public void SetTaskScheduler(TaskScheduler taskScheduler)
{
_taskScheduler = taskScheduler;
if (_taskScheduler != null)
{
if (SessionFactory == null)
{
OpenSessionFactory();
}
_databasePoller = _databasePoller ?? new DatabasePoller(this);
_databasePoller.Start();
_resultCalculator = _resultCalculator ?? new ResultCalculator(this);
_resultCalculator.Start();
_chromatogramGenerator = _chromatogramGenerator ?? new ChromatogramGenerator(this);
_chromatogramGenerator.Start();
}
else
{
if (null != _chromatogramGenerator)
{
_chromatogramGenerator.Stop();
}
if (null != _resultCalculator)
{
_resultCalculator.Stop();
}
if (null != _databasePoller)
{
_databasePoller.Stop();
}
CloseSessionFactory();
}
}
public PeakChromatogramGenerator(double tolerance, Globals.ChromatogramGeneratorMode chromMode,
Globals.IsotopicProfileType isotopicProfileTarget, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
Tolerance = tolerance;
ChromatogramGeneratorMode = chromMode;
IsotopicProfileTarget = isotopicProfileTarget;
TopNPeaksLowerCutOff = 0.3;
ChromWindowWidthForNonAlignedData = 0.4f;
ChromWindowWidthForAlignedData = 0.1f;
ToleranceUnit = toleranceUnit;
_chromGen = new ChromatogramGenerator();
}
private void GenerateChromatogramsBackground(DbMsDataFile msDataFile)
{
ChromatogramGenerator chromatogramGenerator = new ChromatogramGenerator(Workspace);
chromatogramGenerator.GenerateChromatograms(msDataFile, new List <AnalysisChromatograms> {
new AnalysisChromatograms(PeptideAnalysis)
}, UpdateChromatogramProgress);
SafeBeginInvoke(delegate
{
HasChromatograms = true;
WaitingForChromatograms = false;
progressBar1.Visible = false;
tbxStatus.Text = "";
});
}
public void getPeakChromatogramUsingChromGenTest1()
{
var targetMZ = 831.48;
double toleranceInPPM = 20;
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var chromGen = new ChromatogramGenerator();
run.XYData = chromGen.GenerateChromatogram(run.ResultCollection.MSPeakResultList, run.MinLCScan, run.MaxLCScan, targetMZ, toleranceInPPM, 1);
for (var i = 0; i < run.XYData.Xvalues.Length; i++)
{
run.XYData.Xvalues[i] = run.GetTime(i);
}
// run.XYData.Display();
var counter = 0;
var sb = new StringBuilder();
var sortedList = run.ResultCollection.MSPeakResultList.OrderBy(p => p.MSPeak.XValue);
foreach (var peak in sortedList)
{
counter++;
if (peak.MSPeak.XValue > (targetMZ - 0.1) && peak.MSPeak.XValue < (targetMZ + 0.1))
{
sb.Append(peak.ChromID);
sb.Append("\t");
sb.Append(peak.PeakID);
sb.Append("\t");
sb.Append(peak.Scan_num);
sb.Append("\t");
sb.Append(peak.MSPeak.XValue);
sb.Append("\t");
sb.Append(peak.MSPeak.Height);
sb.Append(Environment.NewLine);
}
}
Console.WriteLine(sb.ToString());
}
public void Dispose()
{
if (null != _chromatogramGenerator)
{
_chromatogramGenerator.Dispose();
_chromatogramGenerator = null;
}
if (null != _databasePoller)
{
_databasePoller.Dispose();
_databasePoller = null;
}
if (null != _resultCalculator)
{
_resultCalculator.Dispose();
_resultCalculator = null;
}
}
public void getPeakChromAndStoreInPeakChromObject_Test1()
{
double chromToleranceInPPM = 20;
var targetMZ = 831.48;
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var chromGen = new ChromatogramGenerator();
PeakChrom chrom = new BasicPeakChrom();
chrom.ChromSourceData = chromGen.GeneratePeakChromatogram(run.ResultCollection.MSPeakResultList, run.MinLCScan, run.MaxLCScan, targetMZ, chromToleranceInPPM);
Assert.AreEqual(59, chrom.ChromSourceData.Count);
}
public void getPeakChromatogramInTheFormOfMSPeakResult_Test1()
{
double chromToleranceInPPM = 20;
var targetMZ = 831.48;
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var chromGen = new ChromatogramGenerator();
var filteredMSPeaks = chromGen.GeneratePeakChromatogram(run.ResultCollection.MSPeakResultList, run.MinLCScan, run.MaxLCScan, targetMZ, chromToleranceInPPM);
//Assert.AreEqual(56, filteredMSPeaks.Count);
TestUtilities.DisplayMSPeakResults(filteredMSPeaks);
}
public void getChromatogramsSpeedTest1()
{
var targetMZ = 831.48;
double toleranceInPPM = 20;
var totalIterations = 40;
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile1);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var chromGen = new ChromatogramGenerator();
var speedResults = new List <long>();
var sw = new Stopwatch();
var startScan = 5500;
var stopScan = 8500;
for (var i = 0; i < totalIterations; i++)
{
sw.Reset();
sw.Start();
run.XYData = chromGen.GenerateChromatogram(run.ResultCollection.MSPeakResultList, startScan, stopScan, (targetMZ + totalIterations), toleranceInPPM, 1);
sw.Stop();
speedResults.Add(sw.ElapsedMilliseconds);
}
Console.WriteLine("Average time = " + speedResults.Average());
}
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);
}
}
