private static void TestSpectrumProcessor(TransitionBinner transBinner, AbstractIsoWindowMapper isoMapper,
MsDataFileImpl file, int testSpectrumNum)
{
int lastSpectrum = testSpectrumNum + 60;
int firstSpectrum = testSpectrumNum - 60;
var spectrumProcessor = new SpectrumProcessor(lastSpectrum + 1, isoMapper, transBinner);
// Make a new spectrum processor using the testing constructor that takes in
// a TransitionBinner, which will be the one used for overlap
// Add the spectra to the cache +/- 60 from the spectrum of interest
for (int i = firstSpectrum; i <= lastSpectrum; ++i)
{
var spectrum = file.GetSpectrum(i);
spectrumProcessor.AddSpectrum(i, spectrum);
}
// Check that the caching worked correctly
for (int spectrumIndex = firstSpectrum; spectrumIndex <= lastSpectrum; ++spectrumIndex)
{
ScanCached specData;
Assert.IsTrue(spectrumProcessor.TryGetSpectrum(spectrumIndex, out specData));
// Check that the cached processing results match the output of
// redoing the processing manually by extracting the spectrum from
// the file again and using transBinner to bin the data
var testSpectrum = file.GetSpectrum(spectrumIndex);
double[] expectedBinnedData = new double[transBinner.NumBins];
transBinner.BinData(testSpectrum.Mzs, testSpectrum.Intensities, ref expectedBinnedData);
ScanCached testSpecData;
spectrumProcessor.TryGetSpectrum(spectrumIndex, out testSpecData);
var seenBinnedData = testSpecData.Data;
Assert.AreEqual(expectedBinnedData.Length, seenBinnedData.Length);
for (int i = 0; i < expectedBinnedData.Length; ++i)
{
Assert.AreEqual(expectedBinnedData[i], seenBinnedData[i], 0.0001);
}
}
}
private static TransitionBinner TestTransitionBinnerOverlap(MsDataSpectrum spectrum,
AbstractIsoWindowMapper isoMapper, double[] binnedIntensities)
{
// Multiple transitions overlapping the same peak from the same precursor
var precursorList = new List<double>();
var transitionList = new List<KeyValuePair<double, double>>();
precursorList.Add(710.5); //transition: start - stop index
transitionList.Add(new KeyValuePair<double, double>(380.19,1.0)); // 379.69-380.69 Bin3
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair<double, double>(380.44,1.0)); // 379.94-380.94 Bin4
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair<double, double>(380.49,0.6)); // 380.19-380.79 Bin5
// And a non-overlapping transition for good measure
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair<double, double>(389.19,0.3)); // 389.04 - 389.34 Bin7
// And a transition that won't have any peaks in the spectrum
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair<double, double>(377.0,0.7)); // 376.65-377.35 Bin0
// And now another precursor with some of the transitions overlapping the first
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair<double, double>(380.0,1.0)); // 379.5 - 380.5 Bin2
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair<double, double>(379.55,1.0)); // 379.05 - 380.05 Bin1
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair<double, double>(389.15, 0.4)); // 388.95 - 389.35 Bin6
var transitionBinner = new TransitionBinner(precursorList, transitionList, isoMapper);
double[] binnedData = new double[transitionList.Count];
transitionBinner.BinData(spectrum.Mzs, spectrum.Intensities, ref binnedData);
// Test that m/z, intensity pairs were binned correctly into their transitions
for (int i = 0; i< binnedData.Length; ++i)
{
Assert.AreEqual(binnedIntensities[i], binnedData[i], 0.001);
}
// Get the precursor index for this precursor
