private void setEnrichment(DbTracerDef tracerDef)
{
tbxTracerSymbol.Text = tracerDef.TracerSymbol;
tbxMassDifference.Text = tracerDef.DeltaMass.ToString();
tbxAtomCount.Text = tracerDef.AtomCount.ToString();
tbxAtomicPercentEnrichment.Text = tracerDef.AtomPercentEnrichment.ToString();
cbxEluteEarlier.Checked = tracerDef.IsotopesEluteEarlier;
cbxEluteLater.Checked = tracerDef.IsotopesEluteLater;
}
public TracerDefData(DbTracerDef dbTracerDef)
{
Name = dbTracerDef.Name;
TracerSymbol = dbTracerDef.TracerSymbol;
DeltaMass = dbTracerDef.DeltaMass;
AtomCount = dbTracerDef.AtomCount;
AtomPercentEnrichment = dbTracerDef.AtomPercentEnrichment;
InitialEnrichment = dbTracerDef.InitialEnrichment;
FinalEnrichment = dbTracerDef.FinalEnrichment;
IsotopesEluteEarlier = dbTracerDef.IsotopesEluteEarlier;
IsotopesEluteLater = dbTracerDef.IsotopesEluteLater;
}
private void UpdateDbTracerDef(DbTracerDef dbTracerDef, TracerDefData tracerDefData)
{
dbTracerDef.AtomCount = tracerDefData.AtomCount;
dbTracerDef.AtomPercentEnrichment = tracerDefData.AtomPercentEnrichment;
dbTracerDef.DeltaMass = tracerDefData.DeltaMass;
dbTracerDef.FinalEnrichment = tracerDefData.FinalEnrichment;
dbTracerDef.InitialEnrichment = tracerDefData.InitialEnrichment;
dbTracerDef.IsotopesEluteEarlier = tracerDefData.IsotopesEluteEarlier;
dbTracerDef.IsotopesEluteLater = tracerDefData.IsotopesEluteLater;
dbTracerDef.Name = tracerDefData.Name;
dbTracerDef.TracerSymbol = tracerDefData.TracerSymbol;
}
public TracerDefData(DbTracerDef dbTracerDef)
{
Name = dbTracerDef.Name;
TracerSymbol = dbTracerDef.TracerSymbol;
DeltaMass = dbTracerDef.DeltaMass;
AtomCount = dbTracerDef.AtomCount;
AtomPercentEnrichment = dbTracerDef.AtomPercentEnrichment;
InitialEnrichment = dbTracerDef.InitialEnrichment;
FinalEnrichment = dbTracerDef.FinalEnrichment;
IsotopesEluteEarlier = dbTracerDef.IsotopesEluteEarlier;
IsotopesEluteLater = dbTracerDef.IsotopesEluteLater;
}
protected Workspace CreateWorkspace(string path, DbTracerDef dbTracerDef)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(path, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
var transaction = session.BeginTransaction();
var dbWorkspace = new DbWorkspace
{
ModificationCount = 1,
TracerDefCount = dbTracerDef == null ? 0 : 1,
SchemaVersion = WorkspaceUpgrader.CurrentVersion,
};
session.Save(dbWorkspace);
if (dbTracerDef != null)
{
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
}
var modification = new DbModification
{
DeltaMass = 57.021461,
Symbol = "C",
Workspace = dbWorkspace
};
session.Save(modification);
transaction.Commit();
}
}
var workspace = new Workspace(path);
workspace.SetTaskScheduler(TaskScheduler.Default);
workspace.DatabasePoller.LoadAndMergeChanges(null);
return(workspace);
}
private void setEnrichment(DbTracerDef tracerDef)
{
tbxTracerSymbol.Text = tracerDef.TracerSymbol;
tbxMassDifference.Text = tracerDef.DeltaMass.ToString();
tbxAtomCount.Text = tracerDef.AtomCount.ToString();
tbxAtomicPercentEnrichment.Text = tracerDef.AtomPercentEnrichment.ToString();
cbxEluteEarlier.Checked = tracerDef.IsotopesEluteEarlier;
cbxEluteLater.Checked = tracerDef.IsotopesEluteLater;
}
// TODO(nicksh): 2013-10-03: Re-enable this test once it reliably passes
//[TestMethod]
public void TestPeakFinder()
{
