public PeptideData(DbPeptide dbPeptide)
{
FullSequence = dbPeptide.FullSequence;
Sequence = dbPeptide.Sequence;
ProteinName = dbPeptide.Protein;
ProteinDescription = dbPeptide.ProteinDescription;
}
public PeptideData(DbPeptide dbPeptide)
{
FullSequence = dbPeptide.FullSequence;
Sequence = dbPeptide.Sequence;
ProteinName = dbPeptide.Protein;
ProteinDescription = dbPeptide.ProteinDescription;
}
public static DbPeptideAnalysis CreateDbPeptideAnalysis(ISession session, DbPeptide dbPeptide)
{
int minCharge, maxCharge;
var query = session.CreateQuery("SELECT MIN(s.PrecursorCharge), MAX(s.PrecursorCharge)"
+ "\nFROM " + typeof(DbPeptideSpectrumMatch) +
" s WHERE s.Peptide = :peptide")
.SetParameter("peptide", dbPeptide);
var minMaxCharge = (object[])query.UniqueResult();
if (minMaxCharge == null)
{
return(null);
}
minCharge = Convert.ToInt32(minMaxCharge[0]);
maxCharge = Convert.ToInt32(minMaxCharge[1]);
return(new DbPeptideAnalysis
{
Peptide = dbPeptide,
MinCharge = minCharge,
MaxCharge = maxCharge,
});
}
public SearchResultKey(DbMsDataFile msDataFile, DbPeptide peptide, double retentionTime)
: this(msDataFile.Id.GetValueOrDefault(), peptide.Id.GetValueOrDefault(), retentionTime)
{
}
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);
}
public void TestChromatogramGenerator()
{
String dbPath = Path.Combine(TestContext.TestDir, "test" + Guid.NewGuid() + ".tpg");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(dbPath, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
session.BeginTransaction();
DbWorkspace dbWorkspace = new DbWorkspace
{
TracerDefCount = 1,
};
session.Save(dbWorkspace);
DbTracerDef dbTracerDef = TracerDef.GetN15Enrichment();
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.data_directory.ToString(),
Value = GetDataDirectory()
});
session.Transaction.Commit();
}
}
Workspace workspace = new Workspace(dbPath);
workspace.SetTaskScheduler(TaskScheduler.Default);
var dbMsDataFile = new DbMsDataFile
{
Name = "20090724_HT3_0",
};
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
var msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
Assert.IsTrue(MsDataFileUtil.InitMsDataFile(workspace, msDataFile));
DbPeptide dbPeptide;
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
dbPeptide = new DbPeptide
{
Protein = "TestProtein",
Sequence = "YLAAYLLLVQGGNAAPSAADIK",
FullSequence = "K.YLAAYLLLVQGGNAAPSAADIK.A",
};
session.Save(dbPeptide);
var searchResult = new DbPeptideSpectrumMatch
{
Peptide = dbPeptide,
MsDataFile = session.Load <DbMsDataFile>(msDataFile.Id),
PrecursorCharge = 3,
RetentionTime = 20.557 * 60,
};
session.Save(searchResult);
session.Transaction.Commit();
}
var peptide = new Peptide(workspace, dbPeptide);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
peptideAnalysis.IncChromatogramRefCount();
var peptideFileAnalysis = PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
workspace.DatabasePoller.LoadAndMergeChanges(null);
peptideAnalysis.IncChromatogramRefCount();
var chromatogramGenerator = new ChromatogramGenerator(workspace);
chromatogramGenerator.Start();
while (peptideFileAnalysis.ChromatogramSet == null)
{
Thread.Sleep(100);
}
var chromatogramDatas = peptideFileAnalysis.GetChromatograms();
Assert.IsFalse(chromatogramDatas.Chromatograms.Count == 0);
chromatogramGenerator.Stop();
while (chromatogramGenerator.IsThreadAlive)
{
Thread.Sleep(100);
}
}
public SearchResultKey(DbMsDataFile msDataFile, DbPeptide peptide, double retentionTime)
: this(msDataFile.Id.GetValueOrDefault(), peptide.Id.GetValueOrDefault(), retentionTime)
{
}
public Peptide(Workspace workspace, DbPeptide dbPeptide) : this(workspace, dbPeptide.GetId(), new PeptideData(dbPeptide))
{
}
public void TestChromatogramGenerator()
{
String dbPath = Path.Combine(TestContext.TestDir, "test" + Guid.NewGuid() + ".tpg");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(dbPath, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
session.BeginTransaction();
DbWorkspace dbWorkspace = new DbWorkspace
{
TracerDefCount = 1,
};
session.Save(dbWorkspace);
DbTracerDef dbTracerDef = TracerDef.GetN15Enrichment();
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.data_directory.ToString(),
Value = GetDataDirectory()
});
session.Transaction.Commit();
}
}
Workspace workspace = new Workspace(dbPath);
workspace.SetTaskScheduler(TaskScheduler.Default);
var dbMsDataFile = new DbMsDataFile
{
Name = "20090724_HT3_0",
};
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
var msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
Assert.IsTrue(MsDataFileUtil.InitMsDataFile(workspace, msDataFile));
DbPeptide dbPeptide;
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
dbPeptide = new DbPeptide
{
Protein = "TestProtein",
Sequence = "YLAAYLLLVQGGNAAPSAADIK",
FullSequence = "K.YLAAYLLLVQGGNAAPSAADIK.A",
};
session.Save(dbPeptide);
var searchResult = new DbPeptideSpectrumMatch
{
Peptide = dbPeptide,
MsDataFile = session.Load<DbMsDataFile>(msDataFile.Id),
PrecursorCharge = 3,
RetentionTime = 20.557 * 60,
};
session.Save(searchResult);
session.Transaction.Commit();
}
var peptide = new Peptide(workspace, dbPeptide);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
peptideAnalysis.IncChromatogramRefCount();
var peptideFileAnalysis = PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
workspace.DatabasePoller.LoadAndMergeChanges(null);
peptideAnalysis.IncChromatogramRefCount();
var chromatogramGenerator = new ChromatogramGenerator(workspace);
chromatogramGenerator.Start();
while (peptideFileAnalysis.ChromatogramSet == null)
{
Thread.Sleep(100);
}
var chromatogramDatas = peptideFileAnalysis.GetChromatograms();
Assert.IsFalse(chromatogramDatas.Chromatograms.Count == 0);
chromatogramGenerator.Stop();
while (chromatogramGenerator.IsThreadAlive)
{
Thread.Sleep(100);
}
}
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);
}
