public List <Task> getStandardTaskList(Run run)
{
Task peakChromGen = new PeakChromatogramGenerator(chromPPMTolerance);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task finder = new N14N15TFFTask(5);
Task quant = new N14N15QuantifierTask(1);
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
List <Task> taskList = new List <Task>();
taskList.Add(peakChromGen);
taskList.Add(smoother);
taskList.Add(peakDet);
taskList.Add(chromPeakSel);
taskList.Add(msgen);
taskList.Add(mspeakDet);
taskList.Add(theorFeatureGen);
taskList.Add(finder);
taskList.Add(quant);
taskList.Add(fitScoreCalc);
return(taskList);
}
public void quantifyN14N15RatioTest1()
{
Run run = new BrukerRun(@"F:\Gord\Data\N14N15\HuttlinTurnover\RSPH_Aonly_28_run1_26Oct07_Andromeda_07-09-02\acqus");
MSGeneratorFactory fact = new MSGeneratorFactory();
Task msgen = fact.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 4;
peakDet.SigNoiseThreshold = 3;
peakDet.IsDataThresholded = false;
Task theorFeature = new DeconTools.Backend.ProcessingTasks.TheorFeatureGenerator.TomTheorFeatureGenerator();
List <MassTag> massTags = TestUtilities.CreateN14N15TestMassTagList();
run.CurrentMassTag = massTags[0];
run.CurrentScanSet = new ScanSet(1210);
run.ResultCollection.MassTagResultType = DeconTools.Backend.Globals.MassTagResultType.N14N15_MASSTAG_RESULT;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
theorFeature.Execute(run.ResultCollection);
N14N15TFFTask finder = new N14N15TFFTask(30);
finder.Execute(run.ResultCollection);
N14N15QuantifierTask quant = new N14N15QuantifierTask();
quant.Execute(run.ResultCollection);
N14N15_TResult massTagResult = (N14N15_TResult)run.ResultCollection.GetMassTagResult(run.CurrentMassTag);
TestUtilities.DisplayIsotopicProfileData(massTagResult.IsotopicProfile);
Console.WriteLine("------------------");
TestUtilities.DisplayIsotopicProfileData(massTagResult.IsotopicProfileLabeled);
Console.WriteLine("------------------");
Console.WriteLine("Ratio N14/N15 = " + massTagResult.RatioN14N15);
}
public void find_unlabelledAndUnlabelledIsotopicProfilesTest1()
{
Run run = new BrukerRun(rsph_AOnly_28_run1File);
MSGeneratorFactory fact = new MSGeneratorFactory();
Task msgen = fact.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 4;
peakDet.SigNoiseThreshold = 3;
peakDet.IsDataThresholded = false;
Task theorFeature = new DeconTools.Backend.ProcessingTasks.TheorFeatureGenerator.TomTheorFeatureGenerator();
List <MassTag> massTags = TestUtilities.CreateN14N15TestMassTagList();
run.CurrentMassTag = massTags[0];
run.CurrentScanSet = new ScanSet(1210);
run.ResultCollection.MassTagResultType = DeconTools.Backend.Globals.MassTagResultType.N14N15_MASSTAG_RESULT;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
theorFeature.Execute(run.ResultCollection);
N14N15TFFTask finder = new N14N15TFFTask(30);
finder.Execute(run.ResultCollection);
//TestUtilities.DisplayIsotopicProfileData(finder.LabeledTheorProfile);
N14N15_TResult massTagResult = (N14N15_TResult)run.ResultCollection.GetMassTagResult(run.CurrentMassTag);
TestUtilities.DisplayIsotopicProfileData(massTagResult.IsotopicProfile);
Console.WriteLine("------------------");
TestUtilities.DisplayIsotopicProfileData(massTagResult.IsotopicProfileLabeled);
}
public void run_fullAnalysisTest1()
{
Run run = new BrukerRun(rsph_AOnly_28_run1File);
MassTagCollection massTagColl = new MassTagCollection();
run.ResultCollection.MassTagResultType = DeconTools.Backend.Globals.MassTagResultType.N14N15_MASSTAG_RESULT;
massTagColl.MassTagIDList = fourTestMTs;
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_R_sphaeroides241_P513", "Albert");
importer.chargeStateFilterThreshold = 0.05;
importer.Import(massTagColl);
Assert.AreEqual(7, massTagColl.MassTagList.Count);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(rsph_Aonly_28_run1_scans500_1000_peaks);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
N14N15TFFTask finder = new N14N15TFFTask(0.01);
N14N15QuantifierTask quant = new N14N15QuantifierTask(1);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
List <long> timingResults = new List <long>();
foreach (MassTag mt in massTagColl.MassTagList)
{
run.CurrentMassTag = mt;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
finder.Execute(run.ResultCollection);
quant.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
Console.WriteLine("------------------------------ end --------------------------");
}
catch (Exception ex)
{
Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
}
sw.Stop();
timingResults.Add(sw.ElapsedMilliseconds);
}
foreach (long tr in timingResults)
{
Console.WriteLine(tr);
}
Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());
Console.WriteLine();
}
