public void Test1()
{
string testfile = @"D:\Data\From_Nicola\AC2_Neg_highpH_14Apr13_Sauron_13-04-03.raw";
Run run = new RunFactory().CreateRun(testfile);
TestUtilities.DisplayRunInformation(run);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
ScanSet scanSet = new ScanSet(4100);
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.Execute(run.ResultCollection);
run.PeakList = run.PeakList.Where(p => p.XValue > 742 && p.XValue < 749).ToList();
HornDeconvolutor hornDeconvolutor = new HornDeconvolutor();
hornDeconvolutor.ChargeCarrierMass = -1.00727649;
hornDeconvolutor.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void findMSFeaturesInOrbitrapData_Test1()
{
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();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
//order and get the most intense msfeature
run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IntensityAggregate).ToList();
var testIso = run.ResultCollection.ResultList[0];
Assert.AreEqual(13084442, testIso.IntensityAggregate);
Assert.AreEqual(2, testIso.IsotopicProfile.ChargeState);
Assert.AreEqual(0.01012m, (decimal)Math.Round(testIso.IsotopicProfile.Score, 5));
Assert.AreEqual(3, testIso.IsotopicProfile.Peaklist.Count);
Assert.AreEqual(481.274105402604m, (decimal)testIso.IsotopicProfile.Peaklist[0].XValue);
Assert.AreEqual(481.775412188198m, (decimal)testIso.IsotopicProfile.Peaklist[1].XValue);
Assert.AreEqual(482.276820274024m, (decimal)testIso.IsotopicProfile.Peaklist[2].XValue);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
// TestUtilities.DisplayPeaks(run.PeakList);
}
public void OldDeconvolutorTest_temp1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
#if !Disable_DeconToolsV2
var parameters = new DeconEngineClasses.OldDecon2LSParameters();
var paramFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_Thrash_MaxFit1.xml";
parameters.Load(paramFile);
var scanSet = new ScanSetFactory().CreateScanSet(run, 6005, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var deconvolutor = new HornDeconvolutor(parameters.GetDeconToolsParameters());
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
deconvolutor.Execute(run.ResultCollection);
run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IntensityAggregate).ToList();
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//IsosResult testIso = run.ResultCollection.ResultList[0];
//TestUtilities.DisplayIsotopicProfileData(testIso.IsotopicProfile);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//TestUtilities.DisplayPeaks(run.PeakList);
#endif
}
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 peak_interference_UIMF_expectInterference_test1()
{
var uimfFrame1200_142 = FileRefs.RawDataBasePath + @"\UIMF\Sarc_MS_90_21Aug10_Cheetah_10-08-02_0000_frame1200_scan142.txt";
Run run = new DeconTools.Backend.Runs.MSScanFromTextFileRun(uimfFrame1200_142);
var scanSet = new ScanSet(0);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
msgen.MinMZ = 200;
msgen.MaxMZ = 2000;
var peakDetector = new DeconToolsPeakDetectorV2(4, 3, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
decon.MinIntensityForScore = 10;
decon.DeleteIntensityThreshold = 10;
decon.MaxFitAllowed = 0.4;
decon.MinMZ = 200;
decon.MaxMZ = 2000;
decon.IsMZRangeUsed = false;
var zeroFiller = new DeconToolsZeroFiller();
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
//Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList.Where(p => p.IsotopicProfile.MonoPeakMZ > 428 && p.IsotopicProfile.MonoPeakMZ < 430).First();
var monoPeak = testResult.IsotopicProfile.getMonoPeak();
var lastPeak = testResult.IsotopicProfile.Peaklist[testResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var scanPeaks = run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
var interferenceScore = interferenceScorer.GetInterferenceScore(scanPeaks, testResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width);
stopwatch.Stop();
Console.WriteLine("interference= " + interferenceScore);
Console.WriteLine("Time taken = " + stopwatch.ElapsedMilliseconds);
}
public SaturationIMSScanBasedWorkflow(DeconToolsParameters parameters, Run run, string outputFolderPath = null, BackgroundWorker backgroundWorker = null)
: base(parameters, run, outputFolderPath, backgroundWorker)
{
Check.Require(run is UIMFRun, "Cannot create workflow. Run is required to be a UIMFRun for this type of workflow");
PeakBRSaturatedPeakDetector = parameters.PeakDetectorParameters.PeakToBackgroundRatio * 0.75;
_msGenerator = new UIMF_MSGenerator();
_peakDetector = new DeconToolsPeakDetectorV2(5, 3, Globals.PeakFitType.QUADRATIC, false);
_zeroFiller = new DeconToolsZeroFiller();
//#if Disable_DeconToolsV2
// throw new NotImplementedException("Cannot use class SaturationIMSScanBasedWorkflow since support for C++ based DeconToolsV2 is disabled");
//#else
_deconvolutor = new HornDeconvolutor(parameters)
{
MaxFitAllowed = 0.9,
MinPeptideBackgroundRatio = _peakDetector.PeakToBackgroundRatio
};
//#endif
AdjustMonoIsotopicMasses = true;
