public void simpleAddTest1()
{
//first deconvolute with THRASH
//then deconvolute with RAPID, using comboMode = 'simplyAddIt'
//so there will be duplicate results
Project.Reset();
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6050);
Project.getInstance().RunCollection.Add(run);
ResultCollection results = new ResultCollection(run);
TaskCollection taskCollection = new TaskCollection();
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false);
scansetCreator.Create();
Task msgen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters peakDetParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
peakDetParams.SignalToNoiseThreshold = 3;
peakDetParams.PeakBackgroundRatio = 0.5;
Task peakDetector = new DeconToolsPeakDetector(peakDetParams);
Task thrashDecon = new HornDeconvolutor();
Task rapidDecon = new RapidDeconvolutor();
taskCollection.TaskList.Add(msgen);
taskCollection.TaskList.Add(peakDetector);
taskCollection.TaskList.Add(thrashDecon);
TaskController taskcontroller = new BasicTaskController(taskCollection);
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(644, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
taskCollection.TaskList.Remove(thrashDecon);
taskCollection.TaskList.Add(rapidDecon);
Project.getInstance().RunCollection[0].ResultCollection.ResultList.Clear();
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(2472, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
Project.getInstance().RunCollection[0].ResultCollection.ResultList.Clear();
taskCollection.TaskList.Remove(rapidDecon);
taskCollection.TaskList.Add(thrashDecon);
taskCollection.TaskList.Add(rapidDecon);
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(2472 + 644, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
}
public void xcaliburFile100ScanRAPIDTest1()
{
Project.Reset();
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6999);
Project project = Project.getInstance();
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1);
sscc.Create();
Task msGen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task rapidDecon = new RapidDeconvolutor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(rapidDecon);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
Assert.AreEqual(1, Project.getInstance().RunCollection.Count);
Assert.AreEqual(3, project.TaskCollection.TaskList.Count);
Assert.AreEqual(1000, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Assert.AreEqual(12762, project.RunCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + project.RunCollection[0].ResultCollection.ResultList.Count);
}
public void xcaliburFileMSMSDataTest1()
{
//exploring how only MSMS data is processed...
Project.Reset();
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6004); //only MS/MS data here
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1);
sscc.Create();
Project project = Project.getInstance();
project.RunCollection.Add(run);
Task msGen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 1.3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 2;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornparams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornparams.PeptideMinBackgroundRatio = 2;
Task hornDecon = new HornDeconvolutor(hornparams);
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(hornDecon);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
Assert.AreEqual(1, Project.getInstance().RunCollection.Count);
Assert.AreEqual(3, project.TaskCollection.TaskList.Count);
// Assert.AreEqual(21, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Assert.AreEqual(0, project.RunCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + project.RunCollection[0].ResultCollection.ResultList.Count);
}
public void test1()
{
Run run0 = new XCaliburRun(c2_blankfilePath);
Run run1 = new XCaliburRun(c2_6FilePath);
Run run2 = new XCaliburRun(c2_7FilePath);
Run run3 = new XCaliburRun(c2_8FilePath);
Run run4 = new XCaliburRun(c2_9FilePath);
Run run5 = new XCaliburRun(c2_10FilePath);
Project.getInstance().RunCollection.Add(run0);
Project.getInstance().RunCollection.Add(run1);
Project.getInstance().RunCollection.Add(run2);
Project.getInstance().RunCollection.Add(run3);
Project.getInstance().RunCollection.Add(run4);
Project.getInstance().RunCollection.Add(run5);
foreach (Run run in Project.getInstance().RunCollection)
{
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, 1, 1);
scansetCreator.Create();
}
Task msgen = new GenericMSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new SimpleDecon();
