diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h index 58f4030367a..da52e1f9ce6 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h @@ -63,6 +63,8 @@ namespace OpenMS std::vector getSpectraByRT(double RT, double deltaRT) const override; + std::vector getSpectraRTRange(double rt_start, double rt_end) const override; + size_t getNrSpectra() const override; SpectrumSettings getSpectraMetaInfo(int id) const; diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.h index d75898fe4f0..b2d6cee82ea 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.h @@ -72,6 +72,8 @@ namespace OpenMS std::vector getSpectraByRT(double RT, double deltaRT) const override; + std::vector getSpectraRTRange(double rt_start, double rt_end) const override; + size_t getNrSpectra() const override; SpectrumSettings getSpectraMetaInfo(int id) const; diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h index ef249e33182..1a444185126 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h @@ -21,16 +21,16 @@ namespace OpenMS { /** * @brief An implementation of the OpenSWATH Spectrum Access interface completely in memory - * + * * This implementation of the spectrum access interface ensures that all data * is held completely in memory and is quickly accessible. This class can be * generated by passing any object implementing the Spectrum Access interface * and guarantees to provide the same access to the raw data as the original * object with the added benefits (and downside) of keeping all data in system * memory. - * + * * A possible example - * + * * @code * OpenSwath::ISpectrumAccess * data_access; * fillData(data_access); // assume that data_access points to some data @@ -70,6 +70,8 @@ namespace OpenMS std::vector getSpectraByRT(double RT, double deltaRT) const override; + std::vector getSpectraRTRange(double rt_start, double rt_end) const override; + size_t getNrSpectra() const override; OpenSwath::ChromatogramPtr getChromatogramById(int id) override; diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.h index 5cb55be15a5..fbdcb3ef13f 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.h @@ -89,6 +89,8 @@ namespace OpenMS std::vector getSpectraByRT(double /* RT */, double /* deltaRT */) const override; + std::vector getSpectraRTRange(double /* rt_start */, double /* rt_end */) const override; + size_t getNrSpectra() const override; OpenSwath::ChromatogramPtr getChromatogramById(int /* id */) override; diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h index 75602d9b472..ccc21581f75 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h @@ -24,7 +24,7 @@ namespace OpenMS public: explicit SpectrumAccessTransforming(OpenSwath::SpectrumAccessPtr sptr); - + ~SpectrumAccessTransforming() override = 0; boost::shared_ptr lightClone() const override = 0; @@ -35,6 +35,8 @@ namespace OpenMS std::vector getSpectraByRT(double RT, double deltaRT) const override; + std::vector getSpectraRTRange(double rt_start, double rt_end) const override; + size_t getNrSpectra() const override; OpenSwath::ChromatogramPtr getChromatogramById(int id) override; diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h index f59ee8b3a8d..3a53ff7fc63 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h @@ -126,6 +126,8 @@ namespace OpenMS double dotprod_score_dia = 0; double manhatt_score_dia = 0; + int numSpectraAdd = 1; // num spectra that are summed up when computing DIA scores + OpenSwath_Scores() = default; double get_quick_lda_score(double library_corr_, diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h index 3ac5a933729..69b73fde7b7 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h @@ -28,6 +28,7 @@ class RangeMZ; class RangeMobility; +class RangeRT; namespace OpenMS { @@ -169,6 +170,7 @@ namespace OpenMS * @param mzerror_ppm m/z and mass error (in ppm) for all transitions * @param[in] drift_target target drift value * @param[in] range_im drift time lower and upper bounds + * @param[in] range_rt retention time lower and upper bounds * */ void calculateDIAScores(OpenSwath::IMRMFeature* imrmfeature, @@ -180,7 +182,8 @@ namespace OpenMS OpenSwath_Scores& scores, std::vector& mzerror_ppm, const double drift_target, - const RangeMobility& range_im); + const RangeMobility& range_im, + const RangeRT& range_rt); /** @brief Score a single chromatographic feature using the precursor map. * @@ -286,17 +289,14 @@ namespace OpenMS */ SpectrumSequence fetchSpectrumSwath(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add, const RangeMobility& im_range); - - protected: - - /** @breif converts a ion mobility enhanced spectrum to a non ion mobility spectrum by filtering by drift time + /** @breif similar to fetchSpectrumSwath() however select spectra across entire rt range of the feature */ - OpenSwath::SpectrumPtr filterByDrift_(const OpenSwath::SpectrumPtr& input, const RangeMobility& range_im); + SpectrumSequence fetchSpectrumSwathAuto(OpenSwath::SpectrumAccessPtr swathmap, const RangeMobility& im_range, const RangeRT& rt_range); - /** @breif Adds up an array of spectrum into one spectrum. If the spectra are ion mobility enhanced, first