public XYData GetSpectrumAMTTag23140708_Z3_Sum3()
{
Run run = new MSScanFromTextFileRun(N14N15TestingUtilities.MS_AMTTag23140708_z3_sum3);
var xydata = run.GetMassSpectrum(new ScanSet(1), 0, 50000);
return(xydata);
}
public static XYData GetTestSpectrum(string xydataFileName)
{
Run run = new MSScanFromTextFileRun(xydataFileName);
var xydata = run.GetMassSpectrum(new ScanSet(1), 0, 50000);
return(xydata);
}
public static XYData LoadXYDataFromFile(string testChromatogramDataFile)
{
var tempRun = new MSScanFromTextFileRun(testChromatogramDataFile);
var xydata = tempRun.GetMassSpectrum(new ScanSet(0));
return(xydata);
}
public void ZeroFillerCompareNewAndOld()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var zeroFiller = new DeconToolsZeroFiller(3);
msgen.Execute(run.ResultCollection);
var numZerosToFill = 3;
var newZeroFilled = zeroFiller.ZeroFill(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
// var oldZeroFilled = zeroFiller.ZeroFillOld(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
var lowerMZ = 625.48;
var upperMZ = 626.18;
run.XYData = run.XYData.TrimData(lowerMZ, upperMZ);
newZeroFilled = newZeroFilled.TrimData(lowerMZ, upperMZ);
// oldZeroFilled = oldZeroFilled.TrimData(lowerMZ, upperMZ);
Console.WriteLine("---------- before zerofilling ---------------");
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("---------- after zerofilling ---------------");
TestUtilities.DisplayXYValues(newZeroFilled);
// Console.WriteLine("---------- after zerofilling using DeconEngine ---------------");
// TestUtilities.DisplayXYValues(oldZeroFilled);
}
public void readInTextFileContainingMultipleHeaderLinesTest1()
{
Run textfiledata = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_multipleHeaderLines, '\t', 1, 2);
textfiledata.GetMassSpectrum(new DeconTools.Backend.Core.ScanSet(0), 200, 2000);
TestUtilities.DisplayXYValues(textfiledata.XYData);
}
public void readInTextFileContainingMultipleSpaceDelimitersTest2()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_multipleDelimiters, ' ');
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
msgen.Execute(run.ResultCollection);
TestUtilities.DisplayXYValues(run.XYData);
}
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 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 test1()
{
var textfiledata = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
var xydata = textfiledata.GetMassSpectrum(new DeconTools.Backend.Core.ScanSet(0), 0, 2000);
TestUtilities.DisplayXYValues(xydata);
Assert.AreEqual(2596, xydata.Xvalues.Length);
Assert.AreEqual(582.822204589844, Convert.ToDecimal(xydata.Xvalues[418]));
Assert.AreEqual(2984, xydata.Yvalues[418]);
Assert.AreEqual(1, textfiledata.GetNumMSScans());
}
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 ZeroFillerTest1()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var zeroFiller = new DeconToolsZeroFiller(3);
msgen.Execute(run.ResultCollection);
// Delete data points such that we only retain 50% of the data
var fractionToKeep = 0.50;
var distanceBetweenPoints = (int)(run.XYData.Xvalues.Length / (run.XYData.Xvalues.Length * fractionToKeep));
var newXVals = new List <double>();
var newYVals = new List <double>();
for (var i = 0; i < run.XYData.Xvalues.Length; i += distanceBetweenPoints)
{
if (i < run.XYData.Xvalues.Length)
{
newXVals.Add(run.XYData.Xvalues[i]);
newYVals.Add(run.XYData.Yvalues[i]);
}
}
run.XYData.Xvalues = newXVals.ToArray();
run.XYData.Yvalues = newYVals.ToArray();
var numZerosToFill = 3;
var newZeroFilled = zeroFiller.ZeroFill(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
double lowerMZ = 1000;
double upperMZ = 1300;
run.XYData = run.XYData.TrimData(lowerMZ, upperMZ);
newZeroFilled = newZeroFilled.TrimData(lowerMZ, upperMZ);
Console.WriteLine("---------- before zerofilling ---------------");
TestUtilities.DisplayXYValues(run.XYData, lowerMZ, upperMZ);
Console.WriteLine("---------- after zerofilling ---------------");
TestUtilities.DisplayXYValues(newZeroFilled, lowerMZ, upperMZ);
Assert.IsTrue(newZeroFilled.Xvalues.Length > run.XYData.Xvalues.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);
}
public void smootherTest1()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
Task msgen = new GenericMSGenerator();
msgen.Execute(run.ResultCollection);
var peakdetector = new DeconToolsPeakDetectorV2(3, 3, Globals.PeakFitType.QUADRATIC, true);
peakdetector.Execute(run.ResultCollection);
Assert.AreEqual(84, run.PeakList.Count);
Task smoother = new SavitzkyGolaySmoother(7, 2, false);
smoother.Execute(run.ResultCollection);
peakdetector.Execute(run.ResultCollection);
Assert.AreEqual(46, run.PeakList.Count);
}
