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