public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
MassTag mt = TestUtilities.GetMassTagStandard(1);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = mt;
Task theorFeatureGen = new TomTheorFeatureGenerator();
theorFeatureGen.Execute(run.ResultCollection);
int numPeaksForExtractingChrom = 3;
int toleranceInPPM = 25;
IsotopicProfileMultiChromatogramExtractor multiChromExtractor = new IsotopicProfileMultiChromatogramExtractor(
numPeaksForExtractingChrom, toleranceInPPM);
List <int> ms1Levels = run.GetMSLevelScanValues();
Dictionary <MSPeak, XYData> chromDataForIsotopicProfile = multiChromExtractor.GetChromatogramsForIsotopicProfilePeaks(run.ResultCollection.MSPeakResultList, run.CurrentMassTag.IsotopicProfile, true, ms1Levels);
multiChromExtractor.SmoothChromatograms(chromDataForIsotopicProfile, new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2));
XYData xydata1 = chromDataForIsotopicProfile.Values.First();
XYData xydata2 = chromDataForIsotopicProfile.Values.ElementAt(1);
XYData xydata3 = chromDataForIsotopicProfile.Values.ElementAt(2);
TestUtilities.DisplayXYValues(xydata3);
}
public void processOrbi_Refining_Case01_whatHappensTo_PeakID_396293()
{
var minScan = 200;
var maxScan = 18000;
Run run = new XCaliburRun2(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var workflow = new WholisticChromBasedLCMSFeatureFinderWorkflow(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
#if peaksAreFilteredToNarrowMZ
run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan && p.MSPeak.XValue > 771 && p.MSPeak.XValue < 775).ToList();
#else
run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan).ToList();
#endif
workflow.Execute();
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
var filteredPeakResults = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan && p.MSPeak.XValue > 771 && p.MSPeak.XValue < 775).ToList();
//TestUtilities.DisplayMSPeakResults(filteredPeakResults);
}
public void processOrbiWithNewWorkflowTest2()
{
var minScan = 5500;
var maxScan = 6500;
Run run = new XCaliburRun2(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1, minScan, maxScan);
var workflow = new WholisticChromBasedLCMSFeatureFinderWorkflow(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan).ToList();
run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan && p.MSPeak.XValue > 771 && p.MSPeak.XValue < 775).ToList();
var sw = new Stopwatch();
sw.Start();
workflow.Execute();
sw.Stop();
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
Console.WriteLine("workflow time = " + sw.ElapsedMilliseconds);
}
public void test2()
{
MassTag massTag = new MassTag();
massTag.ID = 56488;
massTag.MonoIsotopicMass = 2275.1694779;
massTag.ChargeState = 3;
massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649;
Run run = new XCaliburRun(xcaliburTestfile);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = massTag;
Task peakChromGen = new PeakChromatogramGenerator(10);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector();
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
TestUtilities.DisplayXYValues(run.ResultCollection);
}
public void getPeakChromatogramTest2()
{
var mt = TestUtilities.GetMassTagStandard(1);
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new TomTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(10, Globals.ChromatogramGeneratorMode.TOP_N_PEAKS);
peakChromGen.TopNPeaksLowerCutOff = 0.4;
peakChromGen.Execute(run.ResultCollection);
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
//Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
run.XYData.Display();
}
public void importPeaksFromOrbitrapFileTest1()
{
var mspeaks = new List <MSPeakResult>();
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(mspeaks);
Assert.AreEqual(105540, mspeaks.Count);
}
public void test3()
{
MassTag massTag = new MassTag();
massTag.ID = 56488;
massTag.MonoIsotopicMass = 2275.1694779;
massTag.ChargeState = 3;
massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649;
massTag.NETVal = 0.3520239f;
Run run = new XCaliburRun(xcaliburTestfile);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = massTag;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector();
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.1);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
Console.WriteLine("Now generating MS....");
msgen.Execute(run.ResultCollection);
Console.WriteLine("----------- RESULTS ----------------------\n");
TestUtilities.DisplayPeaks(run.PeakList);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[massTag];
massTagResult.DisplayToConsole();
Assert.AreEqual(5512, massTagResult.ScanSet.PrimaryScanNumber);
}
private Run setupRun(string runFile, string peaksFile)
{
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(runFile);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(peaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
return(run);
}
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 Test1()
{
var rawdataFile = @"D:\Data\Orbitrap\QC_Shew_09_05-pt5-6_4Jan10_Doc_09-11-08.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var parameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
var mtc = new TargetCollection();
mtc = mtimporter.Import();