filter by drift time and then add up spectra + /** @breif similar to fetchSpectrumSwath() however select spectra across entire rt range of the feature */ - OpenSwath::SpectrumPtr getAddedSpectra_(std::vector&, const RangeMobility& range_im); + SpectrumSequence fetchSpectrumSwathAuto(std::vector swath_maps, const RangeMobility& im_range, const RangeRT& rt_range); }; } diff --git a/src/openms/include/OpenMS/INTERFACES/ISpectrumAccess.h b/src/openms/include/OpenMS/INTERFACES/ISpectrumAccess.h index 64b74694f88..0db43b8633d 100644 --- a/src/openms/include/OpenMS/INTERFACES/ISpectrumAccess.h +++ b/src/openms/include/OpenMS/INTERFACES/ISpectrumAccess.h @@ -32,6 +32,8 @@ namespace Interfaces virtual SpectrumPtr getSpectrumById(const std::string& id) const = 0; /// Return a vector of ids of spectra that are within RT +/- deltaRT virtual std::vector getSpectraByRT(double RT, double deltaRT) const = 0; + /// Return a vector of ids of spectra between rt_start and rt_end + virtual std::vector getSpectraRTRange(double rt_start, double rt_end) const = 0; /// Returns the number of spectra available virtual size_t getNrSpectra() const = 0; /// Returns the meta information for a spectrum diff --git a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.cpp b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.cpp index a72db664b65..01bcb719e75 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.cpp @@ -23,7 +23,7 @@ namespace OpenMS SpectrumAccessOpenMS::SpectrumAccessOpenMS(const SpectrumAccessOpenMS & rhs) : ms_experiment_(rhs.ms_experiment_) { - // this only copies the pointers and not the actual data ... + // this only copies the pointers and not the actual data ... } @@ -159,6 +159,25 @@ namespace OpenMS return result; } + std::vector SpectrumAccessOpenMS::getSpectraRTRange(double rt_start, double rt_end) const + { + + // Start at the rt_start + std::vector result; + auto spectrum = ms_experiment_->RTBegin(rt_start); + if (spectrum == ms_experiment_->end()) return result; + + result.push_back(std::distance(ms_experiment_->begin(), spectrum)); + spectrum++; + + while (spectrum != ms_experiment_->end() && spectrum->getRT() <= rt_end) + { + result.push_back(spectrum - ms_experiment_->begin()); + spectrum++; + } + return result; + } + size_t SpectrumAccessOpenMS::getNrChromatograms() const { return ms_experiment_->getChromatograms().size(); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.cpp b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.cpp index ed886841ee1..4873917e044 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.cpp @@ -104,6 +104,23 @@ namespace OpenMS return result; } + std::vector SpectrumAccessOpenMSCached::getSpectraRTRange(double rt_start, double rt_end) const + { + std::vector result; + auto spectrum = meta_ms_experiment_.RTBegin(rt_start); + if (spectrum == meta_ms_experiment_.end()) return result; + + result.push_back(std::distance(meta_ms_experiment_.begin(), spectrum)); + spectrum++; + + while (spectrum != meta_ms_experiment_.end() && spectrum->getRT() < rt_end) + { + result.push_back(spectrum - meta_ms_experiment_.begin()); + spectrum++; + } + return result; + } + size_t SpectrumAccessOpenMSCached::getNrSpectra() const { return meta_ms_experiment_.size(); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.cpp b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.cpp index 975f0d72e21..1258911d650 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.cpp @@ -48,7 +48,7 @@ namespace OpenMS chromatograms_(rhs.chromatograms_), chromatogram_ids_(rhs.chromatogram_ids_) { - // this only copies the pointers and not the actual data ... + // this only copies the pointers and not the actual data ... } boost::shared_ptr SpectrumAccessOpenMSInMemory::lightClone() const @@ -93,6 +93,25 @@ namespace OpenMS return result; } + std::vector SpectrumAccessOpenMSInMemory::getSpectraRTRange(double rt_start, double rt_end) const + { + + std::vector result; + OpenSwath::SpectrumMeta s; + s.RT = rt_start; + auto spectrum = std::lower_bound(spectra_meta_.begin(), spectra_meta_.end(), s, OpenSwath::SpectrumMeta::RTLess()); + if (spectrum == spectra_meta_.end()) return result; + + result.push_back(std::distance(spectra_meta_.begin(), spectrum)); + ++spectrum; + while ( spectrum != spectra_meta_.end() && spectrum->RT < rt_end) + { + result.push_back(std::distance(spectra_meta_.begin(), spectrum)); + ++spectrum; + } + return result; + } + size_t SpectrumAccessOpenMSInMemory::getNrSpectra() const { OPENMS_PRECONDITION(spectra_.size() == spectra_meta_.size(), "Spectra and meta data needs to match") diff --git a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.cpp b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.cpp index ffc9355cc0a..9db5a8b915d 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.cpp @@ -138,7 +138,7 @@ namespace OpenMS } spectra.reserve(tmp_spectra.size()); spectra_meta.reserve(tmp_spectra.size()); - + for (Size k = 0; k < tmp_spectra.size(); k++) { const MSSpectrumType& spectrum = tmp_spectra[k]; @@ -187,6 +187,11 @@ namespace OpenMS } } + std::vector