public void test1()
{
Run run = new XCaliburRun(lowmwRawfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(1);
Task msgen = new GenericMSGenerator(0, 1000);
msgen.Execute(results);
DeconToolsPeakDetector peakdetector = new DeconToolsPeakDetector();
peakdetector.PeakBackgroundRatio = 0.5;
peakdetector.PeakFitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
peakdetector.SigNoiseThreshold = 3;
peakdetector.IsDataThresholded = true;
peakdetector.Execute(results);
//Task rapidDecon = new RapidDeconvolutor();
//rapidDecon.Execute(results);
Task simpleDecon = new SimpleDecon(0.0005);
simpleDecon.Execute(results);
Console.WriteLine(results.Run.PeakList.Count);
Console.WriteLine(results.ResultList.Count);
string reportedResults = reportResults(results.ResultList);
Console.WriteLine(reportedResults);
}
public void test1()
{
Run run = new ICR2LSRun(icr2LSRawDatafile1);
run.CurrentScanSet = new ScanSet(2210);
Task msGen = new GenericMSGenerator(732, 746);
msGen.Execute(run.ResultCollection);
Task peakdetector = new DeconToolsPeakDetector();
((DeconToolsPeakDetector)peakdetector).PeakBackgroundRatio = 5;
((DeconToolsPeakDetector)peakdetector).SigNoiseThreshold = 2;
peakdetector.Execute(run.ResultCollection);
Console.WriteLine("Peaks detected = " + run.PeakList.Count);
TomN14N15Analyzer analyzer = new TomN14N15Analyzer();
analyzer.ExtractN14N15Values(run.ResultCollection);
Console.WriteLine("Peaks detected = " + run.PeakList.Count);
Assert.AreEqual(14, run.PeakList.Count);
}
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 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 xcaliburSpeed_RAPID_Test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
int startScan = 6005;
int stopScan = 7000;
int numScansSummed = 1;
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, startScan, stopScan, numScansSummed, 1);
scanSetCreator.Create();
ResultCollection results = new ResultCollection(run);
List <timingResult> timingResults = new List <timingResult>();
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
if (results.Run.GetMSLevel(scanset.PrimaryScanNumber) != 1)
{
continue;
}
sw.Reset();
timingResult timeresult = new timingResult();
timeresult.frameNum = -1;
timeresult.scanNum = scanset.PrimaryScanNumber;
sw.Start();
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator();
msgen.Execute(results);
timeresult.msGenTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(results);
timeresult.peakDetectorTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task rapid = new RapidDeconvolutor();
rapid.Execute(results);
timeresult.deconTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
timeresult.resultUpdaterTime = sw.ElapsedMilliseconds;
timingResults.Add(timeresult);
}
reportTimingEachScan(timingResults);
}
public void examineIMFFile_Scan233MZ630()
{
Run run = new IMFRun(imfFilepath);
run.MSParameters = new DeconTools.Backend.Parameters.MSParameters();
run.CurrentScanSet = new ScanSet(233, 229, 237);
run.MSParameters.MinMZ = 100;
run.MSParameters.MaxMZ = 631.5;
int numPeaks = 0;
for (double n = 629; n < 630; n = n + 0.01)
{
ResultCollection rc = new ResultCollection(run);
Task msGen = new GenericMSGenerator(n, run.MSParameters.MaxMZ);
msGen.Execute(rc);
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 zeroFiller = new DeconToolsZeroFiller(3);
//zeroFiller.Execute(rc);
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(rc);
Task decon = new RapidDeconvolutor();
decon.Execute(rc);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < rc.ResultList.Count; i++)
{
IsosResult result = rc.ResultList[i];
if (result.IsotopicProfile.Peaklist[0].XValue > 629 && result.IsotopicProfile.Peaklist[0].XValue < 631)
{
sb.Append(n.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Peaklist[0].XValue.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Score.ToString("0.00"));
sb.Append("\t");
sb.Append(result.Run.PeakList.Count);
sb.Append("\t");
sb.Append(result.Run.XYData.Xvalues.Length);
sb.Append("\n");
}
}
Console.Write(sb.ToString());
}
}
public void MSGeneratorOnAgilentDFileTest1()
{
Run run = new AgilentD_Run(agilentDTestFile);
run.CurrentScanSet = new ScanSet(25);
Task msGen = new GenericMSGenerator();
msGen.Execute(run.ResultCollection);
}
public void MSGeneratoronTextFileTest2()
{
Run run = new MSScanFromTextFileRun(textFile1);
Task msgen = new GenericMSGenerator();
msgen.Execute(run.ResultCollection);
Assert.AreEqual(19716, run.XYData.Xvalues.Length);
}
