From 287915317a8bc7f67ddfc9e9f85b9acf23109aeb Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 4 Jun 2026 17:30:10 +0000 Subject: [PATCH 1/6] Use contains() for membership tests (C++20/23 readability) Replace verbose membership-test idioms with the dedicated contains() member, now available codebase-wide under C++23: map/set/unordered_*: c.find(k) != c.end() -> c.contains(k) c.count(k) > 0 / != 0 -> c.contains(k) c.count(k) == 0 -> !c.contains(k) std::string/String: s.find(x) != npos -> s.contains(x) (C++23) 647 call sites across 195 files. Conversions are restricted to provably equivalent boolean-context forms: - stored-iterator comparisons (auto it = m.find(k); if (it != m.end())) are left untouched - positional string find(x, pos) is skipped (contains has no such overload) - count() == 1 is skipped (not equivalent for multimap/multiset) - count() uses whose numeric value is consumed are left untouched contains() is specified by the standard as exactly these predicates, so there is no behavior change. --- .../include/OpenMS/ANALYSIS/ID/IDBoostGraph.h | 2 +- .../OpenMS/CHEMISTRY/DigestionEnzymeDB.h | 6 +-- .../OpenMS/COMPARISON/SpectrumAlignment.h | 6 +-- .../include/OpenMS/CONCEPT/UniqueIdIndexer.h | 2 +- .../OpenMS/DATASTRUCTURES/StringUtilsSimple.h | 4 +- .../include/OpenMS/KERNEL/ChromatogramTools.h | 2 +- .../OpenMS/KERNEL/MRMTransitionGroup.h | 6 +-- .../METADATA/ID/AppliedProcessingStep.h | 2 +- .../OpenMS/PROCESSING/FILTERING/WindowMower.h | 2 +- .../include/OpenMS/PROCESSING/ID/IDFilter.h | 8 ++-- .../PROCESSING/SPECTRAMERGING/SpectraMerger.h | 2 +- .../DECHARGING/FeatureDeconvolution.cpp | 6 +-- .../ANALYSIS/DECHARGING/ILPDCWrapper.cpp | 6 +-- .../MetaboliteFeatureDeconvolution.cpp | 6 +-- .../ANALYSIS/ID/AccurateMassSearchEngine.cpp | 6 +-- .../source/ANALYSIS/ID/CometModification.cpp | 2 +- .../source/ANALYSIS/ID/IDBoostGraph.cpp | 2 +- .../ID/IDConflictResolverAlgorithm.cpp | 2 +- src/openms/source/ANALYSIS/ID/IDMapper.cpp | 2 +- src/openms/source/ANALYSIS/ID/IDRipper.cpp | 4 +- .../ANALYSIS/ID/IDScoreGetterSetter.cpp | 2 +- .../ID/OpenSearchModificationAnalysis.cpp | 12 +++--- .../source/ANALYSIS/ID/PeptideIndexing.cpp | 2 +- .../ANALYSIS/ID/PeptideProteinResolution.cpp | 2 +- src/openms/source/ANALYSIS/ID/Percolator.cpp | 8 ++-- .../ID/PercolatorFeatureSetHelper.cpp | 2 +- src/openms/source/ANALYSIS/ID/Scores.cpp | 6 +-- .../ID/SimpleSearchEngineAlgorithm.cpp | 2 +- .../ANALYSIS/MAPMATCHING/BaseGroupFinder.cpp | 2 +- .../FeatureGroupingAlgorithmWNet.cpp | 2 +- .../MAPMATCHING/LabeledPairFinder.cpp | 4 +- .../MAPMATCHING/MapAlignmentAlgorithmKD.cpp | 2 +- .../ANALYSIS/MAPMATCHING/QTClusterFinder.cpp | 2 +- .../ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp | 14 +++---- src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp | 2 +- .../NUXL/NuXLModificationsGenerator.cpp | 6 +-- .../ANALYSIS/NUXL/NuXLParameterParsing.cpp | 10 ++--- .../source/ANALYSIS/NUXL/NuXLReport.cpp | 8 ++-- .../ANALYSIS/OPENSWATH/ConfidenceScoring.cpp | 2 +- .../OPENSWATH/DATAACCESS/DataAccessHelper.cpp | 8 ++-- .../source/ANALYSIS/OPENSWATH/MRMAssay.cpp | 20 +++++----- .../source/ANALYSIS/OPENSWATH/MRMDecoy.cpp | 16 ++++---- .../OPENSWATH/MRMFeatureFinderScoring.cpp | 2 +- .../ANALYSIS/OPENSWATH/MRMFeatureSelector.cpp | 16 ++++---- .../ANALYSIS/OPENSWATH/MRMIonSeries.cpp | 8 ++-- .../OPENSWATH/MasstraceCorrelator.cpp | 2 +- .../ANALYSIS/OPENSWATH/OpenSwathHelper.cpp | 14 +++---- .../OPENSWATH/OpenSwathMatrixExporter.cpp | 6 +-- .../OPENSWATH/OpenSwathOSWParquetWriter.cpp | 4 +- .../OpenSwathPeptidoformInference.cpp | 4 +- .../ANALYSIS/OPENSWATH/OpenSwathWorkflow.cpp | 14 +++---- .../OPENSWATH/TargetedSpectraExtractor.cpp | 6 +-- .../ANALYSIS/OPENSWATH/TransitionPQPFile.cpp | 14 +++---- .../OPENSWATH/TransitionParquetFile.cpp | 8 ++-- .../ANALYSIS/OPENSWATH/TransitionTSVFile.cpp | 38 +++++++++---------- .../QUANTITATION/AbsoluteQuantitation.cpp | 2 +- .../QUANTITATION/IsobaricChannelExtractor.cpp | 2 +- .../ANALYSIS/QUANTITATION/ItraqConstants.cpp | 2 +- .../QUANTITATION/PeptideAndProteinQuant.cpp | 4 +- .../QUANTITATION/ProteinInference.cpp | 2 +- .../ANALYSIS/TARGETED/DIAChromHandler.cpp | 4 +- .../TARGETED/MetaboTargetedTargetDecoy.cpp | 8 ++-- .../ANALYSIS/TARGETED/TargetedExperiment.cpp | 22 +++++------ .../ANALYSIS/TOPDOWN/DeconvolvedSpectrum.cpp | 2 +- .../ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.cpp | 10 ++--- src/openms/source/ANALYSIS/TOPDOWN/Qvalue.cpp | 2 +- .../TOPDOWN/SpectralDeconvolution.cpp | 4 +- .../TOPDOWN/TopDownIsobaricQuantification.cpp | 8 ++-- .../source/ANALYSIS/XLMS/OPXLHelper.cpp | 4 +- .../source/ANALYSIS/XLMS/XFDRAlgorithm.cpp | 8 ++-- src/openms/source/APPLICATIONS/INIUpdater.cpp | 6 +-- .../source/APPLICATIONS/OpenSwathBase.cpp | 6 +-- src/openms/source/APPLICATIONS/TOPPBase.cpp | 6 +-- .../source/APPLICATIONS/ToolHandler.cpp | 6 +-- src/openms/source/CHEMISTRY/ElementDB.cpp | 6 +-- .../source/CHEMISTRY/EmpiricalFormula.cpp | 2 +- .../IMS/IMSAlphabetTextParser.cpp | 2 +- .../CHEMISTRY/ModificationDefinitionsSet.cpp | 12 +++--- .../source/CHEMISTRY/ModificationsDB.cpp | 2 +- .../CHEMISTRY/ModomicsJSONDataProvider.cpp | 10 ++--- .../source/CHEMISTRY/MonosaccharideDB.cpp | 2 +- src/openms/source/CHEMISTRY/ProForma.cpp | 32 ++++++++-------- src/openms/source/CHEMISTRY/Residue.cpp | 2 +- src/openms/source/CHEMISTRY/ResidueDB.cpp | 10 ++--- .../source/COMPARISON/SpectrumCheapDPCorr.cpp | 4 +- .../source/CONCEPT/FuzzyStringComparator.cpp | 12 +++--- src/openms/source/CONCEPT/LogStream.cpp | 2 +- src/openms/source/CONCEPT/StreamHandler.cpp | 6 +-- .../source/DATASTRUCTURES/CVMappings.cpp | 2 +- src/openms/source/DATASTRUCTURES/Compomer.cpp | 6 +-- .../source/DATASTRUCTURES/ConvexHull2D.cpp | 6 +-- src/openms/source/DATASTRUCTURES/OSWData.cpp | 4 +- src/openms/source/DATASTRUCTURES/Param.cpp | 22 +++++------ .../source/DATASTRUCTURES/QTCluster.cpp | 2 +- .../FEATUREFINDER/Biosaur2Algorithm.cpp | 18 ++++----- .../FeatureFinderAlgorithmMetaboIdent.cpp | 2 +- .../FeatureFinderIdentificationAlgorithm.cpp | 6 +-- .../FeatureFinderMultiplexAlgorithm.cpp | 2 +- .../FEATUREFINDER/FeatureFindingMetabo.cpp | 2 +- .../MultiplexDeltaMassesGenerator.cpp | 20 +++++----- .../FEATUREFINDER/MultiplexFiltering.cpp | 2 +- .../FORMAT/AbsoluteQuantitationMethodFile.cpp | 12 +++--- src/openms/source/FORMAT/ArrowIOHelpers.cpp | 2 +- src/openms/source/FORMAT/BrukerTimsFile.cpp | 4 +- .../source/FORMAT/ConsensusMapArrowExport.cpp | 8 ++-- .../source/FORMAT/ConsensusMapArrowIO.cpp | 2 +- .../source/FORMAT/ControlledVocabulary.cpp | 2 +- .../MSChromatogramParquetConsumer.cpp | 2 +- .../DATAACCESS/MobilogramParquetConsumer.cpp | 2 +- .../source/FORMAT/ExperimentalDesignFile.cpp | 12 +++--- .../source/FORMAT/FeatureMapArrowIO.cpp | 2 +- src/openms/source/FORMAT/FileTypes.cpp | 2 +- src/openms/source/FORMAT/GNPSMGFFile.cpp | 2 +- .../source/FORMAT/GNPSQuantificationFile.cpp | 2 +- .../FORMAT/HANDLERS/ConsensusXMLHandler.cpp | 6 +-- .../FORMAT/HANDLERS/FeatureXMLHandler.cpp | 6 +-- .../FORMAT/HANDLERS/IndexedMzMLHandler.cpp | 2 +- .../FORMAT/HANDLERS/MascotXMLHandler.cpp | 2 +- .../source/FORMAT/HANDLERS/MzDataHandler.cpp | 2 +- .../FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp | 24 ++++++------ .../FORMAT/HANDLERS/MzIdentMLHandler.cpp | 16 ++++---- .../source/FORMAT/HANDLERS/MzMLHandler.cpp | 34 ++++++++--------- .../FORMAT/HANDLERS/MzMLSqliteHandler.cpp | 2 +- .../FORMAT/HANDLERS/PASEFHillCentroider.cpp | 2 +- .../source/FORMAT/HANDLERS/TraMLHandler.cpp | 4 +- .../HANDLERS/XQuestResultXMLHandler.cpp | 2 +- src/openms/source/FORMAT/IdXMLFile.cpp | 2 +- src/openms/source/FORMAT/InspectInfile.cpp | 6 +-- src/openms/source/FORMAT/InspectOutfile.cpp | 2 +- .../source/FORMAT/MSExperimentArrowExport.cpp | 2 +- src/openms/source/FORMAT/MSPFile.cpp | 2 +- src/openms/source/FORMAT/MSstatsFile.cpp | 4 +- .../source/FORMAT/MascotRemoteQuery.cpp | 14 +++---- src/openms/source/FORMAT/MzTabFile.cpp | 2 +- src/openms/source/FORMAT/MzTabM.cpp | 4 +- src/openms/source/FORMAT/OMSSAXMLFile.cpp | 4 +- src/openms/source/FORMAT/OSWFile.cpp | 2 +- src/openms/source/FORMAT/PEFFFile.cpp | 16 ++++---- src/openms/source/FORMAT/ParamCTDFile.cpp | 32 ++++++++-------- src/openms/source/FORMAT/ParamJSONFile.cpp | 10 ++--- src/openms/source/FORMAT/ParamXMLFile.cpp | 20 +++++----- src/openms/source/FORMAT/PepNovoOutfile.cpp | 4 +- src/openms/source/FORMAT/PercolatorInfile.cpp | 8 ++-- .../FORMAT/ProteinIdentificationArrowIO.cpp | 2 +- src/openms/source/FORMAT/QPXFile.cpp | 14 +++---- src/openms/source/FORMAT/QcMLFile.cpp | 4 +- .../FORMAT/RationalScan2ImConverter.cpp | 2 +- src/openms/source/FORMAT/SVOutStream.cpp | 2 +- src/openms/source/FORMAT/SequestInfile.cpp | 6 +-- src/openms/source/FORMAT/TriqlerFile.cpp | 2 +- .../FORMAT/VALIDATORS/MzDataValidator.cpp | 2 +- .../FORMAT/VALIDATORS/SemanticValidator.cpp | 2 +- src/openms/source/FORMAT/XICParquetFile.cpp | 10 ++--- src/openms/source/FORMAT/XIMParquetFile.cpp | 12 +++--- src/openms/source/FORMAT/XTandemInfile.cpp | 10 ++--- src/openms/source/FORMAT/XTandemXMLFile.cpp | 4 +- .../source/IMAGING/MSImagingGeometry.cpp | 4 +- .../source/IONMOBILITY/IMDataConverter.cpp | 6 +-- src/openms/source/KERNEL/ConsensusMap.cpp | 2 +- .../source/KERNEL/OnDiscMSExperiment.cpp | 4 +- .../AbsoluteQuantitationStandards.cpp | 2 +- src/openms/source/METADATA/CVTermList.cpp | 2 +- .../source/METADATA/ExperimentalDesign.cpp | 8 ++-- .../source/METADATA/ID/IdentificationData.cpp | 8 ++-- .../ID/IdentificationDataConverter.cpp | 6 +-- .../source/METADATA/IdentifierMSRunMapper.cpp | 4 +- src/openms/source/METADATA/MetaInfo.cpp | 4 +- .../source/METADATA/ProteinIdentification.cpp | 8 ++-- .../source/ML/CLUSTERING/ClusteringGrid.cpp | 6 +-- src/openms/source/ML/SVM/SimpleSVM.cpp | 2 +- .../CALIBRATION/InternalCalibration.cpp | 2 +- .../FEATURE/FeatureOverlapFilter.cpp | 2 +- src/openms/source/PROCESSING/ID/IDFilter.cpp | 10 ++--- src/openms/source/QC/Contaminants.cpp | 4 +- src/openms/source/QC/DBSuitability.cpp | 6 +-- src/topp/CVInspector.cpp | 4 +- src/topp/ConsensusID.cpp | 10 ++--- src/topp/DatabaseFilter.cpp | 2 +- src/topp/DecoyDatabase.cpp | 2 +- src/topp/EICExtractor.cpp | 2 +- src/topp/FLASHDeconv.cpp | 16 ++++---- src/topp/FileFilter.cpp | 10 ++--- src/topp/FileInfo.cpp | 14 +++---- src/topp/IDExtractor.cpp | 6 +-- src/topp/IDMerger.cpp | 8 ++-- src/topp/LuciphorAdapter.cpp | 4 +- src/topp/MRMTransitionGroupPicker.cpp | 4 +- src/topp/MetaProSIP.cpp | 12 +++--- src/topp/NucleicAcidSearchEngine.cpp | 4 +- src/topp/OpenNuXL.cpp | 24 ++++++------ src/topp/OpenSwathFeatureXMLToTSV.cpp | 10 ++--- src/topp/OpenSwathRewriteToFeatureXML.cpp | 10 ++--- src/topp/PercolatorAdapter.cpp | 6 +-- src/topp/ProteinQuantifier.cpp | 6 +-- src/topp/RNADigestor.cpp | 2 +- 195 files changed, 631 insertions(+), 631 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/ID/IDBoostGraph.h b/src/openms/include/OpenMS/ANALYSIS/ID/IDBoostGraph.h index a276f193be6..4595f116719 100644 --- a/src/openms/include/OpenMS/ANALYSIS/ID/IDBoostGraph.h +++ b/src/openms/include/OpenMS/ANALYSIS/ID/IDBoostGraph.h @@ -133,7 +133,7 @@ namespace OpenMS template < typename Edge, typename Graph > void examine_edge(Edge e, const Graph & tg) { - if (m.find(e.m_target) == m.end()) + if (!m.contains(e.m_target)) { next_v = boost::add_vertex(tg[e.m_target], gs.back()); m[e.m_target] = next_v; diff --git a/src/openms/include/OpenMS/CHEMISTRY/DigestionEnzymeDB.h b/src/openms/include/OpenMS/CHEMISTRY/DigestionEnzymeDB.h index 8e0d39a37a8..8178ef1180e 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/DigestionEnzymeDB.h +++ b/src/openms/include/OpenMS/CHEMISTRY/DigestionEnzymeDB.h @@ -110,19 +110,19 @@ namespace OpenMS /// returns true if the db contains a enzyme with the given name (supports synonym names) bool hasEnzyme(const String& name) const { - return (enzyme_names_.find(name) != enzyme_names_.end()); + return (enzyme_names_.contains(name)); } /// returns true if the db contains a enzyme with the given regex bool hasRegEx(const String& cleavage_regex) const { - return (enzyme_regex_.find(cleavage_regex) != enzyme_regex_.end()); + return (enzyme_regex_.contains(cleavage_regex)); } /// returns true if the db contains the enzyme of the given pointer bool hasEnzyme(const DigestionEnzymeType* enzyme) const { - return (const_enzymes_.find(enzyme) != const_enzymes_.end() ); + return (const_enzymes_.contains(enzyme) ); } //@} diff --git a/src/openms/include/OpenMS/COMPARISON/SpectrumAlignment.h b/src/openms/include/OpenMS/COMPARISON/SpectrumAlignment.h index 3b89423cd8d..805acc2708a 100644 --- a/src/openms/include/OpenMS/COMPARISON/SpectrumAlignment.h +++ b/src/openms/include/OpenMS/COMPARISON/SpectrumAlignment.h @@ -121,7 +121,7 @@ namespace OpenMS double score_align = diff_align; - if (matrix.find(i - 1) != matrix.end() && matrix[i - 1].find(j - 1) != matrix[i - 1].end()) + if (matrix.contains(i - 1) && matrix[i - 1].contains(j - 1)) { score_align += matrix[i - 1][j - 1]; } @@ -131,7 +131,7 @@ namespace OpenMS } double score_up = tolerance; - if (matrix.find(i) != matrix.end() && matrix[i].find(j - 1) != matrix[i].end()) + if (matrix.contains(i) && matrix[i].contains(j - 1)) { score_up += matrix[i][j - 1]; } @@ -141,7 +141,7 @@ namespace OpenMS } double score_left = tolerance; - if (matrix.find(i - 1) != matrix.end() && matrix[i - 1].find(j) != matrix[i - 1].end()) + if (matrix.contains(i - 1) && matrix[i - 1].contains(j)) { score_left += matrix[i - 1][j]; } diff --git a/src/openms/include/OpenMS/CONCEPT/UniqueIdIndexer.h b/src/openms/include/OpenMS/CONCEPT/UniqueIdIndexer.h index ad2bb31334e..d04c65f7e93 100644 --- a/src/openms/include/OpenMS/CONCEPT/UniqueIdIndexer.h +++ b/src/openms/include/OpenMS/CONCEPT/UniqueIdIndexer.h @@ -155,7 +155,7 @@ namespace OpenMS } // see if UID already present - while (uniqueid_to_index_.find(unique_id) != uniqueid_to_index_.end()) // double entry! + while (uniqueid_to_index_.contains(unique_id)) // double entry! { getBase_()[index].setUniqueId(); unique_id = getBase_()[index].getUniqueId(); diff --git a/src/openms/include/OpenMS/DATASTRUCTURES/StringUtilsSimple.h b/src/openms/include/OpenMS/DATASTRUCTURES/StringUtilsSimple.h index afd6af5c8c3..dbf4b4494ff 100644 --- a/src/openms/include/OpenMS/DATASTRUCTURES/StringUtilsSimple.h +++ b/src/openms/include/OpenMS/DATASTRUCTURES/StringUtilsSimple.h @@ -111,12 +111,12 @@ namespace OpenMS static inline bool hasSubstring(const String & this_s, const String& string) { - return this_s.find(string) != std::string::npos; + return this_s.contains(string); } static inline bool has(const String & this_s, Byte byte) { - return this_s.find(char(byte)) != std::string::npos; + return this_s.contains(char(byte)); } static inline String prefix(const String & this_s, size_t length) diff --git a/src/openms/include/OpenMS/KERNEL/ChromatogramTools.h b/src/openms/include/OpenMS/KERNEL/ChromatogramTools.h index a8563cec6de..e68aa86a93d 100644 --- a/src/openms/include/OpenMS/KERNEL/ChromatogramTools.h +++ b/src/openms/include/OpenMS/KERNEL/ChromatogramTools.h @@ -146,7 +146,7 @@ namespace OpenMS ChromatogramPeak chr_p; chr_p.setRT(it->getRT()); chr_p.setIntensity(p.getIntensity()); - if (chroms_xic.find(mz) == chroms_xic.end()) + if (!chroms_xic.contains(mz)) { // new chromatogram chroms_xic[mz].getPrecursor().setMZ(mz); diff --git a/src/openms/include/OpenMS/KERNEL/MRMTransitionGroup.h b/src/openms/include/OpenMS/KERNEL/MRMTransitionGroup.h index ede34d79b68..32aa1318882 100644 --- a/src/openms/include/OpenMS/KERNEL/MRMTransitionGroup.h +++ b/src/openms/include/OpenMS/KERNEL/MRMTransitionGroup.h @@ -143,7 +143,7 @@ namespace OpenMS inline bool hasTransition(const String& key) const { - return transition_map_.find(key) != transition_map_.end(); + return transition_map_.contains(key); } inline const TransitionType& getTransition(const String& key) @@ -187,7 +187,7 @@ namespace OpenMS inline bool hasChromatogram(const String& key) const { - return chromatogram_map_.find(key) != chromatogram_map_.end(); + return chromatogram_map_.contains(key); } inline ChromatogramType& getChromatogram(const String& key) @@ -241,7 +241,7 @@ namespace OpenMS inline bool hasPrecursorChromatogram(const String& key) const { - return precursor_chromatogram_map_.find(key) != precursor_chromatogram_map_.end(); + return precursor_chromatogram_map_.contains(key); } inline ChromatogramType & getPrecursorChromatogram(const String& key) diff --git a/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h b/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h index 6b4e5f29737..f212dfb1065 100644 --- a/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h +++ b/src/openms/include/OpenMS/METADATA/ID/AppliedProcessingStep.h @@ -84,7 +84,7 @@ namespace OpenMS } for (const auto& pair: scores) { - if (!scores_done.count(pair.first)) + if (!scores_done.contains(pair.first)) { result.push_back(pair); if (primary_only) return result; diff --git a/src/openms/include/OpenMS/PROCESSING/FILTERING/WindowMower.h b/src/openms/include/OpenMS/PROCESSING/FILTERING/WindowMower.h index 3aed1186511..32a7551608f 100644 --- a/src/openms/include/OpenMS/PROCESSING/FILTERING/WindowMower.h +++ b/src/openms/include/OpenMS/PROCESSING/FILTERING/WindowMower.h @@ -90,7 +90,7 @@ namespace OpenMS std::vector indices; for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it) { - if (positions.find(it->getMZ()) != positions.end()) + if (positions.contains(it->getMZ())) { Size index(it - spectrum.begin()); indices.push_back(index); diff --git a/src/openms/include/OpenMS/PROCESSING/ID/IDFilter.h b/src/openms/include/OpenMS/PROCESSING/ID/IDFilter.h index 0298a8b974c..76d4e1b0706 100644 --- a/src/openms/include/OpenMS/PROCESSING/ID/IDFilter.h +++ b/src/openms/include/OpenMS/PROCESSING/ID/IDFilter.h @@ -275,7 +275,7 @@ namespace OpenMS { for (const auto& acc : hit.extractProteinAccessionsSet()) { - if (accessions.count(acc) > 0) + if (accessions.contains(acc)) return true; } return false; @@ -283,12 +283,12 @@ namespace OpenMS bool operator()(const ProteinHit& hit) const { - return accessions.count(hit.getAccession()) > 0; + return accessions.contains(hit.getAccession()); } bool operator()(const PeptideEvidence& evidence) const { - return accessions.count(evidence.getProteinAccession()) > 0; + return accessions.contains(evidence.getProteinAccession()); } }; @@ -330,7 +330,7 @@ namespace OpenMS bool exists(const HitType& hit) const { - return items.count(getHitKey(hit)) > 0; + return items.contains(getHitKey(hit)); } const String& getHitKey(const PeptideEvidence& p) const diff --git a/src/openms/include/OpenMS/PROCESSING/SPECTRAMERGING/SpectraMerger.h b/src/openms/include/OpenMS/PROCESSING/SPECTRAMERGING/SpectraMerger.h index afddde780fd..bd9d480eda1 100644 --- a/src/openms/include/OpenMS/PROCESSING/SPECTRAMERGING/SpectraMerger.h +++ b/src/openms/include/OpenMS/PROCESSING/SPECTRAMERGING/SpectraMerger.h @@ -740,7 +740,7 @@ namespace OpenMS MapType exp_tmp; for (Size i = 0; i < exp.size(); ++i) { - if (merged_indices.count(i) == 0) // save unclustered ones + if (!merged_indices.contains(i)) // save unclustered ones { exp_tmp.addSpectrum(exp[i]); exp[i] = empty_spec; diff --git a/src/openms/source/ANALYSIS/DECHARGING/FeatureDeconvolution.cpp b/src/openms/source/ANALYSIS/DECHARGING/FeatureDeconvolution.cpp index 978663d3aba..a2c26f03473 100644 --- a/src/openms/source/ANALYSIS/DECHARGING/FeatureDeconvolution.cpp +++ b/src/openms/source/ANALYSIS/DECHARGING/FeatureDeconvolution.cpp @@ -810,11 +810,11 @@ namespace OpenMS SignedSize target_cf0 = -1, target_cf1 = -1; // find the index of the ConsensusFeatures for the current pair - if (clique_register.count(f0_idx) > 0) + if (clique_register.contains(f0_idx)) { target_cf0 = clique_register[f0_idx]; } - if (clique_register.count(f1_idx) > 0) + if (clique_register.contains(f1_idx)) { target_cf1 = clique_register[f1_idx]; } @@ -977,7 +977,7 @@ namespace OpenMS for (Size i = 0; i < fm_out.size(); ++i) { // find the index of the ConsensusFeature for the current feature - if (clique_register.count(i) > 0) + if (clique_register.contains(i)) continue; Feature f_single = fm_out_untouched[i]; diff --git a/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp b/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp index d5852b6118c..5ed115f7baf 100644 --- a/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp +++ b/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp @@ -51,7 +51,7 @@ namespace OpenMS { Size f1 = pairs[i].getElementIndex(0); Size f2 = pairs[i].getElementIndex(1); - if ((f2g.find(f1) != f2g.end()) && (f2g.find(f2) != f2g.end())) // edge connects two distinct groups + if ((f2g.contains(f1)) && (f2g.contains(f2))) // edge connects two distinct groups { Size group1 = f2g[f1]; Size group2 = f2g[f2]; @@ -68,13 +68,13 @@ namespace OpenMS g2f.erase(group2); } } - else if ((f2g.find(f1) != f2g.end()) && !(f2g.find(f2) != f2g.end())) // only f1 is part of a group + else if ((f2g.contains(f1)) && !(f2g.contains(f2))) // only f1 is part of a group { Size group1 = f2g[f1]; f2g[f2] = group1; g2f[group1].insert(f2); } - else if (!(f2g.find(f1) != f2g.end()) && f2g.find(f2) != f2g.end()) // only f2 is part of a group + else if (!(f2g.contains(f1)) && f2g.contains(f2)) // only f2 is part of a group { Size group2 = f2g[f2]; f2g[f1] = group2; diff --git a/src/openms/source/ANALYSIS/DECHARGING/MetaboliteFeatureDeconvolution.cpp b/src/openms/source/ANALYSIS/DECHARGING/MetaboliteFeatureDeconvolution.cpp index 59bc2458579..34374c5cd35 100644 --- a/src/openms/source/ANALYSIS/DECHARGING/MetaboliteFeatureDeconvolution.cpp +++ b/src/openms/source/ANALYSIS/DECHARGING/MetaboliteFeatureDeconvolution.cpp @@ -907,11 +907,11 @@ namespace OpenMS SignedSize target_cf0 = -1, target_cf1 = -1; // find the index of the ConsensusFeatures for the current pair - if (clique_register.count(f0_idx) > 0) + if (clique_register.contains(f0_idx)) { target_cf0 = clique_register[f0_idx]; } - if (clique_register.count(f1_idx) > 0) + if (clique_register.contains(f1_idx)) { target_cf1 = clique_register[f1_idx]; } @@ -1023,7 +1023,7 @@ namespace OpenMS for (Size i = 0; i < fm_out.size(); ++i) { // find the index of the ConsensusFeature for the current feature - if (clique_register.count(i) > 0) + if (clique_register.contains(i)) continue; Feature f_single = fm_out_untouched[i]; diff --git a/src/openms/source/ANALYSIS/ID/AccurateMassSearchEngine.cpp b/src/openms/source/ANALYSIS/ID/AccurateMassSearchEngine.cpp index 6ef133184ae..a9515bbf769 100644 --- a/src/openms/source/ANALYSIS/ID/AccurateMassSearchEngine.cpp +++ b/src/openms/source/ANALYSIS/ID/AccurateMassSearchEngine.cpp @@ -741,7 +741,7 @@ namespace OpenMS { for (Size i = 0; i < r.getMatchingHMDBids().size(); ++i) { - if (!hmdb_properties_mapping_.count(r.getMatchingHMDBids()[i])) + if (!hmdb_properties_mapping_.contains(r.getMatchingHMDBids()[i])) { throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, String("DB entry '") + r.getMatchingHMDBids()[i] + "' not found in struct file!"); } @@ -818,7 +818,7 @@ namespace OpenMS StringList names; for (Size i = 0; i < result.getMatchingHMDBids().size(); ++i) { // mapping ok? - if (!hmdb_properties_mapping_.count(result.getMatchingHMDBids()[i])) + if (!hmdb_properties_mapping_.contains(result.getMatchingHMDBids()[i])) { throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, String("DB entry '") + result.getMatchingHMDBids()[i] + "' not found in struct file!"); } @@ -1383,7 +1383,7 @@ namespace OpenMS { String hmdb_id_key(parts[0]); - if (hmdb_properties_mapping_.count(hmdb_id_key)) + if (hmdb_properties_mapping_.contains(hmdb_id_key)) { throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, String("File '") + filename + "' in line '" + line + "' cannot be parsed. The ID entry was already used (see above)!"); } diff --git a/src/openms/source/ANALYSIS/ID/CometModification.cpp b/src/openms/source/ANALYSIS/ID/CometModification.cpp index ee97285ea5a..642ec23f39b 100644 --- a/src/openms/source/ANALYSIS/ID/CometModification.cpp +++ b/src/openms/source/ANALYSIS/ID/CometModification.cpp @@ -104,7 +104,7 @@ namespace OpenMS // Add residues from other (avoiding duplicates) for (char c : other.residues) { - if (residues.find(c) == String::npos) + if (!residues.contains(c)) { residues += c; } diff --git a/src/openms/source/ANALYSIS/ID/IDBoostGraph.cpp b/src/openms/source/ANALYSIS/ID/IDBoostGraph.cpp index 2922d4a2f94..0953b031314 100644 --- a/src/openms/source/ANALYSIS/ID/IDBoostGraph.cpp +++ b/src/openms/source/ANALYSIS/ID/IDBoostGraph.cpp @@ -1095,7 +1095,7 @@ namespace OpenMS auto& ev = peptidePtr->getPeptideEvidences(); for (const auto& e : ev) { - if (accs_to_remove.find(e.getProteinAccession()) == accs_to_remove.end()) + if (!accs_to_remove.contains(e.getProteinAccession())) { newev.emplace_back(e); } diff --git a/src/openms/source/ANALYSIS/ID/IDConflictResolverAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/IDConflictResolverAlgorithm.cpp index 117c11e24d8..1c387829eb8 100644 --- a/src/openms/source/ANALYSIS/ID/IDConflictResolverAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/IDConflictResolverAlgorithm.cpp @@ -215,7 +215,7 @@ namespace OpenMS for (Size j = 0; j < hits.size(); ++j) { const AASequence& seq = hits[j].getSequence(); - if (seen_in_run.count(seq) == 0) + if (!seen_in_run.contains(seq)) { // First occurrence of this sequence in this ID: use its rank rank_sums[seq] += static_cast(j); diff --git a/src/openms/source/ANALYSIS/ID/IDMapper.cpp b/src/openms/source/ANALYSIS/ID/IDMapper.cpp index 6f76701aae5..311a7b4ecd2 100644 --- a/src/openms/source/ANALYSIS/ID/IDMapper.cpp +++ b/src/openms/source/ANALYSIS/ID/IDMapper.cpp @@ -491,7 +491,7 @@ namespace OpenMS { id_mapped = true; was_added = true; - if (mapping[cm_index].count(i) == 0) + if (!mapping[cm_index].contains(i)) { // Store the map index of the peptide feature in the id the feature was mapped to. PeptideIdentification id_pep = ids[i]; diff --git a/src/openms/source/ANALYSIS/ID/IDRipper.cpp b/src/openms/source/ANALYSIS/ID/IDRipper.cpp index 5d6ef9fe2f0..84b2214664c 100644 --- a/src/openms/source/ANALYSIS/ID/IDRipper.cpp +++ b/src/openms/source/ANALYSIS/ID/IDRipper.cpp @@ -39,7 +39,7 @@ namespace OpenMS for (const auto& prot_id : prot_ids) { const String& id_run_id = prot_id.getIdentifier(); - if (this->index_map.find(id_run_id) != this->index_map.end()) + if (this->index_map.contains(id_run_id)) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "IdentificationRun IDs are not unique!", id_run_id); } @@ -397,7 +397,7 @@ IDRipper::OriginAnnotationFormat IDRipper::detectOriginAnnotationFormat_(mapgetMetaValue("file_origin"); // Did we already assign an index to this file_origin? - if (file_origin_map.find(file_origin) == file_origin_map.end()) + if (!file_origin_map.contains(file_origin)) { // If not, assign a new unique index size_t cur_size = file_origin_map.size(); diff --git a/src/openms/source/ANALYSIS/ID/IDScoreGetterSetter.cpp b/src/openms/source/ANALYSIS/ID/IDScoreGetterSetter.cpp index 7e83b0be5a3..336e6babdae 100644 --- a/src/openms/source/ANALYSIS/ID/IDScoreGetterSetter.cpp +++ b/src/openms/source/ANALYSIS/ID/IDScoreGetterSetter.cpp @@ -33,7 +33,7 @@ namespace OpenMS for (const auto &acc : grp.accessions) { // In groups, you usually want to check if at least one member is a real target - if (decoy_accs.find(acc) == decoy_accs.end()) + if (!decoy_accs.contains(acc)) { target = true; break; diff --git a/src/openms/source/ANALYSIS/ID/OpenSearchModificationAnalysis.cpp b/src/openms/source/ANALYSIS/ID/OpenSearchModificationAnalysis.cpp index a66beea6c6d..fd0a2c820ef 100644 --- a/src/openms/source/ANALYSIS/ID/OpenSearchModificationAnalysis.cpp +++ b/src/openms/source/ANALYSIS/ID/OpenSearchModificationAnalysis.cpp @@ -119,7 +119,7 @@ namespace OpenMS String full_name = residue->getFullName(); double diff_mono_mass = residue->getDiffMonoMass(); - if (full_name.find("substitution") == std::string::npos) + if (!full_name.contains("substitution")) { mass_to_modification[diff_mono_mass] = full_name; } @@ -138,7 +138,7 @@ namespace OpenMS // Helper function to add or update modifications auto addOrUpdateModification = [&](const String& mod_name, double mass, double count, int num_charges) { - if (modifications.find(mod_name) == modifications.end()) + if (!modifications.contains(mod_name)) { ModificationPattern pattern; pattern.masses.push_back(mass); @@ -720,13 +720,13 @@ namespace OpenMS stats.total_modified_psms++; // Get or create PTM entry - if (ptm_map.find(ptm_name) == ptm_map.end()) + if (!ptm_map.contains(ptm_name)) { PTMEntry entry; entry.name = ptm_name; // Get theoretical mass - if (name_to_mass.find(ptm_name) != name_to_mass.end()) + if (name_to_mass.contains(ptm_name)) { entry.theoretical_mass = name_to_mass[ptm_name]; } @@ -925,7 +925,7 @@ namespace OpenMS double diff_mono_mass = residue->getDiffMonoMass(); // Skip substitutions - if (full_name.find("substitution") == std::string::npos) + if (!full_name.contains("substitution")) { mass_to_mod[diff_mono_mass] = full_name; } @@ -938,7 +938,7 @@ namespace OpenMS { // Split compound names (e.g. "Oxidation//Deamidated" or "Oxidation+1Da") and resolve each part std::vector parts; - if (mod_name.find("//") != std::string::npos) + if (mod_name.contains("//")) { mod_name.split("//", parts); } diff --git a/src/openms/source/ANALYSIS/ID/PeptideIndexing.cpp b/src/openms/source/ANALYSIS/ID/PeptideIndexing.cpp index c618204222a..53cd2174dd9 100644 --- a/src/openms/source/ANALYSIS/ID/PeptideIndexing.cpp +++ b/src/openms/source/ANALYSIS/ID/PeptideIndexing.cpp @@ -757,7 +757,7 @@ PeptideIndexing::ExitCodes PeptideIndexing::run_(FASTAContainer& proteins, st for (std::vector::iterator p_hit = phits.begin(); p_hit != phits.end(); ++p_hit) { const String& acc = p_hit->getAccession(); - if (acc_to_prot.find(acc) == acc_to_prot.end()) // acc_to_prot only contains found proteins from current run + if (!acc_to_prot.contains(acc)) // acc_to_prot only contains found proteins from current run { // old hit is orphaned ++stats_orphaned_proteins; if (keep_unreferenced_proteins_) diff --git a/src/openms/source/ANALYSIS/ID/PeptideProteinResolution.cpp b/src/openms/source/ANALYSIS/ID/PeptideProteinResolution.cpp index b636a80ab9a..1939a8b1763 100644 --- a/src/openms/source/ANALYSIS/ID/PeptideProteinResolution.cpp +++ b/src/openms/source/ANALYSIS/ID/PeptideProteinResolution.cpp @@ -94,7 +94,7 @@ namespace OpenMS { Size idx = group_it - groups.begin(); prot_acc_to_indist_prot_grp[*acc_it] = idx; - if (decoy_accs.find(*acc_it) != decoy_accs.end()) + if (decoy_accs.contains(*acc_it)) { indist_prot_grp_decoy[idx] = true; } diff --git a/src/openms/source/ANALYSIS/ID/Percolator.cpp b/src/openms/source/ANALYSIS/ID/Percolator.cpp index a88241f5ffb..be9a34e576a 100644 --- a/src/openms/source/ANALYSIS/ID/Percolator.cpp +++ b/src/openms/source/ANALYSIS/ID/Percolator.cpp @@ -1130,7 +1130,7 @@ PercolatorModel Percolator::loadModel(const String& filename) // between feature name and weight. A feature name cannot contain a ':' // without a TAB (names are written as the left-hand side of TAB-split // data rows), so checking for TAB first is unambiguous. - if (line.find('\t') == std::string::npos) + if (!line.contains('\t')) { const size_t colon = line.find(':'); if (colon == std::string::npos) @@ -1141,7 +1141,7 @@ PercolatorModel Percolator::loadModel(const String& filename) } const std::string key = trim(line.substr(0, colon)); const std::string val = trim(line.substr(colon + 1)); - if (known_keys.find(key) == known_keys.end()) + if (!known_keys.contains(key)) { throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename + ": unknown header key '" + key + "'", line); @@ -1159,7 +1159,7 @@ PercolatorModel Percolator::loadModel(const String& filename) else if (key == "bias") { bias = std::stod(val); bias_seen = true; } else if (key == "normalizer") { - if (known_normalizers.find(val) == known_normalizers.end()) + if (!known_normalizers.contains(val)) { throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename + ": invalid normalizer value (expected stdv|uni|none)", @@ -1193,7 +1193,7 @@ PercolatorModel Percolator::loadModel(const String& filename) // Required-key completeness. for (const auto& required : known_keys) { - if (seen_keys.find(required) == seen_keys.end()) + if (!seen_keys.contains(required)) { throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename + ": missing required header key '" + required + "'", ""); diff --git a/src/openms/source/ANALYSIS/ID/PercolatorFeatureSetHelper.cpp b/src/openms/source/ANALYSIS/ID/PercolatorFeatureSetHelper.cpp index 2bb39762ddb..29fa371c1d3 100644 --- a/src/openms/source/ANALYSIS/ID/PercolatorFeatureSetHelper.cpp +++ b/src/openms/source/ANALYSIS/ID/PercolatorFeatureSetHelper.cpp @@ -303,7 +303,7 @@ namespace OpenMS String spectrum_reference = getScanMergeKey_(pit, new_peptide_ids.begin()); //merge in unified map // insert newly identified spectra (PeptideIdentifications) or .. - if (unified.find(spectrum_reference) == unified.end()) + if (!unified.contains(spectrum_reference)) { unified[spectrum_reference] = ins; ++nc; diff --git a/src/openms/source/ANALYSIS/ID/Scores.cpp b/src/openms/source/ANALYSIS/ID/Scores.cpp index 14ce8ea3614..32bf20ebb9a 100644 --- a/src/openms/source/ANALYSIS/ID/Scores.cpp +++ b/src/openms/source/ANALYSIS/ID/Scores.cpp @@ -54,7 +54,7 @@ namespace OpenMS chopped = chopped.chop(6); } const std::set& possible_types = maps.type_to_str.at(type); - return possible_types.find(chopped) != possible_types.end(); + return possible_types.contains(chopped); } Scores::IDType Scores::parseIDType(const String& score_type_in) @@ -123,7 +123,7 @@ namespace OpenMS const auto& maps = getMaps_(); for (const auto& [scoretype, names] : maps.type_to_str) { - if (names.find(name) != names.end()) + if (names.contains(name)) { type = scoretype; return true; @@ -149,7 +149,7 @@ namespace OpenMS for (const auto& [type, names] : maps.type_to_str) { - if (names.find(normalized) != names.end()) + if (names.contains(normalized)) { return true; } diff --git a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp index 25e95e4c6e5..dc849d39ebb 100644 --- a/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp @@ -738,7 +738,7 @@ void SimpleSearchEngineAlgorithm::postProcessHits_(const PeakMap& exp, #pragma omp critical (processed_peptides_access) { // peptide (and all modified variants) already processed so skip it - if (processed_petides.find(c) != processed_petides.end()) + if (processed_petides.contains(c)) { already_processed = true; } diff --git a/src/openms/source/ANALYSIS/MAPMATCHING/BaseGroupFinder.cpp b/src/openms/source/ANALYSIS/MAPMATCHING/BaseGroupFinder.cpp index 755e9d37148..f2fa2e28d1d 100644 --- a/src/openms/source/ANALYSIS/MAPMATCHING/BaseGroupFinder.cpp +++ b/src/openms/source/ANALYSIS/MAPMATCHING/BaseGroupFinder.cpp @@ -26,7 +26,7 @@ namespace OpenMS const ConsensusMap& map = maps[i]; for (ConsensusMap::ColumnHeaders::const_iterator it = map.getColumnHeaders().begin(); it != map.getColumnHeaders().end(); ++it) { - if (used_ids.find(it->first) != used_ids.end()) + if (used_ids.contains(it->first)) { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "file ids have to be unique"); } diff --git a/src/openms/source/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmWNet.cpp b/src/openms/source/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmWNet.cpp index 019df46b68a..b84046e0c99 100644 --- a/src/openms/source/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmWNet.cpp +++ b/src/openms/source/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmWNet.cpp @@ -287,7 +287,7 @@ namespace OpenMS for (Size m : group_maps_[b]) { - if (group_maps_[a].count(m)) return false; // would create duplicate map entry + if (group_maps_[a].contains(m)) return false; // would create duplicate map entry } if (rank_[a] < rank_[b]) swap(a, b); diff --git a/src/openms/source/ANALYSIS/MAPMATCHING/LabeledPairFinder.cpp b/src/openms/source/ANALYSIS/MAPMATCHING/LabeledPairFinder.cpp index de218ec6a26..4366ce84e85 100644 --- a/src/openms/source/ANALYSIS/MAPMATCHING/LabeledPairFinder.cpp +++ b/src/openms/source/ANALYSIS/MAPMATCHING/LabeledPairFinder.cpp @@ -278,8 +278,8 @@ namespace OpenMS for (ConsensusMap::const_iterator match = matches.begin(); match != matches.end(); ++match) { //check if features are not used yet - if (used_features.find(match->begin()->getUniqueId()) == used_features.end() && - used_features.find(match->rbegin()->getUniqueId()) == used_features.end() + if (!used_features.contains(match->begin()->getUniqueId()) && + !used_features.contains(match->rbegin()->getUniqueId()) ) { //if unused, add it to the final set of elements diff --git a/src/openms/source/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmKD.cpp b/src/openms/source/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmKD.cpp index 9623eaee209..24d68c237d8 100644 --- a/src/openms/source/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmKD.cpp +++ b/src/openms/source/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmKD.cpp @@ -220,7 +220,7 @@ void MapAlignmentAlgorithmKD::filterCCs_(const KDTreeFeatureMaps& kd_data, const { // filter out if too many features from same map Size map_idx = kd_data.mapIndex(*idx_it); - if (map_indices.find(map_idx) != map_indices.end()) + if (map_indices.contains(map_idx)) { if (++nr_conflicts > max_nr_conflicts) { diff --git a/src/openms/source/ANALYSIS/MAPMATCHING/QTClusterFinder.cpp b/src/openms/source/ANALYSIS/MAPMATCHING/QTClusterFinder.cpp index 1cef0acf46c..41b1946e3e3 100644 --- a/src/openms/source/ANALYSIS/MAPMATCHING/QTClusterFinder.cpp +++ b/src/openms/source/ANALYSIS/MAPMATCHING/QTClusterFinder.cpp @@ -690,7 +690,7 @@ void QTClusterFinder::createConsensusFeature_(ConsensusFeature& feature, // Skip features that we have already used -> we cannot add them to // be neighbors any more - if (already_used_.find(neighbor_feature) != already_used_.end() ) + if (already_used_.contains(neighbor_feature) ) { continue; } diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp index b1ba852ad3a..4f8173a168c 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLAnnotateAndLocate.cpp @@ -526,7 +526,7 @@ namespace OpenMS for (auto pair_it = alignment.begin(); pair_it != alignment.end(); ++pair_it) { // only annotate experimental peaks with shift - i.e. do not annotated complete loss peaks again - if (peak_is_annotated.find(pair_it->second) != peak_is_annotated.end()) { continue; } + if (peak_is_annotated.contains(pair_it->second)) { continue; } // information on the experimental fragment in the alignment const Size & fragment_index = pair_it->second; @@ -658,20 +658,20 @@ namespace OpenMS for (Size i = 0; i != n_shifts.size(); ++i) { - if (shifted_b_ions.find(i + 1) == shifted_b_ions.end()) { continue; } + if (!shifted_b_ions.contains(i + 1)) { continue; } for (auto& k : shifted_b_ions[i + 1]) { n_shifts[i] += k.intensity; } } for (Size i = 0; i != n_shifts.size(); ++i) { - if (shifted_a_ions.find(i + 1) == shifted_a_ions.end()) { continue; } + if (!shifted_a_ions.contains(i + 1)) { continue; } for (auto& k : shifted_a_ions[i + 1]) { n_shifts[i] += k.intensity; } } for (Size i = 0; i != c_shifts.size(); ++i) { const Size ion_index = c_shifts.size() - i; - if (shifted_y_ions.find(ion_index) == shifted_y_ions.end()) { continue; } + if (!shifted_y_ions.contains(ion_index)) { continue; } for (auto& k : shifted_y_ions[ion_index]) { c_shifts[i] += k.intensity; } } @@ -679,20 +679,20 @@ namespace OpenMS vector c_noshifts(sites_sum_score.size(), 0); for (Size i = 0; i != n_noshifts.size(); ++i) { - if (unshifted_b_ions.find(i + 1) == unshifted_b_ions.end()) { continue; } + if (!unshifted_b_ions.contains(i + 1)) { continue; } for (auto& k : unshifted_b_ions[i + 1]) { n_noshifts[i] += k.intensity; } } for (Size i = 0; i != n_noshifts.size(); ++i) { - if (unshifted_a_ions.find(i + 1) == unshifted_a_ions.end()) { continue; } + if (!unshifted_a_ions.contains(i + 1)) { continue; } for (auto& k : unshifted_a_ions[i + 1]) { n_noshifts[i] += k.intensity; } } for (Size i = 0; i != c_noshifts.size(); ++i) { const Size ion_index = c_noshifts.size() - i; - if (unshifted_y_ions.find(ion_index) == unshifted_y_ions.end()) { continue; } + if (!unshifted_y_ions.contains(ion_index)) { continue; } for (auto& k : unshifted_y_ions[ion_index]) { c_noshifts[i] += k.intensity; } } diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp index 5322677342e..5ae8f67a9f8 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLFDR.cpp @@ -72,7 +72,7 @@ namespace OpenMS for (const auto & pi : xl_pi) { - if (native_id_to_id_index.find(pi.getMetaValue("spectrum_reference")) == native_id_to_id_index.end()) + if (!native_id_to_id_index.contains(pi.getMetaValue("spectrum_reference"))) { peptide_ids.push_back(pi); } diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLModificationsGenerator.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLModificationsGenerator.cpp index 614eaa9396f..aeb4cde4988 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLModificationsGenerator.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLModificationsGenerator.cpp @@ -260,7 +260,7 @@ NuXLModificationMassesResult NuXLModificationsGenerator::initModificationMassesN } } - if (formulas_of_modified_nucleotide.find(sum_formula.toString()) == formulas_of_modified_nucleotide.end()) + if (!formulas_of_modified_nucleotide.contains(sum_formula.toString())) { actual_combinations.push_back(sum_formula); result.mod_combinations[sum_formula.toString()].insert(nt); // add sum formula -> nucleotide @@ -355,7 +355,7 @@ NuXLModificationMassesResult NuXLModificationsGenerator::initModificationMassesN // check if nucleotide formula contains a cross-linkable amino acid bool has_xl_nt(false); - for (auto const & c : nucleotide_style_formula) { if (can_xl.count(c) > 0) { has_xl_nt = true; break;}; } + for (auto const & c : nucleotide_style_formula) { if (can_xl.contains(c)) { has_xl_nt = true; break;}; } if (!has_xl_nt) { // no cross-linked nucleotide => not valid @@ -479,7 +479,7 @@ NuXLModificationMassesResult NuXLModificationsGenerator::initModificationMassesN } // only print ambiguous sequences once - if (printed.find(nucleotide_style_formula) == printed.end()) + if (!printed.contains(nucleotide_style_formula)) { OPENMS_LOG_INFO << nucleotide_style_formula << " "; printed.insert(nucleotide_style_formula); diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLParameterParsing.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLParameterParsing.cpp index 13d6d2ca11e..908eb638c44 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLParameterParsing.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLParameterParsing.cpp @@ -275,10 +275,10 @@ NuXLParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, if (*exp_pc_it == '+' || *exp_pc_it == '-') break; // count occurence of nucleotide - if (exp_pc_nucleotide_count.count(*exp_pc_it) == 0) + if (!exp_pc_nucleotide_count.contains(*exp_pc_it)) { exp_pc_nucleotide_count[*exp_pc_it] = 1; - if (can_xl.count(*exp_pc_it)) { exp_pc_xl_nts.insert(*exp_pc_it); }; + if (can_xl.contains(*exp_pc_it)) { exp_pc_xl_nts.insert(*exp_pc_it); }; } else { @@ -329,7 +329,7 @@ NuXLParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, const set& fragment_adducts = n2fa.second; // all potential fragment adducts that may arise from the unmodified nucleotide // check if nucleotide is cross-linkable and part of the precursor adduct - if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) + if (exp_pc_xl_nts.contains(nucleotide)) { OPENMS_LOG_DEBUG << "\t" << exp_pc_adduct << " found nucleotide: " << String(nucleotide) << " in precursor RNA." << endl; OPENMS_LOG_DEBUG << "\t" << exp_pc_adduct << " nucleotide: " << String(nucleotide) << " has fragment_adducts: " << fragment_adducts.size() << endl; @@ -347,7 +347,7 @@ NuXLParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, for (auto const & n2fa : nucleotide_to_fragment_adducts) { const char & nucleotide = n2fa.first; // the nucleotide without any associated loss - if (exp_pc_nucleotide_count.find(nucleotide) != exp_pc_nucleotide_count.end()) + if (exp_pc_nucleotide_count.contains(nucleotide)) { marker_ion_set.insert(n2fa.second.begin(), n2fa.second.end()); } @@ -363,7 +363,7 @@ NuXLParameterParsing::getFeasibleFragmentAdducts(const String &exp_pc_adduct, set fas = n2fa.second; // all potential fragment adducts that may arise from NT assuming no loss on the precursor adduct // check if nucleotide is cross-linkable and part of the precursor adduct - if (exp_pc_xl_nts.find(nucleotide) != exp_pc_xl_nts.end()) + if (exp_pc_xl_nts.contains(nucleotide)) { OPENMS_LOG_DEBUG << "\t" << exp_pc_adduct << " found nucleotide: " << String(nucleotide) << " in precursor NA adduct." << endl; OPENMS_LOG_DEBUG << "\t" << exp_pc_adduct << " nucleotide: " << String(nucleotide) << " has fragment_adducts: " << fas.size() << endl; diff --git a/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp b/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp index 2da26fc6411..08141f2ad44 100644 --- a/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp +++ b/src/openms/source/ANALYSIS/NUXL/NuXLReport.cpp @@ -152,7 +152,7 @@ namespace OpenMS NuXLReportRow row; // case 1: no peptide identification: store rt, mz, charge and marker ion intensities - if (map_spectra_to_id.find(scan_index) == map_spectra_to_id.end()) + if (!map_spectra_to_id.contains(scan_index)) { row.no_id = true; row.rt = rt; @@ -604,7 +604,7 @@ Output format: // one row per unlocalized peptide for (const auto& [peptide, unlocalizedXLs] : region_loc.peptide2unlocalizedXL) { - if (remaining_peptides.find(peptide) == remaining_peptides.end()) continue; + if (!remaining_peptides.contains(peptide)) continue; // protein, AA, position String l = accession + "\t-\t-\t"; @@ -744,7 +744,7 @@ Output format: for (auto& ph_evidence : ph_evidences) { const String& acc = ph_evidence.getProteinAccession(); - bool is_target = acc2protein_targets.find(acc) != acc2protein_targets.end(); + bool is_target = acc2protein_targets.contains(acc); if (!is_target) continue; // skip decoys peptide2proteins[peptide_sequence].insert(acc); protein2peptides[acc].insert(peptide_sequence); @@ -894,7 +894,7 @@ Output format: else if (auto it = accessionToIndistinguishableGroup.find(accession); it != accessionToIndistinguishableGroup.end()) { // ind. protein group - if (printed_ind_group.count(accession) == 0) + if (!printed_ind_group.contains(accession)) { const ProteinIdentification::ProteinGroup* pg = it->second; String a = ListUtils::concatenate(pg->accessions, ","); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/ConfidenceScoring.cpp b/src/openms/source/ANALYSIS/OPENSWATH/ConfidenceScoring.cpp index 1af6bb5c161..d491a32a15c 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/ConfidenceScoring.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/ConfidenceScoring.cpp @@ -120,7 +120,7 @@ namespace OpenMS // for the "true" assay, we need to choose the same transitions as for the // feature: if (!transition_ids.empty() && - (transition_ids.count(transition.getNativeID()) == 0)) continue; + (!transition_ids.contains(transition.getNativeID()))) continue; // seems like Boost's Bimap doesn't support "operator[]"... intensity_map.left.insert(make_pair(transition.getProductMZ(), transition.getLibraryIntensity())); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.cpp b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.cpp index 891ab13f135..a51dfed3da3 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.cpp @@ -157,19 +157,19 @@ namespace OpenMS // legacy #if 1 const auto& cv_terms = transition.getCVTerms(); - if (cv_terms.find("decoy") != cv_terms.end() && cv_terms.at("decoy")[0].getValue().toString() == "1" ) + if (cv_terms.contains("decoy") && cv_terms.at("decoy")[0].getValue().toString() == "1" ) { t.setDecoy(true); } - else if (cv_terms.find("MS:1002007") != cv_terms.end()) // target SRM transition + else if (cv_terms.contains("MS:1002007")) // target SRM transition { t.setDecoy(false); } - else if (cv_terms.find("MS:1002008") != cv_terms.end()) // decoy SRM transition + else if (cv_terms.contains("MS:1002008")) // decoy SRM transition { t.setDecoy(true); } - else if (cv_terms.find("MS:1002007") != cv_terms.end() && cv_terms.find("MS:1002008") != cv_terms.end()) // both == illegal + else if (cv_terms.contains("MS:1002007") && cv_terms.contains("MS:1002008")) // both == illegal { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Transition " + t.transition_name + " cannot be target and decoy at the same time."); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMAssay.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMAssay.cpp index a09700a642d..01a178dc86b 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MRMAssay.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMAssay.cpp @@ -531,7 +531,7 @@ namespace OpenMS } // Skip if target peptide is not in map, e.g. permutation threshold was reached - if (TargetPeptideMap.find(peptide.id) == TargetPeptideMap.end()) + if (!TargetPeptideMap.contains(peptide.id)) { continue; } @@ -947,7 +947,7 @@ namespace OpenMS ReactionMonitoringTransition tr = *tr_it; if ( - top_intensities.find(tr.getLibraryIntensity()) != top_intensities.end() && + top_intensities.contains(tr.getLibraryIntensity()) && tr.getDecoyTransitionType() != ReactionMonitoringTransition::DECOY && j < (Size)max_transitions) { @@ -974,7 +974,7 @@ namespace OpenMS setProgress(++progress); // Check if peptide has any transitions left - if (peptide_ids.find(peptide.id) != peptide_ids.end()) + if (peptide_ids.contains(peptide.id)) { peptides.push_back(peptide); for (const auto& protein_ref : peptide.protein_refs) @@ -993,7 +993,7 @@ namespace OpenMS setProgress(++progress); // Check if protein has any peptides left - if (ProteinList.find(protein.id) != ProteinList.end()) + if (ProteinList.contains(protein.id)) { proteins.push_back(protein); } @@ -1122,7 +1122,7 @@ namespace OpenMS for (TransitionVectorType::iterator tr_it = m->second.begin(); tr_it != m->second.end(); ++tr_it) { ReactionMonitoringTransition tr = *tr_it; - if (top_intensities.find(tr.getLibraryIntensity()) != top_intensities.end() && j < (Size)max_transitions) + if (top_intensities.contains(tr.getLibraryIntensity()) && j < (Size)max_transitions) { // Set meta value tag for detecting transition tr.setDetectingTransition(true); @@ -1176,7 +1176,7 @@ namespace OpenMS for (const auto &it : compounds) { // extract potential target TransitionIds based on the decoy annotation '0_CompoundName_decoy_[M+H]+_448_0' - if (it.id.find("decoy") != std::string::npos) + if (it.id.contains("decoy")) { String current_decoy = it.id; String potential_target = current_decoy; @@ -1498,7 +1498,7 @@ namespace OpenMS size_t j = 0; for (auto& tr : m.second) { - if (top_intensities.find(tr.library_intensity) != top_intensities.end() && + if (top_intensities.contains(tr.library_intensity) && !tr.getDecoy() && j < static_cast(max_transitions)) { @@ -1522,7 +1522,7 @@ namespace OpenMS { setProgress(++progress); - if (peptide_ids.find(compound.id) != peptide_ids.end()) + if (peptide_ids.contains(compound.id)) { compounds.push_back(compound); for (const auto& protein_ref : compound.protein_refs) @@ -1536,7 +1536,7 @@ namespace OpenMS { setProgress(++progress); - if (protein_list.find(protein.id) != protein_list.end()) + if (protein_list.contains(protein.id)) { proteins.push_back(protein); } @@ -1749,7 +1749,7 @@ namespace OpenMS } // Skip compounds that are not in target peptide map (e.g., those with too many permutations) - if (TargetPeptideMap.find(compound.id) == TargetPeptideMap.end()) + if (!TargetPeptideMap.contains(compound.id)) { continue; } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMDecoy.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMDecoy.cpp index ae427d2c81a..e7095b9dad5 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MRMDecoy.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMDecoy.cpp @@ -602,7 +602,7 @@ namespace OpenMS // Check that the decoy precursor does not happen to be a target precursor AND is not already present. // Use getModifiedPeptideSequence_ to match the key format used when populating allPeptideSequences above. const std::string peptide_key = MRMDecoy::getModifiedPeptideSequence_(peptide) + String(peptide.getChargeState()); - if (allPeptideSequences.find(peptide_key) != allPeptideSequences.end()) + if (allPeptideSequences.contains(peptide_key)) { OPENMS_LOG_DEBUG << "[peptide] Skipping " << peptide.id << " since decoy peptide is also a target peptide or this decoy peptide is already present\n"; exclusion_peptides.insert(peptide.id); @@ -712,7 +712,7 @@ namespace OpenMS decoy_transitions.begin(), decoy_transitions.end(), [&exclusion_peptides](const OpenMS::ReactionMonitoringTransition& tr) { - return exclusion_peptides.find(tr.getPeptideRef()) != exclusion_peptides.end(); + return exclusion_peptides.contains(tr.getPeptideRef()); }), decoy_transitions.end()); dec.setTransitions(std::move(decoy_transitions)); @@ -721,7 +721,7 @@ namespace OpenMS for (const auto& peptide : peptides) { // Check if peptide has any transitions left - if (exclusion_peptides.find(peptide.id) == exclusion_peptides.end()) + if (!exclusion_peptides.contains(peptide.id)) { decoy_peptides.push_back(peptide); for (Size j = 0; j < peptide.protein_refs.size(); ++j) @@ -739,7 +739,7 @@ namespace OpenMS for (const auto& protein : proteins) { // Check if protein has any peptides left - if (protein_ids.find(protein.id) != protein_ids.end()) + if (protein_ids.contains(protein.id)) { decoy_proteins.push_back(protein); } @@ -955,7 +955,7 @@ namespace OpenMS // which includes UniMod annotations. This ensures peptides with the same unmodified // sequence but different modifications are NOT considered duplicates. std::string decoy_key = full_decoy_sequence + String(decoy_compound.charge); - if (allPeptideSequences.find(decoy_key) != allPeptideSequences.end()) + if (allPeptideSequences.contains(decoy_key)) { OPENMS_LOG_DEBUG << "[peptide] Skipping " << decoy_compound.id << " since decoy peptide is also a target peptide or this decoy peptide is already present\n"; exclusion_peptides.insert(decoy_compound.id); @@ -1123,7 +1123,7 @@ namespace OpenMS decoy_transitions.erase( std::remove_if(decoy_transitions.begin(), decoy_transitions.end(), [&exclusion_peptides](const OpenSwath::LightTransition& tr) { - return exclusion_peptides.find(tr.peptide_ref) != exclusion_peptides.end(); + return exclusion_peptides.contains(tr.peptide_ref); }), decoy_transitions.end()); @@ -1132,7 +1132,7 @@ namespace OpenMS std::unordered_set protein_ids; for (const auto& compound : decoy_compounds) { - if (exclusion_peptides.find(compound.id) == exclusion_peptides.end()) + if (!exclusion_peptides.contains(compound.id)) { filtered_compounds.push_back(compound); for (const auto& prot_ref : compound.protein_refs) @@ -1146,7 +1146,7 @@ namespace OpenMS std::vector filtered_proteins; for (const auto& protein : decoy_proteins) { - if (protein_ids.find(protein.id) != protein_ids.end()) + if (protein_ids.contains(protein.id)) { filtered_proteins.push_back(protein); } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp index c97074b6648..d285ca88fc1 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp @@ -1423,7 +1423,7 @@ namespace OpenMS chromatogram.setNativeID(transition->getNativeID()); // Create new transition group if there is none for this peptide - if (transition_group_map.find(transition->getPeptideRef()) == transition_group_map.end()) + if (!transition_group_map.contains(transition->getPeptideRef())) { MRMTransitionGroupType transition_group; transition_group.setTransitionGroupID(transition->getPeptideRef()); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureSelector.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureSelector.cpp index 30309b7837f..b386d58535f 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureSelector.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureSelector.cpp @@ -84,7 +84,7 @@ namespace OpenMS for (const Feature& feature : feature_name_map.at(elem.second)) { const String name1 = elem.second + "_" + String(feature.getUniqueId()); - if (variables.count(name1) == 0) + if (!variables.contains(name1)) { const double score = computeScore_(feature, parameters.score_weights); const Int col_idx = addVariable_(problem, name1, true, score, parameters.variable_type); @@ -135,7 +135,7 @@ namespace OpenMS { const String name1 = time_to_name[cnt1].second + "_" + String(feature_row1[i].getUniqueId()); - if (variables.count(name1) == 0) + if (!variables.contains(name1)) { constraints.push_back(addVariable_(problem, name1, true, 0, parameters.variable_type)); variables.insert(name1); @@ -171,7 +171,7 @@ namespace OpenMS for (Size j = 0; j < feature_row2.size(); ++j) { const String name2 = time_to_name[cnt2].second + "_" + String(feature_row2[j].getUniqueId()); - if (variables.count(name2) == 0) + if (!variables.contains(name2)) { addVariable_(problem, name2, true, 0, parameters.variable_type); variables.insert(name2); @@ -232,12 +232,12 @@ namespace OpenMS { const String component_group_name = removeSpaces_(feature.getMetaValue("PeptideRef").toString()); const double assay_retention_time = feature.getMetaValue("assay_rt"); - if (names.count(component_group_name) == 0) + if (!names.contains(component_group_name)) { time_to_name.emplace_back(assay_retention_time, component_group_name); names.insert(component_group_name); } - if (feature_name_map.count(component_group_name) == 0) + if (!feature_name_map.contains(component_group_name)) { feature_name_map[component_group_name] = std::vector(); } @@ -249,12 +249,12 @@ namespace OpenMS for (const Feature& subordinate : feature.getSubordinates()) { const String component_name = removeSpaces_(subordinate.getMetaValue("native_id").toString()); - if (names.count(component_name)) + if (names.contains(component_name)) { time_to_name.emplace_back(assay_retention_time, component_name); names.insert(component_name); } - if (feature_name_map.count(component_name) == 0) + if (!feature_name_map.contains(component_name)) { feature_name_map[component_name] = std::vector(); } @@ -313,7 +313,7 @@ namespace OpenMS ? removeSpaces_(feature.getMetaValue("PeptideRef").toString()) + "_" + String(feature.getUniqueId()) : removeSpaces_(subordinate.getMetaValue("native_id").toString()) + "_" + String(feature.getUniqueId()); - if (result_names_set.count(feature_name)) + if (result_names_set.contains(feature_name)) { subordinates_filtered.push_back(subordinate); } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMIonSeries.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMIonSeries.cpp index dd2be7289c7..eedc1413de4 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MRMIonSeries.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMIonSeries.cpp @@ -21,7 +21,7 @@ namespace OpenMS std::pair MRMIonSeries::getIon(IonSeries& ionseries, const String& ionid) { - if (ionseries.find(ionid) != ionseries.end()) + if (ionseries.contains(ionid)) { return make_pair(ionid, ionseries[ionid]); } @@ -153,7 +153,7 @@ namespace OpenMS { return interpretation; } - else if (best_annotation[0].find("-") != std::string::npos) + else if (best_annotation[0].contains("-")) { std::vector best_annotation_loss; best_annotation[0].split("-", best_annotation_loss); @@ -173,7 +173,7 @@ namespace OpenMS fragment_loss = -1 * nl_formula.getMonoWeight(); } } - else if (best_annotation[0].find("+") != std::string::npos) + else if (best_annotation[0].contains("+")) { std::vector best_annotation_gain; best_annotation[0].split("+", best_annotation_gain); @@ -249,7 +249,7 @@ namespace OpenMS tr.getMetaValue("annotation").toString().split("/", best_annotation); String annotation; - if (best_annotation[0].find("^") != std::string::npos) + if (best_annotation[0].contains("^")) { std::vector best_annotation_charge; best_annotation[0].split("^", best_annotation_charge); diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MasstraceCorrelator.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MasstraceCorrelator.cpp index bcbd38ea579..2b9027baf81 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MasstraceCorrelator.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MasstraceCorrelator.cpp @@ -223,7 +223,7 @@ namespace OpenMS { setProgress(i); - if (used_already.find(i) != used_already.end()) + if (used_already.contains(i)) { continue; } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathHelper.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathHelper.cpp index 1f71cedb2b9..f15087d126b 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathHelper.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathHelper.cpp @@ -131,7 +131,7 @@ namespace OpenMS std::set matching_proteins; for (Size i = 0; i < targeted_exp.compounds.size(); i++) { - if (matching_compounds.find(targeted_exp.compounds[i].id) != matching_compounds.end()) + if (matching_compounds.contains(targeted_exp.compounds[i].id)) { transition_exp_used.compounds.push_back( targeted_exp.compounds[i] ); for (Size j = 0; j < targeted_exp.compounds[i].protein_refs.size(); j++) @@ -142,7 +142,7 @@ namespace OpenMS } for (Size i = 0; i < targeted_exp.proteins.size(); i++) { - if (matching_proteins.find(targeted_exp.proteins[i].id) != matching_proteins.end()) + if (matching_proteins.contains(targeted_exp.proteins[i].id)) { transition_exp_used.proteins.push_back( targeted_exp.proteins[i] ); } @@ -195,9 +195,9 @@ namespace OpenMS // Separate compounds into priority and regular candidates for (auto & cmp : exp.getCompounds()) { - if (good_ids.count(cmp.id)) + if (good_ids.contains(cmp.id)) { - if (priority_peptides.count(cmp.sequence)) + if (priority_peptides.contains(cmp.sequence)) { priority_candidates.push_back(cmp); } @@ -281,7 +281,7 @@ namespace OpenMS for (auto & cmp : priority_candidates) { - if (cmp.rt >= lo && cmp.rt < hi && picked_sequences.find(cmp.sequence) == picked_sequences.end()) + if (cmp.rt >= lo && cmp.rt < hi && !picked_sequences.contains(cmp.sequence)) bucket.push_back(cmp); } @@ -329,7 +329,7 @@ namespace OpenMS std::vector bucket; for (auto & cmp : candidates) { - if (cmp.rt >= lo && cmp.rt < hi && picked_sequences.find(cmp.sequence) == picked_sequences.end()) + if (cmp.rt >= lo && cmp.rt < hi && !picked_sequences.contains(cmp.sequence)) bucket.push_back(cmp); } @@ -368,7 +368,7 @@ namespace OpenMS prot_ids.insert(pid); for (auto & prot : exp.getProteins()) { - if (prot_ids.count(prot.id)) + if (prot_ids.contains(prot.id)) out_exp.proteins.push_back(prot); } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathMatrixExporter.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathMatrixExporter.cpp index 0936c1a265e..f8bd3bd1894 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathMatrixExporter.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathMatrixExporter.cpp @@ -64,12 +64,12 @@ namespace OpenMS std::set used; for (const auto& row : rows) { - if (names.find(row.run_id) != names.end()) + if (names.contains(row.run_id)) { continue; } String label = row.run_name.empty() ? (String("RUN_ID_") + String(row.run_id)) : row.run_name; - if (used.count(label)) + if (used.contains(label)) { label += "_RUN" + String(row.run_id); } @@ -150,7 +150,7 @@ namespace OpenMS { const PeptideKey key{row.sequence, row.full_peptide_name}; const auto selected_it = selected_precursors.find(key); - if (selected_it == selected_precursors.end() || !selected_it->second.count(row.transition_group_id)) + if (selected_it == selected_precursors.end() || !selected_it->second.contains(row.transition_group_id)) { continue; } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWParquetWriter.