private bool CompareSpectraBinData(
clsCorrelation dataComparer,
clsMSSpectrum fragSpectrum,
clsBinnedData binnedSpectrum)
{
var xData = new List <float>(fragSpectrum.IonCount);
var yData = new List <float>(fragSpectrum.IonCount);
// Make a copy of the data, excluding any Reporter Ion data
for (var index = 0; index < fragSpectrum.IonCount; index++)
{
if (!clsUtilities.CheckPointInMZIgnoreRange(fragSpectrum.IonsMZ[index],
mReporterIons.MZIntensityFilterIgnoreRangeStart,
mReporterIons.MZIntensityFilterIgnoreRangeEnd))
{
xData.Add((float)(fragSpectrum.IonsMZ[index]));
yData.Add((float)(fragSpectrum.IonsIntensity[index]));
}
}
binnedSpectrum.BinnedDataStartX = dataComparer.BinStartX;
binnedSpectrum.BinSize = dataComparer.BinSize;
// Note that the data in xData and yData should have already been filtered to discard data points below the noise threshold intensity
var success = dataComparer.BinData(xData, yData, binnedSpectrum.BinnedIntensities, binnedSpectrum.BinnedIntensitiesOffset);
return(success);
}
private float CompareSpectra(
clsMSSpectrum fragSpectrum1,
clsMSSpectrum fragSpectrum2,
clsBinningOptions binningOptions,
bool considerOffsetBinnedData = true)
{
// Compares the two spectra and returns a similarity score (ranging from 0 to 1)
// Perfect match is 1; no similarity is 0
// Note that both the standard binned data and the offset binned data are compared
// If considerOffsetBinnedData = True, then the larger of the two scores is returned
// similarity scores is returned
//
// If an error, returns -1
var binnedSpectrum1 = new clsBinnedData();
var binnedSpectrum2 = new clsBinnedData();
try
{
var dataComparer = new clsCorrelation(binningOptions);
RegisterEvents(dataComparer);
const clsCorrelation.cmCorrelationMethodConstants eCorrelationMethod = clsCorrelation.cmCorrelationMethodConstants.Pearson;
// Bin the data in the first spectrum
var success = CompareSpectraBinData(dataComparer, fragSpectrum1, binnedSpectrum1);
if (!success)
{
return(-1);
}
// Bin the data in the second spectrum
success = CompareSpectraBinData(dataComparer, fragSpectrum2, binnedSpectrum2);
if (!success)
{
return(-1);
}
// Now compare the binned spectra
// Similarity will be 0 if either instance of BinnedIntensities has fewer than 5 data points
var similarity1 = dataComparer.Correlate(binnedSpectrum1.BinnedIntensities, binnedSpectrum2.BinnedIntensities, eCorrelationMethod);
if (!considerOffsetBinnedData)
{
return(similarity1);
}
var similarity2 = dataComparer.Correlate(binnedSpectrum1.BinnedIntensitiesOffset, binnedSpectrum2.BinnedIntensitiesOffset, eCorrelationMethod);
return(Math.Max(similarity1, similarity2));
}
catch (Exception ex)
{
ReportError("CompareSpectra: " + ex.Message, ex);
return(-1);
}
}