// make sure the precursor -> transition mapping is working for the first precursor
int windowIndexOne;
Assert.IsTrue(isoMapper.TryGetDeconvFromMz(710.5, out windowIndexOne));
// Use the precursor index to get the bins mapping to this precursor
var precursorBins = new HashSet<int>(transitionBinner.BinsForDeconvWindows(new[] {windowIndexOne}));
var expectedPrecursorBins = new HashSet<int>(new[]{0,3,4,5,7});
var setComparer = HashSet<int>.CreateSetComparer();
Assert.IsTrue(setComparer.Equals(expectedPrecursorBins, precursorBins));
// Make sure the precursor -> transition mapping is working for the second precursor
int windowIndexTwo;
Assert.IsTrue(isoMapper.TryGetDeconvFromMz(595.0, out windowIndexTwo));
precursorBins = new HashSet<int>(transitionBinner.BinsForDeconvWindows(new[]{windowIndexOne, windowIndexTwo}));
expectedPrecursorBins = new HashSet<int>(new[]{0,1,2,3,4,5,6,7});
Assert.IsTrue(setComparer.Equals(expectedPrecursorBins, precursorBins));
// m/z values to test mapping of m/z value -> multiplex matching transition bins
var queryVals = new[] {252.0, 377.0, 379.92, 379.95};
var bins = transitionBinner.BinsFromValues(queryVals, true).ToList();
var expectedBins = new List<KeyValuePair<int, int>>
{
new KeyValuePair<int, int>(1, 0),
new KeyValuePair<int, int>(2, 1),
new KeyValuePair<int, int>(2, 2),
new KeyValuePair<int, int>(2, 3),
new KeyValuePair<int, int>(3, 1),
new KeyValuePair<int, int>(3, 2),
new KeyValuePair<int, int>(3, 3),
new KeyValuePair<int, int>(3, 4)
};
AssertEx.AreEqualDeep(expectedBins, bins);
Assert.AreEqual(376.65, transitionBinner.LowerValueFromBin(0),0.0001);
Assert.AreEqual(377.35, transitionBinner.UpperValueFromBin(0),0.0001);
Assert.AreEqual(377.0, transitionBinner.CenterValueFromBin(0),0.0001);
return transitionBinner;
}
private static TransitionBinner TestTransitionBinnerOverlap(MsDataSpectrum spectrum,
AbstractIsoWindowMapper isoMapper, double[] binnedIntensities)
{
// Multiple transitions overlapping the same peak from the same precursor
var precursorList = new List <double>();
var transitionList = new List <KeyValuePair <double, double> >();
precursorList.Add(710.5); //transition: start - stop index
transitionList.Add(new KeyValuePair <double, double>(380.19, 1.0)); // 379.69-380.69 Bin3
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(380.44, 1.0)); // 379.94-380.94 Bin4
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(380.49, 0.6)); // 380.19-380.79 Bin5
// And a non-overlapping transition for good measure
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(389.19, 0.3)); // 389.04 - 389.34 Bin7
// And a transition that won't have any peaks in the spectrum
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(377.0, 0.7)); // 376.65-377.35 Bin0
// And now another precursor with some of the transitions overlapping the first
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair <double, double>(380.0, 1.0)); // 379.5 - 380.5 Bin2
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair <double, double>(379.55, 1.0)); // 379.05 - 380.05 Bin1
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair <double, double>(389.15, 0.4)); // 388.95 - 389.35 Bin6
var transitionBinner = new TransitionBinner(precursorList, transitionList, isoMapper);
double[] binnedData = new double[transitionList.Count];
transitionBinner.BinData(spectrum.Mzs, spectrum.Intensities, ref binnedData);
// Test that m/z, intensity pairs were binned correctly into their transitions
for (int i = 0; i < binnedData.Length; ++i)
{
