/// Create the mapping
void doMap(OpenSwath::SpectrumAccessPtr input, TargetedExpType& transition_exp)
{
for (Size i = 0; i < input->getNrChromatograms(); i++)
{
chromatogram_map[input->getChromatogramNativeID(i)] = boost::numeric_cast<int>(i);
}
for (Size i = 0; i < transition_exp.getPeptides().size(); i++)
{
assay_peptide_map[transition_exp.getPeptides()[i].id] = boost::numeric_cast<int>(i);
}
for (Size i = 0; i < transition_exp.getTransitions().size(); i++)
{
assay_map[transition_exp.getTransitions()[i].getPeptideRef()].push_back(&transition_exp.getTransitions()[i]);
}
}
/// Fill up transition group with paired Transitions and Chromatograms
void getTransitionGroup(OpenSwath::SpectrumAccessPtr input, MRMTransitionGroupType& transition_group, String id)
{
transition_group.setTransitionGroupID(id);
// Go through all transitions
for (Size i = 0; i < assay_map[id].size(); i++)
{
// Check first whether we have a mapping (e.g. see -force option)
const TransitionType* transition = assay_map[id][i];
if (chromatogram_map.find(transition->getNativeID()) == chromatogram_map.end())
{
LOG_DEBUG << "Found no matching chromatogram for id " << transition->getNativeID() << std::endl;
continue;
}
OpenSwath::ChromatogramPtr cptr = input->getChromatogramById(chromatogram_map[transition->getNativeID()]);
MSChromatogram chromatogram;
OpenSwathDataAccessHelper::convertToOpenMSChromatogram(cptr, chromatogram);
chromatogram.setMetaValue("product_mz", transition->getProductMZ());
chromatogram.setMetaValue("precursor_mz", transition->getPrecursorMZ());
chromatogram.setNativeID(transition->getNativeID());
// Now add the transition and the chromatogram to the group
transition_group.addTransition(*transition, transition->getNativeID());
transition_group.addChromatogram(chromatogram, chromatogram.getNativeID());
}
}
OpenSwath::SpectrumPtr OpenSwathScoring::getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map,
double RT, int nr_spectra_to_add)
{
std::vector<std::size_t> indices = swath_map->getSpectraByRT(RT, 0.0);
if (indices.empty() )
{
OpenSwath::SpectrumPtr sptr(new OpenSwath::Spectrum);
return sptr;
}
int closest_idx = boost::numeric_cast<int>(indices[0]);
if (indices[0] != 0 &&
std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0]) - 1).RT - RT) <
std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0])).RT - RT))
{
closest_idx--;
}
if (nr_spectra_to_add == 1)
{
OpenSwath::SpectrumPtr spectrum_ = swath_map->getSpectrumById(closest_idx);
return spectrum_;
}
else
{
std::vector<OpenSwath::SpectrumPtr> all_spectra;
// always add the spectrum 0, then add those right and left
all_spectra.push_back(swath_map->getSpectrumById(closest_idx));
for (int i = 1; i <= nr_spectra_to_add / 2; i++) // cast to int is intended!
{
if (closest_idx - i >= 0)
{
all_spectra.push_back(swath_map->getSpectrumById(closest_idx - i));
}
if (closest_idx + i < (int)swath_map->getNrSpectra())
{
all_spectra.push_back(swath_map->getSpectrumById(closest_idx + i));
}
}
OpenSwath::SpectrumPtr spectrum_ = SpectrumAddition::addUpSpectra(all_spectra, spacing_for_spectra_resampling_, true);
return spectrum_;
}
}
void OpenSwathScoring::calculateDIAScores(OpenSwath::IMRMFeature* imrmfeature, const std::vector<TransitionType> & transitions,
OpenSwath::SpectrumAccessPtr swath_map, OpenSwath::SpectrumAccessPtr ms1_map, OpenMS::DIAScoring & diascoring,
const PeptideType& pep, OpenSwath_Scores & scores)
{
OPENMS_PRECONDITION(transitions.size() > 0, "There needs to be at least one transition.");
std::vector<double> normalized_library_intensity;
getNormalized_library_intensities_(transitions, normalized_library_intensity);
// parameters
int by_charge_state = 1; // for which charge states should we check b/y series
double precursor_mz = transitions[0].precursor_mz;
// find spectrum that is closest to the apex of the peak using binary search
OpenSwath::SpectrumPtr spectrum_ = getAddedSpectra_(swath_map, imrmfeature->getRT(), add_up_spectra_);
OpenSwath::SpectrumPtr* spectrum = &spectrum_;
// Isotope correlation / overlap score: Is this peak part of an
// isotopic pattern or is it the monoisotopic peak in an isotopic
// pattern?