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWParquetWriter.cpp index fc491ffade4..3a10d307091 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWParquetWriter.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWParquetWriter.cpp @@ -412,7 +412,7 @@ namespace OpenMS int64_t next_precursor_id = 1; for (const auto& compound : assay_library.compounds) { - if (compound_to_precursor.find(compound.id) != compound_to_precursor.end()) + if (compound_to_precursor.contains(compound.id)) { continue; } @@ -434,7 +434,7 @@ namespace OpenMS // If numeric id collides with an already-used id, reject the numeric // value and fall back to auto-assigning. This prevents accidental // collisions between user-provided numeric ids and our auto ids. - if (used_precursor_ids.find(precursor_id) != used_precursor_ids.end() || precursor_id <= 0) + if (used_precursor_ids.contains(precursor_id) || precursor_id <= 0) { precursor_id = next_precursor_id++; } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathPeptidoformInference.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathPeptidoformInference.cpp index 0fc3139f35d..52b1ce21fb0 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathPeptidoformInference.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathPeptidoformInference.cpp @@ -193,7 +193,7 @@ namespace OpenMS missing_rows_added.reserve(rows.size()); for (const auto& row : rows) { - if (features_with_precursor_evidence.find(row.feature_id) == features_with_precursor_evidence.end() && + if (!features_with_precursor_evidence.contains(row.feature_id) && missing_rows_added.insert(row.feature_id).second) { // No precursor-specific evidence is available for this feature, so fall back @@ -382,7 +382,7 @@ namespace OpenMS (alignment_group_map.count(row.feature_id) ? alignment_group_map[row.feature_id] : -1); merged_rows.push_back(std::move(merged_row)); - if (row.num_peptidoforms > 0 && num_peptidoforms_by_feature.find(row.feature_id) == num_peptidoforms_by_feature.end()) + if (row.num_peptidoforms > 0 && !num_peptidoforms_by_feature.contains(row.feature_id)) { num_peptidoforms_by_feature[row.feature_id] = row.num_peptidoforms; } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathWorkflow.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathWorkflow.cpp index cc98b116cb3..9e684c4596f 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathWorkflow.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathWorkflow.cpp @@ -600,7 +600,7 @@ namespace OpenMS std::set matching_proteins; for (Size compound_idx = 0; compound_idx < transition_exp.compounds.size(); compound_idx++) { - if (matching_compounds.find(transition_exp.compounds[compound_idx].id) != matching_compounds.end()) + if (matching_compounds.contains(transition_exp.compounds[compound_idx].id)) { context.transition_exp_used_all.compounds.push_back(transition_exp.compounds[compound_idx]); for (Size protein_ref_idx = 0; @@ -613,7 +613,7 @@ namespace OpenMS } for (Size protein_idx = 0; protein_idx < transition_exp.proteins.size(); protein_idx++) { - if (matching_proteins.find(transition_exp.proteins[protein_idx].id) != matching_proteins.end()) + if (matching_proteins.contains(transition_exp.proteins[protein_idx].id)) { context.transition_exp_used_all.proteins.push_back(transition_exp.proteins[protein_idx]); } @@ -988,7 +988,7 @@ namespace OpenMS std::set matching_proteins; for (Size i = 0; i < transition_exp.compounds.size(); i++) { - if (matching_compounds.find(transition_exp.compounds[i].id) != matching_compounds.end()) + if (matching_compounds.contains(transition_exp.compounds[i].id)) { transition_exp_used_all.compounds.push_back( transition_exp.compounds[i] ); for (Size j = 0; j < transition_exp.compounds[i].protein_refs.size(); j++) @@ -999,7 +999,7 @@ namespace OpenMS } for (Size i = 0; i < transition_exp.proteins.size(); i++) { - if (matching_proteins.find(transition_exp.proteins[i].id) != matching_proteins.end()) + if (matching_proteins.contains(transition_exp.proteins[i].id)) { transition_exp_used_all.proteins.push_back( transition_exp.proteins[i] ); } @@ -1336,7 +1336,7 @@ namespace OpenMS // the transitions) if (ms1only) {continue;} - if (chromatogram_map.find(transition->getNativeID()) == chromatogram_map.end()) + if (!chromatogram_map.contains(transition->getNativeID())) { if (mrm_) // in SRM/MRM mode, we can skip missing chromatograms, because it's unlikely that we will map all transitions to the already targeted extracted chromatograms { @@ -1389,7 +1389,7 @@ namespace OpenMS for (int iso = 0; iso <= nr_ms1_isotopes; iso++) { String prec_id = OpenSwathHelper::computePrecursorId(transition_group.getTransitionGroupID(), iso); - if (!ms1_chromatograms.empty() && ms1_chromatogram_map.find(prec_id) != ms1_chromatogram_map.end()) + if (!ms1_chromatograms.empty() && ms1_chromatogram_map.contains(prec_id)) { const MSChromatogram& chromatogram = ms1_chromatograms[ ms1_chromatogram_map[prec_id] ]; transition_group.addPrecursorChromatogram(chromatogram, chromatogram.getNativeID()); @@ -1593,7 +1593,7 @@ namespace OpenMS for (Size i = 0; i < all_transitions.size(); i++) { - if (selected_compounds.find(all_transitions[i].peptide_ref) != selected_compounds.end()) + if (selected_compounds.contains(all_transitions[i].peptide_ref)) { output.push_back(all_transitions[i]); } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp b/src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp index 777eb81ee0e..6cbe10d2d0d 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp @@ -1107,15 +1107,15 @@ namespace OpenMS void TargetedSpectraExtractor::BinnedSpectrumComparator::init(const std::vector& library, const std::map& options) { - if (options.count("bin_size")) + if (options.contains("bin_size")) { bin_size_ = options.at("bin_size"); } - if (options.count("peak_spread")) + if (options.contains("peak_spread")) { peak_spread_ = options.at("peak_spread"); } - if (options.count("bin_offset")) + if (options.contains("bin_offset")) { bin_offset_ = options.at("bin_offset"); } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp b/src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp index f69deecc784..e5a6aebd48c 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp @@ -739,11 +739,11 @@ namespace OpenMS int group_set_index = group_map[transition.group_id]; - if (precursor_mz_map.find(group_set_index) == precursor_mz_map.end()) + if (!precursor_mz_map.contains(group_set_index)) { precursor_mz_map[group_set_index] = transition.precursor; } - if (precursor_decoy_map.find(group_set_index) == precursor_decoy_map.end()) + if (!precursor_decoy_map.contains(group_set_index)) { if (transition.detecting_transition == 1) { @@ -829,7 +829,7 @@ namespace OpenMS gene_name = peptide.getMetaValue("GeneName"); } - if (gene_map.find(gene_name) == gene_map.end()) gene_map[gene_name] = (int)gene_map.size(); + if (!gene_map.contains(gene_name)) gene_map[gene_name] = (int)gene_map.size(); peptide_gene_map.emplace_back(peptide_set_index, gene_map[gene_name]); insert_precursor_sql << @@ -1230,11 +1230,11 @@ namespace OpenMS const auto& tr = targeted_exp.transitions[i]; int group_set_index = group_map[tr.peptide_ref]; - if (precursor_mz_map.find(group_set_index) == precursor_mz_map.end()) + if (!precursor_mz_map.contains(group_set_index)) { precursor_mz_map[group_set_index] = tr.precursor_mz; } - if (precursor_decoy_map.find(group_set_index) == precursor_decoy_map.end()) + if (!precursor_decoy_map.contains(group_set_index)) { if (tr.isDetectingTransition()) { @@ -1314,14 +1314,14 @@ namespace OpenMS for (const auto& prot_ref : compound.protein_refs) { - if (protein_map.find(prot_ref) != protein_map.end()) + if (protein_map.contains(prot_ref)) { peptide_protein_map_vec.emplace_back(peptide_set_index, protein_map[prot_ref]); } } std::string gene_name = compound.gene_name.empty() ? "NA" : compound.gene_name; - if (gene_map.find(gene_name) == gene_map.end()) gene_map[gene_name] = (int)gene_map.size(); + if (!gene_map.contains(gene_name)) gene_map[gene_name] = (int)gene_map.size(); peptide_gene_map_vec.emplace_back(peptide_set_index, gene_map[gene_name]); insert_precursor_sql << diff --git a/src/openms/source/ANALYSIS/OPENSWATH/TransitionParquetFile.cpp b/src/openms/source/ANALYSIS/OPENSWATH/TransitionParquetFile.cpp index a105c420a92..c95ffc656af 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/TransitionParquetFile.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/TransitionParquetFile.cpp @@ -308,7 +308,7 @@ namespace OpenMS for (const auto& accession : info.protein_accessions) { - if (protein_map.find(accession) == protein_map.end()) + if (!protein_map.contains(accession)) { OpenSwath::LightProtein protein; protein.id = accession; @@ -429,7 +429,7 @@ namespace OpenMS std::unordered_set used_precursor_ids; for (const auto& compound : targeted_exp.compounds) { - if (compound_to_precursor.find(compound.id) != compound_to_precursor.end()) + if (compound_to_precursor.contains(compound.id)) { continue; } @@ -448,7 +448,7 @@ namespace OpenMS if (parsed_numeric) { - if (precursor_id <= 0 || used_precursor_ids.find(precursor_id) != used_precursor_ids.end()) + if (precursor_id <= 0 || used_precursor_ids.contains(precursor_id)) { precursor_id = next_precursor_id++; } @@ -472,7 +472,7 @@ namespace OpenMS std::unordered_map precursor_mz; for (const auto& transition : targeted_exp.transitions) { - if (precursor_mz.find(transition.peptide_ref) == precursor_mz.end()) + if (!precursor_mz.contains(transition.peptide_ref)) { precursor_mz[transition.peptide_ref] = transition.precursor_mz; } diff --git a/src/openms/source/ANALYSIS/OPENSWATH/TransitionTSVFile.cpp b/src/openms/source/ANALYSIS/OPENSWATH/TransitionTSVFile.cpp index 3455d0103ab..f000f7ffd08 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/TransitionTSVFile.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/TransitionTSVFile.cpp @@ -290,7 +290,7 @@ namespace OpenMS !extractName(mytransition.rt_calibrated, "RetentionTime", tmp_line, header_dict) && !extractName(mytransition.rt_calibrated, "Tr_recalibrated", tmp_line, header_dict)) { - if (header_dict.find("SpectraSTRetentionTime") != header_dict.end()) + if (header_dict.contains("SpectraSTRetentionTime")) { spectrastRTExtract(tmp_line[header_dict["SpectraSTRetentionTime"]], mytransition.rt_calibrated, spectrast_legacy); } @@ -384,7 +384,7 @@ namespace OpenMS !extractName(mytransition.decoy, "Decoy", tmp_line, header_dict) && !extractName(mytransition.decoy, "IsDecoy", tmp_line, header_dict)); - if (header_dict.find("SpectraSTAnnotation") != header_dict.end()) + if (header_dict.contains("SpectraSTAnnotation")) { skip_transition = spectrastAnnotationExtract(tmp_line[header_dict["SpectraSTAnnotation"]], mytransition); } @@ -498,20 +498,20 @@ namespace OpenMS std::vector all_fragment_annotations; str_inp.split(",", all_fragment_annotations); - if (all_fragment_annotations[0].find("[") == std::string::npos && // non-unique peak annotation - all_fragment_annotations[0].find("]") == std::string::npos && // non-unique peak annotation - all_fragment_annotations[0].find("I") == std::string::npos && // immonium ion - all_fragment_annotations[0].find("p") == std::string::npos && // precursor ion - all_fragment_annotations[0].find("i") == std::string::npos && // isotope ion - all_fragment_annotations[0].find("m") == std::string::npos && - all_fragment_annotations[0].find("?") == std::string::npos + if (!all_fragment_annotations[0].contains("[") && // non-unique peak annotation + !all_fragment_annotations[0].contains("]") && // non-unique peak annotation + !all_fragment_annotations[0].contains("I") && // immonium ion + !all_fragment_annotations[0].contains("p") && // precursor ion + !all_fragment_annotations[0].contains("i") && // isotope ion + !all_fragment_annotations[0].contains("m") && + !all_fragment_annotations[0].contains("?") ) { std::vector best_fragment_annotation_with_deviation; all_fragment_annotations[0].split("/", best_fragment_annotation_with_deviation); String best_fragment_annotation = best_fragment_annotation_with_deviation[0]; - if (best_fragment_annotation.find("^") != std::string::npos) + if (best_fragment_annotation.contains("^")) { std::vector best_fragment_annotation_charge; best_fragment_annotation.split("^", best_fragment_annotation_charge); @@ -523,7 +523,7 @@ namespace OpenMS mytransition.fragment_charge = 1; // assume 1 (most frequent charge state) } - if (best_fragment_annotation.find("-") != std::string::npos) + if (best_fragment_annotation.contains("-")) { std::vector best_fragment_annotation_modification; best_fragment_annotation.split("-", best_fragment_annotation_modification); @@ -532,7 +532,7 @@ namespace OpenMS mytransition.fragment_modification = -1 * String(best_fragment_annotation_modification[1]).toInt(); } - else if (best_fragment_annotation.find("+") != std::string::npos) + else if (best_fragment_annotation.contains("+")) { std::vector best_fragment_annotation_modification; best_fragment_annotation.split("+", best_fragment_annotation_modification); @@ -597,8 +597,8 @@ namespace OpenMS exp.addTransition(rm_trans); // check whether we need a new peptide - if (peptide_map.find(tr_it->group_id) == peptide_map.end() && - compound_map.find(tr_it->group_id) == compound_map.end() ) + if (!peptide_map.contains(tr_it->group_id) && + !compound_map.contains(tr_it->group_id) ) { // should we make a peptide or a compound ? if (tr_it->isPeptide()) @@ -620,7 +620,7 @@ namespace OpenMS // check whether we need new proteins for (size_t i = 0; i < tr_it->ProteinName.size(); ++i) { - if (tr_it->isPeptide() && protein_map.find(tr_it->ProteinName[i]) == protein_map.end()) + if (tr_it->isPeptide() && !protein_map.contains(tr_it->ProteinName[i])) { OpenMS::TargetedExperiment::Protein protein; String protein_name = tr_it->ProteinName[i]; @@ -754,7 +754,7 @@ namespace OpenMS !extractName(mytransition.rt_calibrated, "RetentionTime", tmp_line, header_dict) && !extractName(mytransition.rt_calibrated, "Tr_recalibrated", tmp_line, header_dict)) { - if (header_dict.find("SpectraSTRetentionTime") != header_dict.end()) + if (header_dict.contains("SpectraSTRetentionTime")) { spectrastRTExtract(tmp_line[header_dict["SpectraSTRetentionTime"]], mytransition.rt_calibrated, spectrast_legacy); } @@ -844,7 +844,7 @@ namespace OpenMS !extractName(mytransition.decoy, "Decoy", tmp_line, header_dict) && !extractName(mytransition.decoy, "IsDecoy", tmp_line, header_dict)); - if (header_dict.find("SpectraSTAnnotation") != header_dict.end()) + if (header_dict.contains("SpectraSTAnnotation")) { skip_transition = spectrastAnnotationExtract(tmp_line[header_dict["SpectraSTAnnotation"]], mytransition); } @@ -943,7 +943,7 @@ namespace OpenMS exp.transitions.push_back(std::move(transition)); // --- Create compound if needed --- - if (compound_map.find(mytransition.group_id) == compound_map.end()) + if (!compound_map.contains(mytransition.group_id)) { OpenSwath::LightCompound compound; compound.id = mytransition.group_id; @@ -1013,7 +1013,7 @@ namespace OpenMS // --- Create proteins if needed --- for (Size i = 0; i < mytransition.ProteinName.size(); ++i) { - if (mytransition.isPeptide() && protein_map.find(mytransition.ProteinName[i]) == protein_map.end()) + if (mytransition.isPeptide() && !protein_map.contains(mytransition.ProteinName[i])) { OpenSwath::LightProtein protein; protein.id = mytransition.ProteinName[i]; diff --git a/src/openms/source/ANALYSIS/QUANTITATION/AbsoluteQuantitation.cpp b/src/openms/source/ANALYSIS/QUANTITATION/AbsoluteQuantitation.cpp index 93feedb1057..01deb16470d 100644 --- a/src/openms/source/ANALYSIS/QUANTITATION/AbsoluteQuantitation.cpp +++ b/src/openms/source/ANALYSIS/QUANTITATION/AbsoluteQuantitation.cpp @@ -301,7 +301,7 @@ namespace OpenMS String component_name = (String)unknowns[feature_it].getSubordinates()[sub_it].getMetaValue("native_id"); // apply the calibration curve to components that are in the quant_method - if (quant_methods_.count(component_name)>0) + if (quant_methods_.contains(component_name)) { double calculated_concentration = 0.0; std::map::iterator quant_methods_it = quant_methods_.find(component_name); diff --git a/src/openms/source/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.cpp b/src/openms/source/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.cpp index eabc8a851f5..3e6af9eef7c 100644 --- a/src/openms/source/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.cpp +++ b/src/openms/source/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.cpp @@ -835,7 +835,7 @@ namespace OpenMS ++cl_it) { OPENMS_LOG_INFO << " ch " << String(cl_it->name).fillRight(' ', 4) << " (~" << String(cl_it->center).substr(0, 7).fillRight(' ', 7) << "): "; - if (stats.find(cl_it->name) != stats.end()) + if (stats.contains(cl_it->name)) { // sort double median = Math::median(stats[cl_it->name].mz_deltas.begin(), stats[cl_it->name].mz_deltas.end(), false); diff --git a/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp b/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp index 315d670f9c0..3d2dac5b991 100644 --- a/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp +++ b/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp @@ -218,7 +218,7 @@ namespace OpenMS throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "ItraqConstants: Invalid entry in Param 'channel_active'; key or value is empty ('" + (*it) + "')"); } Int channel = result[0].toInt(); - if (map.find(channel) == map.end()) + if (!map.contains(channel)) { throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "ItraqConstants: Invalid entry in Param 'channel_active'; channel is not valid ('" + String(channel) + "')"); } diff --git a/src/openms/source/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.cpp b/src/openms/source/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.cpp index b36f53a81af..bc83017e91d 100644 --- a/src/openms/source/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.cpp +++ b/src/openms/source/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.cpp @@ -922,7 +922,7 @@ namespace OpenMS if (auto file_level_it = filename_to_channel_map.find(design_filename); file_level_it != filename_to_channel_map.end()) { - if (file_level_it->second.find(0) != file_level_it->second.end()) throw Exception::MissingInformation( + if (file_level_it->second.contains(0)) throw Exception::MissingInformation( __FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, @@ -1301,7 +1301,7 @@ namespace OpenMS const OpenMS::String & hit_accession = hit.getAccession(); const OpenMS::String & hit_sequence = hit.getSequence(); - if (prot_quant_.find(hit_accession) != prot_quant_.end()) + if (prot_quant_.contains(hit_accession)) { if (hit_sequence.empty()) { diff --git a/src/openms/source/ANALYSIS/QUANTITATION/ProteinInference.cpp b/src/openms/source/ANALYSIS/QUANTITATION/ProteinInference.cpp index f99315674fe..0bffc6c0f91 100644 --- a/src/openms/source/ANALYSIS/QUANTITATION/ProteinInference.cpp +++ b/src/openms/source/ANALYSIS/QUANTITATION/ProteinInference.cpp @@ -145,7 +145,7 @@ namespace OpenMS it_file != consensus_map.getColumnHeaders().end(); ++it_file) { - if (ratios.find(it_file->first) != ratios.end()) + if (ratios.contains(it_file->first)) { //sort intensity ratios for map #it_file->first std::sort(ratios[it_file->first].begin(), ratios[it_file->first].end()); diff --git a/src/openms/source/ANALYSIS/TARGETED/DIAChromHandler.cpp b/src/openms/source/ANALYSIS/TARGETED/DIAChromHandler.cpp index 0bc53cca063..e2abe2d3d4e 100644 --- a/src/openms/source/ANALYSIS/TARGETED/DIAChromHandler.cpp +++ b/src/openms/source/ANALYSIS/TARGETED/DIAChromHandler.cpp @@ -86,7 +86,7 @@ std::vector DIAChromHandler::collectIrtChromatogramsForIrt( std::set matching_proteins; for (Size i = 0; i < irt_transitions.compounds.size(); i++) { - if (matching_compounds.find(irt_transitions.compounds[i].id) != matching_compounds.end()) + if (matching_compounds.contains(irt_transitions.compounds[i].id)) { transition_exp_used.compounds.push_back( irt_transitions.compounds[i] ); for (Size j = 0; j < irt_transitions.compounds[i].protein_refs.size(); j++) @@ -97,7 +97,7 @@ std::vector DIAChromHandler::collectIrtChromatogramsForIrt( } for (Size i = 0; i < irt_transitions.proteins.size(); i++) { - if (matching_proteins.find(irt_transitions.proteins[i].id) != matching_proteins.end()) + if (matching_proteins.contains(irt_transitions.proteins[i].id)) { transition_exp_used.proteins.push_back( irt_transitions.proteins[i] ); } diff --git a/src/openms/source/ANALYSIS/TARGETED/MetaboTargetedTargetDecoy.cpp b/src/openms/source/ANALYSIS/TARGETED/MetaboTargetedTargetDecoy.cpp index 33239f0d967..219ebc1f6ac 100644 --- a/src/openms/source/ANALYSIS/TARGETED/MetaboTargetedTargetDecoy.cpp +++ b/src/openms/source/ANALYSIS/TARGETED/MetaboTargetedTargetDecoy.cpp @@ -117,7 +117,7 @@ namespace OpenMS auto found = match_compound_refs_decoy_mz.find(tr.getCompoundRef()); // Check if the compound reference is found and if the product m/z matches any in the set. - if (found != match_compound_refs_decoy_mz.end() && found->second.count(tr.getProductMZ()) > 0) { + if (found != match_compound_refs_decoy_mz.end() && found->second.contains(tr.getProductMZ())) { // Create a new transition object based on the current transition. ReactionMonitoringTransition new_tr = tr; @@ -181,7 +181,7 @@ namespace OpenMS if (it_target != t_exp.getCompounds().end()) { compounds.emplace_back(*it_target); - if (TransitionsMap.find(it_target->id) != TransitionsMap.end()) + if (TransitionsMap.contains(it_target->id)) { transitions.insert(transitions.end(), TransitionsMap[it_target->id].begin(), @@ -191,7 +191,7 @@ namespace OpenMS if (it_decoy != t_exp.getCompounds().end()) { compounds.emplace_back(*it_decoy); - if (TransitionsMap.find(it_decoy->id) != TransitionsMap.end()) + if (TransitionsMap.contains(it_decoy->id)) { transitions.insert(transitions.end(), TransitionsMap[it_decoy->id].begin(), @@ -210,7 +210,7 @@ namespace OpenMS potential_decoy_compound.id = it.decoy_compound_ref; potential_decoy_compound.setMetaValue("decoy", DataValue(1)); - if (TransitionsMap.find(it_target->id) != TransitionsMap.end()) + if (TransitionsMap.contains(it_target->id)) { potential_decoy_transitions = TransitionsMap[it_target->id]; for (size_t i = 0; i < potential_decoy_transitions.size(); ++i) diff --git a/src/openms/source/ANALYSIS/TARGETED/TargetedExperiment.cpp b/src/openms/source/ANALYSIS/TARGETED/TargetedExperiment.cpp index 13f3667c674..f1995cf1e56 100644 --- a/src/openms/source/ANALYSIS/TARGETED/TargetedExperiment.cpp +++ b/src/openms/source/ANALYSIS/TARGETED/TargetedExperiment.cpp @@ -403,7 +403,7 @@ namespace OpenMS { createProteinReferenceMap_(); } - OPENMS_PRECONDITION(protein_reference_map_.find(ref) != protein_reference_map_.end(), "Could not find protein in map") + OPENMS_PRECONDITION(protein_reference_map_.contains(ref), "Could not find protein in map") return *(protein_reference_map_[ref]); } @@ -413,7 +413,7 @@ namespace OpenMS { createProteinReferenceMap_(); } - return protein_reference_map_.find(ref) != protein_reference_map_.end(); + return protein_reference_map_.contains(ref); } void TargetedExperiment::addProtein(const Protein & protein) @@ -480,7 +480,7 @@ namespace OpenMS { createPeptideReferenceMap_(); } - return peptide_reference_map_.find(ref) != peptide_reference_map_.end(); + return peptide_reference_map_.contains(ref); } bool TargetedExperiment::hasCompound(const String & ref) const @@ -489,7 +489,7 @@ namespace OpenMS { createCompoundReferenceMap_(); } - return compound_reference_map_.find(ref) != compound_reference_map_.end(); + return compound_reference_map_.contains(ref); } void TargetedExperiment::addPeptide(const Peptide & rhs) @@ -585,7 +585,7 @@ namespace OpenMS for (ProteinVectorType::const_iterator prot_it = getProteins().begin(); prot_it != getProteins().end(); ++prot_it) { // Create new transition group if it does not yet exist - if (unique_protein_map.find(prot_it->id) != unique_protein_map.end()) + if (unique_protein_map.contains(prot_it->id)) { OPENMS_LOG_ERROR << "Found duplicate protein id (must be unique): " + String(prot_it->id) << std::endl; return true; @@ -598,7 +598,7 @@ namespace OpenMS for (PeptideVectorType::const_iterator pep_it = getPeptides().begin(); pep_it != getPeptides().end(); ++pep_it) { // Create new transition group if it does not yet exist - if (unique_peptide_map.find(pep_it->id) != unique_peptide_map.end()) + if (unique_peptide_map.contains(pep_it->id)) { OPENMS_LOG_ERROR << "Found duplicate peptide id (must be unique): " + String(pep_it->id) << std::endl; return true; @@ -611,7 +611,7 @@ namespace OpenMS for (CompoundVectorType::const_iterator comp_it = getCompounds().begin(); comp_it != getCompounds().end(); ++comp_it) { // Create new transition group if it does not yet exist - if (unique_compounds_map.find(comp_it->id) != unique_compounds_map.end()) + if (unique_compounds_map.contains(comp_it->id)) { OPENMS_LOG_ERROR << "Found duplicate compound id (must be unique): " + String(comp_it->id) << std::endl; return true; @@ -624,7 +624,7 @@ namespace OpenMS for (TransitionVectorType::const_iterator tr_it = getTransitions().begin(); tr_it != getTransitions().end(); ++tr_it) { // Create new transition group if it does not yet exist - if (unique_transition_map.find(tr_it->getNativeID()) != unique_transition_map.end()) + if (unique_transition_map.contains(tr_it->getNativeID())) { OPENMS_LOG_ERROR << "Found duplicate transition id (must be unique): " + String(tr_it->getNativeID()) << std::endl; return true; @@ -637,7 +637,7 @@ namespace OpenMS { for (std::vector::const_iterator prot_it = getPeptides()[i].protein_refs.begin(); prot_it != getPeptides()[i].protein_refs.end(); ++prot_it) { - if (unique_protein_map.find(*prot_it) == unique_protein_map.end()) + if (!unique_protein_map.contains(*prot_it)) { OPENMS_LOG_ERROR << "Protein " << *prot_it << " is not present in the provided data structure." << std::endl; return true; @@ -651,7 +651,7 @@ namespace OpenMS const ReactionMonitoringTransition& tr = getTransitions()[i]; if (!tr.getPeptideRef().empty()) { - if (unique_peptide_map.find(tr.getPeptideRef()) == unique_peptide_map.end()) + if (!unique_peptide_map.contains(tr.getPeptideRef())) { OPENMS_LOG_ERROR << "Peptide " << tr.getPeptideRef() << " is not present in the provided data structure." << std::endl; return true; @@ -659,7 +659,7 @@ namespace OpenMS } else if (!tr.getCompoundRef().empty()) { - if (unique_compounds_map.find(tr.getCompoundRef()) == unique_compounds_map.end()) + if (!unique_compounds_map.contains(tr.getCompoundRef())) { OPENMS_LOG_ERROR << "Compound " << tr.getPeptideRef() << " is not present in the provided data structure." << std::endl; return true; diff --git a/src/openms/source/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.cpp b/src/openms/source/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.cpp index 30350996b45..3711edd1e2b 100644 --- a/src/openms/source/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.cpp +++ b/src/openms/source/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.cpp @@ -123,7 +123,7 @@ namespace OpenMS { for (const auto& p : spec_) { - if (deconvolved_mzs.find(p.getMZ()) != deconvolved_mzs.end()) // if p is deconvolved + if (deconvolved_mzs.contains(p.getMZ())) // if p is deconvolved { continue; } diff --git a/src/openms/source/ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.cpp b/src/openms/source/ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.cpp index 39790f51ba0..b1f382ed22e 100644 --- a/src/openms/source/ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.cpp @@ -187,7 +187,7 @@ void FLASHDeconvAlgorithm::mergeSpectra_(MSExperiment& map, uint ms_level) const auto& native_id = spec.getNativeID(); original_precursor_map[native_id] = spec.getPrecursors(); - if (! spec.getPrecursors().empty() && native_id_precursor_peak_group_map_.find(native_id) != native_id_precursor_peak_group_map_.end()) + if (! spec.getPrecursors().empty() && native_id_precursor_peak_group_map_.contains(native_id)) { auto precursor_pg = native_id_precursor_peak_group_map_[native_id]; auto precursor = spec.getPrecursors()[0]; @@ -213,7 +213,7 @@ void FLASHDeconvAlgorithm::mergeSpectra_(MSExperiment& map, uint ms_level) for (auto& native_id : native_ids) { - if (original_precursor_map.find(native_id) == original_precursor_map.end()) continue; + if (!original_precursor_map.contains(native_id)) continue; mspec.setPrecursors(original_precursor_map[native_id]); } } @@ -316,7 +316,7 @@ void FLASHDeconvAlgorithm::runSpectralDeconvolution_(MSExperiment& map, std::vec for (Size index = 0; index < map.size(); index++) { int scan_number = merge_spec_ == 0 ? getScanNumber(map, index) : - (rt_scan_map.find(map[index].getRT()) == rt_scan_map.end() ? getScanNumber(map, index) : + (!rt_scan_map.contains(map[index].getRT()) ? getScanNumber(map, index) : rt_scan_map[map[index].getRT()]); const auto& spec = map[index]; @@ -326,7 +326,7 @@ void FLASHDeconvAlgorithm::runSpectralDeconvolution_(MSExperiment& map, std::vec String native_id = spec.getNativeID(); PeakGroup precursor_pg; - if (native_id_precursor_peak_group_map_.find(native_id) != native_id_precursor_peak_group_map_.end()) + if (native_id_precursor_peak_group_map_.contains(native_id)) { precursor_pg = native_id_precursor_peak_group_map_[native_id]; } @@ -660,7 +660,7 @@ void FLASHDeconvAlgorithm::updatePrecursorQScores_(std::vector 0 && used_feature_indices.find(pg.getFeatureIndex()) != used_feature_indices.end()) + if (pg.getFeatureIndex() > 0 && used_feature_indices.contains(pg.getFeatureIndex())) continue; used_feature_indices.insert(pg.getFeatureIndex()); diff --git a/src/openms/source/ANALYSIS/TOPDOWN/SpectralDeconvolution.cpp b/src/openms/source/ANALYSIS/TOPDOWN/SpectralDeconvolution.cpp index 3da24ae8d27..f5952dae85a 100644 --- a/src/openms/source/ANALYSIS/TOPDOWN/SpectralDeconvolution.cpp +++ b/src/openms/source/ANALYSIS/TOPDOWN/SpectralDeconvolution.cpp @@ -142,7 +142,7 @@ namespace OpenMS for (const auto& p : spec) { - if (signal_mzs.find(p.getMZ()) != signal_mzs.end()) { continue; } + if (signal_mzs.contains(p.getMZ())) { continue; } nspec.push_back(p); } deconvolved_spectrum_.setOriginalSpectrum(nspec); @@ -1185,7 +1185,7 @@ namespace OpenMS { auto& pg = deconvolved_spectrum_[k]; - if (!indices.empty() && (indices.find(k) == indices.end())) + if (!indices.empty() && (!indices.contains(k))) { continue; } diff --git a/src/openms/source/ANALYSIS/TOPDOWN/TopDownIsobaricQuantification.cpp b/src/openms/source/ANALYSIS/TOPDOWN/TopDownIsobaricQuantification.cpp index c0a7811b688..4f530fe9905 100644 --- a/src/openms/source/ANALYSIS/TOPDOWN/TopDownIsobaricQuantification.cpp +++ b/src/openms/source/ANALYSIS/TOPDOWN/TopDownIsobaricQuantification.cpp @@ -155,7 +155,7 @@ TopDownIsobaricQuantification::TopDownIsobaricQuantification() : DefaultParamHan if (abs(trt.first - p.getRT()) > .01) continue; int scan = trt.second; - if (scan_precursors_map.find(scan) == scan_precursors_map.end()) + if (!scan_precursors_map.contains(scan)) continue; for (auto& pg : scan_precursors_map[scan]) { @@ -183,7 +183,7 @@ TopDownIsobaricQuantification::TopDownIsobaricQuantification() : DefaultParamHan continue; } auto& precursor = dspec.getPrecursorPeakGroup(); - if (precursor.empty() || precursor_cluster_index.find(precursor) != precursor_cluster_index.end()) + if (precursor.empty() || precursor_cluster_index.contains(precursor)) continue; precursor_clusters.push_back(std::vector {precursor}); precursor_cluster_index[precursor] = (int)precursor_clusters.size() - 