Run.PeakList = new List <Peak>();
}
public void agilentDeconTest1()
{
RunFactory runFact = new RunFactory();
Run run = runFact.CreateRun(agilentFile);
MSGeneratorFactory msfactory = new MSGeneratorFactory();
Task msgen = msfactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 7;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
ScanSet scan1821 = new ScanSet(1821);
run.CurrentScanSet = scan1821;
msgen.Execute(run.ResultCollection);
run.XYData = run.XYData.TrimData(450, 520, TODO);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void exporterTest1()
{
Run run = new IMFRun(imfFilepath);
run.CurrentScanSet = new ScanSet(233);
ResultCollection results = new ResultCollection(run);
Task msGen = new GenericMSGenerator();
msGen.Execute(results);
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);
peakDetector.Execute(results);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
Task decon = new HornDeconvolutor(hornParams);
decon.Execute(results);
Exporter <ResultCollection> exporter = new BasicIsosExporter(exporterTest1OutputName);
exporter.Export(results);
}
public void effectOfFWHMOnFitTest()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1160, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
var result1 = results.ResultList[0];
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
var distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
var sb = new StringBuilder();
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(distcreator.Data, run.XYData, 10);
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
for (var fwhm = 0.001; fwhm < 0.050; fwhm = fwhm + 0.0005)
{
distcreator = new MercuryDistributionCreator();
resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / fwhm;
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
areafitter = new AreaFitter();
fitval = areafitter.GetFit(distcreator.Data, run.XYData, 10);
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
}
//Console.Write(sb.ToString());
}
public void uimfTest1()
{
UIMFRun run = new UIMFRun(uimfFile1);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task suspPeakFlagger = new LeftOfMonoPeakLooker();
run.CurrentFrameSet = new FrameSet(501, 500, 502);
run.CurrentScanSet = new ScanSet(250, 246, 254);
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
foreach (var result in run.ResultCollection.ResultList)
{
((LeftOfMonoPeakLooker)suspPeakFlagger).CurrentResult = result;
suspPeakFlagger.Execute(run.ResultCollection);
}
Assert.AreEqual(38, run.ResultCollection.ResultList.Count);
List <IsosResult> flaggedResults = run.ResultCollection.ResultList.Where(p => p.Flags.Count > 0).ToList();
Assert.AreEqual(13, flaggedResults.Count);
TestUtilities.DisplayIsotopicProfileData(flaggedResults[0].IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(flaggedResults[1].IsotopicProfile);
}
public void fitterOnHornDataTest1()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
Task msGen = new GenericMSGenerator(1154, 1158);
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 0.5;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParameters.PeptideMinBackgroundRatio = 2;
Task decon = new HornDeconvolutor(hornParameters);
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
StringBuilder sb = new StringBuilder();
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
Console.WriteLine(sb.ToString());
AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10);
double fitval = areafitter.getFit();
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0209385414928986, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void turnRAPIDScoreIntoHornScoreAndCompareTest1()
{
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6050);
int numScansSummed = 1;
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, numScansSummed, 1, false);
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 rapid = new RapidDeconvolutor();
Task horn = new HornDeconvolutor();
Task fitcalc = new DeconToolsFitScoreCalculator();
run.CurrentScanSet = run.ScanSetCollection.GetScanSet(6005);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
horn.Execute(run.ResultCollection);
//string isosData = reportIsotopicProfiles(run);
//Console.Write(isosData);
//First evaluate HornTransform score
Assert.AreEqual(481.274105402604, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.GetMZ());
Assert.AreEqual(0.0101245114907111, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.Score);
run.ResultCollection.ClearAllResults();
horn.Execute(run.ResultCollection);
fitcalc.Execute(run.ResultCollection);
Assert.AreEqual(0.00583991502104572, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.Score);
run.ResultCollection.ClearAllResults();
//Run RAPID and evaluate the score Rapid gives it
rapid.Execute(run.ResultCollection);
Assert.AreEqual(481.274105402604, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.GetMZ());
Assert.AreEqual(1.52062147024669, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score);
