public static void LoadThermoFiltered2()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.raw");
ThermoStaticData b = ThermoStaticData.LoadAllStaticData(@"small.raw", filterParams: new FilteringParams(numberOfPeaksToKeepPerWindow: 40, applyTrimmingToMs1: true, applyTrimmingToMsMs: true));
ThermoStaticData c = ThermoStaticData.LoadAllStaticData(@"small.raw", filterParams: new FilteringParams(minimumAllowedIntensityRatioToBasePeak: 0.1, applyTrimmingToMs1: true, applyTrimmingToMsMs: true));
ThermoStaticData d = ThermoStaticData.LoadAllStaticData(@"small.raw", filterParams: new FilteringParams(minimumAllowedIntensityRatioToBasePeak: 0.1, numberOfPeaksToKeepPerWindow: 40, applyTrimmingToMs1: true, applyTrimmingToMsMs: true));
var aLen = a.GetOneBasedScan(1).MassSpectrum.Size;
var bLen = b.GetOneBasedScan(1).MassSpectrum.Size;
var cLen = c.GetOneBasedScan(1).MassSpectrum.Size;
var dLen = d.GetOneBasedScan(1).MassSpectrum.Size;
Assert.AreEqual(Math.Min(bLen, cLen), dLen);
var aLen2 = a.GetOneBasedScan(2).MassSpectrum.Size;
var bLen2 = b.GetOneBasedScan(2).MassSpectrum.Size;
var cLen2 = c.GetOneBasedScan(2).MassSpectrum.Size;
var dLen2 = d.GetOneBasedScan(2).MassSpectrum.Size;
Assert.AreEqual(Math.Min(bLen2, cLen2), dLen2);
var aLen3 = a.GetOneBasedScan(3).MassSpectrum.Size;
var bLen3 = b.GetOneBasedScan(3).MassSpectrum.Size;
var cLen3 = c.GetOneBasedScan(3).MassSpectrum.Size;
var dLen3 = d.GetOneBasedScan(3).MassSpectrum.Size;
Assert.AreEqual(Math.Min(bLen3, cLen3), dLen3);
}
public static void WindowFilteringStaticTest()
{
//test window number of 1
ThermoStaticData a_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
ThermoStaticData b_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(numberOfPeaksToKeepPerWindow: 400, numberOfWindows: 1, applyTrimmingToMs1: true));
ThermoStaticData c_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(minimumAllowedIntensityRatioToBasePeak: 0.001, numberOfWindows: 1, applyTrimmingToMs1: true));
ThermoStaticData d_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(minimumAllowedIntensityRatioToBasePeak: 0.001, numberOfPeaksToKeepPerWindow: 400, numberOfWindows: 1, applyTrimmingToMs1: true));
var aLen = a_w.GetOneBasedScan(1).MassSpectrum.Size;
var bLen = b_w.GetOneBasedScan(1).MassSpectrum.Size;
var cLen = c_w.GetOneBasedScan(1).MassSpectrum.Size;
var dLen = d_w.GetOneBasedScan(1).MassSpectrum.Size;
Assert.AreEqual(Math.Min(bLen, cLen), dLen);
var aLen2 = a_w.GetOneBasedScan(2).MassSpectrum.Size;
var bLen2 = b_w.GetOneBasedScan(2).MassSpectrum.Size;
var cLen2 = c_w.GetOneBasedScan(2).MassSpectrum.Size;
var dLen2 = d_w.GetOneBasedScan(2).MassSpectrum.Size;
Assert.AreEqual(Math.Min(bLen2, cLen2), dLen2);
var aLen3 = a_w.GetOneBasedScan(3).MassSpectrum.Size;
var bLen3 = b_w.GetOneBasedScan(3).MassSpectrum.Size;
var cLen3 = c_w.GetOneBasedScan(3).MassSpectrum.Size;
var dLen3 = d_w.GetOneBasedScan(3).MassSpectrum.Size;
Assert.AreEqual(Math.Min(bLen3, cLen3), dLen3);
}
public static void LoadThermoTest3()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.RAW");
Assert.IsTrue(a.GetAllScansList().Where(eb => eb.MsnOrder > 1).Count() > 0);
Assert.IsTrue(a.GetAllScansList().Where(eb => eb.MsnOrder == 1).Count() > 0);
Assert.IsFalse(a.ThermoGlobalParams.MonoisotopicselectionEnabled);
var hehe = a.GetAllScansList().First(b => b.MsnOrder > 1);
var prec = a.GetOneBasedScan(hehe.OneBasedPrecursorScanNumber.Value);
Assert.IsNull(hehe.SelectedIonChargeStateGuess);
