private void TestPeptide(Workspace workspace, PeakFinderPeptide peakFinderPeptide)
{
DbPeptideFileAnalysis dbPeptideFileAnalysis;
using (var session = workspace.OpenSession())
{
dbPeptideFileAnalysis = (DbPeptideFileAnalysis)session.CreateQuery(
"FROM DbPeptideFileAnalysis T WHERE T.MsDataFile.Name = :dataFile AND T.PeptideAnalysis.Peptide.Sequence = :sequence")
.SetParameter("dataFile", peakFinderPeptide.DataFile)
.SetParameter("sequence",
peakFinderPeptide.PeptideSequence)
.UniqueResult();
}
PeptideAnalysis peptideAnalysis = workspace.PeptideAnalyses.FindByKey(dbPeptideFileAnalysis.PeptideAnalysis.Id.GetValueOrDefault());
using (peptideAnalysis.IncChromatogramRefCount())
{
workspace.DatabasePoller.LoadAndMergeChanges(new Dictionary <long, bool> {
{ peptideAnalysis.Id, true }
});
PeptideFileAnalysis peptideFileAnalysis = peptideAnalysis.GetFileAnalysis(dbPeptideFileAnalysis.Id.GetValueOrDefault());
var peaks = CalculatedPeaks.Calculate(peptideFileAnalysis, new CalculatedPeaks[0]);
const string format = "0.000";
Assert.AreEqual(
peakFinderPeptide.ExpectedPeakStart.ToString(format) + "-" + peakFinderPeptide.ExpectedPeakEnd.ToString(format),
(peaks.StartTime.GetValueOrDefault() / 60).ToString(format) + "-" + (peaks.EndTime.GetValueOrDefault() / 60).ToString(format), peakFinderPeptide.PeptideSequence);
}
}
void CalculateAnalysisResults(ResultCalculatorTask task)
{
StatusMessage = "Processing " + task.PeptideAnalysis.Peptide.FullSequence;
var peaksList = new List <CalculatedPeaks>();
var peptideFileAnalyses = task.PeptideAnalysis.FileAnalyses.ToArray();
Array.Sort(peptideFileAnalyses,
(f1, f2) => (null == f1.PsmTimes).CompareTo(null == f2.PsmTimes)
);
foreach (var peptideFileAnalysis in peptideFileAnalyses)
{
if (peptideFileAnalysis.ChromatogramSet == null ||
!peptideFileAnalysis.IsMzKeySetComplete(peptideFileAnalysis.ChromatogramSet.Chromatograms.Keys))
{
continue;
}
var peaks = CalculatedPeaks.Calculate(peptideFileAnalysis, peaksList);
if (peaks.Peaks.Count != 0)
{
peaksList.Add(peaks);
}
}
task.PeptideAnalysis.SetCalculatedPeaks(peaksList);
_workspace.RunOnEventQueue(() => _workspace.RetentionTimeAlignments.MergeFrom(task.Workspace.RetentionTimeAlignments));
if (task.CanSave())
{
using (_session = _workspace.OpenWriteSession())
{
_session.BeginTransaction();
foreach (var peptideFileAnalysis in task.PeptideAnalysis.GetFileAnalyses(false))
{
if (peptideFileAnalysis.ChromatogramSet != null &&
!peptideFileAnalysis.IsMzKeySetComplete(peptideFileAnalysis.ChromatogramSet.Chromatograms.Keys))
{
var dbPeptideFileAnalysis = _session.Get <DbPeptideFileAnalysis>(peptideFileAnalysis.Id);
var dbChromatogramSet = dbPeptideFileAnalysis.ChromatogramSet;
if (null != dbChromatogramSet)
{
foreach (var dbChromatogram in dbPeptideFileAnalysis.ChromatogramSet.Chromatograms)
{
_session.Delete(dbChromatogram);
}
dbPeptideFileAnalysis.ChromatogramSet = null;
_session.Update(dbPeptideFileAnalysis);
_session.Delete(dbChromatogramSet);
}
}
if (null == peptideFileAnalysis.CalculatedPeaks)
{
var dbPeptideFileAnalysis = _session.Get <DbPeptideFileAnalysis>(peptideFileAnalysis.Id);
CalculatedPeaks.DeleteResults(_session, dbPeptideFileAnalysis);
_session.Update(dbPeptideFileAnalysis);
}
else
{
peptideFileAnalysis.CalculatedPeaks.Save(_session);
}
}
_session.Save(new DbChangeLog(task.PeptideAnalysis));
task.FinishLock(_session);
try
{
_session.Transaction.Commit();
}
// ReSharper disable RedundantCatchClause
// ReSharper disable UnusedVariable
catch (Exception e)
// ReSharper restore UnusedVariable
{
throw;
}
// ReSharper restore RedundantCatchClause
}
}
}