public void test1()
{
Run run = new MSScanFromTextFileRun(imfMSScanTextfile);
ResultCollection resultcollection = new ResultCollection(run);
Task msgen = new GenericMSGenerator();
msgen.Execute(resultcollection);
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(resultcollection);
Task rapidDecon = new RapidDeconvolutor();
rapidDecon.Execute(resultcollection);
int counter = 0;
foreach (StandardIsosResult result in resultcollection.ResultList)
{
IsotopicProfile profile = result.IsotopicProfile;
Console.Write("------------ profile" + counter + "; Charge state = " + profile.ChargeState
+ "; Score= " + profile.Score.ToString("0.00") + " ----------------\n");
int peakcounter = 0;
Console.Write("idx" + "\t" + "mz" + "\t" + "intensity" + "\t" + "SN" + "\t" + "FWHM" + "\n");
foreach (MSPeak peak in profile.Peaklist)
{
Console.Write(peakcounter + "\t" + peak.XValue + "\t" + peak.Height + "\t" + peak.SN + "\t" + peak.Width + "\n");
peakcounter++;
}
counter++;
}
Assert.AreEqual(9, resultcollection.ResultList.Count);
Assert.AreEqual(582.820684517665, Convert.ToDecimal(resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].XValue));
Assert.AreEqual(2984.0, resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].Height);
Assert.AreEqual(0.05905123, (decimal)resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].Width);
Assert.AreEqual(157.0526, (decimal)resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].SN);
Assert.AreEqual(4593, resultcollection.ResultList[0].IsotopicProfile.GetAbundance());
Assert.AreEqual(1, resultcollection.ResultList[8].IsotopicProfile.GetNumOfIsotopesInProfile());
Assert.AreEqual(2488.07303881522, Convert.ToDecimal(resultcollection.ResultList[8].IsotopicProfile.AverageMass));
Assert.AreEqual(3, resultcollection.ResultList[8].IsotopicProfile.ChargeState);
Assert.AreEqual(18802, Convert.ToDecimal(resultcollection.ResultList[8].IsotopicProfile.IntensityAggregate));
Assert.AreEqual(2486.09777364184, Convert.ToDecimal(resultcollection.ResultList[8].IsotopicProfile.MonoIsotopicMass));
}
public void examineRAWFile_Scan6757()
{
Run run = new XCaliburRun(xcaliburTestfile);
run.MSParameters = new DeconTools.Backend.Parameters.MSParameters();
run.CurrentScanSet = new ScanSet(6757);
run.MSParameters.MinMZ = 0;
run.MSParameters.MaxMZ = 10000;
ResultCollection rc = new ResultCollection(run);
Task msGen = new GenericMSGenerator(run.MSParameters.MinMZ, run.MSParameters.MaxMZ);
msGen.Execute(rc);
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 zeroFiller = new DeconToolsZeroFiller(3);
//zeroFiller.Execute(rc);
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(rc);
Task decon = new RapidDeconvolutor();
decon.Execute(rc);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < rc.ResultList.Count; i++)
{
IsosResult result = rc.ResultList[i];
if (result.IsotopicProfile.Peaklist[0].XValue > 0 && result.IsotopicProfile.Peaklist[0].XValue < 10000)
{
sb.Append(result.IsotopicProfile.Peaklist[0].XValue.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Score.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Peaklist[0].SN.ToString("0.0"));
sb.Append("\t");
sb.Append(result.Run.PeakList.Count);
sb.Append("\t");
sb.Append(result.Run.XYData.Xvalues.Length);
sb.Append("\n");
}
}
Console.Write(sb.ToString());
}
public void ExportMultipleScansTest1()
{
Run run = new IMFRun(imfFilepath);
ScanSetCollection scanSetCollection = new ScanSetCollection();
scanSetCollection.ScanSetList.Add(new ScanSet(232));
scanSetCollection.ScanSetList.Add(new ScanSet(233));
scanSetCollection.ScanSetList.Add(new ScanSet(234));
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in scanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
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);
Task decon = new RapidDeconvolutor();
decon.Execute(results);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
}
Assert.AreEqual(3, results.ScanResultList.Count);
Assert.AreEqual(92, results.ScanResultList[0].NumPeaks);
Assert.AreEqual(82, results.ScanResultList[1].NumPeaks);
Assert.AreEqual(72, results.ScanResultList[2].NumPeaks);
Assert.AreEqual(11, results.ScanResultList[0].NumIsotopicProfiles);
Assert.AreEqual(9, results.ScanResultList[1].NumIsotopicProfiles);
Assert.AreEqual(9, results.ScanResultList[2].NumIsotopicProfiles);
Assert.AreEqual(830.045752112968, (Decimal)results.ScanResultList[0].BasePeak.XValue);
Assert.AreEqual(10438, results.ScanResultList[0].BasePeak.Height);