Assert.AreEqual(binnedIntensities[i], binnedData[i], 0.001);
}
// Get the precursor index for this precursor
// make sure the precursor -> transition mapping is working for the first precursor
int windowIndexOne;
Assert.IsTrue(isoMapper.TryGetDeconvFromMz(710.5, out windowIndexOne));
// Use the precursor index to get the bins mapping to this precursor
var precursorBins = new HashSet <int>(transitionBinner.BinsForDeconvWindows(new[] { windowIndexOne }));
var expectedPrecursorBins = new HashSet <int>(new[] { 0, 3, 4, 5, 7 });
var setComparer = HashSet <int> .CreateSetComparer();
Assert.IsTrue(setComparer.Equals(expectedPrecursorBins, precursorBins));
// Make sure the precursor -> transition mapping is working for the second precursor
int windowIndexTwo;
Assert.IsTrue(isoMapper.TryGetDeconvFromMz(595.0, out windowIndexTwo));
precursorBins = new HashSet <int>(transitionBinner.BinsForDeconvWindows(new[] { windowIndexOne, windowIndexTwo }));
expectedPrecursorBins = new HashSet <int>(new[] { 0, 1, 2, 3, 4, 5, 6, 7 });
Assert.IsTrue(setComparer.Equals(expectedPrecursorBins, precursorBins));
// m/z values to test mapping of m/z value -> multiplex matching transition bins
var queryVals = new[] { 252.0, 377.0, 379.92, 379.95 };
var bins = transitionBinner.BinsFromValues(queryVals, true).ToList();
var expectedBins = new List <KeyValuePair <int, int> >
{
new KeyValuePair <int, int>(1, 0),
new KeyValuePair <int, int>(2, 1),
new KeyValuePair <int, int>(2, 2),
new KeyValuePair <int, int>(2, 3),
new KeyValuePair <int, int>(3, 1),
new KeyValuePair <int, int>(3, 2),
new KeyValuePair <int, int>(3, 3),
new KeyValuePair <int, int>(3, 4)
};
AssertEx.AreEqualDeep(expectedBins, bins);
Assert.AreEqual(376.65, transitionBinner.LowerValueFromBin(0), 0.0001);
Assert.AreEqual(377.35, transitionBinner.UpperValueFromBin(0), 0.0001);
Assert.AreEqual(377.0, transitionBinner.CenterValueFromBin(0), 0.0001);
return(transitionBinner);
}
private static void TestSpectrumProcessor(TransitionBinner transBinner,AbstractIsoWindowMapper isoMapper,
MsDataFileImpl file, int testSpectrumNum)
{
int lastSpectrum = testSpectrumNum + 60;
int firstSpectrum = testSpectrumNum - 60;
var spectrumProcessor = new SpectrumProcessor(lastSpectrum + 1, isoMapper, transBinner);
// Make a new spectrum processor using the testing constructor that takes in
// a TransitionBinner, which will be the one used for overlap
// Add the spectra to the cache +/- 60 from the spectrum of interest
for (int i = firstSpectrum; i <= lastSpectrum; ++i)
{
var spectrum = file.GetSpectrum(i);
spectrumProcessor.AddSpectrum(i, spectrum);
}
// Check that the caching worked correctly
for (int spectrumIndex = firstSpectrum; spectrumIndex <= lastSpectrum; ++spectrumIndex)
{
ScanCached specData;
Assert.IsTrue(spectrumProcessor.TryGetSpectrum(spectrumIndex, out specData));
// Check that the cached processing results match the output of
// redoing the processing manually by extracting the spectrum from
// the file again and using transBinner to bin the data
var testSpectrum = file.GetSpectrum(spectrumIndex);
double[] expectedBinnedData = new double[transBinner.NumBins];
transBinner.BinData(testSpectrum.Mzs, testSpectrum.Intensities, ref expectedBinnedData);
ScanCached testSpecData;
spectrumProcessor.TryGetSpectrum(spectrumIndex, out testSpecData);
var seenBinnedData = testSpecData.Data;
Assert.AreEqual(expectedBinnedData.Length, seenBinnedData.Length);
for (int i = 0; i < expectedBinnedData.Length; ++i)
{
Assert.AreEqual(expectedBinnedData[i], seenBinnedData[i], 0.0001);
}
}
}