95 template <
typename ExperimentT>
99 double mz_extraction_window,
101 double rt_extraction_window,
107 Size input_size = input.size();
113 int used_filter = getFilterNr_(filter);
114 populatePeptideRTMap_(transition_exp, rt_extraction_window);
122 std::vector<typename ExperimentT::ChromatogramType> chromatograms;
123 prepareSpectra_(settings, chromatograms, transition_exp);
126 startProgress(0, input_size,
"Extracting chromatograms");
127 for (
Size scan_idx = 0; scan_idx < input_size; ++scan_idx)
129 setProgress(scan_idx);
131 if (input[scan_idx].size() == 0)
137 double integrated_intensity = 0;
143 for (
Size k = 0;
k < chromatograms.size(); ++
k)
146 double current_rt = input[scan_idx].getRT();
147 if (outsideExtractionWindow_(transition_exp.
getTransitions()[
k], current_rt, trafo, rt_extraction_window))
155 if (used_filter == 1)
157 extract_value_tophat(input[scan_idx], mz, peak_idx, integrated_intensity, mz_extraction_window, ppm);
159 else if (used_filter == 2)
161 extract_value_bartlett(input[scan_idx], mz, peak_idx, integrated_intensity, mz_extraction_window, ppm);
166 p.setIntensity(integrated_intensity);
167 chromatograms[
k].push_back(p);
173 output.setChromatograms(chromatograms);
194 std::vector< OpenSwath::ChromatogramPtr >& output,
195 const std::vector<ExtractionCoordinates>& extraction_coordinates,
196 double mz_extraction_window,
201 extraction_coordinates, mz_extraction_window, ppm, -1, filter);
223 std::vector< OpenSwath::ChromatogramPtr >& output,
224 const std::vector<ExtractionCoordinates>& extraction_coordinates,
225 double mz_extraction_window,
227 double im_extraction_window,
231 extraction_coordinates, mz_extraction_window, ppm, im_extraction_window, filter);
255 static void prepare_coordinates(std::vector< OpenSwath::ChromatogramPtr > & output_chromatograms,
256 std::vector< ExtractionCoordinates > & coordinates,
258 const double rt_extraction_window,
259 const bool ms1 =
false,
260 const int ms1_isotopes = 0);
262 static void prepare_coordinates(std::vector< OpenSwath::ChromatogramPtr > & output_chromatograms,
263 std::vector< ExtractionCoordinates > & coordinates,
265 const double rt_extraction_window,
266 const bool ms1 =
false,
267 const int ms1_isotopes = 0);
283 template <
typename TransitionExpT>
285 const std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
286 TransitionExpT& transition_exp_used,
288 std::vector<OpenMS::MSChromatogram > & output_chromatograms,
290 double im_extraction_width = 0.0)
292 typedef std::map<String, const typename TransitionExpT::Transition* > TransitionMapType;
293 TransitionMapType trans_map;
294 for (
Size i = 0; i < transition_exp_used.getTransitions().size(); i++)
296 trans_map[transition_exp_used.getTransitions()[i].getNativeID()] = &transition_exp_used.getTransitions()[i];
299 for (
Size i = 0; i < chromatograms.size(); i++)
322 if (!transition_group_id.empty())
325 String r = extract_id_(transition_exp_used, transition_group_id, prec_charge);
332 typename TransitionExpT::Transition transition = (*trans_map[coord.
id]);
334 prec.
setMZ(transition.getPrecursorMZ());
343 prod.
setMZ(transition.getProductMZ());
349 if (!transition.getPeptideRef().empty())
352 String r = extract_id_(transition_exp_used, transition.getPeptideRef(), prec_charge);
359 String r = extract_id_(transition_exp_used, transition.getCompoundRef(), prec_charge);
365 if (coord.
