private bool UpdateProgress(ChromatogramTask chromatogramTask, int progress)
{
// TODO(nicksh)
// if (chromatogramTask.WorkspaceChange.MassVersion != _workspace.WorkspaceChange.MassVersion)
// {
// return false;
// }
lock (this)
{
_progress = progress;
return(_isRunning && !_isSuspended);
}
}
private bool UpdateProgress(ChromatogramTask chromatogramTask, int progress)
{
// TODO(nicksh)
// if (chromatogramTask.WorkspaceChange.MassVersion != _workspace.WorkspaceChange.MassVersion)
// {
// return false;
// }
lock(this)
{
_progress = progress;
return _isRunning && !_isSuspended;
}
}
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 GenerateChromatograms(ChromatogramTask chromatogramTask)
{
int totalAnalyses = chromatogramTask.AnalysisChromatograms.Count;
if (totalAnalyses == 0)
{
return;
}
if (!UpdateProgress(chromatogramTask, 0))
{
return;
}
var msDataFile = chromatogramTask.MsDataFile;
MsDataFileUtil.InitMsDataFile(chromatogramTask.Workspace, msDataFile);
var analyses = new List<AnalysisChromatograms>(chromatogramTask.AnalysisChromatograms);
MsDataFileImpl pwizMsDataFileImpl;
var path = _workspace.GetDataFilePath(msDataFile.Name);
try
{
pwizMsDataFileImpl = new MsDataFileImpl(path);
}
catch (Exception exception)
{
ErrorHandler.LogException("Chromatogram Generator", "Error opening " + path, exception);
_workspace.RejectMsDataFile(msDataFile);
return;
}
using (pwizMsDataFileImpl)
{
var completeAnalyses = new List<AnalysisChromatograms>();
int totalScanCount = pwizMsDataFileImpl.SpectrumCount;
var lastTimeInDataFile =
chromatogramTask.MsDataFile.GetTime(chromatogramTask.MsDataFile.GetSpectrumCount() - 1);
double minTime = lastTimeInDataFile;
double maxTime = msDataFile.GetTime(0);
foreach (var analysis in analyses)
{
minTime = Math.Min(minTime, analysis.FirstTime);
maxTime = Math.Max(maxTime, analysis.LastTime);
}
int firstScan = msDataFile.FindScanIndex(minTime);
for (int iScan = firstScan; analyses.Count > 0 && iScan < totalScanCount; iScan++)
{
double time = msDataFile.GetTime(iScan);
int progress = (int)(100 * (time - minTime) / (maxTime - minTime));
progress = Math.Min(progress, 100);
progress = Math.Max(progress, 0);
if (!UpdateProgress(chromatogramTask, progress))
{
return;
}
List<AnalysisChromatograms> activeAnalyses = new List<AnalysisChromatograms>();
double nextTime = Double.MaxValue;
if (msDataFile.GetMsLevel(iScan, pwizMsDataFileImpl) != 1)
{
continue;
}
foreach (var analysis in analyses)
{
nextTime = Math.Min(nextTime, analysis.FirstTime);
if (analysis.FirstTime <= time)
{
activeAnalyses.Add(analysis);
}
}
if (activeAnalyses.Count == 0)
{
int nextScan = msDataFile.FindScanIndex(nextTime);
iScan = Math.Max(iScan, nextScan - 1);
continue;
}
bool lowMemory = IsLowOnMemory();
// If we have exceeded the number of analyses we should be working on at once,
// throw out any that we haven't started.