1; @@ -226,9 +226,9 @@ TopDownIsobaricQuantification::TopDownIsobaricQuantification() : DefaultParamHan std::vector intensities (0); for (int ms2_scan : precursor_scan_ms2_scans[ms2_scan_precursor_scan[scan]]) { - if (ms2_ints.find(ms2_scan) == ms2_ints.end() || ms2_ints[ms2_scan].empty()) + if (!ms2_ints.contains(ms2_scan) || ms2_ints[ms2_scan].empty()) continue; - if (ms2_scan_precursor_mz.find(ms2_scan) == ms2_scan_precursor_mz.end() || abs(ms2_scan_precursor_mz[ms2_scan] - pre_mz) > .01) + if (!ms2_scan_precursor_mz.contains(ms2_scan) || abs(ms2_scan_precursor_mz[ms2_scan] - pre_mz) > .01) continue; if (intensities.empty()) { diff --git a/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp b/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp index 47fc564a98f..3e3f2a49092 100644 --- a/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp +++ b/src/openms/source/ANALYSIS/XLMS/OPXLHelper.cpp @@ -306,7 +306,7 @@ namespace OpenMS bool already_processed = false; - if (processed_peptides.find(*cit) != processed_peptides.end()) + if (processed_peptides.contains(*cit)) { // peptide (and all modified variants) already processed so skip it already_processed = true; @@ -1144,7 +1144,7 @@ namespace OpenMS PeptideHit& hit = id.getHits()[0]; PeptideIdentification new_id; String current_spectrum = id.getMetaValue(Constants::UserParam::SPECTRUM_REFERENCE); - if (new_peptide_ids.find(current_spectrum) != new_peptide_ids.end()) + if (new_peptide_ids.contains(current_spectrum)) { new_id = (*new_peptide_ids.find(current_spectrum)).second; } diff --git a/src/openms/source/ANALYSIS/XLMS/XFDRAlgorithm.cpp b/src/openms/source/ANALYSIS/XLMS/XFDRAlgorithm.cpp index bd355950b1a..378b1c93d8d 100644 --- a/src/openms/source/ANALYSIS/XLMS/XFDRAlgorithm.cpp +++ b/src/openms/source/ANALYSIS/XLMS/XFDRAlgorithm.cpp @@ -341,7 +341,7 @@ using namespace OpenMS; String id = getId_(ph); ph.setMetaValue("OpenPepXL:id", id); // candidates with the same ID will also have the same types - if (this->cross_link_classes_.find(id) == this->cross_link_classes_.end()) + if (!this->cross_link_classes_.contains(id)) { assignTypes_(ph, this->cross_link_classes_[id]); } @@ -449,9 +449,9 @@ using namespace OpenMS; std::vector< double > & fdr, bool mono) const { // Determine whether targetclass, decoyclass, and fulldecoyclass are present in the histogram map - bool targetclass_present = cum_histograms.find(targetclass) != cum_histograms.end(); - bool decoyclass_present = cum_histograms.find(decoyclass) != cum_histograms.end(); - bool fulldecoyclass_present = cum_histograms.find(fulldecoyclass) != cum_histograms.end(); + bool targetclass_present = cum_histograms.contains(targetclass); + bool decoyclass_present = cum_histograms.contains(decoyclass); + bool fulldecoyclass_present = cum_histograms.contains(fulldecoyclass); for (double current_score = this->min_score_ + (arg_binsize_/2); current_score <= this->max_score_ - (arg_binsize_/2); diff --git a/src/openms/source/APPLICATIONS/INIUpdater.cpp b/src/openms/source/APPLICATIONS/INIUpdater.cpp index 78d3f4d20bf..219cf2dba3d 100644 --- a/src/openms/source/APPLICATIONS/INIUpdater.cpp +++ b/src/openms/source/APPLICATIONS/INIUpdater.cpp @@ -70,7 +70,7 @@ namespace OpenMS new_name = ""; // try with type (as some new tools for one type might have the exact same name as old ones with several types) TDE old_withtype(old_name, ListUtils::create(tools_type)); - if (map_.find(old_withtype) != map_.end()) + if (map_.contains(old_withtype)) { new_name = map_[old_withtype].name; return true; @@ -78,7 +78,7 @@ namespace OpenMS // try without type TDE old_notype(old_name, StringList()); - if (map_.find(old_notype) != map_.end()) + if (map_.contains(old_notype)) { new_name = map_[old_notype].name; return true; @@ -86,7 +86,7 @@ namespace OpenMS // default to ToolHandler const auto& topp = ToolHandler::getTOPPToolList(); - if (topp.find(old_name) != topp.end()) + if (topp.contains(old_name)) { new_name = old_name; return true; diff --git a/src/openms/source/APPLICATIONS/OpenSwathBase.cpp b/src/openms/source/APPLICATIONS/OpenSwathBase.cpp index d5c19a20868..b43b4e9aba5 100644 --- a/src/openms/source/APPLICATIONS/OpenSwathBase.cpp +++ b/src/openms/source/APPLICATIONS/OpenSwathBase.cpp @@ -46,9 +46,9 @@ namespace OpenMS for (const auto& arr : spectrum->getDataArrays()) { // Check for CCS CV term (MS:1002954) or square angstrom unit (UO:0000324) - if (arr->description.find("MS:1002954") != std::string::npos || - arr->description.find("UO:0000324") != std::string::npos || - arr->description.find("collision cross section") != std::string::npos) + if (arr->description.contains("MS:1002954") || + arr->description.contains("UO:0000324") || + arr->description.contains("collision cross section")) { OPENMS_LOG_WARN << "Warning: Ion mobility data appears to be in CCS (Collisional Cross Section) format. " << "OpenSwath expects ion mobility in 1/K0 (inverse reduced ion mobility) units. " diff --git a/src/openms/source/APPLICATIONS/TOPPBase.cpp b/src/openms/source/APPLICATIONS/TOPPBase.cpp index 3d112b3d1b3..d9e2f4cfe16 100755 --- a/src/openms/source/APPLICATIONS/TOPPBase.cpp +++ b/src/openms/source/APPLICATIONS/TOPPBase.cpp @@ -958,7 +958,7 @@ namespace OpenMS { String full_name = it.getName(); String subsection = getSubsection_(full_name); - if (!subsection.empty() && (subsections_TOPP_.count(subsection) == 0)) + if (!subsection.empty() && (!subsections_TOPP_.contains(subsection))) { subsections_TOPP_[subsection] = param.getSectionDescription(subsection); } @@ -1887,10 +1887,10 @@ namespace OpenMS { // subsections (do not check content, but warn if not registered) String subsection = getSubsection_(it.getName()); - if (!subsection.empty() && subsections_TOPP_.count(subsection) == 0) // not found in TOPP subsections + if (!subsection.empty() && !subsections_TOPP_.contains(subsection)) // not found in TOPP subsections { // for multi-level subsections, check only the first level: - if (subsections_.count(subsection.substr(0, subsection.find(':'))) == 0) // not found in normal subsections + if (!subsections_.contains(subsection.substr(0, subsection.find(':')))) // not found in normal subsections { if (!(location == "common::" && subsection == tool_name_)) { diff --git a/src/openms/source/APPLICATIONS/ToolHandler.cpp b/src/openms/source/APPLICATIONS/ToolHandler.cpp index ad664c152e2..ee43546fe84 100644 --- a/src/openms/source/APPLICATIONS/ToolHandler.cpp +++ b/src/openms/source/APPLICATIONS/ToolHandler.cpp @@ -213,7 +213,7 @@ namespace OpenMS std::vector internal_tools = getInternalTools_(); for (std::vector::const_iterator it = internal_tools.begin(); it != internal_tools.end(); ++it) { - if (tools_map.find(it->name) == tools_map.end()) + if (!tools_map.contains(it->name)) { tools_map[it->name] = *it; } @@ -230,7 +230,7 @@ namespace OpenMS { Internal::ToolDescription ret; ToolListType tools = getTOPPToolList(); - if (tools.find(toolname) != tools.end()) + if (tools.contains(toolname)) { return tools[toolname].types; } @@ -304,7 +304,7 @@ namespace OpenMS { ToolListType tools = getTOPPToolList(); String s; - if (tools.find(toolname) != tools.end()) + if (tools.contains(toolname)) { s = tools[toolname].category; } diff --git a/src/openms/source/CHEMISTRY/ElementDB.cpp b/src/openms/source/CHEMISTRY/ElementDB.cpp index 0ae744b3700..8837ceade1d 100644 --- a/src/openms/source/CHEMISTRY/ElementDB.cpp +++ b/src/openms/source/CHEMISTRY/ElementDB.cpp @@ -79,12 +79,12 @@ namespace OpenMS bool ElementDB::hasElement(const string& name) const { - return (names_.find(name) != names_.end()) || (symbols_.find(name) != symbols_.end()); + return (names_.contains(name)) || (symbols_.contains(name)); } bool ElementDB::hasElement(unsigned int atomic_number) const { - return atomic_numbers_.find(atomic_number) != atomic_numbers_.end(); + return atomic_numbers_.contains(atomic_number); } double ElementDB::calculateAvgWeight_(const map& abundance, const map& mass) @@ -614,7 +614,7 @@ namespace OpenMS { // overwrite existing element if it already exists // find() has to be protected here in a parallel context - if (atomic_numbers_.find(an) != atomic_numbers_.end()) + if (atomic_numbers_.contains(an)) { // in order to ensure that existing elements are still valid and memory // addresses do not change, we have to modify the Element in place diff --git a/src/openms/source/CHEMISTRY/EmpiricalFormula.cpp b/src/openms/source/CHEMISTRY/EmpiricalFormula.cpp index 69b864f1ce3..501916ea31e 100644 --- a/src/openms/source/CHEMISTRY/EmpiricalFormula.cpp +++ b/src/openms/source/CHEMISTRY/EmpiricalFormula.cpp @@ -369,7 +369,7 @@ namespace OpenMS bool EmpiricalFormula::hasElement(const Element* element) const { - return formula_.find(element) != formula_.end(); + return formula_.contains(element); } bool EmpiricalFormula::contains(const EmpiricalFormula& ef) const diff --git a/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetTextParser.cpp b/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetTextParser.cpp index 794fac74fab..bb597369e1a 100644 --- a/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetTextParser.cpp +++ b/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetTextParser.cpp @@ -31,7 +31,7 @@ void OpenMS::ims::IMSAlphabetTextParser::parse(std::istream & is) while (std::getline(is, line)) { std::string::size_type i = line.find_first_not_of(delimits); - if (i == std::string::npos || comments.find(line[i]) != std::string::npos) + if (i == std::string::npos || comments.contains(line[i])) { continue; // skip comment lines } diff --git a/src/openms/source/CHEMISTRY/ModificationDefinitionsSet.cpp b/src/openms/source/CHEMISTRY/ModificationDefinitionsSet.cpp index afa72e0507a..62ca437e899 100644 --- a/src/openms/source/CHEMISTRY/ModificationDefinitionsSet.cpp +++ b/src/openms/source/CHEMISTRY/ModificationDefinitionsSet.cpp @@ -232,8 +232,8 @@ namespace OpenMS if (it->isModified()) { String mod = it->getModification()->getFullId(); - if (var_names.find(mod) == var_names.end() && - fixed_names.find(mod) == fixed_names.end()) + if (!var_names.contains(mod) && + !fixed_names.contains(mod)) { return false; } @@ -243,8 +243,8 @@ namespace OpenMS if (peptide.hasNTerminalModification()) { String mod = peptide.getNTerminalModification()->getFullId(); - if (var_names.find(mod) == var_names.end() && - fixed_names.find(mod) == fixed_names.end()) + if (!var_names.contains(mod) && + !fixed_names.contains(mod)) { return false; } @@ -253,8 +253,8 @@ namespace OpenMS if (peptide.hasCTerminalModification()) { String mod = peptide.getCTerminalModification()->getFullId(); - if (var_names.find(mod) == var_names.end() && - fixed_names.find(mod) == fixed_names.end()) + if (!var_names.contains(mod) && + !fixed_names.contains(mod)) { return false; } diff --git a/src/openms/source/CHEMISTRY/ModificationsDB.cpp b/src/openms/source/CHEMISTRY/ModificationsDB.cpp index 06553f1f07a..bcad51b0945 100644 --- a/src/openms/source/CHEMISTRY/ModificationsDB.cpp +++ b/src/openms/source/CHEMISTRY/ModificationsDB.cpp @@ -289,7 +289,7 @@ namespace OpenMS bool has_mod; #pragma omp critical(OpenMS_ModificationsDB) { - has_mod = (modification_names_.find(modification) != modification_names_.end()); + has_mod = (modification_names_.contains(modification)); } return has_mod; } diff --git a/src/openms/source/CHEMISTRY/ModomicsJSONDataProvider.cpp b/src/openms/source/CHEMISTRY/ModomicsJSONDataProvider.cpp index 19e4b6394a9..d50dc1e2ea2 100644 --- a/src/openms/source/CHEMISTRY/ModomicsJSONDataProvider.cpp +++ b/src/openms/source/CHEMISTRY/ModomicsJSONDataProvider.cpp @@ -58,25 +58,25 @@ namespace OpenMS // @throw Exception::MissingInformation if some of the required info for the entry is missing void entryIsWellFormed_(const nlohmann::json::value_type& entry) { - if (entry.find("name") == entry.cend()) + if (!entry.contains("name")) { String msg = "\"name\" entry missing for ribonucleotide"; throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, msg); } - if (entry.find("short_name") == entry.cend()) + if (!entry.contains("short_name")) { String msg = "\"short_name\" entry missing for ribonucleotide"; throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, msg); } - if (entry.find("reference_moiety") == entry.cend()) + if (!entry.contains("reference_moiety")) { String msg = "\"reference_moiety\" entry missing for ribonucleotide"; throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, msg); } - if (entry.find("formula") == entry.cend()) + if (!entry.contains("formula")) { String msg = "\"formula\" entry missing for ribonucleotide"; throw Exception::MissingInformation(__FILE__, __LINE__, @@ -165,7 +165,7 @@ namespace OpenMS OPENMS_PRETTY_FUNCTION, msg, entry["reference_moiety"].dump()); } - if (entry.find("abbrev") != entry.cend()) + if (entry.contains("abbrev")) { ribo->setHTMLCode(entry.at("abbrev").get()); //This is the single letter unicode representation that only SOME mods have } diff --git a/src/openms/source/CHEMISTRY/MonosaccharideDB.cpp b/src/openms/source/CHEMISTRY/MonosaccharideDB.cpp index 018e12f06db..fd9f18189a3 100644 --- a/src/openms/source/CHEMISTRY/MonosaccharideDB.cpp +++ b/src/openms/source/CHEMISTRY/MonosaccharideDB.cpp @@ -121,7 +121,7 @@ namespace OpenMS bool MonosaccharideDB::hasSymbol(const String& symbol) const { - return synonym_to_symbol_.find(symbol) != synonym_to_symbol_.end(); + return synonym_to_symbol_.contains(symbol); } const MonosaccharideDB::Monosaccharide* MonosaccharideDB::getMonosaccharide(const String& symbol) const diff --git a/src/openms/source/CHEMISTRY/ProForma.cpp b/src/openms/source/CHEMISTRY/ProForma.cpp index a19e71d82db..f7bea49e19f 100644 --- a/src/openms/source/CHEMISTRY/ProForma.cpp +++ b/src/openms/source/CHEMISTRY/ProForma.cpp @@ -1705,7 +1705,7 @@ namespace const auto& label = mod.alternatives[0].second.value(); if (label.type == Label::Type::CROSSLINK) { - if (counted_crosslinks.count(label.identifier) > 0) return; + if (counted_crosslinks.contains(label.identifier)) return; counted_crosslinks.insert(label.identifier); } } @@ -2445,14 +2445,14 @@ MSSpectrum ProForma::generateSpectrum( TheoreticalSpectrumGenerator generator; Param param = generator.getParameters(); - param.setValue("add_a_ions", ion_types.find('a') != std::string::npos ? "true" : "false"); - param.setValue("add_b_ions", ion_types.find('b') != std::string::npos ? "true" : "false"); - param.setValue("add_c_ions", ion_types.find('c') != std::string::npos ? "true" : "false"); - param.setValue("add_x_ions", ion_types.find('x') != std::string::npos ? "true" : "false"); - param.setValue("add_y_ions", ion_types.find('y') != std::string::npos ? "true" : "false"); - param.setValue("add_z_ions", ion_types.find('z') != std::string::npos ? "true" : "false"); - param.setValue("add_precursor_peaks", ion_types.find('M') != std::string::npos ? "true" : "false"); - param.setValue("add_abundant_immonium_ions", ion_types.find('I') != std::string::npos ? "true" : "false"); + param.setValue("add_a_ions", ion_types.contains('a') ? "true" : "false"); + param.setValue("add_b_ions", ion_types.contains('b') ? "true" : "false"); + param.setValue("add_c_ions", ion_types.contains('c') ? "true" : "false"); + param.setValue("add_x_ions", ion_types.contains('x') ? "true" : "false"); + param.setValue("add_y_ions", ion_types.contains('y') ? "true" : "false"); + param.setValue("add_z_ions", ion_types.contains('z') ? "true" : "false"); + param.setValue("add_precursor_peaks", ion_types.contains('M') ? "true" : "false"); + param.setValue("add_abundant_immonium_ions", ion_types.contains('I') ? "true" : "false"); param.setValue("add_losses", add_losses ? "true" : "false"); param.setValue("add_metainfo", add_metainfo ? "true" : "false"); generator.setParameters(param); @@ -2501,13 +2501,13 @@ MSSpectrum ProForma::generateSpectrum( TheoreticalSpectrumGeneratorXLMS generator; Param param = generator.getParameters(); - param.setValue("add_a_ions", ion_types.find('a') != std::string::npos ? "true" : "false"); - param.setValue("add_b_ions", ion_types.find('b') != std::string::npos ? "true" : "false"); - param.setValue("add_c_ions", ion_types.find('c') != std::string::npos ? "true" : "false"); - param.setValue("add_x_ions", ion_types.find('x') != std::string::npos ? "true" : "false"); - param.setValue("add_y_ions", ion_types.find('y') != std::string::npos ? "true" : "false"); - param.setValue("add_z_ions", ion_types.find('z') != std::string::npos ? "true" : "false"); - param.setValue("add_precursor_peaks", ion_types.find('M') != std::string::npos ? "true" : "false"); + param.setValue("add_a_ions", ion_types.contains('a') ? "true" : "false"); + param.setValue("add_b_ions", ion_types.contains('b') ? "true" : "false"); + param.setValue("add_c_ions", ion_types.contains('c') ? "true" : "false"); + param.setValue("add_x_ions", ion_types.contains('x') ? "true" : "false"); + param.setValue("add_y_ions", ion_types.contains('y') ? "true" : "false"); + param.setValue("add_z_ions", ion_types.contains('z') ? "true" : "false"); + param.setValue("add_precursor_peaks", ion_types.contains('M') ? "true" : "false"); param.setValue("add_losses", add_losses ? "true" : "false"); param.setValue("add_metainfo", add_metainfo ? "true" : "false"); generator.setParameters(param); diff --git a/src/openms/source/CHEMISTRY/Residue.cpp b/src/openms/source/CHEMISTRY/Residue.cpp index 920ef842ce0..6d1a33ff4d7 100644 --- a/src/openms/source/CHEMISTRY/Residue.cpp +++ b/src/openms/source/CHEMISTRY/Residue.cpp @@ -584,7 +584,7 @@ namespace OpenMS bool Residue::isInResidueSet(const String& residue_set) { - return residue_sets_.find(residue_set) != residue_sets_.end(); + return residue_sets_.contains(residue_set); } std::string Residue::residueTypeToIonLetter(const Residue::ResidueType& res_type) diff --git a/src/openms/source/CHEMISTRY/ResidueDB.cpp b/src/openms/source/CHEMISTRY/ResidueDB.cpp index cbfaa75fd7b..8abe21a0558 100644 --- a/src/openms/source/CHEMISTRY/ResidueDB.cpp +++ b/src/openms/source/CHEMISTRY/ResidueDB.cpp @@ -125,7 +125,7 @@ namespace OpenMS bool found = false; #pragma omp critical (ResidueDB) { - found = residue_names_.find(res_name) != residue_names_.end(); + found = residue_names_.contains(res_name); } return found; } @@ -135,8 +135,8 @@ namespace OpenMS bool found = false; #pragma omp critical (ResidueDB) { - found = (const_residues_.find(residue) != const_residues_.end() || - const_modified_residues_.find(residue) != const_modified_residues_.end()); + found = (const_residues_.contains(residue) || + const_modified_residues_.contains(residue)); } return found; } @@ -366,7 +366,7 @@ namespace OpenMS const auto& rm_entry = residue_mod_names_.find(res_name); if (rm_entry == residue_mod_names_.end()) { - if (residue_names_.find(res_name) == residue_names_.end()) + if (!residue_names_.contains(res_name)) { residue_found = false; } @@ -469,7 +469,7 @@ namespace OpenMS const auto& rm_entry = residue_mod_names_.find(res_name); if (rm_entry == residue_mod_names_.end()) { - if (residue_names_.find(res_name) == residue_names_.end()) + if (!residue_names_.contains(res_name)) { residue_found = false; } diff --git a/src/openms/source/COMPARISON/SpectrumCheapDPCorr.cpp b/src/openms/source/COMPARISON/SpectrumCheapDPCorr.cpp index edd6664daef..8a14c3aba40 100644 --- a/src/openms/source/COMPARISON/SpectrumCheapDPCorr.cpp +++ b/src/openms/source/COMPARISON/SpectrumCheapDPCorr.cpp @@ -178,7 +178,7 @@ namespace OpenMS consensuspeak.setIntensity((xit->getIntensity() * (1 - factor_) + yit->getIntensity() * factor_)); lastconsensus_.push_back(consensuspeak); - if (!(peak_map_.find(xit - x.begin()) != peak_map_.end())) + if (!(peak_map_.contains(xit - x.begin()))) { peak_map_[xit - x.begin()] = yit - y.begin(); } @@ -256,7 +256,7 @@ namespace OpenMS consensuspeak.setMZ((y[ystart + j - 1].getMZ() * (1 - factor_) + x[xstart + i - 1].getMZ() * factor_)); consensuspeak.setIntensity((y[ystart + j - 1].getIntensity() * (1 - factor_) + x[xstart + i - 1].getIntensity() * factor_)); lastconsensus_.push_back(consensuspeak); - if (!(peak_map_.find(xstart + i - 1) != peak_map_.end())) + if (!(peak_map_.contains(xstart + i - 1))) { peak_map_[xstart + i - 1] = ystart + j - 1; } diff --git a/src/openms/source/CONCEPT/FuzzyStringComparator.cpp b/src/openms/source/CONCEPT/FuzzyStringComparator.cpp index 595aa914e83..3edc1513c36 100644 --- a/src/openms/source/CONCEPT/FuzzyStringComparator.cpp +++ b/src/openms/source/CONCEPT/FuzzyStringComparator.cpp @@ -280,8 +280,8 @@ namespace OpenMS for (StringList::const_iterator slit = whitelist_.begin(); slit != whitelist_.end(); ++slit) { - if (line_str_1.find(*slit) != String::npos && - line_str_2.find(*slit) != String::npos) + if (line_str_1.contains(*slit) && + line_str_2.contains(*slit)) { ++whitelist_cases_[*slit]; // *log_dest_ << "whitelist_ case: " << *slit << '\n'; @@ -294,11 +294,11 @@ namespace OpenMS for (std::vector< std::pair >::const_iterator pair_it = matched_whitelist_.begin(); pair_it != matched_whitelist_.end(); ++pair_it) { - if ((line_str_1.find(pair_it->first) != String::npos && - line_str_2.find(pair_it->second) != String::npos + if ((line_str_1.contains(pair_it->first) && + line_str_2.contains(pair_it->second) ) || - (line_str_1.find(pair_it->second) != String::npos && - line_str_2.find(pair_it->first) != String::npos + (line_str_1.contains(pair_it->second) && + line_str_2.contains(pair_it->first) ) ) { diff --git a/src/openms/source/CONCEPT/LogStream.cpp b/src/openms/source/CONCEPT/LogStream.cpp index 48e22c1dace..56b62ee3bbe 100644 --- a/src/openms/source/CONCEPT/LogStream.cpp +++ b/src/openms/source/CONCEPT/LogStream.cpp @@ -144,7 +144,7 @@ namespace OpenMS bool LogStreamBuf::isInCache_(std::string const & line) { //cout << "LogCache (count)" << log_cache_.count(line) << endl; - if (log_cache_.count(line) == 0) + if (!log_cache_.contains(line)) { return false; } diff --git a/src/openms/source/CONCEPT/StreamHandler.cpp b/src/openms/source/CONCEPT/StreamHandler.cpp index 2cea8817d1a..aba6dde2ed1 100644 --- a/src/openms/source/CONCEPT/StreamHandler.cpp +++ b/src/openms/source/CONCEPT/StreamHandler.cpp @@ -83,7 +83,7 @@ namespace OpenMS { Int state = 1; - if (name_to_stream_map_.count(stream_name) == 0) // this is an unknown stream .. register + if (!name_to_stream_map_.contains(stream_name)) // this is an unknown stream .. register { name_to_stream_map_[stream_name] = createStream_(type, stream_name); name_to_type_map_[stream_name] = type; @@ -110,7 +110,7 @@ namespace OpenMS bool StreamHandler::hasStream(const StreamType type, const String & stream_name) { - if (name_to_stream_map_.count(stream_name) != 0) + if (name_to_stream_map_.contains(stream_name)) { return name_to_type_map_[stream_name] == type; } @@ -122,7 +122,7 @@ namespace OpenMS void StreamHandler::unregisterStream(StreamType const type, const String & stream_name) { - if (name_to_stream_map_.count(stream_name) != 0) // check if we know this stream + if (name_to_stream_map_.contains(stream_name)) // check if we know this stream { if (name_to_counter_map_[stream_name] > 1) { diff --git a/src/openms/source/DATASTRUCTURES/CVMappings.cpp b/src/openms/source/DATASTRUCTURES/CVMappings.cpp index e77eb711083..44c0a969673 100644 --- a/src/openms/source/DATASTRUCTURES/CVMappings.cpp +++ b/src/openms/source/DATASTRUCTURES/CVMappings.cpp @@ -92,7 +92,7 @@ namespace OpenMS bool CVMappings::hasCVReference(const String& identifier) { - return cv_references_.find(identifier) != cv_references_.end(); + return cv_references_.contains(identifier); } } // namespace OpenMS diff --git a/src/openms/source/DATASTRUCTURES/Compomer.cpp b/src/openms/source/DATASTRUCTURES/Compomer.cpp index bb4cd02abbe..5000b9b3764 100644 --- a/src/openms/source/DATASTRUCTURES/Compomer.cpp +++ b/src/openms/source/DATASTRUCTURES/Compomer.cpp @@ -82,7 +82,7 @@ namespace OpenMS // std::cerr << "Compomer::add() was given adduct with negative charge! Are you sure this is what you want?!\n"; //} - if (cmp_[side].count(a.getFormula()) == 0) + if (!cmp_[side].contains(a.getFormula())) { cmp_[side][a.getFormula()] = a; } @@ -231,7 +231,7 @@ namespace OpenMS { return false; } - if (cmp_[side].count(a.getFormula()) == 0) + if (!cmp_[side].contains(a.getFormula())) { return false; } @@ -252,7 +252,7 @@ namespace OpenMS throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Compomer::removeAdduct() does not support this value for 'side'!", String(side)); } Compomer tmp(*this); - if (tmp.cmp_[side].count(a.getFormula()) > 0) + if (tmp.cmp_[side].contains(a.getFormula())) { { // how many instances does this side contain? Int amount = tmp.cmp_[side][a.getFormula()].getAmount(); diff --git a/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp b/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp index 6ee303c2e15..147f18a24b7 100644 --- a/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp +++ b/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp @@ -45,7 +45,7 @@ namespace OpenMS //different points now => return false for (const auto& point_pair : rhs.map_points_) { - if (map_points_.find(point_pair.first) != map_points_.end()) + if (map_points_.contains(point_pair.first)) { if (map_points_.at(point_pair.first) != point_pair.second) { @@ -162,7 +162,7 @@ namespace OpenMS { outer_points_.clear(); - if (map_points_.find(point[0]) != map_points_.end()) + if (map_points_.contains(point[0])) { if (map_points_.at(point[0]).encloses(point[1])) { @@ -236,7 +236,7 @@ namespace OpenMS throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION); } - if (map_points_.find(point[0]) != map_points_.end()) + if (map_points_.contains(point[0])) { if (map_points_.at(point[0]).encloses(point[1])) { diff --git a/src/openms/source/DATASTRUCTURES/OSWData.cpp b/src/openms/source/DATASTRUCTURES/OSWData.cpp index e171ebcfb86..fe0ecd67368 100644 --- a/src/openms/source/DATASTRUCTURES/OSWData.cpp +++ b/src/openms/source/DATASTRUCTURES/OSWData.cpp @@ -58,7 +58,7 @@ namespace OpenMS // probably a precursor native ID, e.g. 5543_precursor_i0 .. currently not handled. continue; } - if (transitions_.find(nid) == transitions_.end()) + if (!transitions_.contains(nid)) { throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Transition with nativeID " + (String(nid)) + " not found in OSW data. Make sure the OSW data was loaded!"); } @@ -84,7 +84,7 @@ namespace OpenMS { for (const auto& tr : f.getTransitionIDs()) { - if (transitions_.find(tr) == transitions_.end()) + if (!transitions_.contains(tr)) { throw Exception::Precondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Transition with ID " + String(tr) + " was referenced in Protein/Precursor/Feature but is not known!"); } diff --git a/src/openms/source/DATASTRUCTURES/Param.cpp b/src/openms/source/DATASTRUCTURES/Param.cpp index ddedcf58a21..33a4bd822ad 100644 --- a/src/openms/source/DATASTRUCTURES/Param.cpp +++ b/src/openms/source/DATASTRUCTURES/Param.cpp @@ -45,7 +45,7 @@ namespace OpenMS tags.insert(t[i]); } //check name - if (name.find(':') != std::string::npos) + if (name.contains(':')) { OPENMS_LOG_ERROR << "Error ParamEntry name must not contain ':' characters!" << std::endl; } @@ -185,7 +185,7 @@ namespace OpenMS entries(), nodes() { - if (name.find(':') != std::string::npos) + if (name.contains(':')) { OPENMS_LOG_WARN << "Error ParamNode name must not contain ':' characters!