Assert.AreEqual(0.09454554, (Decimal)results.ScanResultList[0].BasePeak.Width);
Assert.AreEqual(434.9167, (Decimal)results.ScanResultList[0].BasePeak.SN);
Exporter <ResultCollection> exporter = new BasicScansExporter(scansExporterTest1output);
exporter.Export(results);
}
public void MSGeneratorOnTextfileTest1()
{
Run run = new MSScanFromTextFileRun(imfMSScanTextfile, Globals.XYDataFileType.Textfile);
ResultCollection resultcollection = new ResultCollection(run);
Task msgen = new GenericMSGenerator();
msgen.Execute(resultcollection);
Assert.AreEqual(2596, resultcollection.Run.XYData.Xvalues.Length);
}
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 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 fitterOnRapidDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
bool isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
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 DeconToolsPeakDetectorV2(detectorParams);
peakDetector.Execute(results);
Task decon = new RapidDeconvolutor();
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
// theorXYData.Display();
AreaFitter areafitter = new AreaFitter();
double 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(0.0207350903681061m, (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 MSGeneratorOnIMFFileTest2()
{
Run run = new IMFRun(imfFilepath);
run.CurrentScanSet = new ScanSet(233, 229, 237);
Task msgen = new GenericMSGenerator();
msgen.Execute(run.ResultCollection);
Assert.AreEqual(9917, run.XYData.Xvalues.Length);
Assert.AreEqual(1, run.GetMSLevel(run.CurrentScanSet.PrimaryScanNumber));
}
public void DeconToolsPeakDetectionTest1()
{
Run run = new MSScanFromTextFileRun(imfMSScanTextfile);
ResultCollection resultcollection = new ResultCollection(run);
Task msgen = new GenericMSGenerator();
msgen.Execute(resultcollection);
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(resultcollection);
Assert.AreEqual(82, resultcollection.Run.PeakList.Count);
Assert.AreEqual(167.243318707619, Convert.ToDecimal(resultcollection.Run.CurrentScanSet.BackgroundIntensity));
detectorParams.PeakBackgroundRatio = 2;
peakdetector = new DeconToolsPeakDetector(detectorParams);
peakdetector.Execute(resultcollection);
Assert.AreEqual(154, resultcollection.Run.PeakList.Count);
Assert.AreEqual(167.243318707619, Convert.ToDecimal(resultcollection.Run.CurrentScanSet.BackgroundIntensity));
detectorParams.PeakBackgroundRatio = 2;
detectorParams.SignalToNoiseThreshold = 1;
peakdetector = new DeconToolsPeakDetector(detectorParams);
peakdetector.Execute(resultcollection);
Assert.AreEqual(156, resultcollection.Run.PeakList.Count);
Assert.AreEqual(167.243318707619, Convert.ToDecimal(resultcollection.Run.CurrentScanSet.BackgroundIntensity));
detectorParams.PeakBackgroundRatio = 3;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = true;
peakdetector = new DeconToolsPeakDetector(detectorParams);
peakdetector.Execute(resultcollection);
Task scanresultUpdater = new ScanResultUpdater();
scanresultUpdater.Execute(resultcollection);
Assert.AreEqual(82, resultcollection.Run.PeakList.Count);
Assert.AreEqual(1, resultcollection.ScanResultList.Count);
Assert.AreEqual(82, resultcollection.ScanResultList[0].NumPeaks);
Assert.AreEqual(167.243318707619, Convert.ToDecimal(resultcollection.Run.CurrentScanSet.BackgroundIntensity));
}
public void outputToText_xcaliburData_Test1()
{
List <Run> runcoll = new List <Run>();
Run run = new XCaliburRun(xcaliburFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6100, 1, 1);
sscc.Create();
Task msgen = new GenericMSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new RapidDeconvolutor();
Task textScanResultExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.BasicScanResult_TextFileExporter(xcalibur_text_ScanResultOutputFile1);
Task scanResultUpdater = new ScanResultUpdater();
Stopwatch sw;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
scanResultUpdater.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
textScanResultExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("Exporter execution time = \t" + sw.ElapsedMilliseconds);
}
}
//TaskCollection taskColl=new TaskCollection();
//taskColl.TaskList.Add(msgen);
//taskColl.TaskList.Add(peakDetector);
//taskColl.TaskList.Add(decon);
//taskColl.TaskList.Add(sqliteExporter);
//TaskController controller = new BasicTaskController(taskColl);
//controller.Execute(runcoll);
}
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 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 MSGeneratorOnXCaliburFileTest1()
