35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
38 #define run_identifier "unique_run_identifier"
39 #define USE_SP_INTERFACE
112 double lda_quick_score =
113 library_corr * -0.5319046 +
114 library_rmsd * 2.1643962 +
115 norm_rt_score * 8.0353047 +
116 xcorr_coelution_score * 0.1458914 +
117 xcorr_shape_score * -1.6901925 +
118 log_sn_score * -0.8002824;
119 return lda_quick_score;
241 pickExperiment(chromatogram_ptr, output, transition_exp, trafo, empty_swath_ptr, transition_group_map);
254 PeptideRTMap_.clear();
258 PeptideRTMap_[pep.
id] = pep.
rt;
263 std::vector<ProteinHit> protein_hits;
271 protein_hits.push_back(prot_hit);
283 mapExperimentToTransitionList(input, transition_exp, transition_group_map, trafo, rt_extraction_window_);
285 for (TransitionGroupMapType::iterator trgroup_it = transition_group_map.begin(); trgroup_it != transition_group_map.end(); trgroup_it++)
287 if (trgroup_it->second.getChromatograms().size() > 0) {counter++; }
289 std::cout <<
"Will analyse " << counter <<
" peptides with a total of " << transition_exp.
getTransitions().size() <<
" transitions " << std::endl;
296 startProgress(0, transition_group_map.size(),
"picking peaks");
297 for (TransitionGroupMapType::iterator trgroup_it = transition_group_map.begin(); trgroup_it != transition_group_map.end(); trgroup_it++)
300 setProgress(++progress);
308 trgroup_picker.
setParameters(param_.copy(
"TransitionGroupPicker:",
true));
310 scorePeakgroups_(trgroup_it->second, trafo, swath_map, output);
333 template <
typename SpectrumT,
typename TransitionT>
339 std::vector<OpenSwath::ISignalToNoisePtr> signal_noise_estimators;
340 std::vector<MRMFeature> feature_list;
348 signal_noise_estimators.push_back(snptr);
355 expected_rt = newtr.
apply(expected_rt);
358 for (std::vector<MRMFeature>::iterator mrmfeature = transition_group.
getFeaturesMuteable().begin();
368 #ifdef DEBUG_MRMPEAKPICKER
369 std::cout <<
"000000000000000000000000000000000000000000000000000000000000000000000000000 " << std::endl;
370 std::cout <<
"scoring feature " << (*mrmfeature) <<
" == " << mrmfeature->getMetaValue(
"PeptideRef") <<
371 "[ expected RT " << PeptideRTMap_[mrmfeature->getMetaValue(
"PeptideRef")] <<
" / " << expected_rt <<
" ]" <<
372 " with " << transition_group.
size() <<
" nr transitions and nr chromats " << transition_group.
getChromatograms().size() << std::endl;
375 int group_size = boost::numeric_cast<
int>(transition_group.
size());
379 "Error: Transition group " + transition_group.
getTransitionGroupID() +
" has no chromatograms.");
383 std::cerr <<
"Error: transition group " << transition_group.
getTransitionGroupID() <<
" has less than 2 chromatograms. It has " << group_size << std::endl;
389 std::vector<double> normalized_library_intensity;
396 mrmscore_.initializeXCorrMatrix(imrmfeature, itransition_group, normalize);
399 double xcorr_coelution_score = 0;
400 if (use_coelution_score_)
402 xcorr_coelution_score = mrmscore_.calcXcorrCoelutionScore();
403 mrmfeature->addScore(
"var_xcorr_coelution", xcorr_coelution_score);
406 double weighted_coelution_score = 0;
407 if (use_coelution_score_)
409 weighted_coelution_score = mrmscore_.calcXcorrCoelutionScore_weighted(normalized_library_intensity);
410 mrmfeature->addScore(
"var_xcorr_coelution_weighted ", weighted_coelution_score);
417 double xcorr_shape_score = 0;
418 if (use_shape_score_)
420 xcorr_shape_score = mrmscore_.calcXcorrShape_score();
421 mrmfeature->addScore(
"var_xcorr_shape", xcorr_shape_score);
424 double weighted_xcorr_shape = 0;
425 if (use_shape_score_)
427 weighted_xcorr_shape = mrmscore_.calcXcorrShape_score_weighted(normalized_library_intensity);
428 mrmfeature->addScore(
"var_xcorr_shape_weighted", weighted_xcorr_shape);
433 double library_corr = 0, library_rmsd = 0;
434 double library_manhattan, library_dotprod;
435 if (use_library_score_)
437 mrmscore_.calcLibraryScore(imrmfeature, transition_group.