String dbPath = Path.Combine(TestContext.TestDir, "PeakFinderTest.tpg");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(dbPath, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
session.BeginTransaction();
DbWorkspace dbWorkspace = new DbWorkspace
{
TracerDefCount = 1,
SettingCount = 2,
SchemaVersion = WorkspaceUpgrader.CurrentVersion
};
session.Save(dbWorkspace);
DbTracerDef dbTracerDef = TracerDef.GetD3LeuEnrichment();
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.data_directory.ToString(),
Value = GetDataDirectory()
});
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.mass_accuracy.ToString(),
Value = "100000"
});
session.Transaction.Commit();
}
}
Workspace workspace = new Workspace(dbPath);
workspace.SetTaskScheduler(TaskScheduler.Default);
workspace.DatabasePoller.LoadAndMergeChanges(null);
foreach (var peakFinderPeptide in peptides)
{
AddPeptide(workspace, peakFinderPeptide);
}
while (true)
{
string statusMessage;
int progress;
workspace.ChromatogramGenerator.GetProgress(out statusMessage, out progress);
if ("Idle" == statusMessage)
{
break;
}
Thread.Sleep(100);
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
var exceptions = new List <Exception>();
foreach (var peptide in peptides)
{
try
{
TestPeptide(workspace, peptide);
}
catch (Exception exception)
{
exceptions.Add(exception);
Trace.TraceError("{0}:{1}", peptide.PeptideSequence, exception);
}
}
CollectionAssert.AreEqual(new Exception[0], exceptions);
}
private TracerDefData GetTracerDef()
{
string name = NormalizeName(tbxTracerName.Text);
if (_originalTracerDef == null || name != _originalTracerDef.Name)
{
if (Workspace.GetTracerDefs().Any(pair => pair.Name == name))
{
ShowError("There is already a label defined with this name.", tbxTracerName);
return(null);
}
}
foreach (var ch in name.ToLower())
{
if (ch < 'a' || ch > 'z')
{
ShowError("Name can consist only of alphabetic characters", tbxTracerName);
return(null);
}
}
if (IsotopeAbundances.Default.ContainsKey(name) || AminoAcidFormulas.LongNames.ContainsKey(name))
{
ShowError("Name cannot be the same as a 3 letter amino acid code, or an atomic element",
tbxTracerName);
return(null);
}
string tracerSymbol = NormalizeName(tbxTracerSymbol.Text);
if (string.IsNullOrEmpty(tracerSymbol))
{
ShowError("Symbol cannot be blank", tbxTracerSymbol);
return(null);
}
if (!IsotopeAbundances.Default.ContainsKey(tracerSymbol) && !AminoAcidFormulas.LongNames.ContainsKey(tracerSymbol))
{
ShowError("Symbol must be either a three letter amino acid code, or an atomic element",
tbxTracerSymbol);
return(null);
}
double deltaMass;
try
{
deltaMass = double.Parse(tbxMassDifference.Text);
}
catch
{
ShowError("This must be a number", tbxMassDifference);
return(null);
}
if (deltaMass == 0)
{
ShowError("Mass cannot be 0", tbxMassDifference);
return(null);
}
int atomCount;
try
{
atomCount = int.Parse(tbxAtomCount.Text);
}
catch
{
ShowError("This must be a positive integer", tbxAtomCount);
return(null);
}
if (atomCount <= 0)
{
ShowError("This must be a positive integer", tbxAtomCount);
return(null);
}
double atomicPercentEnrichment, initialApe, finalApe;
if (!ValidatePercent(tbxAtomicPercentEnrichment, out atomicPercentEnrichment) ||
!ValidatePercent(tbxInitialApe, out initialApe) ||
!ValidatePercent(tbxFinalApe, out finalApe))
{
return(null);
}
var dbTracerDef = new DbTracerDef
{
AtomCount = atomCount,
AtomPercentEnrichment = atomicPercentEnrichment,
