,
Times = analysis.Times.ToArray(),
ScanIndexes = analysis.ScanIndexes.ToArray(),
ChromatogramCount = analysis.Chromatograms.Count,
};
bool noPoints = false;
if (dbPeptideFileAnalysis.ChromatogramSet.Times.Length == 0)
{
noPoints = true;
dbPeptideFileAnalysis.ChromatogramSet.Times = new double[]{0};
dbPeptideFileAnalysis.ChromatogramSet.ScanIndexes = new int[]{0};
}
_session.Save(dbPeptideFileAnalysis.ChromatogramSet);
foreach (Chromatogram chromatogram in analysis.Chromatograms)
{
DbChromatogram dbChromatogram = new DbChromatogram
{
ChromatogramSet = dbPeptideFileAnalysis.ChromatogramSet,
MzKey = chromatogram.MzKey,
ChromatogramPoints = chromatogram.Points,
MzRange = chromatogram.MzRange,
};
if (noPoints)
{
dbChromatogram.ChromatogramPoints = new []{new ChromatogramPoint(), };
}
_session.Save(dbChromatogram);
}
_session.Update(dbPeptideFileAnalysis);
_session.Save(new DbChangeLog(_workspace, dbPeptideFileAnalysis.PeptideAnalysis));
}
if (chromatogramTask.MsDataFile.IsBinaryDirty)
{
chromatogramTask.MsDataFile.SaveBinary(_session);
}
chromatogramTask.UpdateLock(_session);
_session.Transaction.Commit();
}
}
private void SaveChromatograms(ChromatogramTask chromatogramTask, ICollection <AnalysisChromatograms> analyses, bool finished)
{
if (analyses.Count == 0)
{
return;
}
if (!IsRunning())
{
return;
}
_workspace.RunOnEventQueue(() =>
{
if (
chromatogramTask.Workspace.CompareSettings(_workspace)
.HasChromatogramMassChange)
{
return;
}
foreach (var analysisChromatograms in analyses)
{
PeptideAnalysis peptideAnalysis;
_workspace.PeptideAnalyses.TryGetValue(
analysisChromatograms.PeptideAnalysisId, out peptideAnalysis);
if (peptideAnalysis == null ||
0 == peptideAnalysis.GetChromatogramRefCount())
{
continue;
}
var peptideFileAnalysis =
peptideAnalysis.GetFileAnalysis(
analysisChromatograms.PeptideFileAnalysisId);
if (peptideFileAnalysis == null)
{
continue;
}
peptideFileAnalysis.SetChromatograms(analysisChromatograms);
}
});
if (!chromatogramTask.CanSave())
{
return;
}
using (_session = _workspace.OpenWriteSession())
{
// TODO(nicksh)
// if (chromatogramTask.WorkspaceChange.MassVersion != _workspace.SavedWorkspaceChange.MassVersion)
// {
// return;
// }
_session.BeginTransaction();
foreach (AnalysisChromatograms analysis in analyses)
{
if (!IsRunning())
{
return;
}
var dbPeptideFileAnalysis = _session.Get <DbPeptideFileAnalysis>(analysis.PeptideFileAnalysisId);
if (dbPeptideFileAnalysis == null)
{
continue;
}
if (analysis.MinCharge != dbPeptideFileAnalysis.PeptideAnalysis.MinCharge ||
analysis.MaxCharge != dbPeptideFileAnalysis.PeptideAnalysis.MaxCharge)
{
continue;
}
foreach (DbChromatogramSet dbChromatogramSet in _session.CreateCriteria(typeof(DbChromatogramSet))
.Add(Restrictions.Eq("PeptideFileAnalysis", dbPeptideFileAnalysis)).List())
{
foreach (DbChromatogram dbChromatogram in _session.CreateCriteria(typeof(DbChromatogram))
.Add(Restrictions.Eq("ChromatogramSet", dbChromatogramSet)).List())
{
_session.Delete(dbChromatogram);
}
_session.Delete(dbChromatogramSet);
}