getTransitions(), library_corr, library_rmsd, library_manhattan, library_dotprod);
438 mrmfeature->addScore(
"var_library_corr", library_corr);
439 mrmfeature->addScore(
"var_library_rmsd", library_rmsd);
440 mrmfeature->addScore(
"var_library_manhattan", library_manhattan);
441 mrmfeature->addScore(
"var_library_dotprod", library_dotprod);
445 double rt_score = 0, norm_rt_score = 0;
452 double experimental_rt = mrmfeature->getFeature(native_id).getRT();
453 double normalized_experimental_rt = trafo.
apply(experimental_rt);
455 rt_score = mrmscore_.calcRTScore(*pep, normalized_experimental_rt);
456 norm_rt_score = rt_score / rt_normalization_factor_;
457 mrmfeature->addScore(
"delta_rt", mrmfeature->getRT() - expected_rt);
458 mrmfeature->addScore(
"assay_rt", expected_rt);
459 mrmfeature->addScore(
"norm_RT", normalized_experimental_rt);
460 mrmfeature->addScore(
"rt_score", rt_score);
461 mrmfeature->addScore(
"var_norm_rt_score", norm_rt_score);
465 double intensity_score = 0;
466 if (use_intensity_score_)
468 intensity_score = mrmfeature->getIntensity() / (
double)mrmfeature->getMetaValue(
"total_xic");
469 mrmfeature->addScore(
"var_intensity_score", intensity_score);
472 double total_xic_score = 0;
473 if (use_total_xic_score_)
475 total_xic_score = (
double)mrmfeature->getMetaValue(
"total_xic");
476 mrmfeature->addScore(
"total_xic", total_xic_score);
479 double nr_peaks_score = 0;
480 if (use_nr_peaks_score_)
482 nr_peaks_score = group_size;
483 mrmfeature->addScore(
"nr_peaks", nr_peaks_score);
486 double sn_score = 0, log_sn_score = 0;
489 sn_score = mrmscore_.calcSNScore(imrmfeature, signal_noise_estimators);
496 log_sn_score = std::log(sn_score);
498 mrmfeature->addScore(
"sn_ratio", sn_score);
499 mrmfeature->addScore(
"var_log_sn_score", log_sn_score);
503 double quick_lda_dismiss = 0;
504 double lda_quick_score = -scores.
get_quick_lda_score(library_corr, library_rmsd, norm_rt_score, xcorr_coelution_score, xcorr_shape_score, log_sn_score);
506 if (lda_quick_score < quick_lda_dismiss)
511 double elution_model_fit_score = 0;
512 if (use_elution_model_score_)
514 elution_model_fit_score = emgscoring_.calcElutionFitScore((*mrmfeature), transition_group);
515 mrmfeature->addScore(
"var_elution_model_fit_score", elution_model_fit_score);
518 double xx_lda_prescore;
528 bool swath_present = (swath_map->getNrSpectra() > 0);
531 mrmfeature->addScore(
"main_var_xx_lda_prelim_score", xx_lda_prescore);
532 mrmfeature->setOverallQuality(xx_lda_prescore);
536 mrmfeature->addScore(
"xx_lda_prelim_score", xx_lda_prescore);
541 calculateSwathScores_(transition_group, *mrmfeature, swath_map, normalized_library_intensity, scores);
547 calculate_local_fdr_scores(transition_group, *mrmfeature, trafo);
568 pep_hit_.
setScore(mrmfeature->getScore(
"xx_swath_prelim_score"));
575 mrmfeature->getPeptideIdentifications().push_back(pep_id_);
576 mrmfeature->ensureUniqueId();
577 mrmfeature->setMetaValue(
"PrecursorMZ", transition_group.