diascoring.dia_isotope_scores(transitions, (*spectrum), imrmfeature, scores.isotope_correlation, scores.isotope_overlap);
// Mass deviation score
diascoring.dia_massdiff_score(transitions, (*spectrum), normalized_library_intensity,
scores.massdev_score, scores.weighted_massdev_score);
// Presence of b/y series score
OpenMS::AASequence aas;
OpenSwathDataAccessHelper::convertPeptideToAASequence(pep, aas);
diascoring.dia_by_ion_score((*spectrum), aas, by_charge_state, scores.bseries_score, scores.yseries_score);
// FEATURE we should not punish so much when one transition is missing!
scores.massdev_score = scores.massdev_score / transitions.size();
// DIA dotproduct and manhattan score
diascoring.score_with_isotopes((*spectrum), transitions, scores.dotprod_score_dia, scores.manhatt_score_dia);
// MS1 ppm score : check that the map is not NULL and contains spectra
if (ms1_map && ms1_map->getNrSpectra() > 0)
{
OpenSwath::SpectrumPtr ms1_spectrum = getAddedSpectra_(ms1_map, imrmfeature->getRT(), add_up_spectra_);
diascoring.dia_ms1_massdiff_score(precursor_mz, ms1_spectrum, scores.ms1_ppm_score);
diascoring.dia_ms1_isotope_scores(precursor_mz, ms1_spectrum, pep.getChargeState(), scores.ms1_isotope_correlation, scores.ms1_isotope_overlap);
}
}
void ChromatogramExtractorAlgorithm::extractChromatograms(const OpenSwath::SpectrumAccessPtr input,
std::vector< OpenSwath::ChromatogramPtr >& output,
std::vector<ExtractionCoordinates> extraction_coordinates, double mz_extraction_window,
bool ppm, String filter)
{
Size input_size = input->getNrSpectra();
if (input_size < 1)
{
return;
}
if (output.size() != extraction_coordinates.size())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Output and extraction coordinates need to have the same size");
}
int used_filter = getFilterNr_(filter);
// assert that they are sorted!
if (std::adjacent_find(extraction_coordinates.begin(), extraction_coordinates.end(),
ExtractionCoordinates::SortExtractionCoordinatesReverseByMZ) != extraction_coordinates.end())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Input to extractChromatogram needs to be sorted by m/z");
}
//go through all spectra
startProgress(0, input_size, "Extracting chromatograms");
for (Size scan_idx = 0; scan_idx < input_size; ++scan_idx)
{
setProgress(scan_idx);
OpenSwath::SpectrumPtr sptr = input->getSpectrumById(scan_idx);
OpenSwath::SpectrumMeta s_meta = input->getSpectrumMetaById(scan_idx);
OpenSwath::BinaryDataArrayPtr mz_arr = sptr->getMZArray();
OpenSwath::BinaryDataArrayPtr int_arr = sptr->getIntensityArray();
std::vector<double>::const_iterator mz_start = mz_arr->data.begin();
std::vector<double>::const_iterator mz_end = mz_arr->data.end();
std::vector<double>::const_iterator mz_it = mz_arr->data.begin();
std::vector<double>::const_iterator int_it = int_arr->data.begin();
if (sptr->getMZArray()->data.size() == 0)
continue;
// go through all transitions / chromatograms which are sorted by
// ProductMZ. We can use this to step through the spectrum and at the
// same time step through the transitions. We increase the peak counter
// until we hit the next transition and then extract the signal.
for (Size k = 0; k < extraction_coordinates.size(); ++k)
{
double integrated_intensity = 0;
double current_rt = s_meta.RT;
if (extraction_coordinates[k].rt_end - extraction_coordinates[k].rt_start > 0 &&
(current_rt < extraction_coordinates[k].rt_start ||
current_rt > extraction_coordinates[k].rt_end) )
{
continue;
}
if (used_filter == 1)
{
extract_value_tophat( mz_start, mz_it, mz_end, int_it,
extraction_coordinates[k].mz, integrated_intensity, mz_extraction_window, ppm);
}
else if (used_filter == 2)
{
throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
}
// Time is first, intensity is second
output[k]->binaryDataArrayPtrs[0]->data.push_back(current_rt);
output[k]->binaryDataArrayPtrs[1]->data.push_back(integrated_intensity);
}
}
endProgress();
}
