private DeconvolutedSpectrum GetDeconvolutedSpectrum(int scan, PbfLcMsRun pbfLcMsRun)
{
var spectrum = pbfLcMsRun.GetSpectrum(scan) as ProductSpectrum;
if (spectrum == null)
{
return(null);
}
return(Deconvoluter.GetCombinedDeconvolutedSpectrum(spectrum, 1, 20, 2, new Tolerance(10, ToleranceUnit.Ppm), 0.7));
}
public void TestReadingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pbfFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
var specFilePath = Path.ChangeExtension(pbfFilePath, "raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Loading .pbf into memory");
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra");
// spectrum comparison
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var spec1 = run.GetSpectrum(scanNum);
var spec2 = pbfRun.GetSpectrum(scanNum);
Assert.IsTrue(spec1.Peaks.Length == spec2.Peaks.Length);
for (var i = 0; i < spec1.Peaks.Length; i++)
{
var p1 = spec1.Peaks[i];
var p2 = spec2.Peaks[i];
Assert.True(p1.Equals(p2));
Assert.True(Math.Abs(p1.Mz - p2.Mz) < 1e-8);
Assert.True(Math.Abs(p1.Intensity - p2.Intensity) < 0.001);
}
}
Console.WriteLine(@"Comparing XICs");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
var xic2 = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
Assert.True(xic1.Count == xic2.Count);
for (var i = 0; i < xic1.Count; i++)
{
if (!xic1[i].Equals(xic2[i]))
{
Console.WriteLine(@"{0} {1} {2}", i, xic1[i], xic2[i]);
}
Assert.True(xic1[i].Equals(xic2[i]));
}
Console.WriteLine(@"Done");
}
public void TestReadingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pbfFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
var specFilePath = Path.ChangeExtension(pbfFilePath, "raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Loading .pbf into memory");
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra");
// spectrum comparison
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var spec1 = run.GetSpectrum(scanNum);
var spec2 = pbfRun.GetSpectrum(scanNum);
Assert.IsTrue(spec1.Peaks.Length == spec2.Peaks.Length);
for (var i = 0; i < spec1.Peaks.Length; i++)
{
var p1 = spec1.Peaks[i];
var p2 = spec2.Peaks[i];
Assert.True(p1.Equals(p2));
Assert.True(Math.Abs(p1.Mz - p2.Mz) < 1e-8);
Assert.True(Math.Abs(p1.Intensity - p2.Intensity) < 0.001);
}
}
Console.WriteLine(@"Comparing XICs");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
var xic2 = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
Assert.True(xic1.Count == xic2.Count);
for (var i = 0; i < xic1.Count; i++)
{
if (!xic1[i].Equals(xic2[i]))
{
Console.WriteLine(@"{0} {1} {2}", i, xic1[i], xic2[i]);
}
Assert.True(xic1[i].Equals(xic2[i]));
}
Console.WriteLine(@"Done");
}