public static bool TryInitMsDataFile(IWin32Window parent, MsDataFile msDataFile, out string errorMessage)
{
bool success = false;
string message = null;
using (var longWaitDialog = new LongWaitDialog(parent, Program.AppName))
{
new LongOperationBroker(broker =>
{
broker.UpdateStatusMessage(string.Format("Reading retention times for {0}", msDataFile.Name));
success = MsDataFileUtil.TryInitMsDataFile(msDataFile.Workspace, msDataFile, broker.CancellationToken, out message);
}, longWaitDialog).LaunchJob();
}
errorMessage = message;
return(success);
}
public void Redisplay()
{
if (!IsHandleCreated)
{
return;
}
if (_inRedisplay)
{
return;
}
try
{
_inRedisplay = true;
tbxMinCharge.Text = MinCharge.ToString();
tbxMaxCharge.Text = MaxCharge.ToString();
tbxPeptideSequence.Text = PeptideSequence;
cbxShowPeptideMzs.Enabled = !string.IsNullOrEmpty(PeptideSequence);
tbxMassAccuracy.Text = MassAccuracy.ToString();
TurnoverCalculator turnoverCalculator = null;
if (!string.IsNullOrEmpty(PeptideSequence))
{
turnoverCalculator = new TurnoverCalculator(Workspace, PeptideSequence);
}
msGraphControlEx1.GraphPane.GraphObjList.Clear();
msGraphControlEx1.GraphPane.CurveList.Clear();
if (_spectrumData == null || comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
using (var msDataFileImpl = new MsDataFileImpl(Workspace.GetDataFilePath(MsDataFile.Name)))
{
if (comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
string chromatogramName;
float[] timeArray;
float[] intensityArray;
msDataFileImpl.GetChromatogram(comboChromatogram.SelectedIndex, out chromatogramName, out timeArray, out intensityArray);
_chromatogramDatas[comboChromatogram.SelectedIndex] = new ChromatogramData(chromatogramName, timeArray, intensityArray);
}
_spectrumData = _spectrumData ?? new SpectrumData(msDataFileImpl, ScanIndex);
}
}
ChromatogramData chromatogram = null;
if (comboChromatogram.SelectedIndex >= 0)
{
chromatogram = _chromatogramDatas[comboChromatogram.SelectedIndex];
}
tbxMsLevel.Text = _spectrumData.MsLevel.ToString();
tbxTime.Text = _spectrumData.Time.ToString();
if (chromatogram != null && ScanIndex < chromatogram.TimeArray.Length)
{
tbxChromatogramRetentionTime.Text = chromatogram.TimeArray[ScanIndex].ToString();
tbxChromatogramIonCurrent.Text = chromatogram.IntensityArray[ScanIndex].ToString(NumberFormat);
}
else
{
tbxChromatogramRetentionTime.Text = tbxChromatogramIonCurrent.Text = @"N/A";
}
if (cbxShowProfile.Checked && _spectrumData.ProfileMzs != null)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, new SpectrumGraphItem()
{
Points =
new PointPairList(_spectrumData.ProfileMzs,
_spectrumData.ProfileIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.line,
Color = Color.Blue,
});
}
if (_spectrumData.ProfileIntensities != null)
{
tbxSumOfProfileIntensities.Text = _spectrumData.ProfileIntensities.Sum().ToString(NumberFormat);
}
else
{
tbxSumOfProfileIntensities.Text = "";
}
tbxCentroidIntensitySum.Text = _spectrumData.CentroidIntensities.Sum().ToString(NumberFormat);
var spectrum = new SpectrumGraphItem
{
Points = new PointPairList(_spectrumData.CentroidMzs, _spectrumData.CentroidIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.stick,
Color = Color.Black
};
if (turnoverCalculator != null)
{
var mzRanges = new Dictionary <MzRange, String>();
double monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideSequence);
double peptideIntensity = 0.0;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
foreach (var mzRange in turnoverCalculator.GetMzs(charge))
{
double mass = (mzRange.Center - AminoAcidFormulas.ProtonMass) * charge;
double massDifference = mass - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
mzRanges.Add(mzRange, label);
var chromatogramPoint = MsDataFileUtil.GetPoint(mzRange, _spectrumData.CentroidMzs, _spectrumData.CentroidIntensities);
peptideIntensity += chromatogramPoint.GetIntensity(mzRange, MassAccuracy);
}
}
spectrum.MassAccuracy = MassAccuracy;
spectrum.MzRanges = mzRanges;
tbxPeptideIntensity.Text = peptideIntensity.ToString(NumberFormat);
}
if (cbxShowCentroids.Checked)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, spectrum);
}
if (turnoverCalculator != null && cbxShowPeptideMzs.Checked)
{
double massAccuracy = MassAccuracy;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var mzs = turnoverCalculator.GetMzs(charge);
var height = int.MaxValue;
foreach (var mzRange in mzs)
{
double min = mzRange.MinWithMassAccuracy(massAccuracy);
double max = mzRange.MaxWithMassAccuracy(massAccuracy);
msGraphControlEx1.GraphPane.GraphObjList.Add(new BoxObj(min, height, max - min, height, Color.Goldenrod, Color.Goldenrod)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid
});
}
}
}
msGraphControlEx1.Invalidate();
}
finally
{
_inRedisplay = false;
}
}
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);
}
}