Task isosMergerExporter = new BasicIsosMergerExporter("..\\..\\TestFiles\\MergeTestFiles\\BasicIsosMergerExporterTest1Output_isos.csv");
Task scansupdater = new ScanResultUpdater();
Task scansMergerExporter = new BasicScansMergerExporter("..\\..\\TestFiles\\MergeTestFiles\\BasicIsosMergerExporterTest1Output_scans.csv");
Project.getInstance().TaskCollection.TaskList.Add(msgen);
Project.getInstance().TaskCollection.TaskList.Add(peakDetector);
Project.getInstance().TaskCollection.TaskList.Add(decon);
Project.getInstance().TaskCollection.TaskList.Add(isosMergerExporter);
Project.getInstance().TaskCollection.TaskList.Add(scansupdater);
Project.getInstance().TaskCollection.TaskList.Add(scansMergerExporter);
BasicTaskController taskController = new BasicTaskController(Project.getInstance().TaskCollection);
taskController.Execute(Project.getInstance().RunCollection);
TaskCleaner cleaner = new TaskCleaner(Project.getInstance().TaskCollection);
cleaner.CleanTasks();
}
public void test1()
{
Run xcalRun = new XCaliburRun(xcaliburTestfile, 6000, 6020);
Run mzxmlRun = new MZXMLRun(mzxmlfile1, 1, 21);
List <Run> runCollection = new List <Run>();
runCollection.Add(xcalRun);
runCollection.Add(mzxmlRun);
int numScansSummed = 1;
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(xcalRun, xcalRun.MinScan, xcalRun.MaxScan, numScansSummed, 1, false);
scanSetCreator.Create();
scanSetCreator = new ScanSetCollectionCreator(mzxmlRun, mzxmlRun.MinScan, mzxmlRun.MaxScan, numScansSummed, 1);
scanSetCreator.Create();
Task msgen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detParams.PeakBackgroundRatio = 3;
detParams.SignalToNoiseThreshold = 3;
Task peakDet = new DeconToolsPeakDetector(detParams);
Task horn = new HornDeconvolutor();
TaskCollection taskColl = new TaskCollection();
taskColl.TaskList.Add(msgen);
taskColl.TaskList.Add(peakDet);
taskColl.TaskList.Add(horn);
TaskController taskController = new BasicTaskController(taskColl);
taskController.Execute(runCollection);
Assert.AreEqual(true, TestUtilities.AreIsosResultsTheSame(xcalRun.ResultCollection.ResultList, mzxmlRun.ResultCollection.ResultList));
}
public void xcaliburSimpleTest1()
{
Run run = new XCaliburRun(xcaliburTestfile);
Project.getInstance().RunCollection.Add(run);
ScanSetCollectionCreator scanSetCollectionCreator = new ScanSetCollectionCreator(run, 6000, 6020, 1, 1);
scanSetCollectionCreator.Create();
Task msGenerator = new GenericMSGenerator();
Task msPeakDetector = new DeconToolsPeakDetector();
Task thrashDecon = new HornDeconvolutor();
Task exporter = new BasicIsosResultSqliteExporter("..\\..\\TestFiles\\tempOutput.db3");
Project.getInstance().TaskCollection.TaskList.Add(msGenerator);
Project.getInstance().TaskCollection.TaskList.Add(msPeakDetector);
Project.getInstance().TaskCollection.TaskList.Add(thrashDecon);
Project.getInstance().TaskCollection.TaskList.Add(exporter);
TaskController controller = new BasicTaskController(Project.getInstance().TaskCollection);
controller.Execute(Project.getInstance().RunCollection);
}
public void compareThrashRapidTest2()
{
IsosResultComparer comparer = new IsosResultComparer();
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6050);
Project.getInstance().RunCollection.Add(run);
ResultCollection results = new ResultCollection(run);
TaskCollection taskCollection = new TaskCollection();
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1);
scansetCreator.Create();
Task msgen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters peakDetParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
peakDetParams.SignalToNoiseThreshold = 3;
peakDetParams.PeakBackgroundRatio = 0.5;
Task peakDetector = new DeconToolsPeakDetector(peakDetParams);
Task thrashDecon = new HornDeconvolutor();
Task rapidDecon = new RapidDeconvolutor();
taskCollection.TaskList.Add(msgen);
taskCollection.TaskList.Add(peakDetector);
taskCollection.TaskList.Add(thrashDecon);
TaskController taskcontroller = new BasicTaskController(taskCollection);
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(644, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
List <IsosResult> thrashResults = new List <IsosResult>(Project.getInstance().RunCollection[0].ResultCollection.ResultList);
taskCollection.TaskList.Remove(thrashDecon);
taskCollection.TaskList.Add(rapidDecon);
Project.getInstance().RunCollection[0].ResultCollection.ResultList.Clear();
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(2472, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
List <IsosResult> rapidResults = new List <IsosResult>(Project.getInstance().RunCollection[0].ResultCollection.ResultList);