dbPeptideFileAnalysis.ChromatogramSet = null;
_session.Update(dbPeptideFileAnalysis);
_session.Flush();
dbPeptideFileAnalysis.ChromatogramSet = new DbChromatogramSet
{
PeptideFileAnalysis = dbPeptideFileAnalysis,
Times = analysis.Times.ToArray(),
ScanIndexes = analysis.ScanIndexes.ToArray(),
ChromatogramCount = analysis.Chromatograms.Count,
};
bool noPoints = false;
if (dbPeptideFileAnalysis.ChromatogramSet.Times.Length == 0)
{
noPoints = true;
dbPeptideFileAnalysis.ChromatogramSet.Times = new double[] { 0 };
dbPeptideFileAnalysis.ChromatogramSet.ScanIndexes = new int[] { 0 };
}
_session.Save(dbPeptideFileAnalysis.ChromatogramSet);
foreach (Chromatogram chromatogram in analysis.Chromatograms)
{
DbChromatogram dbChromatogram = new DbChromatogram
{
ChromatogramSet = dbPeptideFileAnalysis.ChromatogramSet,
MzKey = chromatogram.MzKey,
ChromatogramPoints = chromatogram.Points,
MzRange = chromatogram.MzRange,
};
if (noPoints)
{
dbChromatogram.ChromatogramPoints = new [] { new ChromatogramPoint(), };
}
_session.Save(dbChromatogram);
}
_session.Update(dbPeptideFileAnalysis);
_session.Save(new DbChangeLog(_workspace, dbPeptideFileAnalysis.PeptideAnalysis));
}
if (chromatogramTask.MsDataFile.IsBinaryDirty)
{
chromatogramTask.MsDataFile.SaveBinary(_session);
}
chromatogramTask.UpdateLock(_session);
_session.Transaction.Commit();
}
}
public Chromatogram(DbChromatogram dbChromatogram)
: this()
{
MzMin = dbChromatogram.MzMin;
MzMax = dbChromatogram.MzMax;
ChromatogramPoints = ImmutableList.ValueOf(dbChromatogram.ChromatogramPoints);
}
private void SaveChromatograms(ICollection<AnalysisChromatograms> analyses, MsDataFile msDataFile)
{
using (ISession session = workspace.OpenWriteSession())
{
ITransaction transaction = session.BeginTransaction();
foreach (AnalysisChromatograms analysis in analyses)
{
var dbPeptideAnalysis = session.Get<DbPeptideFileAnalysis>(analysis.PeptideFileAnalysis.Id);
if (dbPeptideAnalysis == null)
{
continue;
}
dbPeptideAnalysis.Times = analysis.Times.ToArray();
dbPeptideAnalysis.ScanIndexes = analysis.ScanIndexes.ToArray();
dbPeptideAnalysis.HasChromatograms = true;
session.Update(dbPeptideAnalysis);
var dbChromatogramDict = dbPeptideAnalysis.GetChromatogramDict();
foreach (Chromatogram chromatogram in analysis.Chromatograms)
{
DbChromatogram dbChromatogram;
if (!dbChromatogramDict.TryGetValue(chromatogram.MzKey, out dbChromatogram))
{
dbChromatogram = new DbChromatogram
{
PeptideFileAnalysis = dbPeptideAnalysis,
MzKey = chromatogram.MzKey,
};
}
dbChromatogram.IntensitiesBytes = ArrayConverter.ToBytes(chromatogram.Intensities.ToArray());
dbChromatogram.PeakMzsBytes = ArrayConverter.ToBytes(chromatogram.PeakMzs.ToArray());
dbChromatogram.Mz = chromatogram.Mz;
session.SaveOrUpdate(dbChromatogram);
}
}
if (msDataFile != null)
{
msDataFile.MsDataFileData.Save(session);
}
transaction.Commit();
}
foreach (var analysis in analyses)
{
Debug.Assert(_activePeptideFileAnalysisIds.Contains(analysis.PeptideFileAnalysis.Id.Value));
analysis.PeptideFileAnalysis.HasChromatograms = true;
}
}
