RichPeakChromatogram get_chrom(int i)
{
// this is a simulated SRM experiment where the two traces are not sampled at
// the exact same time points, thus a resampling is necessary before applying
// the algorithm.
static const double rtdata_1[] = {1474.34, 1477.11, 1479.88, 1482.64, 1485.41, 1488.19, 1490.95, 1493.72, 1496.48, 1499.25, 1502.03, 1504.8 , 1507.56, 1510.33, 1513.09, 1515.87, 1518.64, 1521.42};
static const double rtdata_2[] = {1473.55, 1476.31, 1479.08, 1481.84, 1484.61, 1487.39, 1490.15, 1492.92, 1495.69, 1498.45, 1501.23, 1504 , 1506.76, 1509.53, 1512.29, 1515.07, 1517.84, 1520.62};
static const double intdata_1[] = {3.26958, 3.74189, 3.31075, 86.1901, 3.47528, 387.864, 13281 , 6375.84, 39852.6, 2.66726, 612.747, 3.34313, 793.12 , 3.29156, 4.00586, 4.1591 , 3.23035, 3.90591};
static const double intdata_2[] = {3.44054, 2142.31, 3.58763, 3076.97, 6663.55, 45681 , 157694 , 122844 , 86034.7, 85391.1, 15992.8, 2293.94, 6934.85, 2735.18, 459.413, 3.93863, 3.36564, 3.44005};
RichPeakChromatogram chromatogram;
for (int k = 0; k < 18; k++)
{
ChromatogramPeak peak;
if (i == 0)
{
peak.setMZ(rtdata_1[k]);
peak.setIntensity(intdata_1[k]);
}
else if (i == 1)
{
peak.setMZ(rtdata_2[k]);
peak.setIntensity(intdata_2[k]);
}
chromatogram.push_back(peak);
}
return chromatogram;
}
void OpenSwathDataAccessHelper::convertToOpenMSChromatogram(OpenMS::MSChromatogram<> & chromatogram, const OpenSwath::ChromatogramPtr cptr)
{
OpenSwath::BinaryDataArrayPtr rt_arr = cptr->getTimeArray();
OpenSwath::BinaryDataArrayPtr int_arr = cptr->getIntensityArray();
chromatogram.reserve(rt_arr->data.size());
for (Size i = 0; i < rt_arr->data.size(); i++)
{
ChromatogramPeak p;
p.setRT(rt_arr->data[i]);
p.setIntensity(int_arr->data[i]);
chromatogram.push_back(p);
}
}
MSChromatogram<> toChromatogram(const MSSpectrum<>& in)
{
MSChromatogram<> out;
for (Size ic = 0; ic < in.size(); ++ic)
{
ChromatogramPeak peak;
peak.setMZ(in[ic].getMZ());
peak.setIntensity(in[ic].getIntensity());
out.push_back(peak);
}
out.setChromatogramType(ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM);
return out;
}
void PeakPickerHiRes::pick(const MSChromatogram& input, MSChromatogram& output, std::vector<PeakBoundary>& boundaries) const
{
// copy meta data of the input chromatogram
output.clear(true);
output.ChromatogramSettings::operator=(input);
output.MetaInfoInterface::operator=(input);
output.setName(input.getName());
MSSpectrum input_spectrum;
MSSpectrum output_spectrum;
for (MSChromatogram::const_iterator it = input.begin(); it != input.end(); ++it)
{
Peak1D p;
p.setMZ(it->getRT());
p.setIntensity(it->getIntensity());
input_spectrum.push_back(p);
}
pick(input_spectrum, output_spectrum, boundaries, false); // no spacing checks!
for (MSSpectrum::const_iterator it = output_spectrum.begin(); it != output_spectrum.end(); ++it)
{
ChromatogramPeak p;
p.setRT(it->getMZ());
p.setIntensity(it->getIntensity());
output.push_back(p);
}
// copy float data arrays (for FWHM)
output.getFloatDataArrays().resize(output_spectrum.getFloatDataArrays().size());
for (Size i = 0; i < output_spectrum.getFloatDataArrays().size(); ++i)
{
output.getFloatDataArrays()[i].insert(output.getFloatDataArrays()[i].begin(), output_spectrum.getFloatDataArrays()[i].begin(), output_spectrum.getFloatDataArrays()[i].end());
output.getFloatDataArrays()[i].setName(output_spectrum.getFloatDataArrays()[i].getName());
}
}
END_SECTION START_SECTION((PositionType const& getPosition() const)) TEST_REAL_SIMILAR(ChromatogramPeak().getPosition()[0], 0.0) END_SECTION START_SECTION((CoordinateType getRT() const)) TEST_REAL_SIMILAR(ChromatogramPeak().getRT(), 0.0) END_SECTION START_SECTION((CoordinateType getPos() const)) TEST_REAL_SIMILAR(ChromatogramPeak().getPos(), 0.0) END_SECTION START_SECTION((void setIntensity(IntensityType intensity))) ChromatogramPeak p; p.setIntensity(17.8f); TEST_REAL_SIMILAR(p.getIntensity(), 17.8) END_SECTION START_SECTION((void setPosition(PositionType const &position))) ChromatogramPeak::PositionType pos; pos[0] = 1.0; ChromatogramPeak p; p.setPosition(pos); TEST_REAL_SIMILAR(p.getPosition()[0], 1.0) END_SECTION START_SECTION((PositionType& getPosition())) ChromatogramPeak::PositionType pos; pos[0] = 1.0;
