private void SetLcMsMatches(int ms2ScanNumber)
{
var productSpec = _run.GetSpectrum(ms2ScanNumber) as ProductSpectrum;
if (productSpec == null)
{
return;
}
var isolationWindow = productSpec.IsolationWindow;
var minMz = isolationWindow.MinMz;
var maxMz = isolationWindow.MaxMz;
List <Peak> precursorPeakList = null;
var precursorSpec = _run.GetSpectrum(_run.GetPrecursorScanNum(ms2ScanNumber));
if (precursorSpec != null)
{
precursorPeakList = precursorSpec.GetPeakListWithin(minMz, maxMz);
}
List <Peak> nextMs1PeakList = null;
var nextScanNum = _run.GetNextScanNum(ms2ScanNumber, 1);
var nextSpec = _run.GetSpectrum(nextScanNum);
if (nextSpec != null)
{
nextMs1PeakList = nextSpec.GetPeakListWithin(minMz, maxMz);
}
List <Peak> peakList;
if (precursorPeakList != null && nextMs1PeakList != null)
{
peakList = PeakListUtils.Sum(precursorPeakList, nextMs1PeakList, _comparer);
}
else if (precursorPeakList != null)
{
peakList = precursorPeakList;
}
else if (nextMs1PeakList != null)
{
peakList = nextMs1PeakList;
}
else
{
return;
}
// Sort by intensity
peakList.Sort(new IntensityComparer());
var remainingPeakList = new LinkedList <Peak>(peakList);
SetLcMsMatches(remainingPeakList, ms2ScanNumber, MaxNumPeaksToConsider);
}
public void TestReadingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"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 checksum = pbfRun.PbfFileChecksum;
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);
var run = new InMemoryLcMsRun(MassSpecDataReaderFactory.GetMassSpecDataReader(specFilePath), 0, 0);
Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra");
// spectrum comparison
//for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
foreach (var scanNum in run.AllScanNumbers)
{
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");
}