getTransitions()[0].getPrecursorMZ());
578 mrmfeature->setSubordinates(mrmfeature->getFeatures());
579 double total_intensity = 0, total_peak_apices = 0;
580 for (std::vector<Feature>::iterator sub_it = mrmfeature->getSubordinates().begin(); sub_it != mrmfeature->getSubordinates().end(); sub_it++)
582 if (!write_convex_hull_) {sub_it->getConvexHulls().clear(); }
583 sub_it->ensureUniqueId();
584 if (sub_it->getMZ() > quantification_cutoff_)
586 total_intensity += sub_it->getIntensity();
587 total_peak_apices += (
DoubleReal)sub_it->getMetaValue(
"peak_apex_int");
591 mrmfeature->setIntensity(total_intensity);
592 mrmfeature->setMetaValue(
"peak_apices_sum", total_peak_apices);
593 feature_list.push_back((*mrmfeature));
596 delete itransition_group;
601 std::reverse(feature_list.begin(), feature_list.end());
603 for (
Size i = 0; i < feature_list.size(); i++)
605 if (stop_report_after_feature_ >= 0 && i >= (
Size)stop_report_after_feature_) {
break; }
606 output.push_back(feature_list[i]);
613 std::vector<std::size_t> indices = swath_map->getSpectraByRT(RT, 0.0);
614 int closest_idx = boost::numeric_cast<
int>(indices[0]);
615 if (indices[0] != 0 &&
616 std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0]) - 1).RT - RT) <
617 std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0])).RT - RT))
622 if (nr_spectra_to_add == 1)
629 std::vector<OpenSwath::SpectrumPtr> all_spectra;
631 all_spectra.push_back(swath_map->getSpectrumById(closest_idx));
632 for (
int i = 1; i <= nr_spectra_to_add / 2; i++)
634 all_spectra.push_back(swath_map->getSpectrumById(closest_idx - i));
635 all_spectra.push_back(swath_map->getSpectrumById(closest_idx + i));
642 template <
typename SpectrumT,
typename TransitionT>
649 int by_charge_state = 1;
659 double isotope_corr = 0, isotope_overlap = 0;
661 (*spectrum), imrmfeature, isotope_corr, isotope_overlap);
663 double ppm_score = 0, ppm_score_weighted = 0;
665 (*spectrum), normalized_library_intensity, ppm_score, ppm_score_weighted);
668 double bseries_score = 0, yseries_score = 0;
671 diascoring_.dia_by_ion_score((*spectrum), aas, by_charge_state, bseries_score, yseries_score);
672 mrmfeature->
addScore(
"var_isotope_correlation_score", isotope_corr);
673 mrmfeature->
addScore(
"var_isotope_overlap_score", isotope_overlap);
674 #ifdef DEBUG_MRMPEAKPICKER
675 cout <<
"added corr isotope_score " << isotope_corr << endl;
676 cout <<
"added overlap isotope_score " << isotope_overlap << endl;
680 double massdev_score = ppm_score / transition_group.
size();
681 double massdev_score_weighted = ppm_score_weighted;
682 mrmfeature->
addScore(
"var_massdev_score", massdev_score);
683 mrmfeature->
addScore(
"var_massdev_score_weighted", massdev_score_weighted);
684 #ifdef DEBUG_MRMPEAKPICKER
685 cout <<
"added score massdev_score " << massdev_score << endl;
686 cout <<
"added score weighted massdev_score " << massdev_score_weighted << endl;
689 mrmfeature->
addScore(
"var_bseries_score", bseries_score);
690 mrmfeature->
addScore(
"var_yseries_score", yseries_score);
691 #ifdef DEBUG_MRMPEAKPICKER
692 cout <<
"added score bseries_score " << bseries_score << endl;
693 cout <<
"added score yseries_score " << yseries_score << endl;
696 double dotprod_score_dia;
697 double manhatt_score_dia;
699 diascoring_.score_with_isotopes((*spectrum), transition_group.
getTransitions(), dotprod_score_dia, manhatt_score_dia);
701 mrmfeature->
addScore(
"var_dotprod_score", dotprod_score_dia);
702 mrmfeature->
addScore(
"var_manhatt_score", manhatt_score_dia);
709 mrmfeature->
addScore(
"main_var_xx_swath_prelim_score", xx_swath_prescore);
711 #ifdef DEBUG_MRMPEAKPICKER
712 cout <<
"added xx_swath_prescore (everything above 2 is good) " << xx_swath_prescore << endl;
720 void updateMembers_();
757 #undef run_identifier
double isotope_overlap
Definition: MRMFeatureFinderScoring.h:92
bool use_sn_score_
Definition: MRMFeatureFinderScoring.h:735
std::string getPeptideRef() const
Definition: TransitionExperiment.h:66
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:135
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
std::string id
Definition: TransitionExperiment.h:116
double isotope_correlation
Definition: MRMFeatureFinderScoring.h:91
int getChargeState() const
Definition: TransitionExperiment.h:106
const std::vector< TransitionType > & getTransitions() const
Definition: MRMTransitionGroup.h:122
A more convenient string class.