var run = new RunFactory().CreateRun(rawdataFile);
//RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
var expectedPeaksFilename = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(expectedPeaksFilename, null);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var testMassTagID = 3513677;
var massTagChargeState = 2;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == massTagChargeState select n).First();
var parameters = WorkflowParameters.CreateParameters(parameterFile);
var workflow = TargetedWorkflow.CreateWorkflow(parameters);
workflow.Run = run;
workflow.Execute();
workflow.Result.DisplayToConsole();
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
workflow.Execute();
workflow.Result.DisplayToConsole();
}
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 processOrbi_Scans3000_6000_Test1()
{
var minScan = 5500;
var maxScan = 6500;
Run run = new XCaliburRun2(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1, minScan, maxScan);
var workflow = new WholisticChromBasedLCMSFeatureFinderWorkflow(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan).ToList();
run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan && p.MSPeak.XValue > 771 && p.MSPeak.XValue < 775).ToList();
workflow.ExecuteWorkflow2(run);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
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 importPeaksFromUIMFFileTest1() //NOTE: 2012_11_15 - The importer imports UIMF peaks as if they were orbi peaks. All IMS scan info is ignored
{
var testPeakFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_O16O18Testing\RawData\Alz_O18_Run03_7Sep12_Cheetah_11-12-23_peaks.txt";
var mspeaks = new List <MSPeakResult>();
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(testPeakFile);
peakImporter.ImportPeaks(mspeaks);
Assert.AreEqual(202928, mspeaks.Count);
var testResult = mspeaks[0];
Assert.AreEqual(1, testResult.PeakID);
Assert.AreEqual(-1, testResult.FrameNum);
Assert.AreEqual(1, testResult.Scan_num);
Assert.AreEqual(386.74464, (decimal)testResult.MSPeak.XValue);
Assert.AreEqual(49599, testResult.MSPeak.Height);
Assert.AreEqual(199.19, (decimal)testResult.MSPeak.SignalToNoise);
Assert.AreEqual(-1, testResult.MSPeak.MSFeatureID);
// 43 800 213 357.38662 1528 0.071 100 16
}
public void find_targetMassTag_131959Test1()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
var massTagColl = masstagImporter.Import();
Assert.AreEqual(2719, massTagColl.TargetList.Count);
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//int mtID = 635428;
var mtID = 131959;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2);
Task zeroFill = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 1);
Task msPeakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var basicChromPeakSelParam = new ChromPeakSelectorParameters();
basicChromPeakSelParam.NETTolerance = 0.1f;
basicChromPeakSelParam.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
Task chromPeakSel = new BasicChromPeakSelector(basicChromPeakSelParam);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentMassTag = massTagColl.TargetList.Find(p => p.ID == mtID);
var mt = run.CurrentMassTag;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Task theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
Task targetedFeatureFinder = new BasicTFF();
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
theorFeatureGen.Execute(run.ResultCollection);
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.NormalizedElutionTime.ToString("0.000") + "; Sequence = " + mt.Code + "; EmpiricalFormula= " + mt.EmpiricalFormula + "\n");
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
msPeakDet.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
var massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
//Console.WriteLine("------------------------------ end --------------------------");
}
private void getTestMSPeaklistForChromagramGen(Run run)
{
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(peaks_rsph_AOnly_28_run1File_Scans1000_1500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
}
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();
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
MassTagCollection massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(cysteineMassTagSourceFile1, '\t');
mtidImporter.Import(massTagColl);
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky");
importer.Import(massTagColl);
Assert.AreEqual(737, massTagColl.MassTagIDList.Count);
Assert.AreEqual(826, massTagColl.MassTagList.Count);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
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, 0.75, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(6);
Task exporter = new BasicMTResultSQLiteExporter(cysteineAnalysisOutput1);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
int successCounter = 0;
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);
targetedFeatureFinder.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);
if (mt == massTagColl.MassTagList.Last())
{
exporter.Execute(run.ResultCollection);
}
}
exporter.Cleanup();
//List<IMassTagResult> successfulResults = run.ResultCollection.GetSuccessfulMassTagResults();
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();
}