public static Run CreateResultsFromThreeScansOfStandardOrbitrapData()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6000, 6020, 1, 1, false);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
Task peakDetector = new DeconToolsPeakDetectorV2();
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
msScanInfoCreator.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
}
return(run);
}
public void deconWithRAPID_Then_ValidateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
ScanSet scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
MSGenerator msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
RapidDeconvolutor decon = new RapidDeconvolutor();
ResultValidatorTask validator = new ResultValidatorTask();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
validator.Execute(run.ResultCollection);
Assert.AreEqual(190, run.ResultCollection.ResultList.Count);
IsosResult testResult = run.ResultCollection.ResultList[0];
Assert.AreEqual(0.0213668719893332m, (decimal)testResult.InterferenceScore);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void deconWithTHRASH_Then_ValidateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
var validator = new ResultValidatorTask();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
validator.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList[0];
Assert.AreEqual(0.0532199478712594m, (decimal)testResult.InterferenceScore);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void outputToText_xcaliburData_Test1()
{
string testFile = xcalibur_text_IsosResultOutputFile1;
List <Run> runcoll = new List <Run>();
Run run = new XCaliburRun(xcaliburFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6020, 1, 1, false);
sscc.Create();
Task msgen = new GenericMSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task flagger = new ResultValidatorTask();
Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.BasicIsosResultTextFileExporter(testFile);
Task peakExporter = new DeconTools.Backend.ProcessingTasks.PeakListExporters.PeakListSQLiteExporter(100000, peakExporter1);
Stopwatch sw;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
isosExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("Exporter execution time = \t" + sw.ElapsedMilliseconds);
}
peakExporter.Execute(run.ResultCollection);
}
Assert.AreEqual(true, File.Exists(testFile));
FileInfo fi = new FileInfo(testFile);
//Assert.AreEqual(25881, fi.Length);
Console.Write(fi.Length);
}
public void outputToText_xcaliburData_Test2()
{
string testFile = xcalibur_text_IsosResultOutputFile1;
List <Run> runcoll = new List <Run>();
Run run = new XCaliburRun(xcaliburFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6020, 1, 1, false);
sscc.Create();
Task msgen = new GenericMSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task flagger = new ResultValidatorTask();
BasicIsosResultTextFileExporter isosExporter = new BasicIsosResultTextFileExporter(testFile);
Stopwatch sw;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
}
isosExporter.ExportIsosResults(run.ResultCollection.ResultList);
Assert.AreEqual(true, File.Exists(testFile));
FileInfo fi = new FileInfo(testFile);
//Assert.AreEqual(25881, fi.Length);
Console.Write(fi.Length);
}
public static Run CreateResultsFromTwoFramesOfStandardUIMFData()
{
var run = new UIMFRun(FileRefs.RawDataMSFiles.UIMFStdFile1);
run.ResultCollection.ResultType = Globals.ResultType.UIMF_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 500, 501, 3, 1);
run.IMSScanSetCollection.Create(run, 250, 270, 9, 1);
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetectorV2();
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor();
Task driftTimeextractor = new UIMFDriftTimeExtractor();
foreach (var frame in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = frame;
foreach (IMSScanSet scan in run.IMSScanSetCollection.ScanSetList)
{
run.CurrentIMSScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
driftTimeextractor.Execute(run.ResultCollection);
msScanInfoCreator.Execute(run.ResultCollection);
ticExtractor.Execute(run.ResultCollection);
}
}
return(run);
}
public void outputToText_uimf_test1()
{
if (File.Exists(uimf_text_IsosResultOutputFile1))
{
File.Delete(uimf_text_IsosResultOutputFile1);
}
List <Run> runcoll = new List <Run>();
Run run = new UIMFRun(uimfFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 240, 9, 1, false);
sscc.Create();
FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fsc.Create();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor();
Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.UIMFIsosResultTextFileExporter(uimf_text_IsosResultOutputFile1, 1000000);
Task flagger = new ResultValidatorTask();
Stopwatch sw;
foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
origIntensExtr.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
isosExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("execution time = \t" + sw.ElapsedMilliseconds);
}
}
}
Assert.AreEqual(true, File.Exists(uimf_text_IsosResultOutputFile1));
FileInfo fi = new FileInfo(uimf_text_IsosResultOutputFile1);
Assert.AreEqual(99743, fi.Length);
Console.Write(fi.Length);
}