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);
}
}
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);
}
}
private void AddPeptide(Workspace workspace, PeakFinderPeptide peakFinderPeptide)
{
var msDataFile = GetMsDataFile(workspace, peakFinderPeptide.DataFile);
Peptide peptide;
using (var session = workspace.OpenWriteSession())
{
var dbMsDataFile = new DbMsDataFile
{
Name = peakFinderPeptide.DataFile,
Label = peakFinderPeptide.DataFile,
};
if (msDataFile == null)
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
var dbPeptide = (DbPeptide)
session.CreateCriteria <DbPeptide>().Add(Restrictions.Eq("Sequence",
peakFinderPeptide.PeptideSequence)).
UniqueResult();
if (dbPeptide == null)
{
dbPeptide = new DbPeptide
{
FullSequence = peakFinderPeptide.PeptideSequence,
Sequence = peakFinderPeptide.PeptideSequence,
};
session.BeginTransaction();
session.Save(dbPeptide);
session.Transaction.Commit();
}
session.BeginTransaction();
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.FirstDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MinCharge,
Peptide = dbPeptide,
MsDataFile = session.Load <DbMsDataFile>(msDataFile.Id),
});
if (peakFinderPeptide.LastDetectedTime != peakFinderPeptide.FirstDetectedTime)
{
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.LastDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MaxCharge,
Peptide = dbPeptide,
MsDataFile = session.Load <DbMsDataFile>(msDataFile.Id),
});
}
session.Transaction.Commit();
peptide = new Peptide(workspace, dbPeptide);
}
MsDataFileUtil.InitMsDataFile(workspace, msDataFile);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
if (peptideAnalysis == null)
{
Assert.Fail();
}
PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
}
private void AddPeptide(Workspace workspace, PeakFinderPeptide peakFinderPeptide)
{
var msDataFile = GetMsDataFile(workspace, peakFinderPeptide.DataFile);
Peptide peptide;
using (var session = workspace.OpenWriteSession())
{
var dbMsDataFile = new DbMsDataFile
{
Name = peakFinderPeptide.DataFile,
Label = peakFinderPeptide.DataFile,
};
if (msDataFile == null)
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
var dbPeptide = (DbPeptide)
session.CreateCriteria<DbPeptide>().Add(Restrictions.Eq("Sequence",
peakFinderPeptide.PeptideSequence)).
UniqueResult();
if (dbPeptide == null)
{
dbPeptide = new DbPeptide
{
FullSequence = peakFinderPeptide.PeptideSequence,
Sequence = peakFinderPeptide.PeptideSequence,
};
session.BeginTransaction();
session.Save(dbPeptide);
session.Transaction.Commit();
}
session.BeginTransaction();
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.FirstDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MinCharge,
Peptide = dbPeptide,
MsDataFile = session.Load<DbMsDataFile>(msDataFile.Id),
});
if (peakFinderPeptide.LastDetectedTime != peakFinderPeptide.FirstDetectedTime)
{
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.LastDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MaxCharge,
Peptide = dbPeptide,
MsDataFile = session.Load<DbMsDataFile>(msDataFile.Id),
});
}
session.Transaction.Commit();
peptide = new Peptide(workspace, dbPeptide);
}
MsDataFileUtil.InitMsDataFile(workspace, msDataFile);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
if (peptideAnalysis == null)
{
Assert.Fail();
}
PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
}