DeltaMass = deltaMass,
InitialEnrichment = initialApe,
FinalEnrichment = finalApe,
IsotopesEluteEarlier = cbxEluteEarlier.Checked,
IsotopesEluteLater = cbxEluteLater.Checked,
Name = name,
TracerSymbol = tracerSymbol,
};
return(new TracerDefData(dbTracerDef));
}
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);
}
}
protected Workspace CreateWorkspace(string path, DbTracerDef dbTracerDef)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(path, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
var transaction = session.BeginTransaction();
var dbWorkspace = new DbWorkspace
{
ModificationCount = 1,
TracerDefCount = dbTracerDef == null ? 0 : 1,
SchemaVersion = WorkspaceUpgrader.CurrentVersion,
};
session.Save(dbWorkspace);
if (dbTracerDef != null)
{
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
}
var modification = new DbModification
{
DeltaMass = 57.021461,
Symbol = "C",
Workspace = dbWorkspace
};
session.Save(modification);
transaction.Commit();
}
}
var workspace = new Workspace(path);
workspace.SetTaskScheduler(TaskScheduler.Default);
workspace.DatabasePoller.LoadAndMergeChanges(null);
return workspace;
}
private TracerDefData GetTracerDef()
{
string name = NormalizeName(tbxTracerName.Text);
if (_originalTracerDef == null || name != _originalTracerDef.Name)
{
if (Workspace.GetTracerDefs().Any(pair=>pair.Name == name))
{
ShowError("There is already a label defined with this name.", tbxTracerName);
return null;
}
}
foreach (var ch in name.ToLower())
{
if (ch < 'a' || ch > 'z')
{
ShowError("Name can consist only of alphabetic characters", tbxTracerName);
return null;
}
}
if (IsotopeAbundances.Default.ContainsKey(name) || AminoAcidFormulas.LongNames.ContainsKey(name))
{
ShowError("Name cannot be the same as a 3 letter amino acid code, or an atomic element",
tbxTracerName);
return null;
}
string tracerSymbol = NormalizeName(tbxTracerSymbol.Text);
if (string.IsNullOrEmpty(tracerSymbol))
{
ShowError("Symbol cannot be blank", tbxTracerSymbol);
return null;
}
if (!IsotopeAbundances.Default.ContainsKey(tracerSymbol) && !AminoAcidFormulas.LongNames.ContainsKey(tracerSymbol))
{
ShowError("Symbol must be either a three letter amino acid code, or an atomic element",
tbxTracerSymbol);
return null;
}
double deltaMass;
try
{
deltaMass = double.Parse(tbxMassDifference.Text);
}
catch
{
ShowError("This must be a number", tbxMassDifference);
return null;
}
if (deltaMass == 0)
{
ShowError("Mass cannot be 0", tbxMassDifference);
return null;
}
int atomCount;
try
{
atomCount = int.Parse(tbxAtomCount.Text);
}
catch
{
ShowError("This must be a positive integer", tbxAtomCount);
return null;
}
if (atomCount <= 0)
{
ShowError("This must be a positive integer", tbxAtomCount);
return null;
}
double atomicPercentEnrichment, initialApe, finalApe;
if (!ValidatePercent(tbxAtomicPercentEnrichment, out atomicPercentEnrichment)
|| !ValidatePercent(tbxInitialApe, out initialApe)
|| !ValidatePercent(tbxFinalApe, out finalApe))
{
return null;
}
var dbTracerDef = new DbTracerDef
{
AtomCount = atomCount,
AtomPercentEnrichment = atomicPercentEnrichment,
DeltaMass = deltaMass,
InitialEnrichment = initialApe,
FinalEnrichment = finalApe,
IsotopesEluteEarlier = cbxEluteEarlier.Checked,
IsotopesEluteLater = cbxEluteLater.Checked,
Name = name,
TracerSymbol = tracerSymbol,
};
return new TracerDefData(dbTracerDef);
}