SpectrumAccessSqMass::getSpectraRTRange(double rt_start, double rt_end) const + { + throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION); + } + size_t SpectrumAccessSqMass::getNrSpectra() const { size_t res; diff --git a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.cpp b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.cpp index ab54a4afad5..80c5c47bf17 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.cpp @@ -40,6 +40,11 @@ namespace OpenMS return sptr_->getSpectraByRT(RT, deltaRT); } + std::vector SpectrumAccessTransforming::getSpectraRTRange(double rt_start, double rt_end) const + { + return sptr_->getSpectraRTRange(rt_start, rt_end); + } + size_t SpectrumAccessTransforming::getNrSpectra() const { return sptr_->getNrSpectra(); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp index f76e841538a..4fa20ade364 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp @@ -72,8 +72,8 @@ namespace OpenMS defaults_.setValidStrings("write_convex_hull", {"true","false"}); defaults_.setValue("spectrum_addition_method", "simple", "For spectrum addition, either use simple concatenation or use peak resampling", {"advanced"}); defaults_.setValidStrings("spectrum_addition_method", {"simple", "resample"}); - defaults_.setValue("add_up_spectra", 1, "Add up spectra around the peak apex (needs to be a non-even integer)", {"advanced"}); - defaults_.setMinInt("add_up_spectra", 1); + defaults_.setValue("add_up_spectra", 1, "Add up spectra around the peak apex (needs to be a non-even integer), if set to -1 all spectra across peak width are summed", {"advanced"}); + //defaults_.setMinInt("add_up_spectra", 1); defaults_.setValue("spacing_for_spectra_resampling", 0.005, "If spectra are to be added, use this spacing to add them up", {"advanced"}); defaults_.setMinFloat("spacing_for_spectra_resampling", 0.0); defaults_.setValue("uis_threshold_sn", -1, "S/N threshold to consider identification transition (set to -1 to consider all)"); @@ -169,7 +169,7 @@ namespace OpenMS void MRMFeatureFinderScoring::pickExperiment(const OpenSwath::SpectrumAccessPtr& input, FeatureMap& output, const OpenSwath::LightTargetedExperiment& transition_exp, - const TransformationDescription& trafo, + const TransformationDescription& trafo, const std::vector& swath_maps, TransitionGroupMapType& transition_group_map) { @@ -306,7 +306,7 @@ namespace OpenMS { MRMFeature idmrmfeature = trgr_ident.getFeaturesMuteable()[feature_idx]; OpenSwath::IMRMFeature* idimrmfeature; - idimrmfeature = new MRMFeatureOpenMS(idmrmfeature); + idimrmfeature = new MRMFeatureOpenMS(idmrmfeature); // get drift time upper/lower offset (this assumes that all chromatograms // are derived from the same precursor with the same drift time) @@ -549,6 +549,9 @@ namespace OpenMS for (SignedSize feature_idx = 0; feature_idx < (SignedSize) mrmfeatures.size(); ++feature_idx) { auto& mrmfeature = mrmfeatures[feature_idx]; + + RangeRT rt_range(mrmfeature.getMetaValue("leftWidth"), mrmfeature.getMetaValue("rightWidth")); + OpenSwath::IMRMFeature* imrmfeature; imrmfeature = new MRMFeatureOpenMS(mrmfeature); @@ -686,7 +689,7 @@ namespace OpenMS scorer.calculateDIAScores(imrmfeature, transition_group_detection.getTransitions(), swath_maps, ms1_map_, diascoring_, *pep, scores, masserror_ppm, - drift_target, im_range); + drift_target, im_range, rt_range); mrmfeature.setMetaValue("masserror_ppm", masserror_ppm); } if (sonar_present && su_.use_sonar_scores) @@ -826,6 +829,8 @@ namespace OpenMS // Add the DIA / SWATH scores, ion mobility scores and SONAR scores if (swath_present && su_.use_dia_scores_) { + mrmfeature.addScore("num_spectra_add", scores.numSpectraAdd); + if (su_.use_ms2_isotope_scores) { mrmfeature.addScore("var_isotope_correlation_score", scores.isotope_correlation); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp index 85bbb82194f..e3f6115f1bd 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp @@ -81,6 +81,7 @@ namespace OpenMS "EXP_IM REAL," \ "DELTA_IM REAL," \ "TOTAL_MI REAL NULL," \ + "NUM_SPEC_ADD INT NULL," \ "VAR_BSERIES_SCORE REAL NULL," \ "VAR_DOTPROD_SCORE REAL NULL," \ "VAR_INTENSITY_SCORE REAL NULL," \ @@ -258,7 +259,7 @@ namespace OpenMS << feature_it.getMetaValue("rightWidth") << "); "; sql_feature_ms2 << "INSERT INTO FEATURE_MS2 " \ - "(FEATURE_ID, AREA_INTENSITY, TOTAL_AREA_INTENSITY, APEX_INTENSITY, EXP_IM, DELTA_IM, TOTAL_MI, "\ + "(FEATURE_ID, AREA_INTENSITY, TOTAL_AREA_INTENSITY, APEX_INTENSITY, EXP_IM, DELTA_IM, TOTAL_MI, NUM_SPEC_ADD," \ "VAR_BSERIES_SCORE, VAR_DOTPROD_SCORE, VAR_INTENSITY_SCORE, " \ "VAR_ISOTOPE_CORRELATION_SCORE, VAR_ISOTOPE_OVERLAP_SCORE, VAR_LIBRARY_CORR, "\ "VAR_LIBRARY_DOTPROD, VAR_LIBRARY_MANHATTAN, VAR_LIBRARY_RMSD, VAR_LIBRARY_ROOTMEANSQUARE, "\ @@ -276,6 +277,7 @@ namespace OpenMS << getScore(feature_it, "im_drift") << ", " << getScore(feature_it, "im_delta") << ", " << getScore(feature_it, "total_mi") << ", " + << getScore(feature_it, "num_spectra_add") << ", " << getScore(feature_it, "var_bseries_score") << ", " << getScore(feature_it, "var_dotprod_score") << ", " << getScore(feature_it, "var_intensity_score") << ", " diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathScoring.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathScoring.cpp index 6fcd0464923..dd6d9ed8f75 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathScoring.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathScoring.cpp @@ -79,7 +79,8 @@ namespace OpenMS OpenSwath_Scores& scores, std::vector& masserror_ppm, const double drift_target,// TODO is this needed - const RangeMobility& im_range) + const RangeMobility& im_range, + const RangeRT& rt_range) { OPENMS_PRECONDITION(imrmfeature != nullptr, "Feature to be scored cannot be null"); OPENMS_PRECONDITION(transitions.size() > 0, "There needs to be at least one transition."); @@ -107,11 +108,19 @@ namespace OpenMS std::vector normalized_library_intensity; getNormalized_library_intensities_(transitions, normalized_library_intensity); - // find spectrum that is closest to the apex of the peak using binary search - std::vector spectra = fetchSpectrumSwath(used_swath_maps, imrmfeature->getRT(), add_up_spectra_, im_range); + SpectrumSequence spectra; + if (add_up_spectra_ == -1) // automatically determine how many spectra to add using the rt boundaries + { + spectra = fetchSpectrumSwathAuto(used_swath_maps, im_range, rt_range); + scores.numSpectraAdd = spectra.size(); + } + else // spectrum addition is a constant number + { + spectra = fetchSpectrumSwath(used_swath_maps, imrmfeature->getRT(), add_up_spectra_, im_range); + scores.numSpectraAdd = add_up_spectra_; + } // set the DIA parameters - // TODO Cache these parameters double dia_extract_window_ = (double)diascoring.getParameters().getValue("dia_extraction_window"); bool dia_extraction_ppm_ = diascoring.getParameters().getValue("dia_extraction_unit") == "ppm"; @@ -515,6 +524,23 @@ namespace OpenMS } } + SpectrumSequence OpenSwathScoring::fetchSpectrumSwathAuto(OpenSwath::SpectrumAccessPtr swathmap, const RangeMobility& im_range, const RangeRT& rt_range) + { + + SpectrumSequence all_spectra = swathmap->getMultipleSpectraAuto(rt_range.getMin(), rt_range.getMax()); + if (spectra_addition_method_ == ADDITION) + { + return all_spectra; // return vector, addition is done later + } + else // (spectra_addition_method_ == RESAMPLE) + { + std::vector spectrum_out; + //added_spec = SpectrumAddition::addUpSpectra(all_spectra, spacing_for_spectra_resampling_, true); + spectrum_out.push_back(SpectrumAddition::addUpSpectra(all_spectra, im_range, spacing_for_spectra_resampling_, true)); + return spectrum_out; + } + } + SpectrumSequence OpenSwathScoring::fetchSpectrumSwath(std::vector swath_maps, double RT, int nr_spectra_to_add, const RangeMobility& im_range) { OPENMS_PRECONDITION(nr_spectra_to_add >= 1, "nr_spectra_to_add must be at least 1.") @@ -575,4 +601,64 @@ namespace OpenMS } } } -} + + SpectrumSequence OpenSwathScoring::fetchSpectrumSwathAuto(std::vector swath_maps, const RangeMobility& im_range, const RangeRT& rt_range) + { + OPENMS_PRECONDITION(!swath_maps.empty(), "swath_maps vector cannot be empty") + + // This is not SONAR data + if (swath_maps.size() == 1) + { + return fetchSpectrumSwathAuto(swath_maps[0].sptr, im_range, rt_range); + } + else + { + // data is not IM enhanced + if (!im_range.isEmpty()) + { + // multiple SWATH maps for a single precursor -> this is SONAR data, in all cases only return a single spectrum + SpectrumSequence all_spectra; + + if (spectra_addition_method_ == ADDITION) + { + for (size_t i = 0; i < swath_maps.size(); ++i) + { + SpectrumSequence spectrumSequence = swath_maps[i].sptr->getMultipleSpectraAuto(im_range.getMin(), im_range.getMax(), rt_range.getMin(), rt_range.getMax()); + } + } + else // (spectra_addition_method_ == RESAMPLE) + { + for (size_t i = 0; i < swath_maps.size(); ++i) + { + SpectrumSequence spectrumSequence = swath_maps[i].sptr->getMultipleSpectraAuto(im_range.getMin(), im_range.getMax(), rt_range.getMin(), rt_range.getMax()); + all_spectra.push_back(SpectrumAddition::addUpSpectra(spectrumSequence, spacing_for_spectra_resampling_, true)); + } + } + return { SpectrumAddition::addUpSpectra(all_spectra, spacing_for_spectra_resampling_, true) }; + } + else // im_range.isEmpty() + { + // multiple SWATH maps for a single precursor -> this is SONAR data, in all cases only return a single spectrum + SpectrumSequence all_spectra; + + if (spectra_addition_method_ == ADDITION) + { + for (size_t i = 0; i < swath_maps.size(); ++i) + { + SpectrumSequence spectrumSequence = swath_maps[i].sptr->getMultipleSpectraAuto(rt_range.getMin(), rt_range.getMax()); + all_spectra.push_back(SpectrumAddition::concatenateSpectra(spectrumSequence)); + } + } + else // (spectra_addition_method_ == RESAMPLE) + { + for (size_t i = 0; i < swath_maps.size(); ++i) + { + SpectrumSequence spectrumSequence = swath_maps[i].sptr->getMultipleSpectraAuto(rt_range.getMin(), rt_range.getMax()); + all_spectra.push_back(SpectrumAddition::addUpSpectra(spectrumSequence, spacing_for_spectra_resampling_, true)); + } + } + return { SpectrumAddition::addUpSpectra(all_spectra, spacing_for_spectra_resampling_, true) }; + } + } + } +} \ No newline at end of