public void serializeUIMFDataTest1()
{
Run run = new UIMFRun(uimfFilepath2);
List <Run> runCollection = new List <Run>();
runCollection.Add(run);
int startFrame = 1200;
int stopFrame = 1205;
int numFramesSummed = 3;
int numScansSummed = 3;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, numScansSummed, 1);
scanSetCreator.Create();
Task msgen = new UIMF_MSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = true;
Task peakdetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new RapidDeconvolutor();
TaskCollection taskcollection = new TaskCollection();
taskcollection.TaskList.Add(msgen);
taskcollection.TaskList.Add(peakdetector);
taskcollection.TaskList.Add(decon);
TaskController taskcontroller = new UIMF_TaskController(taskcollection);
taskcontroller.IsosResultThresholdNum = 50;
taskcontroller.Execute(runCollection);
ResultCollection results;
IsosResultDeSerializer deserializer = new IsosResultDeSerializer(run.Filename + "_tmp.bin");
int counter = 0;
do
{
counter++;
results = deserializer.GetNextSetOfResults();
} while (results != null);
Assert.AreEqual(8, counter);
}
public void test1_summing()
{
Project.Reset();
Project project = Project.getInstance();
UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1201);
project.RunCollection.Add(run);
int numFramesSummed = 3;
int numScansSummed = 3;
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 250, 270, numScansSummed, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, numFramesSummed, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(200, 2000);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new HornDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
Task originalIntensitiesExtractor = new OriginalIntensitiesExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
project.TaskCollection.TaskList.Add(originalIntensitiesExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
ResultCollection rc = project.RunCollection[0].ResultCollection;
Assert.AreEqual(180, rc.ResultList.Count);
StringBuilder sb = new StringBuilder();
IsosResultUtilities.DisplayResults(sb, rc.ResultList);
Console.Write(sb.ToString());
}
public void multipleFrames_horn_test1()
{
Project.Reset();
Project project = Project.getInstance();
project.LoadOldDecon2LSParameters(uimfParameters1);
UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1203);
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(0, 5000);
Task zeroFiller = new DeconToolsZeroFiller(3);
Task peakDetector = new DeconToolsPeakDetector(project.Parameters.OldDecon2LSParameters.PeakProcessorParameters);
Task decon = new HornDeconvolutor(project.Parameters.OldDecon2LSParameters.HornTransformParameters);
Task scanResultsUpdater = new ScanResultUpdater();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(zeroFiller);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
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);
Console.WriteLine("Peaks found = " + project.RunCollection[0].ResultCollection.ScanResultList[0].NumPeaks);
StringBuilder sb = new StringBuilder();
}
public void test1()
{
Project project = Project.getInstance();
//TODO: add project parameters (for summing)
Run run = new UIMFRun(uimfFilepath, 1200, 1202, 300, 400);
project.RunCollection.Add(run);
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, ((UIMFRun)run).MinFrame, ((UIMFRun)run).MaxFrame, 1, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetcreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false);
scanSetcreator.Create();
Task msGen = new UIMF_MSGenerator(200, 2000);
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();
Task scanresultUpdater = new ScanResultUpdater();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(rapidDecon);
project.TaskCollection.TaskList.Add(scanresultUpdater);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
UIMFScansExporter scansExporter = new UIMFScansExporter(uimfScansExporterTest1output);
scansExporter.Export(project.RunCollection[0].ResultCollection);
}
public void smallExportTest1()
{
Project project = Project.getInstance();
//TODO: add project parameters (for summing)
project.RunCollection.Add(new UIMFRun(uimfFilepath, 1200, 1202, 250, 300));
Task msGen = new UIMF_MSGenerator(200, 2000);
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 decon = new HornDeconvolutor();
Task driftTimeExtractor = new UIMFDriftTimeExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(driftTimeExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
UIMFIsosExporter isosExporter = new UIMFIsosExporter(uimfIsosExporterTest1output);
isosExporter.Export(project.RunCollection[0].ResultCollection);
}
public void multipleFrames_horn_test4()
{
Project.Reset();
//Project.getInstance().LoadOldDecon2LSParameters(uimfParameters1);
UIMFRun run = new UIMFRun(uimfFilepath, 1202, 1202);
Project.getInstance().RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(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);
Task scanResultsUpdater = new ScanResultUpdater();
Project.getInstance().TaskCollection.TaskList.Add(msGen);
Project.getInstance().TaskCollection.TaskList.Add(zeroFiller);
Project.getInstance().TaskCollection.TaskList.Add(peakDetector);
Project.getInstance().TaskCollection.TaskList.Add(decon);
Project.getInstance().TaskCollection.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new UIMF_TaskController(Project.getInstance().TaskCollection);
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[0].NumPeaks);
StringBuilder sb = new StringBuilder();
}
public void test1()
{
Project.Reset();
Project project = Project.getInstance();
UIMFRun run = new UIMFRun(uimfFilepath, 1200, 1202);
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(200, 2000);
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();
Task scanResultsUpdater = new ScanResultUpdater();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(rapidDecon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
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);
Assert.AreEqual(1, Project.getInstance().RunCollection.Count);
Assert.AreEqual(4, project.TaskCollection.TaskList.Count);
Assert.AreEqual(600, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
UIMFRun uimfRun = (UIMFRun)(project.RunCollection[0]);
Assert.AreEqual(3, uimfRun.FrameSetCollection.FrameSetList.Count);
StringBuilder sb = new StringBuilder();
foreach (IsosResult result in project.RunCollection[0].ResultCollection.ResultList)
{
Assert.IsInstanceOfType(typeof(UIMFIsosResult), result);
UIMFIsosResult uimfResult = (UIMFIsosResult)result;
sb.Append(uimfResult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(uimfResult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.Peaklist[0].XValue);
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.GetAbundance());
sb.Append("\t");
//sb.Append(uimfResult.IsotopicProfile.
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
public void test1()
{
Run uimfrun = new UIMFRun(inputUIMFFile1);
int startFrame = 800;
int stopFrame = 800;
int numFramesSummed = 3;
int numScansSummed = 9;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(uimfrun, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(uimfrun, 230, 240, numScansSummed, 1, false);
scansetCreator.Create();
Project project = Project.getInstance();
project.RunCollection.Add(uimfrun);
Task msGen = new UIMF_MSGenerator(200, 2000);
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 decon = new HornDeconvolutor();
Task driftTimeExtractor = new UIMFDriftTimeExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(driftTimeExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
Assert.AreEqual(252, project.RunCollection[0].ResultCollection.ResultList.Count);
if (File.Exists(outputFile1))
{
File.Delete(outputFile1);
}
Stopwatch sw = new Stopwatch();
sw.Start();
UIMFSQLiteIsosExporter isosExporter = new UIMFSQLiteIsosExporter(outputFile1);
isosExporter.Export(project.RunCollection[0].ResultCollection);
sw.Stop();
Console.Write("\n\n----------- Time taken for UIMFSQLiteIsosExporter (milliseconds) = \t" + sw.ElapsedMilliseconds);
}