Assert.IsNull(hehe.SelectedIonIntensity);
hehe.ComputeSelectedPeakIntensity(prec.MassSpectrum);
Assert.AreEqual(1017759, hehe.SelectedIonIntensity, 1);
Assert.IsNull(hehe.SelectedIonMonoisotopicGuessIntensity);
hehe.ComputeMonoisotopicPeakIntensity(prec.MassSpectrum);
Assert.AreEqual(1017759, hehe.SelectedIonMonoisotopicGuessIntensity, 1);
}
public static void LoadThermoFiltered()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
ThermoStaticData b = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(numberOfPeaksToKeepPerWindow: 400, applyTrimmingToMs1: true));
ThermoStaticData c = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(minimumAllowedIntensityRatioToBasePeak: 0.001, applyTrimmingToMs1: true));
ThermoStaticData d = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(minimumAllowedIntensityRatioToBasePeak: 0.001, numberOfPeaksToKeepPerWindow: 400, applyTrimmingToMs1: true));
var aLen = a.GetOneBasedScan(1).MassSpectrum.Size;
var bLen = b.GetOneBasedScan(1).MassSpectrum.Size;
var cLen = c.GetOneBasedScan(1).MassSpectrum.Size;
var dLen = d.GetOneBasedScan(1).MassSpectrum.Size;
Assert.AreEqual(Math.Min(bLen, cLen), dLen);
}
public static void MultiWindowFiltering()
{
//tests for filtering with window
ThermoStaticData a_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(numberOfWindows: 1, applyTrimmingToMs1: true));
Assert.AreEqual(1120, a_w.GetOneBasedScan(1).MassSpectrum.Size);
//number of 2
ThermoStaticData b_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(numberOfPeaksToKeepPerWindow: 200, numberOfWindows: 3, applyTrimmingToMs1: true));
Assert.AreEqual(600, b_w.GetOneBasedScan(1).MassSpectrum.Size);
//number of 4
ThermoStaticData c_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(numberOfPeaksToKeepPerWindow: 200, numberOfWindows: 4, applyTrimmingToMs1: true));
Assert.AreEqual(800, c_w.GetOneBasedScan(1).MassSpectrum.Size);
//number of 6, which doesn't divide 1120
ThermoStaticData d_w = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw", filterParams: new FilteringParams(numberOfPeaksToKeepPerWindow: 150, numberOfWindows: 6, applyTrimmingToMs1: true));
Assert.AreEqual(900, d_w.GetOneBasedScan(1).MassSpectrum.Size);
}
public static void LoadCompressedMzml()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.RAW");
Mzml b = Mzml.LoadAllStaticData(@"smallCentroid.mzML");
Assert.AreEqual(a.NumSpectra, b.NumSpectra);
Assert.AreEqual(a.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
Assert.AreEqual(a.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
Assert.AreEqual(a.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
}
public static void LoadThermoTest2()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
Assert.AreEqual(360, a.NumSpectra);
Assert.GreaterOrEqual(1000, a.GetOneBasedScan(1).MassSpectrum.Extract(0, 500).Last().Mz);
Assert.AreEqual(2, a.GetOneBasedScan(1).MassSpectrum.FilterByY(5e6, double.MaxValue).Count());
var ye = a.GetOneBasedScan(1).MassSpectrum.CopyTo2DArray();
Assert.AreEqual(77561752, a.GetOneBasedScan(1).TotalIonCurrent);
Assert.AreEqual(144, a.GetClosestOneBasedSpectrumNumber(2));
MzSpectrum newSpectrum = new MzSpectrum(a.GetOneBasedScan(51).MassSpectrum.XArray, a.GetOneBasedScan(51).MassSpectrum.YArray, true);
Assert.AreEqual(1120, a.GetOneBasedScan(1).MassSpectrum.Size);
var newDeconvolution = a.GetOneBasedScan(1).MassSpectrum.Deconvolute(new MzRange(double.MinValue, double.MaxValue), 1, 10, 1, 4).ToList();