//Run the DeconToolsFitScoreCalculator
fitcalc.Execute(run.ResultCollection);
//Evaluate the score given by the fitscore calculator
Assert.AreNotEqual(1.52062147024669, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score);
Assert.AreEqual(0.00583991502104572m, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score);
}
public void fitterOnHornDataTest2()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
Task msGen = new GenericMSGenerator(579, 582);
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 0.5;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
IsosResult result1 = results.ResultList[1];
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
StringBuilder sb = new StringBuilder();
XYData theorXYData = distcreator.Data;
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
distcreator.OffsetDistribution(result1.IsotopicProfile);
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
Console.WriteLine(sb.ToString());
AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10);
double fitval = areafitter.getFit();
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0704215577242672, (decimal)fitval);
}
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 uimf_data_preLoaded() // in this case, data is preloaded, preventing re-accessing the same drifttimes over and over
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
((UIMFRun)run).GetFrameDataAllFrameSets(); // this is the key line... loads data necessary for drift time calc and correction
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
public void uimf_data_not_preLoaded() // in this case the drift time is calculated every time by looking up sqlite data from uimf file
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
public void Test1()
{
var peakAssociator = new PeakToMSFeatureAssociator();
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();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
peakAssociator.Execute(run.ResultCollection);
var numPeaksAssociatedWithFeatures = 0;
foreach (var msfeature in run.ResultCollection.ResultList)
{
foreach (var peak in msfeature.IsotopicProfile.Peaklist)
{
numPeaksAssociatedWithFeatures++;
}
}
var numPeaksInPeakListWithAssociations = 0;
foreach (MSPeak peak in run.PeakList)
{
Console.WriteLine(peak.MSFeatureID + "\t" + peak.XValue + "\t" + peak.Height + "\t");
if (peak.MSFeatureID != -1)
{
numPeaksInPeakListWithAssociations++;
}
}
//I don't think I can assume this... msfeature1 might overlap and share a peak with msfeature2
//Assert.AreEqual(numPeaksAssociatedWithFeatures, numPeaksInPeakListWithAssociations);
Console.WriteLine("total peaks associated with MSFeatures = " + numPeaksAssociatedWithFeatures);
Console.WriteLine("total peaks in original peaklist that were associated = " + numPeaksInPeakListWithAssociations);
Console.WriteLine("fraction peaks assigned = " + (double)(numPeaksInPeakListWithAssociations / (double)run.PeakList.Count));
}
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 OldDeconvolutorOrbitrapTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6005, 6200, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var deconvolutor = new HornDeconvolutor();
deconvolutor.MinPeptideBackgroundRatio = 3;
//deconvolutor.IsMZRangeUsed = true;
//deconvolutor.MinMZ = 575;
//deconvolutor.MaxMZ = 585;
foreach (var scanSet in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.CurrentScanSet.BackgroundIntensity = peakDetector.BackgroundIntensity;
var stopwatch = new Stopwatch();
stopwatch.Start();
deconvolutor.Execute(run.ResultCollection);
stopwatch.Stop();
Console.WriteLine("Time for decon= \t" + stopwatch.ElapsedMilliseconds);
}
//Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
////order and get the most intense msfeature
//run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IsotopicProfile.IntensityAggregate).ToList();
//IsosResult testIso = run.ResultCollection.ResultList[0];
//Assert.AreEqual(13084442, testIso.IsotopicProfile.IntensityAggregate);
//Assert.AreEqual(2, testIso.IsotopicProfile.ChargeState);
//Assert.AreEqual(0.01012m, (decimal)Math.Round(testIso.IsotopicProfile.Score, 5));
//Assert.AreEqual(3, testIso.IsotopicProfile.Peaklist.Count);
//Assert.AreEqual(481.274105402604m, (decimal)testIso.IsotopicProfile.Peaklist[0].XValue);
//Assert.AreEqual(481.775412188198m, (decimal)testIso.IsotopicProfile.Peaklist[1].XValue);
//Assert.AreEqual(482.276820274024m, (decimal)testIso.IsotopicProfile.Peaklist[2].XValue);
//TestUtilities.DisplayIsotopicProfileData(testIso.IsotopicProfile);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//TestUtilities.DisplayPeaks(run.PeakList);
}
public void fitterOnHornDataTest2()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(579, 582, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
var result1 = results.ResultList[1];
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
var distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
var sb = new StringBuilder();
var theorXYData = distcreator.Data;