{
Run run = new XCaliburRun(xcaliburTestfile);
run.CurrentScanSet = new ScanSet(6067);
ResultCollection resultcollection = new ResultCollection(run);
Task msgen = new GenericMSGenerator();
msgen.Execute(resultcollection);
Assert.AreEqual(27053, run.XYData.Xvalues.Length);
Assert.AreEqual(1, run.GetMSLevel(run.CurrentScanSet.PrimaryScanNumber));
Assert.AreEqual(3558996224, (long)run.CurrentScanSet.TICValue);
}
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 examineEffectOfIntensityCutoffOnRapidTest1()
{
Project project = Project.getInstance();
project.Parameters.OldDecon2LSParameters = new OldDecon2LSParameters();
Run run = new XCaliburRun(xcaliburTestfile, 6000, 7000);
project.RunCollection.Add(run);
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1);
scansetCreator.Create();
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
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);
for (int i = 1; i < 6; i++)
{
results.ResultList.Clear();
Task rapidDecon = new RapidDeconvolutor(i, DeconTools.Backend.ProcessingTasks.IDeconvolutor.DeconResultComboMode.simplyAddIt);
rapidDecon.Execute(results);
//Console.WriteLine(scanset.PrimaryScanNumber + "\t" + i + "\t" +
// results.ResultList.Count + "\t" + results.Run.CurrentScanSet.BackgroundIntensity);
}
}
}
public void outputToSqlite_xcaliburData_Test1()
{
List <Run> runcoll = new List <Run>();
Run run = new XCaliburRun(xcaliburFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6100, 1, 1, false);
sscc.Create();
Task msgen = new GenericMSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new RapidDeconvolutor();
Task sqliteScanResultExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.BasicScanResult_SqliteExporter(xcalibur_sqlite_ScanResultOutputFile1);
Task peakExporter = new DeconTools.Backend.ProcessingTasks.PeakListExporters.PeakListSQLiteExporter(100000, peakExporter1);
Task scanResultUpdater = new ScanResultUpdater();
Stopwatch sw;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
scanResultUpdater.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
sqliteScanResultExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("SqliteExporter execution time = \t" + sw.ElapsedMilliseconds);
}
peakExporter.Execute(run.ResultCollection);
}
}
public void exportToSqliteTest1()
{
if (File.Exists(sqliteOutfileName))
{
File.Delete(sqliteOutfileName);
}
Run run = new XCaliburRun(xcaliburTestfile);
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, 6000, 6020, 1, 1, false);
scansetCreator.Create();
Task msgen = new GenericMSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
((DeconToolsPeakDetector)peakDetector).StorePeakData = true;
Task exporter = new PeakListSQLiteExporter(1000000, sqliteOutfileName); //trigger of 1E5 = 310 sec (memory = 150 MB); trigger of 1E6 = 231 Sec (memory = 250 MB);
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
Stopwatch sw = new Stopwatch();
sw.Start();
exporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 5)
{
Console.WriteLine("PeakListExporter execution time = " + sw.ElapsedMilliseconds);
}
}
exporter.Cleanup();
Assert.AreEqual(true, File.Exists(sqliteOutfileName));
FileInfo fi = new FileInfo(sqliteOutfileName);
Assert.AreEqual(81920, fi.Length);
Console.Write(fi.Length);
}
public void FindMSPeaksTest1()
{
ParameterLoader loader = new ParameterLoader();
loader.LoadParametersFromFile(parameterFilename);
Run run = new IMFRun(imfFilepath);
run.CurrentScanSet = new ScanSet(1, 1, 100000);
ResultCollection resultcollection = new ResultCollection(run);
Task msgen = new GenericMSGenerator();
msgen.Execute(resultcollection);
DeconToolsPeakDetector peakfinder = new DeconToolsPeakDetector(loader.PeakParameters);
peakfinder.Execute(resultcollection);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < resultcollection.Run.PeakList.Count; i++)
{
MSPeak mspeak = (MSPeak)resultcollection.Run.PeakList[i];
sb.Append(resultcollection.Run.PeakList[i].XValue);
sb.Append("\t");
sb.Append(resultcollection.Run.PeakList[i].Height);
sb.Append("\t");
sb.Append(mspeak.SN);
sb.Append("\t");
sb.Append(resultcollection.Run.PeakList[i].Width);
sb.Append("\t");
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
Assert.AreEqual(2438, resultcollection.Run.PeakList.Count);
Assert.AreEqual(547.316411323136, Convert.ToDecimal(resultcollection.Run.PeakList[982].XValue));
Assert.AreEqual(100385, resultcollection.Run.PeakList[982].Height);
}