Definition: String.h:56
void setIdentifier(const String &id)
sets the indentifier
void setScore(DoubleReal score)
sets the score of the peptide hit
void setHits(const std::vector< ProteinHit > &hits)
Sets the protein hits.
Size size() const
Definition: MRMTransitionGroup.h:107
OpenSwath::LightPeptide PeptideType
Definition: MRMFeatureFinderScoring.h:215
bool use_shape_score_
Definition: MRMFeatureFinderScoring.h:728
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
Definition: FeatureMap.h:410
This class implements different scores for peaks found in SRM/MRM.
Definition: MRMScoring.h:75
void setSequence(const String &sequence)
sets the protein sequence
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:60
MRMTransitionGroup< MSSpectrum< ChromatogramPeak >, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:218
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:752
OpenSwath::SpectrumPtr getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add)
Returns the addition of "nr_spectra_to_add" spectra around the given RT.
Definition: MRMFeatureFinderScoring.h:611
OpenSwath::MRMScoring mrmscore_
Definition: MRMFeatureFinderScoring.h:751
const std::vector< SpectrumType > & getChromatograms() const
Definition: MRMTransitionGroup.h:148
A container for features.
Definition: FeatureMap.h:111
OpenSwath::LightTransition TransitionType
Definition: MRMFeatureFinderScoring.h:213
static void convertPeptideToAASequence(const OpenSwath::LightPeptide &peptide, AASequence &aa_sequence)
convert from the LightPeptide to an OpenMS AASequence (with correct modifications) ...
std::map< OpenMS::String, double > PeptideRTMap_
Definition: MRMFeatureFinderScoring.h:747
An implementation of the OpenSWATH Transition Group Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:109
The MRMFeatureFinder finds and scores peaks of transitions that coelute.
Definition: MRMFeatureFinderScoring.h:200
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:742
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:738
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:219
#define run_identifier
Definition: MRMFeatureFinderScoring.h:38
void getLibraryIntensity(std::vector< double > &result) const
Definition: MRMTransitionGroup.h:189
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
QualityLess OverallQualityLess
Compare by quality.
Definition: Feature.h:97
std::string protein_ref
Definition: TransitionExperiment.h:104
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:203
void setParameters(const Param ¶m)
Sets the parameters.
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:753
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
Definition: ITransition.h:65
bool use_nr_peaks_score_
Definition: MRMFeatureFinderScoring.h:734
The representation of a transition group that has information about the individual chromatograms as w...
Definition: MRMTransitionGroup.h:56
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:737
OPENSWATHALGO_DLLAPI void normalize_sum(double x[], unsigned int n)
divide each element of x by the sum of the vector
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:216
double library_rmsd
Definition: MRMFeatureFinderScoring.h:89
Definition: TransitionExperiment.h:99
void scorePeakgroups_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap< Feature > &output)
Score all peak groups.
Definition: MRMFeatureFinderScoring.h:334
std::string sequence
Definition: TransitionExperiment.h:117
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
A method or algorithm argument contains illegal values.
Definition: Exception.h:634
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:73
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:125
DoubleReal spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:739
void setCharge(Int charge)
sets the charge of the peptide
The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors...
Definition: MRMTransitionGroupPicker.h:76
DoubleReal quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:724
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Spectrum > SpectrumPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:227
Representation of a peptide hit.
Definition: PeptideHit.h:54
static OpenSwath::SpectrumAccessPtr getSpectrumAccessOpenMSPtr(OpenMS::MSExperiment< OpenMS::Peak1D > &exp)
Simple Factory method to get a SpectrumAccess Ptr from an MSExperiment.