Assert.IsTrue(newDeconvolution.Any(b => Math.Abs(b.peaks.First().mz.ToMass(b.charge) - 523.257) < 0.001));
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML"), false);
var sdafaf = a.Deconvolute(null, null, 1, 30, 10, 3, 10, b => true).OrderByDescending(b => b.NumPeaks).First();
Assert.IsTrue(Math.Abs(262.64 - sdafaf.Mass.ToMz(2)) <= 0.01);
using (ThermoDynamicData dynamicThermo = ThermoDynamicData.InitiateDynamicConnection(@"05-13-16_cali_MS_60K-res_MS.raw"))
{
Assert.AreEqual(136, dynamicThermo.GetClosestOneBasedSpectrumNumber(1.89));
dynamicThermo.ClearCachedScans();
}
Mzml readCovertedMzmlFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML"));
Assert.AreEqual(a.GetAllScansList().First().Polarity, readCovertedMzmlFile.GetAllScansList().First().Polarity);
}
public static void TestSummedMsDataFile()
{
ThermoStaticData rawFile = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
// 3 scans
SummedMsDataFile summed3 = new SummedMsDataFile(rawFile, 3, 10);
Assert.AreEqual(rawFile.NumSpectra - 2, summed3.NumSpectra);
var resultingTic = summed3.GetOneBasedScan(1).TotalIonCurrent;
var mySummedTic = rawFile.GetOneBasedScan(1).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(2).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(3).MassSpectrum.SumOfAllY;
var instrumentSummedTic = rawFile.GetOneBasedScan(1).TotalIonCurrent + rawFile.GetOneBasedScan(2).TotalIonCurrent + rawFile.GetOneBasedScan(3).TotalIonCurrent;
// Tics are approximately what they should be
Assert.IsTrue(Math.Abs(resultingTic - mySummedTic) / mySummedTic < 1e-4);
Assert.IsTrue(Math.Abs(resultingTic - instrumentSummedTic) / instrumentSummedTic < 1e-1);
// Equal to representative
Assert.AreEqual(summed3.GetOneBasedScan(1).RetentionTime, rawFile.GetOneBasedScan(2).RetentionTime);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size <= rawFile.GetOneBasedScan(1).MassSpectrum.Size + rawFile.GetOneBasedScan(2).MassSpectrum.Size + rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(1).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(2).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY == rawFile.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY);
// Interval of 893-899 mz
Assert.AreEqual(2, rawFile.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(2, rawFile.GetOneBasedScan(2).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(1, rawFile.GetOneBasedScan(3).MassSpectrum.NumPeaksWithinRange(893, 899));
// One peak persists across the three scans! So instead of 5 see three peaks in summed
Assert.AreEqual(3, summed3.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.FirstX, Math.Min(Math.Min(rawFile.GetOneBasedScan(1).MassSpectrum.FirstX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.FirstX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.FirstX.Value));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.LastX, Math.Max(Math.Max(rawFile.GetOneBasedScan(1).MassSpectrum.LastX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.LastX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.LastX.Value));
// 5 scans
SummedMsDataFile summed5 = new SummedMsDataFile(rawFile, 5, 10);
Assert.AreEqual(rawFile.NumSpectra - 4, summed5.NumSpectra);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(summed5, "testSummed.mzML", false);
var ok = Mzml.LoadAllStaticData("testSummed.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(ok, "testSummed2.mzML", false);
Mzml.LoadAllStaticData("testSummed2.mzML");
}