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::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::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;
}
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;
}
OpenMS::Interfaces::SpectrumPtr MzMLSpectrumDecoder::decodeBinaryData(std::vector<BinaryData>& data_)
{
Internal::MzMLHandlerHelper::decodeBase64Arrays(data_);
OpenMS::Interfaces::SpectrumPtr sptr(new OpenMS::Interfaces::Spectrum);
//look up the precision and the index of the intensity and m/z array
bool x_precision_64 = true;
bool int_precision_64 = true;
SignedSize x_index = -1;
SignedSize int_index = -1;
Internal::MzMLHandlerHelper::computeDataProperties_(data_, x_precision_64, x_index, "m/z array");
Internal::MzMLHandlerHelper::computeDataProperties_(data_, int_precision_64, int_index, "intensity array");
//Abort if no m/z or intensity array is present
if (int_index == -1 || x_index == -1)
{
// Warning ...
return sptr;
}
// Error if intensity or m/z is encoded as int32|64 - they should be float32|64!
if ((data_[x_index].ints_32.size() > 0) || (data_[x_index].ints_64.size() > 0))
{
//fatalError(LOAD, "Encoding m/z array as integer is not allowed!");
}
if ((data_[int_index].ints_32.size() > 0) || (data_[int_index].ints_64.size() > 0))
{
//fatalError(LOAD, "Encoding intensity array as integer is not allowed!");
}
// Warn if the decoded data has a different size than the defaultArrayLength
Size mz_size = x_precision_64 ? data_[x_index].floats_64.size() : data_[x_index].floats_32.size();
Size int_size = int_precision_64 ? data_[int_index].floats_64.size() : data_[int_index].floats_32.size();
// Check if int-size and mz-size are equal
if (mz_size != int_size)
{
std::cout << "Warning, intensity and m/z array length are unequal" << std::endl;
return sptr;
}
Size default_array_length_ = mz_size;
// maybe some checks here about internal consistency e.g. with defaultArrayLength ...
//create meta data arrays and reserve enough space for the content
if (data_.size() > 2)
{
// --> TODO the other arrays ... create and resize those ...
}
// Copy meta data from m/z and intensity binary
// We don't have this as a separate location => store it in spectrum
// --> maybe TODO
OpenMS::Interfaces::BinaryDataArrayPtr intensity_array(new OpenMS::Interfaces::BinaryDataArray);
OpenMS::Interfaces::BinaryDataArrayPtr x_array(new OpenMS::Interfaces::BinaryDataArray);
for (Size n = 0; n < default_array_length_; n++)
{
DoubleReal xcoord = x_precision_64 ? data_[x_index].floats_64[n] : data_[x_index].floats_32[n];
DoubleReal intensity = int_precision_64 ? data_[int_index].floats_64[n] : data_[int_index].floats_32[n];
x_array->data.push_back(xcoord);
intensity_array->data.push_back(intensity);
// TODO the other arrays
}
sptr->setMZArray(x_array);
sptr->setIntensityArray(intensity_array);
return sptr;
}
