PWIZ_API_DECL
msdata::SpectrumPtr SpectrumList_MZWindow::spectrum(size_t index, bool getBinaryData) const
{
SpectrumPtr spectrum = inner_->spectrum(index, getBinaryData);
if (!getBinaryData) return spectrum;
vector<MZIntensityPair> data;
spectrum->getMZIntensityPairs(data);
vector<MZIntensityPair>::const_iterator begin = lower_bound(
data.begin(), data.end(), MZIntensityPair(mzLow_,0), hasLowerMZ);
vector<MZIntensityPair>::const_iterator end = upper_bound(
data.begin(), data.end(), MZIntensityPair(mzHigh_,0), hasLowerMZ);
vector<MZIntensityPair> newData;
copy(begin, end, back_inserter(newData));
BinaryDataArrayPtr intensityArray = spectrum->getIntensityArray();
CVID intensityUnits = intensityArray.get() ? intensityArray->cvParam(MS_intensity_unit).cvid : CVID_Unknown;
SpectrumPtr newSpectrum(new Spectrum(*spectrum));
newSpectrum->binaryDataArrayPtrs.clear();
newSpectrum->setMZIntensityPairs(newData, intensityUnits);
return newSpectrum;
}
PWIZ_API_DECL SpectrumPtr SpectrumList_MetadataFixer::spectrum(size_t index, bool getBinaryData) const
{
// always get binary data
SpectrumPtr s = inner_->spectrum(index, true);
BinaryDataArrayPtr mzArray = s->getMZArray();
BinaryDataArrayPtr intensityArray = s->getIntensityArray();
if (!mzArray.get() || !intensityArray.get())
return s;
vector<double>& mzs = mzArray->data;
vector<double>& intensities = intensityArray->data;
double tic = 0;
if (!mzs.empty())
{
double bpmz, bpi = -1;
for (size_t i=0, end=mzs.size(); i < end; ++i)
{
tic += intensities[i];
if (bpi < intensities[i])
{
bpi = intensities[i];
bpmz = mzs[i];
}
}
replaceCvParam(*s, MS_base_peak_intensity, bpi, MS_number_of_counts);
replaceCvParam(*s, MS_base_peak_m_z, bpmz, MS_m_z);
replaceCvParam(*s, MS_lowest_observed_m_z, mzs.front(), MS_m_z);
replaceCvParam(*s, MS_highest_observed_m_z, mzs.back(), MS_m_z);
}
replaceCvParam(*s, MS_TIC, tic, MS_number_of_counts);
return s;
}
