OpenSwath::ChromatogramPtr SpectrumAccessOpenMS::getChromatogramById(int id)
{
const MSChromatogramType& chromatogram = ms_experiment_->getChromatograms()[id];
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr rt_array(new OpenSwath::BinaryDataArray);
for (MSChromatogramType::const_iterator it = chromatogram.begin(); it != chromatogram.end(); it++)
{
rt_array->data.push_back(it->getRT());
intensity_array->data.push_back(it->getIntensity());
}
// push back rt first, then intensity.
// FEATURE (hroest) annotate which is which
std::vector<OpenSwath::BinaryDataArrayPtr> binaryDataArrayPtrs;
binaryDataArrayPtrs.push_back(rt_array);
binaryDataArrayPtrs.push_back(intensity_array);
OpenSwath::ChromatogramPtr cptr(new OpenSwath::Chromatogram);
cptr->binaryDataArrayPtrs = binaryDataArrayPtrs;
return cptr;
}
OpenSwath::ChromatogramPtr SpectrumAccessOpenMSCached::getChromatogramById(int id) const
{
if (cache_.getChromatogramIndex().empty())
{
// remove const from the cache since we need to recalculate the index
// and re-read the data.
(const_cast<CachedmzML*>(&cache_))->createMemdumpIndex(filename_cached_);
}
OpenSwath::BinaryDataArrayPtr rt_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
std::ifstream ifs_((filename_cached_).c_str(), std::ios::binary);
ifs_.seekg(cache_.getChromatogramIndex()[id]);
cache_.readChromatogramFast(rt_array, intensity_array, ifs_);
// push back rt first, then intensity.
// FEATURE (hroest) annotate which is which
std::vector<OpenSwath::BinaryDataArrayPtr> binaryDataArrayPtrs;
binaryDataArrayPtrs.push_back(rt_array);
binaryDataArrayPtrs.push_back(intensity_array);
OpenSwath::ChromatogramPtr cptr(new OpenSwath::Chromatogram);
cptr->binaryDataArrayPtrs = binaryDataArrayPtrs;
return cptr;
}