double log_sn_score
Definition: MRMFeatureFinderScoring.h:97
An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:152
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:76
double massdev_score
Definition: MRMFeatureFinderScoring.h:93
bool use_coelution_score_
Definition: MRMFeatureFinderScoring.h:727
DoubleReal rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:745
double get_quick_lda_score(double library_corr, double library_rmsd, double norm_rt_score, double xcorr_coelution_score, double xcorr_shape_score, double log_sn_score)
Definition: MRMFeatureFinderScoring.h:99
double yseries_score
Definition: MRMFeatureFinderScoring.h:96
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:748
std::vector< MRMFeature > & getFeaturesMuteable()
Definition: MRMTransitionGroup.h:179
void setStrictFlag(bool f)
Definition: MRMFeatureFinderScoring.h:325
bool use_rt_score_
Definition: MRMFeatureFinderScoring.h:729
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS Targeted experiment to the light Targeted Experiment
std::string id
Definition: TransitionExperiment.h:105
void calculateSwathScores_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, MRMFeature &mrmfeature_, OpenSwath::SpectrumAccessPtr swath_map, std::vector< double > &normalized_library_intensity, OpenSwath_Scores scores)
Definition: MRMFeatureFinderScoring.h:643
double xcorr_coelution_score
Definition: MRMFeatureFinderScoring.h:94
void setSequence(const AASequence &sequence)
sets the peptide sequence
void setAccession(const String &accession)
sets the accession of the protein
Representation of a protein hit.
Definition: ProteinHit.h:54
Definition: TransitionExperiment.h:46
std::vector< LightPeptide > & getPeptides()
Definition: TransitionExperiment.h:130
DoubleReal rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:723
Definition: ITransition.h:56
std::map< OpenMS::String, const ProteinType * > ProteinRefMap_
Definition: MRMFeatureFinderScoring.h:749
void pickExperiment(MSExperiment< Peak1D > &chromatograms, FeatureMap< Feature > &output, TargetedExperiment &transition_exp_, TransformationDescription trafo, MSExperiment< Peak1D > &swath_map)
Definition: MRMFeatureFinderScoring.h:231
void setOverallQuality(QualityType q)
Set the overall quality.
A structure to hold the different scores computed by the FeatureFinder.
Definition: MRMFeatureFinderScoring.h:85
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:214
bool use_intensity_score_
Definition: MRMFeatureFinderScoring.h:732
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
void addScore(const String &score_name, double score)
set a single peakgroup score
double xcorr_shape_score
Definition: MRMFeatureFinderScoring.h:95
void pickTransitionGroup(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group)
Definition: MRMTransitionGroupPicker.h:202
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
double calculate_swath_lda_prescore(OpenSwath_Scores scores)
Definition: MRMFeatureFinderScoring.h:148
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
double norm_rt_score
Definition: MRMFeatureFinderScoring.h:90
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< ISignalToNoise > ISignalToNoisePtr
Definition: ITransition.h:78
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:217
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
double rt
Definition: TransitionExperiment.h:101
double elution_model_fit_score
Definition: MRMFeatureFinderScoring.h:87
bool use_total_xic_score_
Definition: MRMFeatureFinderScoring.h:733
void addProteinAccession(const String &accession)
adds an accession of a protein which contains this peptide hit
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
bool use_elution_model_score_
Definition: MRMFeatureFinderScoring.h:731
Definition: TransitionExperiment.h:114
Definition: TransitionExperiment.h:120
const String & getTransitionGroupID() const
Definition: MRMTransitionGroup.h:112
std::string sequence
Definition: TransitionExperiment.h:103
double library_corr
Definition: MRMFeatureFinderScoring.h:88
MSSpectrum< ChromatogramPeak > RichPeakChromatogram
Type definitions.
Definition: MRMFeatureFinderScoring.h:212
const TransitionType & getTransition(String key)
Definition: MRMTransitionGroup.h:138
void pickExperiment(OpenSwath::SpectrumAccessPtr input, FeatureMap< Feature > &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map)
Definition: MRMFeatureFinderScoring.h:245
static OpenSwath::SpectrumPtr addUpSpectra(std::vector< OpenSwath::SpectrumPtr > all_spectra, double sampling_rate, double filter_zeros)
adds up a list of Spectra by resampling them and then addition of intensities
void setIdentifier(const String &id)
Sets the identifier.
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
double calculate_lda_prescore(OpenSwath_Scores scores)
Definition: MRMFeatureFinderScoring.h:122
bool use_library_score_
Definition: MRMFeatureFinderScoring.h:730
double DoubleReal
Double-precision real type.
Definition: Types.h:118
bool strict_
Definition: MRMFeatureFinderScoring.h:743
Definition: TransitionExperiment.h:93
An implementation of the OpenSWATH MRM Feature Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:84