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
distcreator.OffsetDistribution(result1.IsotopicProfile);
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
//Console.WriteLine(sb.ToString());
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0763818319332606m, (decimal)fitval);
}
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 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 fitterOnHornDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
var deconParameters = new DeconToolsParameters();
deconParameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 2; // PeptideMinBackgroundRatio
Task decon = new HornDeconvolutor(deconParameters);
decon.Execute(results);
var result1 = results.ResultList[0];
var distcreator = new MercuryDistributionCreator();
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
var theorXYData = distcreator.Data;
//StringBuilder sb = new StringBuilder();
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
//Console.WriteLine(sb.ToString());
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0207350903681061m, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void Test1()
{
var rawfilename = @"D:\Data\O16O18\GlueGrant\GG_MO_Trauma_374020_20May11_Sphinx_11-03-28.RAW";
var exportedIsos = Path.Combine(Path.GetDirectoryName(rawfilename), Path.GetFileName(rawfilename).Replace(".RAW", "_test_isos.csv"));
if (File.Exists(exportedIsos))
{
File.Delete(exportedIsos);
}
var run = new RunFactory().CreateRun(rawfilename);
run.ResultCollection.ResultType = Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 5000, 5000, 1, 1);
run.CurrentScanSet = run.ScanSetCollection.ScanSetList[0];
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 1.3;
peakDet.SignalToNoiseThreshold = 2;
var decon = new HornDeconvolutor();
decon.IsO16O18Data = true;
var appender = new O16O18PeakDataAppender();
var exporter = IsosExporterFactory.CreateIsosExporter(run.ResultCollection.ResultType, Backend.Globals.ExporterType.Text, exportedIsos);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
appender.Execute(run.ResultCollection);
var testResult = (O16O18IsosResult)run.ResultCollection.ResultList[1];
Assert.AreEqual(DeconTools.Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT, run.ResultCollection.ResultType);
Assert.AreEqual(5905390, testResult.IsotopicProfile.GetMonoAbundance());
Assert.AreEqual(3017899, testResult.MonoPlus2Abundance);
Assert.AreEqual(162389, testResult.MonoPlus4Abundance);
exporter.Execute(run.ResultCollection);
run.Close();
}
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 examineFPGAFileTest1()
{
UIMFRun run = new UIMFRun(uimfFPGAFilePath);
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();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 300, 300, 1, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 5, 5, 1, 1);
fscc.Create();
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msGen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.XYData);
originalIntensitiesExtractor.Execute(run.ResultCollection);
TestUtilities.DisplayXYValues(run.XYData);
}
}
}
public void peak_interference_weakFeature_test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList.Where(p => p.IsotopicProfile.MonoPeakMZ > 597 && p.IsotopicProfile.MonoPeakMZ < 598).First();
var monoPeak = testResult.IsotopicProfile.getMonoPeak();
var lastPeak = testResult.IsotopicProfile.Peaklist[testResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var scanPeaks = run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
var interferenceScore = interferenceScorer.GetInterferenceScore(scanPeaks, testResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width);
stopwatch.Stop();
Console.WriteLine("interference= " + interferenceScore);
Console.WriteLine("Time taken = " + stopwatch.ElapsedMilliseconds);
}
public void interference_allFeaturesInScan_test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
foreach (var isosResult in run.ResultCollection.ResultList)
{
var monoPeak = isosResult.IsotopicProfile.getMonoPeak();
var lastPeak = isosResult.IsotopicProfile.Peaklist[isosResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var interferenceScore = interferenceScorer.GetInterferenceScore(run.XYData, isosResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width, startIndexOfXYData);
stopwatch.Stop();
Console.WriteLine("interference= \t" + interferenceScore);
}
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
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 void test1()
{
Run run = new MSScanFromTextFileRun(sourceXYData);
MSGeneratorFactory fact = new MSGeneratorFactory();
Task msGen = fact.CreateMSGenerator(run.MSFileType);
msGen.Execute(run.ResultCollection);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false);
peakDet.Execute(run.ResultCollection);
HornDeconvolutor decon = new HornDeconvolutor();
decon.Execute(run.ResultCollection);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//TestUtilities.DisplayPeaks(run.PeakList);
}