Console.WriteLine("Thrash result count = " + thrashResults.Count);
Console.WriteLine("RAPID result count = " + rapidResults.Count);
List <IsosResult> intersectedResults = comparer.GetIntersectionBetweenTwoIsosResultSets(thrashResults, rapidResults);
List <IsosResult> intersectedResults2 = comparer.GetIntersectionTheManualWay(thrashResults, rapidResults);
//List<IsosResult> intersectedResults3 = comparer.GetIntersectionTheManualWay(rapidResults, thrashResults);
List <IsosResult> unmatchedResults1 = comparer.GetUniqueBetweenTwoIsosResultSets(rapidResults, thrashResults);
List <IsosResult> unmatchedResults2 = comparer.GetUniqueBetweenTwoIsosResultSets(thrashResults, rapidResults);
Console.WriteLine("Intersected result count = " + intersectedResults.Count);
Console.WriteLine("Manual Intersected result count = " + intersectedResults2.Count);
//Console.WriteLine("Manual Intersected result count = " + intersectedResults3.Count);
Console.WriteLine("unmatched result count = " + unmatchedResults1.Count);
Console.WriteLine("unmatched result count2 = " + unmatchedResults2.Count);
}
public void multiIMFFileDeconTest1()
{
imfFileList.Clear();
imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_QS_16V_0000.Accum_1.IMF");
imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_QS_16V_0000.Accum_2.IMF");
imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_SQ_14V_0000.Accum_1.IMF");
Project.Reset();
Project project = Project.getInstance();
foreach (string strItem in imfFileList)
{
Run run = new IMFRun(strItem, 233, 233);
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1);
sscc.Create();
}
Task msGen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornparams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornparams.PeptideMinBackgroundRatio = 5;
Task hornDecon = new HornDeconvolutor(hornparams);
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(hornDecon);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
Assert.AreEqual(3, Project.getInstance().RunCollection.Count);
Assert.AreEqual(3, project.TaskCollection.TaskList.Count);
Assert.AreEqual(1, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Assert.AreEqual(12, project.RunCollection[0].ResultCollection.ResultList.Count);
int totalScans = 0;
int totalFeatures = 0;
for (int i = 0; i < project.RunCollection.Count; i++)
{
Console.WriteLine("Run name = " + project.RunCollection[i].Filename);
Console.WriteLine("Scans analyzed = " + project.RunCollection[i].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + project.RunCollection[i].ResultCollection.ResultList.Count);
totalFeatures += project.RunCollection[i].ResultCollection.ResultList.Count;
totalScans += project.RunCollection[i].ScanSetCollection.ScanSetList.Count;
}
Console.WriteLine("------------------------------------------------");
Console.WriteLine("Total Features found = " + totalFeatures);
Console.WriteLine("Total Scans = " + totalScans);
Console.WriteLine("Total Time required (ms) = " + sw.ElapsedMilliseconds);
}
public void imf_projectRef_horn_test2()
{
Project.Reset();
//Project.getInstance().RunCollection = new List<Run>();
Run run = new IMFRun(imfFilePath);
Project.getInstance().RunCollection.Add(run);
Project.getInstance().LoadOldDecon2LSParameters(imfParameters1);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
Task msGen = new GenericMSGenerator(0, 5000);
Task zeroFiller = new DeconToolsZeroFiller(3);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 4;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParams.CompleteFit = true;
hornParams.LeftFitStringencyFactor = 2.5;
hornParams.RightFitStringencyFactor = 0.5;
hornParams.PeptideMinBackgroundRatio = 4;
hornParams.MaxFit = 0.4;
hornParams.UseMZRange = false;
hornParams.UseMercuryCaching = true;
Task decon = new HornDeconvolutor(hornParams);
HornDeconvolutor horn = (HornDeconvolutor)decon;
Task scanResultsUpdater = new ScanResultUpdater();
TaskCollection tc = new TaskCollection();
tc.TaskList.Add(msGen);
tc.TaskList.Add(zeroFiller);
tc.TaskList.Add(peakDetector);
tc.TaskList.Add(decon);
tc.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(tc);
controller.Execute(Project.getInstance().RunCollection);
sw.Stop();
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + Project.getInstance().RunCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Peaks found = " + Project.getInstance().RunCollection[0].ResultCollection.ScanResultList.Sum(p => p.NumPeaks));
StringBuilder sb = new StringBuilder();
}