file diff --git a/src/openms/source/INTERFACES_IMPL/MockImplementation.cpp b/src/openms/source/INTERFACES_IMPL/MockImplementation.cpp index e2107434ccc..dc18e5066a8 100644 --- a/src/openms/source/INTERFACES_IMPL/MockImplementation.cpp +++ b/src/openms/source/INTERFACES_IMPL/MockImplementation.cpp @@ -35,6 +35,11 @@ namespace OpenMS::Interfaces { return std::vector(); } + /// Return a vector of ids of spectra that are between rt_start and rt_end + std::vector getSpectraRTRange(double /* rt_start */, double /* rt_end */) const override + { + return std::vector(); + } /// Returns the number of spectra available size_t getNrSpectra() const override { diff --git a/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h b/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h index 5ee28ef6ba0..1160cb24877 100644 --- a/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h +++ b/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h @@ -50,6 +50,8 @@ namespace OpenSwath /// Return a vector of ids of spectra that are within RT +/- deltaRT virtual std::vector getSpectraByRT(double RT, double deltaRT) const = 0; + /// Return a vector of ids of spectra that are between rt_start and rt_end + virtual std::vector getSpectraRTRange(double rt_start, double rt_end) const = 0; /// Returns the number of spectra available virtual size_t getNrSpectra() const = 0; /// Returns the meta information for a spectrum @@ -74,6 +76,15 @@ namespace OpenSwath */ SpectrumSequence getMultipleSpectra(double RT, int nr_spectra_to_fetch, double drift_start, double drift_end); + + /* @breif Fetches a spectrumSequnce (multiple spectra pointers) across the range of RT specified. Filters all specta by the specified @p drift_start and @p drift_end + */ + SpectrumSequence getMultipleSpectraAuto(double drift_start, double drift_end, double rt_start, double rt_end); + + /* @breif Fetches a spectrumSequnce (multiple spectra pointers) across the range of RT specified. + */ + SpectrumSequence getMultipleSpectraAuto(double rt_start, double rt_end); + /// filters a spectrum by drift time, spectrum pointer returned is a copy static SpectrumPtr filterByDrift(const SpectrumPtr& input, double drift_start, double drift_end) { diff --git a/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.cpp b/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.cpp index f018da79648..684e9288bd7 100644 --- a/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.cpp +++ b/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.cpp @@ -90,6 +90,41 @@ namespace OpenSwath return all_spectra; } + SpectrumSequence ISpectrumAccess::getMultipleSpectraAuto(double rt_start, double rt_end) + { + std::vector indices = getSpectraRTRange(rt_start, rt_end); + SpectrumSequence all_spectra; + + if (indices.empty() ) + { + return all_spectra; + } + + for (const auto i:indices) + { + all_spectra.push_back(getSpectrumById(indices[i])); + } + + return all_spectra; + } + + SpectrumSequence ISpectrumAccess::getMultipleSpectraAuto(double drift_start, double drift_end, double rt_start, double rt_end) + { + std::vector indices = getSpectraRTRange(rt_start, rt_end); + SpectrumSequence all_spectra; + + if (indices.empty() ) + { + return all_spectra; + } + + for (const auto i:indices) + { + all_spectra.push_back(getSpectrumById(indices[i], drift_start, drift_end)); + } + + return all_spectra; + } SpectrumPtr ISpectrumAccess::getSpectrumById(int id, double drift_start, double drift_end) { diff --git a/src/tests/topp/FeatureFinderIdentification_1_output.featureXML b/src/tests/topp/FeatureFinderIdentification_1_output.featureXML index 47f4282cbec..9e0b5d1a76f 100644 --- a/src/tests/topp/FeatureFinderIdentification_1_output.featureXML +++ b/src/tests/topp/FeatureFinderIdentification_1_output.featureXML @@ -1,6 +1,6 @@ - + @@ -196,6 +196,7 @@ + @@ -294,7 +295,8 @@ - + + @@ -382,7 +384,7 @@ - + @@ -394,6 +396,7 @@ + @@ -500,6 +503,7 @@ + @@ -599,6 +603,7 @@ + @@ -707,10 +712,10 @@ - - + + - + @@ -718,10 +723,11 @@ - + + - + @@ -807,9 +813,9 @@ - + - + @@ -818,6 +824,7 @@ + @@ -913,9 +920,9 @@ - + - + @@ -923,7 +930,8 @@ - + + @@ -1030,6 +1038,7 @@ + @@ -1115,12 +1124,12 @@ - + - - + + - + @@ -1129,9 +1138,10 @@ + - + @@ -1231,9 +1241,9 @@ - + - + @@ -1242,9 +1252,10 @@ + - + @@ -1329,7 +1340,7 @@ - + @@ -1340,7 +1351,8 @@ - + + @@ -1439,7 +1451,8 @@ - + + @@ -1525,7 +1538,7 @@ - + @@ -1539,6 +1552,7 @@ + @@ -1638,6 +1652,7 @@ + @@ -1744,6 +1759,7 @@ + @@ -1843,6 +1859,7 @@ + @@ -1937,7 +1954,7 @@ - + @@ -1949,6 +1966,7 @@ + @@ -2036,10 +2054,10 @@ - - + + - + @@ -2048,6 +2066,7 @@ + @@ -2146,10 +2165,11 @@ - + + - + @@ -2246,6 +2266,7 @@ + @@ -2331,7 +2352,7 @@ - + @@ -2344,7 +2365,8 @@ - + + @@ -2444,9 +2466,10 @@ + - + @@ -2545,10 +2568,10 @@ - - + + - + @@ -2556,7 +2579,8 @@ - + + diff --git a/src/tests/topp/FeatureFinderIdentification_3_output.featureXML b/src/tests/topp/FeatureFinderIdentification_3_output.featureXML index 4313ea4f603..bee73210a79 100644 --- a/src/tests/topp/FeatureFinderIdentification_3_output.featureXML +++ b/src/tests/topp/FeatureFinderIdentification_3_output.featureXML @@ -1,6 +1,6 @@ - + @@ -105,7 +105,7 @@ 2024.601233363805477 461.747653035420967 - 1.567024e08 + 1.567165e08 0.0 0.0 4.055415 @@ -179,7 +179,7 @@ - + 2024.601233363805477 @@ -263,22 +263,23 @@ - + - - - - - + + + + + - + + - - + + @@ -287,15 +288,15 @@ - - - - - - - - - + + + + + + + + + @@ -495,7 +496,8 @@ - + + @@ -507,22 +509,22 @@ - - - - - - - - - + + + + + + + + + 2123.350439084953905 455.75528053542098 - 9.999641e06 + 9.999901e06 0.0 0.0 2.101267 @@ -700,7 +702,7 @@ - + @@ -719,22 +721,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -743,22 +746,22 @@ - - - - - - - - - + + + + + + + + + 1760.256570937733613 569.752618393021066 - 2.062863e07 + 2.062843e07 0.0 0.0 4.25113 @@ -836,7 +839,7 @@ - + 1760.256570937733613 @@ -898,7 +901,7 @@ - + @@ -924,22 +927,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -948,15 +952,15 @@ - - - - - - - - - + + + + + + + + + @@ -1145,6 +1149,7 @@ + @@ -1156,15 +1161,15 @@ - - + + - - - - - - + + + + + + @@ -1460,10 +1465,10 @@ - - + + - + @@ -1471,10 +1476,11 @@ - + + - + @@ -1483,42 +1489,42 @@ - - - - - - - - - + + + + + + + + + 1850.920897815956096 - 325.490781803337597 + 325.490781803337711 6.743887e07 0.0 0.0 4.110307 3 - - - - + + + + - - - - + + + + 1850.920897815956096 - 325.490781803337597 + 325.490781803337711 4.239007e07 0.0 0.0 @@ -1626,7 +1632,7 @@ - + @@ -1638,7 +1644,7 @@ 1850.920897815956096 - 325.825233415937589 + 325.825233415937703 2.189072e07 0.0 0.0 @@ -1746,7 +1752,7 @@ - + @@ -1769,15 +1775,15 @@ - + - + - + @@ -1786,11 +1792,12 @@ - - - + + + + - + @@ -1798,21 +1805,21 @@ - + - - - - + + + + 2074.915570123923317 554.26060201207099 - 3.181611e07 + 3.181606e07 0.0 0.0 4.159474 @@ -1952,7 +1959,7 @@ - + @@ -1978,22 +1985,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -2002,15 +2010,15 @@ - - - - - - - - - + + + + + + + + + @@ -2234,6 +2242,7 @@ + @@ -2245,15 +2254,15 @@ - - + + - - - - + + + + @@ -2518,12 +2527,12 @@ - + - - + + - + @@ -2532,9 +2541,10 @@ + - + @@ -2543,22 +2553,22 @@ - - - - - - - - - + + + + + + + + + 2007.51161653760937 379.715100772820961 - 6.460103e07 + 6.460121e07 0.0 0.0 4.052185 @@ -2642,7 +2652,7 @@ - + 2007.51161653760937 @@ -2710,7 +2720,7 @@ - + @@ -2743,22 +2753,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -2767,22 +2778,22 @@ - - - - - - - - - + + + + + + + + + 2298.147152282906063 435.910228820904251 - 2.258121e05 + 2.258134e05 0.0 0.0 1.807564 @@ -2858,7 +2869,7 @@ - + @@ -2877,22 +2888,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -2901,15 +2913,15 @@ - - - - - - - - - + + + + + + + + + @@ -3067,7 +3079,8 @@ - + + @@ -3079,42 +3092,42 @@ - - + + - - - - - - + + + + + + 2005.797032003118829 - 404.203412328070954 + 404.203412328071011 1.084341e06 0.0 0.0 2.643994 2 - - - - + + + + - - - - + + + + 2005.797032003118829 - 404.203412328070954 + 404.203412328071011 3.877037e05 0.0 0.0 @@ -3154,7 +3167,7 @@ - + @@ -3166,7 +3179,7 @@ 2005.797032003118829 - 404.705089746970941 + 404.705089746970998 3.159881e04 0.0 0.0 @@ -3206,7 +3219,7 @@ - + @@ -3214,7 +3227,7 @@ - + @@ -3229,50 +3242,51 @@ - + - - - - - - - - - + + + + + + + + + - - - - + + + + + - + - - - - - - - - - + + + + + + + + + 1782.511510691123931 300.195528597604323 - 1.344963e07 + 1.345011e07 0.0 0.0 2.770415 @@ -3361,7 +3375,7 @@ - + 1782.511510691123931 @@ -3434,7 +3448,7 @@ - + @@ -3453,22 +3467,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -3477,15 +3492,15 @@ - - - - - - - - - + + + + + + + + + @@ -3756,7 +3771,7 @@ - + @@ -3782,22 +3797,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -3806,22 +3822,22 @@ - - - - - - - - - + + + + + + + + + 1782.343337341021197 449.74438990042097 - 1.970546e06 + 1.970547e06 0.0 0.0 3.142703 @@ -4013,7 +4029,7 @@ - + @@ -4032,22 +4048,23 @@ - + - - - - - + + + + + - + + - - + + @@ -4056,22 +4073,22 @@ - - - - - - - - - + + + + + + + + + 1978.659105381943846 300.165352089204305 - 4.486403e06 + 4.486422e06 0.0 0.0 0.361495 @@ -4215,7 +4232,7 @@ - + @@ -4239,24 +4256,25 @@ - + - - - - - - - + + + + + + + - + + - - + + @@ -4265,22 +4283,22 @@ - - - - - - - - - + + + + + + + + + 1943.300401185303599 395.239463487570902 - 1.828232e08 + 1.828159e08 0.0 0.0 4.097497 @@ -4412,7 +4430,7 @@ - + @@ -4431,22 +4449,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -4455,22 +4474,22 @@ - - - - - - - - - + + + + + + + + + 2391.850923476116805 501.795134726820947 - 7.776416e07 + 7.776408e07 0.0 0.0 4.177951 @@ -4551,7 +4570,7 @@ - + 2391.850923476116805 @@ -4616,7 +4635,7 @@ - + @@ -4635,22 +4654,23 @@ - - - - - - - + + + + + + + - + + - - + + @@ -4659,15 +4679,15 @@ - - - - - - - - - + + + + + + + + + @@ -4862,6 +4882,7 @@ + @@ -4873,22 +4894,22 @@ - - - - - - - - - + + + + + + + + + 2090.165897832880546 421.758354535420949 - 2.059761e07 + 2.059762e07 0.0 0.0 3.872574 @@ -5128,7 +5149,7 @@ - + @@ -5146,23 +5167,24 @@ - - + + - - - - - + + + + + - + + - - + + @@ -5171,22 +5193,22 @@ - - - - - - - - - + + + + + + + + + 1696.5216111905047 613.30659575872096 - 5.309605e05 + 5.309618e05 0.0 0.0 3.230933 @@ -5382,7 +5404,7 @@ - + @@ -5401,22 +5423,23 @@ - - - - - - - + + + + + + + - + + - + @@ -5425,42 +5448,42 @@ - - - - - - - - - + + + + + + + + + 2336.464351141332372 - 464.250362519470968 + 464.250362519471025 2.355746e08 0.0 0.0 3.823007 2 - - - - + + + + - - - - + + + + 2336.464351141332372 - 464.250362519470968 + 464.250362519471025 8.306482e07 0.0 0.0 @@ -5532,7 +5555,7 @@ - + @@ -5544,7 +5567,7 @@ 2336.464351141332372 - 464.752039938370956 + 464.752039938371013 4.381629e07 0.0 0.0 @@ -5616,7 +5639,7 @@ - + @@ -5624,7 +5647,7 @@ - + @@ -5653,43 +5676,44 @@ - + - - - - - - - + + + + + + + - - - - + + + + + - + - - - - - - - - - + + + + + + + + + diff --git a/src/tests/topp/FeatureFinderIdentification_5_candidates.featureXML b/src/tests/topp/FeatureFinderIdentification_5_candidates.featureXML index 5680f8bd0ff..2108bbba67d 100644 --- a/src/tests/topp/FeatureFinderIdentification_5_candidates.featureXML +++ b/src/tests/topp/FeatureFinderIdentification_5_candidates.featureXML @@ -1,6 +1,6 @@ - + 2024.601233363805477 @@ -162,6 +162,7 @@ + @@ -364,6 +365,7 @@ + @@ -582,6 +584,7 @@ + @@ -762,6 +765,7 @@ + @@ -872,6 +876,7 @@ + @@ -1062,6 +1067,7 @@ + @@ -1350,6 +1356,7 @@ + @@ -1646,6 +1653,7 @@ + @@ -1826,6 +1834,7 @@ + @@ -2044,6 +2053,7 @@ + @@ -2174,6 +2184,7 @@ + @@ -2454,6 +2465,7 @@ + @@ -2646,6 +2658,7 @@ + @@ -2764,6 +2777,7 @@ + @@ -2880,6 +2894,7 @@ + @@ -3040,6 +3055,7 @@ + @@ -3200,6 +3216,7 @@ + @@ -3310,6 +3327,7 @@ + @@ -3512,6 +3530,7 @@ + @@ -3816,6 +3835,7 @@ + @@ -4048,6 +4068,7 @@ + @@ -4170,6 +4191,7 @@ + @@ -4332,6 +4354,7 @@ + @@ -4452,6 +4475,7 @@ + @@ -4654,6 +4678,7 @@ + @@ -4830,6 +4855,7 @@ + @@ -5014,6 +5040,7 @@ + @@ -5186,6 +5213,7 @@ + @@ -5372,6 +5400,7 @@ + @@ -5568,6 +5597,7 @@ + @@ -5848,6 +5878,7 @@ + @@ -6084,6 +6115,7 @@ + @@ -6222,6 +6254,7 @@ + @@ -6336,6 +6369,7 @@ + @@ -6456,6 +6490,7 @@ + @@ -6570,6 +6605,7 @@ + @@ -6794,6 +6830,7 @@ + diff --git a/src/tests/topp/FeatureFinderMetaboIdent_1_output.featureXML b/src/tests/topp/FeatureFinderMetaboIdent_1_output.featureXML index 698628d9e89..b4068c5050a 100644 --- a/src/tests/topp/FeatureFinderMetaboIdent_1_output.featureXML +++ b/src/tests/topp/FeatureFinderMetaboIdent_1_output.featureXML @@ -154,7 +154,7 @@ - + @@ -168,21 +168,22 @@ - + - - - - - + + + + + - + + - - + + @@ -190,15 +191,15 @@ - - + + - - - - - - + + + + + + @@ -361,6 +362,7 @@ + @@ -544,6 +546,7 @@ + @@ -727,6 +730,7 @@ + @@ -737,15 +741,15 @@ - - - - - - - - - + + + + + + + + + @@ -922,6 +926,7 @@ + @@ -1089,9 +1094,9 @@ - + - + @@ -1099,6 +1104,7 @@ + @@ -1111,15 +1117,15 @@ - - + + - - - - + + + + diff --git a/src/tests/topp/OpenSwathAnalyzer_2_output.featureXML b/src/tests/topp/OpenSwathAnalyzer_2_output.featureXML index c93b24433ff..105e80b96c4 100644 --- a/src/tests/topp/OpenSwathAnalyzer_2_output.featureXML +++ b/src/tests/topp/OpenSwathAnalyzer_2_output.featureXML @@ -89,6 +89,7 @@ + @@ -177,7 +178,7 @@ - + @@ -196,6 +197,7 @@ + @@ -286,7 +288,7 @@ - + @@ -303,6 +305,7 @@ + diff --git a/src/tests/topp/OpenSwathAnalyzer_5_output.featureXML b/src/tests/topp/OpenSwathAnalyzer_5_output.featureXML index 03673e8194e..be9c8298f1c 100644 --- a/src/tests/topp/OpenSwathAnalyzer_5_output.featureXML +++ b/src/tests/topp/OpenSwathAnalyzer_5_output.featureXML @@ -89,15 +89,16 @@ - + + - - - + + + @@ -177,7 +178,7 @@ - + @@ -196,15 +197,16 @@ - + + - - - + + + @@ -286,7 +288,7 @@ - + @@ -303,15 +305,16 @@ - + + - - - + + + diff --git a/src/tests/topp/OpenSwathAnalyzer_6_output.featureXML b/src/tests/topp/OpenSwathAnalyzer_6_output.featureXML index 02f7c3e936b..9dd7c377392 100644 --- a/src/tests/topp/OpenSwathAnalyzer_6_output.featureXML +++ b/src/tests/topp/OpenSwathAnalyzer_6_output.featureXML @@ -89,6 +89,7 @@ + @@ -177,7 +178,7 @@ - + @@ -196,6 +197,7 @@ + @@ -286,7 +288,7 @@ - + @@ -303,6 +305,7 @@ + diff --git a/src/tests/topp/OpenSwathWorkflow_11_output.featureXML b/src/tests/topp/OpenSwathWorkflow_11_output.featureXML index f02e19384f2..09823b9766a 100644 --- a/src/tests/topp/OpenSwathWorkflow_11_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_11_output.featureXML @@ -83,7 +83,7 @@ - + @@ -92,11 +92,12 @@ - - - - - + + + + + + @@ -105,7 +106,7 @@ - + @@ -199,11 +200,12 @@ - - - - - + + + + + + diff --git a/src/tests/topp/OpenSwathWorkflow_16_output.featureXML b/src/tests/topp/OpenSwathWorkflow_16_output.featureXML index 6c3d0dbc2ce..7c289ef4127 100644 --- a/src/tests/topp/OpenSwathWorkflow_16_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_16_output.featureXML @@ -128,6 +128,7 @@ + @@ -273,7 +274,8 @@ - + + @@ -420,6 +422,7 @@ + @@ -565,7 +568,8 @@ - + + @@ -711,7 +715,8 @@ - + + @@ -857,7 +862,8 @@ - + + diff --git a/src/tests/topp/OpenSwathWorkflow_17_b_output.featureXML b/src/tests/topp/OpenSwathWorkflow_17_b_output.featureXML index bbf77640599..38616c328a1 100644 --- a/src/tests/topp/OpenSwathWorkflow_17_b_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_17_b_output.featureXML @@ -7,7 +7,7 @@ - 25.199999999999999 + 25.199999523162841 412.5 1.4904e05 0.0 @@ -16,7 +16,7 @@ 0 - 25.199999999999999 + 25.199999523162841 100.010000000000005 2.484e04 0.0 @@ -32,7 +32,7 @@ - 25.199999999999999 + 25.199999523162841 101.010000000000005 4.968e04 0.0 @@ -48,7 +48,7 @@ - 25.199999999999999 + 25.199999523162841 102.019999999999996 7.452e04 0.0 @@ -64,7 +64,7 @@ - 25.199999999999999 + 25.199999523162841 412.5 0.0 0.0 @@ -94,16 +94,17 @@ - + - - - + + + - + + @@ -119,7 +120,7 @@ - + @@ -207,7 +208,7 @@ - + @@ -223,7 +224,8 @@ - + + diff --git a/src/tests/topp/OpenSwathWorkflow_17_output.featureXML b/src/tests/topp/OpenSwathWorkflow_17_output.featureXML index ff75f3936ce..924ef5f1e28 100644 --- a/src/tests/topp/OpenSwathWorkflow_17_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_17_output.featureXML @@ -7,7 +7,7 @@ - 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176.666667143504157 + 176.66666618982984 385.0 9643.0 0.0 @@ -3483,13 +3507,13 @@ - + - 176.666667143504157 + 176.66666618982984 485.0 1.9286e04 0.0 @@ -3500,13 +3524,13 @@ - + - 176.666667143504157 + 176.66666618982984 585.0 2.8929e04 0.0 @@ -3517,13 +3541,13 @@ - + - 176.666667143504157 + 176.66666618982984 685.0 3.8572e04 0.0 @@ -3534,13 +3558,13 @@ - + - 176.666667143504157 + 176.66666618982984 459.5 9640.333008 0.0 @@ -3553,7 +3577,7 @@ - + @@ -3563,19 +3587,19 @@ - + - + - - + + - + @@ -3583,27 +3607,28 @@ - - - - - - + + + + + + + - + - - + + - + - + diff --git a/src/tests/topp/OpenSwathWorkflow_22_output.featureXML b/src/tests/topp/OpenSwathWorkflow_22_output.featureXML index 6de0ac9873b..4a38fc9db54 100644 --- a/src/tests/topp/OpenSwathWorkflow_22_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_22_output.featureXML @@ -140,14 +140,15 @@ - + + - - + + @@ -155,9 +156,9 @@ - + - + @@ -298,14 +299,15 @@ - + + - - + + @@ -313,9 +315,9 @@ - + - + diff --git a/src/tests/topp/OpenSwathWorkflow_23_output.featureXML b/src/tests/topp/OpenSwathWorkflow_23_output.featureXML index 3fa5df55ec3..5c4465a0400 100644 --- a/src/tests/topp/OpenSwathWorkflow_23_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_23_output.featureXML @@ -136,6 +136,7 @@ + @@ -297,6 +298,7 @@ + @@ -458,6 +460,7 @@ + diff --git a/src/tests/topp/OpenSwathWorkflow_2_output.featureXML b/src/tests/topp/OpenSwathWorkflow_2_output.featureXML index 3e8f173a4ae..4932aaeb961 100644 --- a/src/tests/topp/OpenSwathWorkflow_2_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_2_output.featureXML @@ -92,15 +92,16 @@ - + + - - - + + + @@ -175,9 +176,9 @@ - + - + @@ -193,15 +194,16 @@ - + + - - - + + + @@ -277,7 +279,7 @@ - + @@ -294,15 +296,16 @@ - + + - - - + + + @@ -379,7 +382,7 @@ - + @@ -395,15 +398,16 @@ - + + - - - + + + diff --git a/src/tests/topp/OpenSwathWorkflow_3_output.featureXML b/src/tests/topp/OpenSwathWorkflow_3_output.featureXML index b58f10ac7e8..97321926e94 100644 --- a/src/tests/topp/OpenSwathWorkflow_3_output.featureXML +++ b/src/tests/topp/OpenSwathWorkflow_3_output.featureXML @@ -104,6 +104,7 @@ + @@ -206,9 +207,9 @@ - + - + @@ -224,6 +225,7 @@ + @@ -239,7 +241,7 @@ - + @@ -327,7 +329,7 @@ - + @@ -344,6 +346,7 @@ + @@ -353,7 +356,7 @@ - + @@ -448,7 +451,7 @@ - + @@ -464,6 +467,7 @@ + @@ -583,7 +587,8 @@ - + + @@ -597,7 +602,7 @@ - + @@ -703,7 +708,8 @@ - + + @@ -717,7 +723,7 @@ - + diff --git a/workflow/cwl/OpenSwathAnalyzer.cwl b/workflow/cwl/OpenSwathAnalyzer.cwl index 615ae32bd29..8ce47255c4e 100644 --- a/workflow/cwl/OpenSwathAnalyzer.cwl +++ b/workflow/cwl/OpenSwathAnalyzer.cwl @@ -67,7 +67,7 @@ inputs: doc: For spectrum addition, either use simple concatenation or use peak resampling type: string? algorithm__add_up_spectra: - doc: Add up spectra around the peak apex (needs to be a non-even integer) + doc: Add up spectra around the peak apex (needs to be a non-even integer), if set to -1 all spectra across peak width are summed type: long? algorithm__spacing_for_spectra_resampling: doc: If spectra are to be added, use this spacing to add them up diff --git a/workflow/cwl/OpenSwathRTNormalizer.cwl b/workflow/cwl/OpenSwathRTNormalizer.cwl index 51706994abb..816f0a946b7 100644 --- a/workflow/cwl/OpenSwathRTNormalizer.cwl +++ b/workflow/cwl/OpenSwathRTNormalizer.cwl @@ -76,7 +76,7 @@ inputs: doc: For spectrum addition, either use simple concatenation or use peak resampling type: string? algorithm__add_up_spectra: - doc: Add up spectra around the peak apex (needs to be a non-even integer) + doc: Add up spectra around the peak apex (needs to be a non-even integer), if set to -1 all spectra across peak width are summed type: long? algorithm__spacing_for_spectra_resampling: doc: If spectra are to be added, use this spacing to add them up diff --git a/workflow/cwl/OpenSwathWorkflow.cwl b/workflow/cwl/OpenSwathWorkflow.cwl index eb69f9b56de..432e4e8d4c4 100644 --- a/workflow/cwl/OpenSwathWorkflow.cwl +++ b/workflow/cwl/OpenSwathWorkflow.cwl @@ -232,7 +232,7 @@ inputs: doc: For spectrum addition, either use simple concatenation or use peak resampling type: string? Scoring__add_up_spectra: - doc: Add up spectra around the peak apex (needs to be a non-even integer) + doc: Add up spectra around the peak apex (needs to be a non-even integer), if set to -1 all spectra across peak width are summed type: long? Scoring__spacing_for_spectra_resampling: doc: If spectra are to be added, use this spacing to add them up