OpenSwath::SpectrumPtr OpenSwathDataAccessHelper::convertToSpectrumPtr(const OpenMS::MSSpectrum<> & spectrum)
{
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr mz_array(new OpenSwath::BinaryDataArray);
for (MSSpectrum<>::const_iterator it = spectrum.begin(); it != spectrum.end(); it++)
{
mz_array->data.push_back(it->getMZ());
intensity_array->data.push_back(it->getIntensity());
}
OpenSwath::SpectrumPtr sptr(new OpenSwath::Spectrum);
sptr->setMZArray(mz_array);
sptr->setIntensityArray(intensity_array);
return sptr;
}
OpenSwath::SpectrumPtr SpectrumAccessOpenMS::getSpectrumById(int id)
{
const MSSpectrumType& spectrum = (*ms_experiment_)[id];
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr mz_array(new OpenSwath::BinaryDataArray);
for (MSSpectrumType::const_iterator it = spectrum.begin(); it != spectrum.end(); it++)
{
mz_array->data.push_back(it->getMZ());
intensity_array->data.push_back(it->getIntensity());
}
OpenSwath::SpectrumPtr sptr(new OpenSwath::Spectrum);
sptr->setMZArray(mz_array);
sptr->setIntensityArray(intensity_array);
return sptr;
}
OpenSwath::SpectrumPtr SpectrumAccessOpenMSCached::getSpectrumById(int id) const
{
if (cache_.getSpectraIndex().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 mz_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
int ms_level = -1;
double rt = -1.0;
// FEATURE check if we can keep the filestream open -> risky if someone else
// accesses the file in the meantime
std::ifstream ifs_((filename_cached_).c_str(), std::ios::binary);
ifs_.seekg(cache_.getSpectraIndex()[id]);
cache_.readSpectrumFast(mz_array, intensity_array, ifs_, ms_level, rt);
OpenSwath::SpectrumPtr sptr(new OpenSwath::Spectrum);
sptr->setMZArray(mz_array);
sptr->setIntensityArray(intensity_array);
return sptr;
}