\n"; } @@ -245,7 +245,7 @@ namespace OpenMS Param::ParamNode* Param::ParamNode::findParentOf(const std::string& local_name) { //cout << "findParentOf nodename: " << this->name << " - nodes: " << this->nodes.size() << " - find: "<< name << '\n'; - if (local_name.find(':') != std::string::npos) //several subnodes to browse through + if (local_name.contains(':')) //several subnodes to browse through { size_t pos = local_name.find(':'); std::string prefix = local_name.substr(0, pos); @@ -305,7 +305,7 @@ namespace OpenMS std::string prefix2 = prefix + node.name; ParamNode* insert_node = this; - while (prefix2.find(':') != std::string::npos) + while (prefix2.contains(':')) { size_t pos = prefix2.find(':'); std::string local_name = prefix2.substr(0, pos); @@ -368,7 +368,7 @@ namespace OpenMS //std::cerr << " - inserting: " << prefix2 << '\n'; ParamNode* insert_node = this; - while (prefix2.find(':') != std::string::npos) + while (prefix2.contains(':')) { size_t pos = prefix2.find(':'); std::string local_name = prefix2.substr(0, pos); @@ -479,7 +479,7 @@ namespace OpenMS //check for commas for (size_t i = 0; i < strings.size(); ++i) { - if (strings[i].find(',') != std::string::npos) + if (strings[i].contains(',')) { throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Comma characters in Param string restrictions are not allowed!"); } @@ -944,7 +944,7 @@ namespace OpenMS } //with multiple argument - if (options_with_multiple_argument.find(arg) != options_with_multiple_argument.end()) + if (options_with_multiple_argument.contains(arg)) { //next argument is an option if (arg1_is_option) @@ -971,12 +971,12 @@ namespace OpenMS } } //without argument - else if (options_without_argument.find(arg) != options_without_argument.end()) + else if (options_without_argument.contains(arg)) { root_.insert(ParamEntry("", "true", ""), options_without_argument.find(arg)->second); } //with one argument - else if (options_with_one_argument.find(arg) != options_with_one_argument.end()) + else if (options_with_one_argument.contains(arg)) { //next argument is not an option if (!arg1_is_option) @@ -1620,7 +1620,7 @@ OPENMS_THREAD_CRITICAL(LOGSTREAM) void Param::addTag(const std::string& key, const std::string& tag) { - if (tag.find(',') != std::string::npos) + if (tag.contains(',')) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Param tags may not contain comma characters", tag); } @@ -1632,7 +1632,7 @@ OPENMS_THREAD_CRITICAL(LOGSTREAM) ParamEntry& entry = getEntry_(key); for (size_t i = 0; i != tags.size(); ++i) { - if (tags[i].find(',') != std::string::npos) + if (tags[i].contains(',')) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Param tags may not contain comma characters", tags[i]); } diff --git a/src/openms/source/DATASTRUCTURES/QTCluster.cpp b/src/openms/source/DATASTRUCTURES/QTCluster.cpp index 3aa1a0a0c3c..5d57ff7402b 100644 --- a/src/openms/source/DATASTRUCTURES/QTCluster.cpp +++ b/src/openms/source/DATASTRUCTURES/QTCluster.cpp @@ -140,7 +140,7 @@ namespace OpenMS { NeighborMap& neighbors_ = data_->neighbors_; - if (neighbors_.find(map_index) == neighbors_.end() || distance < neighbors_[map_index].distance) + if (!neighbors_.contains(map_index) || distance < neighbors_[map_index].distance) { neighbors_[map_index] = Neighbor {distance, element}; changed_ = true; diff --git a/src/openms/source/FEATUREFINDER/Biosaur2Algorithm.cpp b/src/openms/source/FEATUREFINDER/Biosaur2Algorithm.cpp index 661a07d208a..978d1eedf9d 100644 --- a/src/openms/source/FEATUREFINDER/Biosaur2Algorithm.cpp +++ b/src/openms/source/FEATUREFINDER/Biosaur2Algorithm.cpp @@ -1539,9 +1539,9 @@ void Biosaur2Algorithm::linkScanToHills_(const MSSpectrum& spectrum, const int fi = use_im_current ? im_bin_per_peak[static_cast(idx)] : 0; // Collect candidate previous-scan peaks from neighboring m/z bins. - bool flag1 = prev_fast_dict.find(fm) != prev_fast_dict.end(); - bool flag2 = prev_fast_dict.find(fm - 1) != prev_fast_dict.end(); - bool flag3 = prev_fast_dict.find(fm + 1) != prev_fast_dict.end(); + bool flag1 = prev_fast_dict.contains(fm); + bool flag2 = prev_fast_dict.contains(fm - 1); + bool flag3 = prev_fast_dict.contains(fm + 1); Size assigned_hill = numeric_limits::max(); @@ -1614,7 +1614,7 @@ void Biosaur2Algorithm::linkScanToHills_(const MSSpectrum& spectrum, { continue; } - if (banned_prev_idx_set.find(idx_prev) != banned_prev_idx_set.end()) + if (banned_prev_idx_set.contains(idx_prev)) { continue; } @@ -2165,10 +2165,10 @@ map> Biosaur2Algorithm::performInitialIsotopeCalibrati { isotope_calib_map[ic] = calibrateMass_(isotope_errors[ic]); } - else if (ic > 1 && isotope_calib_map.find(ic - 1) != isotope_calib_map.end()) + else if (ic > 1 && isotope_calib_map.contains(ic - 1)) { auto prev = isotope_calib_map[ic - 1]; - auto prev2 = isotope_calib_map.find(ic - 2) != isotope_calib_map.end() ? + auto prev2 = isotope_calib_map.contains(ic - 2) ? isotope_calib_map[ic - 2] : make_pair(0.0, itol_ppm); double shift_delta = prev.first - prev2.first; @@ -2738,7 +2738,7 @@ vector Biosaur2Algorithm::selectNonOverlappin const double mono_mz_center = mono_hill.mz_weighted_mean; // Skip patterns whose monoisotopic hill is already used. - if (occupied_hills.find(mono_hill.hill_idx) != occupied_hills.end()) + if (occupied_hills.contains(mono_hill.hill_idx)) { continue; } @@ -2746,7 +2746,7 @@ vector Biosaur2Algorithm::selectNonOverlappin bool iso_conflict = false; for (const auto& iso : pc.isotopes) { - if (occupied_hills.find(iso.hill_idx) != occupied_hills.end()) + if (occupied_hills.contains(iso.hill_idx)) { iso_conflict = true; break; @@ -2760,7 +2760,7 @@ vector Biosaur2Algorithm::selectNonOverlappin vector tmp_iso; for (const auto& iso : pc.isotopes) { - if (occupied_hills.find(iso.hill_idx) == occupied_hills.end()) + if (!occupied_hills.contains(iso.hill_idx)) { tmp_iso.push_back(iso); } diff --git a/src/openms/source/FEATUREFINDER/FeatureFinderAlgorithmMetaboIdent.cpp b/src/openms/source/FEATUREFINDER/FeatureFinderAlgorithmMetaboIdent.cpp index cc0fb1b097a..a5c6a06d7c5 100644 --- a/src/openms/source/FEATUREFINDER/FeatureFinderAlgorithmMetaboIdent.cpp +++ b/src/openms/source/FEATUREFINDER/FeatureFinderAlgorithmMetaboIdent.cpp @@ -917,7 +917,7 @@ namespace OpenMS library_.getCompounds().begin(); it != library_.getCompounds().end(); ++it) { - if (!found_refs.count(it->id)) + if (!found_refs.contains(it->id)) { PeptideIdentification peptide; peptide.setIdentifier("id"); diff --git a/src/openms/source/FEATUREFINDER/FeatureFinderIdentificationAlgorithm.cpp b/src/openms/source/FEATUREFINDER/FeatureFinderIdentificationAlgorithm.cpp index d5eaf905435..e8cf3451e80 100644 --- a/src/openms/source/FEATUREFINDER/FeatureFinderIdentificationAlgorithm.cpp +++ b/src/openms/source/FEATUREFINDER/FeatureFinderIdentificationAlgorithm.cpp @@ -1434,7 +1434,7 @@ namespace OpenMS RTMap &external_ids = ref_rt_map[peptide_id].second; for (RTRegion& reg : rt_regions) { - if (reg.ids.count(charge)) + if (reg.ids.contains(charge)) { OPENMS_LOG_DEBUG_NOFILE << "Charge " << charge << ", Region# " << counter + 1 << " (RT: " << float(reg.start) << "-" << float(reg.end) @@ -1637,7 +1637,7 @@ namespace OpenMS for (RTMap::const_iterator rt_it = rt_internal.begin(); rt_it != rt_internal.end(); ++rt_it) { - if (!assigned_ids.count(rt_it->second)) + if (!assigned_ids.contains(rt_it->second)) { const PeptideIdentification& pep_id = *(rt_it->second); features.getUnassignedPeptideIdentifications().push_back(pep_id); @@ -1680,7 +1680,7 @@ namespace OpenMS // - IM_min/max: spread of IM distribution (large spread may indicate issues) // Note: Uses full peptide ref (with region number) as this is the key in im_stats_ String full_peptide_ref = peptide_ref; // keep full ref with region number - if (im_stats_.count(full_peptide_ref)) + if (im_stats_.contains(full_peptide_ref)) { const IMStats& stats = im_stats_.at(full_peptide_ref); feat.setMetaValue("IM_median", stats.median); diff --git a/src/openms/source/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.cpp b/src/openms/source/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.cpp index b6d4f1e1628..a37eb7d2633 100644 --- a/src/openms/source/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.cpp +++ b/src/openms/source/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.cpp @@ -233,7 +233,7 @@ namespace OpenMS // find splines for the mass traces of the lightest and other peptide size_t idx_1 = isotope; size_t idx_2 = peptide * isotopes_per_peptide_max_ + isotope; - if ((spline_chromatograms.find(idx_1) == spline_chromatograms.end()) || (spline_chromatograms.find(idx_2) == spline_chromatograms.end())) + if ((!spline_chromatograms.contains(idx_1)) || (!spline_chromatograms.contains(idx_2))) { continue; } diff --git a/src/openms/source/FEATUREFINDER/FeatureFindingMetabo.cpp b/src/openms/source/FEATUREFINDER/FeatureFindingMetabo.cpp index 4f46a389a62..bfc27d9c8d8 100644 --- a/src/openms/source/FEATUREFINDER/FeatureFindingMetabo.cpp +++ b/src/openms/source/FEATUREFINDER/FeatureFindingMetabo.cpp @@ -976,7 +976,7 @@ namespace OpenMS bool trace_coll = false; // trace collision? for (Size lab_idx = 0; lab_idx < labels.size(); ++lab_idx) { - if (trace_excl_map.find(labels[lab_idx]) != trace_excl_map.end()) + if (trace_excl_map.contains(labels[lab_idx])) { trace_coll = true; break; diff --git a/src/openms/source/FEATUREFINDER/MultiplexDeltaMassesGenerator.cpp b/src/openms/source/FEATUREFINDER/MultiplexDeltaMassesGenerator.cpp index 8cd3c50e48b..31ba586e0f5 100644 --- a/src/openms/source/FEATUREFINDER/MultiplexDeltaMassesGenerator.cpp +++ b/src/openms/source/FEATUREFINDER/MultiplexDeltaMassesGenerator.cpp @@ -113,10 +113,10 @@ namespace OpenMS bool no_label = (samples_labels_.size() == 1) && (samples_labels_[0].size() == 1) && samples_labels_[0][0] == "no_label"; - bool labelling_SILAC = ((labels_.find("Arg") != std::string::npos) || (labels_.find("Lys") != std::string::npos)); - bool labelling_Leu = (labels_.find("Leu") != std::string::npos); - bool labelling_Dimethyl = (labels_.find("Dimethyl") != std::string::npos); - bool labelling_ICPL = (labels_.find("ICPL") != std::string::npos); + bool labelling_SILAC = ((labels_.contains("Arg")) || (labels_.contains("Lys"))); + bool labelling_Leu = (labels_.contains("Leu")); + bool labelling_Dimethyl = (labels_.contains("Dimethyl")); + bool labelling_ICPL = (labels_.contains("ICPL")); bool labelling_numeric = false; if (!(no_label || labelling_SILAC || labelling_Leu || labelling_Dimethyl || labelling_ICPL)) @@ -171,7 +171,7 @@ namespace OpenMS { for (std::vector::size_type j = 0; j < samples_labels_[i].size(); ++j) { - if (all_labels.find(samples_labels_[i][j]) == std::string::npos) + if (!all_labels.contains(samples_labels_[i][j])) { std::stringstream stream; stream << "The label " << samples_labels_[i][j] << " is unknown."; @@ -205,11 +205,11 @@ namespace OpenMS for (unsigned j = 0; j < samples_labels_[i].size(); ++j) { - bool Arg6There = (samples_labels_[i][j].find("Arg6") != std::string::npos); // Is Arg6 in the SILAC label? - bool Arg10There = (samples_labels_[i][j].find("Arg10") != std::string::npos); - bool Lys4There = (samples_labels_[i][j].find("Lys4") != std::string::npos); - bool Lys6There = (samples_labels_[i][j].find("Lys6") != std::string::npos); - bool Lys8There = (samples_labels_[i][j].find("Lys8") != std::string::npos); + bool Arg6There = (samples_labels_[i][j].contains("Arg6")); // Is Arg6 in the SILAC label? + bool Arg10There = (samples_labels_[i][j].contains("Arg10")); + bool Lys4There = (samples_labels_[i][j].contains("Lys4")); + bool Lys6There = (samples_labels_[i][j].contains("Lys6")); + bool Lys8There = (samples_labels_[i][j].contains("Lys8")); // construct label set for (unsigned k = 1; k < Arg6There * (ArgPerPeptide + 1); ++k) diff --git a/src/openms/source/FEATUREFINDER/MultiplexFiltering.cpp b/src/openms/source/FEATUREFINDER/MultiplexFiltering.cpp index d0f7b294309..414e1441605 100644 --- a/src/openms/source/FEATUREFINDER/MultiplexFiltering.cpp +++ b/src/openms/source/FEATUREFINDER/MultiplexFiltering.cpp @@ -324,7 +324,7 @@ namespace OpenMS for (const auto &it : satellites) { size_t idx_masstrace = it.first; // mass trace index i.e. the index within the peptide multiplet pattern - if (rt_boundaries.find(idx_masstrace) == rt_boundaries.end()) + if (!rt_boundaries.contains(idx_masstrace)) { // That's the first satellite within this mass trace. rt_boundaries[idx_masstrace] = std::make_pair((it.second).getRTidx(), (it.second).getRTidx()); diff --git a/src/openms/source/FORMAT/AbsoluteQuantitationMethodFile.cpp b/src/openms/source/FORMAT/AbsoluteQuantitationMethodFile.cpp index bbd060a9d40..ea2df687f97 100644 --- a/src/openms/source/FORMAT/AbsoluteQuantitationMethodFile.cpp +++ b/src/openms/source/FORMAT/AbsoluteQuantitationMethodFile.cpp @@ -79,14 +79,14 @@ namespace OpenMS aqm.setComponentName(headers.count("component_name") ? tl[headers.at("component_name")] : ""); aqm.setFeatureName(headers.count("feature_name") ? tl[headers.at("feature_name")] : ""); aqm.setISName(headers.count("IS_name") ? tl[headers.at("IS_name")] : ""); - aqm.setLLOD(!headers.count("llod") || tl[headers.at("llod")].empty() ? 0 : std::stod(tl[headers.at("llod")])); - aqm.setULOD(!headers.count("ulod") || tl[headers.at("ulod")].empty() ? 0 : std::stod(tl[headers.at("ulod")])); - aqm.setLLOQ(!headers.count("lloq") || tl[headers.at("lloq")].empty() ? 0 : std::stod(tl[headers.at("lloq")])); - aqm.setULOQ(!headers.count("uloq") || tl[headers.at("uloq")].empty() ? 0 : std::stod(tl[headers.at("uloq")])); + aqm.setLLOD(!headers.contains("llod") || tl[headers.at("llod")].empty() ? 0 : std::stod(tl[headers.at("llod")])); + aqm.setULOD(!headers.contains("ulod") || tl[headers.at("ulod")].empty() ? 0 : std::stod(tl[headers.at("ulod")])); + aqm.setLLOQ(!headers.contains("lloq") || tl[headers.at("lloq")].empty() ? 0 : std::stod(tl[headers.at("lloq")])); + aqm.setULOQ(!headers.contains("uloq") || tl[headers.at("uloq")].empty() ? 0 : std::stod(tl[headers.at("uloq")])); aqm.setConcentrationUnits(headers.count("concentration_units") ? tl[headers.at("concentration_units")] : ""); - aqm.setNPoints(!headers.count("n_points") || tl[headers.at("n_points")].empty() ? 0 : std::stoi(tl[headers.at("n_points")])); + aqm.setNPoints(!headers.contains("n_points") || tl[headers.at("n_points")].empty() ? 0 : std::stoi(tl[headers.at("n_points")])); aqm.setCorrelationCoefficient( - !headers.count("correlation_coefficient") || tl[headers.at("correlation_coefficient")].empty() + !headers.contains("correlation_coefficient") || tl[headers.at("correlation_coefficient")].empty() ? 0 : std::stod(tl[headers.at("correlation_coefficient")]) ); diff --git a/src/openms/source/FORMAT/ArrowIOHelpers.cpp b/src/openms/source/FORMAT/ArrowIOHelpers.cpp index 71ba98d25ac..605306f1490 100644 --- a/src/openms/source/FORMAT/ArrowIOHelpers.cpp +++ b/src/openms/source/FORMAT/ArrowIOHelpers.cpp @@ -240,7 +240,7 @@ void readMetaValues( for (int64_t i = 0; i < struct_arr->length(); ++i) { std::string name = name_arr->GetString(i); - if (excluded_keys.count(name)) continue; + if (excluded_keys.contains(name)) continue; std::string value_str = value_arr->GetString(i); std::string type_str = type_arr->GetString(i); diff --git a/src/openms/source/FORMAT/BrukerTimsFile.cpp b/src/openms/source/FORMAT/BrukerTimsFile.cpp index 17a87928f78..e76ae98637a 100644 --- a/src/openms/source/FORMAT/BrukerTimsFile.cpp +++ b/src/openms/source/FORMAT/BrukerTimsFile.cpp @@ -958,7 +958,7 @@ namespace OpenMS if (dm == 0 && ds == 0) continue; if (auto nkey = neighborKey(mz_bin, scan_id, dm, ds)) { - if (grid_.count(*nkey)) ++neighbors; + if (grid_.contains(*nkey)) ++neighbors; } } } @@ -1000,7 +1000,7 @@ namespace OpenMS if (dm == 0 && ds == 0) continue; if (auto nkey = neighborKey(mz_bin, scan_id, dm, ds)) { - if (grid_.count(*nkey)) ++neighbors; + if (grid_.contains(*nkey)) ++neighbors; } } } diff --git a/src/openms/source/FORMAT/ConsensusMapArrowExport.cpp b/src/openms/source/FORMAT/ConsensusMapArrowExport.cpp index 0f893411d2f..347b5367d1b 100644 --- a/src/openms/source/FORMAT/ConsensusMapArrowExport.cpp +++ b/src/openms/source/FORMAT/ConsensusMapArrowExport.cpp @@ -271,7 +271,7 @@ std::shared_ptr ConsensusMapArrowExport::exportToArrow(const Conse { for (const auto& acc : ig.accessions) { - if (pg_qvalue_lookup.find(acc) == pg_qvalue_lookup.end()) + if (!pg_qvalue_lookup.contains(acc)) { pg_qvalue_lookup[acc] = ig.probability; } @@ -358,7 +358,7 @@ std::shared_ptr ConsensusMapArrowExport::exportToArrow(const Conse { acc_str = "UNIMOD:" + std::to_string(mod->getUniModRecordId()); } - if (mod_map.find(name) == mod_map.end()) + if (!mod_map.contains(name)) { mod_map[name] = {acc_str, {}}; } @@ -376,7 +376,7 @@ std::shared_ptr ConsensusMapArrowExport::exportToArrow(const Conse { acc_str = "UNIMOD:" + std::to_string(mod->getUniModRecordId()); } - if (mod_map.find(name) == mod_map.end()) + if (!mod_map.contains(name)) { mod_map[name] = {acc_str, {}}; } @@ -477,7 +477,7 @@ std::shared_ptr ConsensusMapArrowExport::exportToArrow(const Conse best_hit->getKeys(keys); for (const auto& key : keys) { - if (excluded_hit_mvs.count(key)) continue; + if (excluded_hit_mvs.contains(key)) continue; const DataValue& val = best_hit->getMetaValue(key); if ((val.valueType() == DataValue::INT_VALUE || val.valueType() == DataValue::DOUBLE_VALUE) && Scores::isKnownScoreType(key)) diff --git a/src/openms/source/FORMAT/ConsensusMapArrowIO.cpp b/src/openms/source/FORMAT/ConsensusMapArrowIO.cpp index 56a99adf3ca..8f011538ec7 100644 --- a/src/openms/source/FORMAT/ConsensusMapArrowIO.cpp +++ b/src/openms/source/FORMAT/ConsensusMapArrowIO.cpp @@ -52,7 +52,7 @@ namespace // anonymous mii.getKeys(keys); for (const auto& key : keys) { - if (excluded_keys.count(key)) continue; + if (excluded_keys.contains(key)) continue; const DataValue& val = mii.getMetaValue(key); (void)struct_b->Append(); (void)name_b->Append(key); diff --git a/src/openms/source/FORMAT/ControlledVocabulary.cpp b/src/openms/source/FORMAT/ControlledVocabulary.cpp index c99f39c1648..76534c0abe6 100644 --- a/src/openms/source/FORMAT/ControlledVocabulary.cpp +++ b/src/openms/source/FORMAT/ControlledVocabulary.cpp @@ -573,7 +573,7 @@ namespace OpenMS bool ControlledVocabulary::exists(const String& id) const { - return terms_.find(id) != terms_.end(); + return terms_.contains(id); } const ControlledVocabulary::CVTerm* ControlledVocabulary::checkAndGetTermByName(const OpenMS::String& name) const diff --git a/src/openms/source/FORMAT/DATAACCESS/MSChromatogramParquetConsumer.cpp b/src/openms/source/FORMAT/DATAACCESS/MSChromatogramParquetConsumer.cpp index 11f76feace0..404593017db 100644 --- a/src/openms/source/FORMAT/DATAACCESS/MSChromatogramParquetConsumer.cpp +++ b/src/openms/source/FORMAT/DATAACCESS/MSChromatogramParquetConsumer.cpp @@ -138,7 +138,7 @@ namespace OpenMS { // fall through to auto-assigned ID } - while (used_ids.count(next_id)) + while (used_ids.contains(next_id)) { ++next_id; } diff --git a/src/openms/source/FORMAT/DATAACCESS/MobilogramParquetConsumer.cpp b/src/openms/source/FORMAT/DATAACCESS/MobilogramParquetConsumer.cpp index 2092f4634ee..f519ab51689 100644 --- a/src/openms/source/FORMAT/DATAACCESS/MobilogramParquetConsumer.cpp +++ b/src/openms/source/FORMAT/DATAACCESS/MobilogramParquetConsumer.cpp @@ -152,7 +152,7 @@ namespace OpenMS { // fall through to auto-assigned ID } - while (used_ids.count(next_id)) + while (used_ids.contains(next_id)) { ++next_id; } diff --git a/src/openms/source/FORMAT/ExperimentalDesignFile.cpp b/src/openms/source/FORMAT/ExperimentalDesignFile.cpp index e7b41ced1b2..8b1023e5e88 100644 --- a/src/openms/source/FORMAT/ExperimentalDesignFile.cpp +++ b/src/openms/source/FORMAT/ExperimentalDesignFile.cpp @@ -114,7 +114,7 @@ namespace OpenMS const String &h = header[i]; // A header is unexpected if it is neither required nor optional and we do not allow other headers - const bool header_unexpected = (required.find(h) == required.end()) && (optional.find(h) == optional.end()); + const bool header_unexpected = (!required.contains(h)) && (!optional.contains(h)); parseErrorIf_(!allow_other_header && header_unexpected, filename, "Header not allowed in this section of the Experimental Design: " + h); column_map[h] = i; } @@ -192,8 +192,8 @@ namespace OpenMS {"Fraction_Group", "Fraction", "Spectra_Filepath"}, {"Label", "Sample"}, true ); - has_label = fs_column_header_to_index.find("Label") != fs_column_header_to_index.end(); - has_sample = fs_column_header_to_index.find("Sample") != fs_column_header_to_index.end(); + has_label = fs_column_header_to_index.contains("Label"); + has_sample = fs_column_header_to_index.contains("Sample"); if (!has_label) // add label column to end of header { @@ -358,8 +358,8 @@ namespace OpenMS {"Fraction_Group", "Fraction", "Spectra_Filepath"}, {"Label", "Sample"}, false ); - has_label = fs_column_header_to_index.find("Label") != fs_column_header_to_index.end(); - has_sample = fs_column_header_to_index.find("Sample") != fs_column_header_to_index.end(); + has_label = fs_column_header_to_index.contains("Label"); + has_sample = fs_column_header_to_index.contains("Sample"); n_col = fs_column_header_to_index.size(); } @@ -422,7 +422,7 @@ namespace OpenMS { // Parse Error if sample appears multiple times const String& sample = cells[sample_columnname_to_columnindex_["Sample"]]; - parseErrorIf_(sample_sample_to_rowindex_.find(sample) != sample_sample_to_rowindex_.end(), + parseErrorIf_(sample_sample_to_rowindex_.contains(sample), tsv_file, "Sample: " + String(sample) + " appears multiple times in the sample table"); sample_sample_to_rowindex_[sample] = line_number++; diff --git a/src/openms/source/FORMAT/FeatureMapArrowIO.cpp b/src/openms/source/FORMAT/FeatureMapArrowIO.cpp index ea53b6d6d68..ac3bc434fdb 100644 --- a/src/openms/source/FORMAT/FeatureMapArrowIO.cpp +++ b/src/openms/source/FORMAT/FeatureMapArrowIO.cpp @@ -52,7 +52,7 @@ namespace // anonymous mii.getKeys(keys); for (const auto& key : keys) { - if (excluded_keys.count(key)) continue; + if (excluded_keys.contains(key)) continue; const DataValue& val = mii.getMetaValue(key); (void)struct_b->Append(); (void)name_b->Append(key); diff --git a/src/openms/source/FORMAT/FileTypes.cpp b/src/openms/source/FORMAT/FileTypes.cpp index a5a0c4eac5a..a3334e6bacf 100644 --- a/src/openms/source/FORMAT/FileTypes.cpp +++ b/src/openms/source/FORMAT/FileTypes.cpp @@ -32,7 +32,7 @@ namespace OpenMS { // Check that there are no double-spaces in the description, since Qt will replace " " with " " in filters supplied to QFileDialog::getSaveFileName. // And if you later ask for the selected filter, you will get a different string back. - assert(description.find(" ") == std::string::npos); + assert(!description.contains(" ")); } }; diff --git a/src/openms/source/FORMAT/GNPSMGFFile.cpp b/src/openms/source/FORMAT/GNPSMGFFile.cpp index c71a7e0a8ec..6e899adefb6 100644 --- a/src/openms/source/FORMAT/GNPSMGFFile.cpp +++ b/src/openms/source/FORMAT/GNPSMGFFile.cpp @@ -301,7 +301,7 @@ namespace OpenMS int map_index = pep.first; // open on-disc experiments - if (map_index2file_index.find(map_index) == map_index2file_index.end()) + if (!map_index2file_index.contains(map_index)) { specs_list[num_msmaps_cached].openFile(mzml_file_paths[map_index], false); // open on-disc experiment and load meta-data map_index2file_index[map_index] = num_msmaps_cached; diff --git a/src/openms/source/FORMAT/GNPSQuantificationFile.cpp b/src/openms/source/FORMAT/GNPSQuantificationFile.cpp index 8b946eab18d..493c1c06f13 100644 --- a/src/openms/source/FORMAT/GNPSQuantificationFile.cpp +++ b/src/openms/source/FORMAT/GNPSQuantificationFile.cpp @@ -67,7 +67,7 @@ namespace OpenMS for (const auto& fh: cf.getFeatures()) index_to_feature[fh.getMapIndex()] = fh; for (size_t i = 0; i < consensus_map.getColumnHeaders().size(); i++) { - if (index_to_feature.count(i)) + if (index_to_feature.contains(i)) { out << index_to_feature[i].getRT() << index_to_feature[i].getMZ() << index_to_feature[i].getIntensity() << index_to_feature[i].getCharge() << index_to_feature[i].getWidth(); } diff --git a/src/openms/source/FORMAT/HANDLERS/ConsensusXMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/ConsensusXMLHandler.cpp index 395128ca343..1ddaa49fafb 100644 --- a/src/openms/source/FORMAT/HANDLERS/ConsensusXMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/ConsensusXMLHandler.cpp @@ -340,7 +340,7 @@ namespace OpenMS::Internal // Note: technically, it would be preferable to prefix the UID for faster string comparison, but this results in random write-orderings during file store (breaks tests) String identifier = prot_id_.getSearchEngine() + '_' + attributeAsString_(attributes, "date") + '_' + String(UniqueIdGenerator::getUniqueId()); - if (id_identifier_.find(id) == id_identifier_.end()) + if (!id_identifier_.contains(id)) { prot_id_.setIdentifier(identifier); id_identifier_[id] = identifier; @@ -439,7 +439,7 @@ namespace OpenMS::Internal else if (tag == "PeptideIdentification" || tag == "UnassignedPeptideIdentification") { String id = attributeAsString_(attributes, "identification_run_ref"); - if (id_identifier_.find(id) == id_identifier_.end()) + if (!id_identifier_.contains(id)) { warning(LOAD, String("Peptide identification without ProteinIdentification found (id: '") + id + "')!"); } @@ -830,7 +830,7 @@ namespace OpenMS::Internal { String indent = String(indentation_level, '\t'); - if (identifier_id_.find(id.getIdentifier()) == identifier_id_.end()) + if (!identifier_id_.contains(id.getIdentifier())) { warning(STORE, String("Omitting peptide identification because of missing ProteinIdentification with identifier '") + id.getIdentifier() + "' while writing '" + filename + "'!"); diff --git a/src/openms/source/FORMAT/HANDLERS/FeatureXMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/FeatureXMLHandler.cpp index 51684ba974d..e881c2c5b01 100644 --- a/src/openms/source/FORMAT/HANDLERS/FeatureXMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/FeatureXMLHandler.cpp @@ -447,7 +447,7 @@ namespace OpenMS::Internal // Note: technically, it would be preferable to prefix the UID for faster string comparison, but this results in random write-orderings during file store (breaks tests) String identifier = prot_id_.getSearchEngine() + '_' + attributeAsString_(attributes, "date") + '_' + String(UniqueIdGenerator::getUniqueId()); - if (id_identifier_.find(id) == id_identifier_.end()) + if (!id_identifier_.contains(id)) { prot_id_.setIdentifier(identifier); id_identifier_[id] = identifier; @@ -547,7 +547,7 @@ namespace OpenMS::Internal else if (tag == "PeptideIdentification" || tag == "UnassignedPeptideIdentification") { String id = attributeAsString_(attributes, "identification_run_ref"); - if (id_identifier_.find(id) == id_identifier_.end()) + if (!id_identifier_.contains(id)) { warning(LOAD, String("Peptide identification without ProteinIdentification found (id: '") + id + "')!"); } @@ -953,7 +953,7 @@ namespace OpenMS::Internal { String indent = String(indentation_level, '\t'); - if (identifier_id_.find(id.getIdentifier()) == identifier_id_.end()) + if (!identifier_id_.contains(id.getIdentifier())) { warning(STORE, String("Omitting peptide identification because of missing ProteinIdentification with identifier '") + id.getIdentifier() + "' while writing '" + filename + "'!"); return; diff --git a/src/openms/source/FORMAT/HANDLERS/IndexedMzMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/IndexedMzMLHandler.cpp index cb9accd1fde..05f651eed80 100644 --- a/src/openms/source/FORMAT/HANDLERS/IndexedMzMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/IndexedMzMLHandler.cpp @@ -252,7 +252,7 @@ namespace OpenMS::Internal void IndexedMzMLHandler::getMSSpectrumByNativeId(const std::string& id, MSSpectrum& s) { - if (spectra_native_ids_.find(id) == spectra_native_ids_.end()) + if (!spectra_native_ids_.contains(id)) { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, String( "Could not find spectrum id " + String(id) )); diff --git a/src/openms/source/FORMAT/HANDLERS/MascotXMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MascotXMLHandler.cpp index 4692e95b948..ef8b12867f9 100644 --- a/src/openms/source/FORMAT/HANDLERS/MascotXMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/MascotXMLHandler.cpp @@ -337,7 +337,7 @@ namespace OpenMS::Internal vector parts; actual_title_ = title; - if (modified_peptides_.find(title) != modified_peptides_.end()) + if (modified_peptides_.contains(title)) { vector& temp_hits = modified_peptides_[title]; vector temp_peptide_hits = id_data_[actual_query_ - 1].getHits(); diff --git a/src/openms/source/FORMAT/HANDLERS/MzDataHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MzDataHandler.cpp index bd62d1148d0..4416d483a6c 100644 --- a/src/openms/source/FORMAT/HANDLERS/MzDataHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/MzDataHandler.cpp @@ -951,7 +951,7 @@ namespace OpenMS::Internal { Int precursor_ms_level = spec.getMSLevel() - 1; SignedSize precursor_id = -1; - if (level_id.find(precursor_ms_level) != level_id.end()) + if (level_id.contains(precursor_ms_level)) { precursor_id = level_id[precursor_ms_level]; } diff --git a/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp index d465b265467..a955de2b95f 100644 --- a/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp @@ -413,7 +413,7 @@ namespace OpenMS::Internal hit_pev_.push_back(pepevs); String pepref = String("OpenMS") + String(UniqueIdGenerator::getUniqueId()); - if (pepset.find(ph->getSequence()) != pepset.end()) + if (pepset.contains(ph->getSequence())) { pepset.insert(ph->getSequence()); pep_map_.insert(make_pair(pepref, ph->getSequence())); @@ -663,7 +663,7 @@ namespace OpenMS::Internal cv_.getAllChildTerms(software_terms, "MS:1000531"); for (map >::const_iterator it = swn.first.getCVTerms().begin(); it != swn.first.getCVTerms().end(); ++it) { - if (software_terms.find(it->first) != software_terms.end()) + if (software_terms.contains(it->first)) { swname = it->second.front().getName(); break; @@ -1118,7 +1118,7 @@ namespace OpenMS::Internal pair > params = parseParamGroup_(sub->getChildNodes()); for (map >::const_iterator it = params.first.getCVTerms().begin(); it != params.first.getCVTerms().end(); ++it) { - if (enzymes_terms.find(it->first) != enzymes_terms.end()) + if (enzymes_terms.contains(it->first)) { enzymename = it->second.front().getName(); } @@ -1186,7 +1186,7 @@ namespace OpenMS::Internal cv_.getAllChildTerms(threshold_terms, "MS:1002482"); //statistical threshold for (map >::const_iterator thit = tcv.getCVTerms().begin(); thit != tcv.getCVTerms().end(); ++thit) { - if (threshold_terms.find(thit->first) != threshold_terms.end()) + if (threshold_terms.contains(thit->first)) { if (thit->first != "MS:1001494") // no threshold { @@ -1889,7 +1889,7 @@ namespace OpenMS::Internal ph_alpha.setMetaValue(Constants::UserParam::OPENPEPXL_XL_MOD, xl_mod_map_.at(peptides[alpha[0]])); ph_alpha.setMetaValue(Constants::UserParam::OPENPEPXL_XL_MASS,DataValue(xl_mass_map_.at(peptides[alpha[0]]))); } - else if ( xl_mod_map_.find(peptides[alpha[0]]) != xl_mod_map_.end() ) + else if ( xl_mod_map_.contains(peptides[alpha[0]]) ) { ph_alpha.setMetaValue(Constants::UserParam::OPENPEPXL_XL_MOD, xl_mod_map_.at(peptides[alpha[0]])); } @@ -1994,7 +1994,7 @@ namespace OpenMS::Internal { bool idec = false; OpenMS::PeptideEvidence pev; - if (pe_ev_map_.find(pev_it->second) != pe_ev_map_.end()) + if (pe_ev_map_.contains(pev_it->second)) { MzIdentMLDOMHandler::PeptideEvidence& pv = pe_ev_map_[pev_it->second]; if (pv.pre != '-') pev.setAABefore(pv.pre); @@ -2045,7 +2045,7 @@ namespace OpenMS::Internal } } - if (pv_db_map_.find(pev_it->second) != pv_db_map_.end()) + if (pv_db_map_.contains(pev_it->second)) { String& dpv = pv_db_map_[pev_it->second]; DBSequence& db = db_sq_map_[dpv]; @@ -2128,7 +2128,7 @@ namespace OpenMS::Internal bool scoretype = false; for (map>::const_iterator scoreit = param_cv.getCVTerms().begin(); scoreit != param_cv.getCVTerms().end(); ++scoreit) { - if (q_score_child_terms_.find(scoreit->first) != q_score_child_terms_.end() || scoreit->first == "MS:1002354") + if (q_score_child_terms_.contains(scoreit->first) || scoreit->first == "MS:1002354") { if (scoreit->first != "MS:1002055") // do not use peptide-level q-values for now { @@ -2140,7 +2140,7 @@ namespace OpenMS::Internal } } else if (scoreit->first != "MS:1001143" && // the parent term itself has no numeric value; handled in the special case below - specific_score_child_terms_.find(scoreit->first) != specific_score_child_terms_.end()) + specific_score_child_terms_.contains(scoreit->first)) { score = toDoubleOrZero_(scoreit->second.front().getValue().toString()); // cast fix needed as DataValue is init with XercesString spectrum_identification.setHigherScoreBetter(ControlledVocabulary::CVTerm::isHigherBetterScore(cv_.getTerm(scoreit->first))); @@ -2148,7 +2148,7 @@ namespace OpenMS::Internal scoretype = true; break; } - else if (e_score_child_terms_.find(scoreit->first) != e_score_child_terms_.end()) + else if (e_score_child_terms_.contains(scoreit->first)) { score = toDoubleOrZero_(scoreit->second.front().getValue().toString()); // cast fix needed as DataValue is init with XercesString spectrum_identification.setHigherScoreBetter(false); @@ -2202,7 +2202,7 @@ namespace OpenMS::Internal { bool idec = false; OpenMS::PeptideEvidence pev; - if (pe_ev_map_.find(pev_it->second) != pe_ev_map_.end()) + if (pe_ev_map_.contains(pev_it->second)) { MzIdentMLDOMHandler::PeptideEvidence& pv = pe_ev_map_[pev_it->second]; if (pv.pre != '-') pev.setAABefore(pv.pre); @@ -2255,7 +2255,7 @@ namespace OpenMS::Internal } } - if (pv_db_map_.find(pev_it->second) != pv_db_map_.end()) + if (pv_db_map_.contains(pev_it->second)) { String& dpv = pv_db_map_[pev_it->second]; DBSequence& db = db_sq_map_[dpv]; diff --git a/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp index 99c9a96d666..161de53b91b 100644 --- a/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp @@ -250,7 +250,7 @@ namespace OpenMS::Internal to_ignore.insert("peptideSequence"); } - if (to_ignore.find(tag_) != to_ignore.end()) + if (to_ignore.contains(tag_)) { return; } @@ -423,7 +423,7 @@ namespace OpenMS::Internal tag_ = sm_.convert(qname); open_tags_.pop_back(); - if (to_ignore.find(tag_) != to_ignore.end()) + if (to_ignore.contains(tag_)) { return; } @@ -719,7 +719,7 @@ namespace OpenMS::Internal sdat_id = "SDAT_" + String(UniqueIdGenerator::getUniqueId()); FileTypes::Type type = FileHandler::getTypeByFileName(sdat_file); - if (formats_map.find(type) == formats_map.end()) type = FileTypes::MZML; // default + if (!formats_map.contains(type)) type = FileTypes::MZML; // default //xml spectra_data += String("\t\t"); @@ -869,7 +869,7 @@ namespace OpenMS::Internal if (is_ppxl) { - if (ppxl_specref_2_element.find(sid)==ppxl_specref_2_element.end()) + if (!ppxl_specref_2_element.contains(sid)) { ppxl_specref_2_element[sid] = sidres; } @@ -1553,12 +1553,12 @@ namespace OpenMS::Internal // Otherwise fall through to the dedicated alias branches below (e.g. Mascot/OMSSA), which would // otherwise be unreachable for score types that happen to be valid (non-score) PSI-MS term names. if (const auto* term = cv_.checkAndGetTermByName(st); - term != nullptr && peptide_result_details_.find(term->id) != peptide_result_details_.end()) + term != nullptr && peptide_result_details_.contains(term->id)) { (sii_tmp += "\t\t\t\t\t") += term->toXMLString(cv_ns, sc); copy_hit.removeMetaValue(term->id); } - else if (cv_.exists(st) && peptide_result_details_.find(st) != peptide_result_details_.end()) + else if (cv_.exists(st) && peptide_result_details_.contains(st)) { const auto& term = cv_.getTerm(st); (sii_tmp += "\t\t\t\t\t") += term.toXMLString(cv_ns, sc); @@ -2198,12 +2198,12 @@ namespace OpenMS::Internal // Only consume the score type here if it maps to a PSM-level search-engine statistic (MS:1001143 subtree); // otherwise fall through to the dedicated alias branches below. if (const auto* term = cv_.checkAndGetTermByName(st); - term != nullptr && peptide_result_details_.find(term->id) != peptide_result_details_.end()) + term != nullptr && peptide_result_details_.contains(term->id)) { (sii_tmp += "\t\t\t\t\t") += term->toXMLString(cv_ns, sc); copy_hit.removeMetaValue(term->id); } - else if (cv_.exists(st) && peptide_result_details_.find(st) != peptide_result_details_.end()) + else if (cv_.exists(st) && peptide_result_details_.contains(st)) { const auto& term = cv_.getTerm(st); (sii_tmp += "\t\t\t\t\t") += term.toXMLString(cv_ns, sc); diff --git a/src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp index 7bbf4698b13..eec0a4d93a8 100644 --- a/src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp @@ -788,7 +788,7 @@ namespace OpenMS::Internal String source_file_ref; if (optionalAttributeAsString_(source_file_ref, attributes, s_source_file_ref)) { - if (source_files_.find(source_file_ref) != source_files_.end()) + if (source_files_.contains(source_file_ref)) { spec_.setSourceFile(source_files_[source_file_ref]); } @@ -3497,7 +3497,7 @@ namespace OpenMS::Internal for (std::vector::iterator key = keys.begin(); key != keys.end(); ++key) { - if (exclude.count(*key)) continue; // skip excluded entries + if (exclude.contains(*key)) continue; // skip excluded entries // special treatment of GO and BTO terms // @@ -4139,63 +4139,63 @@ namespace OpenMS::Internal { ++file_content[exp[i].getInstrumentSettings().getScanMode()]; } - if (file_content.find(InstrumentSettings::ScanMode::MASSSPECTRUM) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::MASSSPECTRUM)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::MS1SPECTRUM) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::MS1SPECTRUM)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::MSNSPECTRUM) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::MSNSPECTRUM)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::SIM) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::SIM)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::SRM) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::SRM)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::CRM) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::CRM)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::PRECURSOR) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::PRECURSOR)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::CNG) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::CNG)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::CNL) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::CNL)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::EMR) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::EMR)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::EMISSION) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::EMISSION)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::ABSORPTION) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::ABSORPTION)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::EMC) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::EMC)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::TDF) != file_content.end()) + if (file_content.contains(InstrumentSettings::ScanMode::TDF)) { os << "\t\t\t\n"; } - if (file_content.find(InstrumentSettings::ScanMode::UNKNOWN) != file_content.end() || file_content.empty()) + if (file_content.contains(InstrumentSettings::ScanMode::UNKNOWN) || file_content.empty()) { os << "\t\t\t\n"; } diff --git a/src/openms/source/FORMAT/HANDLERS/MzMLSqliteHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MzMLSqliteHandler.cpp index ff69feccba4..cc41c34e540 100644 --- a/src/openms/source/FORMAT/HANDLERS/MzMLSqliteHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/MzMLSqliteHandler.cpp @@ -127,7 +127,7 @@ namespace OpenMS::Internal Size id_orig = sqlite3_column_int( stmt, 0 ); // map the sql table id to the index in the "containers" vector - if (sql_container_map.find(id_orig) == sql_container_map.end()) + if (!sql_container_map.contains(id_orig)) { Size tmp = sql_container_map.size(); sql_container_map[id_orig] = tmp; diff --git a/src/openms/source/FORMAT/HANDLERS/PASEFHillCentroider.cpp b/src/openms/source/FORMAT/HANDLERS/PASEFHillCentroider.cpp index 6f0e9b60183..dc7da6fd477 100644 --- a/src/openms/source/FORMAT/HANDLERS/PASEFHillCentroider.cpp +++ b/src/openms/source/FORMAT/HANDLERS/PASEFHillCentroider.cpp @@ -269,7 +269,7 @@ namespace OpenMS::Internal::PASEFHillCentroider for (int tidx : it->second) { if (tidx < 0 || static_cast(tidx) >= tails.size()) continue; - if (claimed_tail_idx.count(tidx)) continue; + if (claimed_tail_idx.contains(tidx)) continue; const auto& t = tails[static_cast(tidx)]; const double dppm = std::abs(mz_cur - t.mz) / mz_cur * 1e6; if (dppm > mz_tol_ppm) continue; diff --git a/src/openms/source/FORMAT/HANDLERS/TraMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/TraMLHandler.cpp index 024bc7f9887..f887926f939 100644 --- a/src/openms/source/FORMAT/HANDLERS/TraMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/TraMLHandler.cpp @@ -83,7 +83,7 @@ namespace OpenMS::Internal } // skip tags where nothing is to do - if (tags_to_ignore.find(tag_) != tags_to_ignore.end()) + if (tags_to_ignore.contains(tag_)) { return; } @@ -327,7 +327,7 @@ namespace OpenMS::Internal } // skip tags where nothing is to do - if (tags_to_ignore.find(tag_) != tags_to_ignore.end()) + if (tags_to_ignore.contains(tag_)) { return; } diff --git a/src/openms/source/FORMAT/HANDLERS/XQuestResultXMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/XQuestResultXMLHandler.cpp index 274c8bc6deb..de3aab254e6 100644 --- a/src/openms/source/FORMAT/HANDLERS/XQuestResultXMLHandler.cpp +++ b/src/openms/source/FORMAT/HANDLERS/XQuestResultXMLHandler.cpp @@ -138,7 +138,7 @@ namespace OpenMS::Internal PeptideEvidence pep_ev; const String& accession = *prot_list_it; - if (this->accessions_.find(accession) == this->accessions_.end()) + if (!this->accessions_.contains(accession)) { this->accessions_.insert(accession); diff --git a/src/openms/source/FORMAT/IdXMLFile.cpp b/src/openms/source/FORMAT/IdXMLFile.cpp index 2a56974ccf4..95417ac9b03 100644 --- a/src/openms/source/FORMAT/IdXMLFile.cpp +++ b/src/openms/source/FORMAT/IdXMLFile.cpp @@ -516,7 +516,7 @@ namespace OpenMS //search parameters String ref = attributeAsString_(attributes, "search_parameters_ref"); - if (parameters_.find(ref) == parameters_.end()) + if (!parameters_.contains(ref)) { fatalError(LOAD, String("Invalid search parameters reference '") + ref + "'"); } diff --git a/src/openms/source/FORMAT/InspectInfile.cpp b/src/openms/source/FORMAT/InspectInfile.cpp index 2280528387c..34b7df556db 100644 --- a/src/openms/source/FORMAT/InspectInfile.cpp +++ b/src/openms/source/FORMAT/InspectInfile.cpp @@ -258,7 +258,7 @@ namespace OpenMS PTMXMLFile().load(modifications_filename, ptm_informations); } // if the modification cannot be found - if (ptm_informations.find(mod_parts.front()) != ptm_informations.end()) + if (ptm_informations.contains(mod_parts.front())) { mass = ptm_informations[mod_parts.front()].first; // composition residues = ptm_informations[mod_parts.front()].second; // residues @@ -335,7 +335,7 @@ namespace OpenMS { type = mod_parts.front(); type.toUpper(); - if (types.find(type) != String::npos) + if (types.contains(type)) { mod_parts.erase(mod_parts.begin()); } @@ -365,7 +365,7 @@ namespace OpenMS } // insert the modification - if (PTMname_residues_mass_type_.find(name) == PTMname_residues_mass_type_.end()) + if (!PTMname_residues_mass_type_.contains(name)) { PTMname_residues_mass_type_[name] = vector(3); PTMname_residues_mass_type_[name][0] = residues; diff --git a/src/openms/source/FORMAT/InspectOutfile.cpp b/src/openms/source/FORMAT/InspectOutfile.cpp index 47667154afb..1704831ee6c 100644 --- a/src/openms/source/FORMAT/InspectOutfile.cpp +++ b/src/openms/source/FORMAT/InspectOutfile.cpp @@ -182,7 +182,7 @@ namespace OpenMS // map the database position of the protein to its position in the // protein hits and insert it, if it's a new protein - if (rn_position_map.find(record_number) == rn_position_map.end()) + if (!rn_position_map.contains(record_number)) { rn_position_map[record_number] = protein_identification.getHits().size(); protein_identification.insertHit(protein_hit); diff --git a/src/openms/source/FORMAT/MSExperimentArrowExport.cpp b/src/openms/source/FORMAT/MSExperimentArrowExport.cpp index 0b78609a82c..dd3bf4c8230 100644 --- a/src/openms/source/FORMAT/MSExperimentArrowExport.cpp +++ b/src/openms/source/FORMAT/MSExperimentArrowExport.cpp @@ -47,7 +47,7 @@ bool passesMSLevelFilter(const MSSpectrum& spec, const std::unordered_set& ms_levels_set) { if (ms_levels_set.empty()) return true; - return ms_levels_set.find(spec.getMSLevel()) != ms_levels_set.end(); + return ms_levels_set.contains(spec.getMSLevel()); } /// Get iterator range for RT-filtered spectra using binary search diff --git a/src/openms/source/FORMAT/MSPFile.cpp b/src/openms/source/FORMAT/MSPFile.cpp index b5c2fee8603..202deb04489 100644 --- a/src/openms/source/FORMAT/MSPFile.cpp +++ b/src/openms/source/FORMAT/MSPFile.cpp @@ -183,7 +183,7 @@ namespace OpenMS mod_split[i].split(',', single_mod); String mod_name = single_mod[2]; - if (modname_to_unimod.find(mod_name) != modname_to_unimod.end()) + if (modname_to_unimod.contains(mod_name)) { mod_name = modname_to_unimod[mod_name]; } diff --git a/src/openms/source/FORMAT/MSstatsFile.cpp b/src/openms/source/FORMAT/MSstatsFile.cpp index 76c829c3f8b..03f77fc3b22 100644 --- a/src/openms/source/FORMAT/MSstatsFile.cpp +++ b/src/openms/source/FORMAT/MSstatsFile.cpp @@ -121,7 +121,7 @@ void MSstatsFile::constructFile_(const String& retention_time_summarization_meth set intensities{}; for (const auto &p : line.second) { - if (retention_times.find(get<1>(p)) != retention_times.end()) + if (retention_times.contains(get<1>(p))) { OPENMS_LOG_WARN << "Peptide ion appears multiple times at the same retention time." " This is not expected." @@ -751,7 +751,7 @@ void MSstatsFile::assembleRunMap_( for (ExperimentalDesign::MSFileSectionEntry const& r : msfile_section) { std::pair< String, unsigned> tpl = std::make_pair(File::basename(r.path), r.fraction); - if (run_map.find(tpl) == run_map.end()) + if (!run_map.contains(tpl)) { run_map[tpl] = run_counter++; } diff --git a/src/openms/source/FORMAT/MascotRemoteQuery.cpp b/src/openms/source/FORMAT/MascotRemoteQuery.cpp index 041182b0dc3..f46e54f375d 100644 --- a/src/openms/source/FORMAT/MascotRemoteQuery.cpp +++ b/src/openms/source/FORMAT/MascotRemoteQuery.cpp @@ -266,15 +266,15 @@ namespace OpenMS if (hasError()) return; - if (response.find("Logged in successfu") != string::npos) + if (response.contains("Logged in successfu")) { OPENMS_LOG_INFO << "Login successful!" << std::endl; } - else if (response.find("Error: You have entered an invalid password") != string::npos) + else if (response.contains("Error: You have entered an invalid password")) { error_message_ = "Error: You have entered an invalid password"; } - else if (response.find("is not a valid user") != string::npos) + else if (response.contains("is not a valid user")) { error_message_ = "Error: Username is not valid"; } @@ -311,7 +311,7 @@ namespace OpenMS if (hasError()) return; // Check for "Click here to see Search Report" - if (response.find("Click here to see Search Report") == string::npos) + if (!response.contains("Click here to see Search Report")) { // Check for Mascot error codes regex mascot_error_regex(R"(\[M[0-9]{5}\])"); @@ -363,7 +363,7 @@ namespace OpenMS if (hasError()) return; // Check if this is a decoy response - if (xml_response.find("") != string::npos) + if (xml_response.contains("")) { mascot_decoy_xml_ = std::move(xml_response); return; @@ -393,8 +393,8 @@ namespace OpenMS if (hasError()) return {}; // Handle Mascot 2.4 continuation links (these are in-body HTML, NOT HTTP redirects) - while (response.find("Finished after") != string::npos && - response.find("adduct_opt)->getName(); // M+H;1+ -> [M+H]1+ - if (adduct_name.find(';') != std::string::npos) // wrong format -> reformat + if (adduct_name.contains(';')) // wrong format -> reformat { String prefix = adduct_name.substr(0, adduct_name.find(';')); String suffix = adduct_name.substr(adduct_name.find(';') + 1, adduct_name.size()); diff --git a/src/openms/source/FORMAT/OMSSAXMLFile.cpp b/src/openms/source/FORMAT/OMSSAXMLFile.cpp index a54d2d4f486..0f5a4ceb444 100644 --- a/src/openms/source/FORMAT/OMSSAXMLFile.cpp +++ b/src/openms/source/FORMAT/OMSSAXMLFile.cpp @@ -127,7 +127,7 @@ namespace OpenMS */ - if (mods_map_.find(actual_mod_type_.toInt()) != mods_map_.end() && !mods_map_[actual_mod_type_.toInt()].empty()) + if (mods_map_.contains(actual_mod_type_.toInt()) && !mods_map_[actual_mod_type_.toInt()].empty()) { if (mods_map_[actual_mod_type_.toInt()].size() > 1) { @@ -388,7 +388,7 @@ namespace OpenMS set mod_names = mod_set.getVariableModificationNames(); for (set::const_iterator it = mod_names.begin(); it != mod_names.end(); ++it) { - if (!(mods_to_num_.find(*it) != mods_to_num_.end())) + if (!(mods_to_num_.contains(*it))) { mods_map_[omssa_mod_num].push_back(ModificationsDB::getInstance()->getModification(*it)); mods_to_num_[*it] = omssa_mod_num; diff --git a/src/openms/source/FORMAT/OSWFile.cpp b/src/openms/source/FORMAT/OSWFile.cpp index c66a1fac6ce..70c46a9b9e3 100644 --- a/src/openms/source/FORMAT/OSWFile.cpp +++ b/src/openms/source/FORMAT/OSWFile.cpp @@ -2053,7 +2053,7 @@ namespace OpenMS Sql::extractDouble(stmt, 4), Sql::extractDouble(stmt, 5) }; - if (!existing_ids.count(aligned_feature_id)) + if (!existing_ids.contains(aligned_feature_id)) { new_feature_ids.push_back(aligned_feature_id); existing_ids.insert(aligned_feature_id); diff --git a/src/openms/source/FORMAT/PEFFFile.cpp b/src/openms/source/FORMAT/PEFFFile.cpp index d1bb454a0eb..0c742192242 100644 --- a/src/openms/source/FORMAT/PEFFFile.cpp +++ b/src/openms/source/FORMAT/PEFFFile.cpp @@ -811,7 +811,7 @@ namespace OpenMS size_t local_pos = var->position - 1 - start; // Position within peptide // Check for conflicting variants at same position - if (modified_positions.count(local_pos)) + if (modified_positions.contains(local_pos)) { has_conflict = true; break; @@ -1157,7 +1157,7 @@ namespace OpenMS size_t local_pos = var->position - 1 - start; // Check for conflicting variants at same position - if (modified_positions.count(local_pos)) + if (modified_positions.contains(local_pos)) { has_conflict = true; break; @@ -1757,7 +1757,7 @@ namespace OpenMS else if (line[start] == '>') { // Check if description contains PEFF annotations (backslash keywords) - if (line.find('\\') != std::string::npos) + if (line.contains('\\')) { return true; } @@ -2097,7 +2097,7 @@ namespace OpenMS const char up = static_cast(std::toupper(static_cast(c))); // IUPAC nucleotide ambiguity codes. const std::string allowed = "ACGTURYSWKMBDHVN"; - return allowed.find(up) != std::string::npos; + return allowed.contains(up); }; // Parse each annotation @@ -2136,7 +2136,7 @@ namespace OpenMS String value = annotation.substr(eq_pos + 1); // Fix #7: Detect duplicate keys (spec section 3.3.3: same key MUST NOT appear twice) - if (seen_keys.count(key)) + if (seen_keys.contains(key)) { OPENMS_LOG_WARN << "PEFF: Duplicate key '" << key << "' in entry '" << entry.identifier << "'.\n"; } @@ -2258,7 +2258,7 @@ namespace OpenMS (void)annot_id; std::vector pos_tokens; - if (pos_field.find(',') != String::npos) + if (pos_field.contains(',')) { pos_field.split(',', pos_tokens); } @@ -2310,7 +2310,7 @@ namespace OpenMS if (!parts_check.empty()) { auto [annot_id, pos_field] = extractAnnotationId(parts_check[0]); - if (pos_field.find(',') != String::npos) + if (pos_field.contains(',')) { std::vector positions; pos_field.split(',', positions); @@ -2709,7 +2709,7 @@ namespace OpenMS { mod.position = 0; } - else if (pos_field.find(',') != String::npos) + else if (pos_field.contains(',')) { // Take first position; caller will handle expansion std::vector positions; diff --git a/src/openms/source/FORMAT/ParamCTDFile.cpp b/src/openms/source/FORMAT/ParamCTDFile.cpp index 473e888dd6c..88c548e6327 100644 --- a/src/openms/source/FORMAT/ParamCTDFile.cpp +++ b/src/openms/source/FORMAT/ParamCTDFile.cpp @@ -111,22 +111,22 @@ namespace OpenMS os << param_it->value.toString() << R"(" type="double")"; break; case ParamValue::STRING_VALUE: - if (tag_list.find(TOPPBase::TAG_INPUT_FILE) != tag_list.end()) + if (tag_list.contains(TOPPBase::TAG_INPUT_FILE)) { os << escapeXML(param_it->value.toString()) << R"(" type="input-file")"; tag_list.erase(TOPPBase::TAG_INPUT_FILE); } - else if (tag_list.find(TOPPBase::TAG_OUTPUT_FILE) != tag_list.end()) + else if (tag_list.contains(TOPPBase::TAG_OUTPUT_FILE)) { os << escapeXML(param_it->value.toString()) << R"(" type="output-file")"; tag_list.erase(TOPPBase::TAG_OUTPUT_FILE); } - else if (tag_list.find(TOPPBase::TAG_OUTPUT_DIR) != tag_list.end()) + else if (tag_list.contains(TOPPBase::TAG_OUTPUT_DIR)) { os << escapeXML(param_it->value.toString()) << R"(" type="output-dir")"; tag_list.erase(TOPPBase::TAG_OUTPUT_DIR); } - else if (tag_list.find(TOPPBase::TAG_OUTPUT_PREFIX) != tag_list.end()) + else if (tag_list.contains(TOPPBase::TAG_OUTPUT_PREFIX)) { os << escapeXML(param_it->value.toString()) << R"(" type="output-prefix")"; tag_list.erase(TOPPBase::TAG_OUTPUT_PREFIX); @@ -139,7 +139,7 @@ namespace OpenMS else { std::string value = param_it->value.toString(); - if (value.find('\t') != std::string::npos) + if (value.contains('\t')) { replace(value, '\t', " "); } @@ -147,12 +147,12 @@ namespace OpenMS } break; case ParamValue::STRING_LIST: - if (tag_list.find(TOPPBase::TAG_INPUT_FILE) != tag_list.end()) + if (tag_list.contains(TOPPBase::TAG_INPUT_FILE)) { os << R"(" type="input-file")"; tag_list.erase(TOPPBase::TAG_INPUT_FILE); } - else if (tag_list.find(TOPPBase::TAG_OUTPUT_FILE) != tag_list.end()) + else if (tag_list.contains(TOPPBase::TAG_OUTPUT_FILE)) { os << R"(" type="output-file")"; tag_list.erase(TOPPBase::TAG_OUTPUT_FILE); @@ -177,7 +177,7 @@ namespace OpenMS os << " description=\"" << escapeXML(description) << "\""; - if (tag_list.find("required") != tag_list.end()) + if (tag_list.contains("required")) { os << R"( required="true")"; tag_list.erase("required"); @@ -187,7 +187,7 @@ namespace OpenMS os << R"( required="false")"; } - if (tag_list.find("advanced") != tag_list.end()) + if (tag_list.contains("advanced")) { os << R"( advanced="true")"; tag_list.erase("advanced"); @@ -269,7 +269,7 @@ namespace OpenMS if (!restrictions.empty()) { - if (param_it->tags.find("input file") != param_it->tags.end() || param_it->tags.find("output file") != param_it->tags.end() || param_it->tags.find("output prefix") != param_it->tags.end()) + if (param_it->tags.contains("input file") || param_it->tags.contains("output file") || param_it->tags.contains("output prefix")) { os << " supported_formats=\"" << escapeXML(restrictions) << "\""; } @@ -294,7 +294,7 @@ namespace OpenMS case ParamValue::STRING_LIST: for (auto item : static_cast&>(param_it->value)) { - if (item.find('\t') != std::string::npos) + if (item.contains('\t')) { replace(item, '\t', " "); } @@ -340,15 +340,15 @@ namespace OpenMS std::string ParamCTDFile::escapeXML(const std::string& to_escape) { std::string copy = to_escape; - if (copy.find('&') != std::string::npos) + if (copy.contains('&')) replace(copy, '&', "&"); - if (copy.find('>') != std::string::npos) + if (copy.contains('>')) replace(copy, '>', ">"); - if (copy.find('"') != std::string::npos) + if (copy.contains('"')) replace(copy, '"', """); - if (copy.find('<') != std::string::npos) + if (copy.contains('<')) replace(copy, '<', "<"); - if (copy.find('\'') != std::string::npos) + if (copy.contains('\'')) replace(copy, '\'', "'"); return copy; diff --git a/src/openms/source/FORMAT/ParamJSONFile.cpp b/src/openms/source/FORMAT/ParamJSONFile.cpp index 3104f81893d..392ea8cf278 100644 --- a/src/openms/source/FORMAT/ParamJSONFile.cpp +++ b/src/openms/source/FORMAT/ParamJSONFile.cpp @@ -97,10 +97,10 @@ namespace OpenMS { value = node.get() ? "true" : "false"; } - else if (entry.tags.count("input file")) + else if (entry.tags.contains("input file")) { // If this is an input file and 'is_executable' is set. this can be of 'class: File' or 'type: string' - if (entry.tags.count("is_executable")) + if (entry.tags.contains("is_executable")) { if (node.is_object()) { @@ -132,7 +132,7 @@ namespace OpenMS } else if (entry.value.valueType() == ParamValue::ValueType::STRING_LIST) { - if (entry.tags.count("input file")) + if (entry.tags.contains("input file")) { value = node["path"].get>(); } @@ -265,7 +265,7 @@ namespace OpenMS { node = param_it->value.toBool(); } else { - if (tags.count("file") > 0 && tags.count("output") == 0) { + if (tags.contains("file") && !tags.contains("output")) { node["class"] = "File"; node["path"] = param_it->value.toString(); } else { @@ -280,7 +280,7 @@ namespace OpenMS node = param_it->value.toDoubleVector(); break; case ParamValue::STRING_LIST: - if (tags.count("file") > 0 && tags.count("output") == 0) { + if (tags.contains("file") && !tags.contains("output")) { node["class"] = "File"; node["path"] = param_it->value.toStringVector(); } else { diff --git a/src/openms/source/FORMAT/ParamXMLFile.cpp b/src/openms/source/FORMAT/ParamXMLFile.cpp index f2f903f85f6..31c271464b0 100644 --- a/src/openms/source/FORMAT/ParamXMLFile.cpp +++ b/src/openms/source/FORMAT/ParamXMLFile.cpp @@ -111,17 +111,17 @@ namespace OpenMS break; case ParamValue::STRING_VALUE: - if (tag_list.find("input file") != tag_list.end()) + if (tag_list.contains("input file")) { os << indentation << "name) << "\" value=\"" << writeXMLEscape(it->value.toString()) << R"(" type="input-file")"; tag_list.erase("input file"); } - else if (tag_list.find("output file") != tag_list.end()) + else if (tag_list.contains("output file")) { os << indentation << "name) << "\" value=\"" << writeXMLEscape(it->value.toString()) << R"(" type="output-file")"; tag_list.erase("output file"); } - else if (tag_list.find("output prefix") != tag_list.end()) + else if (tag_list.contains("output prefix")) { os << indentation << "name) << "\" value=\"" << writeXMLEscape(it->value.toString()) << R"(" type="output-prefix")"; tag_list.erase("output prefix"); @@ -141,12 +141,12 @@ namespace OpenMS break; case ParamValue::STRING_LIST: - if (tag_list.find("input file") != tag_list.end()) + if (tag_list.contains("input file")) { os << indentation << "name) << R"(" type="input-file")"; tag_list.erase("input file"); } - else if (tag_list.find("output file") != tag_list.end()) + else if (tag_list.contains("output file")) { os << indentation << "name) << R"(" type="output-file")"; tag_list.erase("output file"); @@ -178,7 +178,7 @@ namespace OpenMS os << " description=\"" << writeXMLEscape(d) << "\""; // required - if (tag_list.find("required") != tag_list.end()) + if (tag_list.contains("required")) { os << " required=\"true\""; tag_list.erase("required"); @@ -189,7 +189,7 @@ namespace OpenMS } // advanced - if (tag_list.find("advanced") != tag_list.end()) + if (tag_list.contains("advanced")) { os << " advanced=\"true\""; tag_list.erase("advanced"); @@ -273,9 +273,9 @@ namespace OpenMS // for files we store the restrictions as supported_formats if (!restrictions.empty()) { - if (it->tags.find("input file") != it->tags.end() - || it->tags.find("output file") != it->tags.end() - || it->tags.find("output prefix") != it->tags.end()) + if (it->tags.contains("input file") + || it->tags.contains("output file") + || it->tags.contains("output prefix")) { os << " supported_formats=\"" << writeXMLEscape(restrictions) << "\""; } diff --git a/src/openms/source/FORMAT/PepNovoOutfile.cpp b/src/openms/source/FORMAT/PepNovoOutfile.cpp index 5e7350d585b..106556b6f13 100644 --- a/src/openms/source/FORMAT/PepNovoOutfile.cpp +++ b/src/openms/source/FORMAT/PepNovoOutfile.cpp @@ -100,7 +100,7 @@ namespace OpenMS if (mod_it.empty()) continue; //cout<<*mod_it<second<getModification(pnovo_modkey_to_mod_id.find(mod_it)->second); @@ -167,7 +167,7 @@ namespace OpenMS bool success = false; if (!index_to_precursor.empty()) { - if (index_to_precursor.find(index) != index_to_precursor.end()) + if (index_to_precursor.contains(index)) { peptide_identification.setRT(index_to_precursor.find(index)->second.first); peptide_identification.setMZ(index_to_precursor.find(index)->second.second); diff --git a/src/openms/source/FORMAT/PercolatorInfile.cpp b/src/openms/source/FORMAT/PercolatorInfile.cpp index 8256fe459de..3339ac1141c 100644 --- a/src/openms/source/FORMAT/PercolatorInfile.cpp +++ b/src/openms/source/FORMAT/PercolatorInfile.cpp @@ -124,7 +124,7 @@ namespace OpenMS annos.getRow(i, row); //Check if mapping already has PSM, if it does add - if (anno_mapping.find(row[to_idx_a.at("psm_id")].toInt()) == anno_mapping.end()) + if (!anno_mapping.contains(row[to_idx_a.at("psm_id")].toInt())) { //Make a new vector of annotations PeptideHit::PeakAnnotation peak_temp; @@ -244,7 +244,7 @@ namespace OpenMS if (file_name_column_index >= 0) { raw_file_name = row[file_name_column_index]; - if (map_filename_to_idx.find(raw_file_name) == map_filename_to_idx.end()) + if (!map_filename_to_idx.contains(raw_file_name)) { filenames.push_back(raw_file_name); map_filename_to_idx[raw_file_name] = filenames.size() - 1; @@ -370,7 +370,7 @@ namespace OpenMS // add annotations if (SageAnnotation) { - if (anno_mapping.find(sSpecId.toInt()) != anno_mapping.end()) + if (anno_mapping.contains(sSpecId.toInt())) { // copy annotations from mapping to PeptideHit vector pep_vec; @@ -554,7 +554,7 @@ namespace OpenMS const auto& hits = stamped[pid_idx].getHits(); for (size_t hit_idx = 0; hit_idx < hits.size(); ++hit_idx) { - if (skipped.count({pid_idx, hit_idx})) continue; + if (skipped.contains({pid_idx, hit_idx})) continue; const PeptideHit& hit = hits[hit_idx]; StringList feats; diff --git a/src/openms/source/FORMAT/ProteinIdentificationArrowIO.cpp b/src/openms/source/FORMAT/ProteinIdentificationArrowIO.cpp index 7907a590520..00969ed92bf 100644 --- a/src/openms/source/FORMAT/ProteinIdentificationArrowIO.cpp +++ b/src/openms/source/FORMAT/ProteinIdentificationArrowIO.cpp @@ -58,7 +58,7 @@ namespace // anonymous mii.getKeys(keys); for (const auto& key : keys) { - if (excluded_keys.count(key)) continue; + if (excluded_keys.contains(key)) continue; const DataValue& val = mii.getMetaValue(key); (void)struct_b->Append(); (void)name_b->Append(key); diff --git a/src/openms/source/FORMAT/QPXFile.cpp b/src/openms/source/FORMAT/QPXFile.cpp index 7e6e66ef484..2c5f216e767 100644 --- a/src/openms/source/FORMAT/QPXFile.cpp +++ b/src/openms/source/FORMAT/QPXFile.cpp @@ -309,7 +309,7 @@ std::shared_ptr QPXFile::exportToArrow( acc_str = "UNIMOD:" + std::to_string(mod->getUniModRecordId()); } std::string pos_str = std::string(residue.getOneLetterCode()) + "." + std::to_string(pos + 1); - if (mod_map.find(name) == mod_map.end()) + if (!mod_map.contains(name)) { mod_map[name] = {acc_str, {}}; } @@ -328,7 +328,7 @@ std::shared_ptr QPXFile::exportToArrow( acc_str = "UNIMOD:" + std::to_string(mod->getUniModRecordId()); } std::string pos_str = "C-term." + std::to_string(seq.size() + 1); - if (mod_map.find(name) == mod_map.end()) + if (!mod_map.contains(name)) { mod_map[name] = {acc_str, {}}; } @@ -418,7 +418,7 @@ std::shared_ptr QPXFile::exportToArrow( hit.getKeys(keys); for (const auto& key : keys) { - if (excluded_hit_mvs_psm.count(key)) continue; + if (excluded_hit_mvs_psm.contains(key)) continue; const DataValue& val = hit.getMetaValue(key); if ((val.valueType() == DataValue::INT_VALUE || val.valueType() == DataValue::DOUBLE_VALUE) && Scores::isKnownScoreType(key)) @@ -568,7 +568,7 @@ std::shared_ptr QPXFile::exportToArrow( hit.getKeys(keys); for (const auto& key : keys) { - if (excluded_hit_mvs_psm.count(key)) continue; + if (excluded_hit_mvs_psm.contains(key)) continue; const DataValue& val = hit.getMetaValue(key); // Skip known scores (already in additional_scores) if ((val.valueType() == DataValue::INT_VALUE || val.valueType() == DataValue::DOUBLE_VALUE) @@ -981,7 +981,7 @@ std::shared_ptr QPXFile::exportPSMsToQPXArrow( { acc_str = "UNIMOD:" + std::to_string(mod->getUniModRecordId()); } - if (mod_map.find(name) == mod_map.end()) + if (!mod_map.contains(name)) { mod_map[name] = {acc_str, {}}; } @@ -999,7 +999,7 @@ std::shared_ptr QPXFile::exportPSMsToQPXArrow( { acc_str = "UNIMOD:" + std::to_string(mod->getUniModRecordId()); } - if (mod_map.find(name) == mod_map.end()) + if (!mod_map.contains(name)) { mod_map[name] = {acc_str, {}}; } @@ -1098,7 +1098,7 @@ std::shared_ptr QPXFile::exportPSMsToQPXArrow( hit.getKeys(keys); for (const auto& key : keys) { - if (excluded_hit_mvs.count(key)) continue; + if (excluded_hit_mvs.contains(key)) continue; const DataValue& val = hit.getMetaValue(key); if ((val.valueType() == DataValue::INT_VALUE || val.valueType() == DataValue::DOUBLE_VALUE) && Scores::isKnownScoreType(key)) diff --git a/src/openms/source/FORMAT/QcMLFile.cpp b/src/openms/source/FORMAT/QcMLFile.cpp index b8359524cdc..85adb0d3eef 100644 --- a/src/openms/source/FORMAT/QcMLFile.cpp +++ b/src/openms/source/FORMAT/QcMLFile.cpp @@ -793,7 +793,7 @@ namespace OpenMS to_ignore.insert("binary"); // ... } - if (to_ignore.find(tag_) != to_ignore.end()) + if (to_ignore.contains(tag_)) { return; } @@ -920,7 +920,7 @@ namespace OpenMS //close current tag open_tags_.pop_back(); - if (to_ignore.find(tag_) != to_ignore.end()) + if (to_ignore.contains(tag_)) { return; } diff --git a/src/openms/source/FORMAT/RationalScan2ImConverter.cpp b/src/openms/source/FORMAT/RationalScan2ImConverter.cpp index 6879f644f14..90c5623050e 100644 --- a/src/openms/source/FORMAT/RationalScan2ImConverter.cpp +++ b/src/openms/source/FORMAT/RationalScan2ImConverter.cpp @@ -185,7 +185,7 @@ namespace OpenMS frame_to_cal[frame_id] = cal_id; // Verify calibration ID exists - if (calibrations.find(cal_id) == calibrations.end()) + if (!calibrations.contains(cal_id)) { OPENMS_LOG_WARN << "Frame " << frame_id << " references unknown TimsCalibration Id=" << cal_id diff --git a/src/openms/source/FORMAT/SVOutStream.cpp b/src/openms/source/FORMAT/SVOutStream.cpp index 5fab31af25a..3b0a5771c8d 100644 --- a/src/openms/source/FORMAT/SVOutStream.cpp +++ b/src/openms/source/FORMAT/SVOutStream.cpp @@ -59,7 +59,7 @@ namespace OpenMS SVOutStream& SVOutStream::operator<<(String str) { - if (str.find('\n') != String::npos) + if (str.contains('\n')) { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "argument must not contain newline characters"); } diff --git a/src/openms/source/FORMAT/SequestInfile.cpp b/src/openms/source/FORMAT/SequestInfile.cpp index 49c64deaf4f..4bbd3a6f8c5 100644 --- a/src/openms/source/FORMAT/SequestInfile.cpp +++ b/src/openms/source/FORMAT/SequestInfile.cpp @@ -771,7 +771,7 @@ namespace OpenMS PTMXMLFile().load(modifications_filename, ptm_informations); } // if the modification cannot be found - if (ptm_informations.find(mod_parts.front()) != ptm_informations.end()) + if (ptm_informations.contains(mod_parts.front())) { mass = ptm_informations[mod_parts.front()].first; // composition residues = ptm_informations[mod_parts.front()].second; // residues @@ -848,7 +848,7 @@ namespace OpenMS { type = mod_parts.front(); type.toUpper(); - if (types.find(type) != String::npos) + if (types.contains(type)) { mod_parts.erase(mod_parts.begin()); } @@ -878,7 +878,7 @@ namespace OpenMS } // insert the modification - if (PTMname_residues_mass_type_.find(name) == PTMname_residues_mass_type_.end()) + if (!PTMname_residues_mass_type_.contains(name)) { PTMname_residues_mass_type_[name] = vector(3); PTMname_residues_mass_type_[name][0] = residues; diff --git a/src/openms/source/FORMAT/TriqlerFile.cpp b/src/openms/source/FORMAT/TriqlerFile.cpp index 72996780b36..8ebdb2e9fd0 100644 --- a/src/openms/source/FORMAT/TriqlerFile.cpp +++ b/src/openms/source/FORMAT/TriqlerFile.cpp @@ -321,7 +321,7 @@ void TriqlerFile::assembleRunMap_( for (ExperimentalDesign::MSFileSectionEntry const& r : msfile_section) { std::pair< String, unsigned> tpl = std::make_pair(File::basename(r.path), r.fraction); - if (run_map.find(tpl) == run_map.end()) + if (!run_map.contains(tpl)) { run_map[tpl] = run_counter++; } diff --git a/src/openms/source/FORMAT/VALIDATORS/MzDataValidator.cpp b/src/openms/source/FORMAT/VALIDATORS/MzDataValidator.cpp index 3f67d3afacc..21a625c1a08 100644 --- a/src/openms/source/FORMAT/VALIDATORS/MzDataValidator.cpp +++ b/src/openms/source/FORMAT/VALIDATORS/MzDataValidator.cpp @@ -81,7 +81,7 @@ namespace OpenMS::Internal if (cv_.exists(parsed_term.unit_accession)) { // check whether this unit is allowed within the cv term - if (term.units.find(parsed_term.unit_accession) == term.units.end()) + if (!term.units.contains(parsed_term.unit_accession)) { // last chance, a child term of the units was used auto lambda = [&parsed_term] (const String& child) diff --git a/src/openms/source/FORMAT/VALIDATORS/SemanticValidator.cpp b/src/openms/source/FORMAT/VALIDATORS/SemanticValidator.cpp index 034ebfee0f7..f69ed303ecd 100644 --- a/src/openms/source/FORMAT/VALIDATORS/SemanticValidator.cpp +++ b/src/openms/source/FORMAT/VALIDATORS/SemanticValidator.cpp @@ -324,7 +324,7 @@ namespace OpenMS::Internal if (cv_.exists(parsed_term.unit_accession)) { // check whether this unit is allowed within the cv term - if (term.units.find(parsed_term.unit_accession) == term.units.end()) + if (!term.units.contains(parsed_term.unit_accession)) { // last chance, a child term of the units was used set child_terms; diff --git a/src/openms/source/FORMAT/XICParquetFile.cpp b/src/openms/source/FORMAT/XICParquetFile.cpp index 91d6de5c0bb..11f11875a9d 100644 --- a/src/openms/source/FORMAT/XICParquetFile.cpp +++ b/src/openms/source/FORMAT/XICParquetFile.cpp @@ -696,8 +696,8 @@ namespace OpenMS cond.column = it->second; } - const bool unsupported_col = unsupported.count(upper_(cond.column)) > 0; - const bool exists_in_schema = name_map.find(upper_(cond.column)) != name_map.end(); + const bool unsupported_col = unsupported.contains(upper_(cond.column)); + const bool exists_in_schema = name_map.contains(upper_(cond.column)); if (unsupported_col || !exists_in_schema) { dropped_columns.push_back(original); @@ -1604,12 +1604,12 @@ namespace OpenMS for (const auto& name : requested_columns) { const String upper_name = upper_(name); - if (allowed_columns.find(upper_name) == allowed_columns.end()) + if (!allowed_columns.contains(upper_name)) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Unsupported analyte column", name); } - if (schema_columns.find(upper_name) == schema_columns.end()) + if (!schema_columns.contains(upper_name)) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Column not found in parquet schema", name); @@ -1626,7 +1626,7 @@ namespace OpenMS auto want = [&](const String& name) -> bool { - return requested_set.find(name) != requested_set.end(); + return requested_set.contains(name); }; auto table = readParquetTableColumns_(filenames_, normalized_columns); diff --git a/src/openms/source/FORMAT/XIMParquetFile.cpp b/src/openms/source/FORMAT/XIMParquetFile.cpp index 8796b06625d..0abc320f7c2 100644 --- a/src/openms/source/FORMAT/XIMParquetFile.cpp +++ b/src/openms/source/FORMAT/XIMParquetFile.cpp @@ -784,8 +784,8 @@ namespace OpenMS cond.column = it->second; } - const bool unsupported_col = unsupported.count(upper_(cond.column)) > 0; - const bool exists_in_schema = name_map.find(upper_(cond.column)) != name_map.end(); + const bool unsupported_col = unsupported.contains(upper_(cond.column)); + const bool exists_in_schema = name_map.contains(upper_(cond.column)); if (unsupported_col || !exists_in_schema) { dropped_columns.push_back(original); @@ -1715,12 +1715,12 @@ namespace OpenMS for (const auto& name : requested_columns) { const String upper_name = upper_(name); - if (allowed_columns.find(upper_name) == allowed_columns.end()) + if (!allowed_columns.contains(upper_name)) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Unsupported analyte column", name); } - if (schema_columns.find(upper_name) == schema_columns.end()) + if (!schema_columns.contains(upper_name)) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Column not found in parquet schema", name); @@ -1745,7 +1745,7 @@ namespace OpenMS bool has_precursor_discriminator = false; for (const auto& key : precursor_discriminators) { - if (requested_set.find(key) != requested_set.end()) + if (requested_set.contains(key)) { has_precursor_discriminator = true; break; @@ -1761,7 +1761,7 @@ namespace OpenMS auto want = [&](const String& name) -> bool { - return requested_set.find(name) != requested_set.end(); + return requested_set.contains(name); }; auto table = readParquetTableColumns_(filenames_, normalized_columns); diff --git a/src/openms/source/FORMAT/XTandemInfile.cpp b/src/openms/source/FORMAT/XTandemInfile.cpp index 8ea137d574c..270c3dc4fb1 100644 --- a/src/openms/source/FORMAT/XTandemInfile.cpp +++ b/src/openms/source/FORMAT/XTandemInfile.cpp @@ -119,13 +119,13 @@ namespace OpenMS orig = "["; } // check double usage - if (origin_set.find(orig) != origin_set.end()) + if (origin_set.contains(orig)) { OPENMS_LOG_WARN << "X! Tandem config file: Duplicate modification assignment to origin '" << orig << "'. " << "X! Tandem will ignore the first modification '" << origin_set.find(orig)->second << "'!\n"; } // check if already used before (i.e. we are currently looking at variable mods) - if (affected_origins.find(orig) != affected_origins.end()) + if (affected_origins.contains(orig)) { OPENMS_LOG_INFO << "X! Tandem config file: Fixed modification and variable modification to origin '" << orig << "' detected. " << "Using corrected mass of " << mod_mass - affected_origins.find(orig)->second << " instead of " << mod_mass << ".\n"; @@ -318,8 +318,8 @@ namespace OpenMS } if (!force_default_mods_ && - (var_mods.find("Gln->pyro-Glu (N-term Q)") != var_mods.end()) && - (var_mods.find("Glu->pyro-Glu (N-term E)") != var_mods.end())) + (var_mods.contains("Gln->pyro-Glu (N-term Q)")) && + (var_mods.contains("Glu->pyro-Glu (N-term E)"))) { writeNote_(os, "protein, quick pyrolidone", true); OPENMS_LOG_INFO << "Modifications 'Gln->pyro-Glu (N-term Q)' and 'Glu->pyro-Glu (N-term E)' are handled implicitly by the X! Tandem option 'protein, quick pyrolidone'. Set the 'force' flag in XTandemAdapter to force explicit inclusion of these modifications." << endl; @@ -327,7 +327,7 @@ namespace OpenMS // special case for "Acetyl (N-term)" modification: if (!force_default_mods_ && - (var_mods.find("Acetyl (N-term)") != var_mods.end())) + (var_mods.contains("Acetyl (N-term)"))) { writeNote_(os, "protein, quick acetyl", true); OPENMS_LOG_INFO << "Modification 'Acetyl (N-term)' is handled implicitly by the X! Tandem option 'protein, quick acetyl'. Set the 'force' flag in XTandemAdapter to force explicit inclusion of this modification." << endl; diff --git a/src/openms/source/FORMAT/XTandemXMLFile.cpp b/src/openms/source/FORMAT/XTandemXMLFile.cpp index 343d81b8fe3..28b0d769006 100644 --- a/src/openms/source/FORMAT/XTandemXMLFile.cpp +++ b/src/openms/source/FORMAT/XTandemXMLFile.cpp @@ -116,7 +116,7 @@ namespace OpenMS String seq = attributeAsString_(attributes, "seq"); // is this the same peptide as before, just in a different protein (scores will be the same)? - if ((peptide_hits_.find(id) == peptide_hits_.end()) || (seq != previous_seq_)) + if ((!peptide_hits_.contains(id)) || (seq != previous_seq_)) { PeptideHit hit; // can't parse sequences permissively because that would skip characters @@ -300,7 +300,7 @@ namespace OpenMS if (tag_ == "protein") { UInt uid = attributeAsInt_(attributes, "uid"); - if (protein_uids_.find(uid) == protein_uids_.end()) // new protein + if (!protein_uids_.contains(uid)) // new protein { ProteinHit hit; // accession may be overwritten based on '', but set it for now: diff --git a/src/openms/source/IMAGING/MSImagingGeometry.cpp b/src/openms/source/IMAGING/MSImagingGeometry.cpp index 73f24bb0a06..fe32c019a8a 100644 --- a/src/openms/source/IMAGING/MSImagingGeometry.cpp +++ b/src/openms/source/IMAGING/MSImagingGeometry.cpp @@ -61,7 +61,7 @@ namespace OpenMS } const UInt64 key = packKey_(x, y); - if (lookup_.find(key) != lookup_.end()) + if (lookup_.contains(key)) { throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Duplicate pixel coordinate", @@ -74,7 +74,7 @@ namespace OpenMS bool MSImagingGeometry::hasPixel(UInt x, UInt y) const { - return lookup_.find(packKey_(x, y)) != lookup_.end(); + return lookup_.contains(packKey_(x, y)); } Size MSImagingGeometry::getSpectrumIndex(UInt x, UInt y) const diff --git a/src/openms/source/IONMOBILITY/IMDataConverter.cpp b/src/openms/source/IONMOBILITY/IMDataConverter.cpp index 78d131fe479..8d595b4e571 100644 --- a/src/openms/source/IONMOBILITY/IMDataConverter.cpp +++ b/src/openms/source/IONMOBILITY/IMDataConverter.cpp @@ -354,15 +354,15 @@ namespace OpenMS if (cv.isChildOf(cv_term.id, "MS:1002893")) // is child of generic 'ion mobility array'? { - if (cv_term.units.find("MS:1002814") != cv_term.units.end()) + if (cv_term.units.contains("MS:1002814")) { // MS:1002814 ! volt-second per square centimeter unit = DriftTimeUnit::VSSC; } - else if (cv_term.units.find("UO:0000028") != cv_term.units.end()) + else if (cv_term.units.contains("UO:0000028")) { // UO:0000028 ! millisecond unit = DriftTimeUnit::MILLISECOND; } - else if (cv_term.units.find("UO:0000324") != cv_term.units.end()) + else if (cv_term.units.contains("UO:0000324")) { // UO:0000324 ! square angstrom (CCS) unit = DriftTimeUnit::CCS; } diff --git a/src/openms/source/KERNEL/ConsensusMap.cpp b/src/openms/source/KERNEL/ConsensusMap.cpp index ff541af4b80..ff745f7cd15 100644 --- a/src/openms/source/KERNEL/ConsensusMap.cpp +++ b/src/openms/source/KERNEL/ConsensusMap.cpp @@ -671,7 +671,7 @@ OPENMS_THREAD_CRITICAL(LOGSTREAM) const ConsensusFeature& elem = (*this)[i]; for (ConsensusFeature::HandleSetType::const_iterator it = elem.begin(); it != elem.end(); ++it) { - if (column_description_.find(it->getMapIndex()) == column_description_.end()) + if (!column_description_.contains(it->getMapIndex())) { ++stats_wrongMID; ++wrong_ID_count[it->getMapIndex()]; diff --git a/src/openms/source/KERNEL/OnDiscMSExperiment.cpp b/src/openms/source/KERNEL/OnDiscMSExperiment.cpp index fb91c42a918..2f6a25f76e5 100644 --- a/src/openms/source/KERNEL/OnDiscMSExperiment.cpp +++ b/src/openms/source/KERNEL/OnDiscMSExperiment.cpp @@ -73,7 +73,7 @@ namespace OpenMS } } - if (chromatograms_native_ids_.find(id) == chromatograms_native_ids_.end()) + if (!chromatograms_native_ids_.contains(id)) { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, String("Could not find chromatogram with id '") + id + "'."); @@ -105,7 +105,7 @@ namespace OpenMS } } - if (spectra_native_ids_.find(id) == spectra_native_ids_.end()) + if (!spectra_native_ids_.contains(id)) { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, String("Could not find spectrum with id '") + id + "'."); diff --git a/src/openms/source/METADATA/AbsoluteQuantitationStandards.cpp b/src/openms/source/METADATA/AbsoluteQuantitationStandards.cpp index 0db485f97db..0daabbb8d34 100644 --- a/src/openms/source/METADATA/AbsoluteQuantitationStandards.cpp +++ b/src/openms/source/METADATA/AbsoluteQuantitationStandards.cpp @@ -109,7 +109,7 @@ namespace OpenMS } std::map> components_to_concentrations; mapComponentsToConcentrations(filtered_rc, feature_maps, components_to_concentrations); - if (components_to_concentrations.count(component_name)) + if (components_to_concentrations.contains(component_name)) { feature_concentrations = components_to_concentrations.at(component_name); } diff --git a/src/openms/source/METADATA/CVTermList.cpp b/src/openms/source/METADATA/CVTermList.cpp index 2eae00e9ec1..334cca9c94e 100644 --- a/src/openms/source/METADATA/CVTermList.cpp +++ b/src/openms/source/METADATA/CVTermList.cpp @@ -70,7 +70,7 @@ namespace OpenMS bool CVTermList::hasCVTerm(const String& accession) const { - return cv_terms_.find(accession) != cv_terms_.end(); + return cv_terms_.contains(accession); } bool CVTermList::operator==(const CVTermList& cv_term_list) const diff --git a/src/openms/source/METADATA/ExperimentalDesign.cpp b/src/openms/source/METADATA/ExperimentalDesign.cpp index b25aeb4ecd3..dff63d8181c 100644 --- a/src/openms/source/METADATA/ExperimentalDesign.cpp +++ b/src/openms/source/METADATA/ExperimentalDesign.cpp @@ -624,7 +624,7 @@ namespace OpenMS template void ExperimentalDesign::errorIfAlreadyExists(std::set &container, T &item, const String &message) { - if (container.find(item) != container.end()) + if (container.contains(item)) { throw Exception::MissingInformation( __FILE__, @@ -755,7 +755,7 @@ namespace OpenMS msfile_section_.erase(std::remove_if(msfile_section_.begin(), msfile_section_.end(), [&bns](MSFileSectionEntry& e) { - return bns.find(File::basename(e.path)) == bns.end(); + return !bns.contains(File::basename(e.path)); }), msfile_section_.end()); const Size diff = before - msfile_section_.size(); @@ -852,12 +852,12 @@ namespace OpenMS bool ExperimentalDesign::SampleSection::hasSample(const String& sample) const { - return sample_to_rowindex_.find(sample) != sample_to_rowindex_.end(); + return sample_to_rowindex_.contains(sample); } bool ExperimentalDesign::SampleSection::hasFactor(const String &factor) const { - return columnname_to_columnindex_.find(factor) != columnname_to_columnindex_.end(); + return columnname_to_columnindex_.contains(factor); } String ExperimentalDesign::SampleSection::getFactorValue(unsigned sample_idx, const String &factor) const diff --git a/src/openms/source/METADATA/ID/IdentificationData.cpp b/src/openms/source/METADATA/ID/IdentificationData.cpp index 140ab3ec04a..217e7805501 100644 --- a/src/openms/source/METADATA/ID/IdentificationData.cpp +++ b/src/openms/source/METADATA/ID/IdentificationData.cpp @@ -42,7 +42,7 @@ namespace OpenMS { removeFromSetIf_(container, [&lookup](typename ContainerType::iterator it) { - return !lookup.count(uintptr_t(&(*it))); + return !lookup.contains(uintptr_t(&(*it))); }); } @@ -102,7 +102,7 @@ namespace OpenMS removeFromSetIf_(element.parent_matches, [&](const ParentMatches::iterator it) { - return !lookup.count(it->first); + return !lookup.contains(it->first); }); } @@ -845,7 +845,7 @@ namespace OpenMS } removeFromSetIf_(observation_matches_, [&](ObservationMatches::iterator it) { - return !id_vars.count(it->identified_molecule_var); + return !id_vars.contains(it->identified_molecule_var); }); // remove observation matches based on observation match groups: @@ -897,7 +897,7 @@ namespace OpenMS removeFromSetIfNotHashed_(identified_oligos_, identified_oligo_lookup_); removeFromSetIf_(adducts_, [&](Adducts::iterator it) { - return !adduct_refs.count(it); + return !adduct_refs.contains(it); }); } // update look-up tables of addresses: diff --git a/src/openms/source/METADATA/ID/IdentificationDataConverter.cpp b/src/openms/source/METADATA/ID/IdentificationDataConverter.cpp index cb0e124e370..b870555e77b 100644 --- a/src/openms/source/METADATA/ID/IdentificationDataConverter.cpp +++ b/src/openms/source/METADATA/ID/IdentificationDataConverter.cpp @@ -497,7 +497,7 @@ namespace OpenMS // generate hits in different ID runs for different processing steps: for (const ID::AppliedProcessingStep& applied : parent.steps_and_scores) { - if (applied.scores.empty() && !steps.count(applied.processing_step_opt)) + if (applied.scores.empty() && !steps.contains(applied.processing_step_opt)) { continue; // no scores and no associated peptides -> skip } @@ -818,7 +818,7 @@ namespace OpenMS ID::ProcessingSoftwareRef sw_ref = (*applied.processing_step_opt)->software_ref; // mention each search engine only once: - if (!sw_refs.count(sw_ref)) + if (!sw_refs.contains(sw_ref)) { MzTabParameter param; param.setName(sw_ref->getName()); @@ -837,7 +837,7 @@ namespace OpenMS for (const pair& score_pair : applied.getScoresInOrder()) { - if (!score_map.count(score_pair.first)) // new score type + if (!score_map.contains(score_pair.first)) // new score type { score_map.insert(make_pair(score_pair.first, score_map.size() + 1)); } diff --git a/src/openms/source/METADATA/IdentifierMSRunMapper.cpp b/src/openms/source/METADATA/IdentifierMSRunMapper.cpp index 8fe105cc5d9..c8f27bd6beb 100644 --- a/src/openms/source/METADATA/IdentifierMSRunMapper.cpp +++ b/src/openms/source/METADATA/IdentifierMSRunMapper.cpp @@ -81,7 +81,7 @@ namespace OpenMS bool IdentifierMSRunMapper::hasIdentifier(const String& identifier) const { - return identifier_to_msrunpath_.find(identifier) != identifier_to_msrunpath_.end(); + return identifier_to_msrunpath_.contains(identifier); } const String& IdentifierMSRunMapper::getIdentifier(const StringList& ms_run_paths) const @@ -127,7 +127,7 @@ namespace OpenMS bool IdentifierMSRunMapper::hasRunPath(const StringList& ms_run_paths) const { - return runpath_to_identifier_.find(ms_run_paths) != runpath_to_identifier_.end(); + return runpath_to_identifier_.contains(ms_run_paths); } bool IdentifierMSRunMapper::tryGetIdentifier(const StringList& ms_run_paths, String& identifier) const diff --git a/src/openms/source/METADATA/MetaInfo.cpp b/src/openms/source/METADATA/MetaInfo.cpp index 64aa014955f..8b474fe41d1 100644 --- a/src/openms/source/METADATA/MetaInfo.cpp +++ b/src/openms/source/METADATA/MetaInfo.cpp @@ -131,14 +131,14 @@ namespace OpenMS UInt index = registry_.getIndex(name); if (index != UInt(-1)) { - return (index_to_value_.find(index) != index_to_value_.end()); + return (index_to_value_.contains(index)); } return false; } bool MetaInfo::exists(UInt index) const { - return (index_to_value_.find(index) != index_to_value_.end()); + return (index_to_value_.contains(index)); } void MetaInfo::removeValue(const String& name) diff --git a/src/openms/source/METADATA/ProteinIdentification.cpp b/src/openms/source/METADATA/ProteinIdentification.cpp index fce851e8177..6b732407bbe 100644 --- a/src/openms/source/METADATA/ProteinIdentification.cpp +++ b/src/openms/source/METADATA/ProteinIdentification.cpp @@ -351,7 +351,7 @@ namespace OpenMS for (const ProteinHit& protein : getHits()) { const String& acc = protein.getAccession(); - if (groupedAccessions.find(acc) == groupedAccessions.end()) + if (!groupedAccessions.contains(acc)) { groupedAccessions.insert(acc); ProteinGroup pg; @@ -640,7 +640,7 @@ namespace OpenMS const String& accession = this->protein_hits_[i].getAccession(); double coverage = 0.0; - if (map_acc_2_evidence.find(accession) != map_acc_2_evidence.end()) + if (map_acc_2_evidence.contains(accession)) { const set& evidences = map_acc_2_evidence.find(accession)->second; for (const auto & evidence : evidences) @@ -684,7 +684,7 @@ namespace OpenMS for (auto & protein_hit : protein_hits_) { const String& accession = protein_hit.getAccession(); - if (prot2mod.find(accession) != prot2mod.end()) + if (prot2mod.contains(accession)) { protein_hit.setModifications(prot2mod[accession]); } @@ -708,7 +708,7 @@ namespace OpenMS for (auto & protein_hit : protein_hits_) { const String& accession = protein_hit.getAccession(); - if (prot2mod.find(accession) != prot2mod.end()) + if (prot2mod.contains(accession)) { protein_hit.setModifications(prot2mod[accession]); } diff --git a/src/openms/source/ML/CLUSTERING/ClusteringGrid.cpp b/src/openms/source/ML/CLUSTERING/ClusteringGrid.cpp index 52aca4908e9..45af4853cb4 100644 --- a/src/openms/source/ML/CLUSTERING/ClusteringGrid.cpp +++ b/src/openms/source/ML/CLUSTERING/ClusteringGrid.cpp @@ -32,7 +32,7 @@ std::vector ClusteringGrid::getGridSpacingY() const void ClusteringGrid::addCluster(const CellIndex &cell_index, const int &cluster_index) { - if (cells_.find(cell_index) == cells_.end()) + if (!cells_.contains(cell_index)) { // If hash grid cell does not yet exist, create a new one. std::list clusters; @@ -48,7 +48,7 @@ void ClusteringGrid::addCluster(const CellIndex &cell_index, const int &cluster_ void ClusteringGrid::removeCluster(const CellIndex &cell_index, const int &cluster_index) { - if (cells_.find(cell_index) != cells_.end()) + if (cells_.contains(cell_index)) { cells_.find(cell_index)->second.remove(cluster_index); if (cells_.find(cell_index)->second.empty()) @@ -85,7 +85,7 @@ ClusteringGrid::CellIndex ClusteringGrid::getIndex(const Point &position) const bool ClusteringGrid::isNonEmptyCell(const CellIndex &cell_index) const { - return cells_.find(cell_index) != cells_.end(); + return cells_.contains(cell_index); } int ClusteringGrid::getCellCount() const diff --git a/src/openms/source/ML/SVM/SimpleSVM.cpp b/src/openms/source/ML/SVM/SimpleSVM.cpp index feb934a23be..d249bf5bd95 100644 --- a/src/openms/source/ML/SVM/SimpleSVM.cpp +++ b/src/openms/source/ML/SVM/SimpleSVM.cpp @@ -553,7 +553,7 @@ void scaleDataUsingTrainingRanges(SimpleSVM::PredictorMap& predictors, const map auto val_end = pred_it->second.end(); for (; val_begin != val_end; ++val_begin) { - if (scaling.count(pred_it->first) == 0) + if (!scaling.contains(pred_it->first)) { //std::cout << "Predictor: '" << pred_it->first << "' not found in scale map because it was uninformative during training." << std::endl; continue; diff --git a/src/openms/source/PROCESSING/CALIBRATION/InternalCalibration.cpp b/src/openms/source/PROCESSING/CALIBRATION/InternalCalibration.cpp index dae43c35d06..5bcd7f5385a 100644 --- a/src/openms/source/PROCESSING/CALIBRATION/InternalCalibration.cpp +++ b/src/openms/source/PROCESSING/CALIBRATION/InternalCalibration.cpp @@ -429,7 +429,7 @@ namespace OpenMS { sv << "invalid"; // this only happens if ALL models are invalid (since otherwise they would use 'neighbour') } - else if (invalid_models.count(i) > 0) + else if (invalid_models.contains(i)) { sv << "neighbor"; } diff --git a/src/openms/source/PROCESSING/FEATURE/FeatureOverlapFilter.cpp b/src/openms/source/PROCESSING/FEATURE/FeatureOverlapFilter.cpp index 1fa0da57129..e6b946187a8 100644 --- a/src/openms/source/PROCESSING/FEATURE/FeatureOverlapFilter.cpp +++ b/src/openms/source/PROCESSING/FEATURE/FeatureOverlapFilter.cpp @@ -200,7 +200,7 @@ namespace OpenMS std::unordered_set removed_uids; for (auto& f : fmap) { - if (removed_uids.count(f.getUniqueId()) == 0) + if (!removed_uids.contains(f.getUniqueId())) { for (auto& overlap : quadtree.query(getBox(&f))) { diff --git a/src/openms/source/PROCESSING/ID/IDFilter.cpp b/src/openms/source/PROCESSING/ID/IDFilter.cpp index 939060ff251..0ced1213023 100644 --- a/src/openms/source/PROCESSING/ID/IDFilter.cpp +++ b/src/openms/source/PROCESSING/ID/IDFilter.cpp @@ -150,7 +150,7 @@ namespace OpenMS if (seq[i].isModified()) { String mod_name = seq[i].getModification()->getFullId(); - if (mods_.count(mod_name) > 0) + if (mods_.contains(mod_name)) return true; } } @@ -159,13 +159,13 @@ namespace OpenMS if (seq.hasNTerminalModification()) { String mod_name = seq.getNTerminalModification()->getFullId(); - if (mods_.count(mod_name) > 0) + if (mods_.contains(mod_name)) return true; } if (seq.hasCTerminalModification()) { String mod_name = seq.getCTerminalModification()->getFullId(); - if (mods_.count(mod_name) > 0) + if (mods_.contains(mod_name)) return true; } @@ -187,7 +187,7 @@ namespace OpenMS bool operator()(const PeptideHit& hit) const { const String& query = (ignore_mods_ ? hit.getSequence().toUnmodifiedString() : hit.getSequence().toString()); - return (sequences_.count(query) > 0); + return (sequences_.contains(query)); } }; @@ -385,7 +385,7 @@ namespace OpenMS ProteinIdentification::ProteinGroup filtered; for (const String& acc : group.accessions) { - if (valid_accessions.find(acc) != valid_accessions.end()) + if (valid_accessions.contains(acc)) { filtered.accessions.push_back(acc); } diff --git a/src/openms/source/QC/Contaminants.cpp b/src/openms/source/QC/Contaminants.cpp index 051d5928e7b..04f6f691b05 100644 --- a/src/openms/source/QC/Contaminants.cpp +++ b/src/openms/source/QC/Contaminants.cpp @@ -118,7 +118,7 @@ namespace OpenMS ++utotal; // peptide is not in contaminant database - if (!digested_db_.count(key)) + if (!digested_db_.contains(key)) { fu_hit.setMetaValue("is_contaminant", 0); continue; @@ -159,7 +159,7 @@ namespace OpenMS ++total; sum_total += intensity; // peptide is not in contaminant database - if (!digested_db_.count(key)) + if (!digested_db_.contains(key)) { pep_hit.setMetaValue("is_contaminant", 0); return; diff --git a/src/openms/source/QC/DBSuitability.cpp b/src/openms/source/QC/DBSuitability.cpp index 6b87bb092c2..9cc756d0114 100644 --- a/src/openms/source/QC/DBSuitability.cpp +++ b/src/openms/source/QC/DBSuitability.cpp @@ -225,7 +225,7 @@ namespace OpenMS const set& accessions = hit.extractProteinAccessionsSet(); for (const String& acc : accessions) { - if (acc.find(Constants::UserParam::CONCAT_PEPTIDE) == String::npos && !boost::regex_search(String(acc).toLower(), decoy_pattern_)) + if (!acc.contains(Constants::UserParam::CONCAT_PEPTIDE) && !boost::regex_search(String(acc).toLower(), decoy_pattern_)) { return false; } @@ -610,7 +610,7 @@ namespace OpenMS const set accessions = hit.extractProteinAccessionsSet(); for (const String& acc : accessions) { - if (acc.find(Constants::UserParam::CONCAT_PEPTIDE) != String::npos)// skip novo accessions + if (acc.contains(Constants::UserParam::CONCAT_PEPTIDE))// skip novo accessions { continue; } @@ -679,7 +679,7 @@ namespace OpenMS top_hit.getKeys(meta_keys); for (const String& key : meta_keys) { - if (key.find(score_name) != String::npos) + if (key.contains(score_name)) { score = top_hit.getMetaValue(key); score_found = true; diff --git a/src/topp/CVInspector.cpp b/src/topp/CVInspector.cpp index 9b2d0393a68..2d9b753b7ee 100644 --- a/src/topp/CVInspector.cpp +++ b/src/topp/CVInspector.cpp @@ -367,7 +367,7 @@ class TOPPCVInspector : if (tit->getAllowChildren()) { // check whether we want to ignore this term - if (!(tit->getAccession().has(':') && ignore_cv_list.find(tit->getAccession().prefix(':')) != ignore_cv_list.end())) + if (!(tit->getAccession().has(':') && ignore_cv_list.contains(tit->getAccession().prefix(':')))) { cv.getAllChildTerms(allowed_terms, tit->getAccession()); } @@ -390,7 +390,7 @@ class TOPPCVInspector : set unused_terms; for (const auto& [acc, _] : terms) { - if (used_terms.find(acc) == used_terms.end()) + if (!used_terms.contains(acc)) { unused_terms.insert(acc); } diff --git a/src/topp/ConsensusID.cpp b/src/topp/ConsensusID.cpp index c3be19c00ea..5fe4b45554a 100644 --- a/src/topp/ConsensusID.cpp +++ b/src/topp/ConsensusID.cpp @@ -443,23 +443,23 @@ class TOPPConsensusID : std::copy(sp.variable_modifications.begin(), sp.variable_modifications.end(), std::inserter(var_mods_set, var_mods_set.end())); } - if (specs.find(EnzymaticDigestion::SPEC_NONE) != specs.end()) + if (specs.contains(EnzymaticDigestion::SPEC_NONE)) { new_sp.enzyme_term_specificity = EnzymaticDigestion::SPEC_NONE; } - else if (specs.find(EnzymaticDigestion::SPEC_SEMI) != specs.end()) + else if (specs.contains(EnzymaticDigestion::SPEC_SEMI)) { new_sp.enzyme_term_specificity = EnzymaticDigestion::SPEC_SEMI; } - else if (specs.find(EnzymaticDigestion::SPEC_NONTERM) != specs.end()) + else if (specs.contains(EnzymaticDigestion::SPEC_NONTERM)) { new_sp.enzyme_term_specificity = EnzymaticDigestion::SPEC_NONTERM; } - else if (specs.find(EnzymaticDigestion::SPEC_NOCTERM) != specs.end()) + else if (specs.contains(EnzymaticDigestion::SPEC_NOCTERM)) { new_sp.enzyme_term_specificity = EnzymaticDigestion::SPEC_NOCTERM; } - else if (specs.find(EnzymaticDigestion::SPEC_FULL) != specs.end()) + else if (specs.contains(EnzymaticDigestion::SPEC_FULL)) { new_sp.enzyme_term_specificity = EnzymaticDigestion::SPEC_FULL; } diff --git a/src/topp/DatabaseFilter.cpp b/src/topp/DatabaseFilter.cpp index d4ae59df302..80ec44312f9 100644 --- a/src/topp/DatabaseFilter.cpp +++ b/src/topp/DatabaseFilter.cpp @@ -88,7 +88,7 @@ class TOPPDatabaseFilter : for (const auto& entry : db) { const String& fasta_accession = entry.identifier; - const bool found = id_accessions.find(fasta_accession) != id_accessions.end(); + const bool found = id_accessions.contains(fasta_accession); if ((found && whitelist) || (! found && ! whitelist)) // either found in the whitelist or not found in the blacklist { db_new.push_back(entry); diff --git a/src/topp/DecoyDatabase.cpp b/src/topp/DecoyDatabase.cpp index f4d7a615626..5835585cc5d 100644 --- a/src/topp/DecoyDatabase.cpp +++ b/src/topp/DecoyDatabase.cpp @@ -385,7 +385,7 @@ class TOPPDecoyDatabase : //------------------------------------------------------------- while (f.readNext(entry)) { - if (identifiers.find(entry.identifier) != identifiers.end()) + if (identifiers.contains(entry.identifier)) { OPENMS_LOG_WARN << "DecoyDatabase: Warning, identifier '" << entry.identifier << "' occurs more than once!" << endl; } diff --git a/src/topp/EICExtractor.cpp b/src/topp/EICExtractor.cpp index 14f0f8847d4..d8e7d23f203 100644 --- a/src/topp/EICExtractor.cpp +++ b/src/topp/EICExtractor.cpp @@ -346,7 +346,7 @@ class TOPPEICExtractor : { if (cf.getRT() < 0) { - if (mz_doubles.find(cf.getMZ()) == mz_doubles.end()) + if (!mz_doubles.contains(cf.getMZ())) { mz_doubles.insert(cf.getMZ()); } diff --git a/src/topp/FLASHDeconv.cpp b/src/topp/FLASHDeconv.cpp index e49abd74753..4b264607c14 100644 --- a/src/topp/FLASHDeconv.cpp +++ b/src/topp/FLASHDeconv.cpp @@ -269,7 +269,7 @@ class TOPPFLASHDeconv : public TOPPBase for (const auto& it : map) { uint ms_level = it.getMSLevel(); - if (per_ms_level_spec_count.find(ms_level) == per_ms_level_spec_count.end()) per_ms_level_spec_count[ms_level] = 0; + if (!per_ms_level_spec_count.contains(ms_level)) per_ms_level_spec_count[ms_level] = 0; per_ms_level_spec_count[ms_level]++; } @@ -279,8 +279,8 @@ class TOPPFLASHDeconv : public TOPPBase scan_rt_map[deconvolved_spectrum.getScanNumber()] = deconvolved_spectrum.getOriginalSpectrum().getRT(); if (deconvolved_spectrum.empty()) continue; - if (per_ms_level_deconv_spec_count.find(ms_level) == per_ms_level_deconv_spec_count.end()) per_ms_level_deconv_spec_count[ms_level] = 0; - if (per_ms_level_mass_count.find(ms_level) == per_ms_level_mass_count.end()) per_ms_level_mass_count[ms_level] = 0; + if (!per_ms_level_deconv_spec_count.contains(ms_level)) per_ms_level_deconv_spec_count[ms_level] = 0; + if (!per_ms_level_mass_count.contains(ms_level)) per_ms_level_mass_count[ms_level] = 0; per_ms_level_deconv_spec_count[ms_level]++; per_ms_level_mass_count[ms_level] += (int)deconvolved_spectrum.size(); @@ -323,7 +323,7 @@ class TOPPFLASHDeconv : public TOPPBase std::vector out_spec_streams = std::vector(out_spec_file.size()); for (Size i = 0; i < out_spec_file.size(); i++) { - if (out_spec_file[i].empty() || (! keep_empty_out && per_ms_level_deconv_spec_count.find(i + 1) == per_ms_level_deconv_spec_count.end())) + if (out_spec_file[i].empty() || (! keep_empty_out && !per_ms_level_deconv_spec_count.contains(i + 1))) continue; OPENMS_LOG_INFO << "writing spectrum tsv for MS level " << (i + 1) << " ..." << endl; @@ -347,7 +347,7 @@ class TOPPFLASHDeconv : public TOPPBase for (Size i = 0; i < out_spec_file.size(); i++) { - if (out_spec_file[i].empty() || (! keep_empty_out && per_ms_level_deconv_spec_count.find(i + 1) == per_ms_level_deconv_spec_count.end())) + if (out_spec_file[i].empty() || (! keep_empty_out && !per_ms_level_deconv_spec_count.contains(i + 1))) continue; out_spec_streams[i].close(); } @@ -382,7 +382,7 @@ class TOPPFLASHDeconv : public TOPPBase for (Size i = 0; i < out_topfd_feature_file.size(); i++) { if (out_topfd_feature_file[i].empty() - || (! keep_empty_out && per_ms_level_deconv_spec_count.find(i + 1) == per_ms_level_deconv_spec_count.end())) + || (! keep_empty_out && !per_ms_level_deconv_spec_count.contains(i + 1))) continue; OPENMS_LOG_INFO << "writing topfd *.feature for MS level " << (i + 1) << " ..." << endl; @@ -405,7 +405,7 @@ class