for (int iAnalysis = activeAnalyses.Count - 1; iAnalysis >= 0
&& (activeAnalyses.Count > _maxConcurrentAnalyses || lowMemory); iAnalysis--)
{
var analysis = activeAnalyses[iAnalysis];
if (analysis.Times.Count > 0)
{
continue;
}
activeAnalyses.RemoveAt(iAnalysis);
analyses.Remove(analysis);
}
double[] mzArray, intensityArray;
pwizMsDataFileImpl.GetSpectrum(iScan, out mzArray, out intensityArray);
if (!pwizMsDataFileImpl.IsCentroided(iScan))
{
var centroider = new Centroider(mzArray, intensityArray);
centroider.GetCentroidedData(out mzArray, out intensityArray);
}
foreach (var analysis in activeAnalyses)
{
var points = new List<ChromatogramPoint>();
foreach (var chromatogram in analysis.Chromatograms)
{
points.Add(MsDataFileUtil.GetPoint(chromatogram.MzRange, mzArray, intensityArray));
}
analysis.AddPoints(iScan, time, points);
}
var incompleteAnalyses = new List<AnalysisChromatograms>();
foreach (var analysis in analyses)
{
if (analysis.LastTime <= time)
{
completeAnalyses.Add(analysis);
}
else
{
incompleteAnalyses.Add(analysis);
}
}
SaveChromatograms(chromatogramTask, completeAnalyses, false);
completeAnalyses.Clear();
analyses = incompleteAnalyses;
}
completeAnalyses.AddRange(analyses);
SaveChromatograms(chromatogramTask, completeAnalyses, 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 GenerateChromatograms(ChromatogramTask chromatogramTask)
{
int totalAnalyses = chromatogramTask.AnalysisChromatograms.Count;
if (totalAnalyses == 0)
{
return;
}
if (!UpdateProgress(chromatogramTask, 0))
{
return;
}
var msDataFile = chromatogramTask.MsDataFile;
MsDataFileUtil.InitMsDataFile(chromatogramTask.Workspace, msDataFile);
var analyses = new List <AnalysisChromatograms>(chromatogramTask.AnalysisChromatograms);
MsDataFileImpl pwizMsDataFileImpl;
var path = _workspace.GetDataFilePath(msDataFile.Name);
try
{
pwizMsDataFileImpl = new MsDataFileImpl(path);
}
catch (Exception exception)
{
ErrorHandler.LogException("Chromatogram Generator", "Error opening " + path, exception);
_workspace.RejectMsDataFile(msDataFile);
return;
}
using (pwizMsDataFileImpl)
{
var completeAnalyses = new List <AnalysisChromatograms>();
int totalScanCount = pwizMsDataFileImpl.SpectrumCount;
var lastTimeInDataFile =
chromatogramTask.MsDataFile.GetTime(chromatogramTask.MsDataFile.GetSpectrumCount() - 1);
double minTime = lastTimeInDataFile;
double maxTime = msDataFile.GetTime(0);
foreach (var analysis in analyses)
{
minTime = Math.Min(minTime, analysis.FirstTime);
maxTime = Math.Max(maxTime, analysis.LastTime);
}
int firstScan = msDataFile.FindScanIndex(minTime);
for (int iScan = firstScan; analyses.Count > 0 && iScan < totalScanCount; iScan++)
{
double time = msDataFile.GetTime(iScan);
int progress = (int)(100 * (time - minTime) / (maxTime - minTime));
progress = Math.Min(progress, 100);
progress = Math.Max(progress, 0);
if (!UpdateProgress(chromatogramTask, progress))
{
return;
}
List <AnalysisChromatograms> activeAnalyses = new List <AnalysisChromatograms>();
double nextTime = Double.MaxValue;
if (msDataFile.GetMsLevel(iScan, pwizMsDataFileImpl) != 1)
{
continue;
}
foreach (var analysis in analyses)
{
nextTime = Math.Min(nextTime, analysis.FirstTime);
if (analysis.FirstTime <= time)
{
activeAnalyses.Add(analysis);
}
}
if (activeAnalyses.Count == 0)
{
int nextScan = msDataFile.FindScanIndex(nextTime);
iScan = Math.Max(iScan, nextScan - 1);
continue;
}
bool lowMemory = IsLowOnMemory();
// If we have exceeded the number of analyses we should be working on at once,
// throw out any that we haven't started.
for (int iAnalysis = activeAnalyses.Count - 1; iAnalysis >= 0 &&
(activeAnalyses.Count > _maxConcurrentAnalyses || lowMemory); iAnalysis--)
{
var analysis = activeAnalyses[iAnalysis];
if (analysis.Times.Count > 0)
{
continue;
}
activeAnalyses.RemoveAt(iAnalysis);
analyses.Remove(analysis);
}
double[] mzArray, intensityArray;
pwizMsDataFileImpl.GetSpectrum(iScan, out mzArray, out intensityArray);
if (!pwizMsDataFileImpl.IsCentroided(iScan))
{
var centroider = new Centroider(mzArray, intensityArray);
centroider.GetCentroidedData(out mzArray, out intensityArray);
}
foreach (var analysis in activeAnalyses)
{
var points = new List <ChromatogramPoint>();
foreach (var chromatogram in analysis.Chromatograms)
{
points.Add(MsDataFileUtil.GetPoint(chromatogram.MzRange, mzArray, intensityArray));
}
analysis.AddPoints(iScan, time, points);
}
var incompleteAnalyses = new List <AnalysisChromatograms>();
foreach (var analysis in analyses)
{
if (analysis.LastTime <= time)
{
completeAnalyses.Add(analysis);
}
else
{
incompleteAnalyses.Add(analysis);
}
}
SaveChromatograms(chromatogramTask, completeAnalyses, false);
completeAnalyses.Clear();
analyses = incompleteAnalyses;
}
completeAnalyses.AddRange(analyses);
SaveChromatograms(chromatogramTask, completeAnalyses, true);
}
}