ion_mobility >= 0 && im_extraction_width > 0.0)
383 output_chromatograms.push_back(chrom);
388 template <
typename SpectrumT>
392 double& integrated_intensity,
393 const double extract_window,
396 integrated_intensity = 0;
397 if (input.size() == 0)
406 left = mz - mz * extract_window / 2.0 * 1.0e-6;
407 right = mz + mz * extract_window / 2.0 * 1.0e-6;
411 left = mz - extract_window / 2.0;
412 right = mz + extract_window / 2.0;
418 while (peak_idx < input.size() && input[peak_idx].getMZ() < mz)
427 if (peak_idx >= input.size())
429 walker = input.size() - 1;
433 if (input[walker].getMZ() > left && input[walker].getMZ() < right)
435 integrated_intensity += input[walker].getIntensity();
446 if (walker == 0 && input[walker].getMZ() > left && input[walker].getMZ() < right)
448 integrated_intensity += input[walker].getIntensity();
451 while (walker > 0 && input[walker].getMZ() > left && input[walker].getMZ() < right)
453 integrated_intensity += input[walker].getIntensity(); walker--;
459 if (walker < input.size() )
463 while (walker < input.size() && input[walker].getMZ() > left && input[walker].getMZ() < right)
465 integrated_intensity += input[walker].getIntensity(); walker++;
470 template <
typename SpectrumT>
474 double& integrated_intensity,
475 const double extract_window,
478 integrated_intensity = 0;
479 if (input.size() == 0)
485 double left, right, half_window_size, weight;
488 half_window_size = mz * extract_window / 2.0 * 1.0e-6;
489 left = mz - mz * extract_window / 2.0 * 1.0e-6;
490 right = mz + mz * extract_window / 2.0 * 1.0e-6;
494 half_window_size = extract_window / 2.0;
495 left = mz - extract_window / 2.0;
496 right = mz + extract_window / 2.0;
502 while (peak_idx < input.size() && input[peak_idx].getMZ() < mz)
511 if (peak_idx >= input.size())
513 walker = input.size() - 1;
517 if (input[walker].getMZ() > left && input[walker].getMZ() < right)
519 weight = 1 - fabs(input[walker].getMZ() - mz) / half_window_size;
520 integrated_intensity += input[walker].getIntensity() * weight;
531 if (walker == 0 && input[walker].getMZ() > left && input[walker].getMZ() < right)
533 integrated_intensity += input[walker].getIntensity();
536 while (walker > 0 && input[walker].getMZ() > left && input[walker].getMZ() < right)
538 weight = 1 - fabs(input[walker].getMZ() - mz) / half_window_size;
539 integrated_intensity += input[walker].getIntensity() * weight; walker--;
545 if (walker < input.size() )
549 while (walker<input.size() && input[walker].getMZ()> left && input[walker].getMZ() < right)
551 weight = 1 - fabs(input[walker].getMZ() - mz) / half_window_size;
552 integrated_intensity += input[walker].getIntensity() * weight; walker++;
565 template <
typename TransitionExpT>
566 static String extract_id_(TransitionExpT& transition_exp_used,
const String&
id,
int& prec_charge);
582 template <
class SpectrumSettingsT,
class ChromatogramT>
584 std::vector<ChromatogramT>& chromatograms,
596 if (settings.getPrecursors().size() > 0)
604 for (
Size pep_idx = 0; pep_idx < transition_exp.
getPeptides().size(); pep_idx++)
607 if (pep->
id == pepref)
614 for (
Size comp_idx = 0; comp_idx < transition_exp.
getCompounds().size(); comp_idx++)
617 if (comp->
id == compref)
625 chrom.setPrecursor(prec);
630 chrom.setProduct(prod);
633 chrom.setInstrumentSettings(settings.getInstrumentSettings());
634 chrom.setAcquisitionInfo(settings.getAcquisitionInfo());
635 chrom.setSourceFile(settings.getSourceFile());
637 for (
Size j = 0; j < settings.getDataProcessing().size(); ++j)
639 settings.getDataProcessing()[j]->setMetaValue(
"performed_on_spectra",
"true");
640 chrom.getDataProcessing().push_back(settings.getDataProcessing()[j]);
646 chromatograms.push_back(chrom);
655 double rt_extraction_window);
658 int getFilterNr_(
const String& filter);
662 double rt_extraction_window);
675 prec_charge = comp.
charge;
702 if (
c.hasCharge()) {prec_charge =
c.getChargeState();}