TOPPFLASHDeconv : public TOPPBase for (Size i = 0; i < out_topfd_file.size(); i++) { - if (out_topfd_file[i].empty() || (! keep_empty_out && per_ms_level_deconv_spec_count.find(i + 1) == per_ms_level_deconv_spec_count.end())) + if (out_topfd_file[i].empty() || (! keep_empty_out && !per_ms_level_deconv_spec_count.contains(i + 1))) continue; OPENMS_LOG_INFO << "writing topfd *.msalign for MS level " << (i + 1) << " ..." << endl; @@ -429,7 +429,7 @@ class TOPPFLASHDeconv : public TOPPBase for (Size i = 0; i < out_topfd_file.size(); i++) { - if (out_topfd_file[i].empty() || (! keep_empty_out && per_ms_level_deconv_spec_count.find(i + 1) == per_ms_level_deconv_spec_count.end())) + if (out_topfd_file[i].empty() || (! keep_empty_out && !per_ms_level_deconv_spec_count.contains(i + 1))) continue; out_topfd_streams[i].close(); } diff --git a/src/topp/FileFilter.cpp b/src/topp/FileFilter.cpp index 95cd82afc34..144c4d9d37a 100644 --- a/src/topp/FileFilter.cpp +++ b/src/topp/FileFilter.cpp @@ -1455,7 +1455,7 @@ class TOPPFileFilter : for (const FeatureHandle& fh : cm) { UInt64 map_index = fh.getMapIndex(); - if (map_ids.empty() || map_ids.find(map_index) != map_ids.end()) + if (map_ids.empty() || map_ids.contains(map_index)) { Peak2D p; p.setMZ(fh.getMZ()); @@ -1506,14 +1506,14 @@ class TOPPFileFilter : if (is_blacklist) { // blacklist: add all spectra not contained in list - if (list_idx.find(i) == list_idx.end()) + if (!list_idx.contains(i)) { exp2.addSpectrum(exp[i]); } } else // whitelist: add all non MS2 spectra, and MS2 only if in list { - if (exp[i].getMSLevel() != 2 || list_idx.find(i) != list_idx.end()) + if (exp[i].getMSLevel() != 2 || list_idx.contains(i)) { exp2.addSpectrum(exp[i]); } @@ -1594,14 +1594,14 @@ class TOPPFileFilter : if (is_blacklist) { // blacklist: add all spectra not contained in list - if (list_idx.find(i) == list_idx.end()) + if (!list_idx.contains(i)) { exp2.addSpectrum(exp[i]); } } else // whitelist: add all non-MS2 spectra + matched MS2 spectra { - if (exp[i].getMSLevel() != 2 || list_idx.find(i) != list_idx.end()) + if (exp[i].getMSLevel() != 2 || list_idx.contains(i)) { exp2.addSpectrum(exp[i]); } diff --git a/src/topp/FileInfo.cpp b/src/topp/FileInfo.cpp index be3337587d2..1fb93015ae3 100644 --- a/src/topp/FileInfo.cpp +++ b/src/topp/FileInfo.cpp @@ -899,7 +899,7 @@ class TOPPFileInfo : public TOPPBase { for (char c : entry.sequence) { - if (NUCLEOTIDE_CHARS.find(c) == std::string_view::npos) + if (!NUCLEOTIDE_CHARS.contains(c)) { is_nucleic_acid = false; break; @@ -1475,13 +1475,13 @@ class TOPPFileInfo : public TOPPBase } // annotate peak type (profile / centroided) from meta data - if (level_annotated_picked.count(level) == 0) + if (!level_annotated_picked.contains(level)) { level_annotated_picked[level] = static_cast(spectrum.getType(false)); } // estimate peak type once for every level (take a spectrum with enough peaks for stable estimation) - if (level_estimated_picked.count(level) == 0 && spectrum.size() > 10) + if (!level_estimated_picked.contains(level) && spectrum.size() > 10) { level_estimated_picked[level] = static_cast(PeakTypeEstimator::estimateType(spectrum.begin(), spectrum.end())); } @@ -1609,7 +1609,7 @@ class TOPPFileInfo : public TOPPBase os << String(" ") + ChromatogramSettings::ChromatogramNames[static_cast(it->first)] + ": " << it->second << '\n'; } - if (getFlag_("d") && chrom_types.find(ChromatogramSettings::ChromatogramType::SELECTED_REACTION_MONITORING_CHROMATOGRAM) != chrom_types.end()) + if (getFlag_("d") && chrom_types.contains(ChromatogramSettings::ChromatogramType::SELECTED_REACTION_MONITORING_CHROMATOGRAM)) { os << '\n' << " -- Detailed chromatogram listing -- " @@ -1714,7 +1714,7 @@ class TOPPFileInfo : public TOPPBase for (Size m = 0; m < exp[s].getFloatDataArrays().size(); ++m) { String name = exp[s].getFloatDataArrays()[m].getName(); - if (names.find(name) != names.end()) + if (names.contains(name)) { os << "Error: Duplicate meta data array name '" << name << "' in spectrum (RT: " << exp[s].getRT() << ")" << '\n'; @@ -1727,7 +1727,7 @@ class TOPPFileInfo : public TOPPBase for (Size m = 0; m < exp[s].getIntegerDataArrays().size(); ++m) { String name = exp[s].getIntegerDataArrays()[m].getName(); - if (names.find(name) != names.end()) + if (names.contains(name)) { os << "Error: Duplicate meta data array name '" << name << "' in spectrum (RT: " << exp[s].getRT() << ")" << '\n'; @@ -1740,7 +1740,7 @@ class TOPPFileInfo : public TOPPBase for (Size m = 0; m < exp[s].getStringDataArrays().size(); ++m) { String name = exp[s].getStringDataArrays()[m].getName(); - if (names.find(name) != names.end()) + if (names.contains(name)) { os << "Error: Duplicate meta data array name '" << name << "' in spectrum (RT: " << exp[s].getRT() << ")" << '\n'; diff --git a/src/topp/IDExtractor.cpp b/src/topp/IDExtractor.cpp index a8960ac1200..d38d1335e57 100644 --- a/src/topp/IDExtractor.cpp +++ b/src/topp/IDExtractor.cpp @@ -137,7 +137,7 @@ class TOPPIDExtractor : { chosen_ids.push_back(it->second.getHits()[0].getSequence().toString()); chosen_identifications.push_back(it->second); - if (identifiers.find(it->second.getIdentifier()) == identifiers.end()) + if (!identifiers.contains(it->second.getIdentifier())) { temp_identifications.clear(); } @@ -169,7 +169,7 @@ class TOPPIDExtractor : { chosen_ids.push_back(identifications[indices[index]].getHits()[0].getSequence().toString()); chosen_identifications.push_back(identifications[indices[index]]); - if (identifiers.find(identifications[indices[index]].getIdentifier()) == identifiers.end()) + if (!identifiers.contains(identifications[indices[index]].getIdentifier())) { temp_identifications.clear(); } @@ -195,7 +195,7 @@ class TOPPIDExtractor : { temp_protein_hits = protein_identifications[i].getHits(); chosen_protein_hits.clear(); - if (identifiers.find(protein_identifications[i].getIdentifier()) != identifiers.end()) + if (identifiers.contains(protein_identifications[i].getIdentifier())) { temp_identifications = identifiers[protein_identifications[i].getIdentifier()]; for (Size j = 0; j < temp_protein_hits.size(); ++j) diff --git a/src/topp/IDMerger.cpp b/src/topp/IDMerger.cpp index b6f1ae22347..8df8ba7d63b 100644 --- a/src/topp/IDMerger.cpp +++ b/src/topp/IDMerger.cpp @@ -426,7 +426,7 @@ class TOPPIDMerger : const PeptideHit& hit = pep_it->getHits()[0]; OPENMS_LOG_DEBUG << "peptide: " << hit.getSequence().toString() << endl; // skip ahead if peptide is not new: - if (sequences.find(hit.getSequence()) != sequences.end()) continue; + if (sequences.contains(hit.getSequence())) continue; OPENMS_LOG_DEBUG << "new peptide!" << endl; pep_it->getHits().resize(1); // restrict to best hit for simplicity peptides.push_back(*pep_it); @@ -438,7 +438,7 @@ class TOPPIDMerger : { OPENMS_LOG_DEBUG << "accession: " << acc << endl; // skip ahead if accession is not new: - if (accessions.find(acc) != accessions.end()) + if (accessions.contains(acc)) { continue; } @@ -446,7 +446,7 @@ class TOPPIDMerger : // first find the right protein identification: const String& id = pep_it->getIdentifier(); OPENMS_LOG_DEBUG << "identifier: " << id << endl; - if (proteins_by_id.find(id) == proteins_by_id.end()) + if (!proteins_by_id.contains(id)) { writeLogError_("Error: identifier '" + id + "' linking peptides and proteins not found. Skipping."); continue; @@ -461,7 +461,7 @@ class TOPPIDMerger : continue; } // we may need to copy protein ID meta data, if we haven't yet: - if (selected_proteins.find(id) == selected_proteins.end()) + if (!selected_proteins.contains(id)) { OPENMS_LOG_DEBUG << "adding protein identification" << endl; selected_proteins_order.push_back(id); diff --git a/src/topp/LuciphorAdapter.cpp b/src/topp/LuciphorAdapter.cpp index 1a6b92aeec0..de03d8ee9a4 100644 --- a/src/topp/LuciphorAdapter.cpp +++ b/src/topp/LuciphorAdapter.cpp @@ -330,7 +330,7 @@ class LuciphorAdapter : l_psm.predicted_pep_score = elements[8].toDouble(); l_psm.global_flr = elements[10].toDouble(); l_psm.local_flr = elements[11].toDouble(); - if (l_psms.count(l_psm.scan_idx) > 0) + if (l_psms.contains(l_psm.scan_idx)) { return "Duplicate scannr existing " + String(l_psm.scan_nr) + "."; } @@ -618,7 +618,7 @@ class LuciphorAdapter : addScoreToMetaValues_(scored_hit, pep.getScoreType()); struct LuciphorPSM l_psm; - if (l_psms.count(scan_idx) > 0) + if (l_psms.contains(scan_idx)) { l_psm = l_psms.at(scan_idx); AASequence original_seq = scored_hit.getSequence(); diff --git a/src/topp/MRMTransitionGroupPicker.cpp b/src/topp/MRMTransitionGroupPicker.cpp index a0da35000c4..a043c37b892 100644 --- a/src/topp/MRMTransitionGroupPicker.cpp +++ b/src/topp/MRMTransitionGroupPicker.cpp @@ -155,7 +155,7 @@ class TOPPMRMTransitionGroupPicker { for (Size i = 0; i < assay_it->second.size(); i++) { - if (chromatogram_map.find(assay_it->second[i]->getNativeID()) == chromatogram_map.end()) + if (!chromatogram_map.contains(assay_it->second[i]->getNativeID())) { return false; } @@ -175,7 +175,7 @@ class TOPPMRMTransitionGroupPicker // Check first whether we have a mapping (e.g. see -force option) const TransitionType* transition = assay_map[id][i]; - if (chromatogram_map.find(transition->getNativeID()) == chromatogram_map.end()) + if (!chromatogram_map.contains(transition->getNativeID())) { OPENMS_LOG_DEBUG << "Found no matching chromatogram for id " << transition->getNativeID() << std::endl; continue; diff --git a/src/topp/MetaProSIP.cpp b/src/topp/MetaProSIP.cpp index b8896b1abb7..1cd42d880e8 100644 --- a/src/topp/MetaProSIP.cpp +++ b/src/topp/MetaProSIP.cpp @@ -305,7 +305,7 @@ class MetaProSIPInterpolation y.push_back(it->second); } - if (rate2score.find(100.0) == rate2score.end() && x[x.size() - 1] < 100.0) + if (!rate2score.contains(100.0) && x[x.size() - 1] < 100.0) { x.push_back(100.0); y.push_back(0); @@ -369,7 +369,7 @@ class MetaProSIPClustering // build histogram of rates for (vector::const_iterator iit = cit->incorporations.begin(); iit != cit->incorporations.end(); ++iit) { - if (hist.find(iit->rate) == hist.end()) + if (!hist.contains(iit->rate)) { hist[iit->rate] = 1.0; } @@ -1017,7 +1017,7 @@ class MetaProSIPReporting String protein_accession = prot_it->first; String protein_description = "none"; - if (proteinid_to_description.find(protein_accession.trim().toUpper()) != proteinid_to_description.end()) + if (proteinid_to_description.contains(protein_accession.trim().toUpper())) { protein_description = proteinid_to_description.at(protein_accession.trim().toUpper()); } @@ -1146,7 +1146,7 @@ class MetaProSIPReporting String protein_accession = v_it->accessions[ac]; accessions_string += protein_accession; - if (proteinid_to_description.find(protein_accession.trim().toUpper()) != proteinid_to_description.end()) + if (proteinid_to_description.contains(protein_accession.trim().toUpper())) { if (description_string == "none") { @@ -1264,7 +1264,7 @@ class MetaProSIPReporting current_accession.trim().toUpper(); accession_string += current_accession; - if (proteinid_to_description.find(current_accession) != proteinid_to_description.end()) + if (proteinid_to_description.contains(current_accession)) { if (protein_descriptions == "none") { @@ -1899,7 +1899,7 @@ class MetaProSIPXICExtraction for (; it != peak_map.areaEndConst(); ++it) { double rt = it.getRT(); - if (xic.find(rt) != xic.end()) + if (xic.contains(rt)) { xic[rt] += it->getIntensity(); } diff --git a/src/topp/NucleicAcidSearchEngine.cpp b/src/topp/NucleicAcidSearchEngine.cpp index 7128fddbc47..f616cf94b5d 100644 --- a/src/topp/NucleicAcidSearchEngine.cpp +++ b/src/topp/NucleicAcidSearchEngine.cpp @@ -1175,7 +1175,7 @@ class NucleicAcidSearchEngine : Param param = spectrum_generator.getParameters(); vector temp = getStringList_("fragment:ions"); set selected_ions(temp.begin(), temp.end()); - if (resolve_ambiguous_mods_ && !selected_ions.count("a-B")) + if (resolve_ambiguous_mods_ && !selected_ions.contains("a-B")) { OPENMS_LOG_WARN << "Warning: option 'modifications:resolve_ambiguities' requires a-B ions in parameter 'fragment:ions' - disabling the option." << endl; resolve_ambiguous_mods_ = false; @@ -1183,7 +1183,7 @@ class NucleicAcidSearchEngine : for (const auto& code : fragment_ion_codes_) { String param_name = "add_" + code + "_ions"; - if (selected_ions.count(code)) + if (selected_ions.contains(code)) { param.setValue(param_name, "true"); } diff --git a/src/topp/OpenNuXL.cpp b/src/topp/OpenNuXL.cpp index 9231bb19083..7928ae55361 100644 --- a/src/topp/OpenNuXL.cpp +++ b/src/topp/OpenNuXL.cpp @@ -221,11 +221,11 @@ struct NuXLLinearRescore predictors[f].push_back(value); } // only add label for training data (rank = 0 and previously selected for training) - if (psm_rank == 0 && top_indices.count(index) != 0) + if (psm_rank == 0 && top_indices.contains(index)) { labels[current_row] = 1.0; } - else if (psm_rank == 0 && bottom_indices.count(index) != 0) + else if (psm_rank == 0 && bottom_indices.contains(index)) { labels[current_row] = 0.0; } @@ -360,7 +360,7 @@ struct NuXLLinearRescore predictors[f].push_back(value); } // only add label for training data (rank = 0 and previously selected for training) - if (psm_rank == 0 && training_indices.count(index) > 0) + if (psm_rank == 0 && training_indices.contains(index)) { labels[current_row] = is_target; } @@ -3554,7 +3554,7 @@ static void scoreXLIons_( { const Residue& r = fixed_and_variable_modified_peptide[i]; if (!r.isModified()) continue; - if (variable_modifications.val.find(r.getModification()) != variable_modifications.val.end()) + if (variable_modifications.val.contains(r.getModification())) { ++n_var_mods; } @@ -3565,9 +3565,9 @@ static void scoreXLIons_( auto c_term_mod = fixed_and_variable_modified_peptide.getCTerminalModification(); if (n_term_mod != nullptr && - variable_modifications.val.find(n_term_mod) != variable_modifications.val.end()) ++n_var_mods; + variable_modifications.val.contains(n_term_mod)) ++n_var_mods; if (c_term_mod != nullptr && - variable_modifications.val.find(c_term_mod) != variable_modifications.val.end()) ++n_var_mods; + variable_modifications.val.contains(c_term_mod)) ++n_var_mods; ph.setMetaValue(String("variable_modifications"), n_var_mods); ph.setMetaValue(String("n_theoretical_peaks"), ah.n_theoretical_peaks); @@ -3817,7 +3817,7 @@ static void scoreXLIons_( for (auto & ph : pid.getHits()) { const String& unmodified_sequence = ph.getSequence().toUnmodifiedString(); - if (sequence_is_topPSM.find(unmodified_sequence) != sequence_is_topPSM.end()) + if (sequence_is_topPSM.contains(unmodified_sequence)) { ph.setMetaValue("CountSequenceIsTop", sequence_is_topPSM[unmodified_sequence]); ph.setMetaValue("CountSequenceCharges", sequence_charges[unmodified_sequence].size()); @@ -4626,7 +4626,7 @@ static void scoreXLIons_( vector idx_to_keep; // inverse for (size_t i = 0; i != s.size(); ++i) { // add indices we don't want to remove - if (idx_to_remove.find(i) == idx_to_remove.end()) idx_to_keep.push_back(i); + if (!idx_to_remove.contains(i)) idx_to_keep.push_back(i); } filtered_peaks_count += idx_to_remove.size(); s.select(idx_to_keep); @@ -4881,7 +4881,7 @@ static void scoreXLIons_( const String other_native_id = f->getMetaValue("native_id"); // skip self-comparison and already identified spectra - if (this_native_id == other_native_id || skip_peptide_spectrum.count(other_native_id) > 0) continue; + if (this_native_id == other_native_id || skip_peptide_spectrum.contains(other_native_id)) continue; const MSSpectrum& this_spec = spectra[lookup.findByNativeID(this_native_id)]; const MSSpectrum& other_spec = spectra[lookup.findByNativeID(other_native_id)]; @@ -5387,7 +5387,7 @@ static void scoreXLIons_( #endif { // skip peptide (and all modified variants) if already processed - if (processed_petides.find(*cit) != processed_petides.end()) + if (processed_petides.contains(*cit)) { already_processed = true; } @@ -5692,7 +5692,7 @@ static void scoreXLIons_( const PeakSpectrum & exp_spectrum = spectra[scan_index]; ////////////////////////////////////////// // ID-Filter - if (skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) { continue; } + if (skip_peptide_spectrum.contains(exp_spectrum.getNativeID())) { continue; } #pragma omp atomic ++nr_candidates[scan_index]; // count candidate for spectrum @@ -5900,7 +5900,7 @@ static void scoreXLIons_( const String& precursor_na_adduct = *mod_combinations_it->second.begin(); // For fast scoring it should be sufficient to only consider any of the adducts for this mass and formula (e.g., C-H3N vs U-H2O) MSSpectrum& exp_spectrum = spectra[scan_index]; - if (precursor_na_adduct != "none" && skip_peptide_spectrum.find(exp_spectrum.getNativeID()) != skip_peptide_spectrum.end()) continue; + if (precursor_na_adduct != "none" && skip_peptide_spectrum.contains(exp_spectrum.getNativeID())) continue; #pragma omp atomic ++nr_candidates[scan_index]; diff --git a/src/topp/OpenSwathFeatureXMLToTSV.cpp b/src/topp/OpenSwathFeatureXMLToTSV.cpp index c971764c239..ac82ec1ccfc 100644 --- a/src/topp/OpenSwathFeatureXMLToTSV.cpp +++ b/src/topp/OpenSwathFeatureXMLToTSV.cpp @@ -157,24 +157,24 @@ void write_out_body_(std::ostream &os, Feature *feature_it, TargetedExperiment & } // handle decoy tag - if (peptide_transition_map.find(peptide_ref) != peptide_transition_map.end() && !peptide_transition_map[peptide_ref].empty()) + if (peptide_transition_map.contains(peptide_ref) && !peptide_transition_map[peptide_ref].empty()) { const ReactionMonitoringTransition *transition = peptide_transition_map[peptide_ref][0]; #if 1 const auto& terms = transition->getCVTerms(); - if (terms.find("decoy") != terms.end()) + if (terms.contains("decoy")) { decoy = transition->getCVTerms().at("decoy")[0].getValue().toString(); } - else if (terms.find("MS:1002007") != terms.end() ) // target SRM transition + else if (terms.contains("MS:1002007") ) // target SRM transition { decoy = "0"; } - else if (terms.find("MS:1002008") != terms.end() ) // decoy SRM transition + else if (terms.contains("MS:1002008") ) // decoy SRM transition { decoy = "1"; } - else if (terms.find("MS:1002007") != terms.end() && terms.find("MS:1002008") != terms.end() ) // both == illegal + else if (terms.contains("MS:1002007") && terms.contains("MS:1002008") ) // both == illegal { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Peptide " + peptide_ref + " cannot be target and decoy at the same time."); diff --git a/src/topp/OpenSwathRewriteToFeatureXML.cpp b/src/topp/OpenSwathRewriteToFeatureXML.cpp index 68eaf020847..c32805ddbd6 100644 --- a/src/topp/OpenSwathRewriteToFeatureXML.cpp +++ b/src/topp/OpenSwathRewriteToFeatureXML.cpp @@ -107,9 +107,9 @@ class TOPPOpenSwathRewriteToFeatureXML : } } - if (header_dict_inv.find("id") == header_dict_inv.end() || - header_dict_inv.find("m_score") == header_dict_inv.end() || - header_dict_inv.find("d_score") == header_dict_inv.end() ) + if (!header_dict_inv.contains("id") || + !header_dict_inv.contains("m_score") || + !header_dict_inv.contains("d_score") ) { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Error: The tsv file is expected to have at least the following headers: id, m_score, d_score. " ); } @@ -148,13 +148,13 @@ class TOPPOpenSwathRewriteToFeatureXML : throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Error: Could not convert String" + ((String)current_row[header_dict_inv["d_score"]]) + " on line " + String(line_nr)); } - if (feature_map_ref.find(id) != feature_map_ref.end() ) + if (feature_map_ref.contains(id) ) { Feature* feature = feature_map_ref.find(id)->second; feature->setMetaValue("m_score", m_score); feature->setMetaValue("d_score", d_score); // we are not allowed to have duplicate unique ids - if (added_already.find(id) != added_already.end()) + if (added_already.contains(id)) { throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Error: Duplicate id found in CSV file: " + id ); } diff --git a/src/topp/PercolatorAdapter.cpp b/src/topp/PercolatorAdapter.cpp index 6cb44833625..7602a58b763 100644 --- a/src/topp/PercolatorAdapter.cpp +++ b/src/topp/PercolatorAdapter.cpp @@ -570,7 +570,7 @@ class PercolatorAdapter : writeDebug_("PSM identifier in pout file: " + spec_ref, 10); // retain only the best result in the unlikely case that a PSMId+peptide combination occurs multiple times - if (pep_map.find(spec_ref) == pep_map.end()) + if (!pep_map.contains(spec_ref)) { pep_map.insert( map::value_type ( spec_ref, res ) ); } @@ -994,7 +994,7 @@ class PercolatorAdapter : StringList numeric_features; for (const String& f : feature_set) { - if (pin_metadata_not_feature.count(f)) continue; + if (pin_metadata_not_feature.contains(f)) continue; numeric_features.push_back(f); } if (all_peptide_ids.empty() || all_peptide_ids.front().getHits().empty() @@ -1026,7 +1026,7 @@ class PercolatorAdapter : const auto& pid = all_peptide_ids[i]; for (size_t j = 0; j < pid.getHits().size(); ++j) { - if (skipped.count({i, j})) continue; + if (skipped.contains({i, j})) continue; const PeptideHit& hit = pid.getHits()[j]; // Build feature row from stamped meta values. diff --git a/src/topp/ProteinQuantifier.cpp b/src/topp/ProteinQuantifier.cpp index 711ff7541e7..44f4d773ac2 100644 --- a/src/topp/ProteinQuantifier.cpp +++ b/src/topp/ProteinQuantifier.cpp @@ -442,12 +442,12 @@ class TOPPProteinQuantifier : for (Size c = 1; c <= ed.getNumberOfLabels(); ++c) { bool no_quant = false; - if (filename_to_chargemap.find(filename) != filename_to_chargemap.end()) + if (filename_to_chargemap.contains(filename)) { - if (const auto& charge_map = filename_to_chargemap.at(filename); charge_map.find(charge) != charge_map.end()) + if (const auto& charge_map = filename_to_chargemap.at(filename); charge_map.contains(charge)) { const auto& channel_to_abundance = charge_map.at(charge); - if (channel_to_abundance.find(c) != channel_to_abundance.end()) + if (channel_to_abundance.contains(c)) { out << channel_to_abundance.at(c); } diff --git a/src/topp/RNADigestor.cpp b/src/topp/RNADigestor.cpp index 8014ae5b4ab..35b0fe67fa8 100644 --- a/src/topp/RNADigestor.cpp +++ b/src/topp/RNADigestor.cpp @@ -118,7 +118,7 @@ class TOPPRNADigestor : for (vector::const_iterator frag_it = fragments.begin(); frag_it != fragments.end(); ++frag_it) { - if (!unique || !unique_fragments.count(*frag_it)) + if (!unique || !unique_fragments.contains(*frag_it)) { String id = entry.identifier + "_" + String(counter); String desc; From 72a5296cb5e3554b4a6efdb4dfdbc30cf0c460e5 Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Fri, 5 Jun 2026 04:41:50 +0200 Subject: [PATCH 2/6] TOPPView: Apply TOPP tool improvements (#9447) * Feature: make 'threads' parameter more prominent (default to max of system) and hide input/output parameters from the Param editor which are already used in the dropdown menus" of the 'Apply TOPP tool dialog' * fix typo --- .../OpenMS/VISUAL/DIALOGS/ToolsDialog.h | 42 +++- .../source/VISUAL/DIALOGS/ToolsDialog.cpp | 199 +++++++++++++++--- 2 files changed, 200 insertions(+), 41 deletions(-) diff --git a/src/openms_gui/include/OpenMS/VISUAL/DIALOGS/ToolsDialog.h b/src/openms_gui/include/OpenMS/VISUAL/DIALOGS/ToolsDialog.h index 48887770059..a91a9d39749 100644 --- a/src/openms_gui/include/OpenMS/VISUAL/DIALOGS/ToolsDialog.h +++ b/src/openms_gui/include/OpenMS/VISUAL/DIALOGS/ToolsDialog.h @@ -16,8 +16,10 @@ class QLabel; class QComboBox; +class QCheckBox; class QPushButton; class QString; +class QWidget; #include @@ -73,21 +75,37 @@ namespace OpenMS private: /// ParamEditor for reading ini-files - ParamEditor * editor_; + ParamEditor * editor_ = nullptr; + /// Label for CPU usage row + QLabel* cpu_usage_label_ = nullptr; + /// Container for thread controls (FastMode + manual controls) + QWidget* threads_widget_ = nullptr; + /// Enables automatic use of all available threads + QCheckBox* fast_mode_checkbox_ = nullptr; + /// Manual thread count dropdown (1..max) + QComboBox* threads_combo_ = nullptr; + /// Maximum available thread count from OpenMP + const int max_threads_; /// tools description label QLabel * tool_desc_; /// ComboBox for choosing a TOPP-tool QComboBox * tools_combo_; /// Button to rerun the automatic plugin detection - QPushButton* reload_plugins_button_; + QPushButton * reload_plugins_button_; /// for choosing an input parameter QComboBox * input_combo_; /// for choosing an output parameter QComboBox * output_combo_; /// Param for loading the ini-file Param arg_param_; - /// Param for loading configuration information in the ParamEditor - Param vis_param_; + /// Intact tool parameters (after :1:) for the currently selected tool; used for applying changes from gui_param_ and for executing the tool + Param single_tool_param_; + /// Param containing only parameters shown/edited in the ParamEditor (GUI subset) + Param gui_param_; + /// Param object containing all TOPP tool/util params + const Param tool_params_; + /// Param object containing all plugin params + Param plugin_params_; /// ok-button connected with slot ok_() QPushButton * ok_button_; /// Location of the temporary INI file this dialog works on @@ -98,12 +116,8 @@ namespace OpenMS QString filename_; /// Mapping of file extension to layer type to determine the type of a tool std::map tool_map_; - /// Param object containing all TOPP tool/util params - Param tool_params_; - /// Param object containing all plugin params - Param plugin_params_; /// Pointer to the tool scanner for access to the plugins and to rerun the plugins detection - TVToolDiscovery* tool_scanner_; + TVToolDiscovery * tool_scanner_; /// The layer type of the current layer to determine all usable plugins LayerDataBase::DataType layer_type_; @@ -117,6 +131,14 @@ namespace OpenMS void setInputOutputCombo_(const Param& p); /// Create a list of all TOPP tool/util/plugins that are compatible with the active layer type QStringList createToolsList_(); + /// Populate and initialize thread controls + void initializeThreadsControls_(); + /// Apply the selected thread mode/value back to single_tool_param_ + void applyThreadsToSingleToolParam_(); + /// Build GUI-only editor parameters from internal parameter state and update the editor with them + void updateGUIParamFromSingleToolParam_(); + /// Merge edited GUI-only parameters back into internal parameter state + void mergeGUIParamIntoSingleToolParam_(); protected slots: @@ -132,6 +154,8 @@ protected slots: void storeINI_(); /// rerun the automatic plugin detection void reloadPlugins_(); + /// Slot toggling between fast and manual thread mode + void fastModeToggled_(bool checked); }; } diff --git a/src/openms_gui/source/VISUAL/DIALOGS/ToolsDialog.cpp b/src/openms_gui/source/VISUAL/DIALOGS/ToolsDialog.cpp index 812ec4decc2..b8fcb674f75 100644 --- a/src/openms_gui/source/VISUAL/DIALOGS/ToolsDialog.cpp +++ b/src/openms_gui/source/VISUAL/DIALOGS/ToolsDialog.cpp @@ -25,11 +25,22 @@ #include #include #include +#include #include #include #include #include #include +#include + + +#include +#ifdef _OPENMP +#include +#else +// provide dummy omp_get_max_threads if OpenMP is not available +inline int omp_get_max_threads() { return 1; } +#endif #include @@ -45,14 +56,14 @@ namespace OpenMS String default_dir, LayerDataBase::DataType layer_type, const String& layer_name, - TVToolDiscovery* tool_scanner) : - QDialog(parent), - ini_file_(std::move(ini_file)), - default_dir_(std::move(default_dir)), - tool_params_(params.copy("tool_params:", true)), - plugin_params_(), - tool_scanner_(tool_scanner), - layer_type_(layer_type) + TVToolDiscovery* tool_scanner) + : QDialog(parent), + max_threads_(std::max(1, omp_get_max_threads())), + ini_file_(std::move(ini_file)), + default_dir_(std::move(default_dir)), + tool_params_(params.copy("tool_params:", true)), + tool_scanner_(tool_scanner), + layer_type_(layer_type) { auto main_grid = new QGridLayout(this); @@ -88,14 +99,24 @@ namespace OpenMS main_grid->addWidget(reload_plugins_button_, 0, 2); label = new QLabel("input argument:"); + const QString input_tooltip = "Select the input parameter for the tool to which the current layer's data will be forwarded to."; + label->setToolTip(input_tooltip); main_grid->addWidget(label, 2, 0); input_combo_ = new QComboBox; + input_combo_->setToolTip(input_tooltip); main_grid->addWidget(input_combo_, 2, 1); + // remove/readd input files to visible GUI param (the one in the dropdown is removed, all others are present) + connect(input_combo_, &QComboBox::activated, this, &ToolsDialog::updateGUIParamFromSingleToolParam_); label = new QLabel("output argument:"); + const QString output_tooltip = "Select the output parameter for the tool, which is grabbed and added as a new layer in TOPPView."; + label->setToolTip(output_tooltip); main_grid->addWidget(label, 3, 0); output_combo_ = new QComboBox; + output_combo_->setToolTip(output_tooltip); main_grid->addWidget(output_combo_, 3, 1); + // remove/readd input files to visible GUI param (the one in the dropdown is removed, all others are present) + connect(output_combo_, &QComboBox::activated, this, &ToolsDialog::updateGUIParamFromSingleToolParam_); // tools description label tool_desc_ = new QLabel; @@ -103,9 +124,14 @@ namespace OpenMS tool_desc_->setWordWrap(true); main_grid->addWidget(tool_desc_, 1, 2, 3, 1); + initializeThreadsControls_(); + cpu_usage_label_ = new QLabel("CPU utilization:"); + main_grid->addWidget(cpu_usage_label_, 4, 0); + main_grid->addWidget(threads_widget_, 4, 1); + //Add advanced mode check box editor_ = new ParamEditor(this); - main_grid->addWidget(editor_, 4, 0, 1, 5); + main_grid->addWidget(editor_, 5, 0, 1, 5); auto hbox = new QHBoxLayout; auto load_button = new QPushButton(tr("&Load")); @@ -117,13 +143,17 @@ namespace OpenMS hbox->addStretch(); ok_button_ = new QPushButton(tr("&Ok")); + ok_button_->setAutoDefault(false); + ok_button_->setDefault(false); connect(ok_button_, &QPushButton::clicked, this, &ToolsDialog::ok_); hbox->addWidget(ok_button_); auto cancel_button = new QPushButton(tr("&Cancel")); + cancel_button->setAutoDefault(false); + cancel_button->setDefault(false); connect(cancel_button, &QPushButton::clicked, this, &ToolsDialog::reject); hbox->addWidget(cancel_button); - main_grid->addLayout(hbox, 5, 0, 1, 5); + main_grid->addLayout(hbox, 6, 0, 1, 5); setLayout(main_grid); @@ -244,7 +274,8 @@ namespace OpenMS { tool_desc_->clear(); arg_param_.clear(); - vis_param_.clear(); + single_tool_param_.clear(); + gui_param_.clear(); editor_->clear(); } auto tool_name = getTool(); @@ -255,14 +286,12 @@ namespace OpenMS } tool_desc_->setText(toQString(String(arg_param_.getSectionDescription(tool_name)))); - vis_param_ = arg_param_.copy(tool_name + ":1:", true); - vis_param_.remove("log"); - vis_param_.remove("no_progress"); - vis_param_.remove("debug"); - - editor_->load(vis_param_); + single_tool_param_ = arg_param_.copy(tool_name + ":1:", true); setInputOutputCombo_(arg_param_); + + updateGUIParamFromSingleToolParam_(); + editor_->setFocus(Qt::MouseFocusReason); } @@ -306,7 +335,9 @@ namespace OpenMS else { editor_->store(); - arg_param_.insert(getTool() + ":1:", vis_param_); + mergeGUIParamIntoSingleToolParam_(); + applyThreadsToSingleToolParam_(); + arg_param_.insert(getTool() + ":1:", single_tool_param_); if (!File::writable(ini_file_)) { QMessageBox::critical(this, "Error", (String("Could not write to '") + ini_file_ + "'!").c_str()); @@ -330,13 +361,13 @@ namespace OpenMS if (!arg_param_.empty()) { arg_param_.clear(); - vis_param_.clear(); + single_tool_param_.clear(); + gui_param_.clear(); editor_->clear(); } try { - ParamXMLFile paramFile; - paramFile.load(filename_.toStdString(), arg_param_); + ParamXMLFile().load(filename_.toStdString(), arg_param_); } catch (Exception::BaseException& e) { @@ -356,15 +387,12 @@ namespace OpenMS return; } tools_combo_->setCurrentIndex(pos); - //Extract the required parameters - vis_param_ = arg_param_.copy(getTool() + ":1:", true); - vis_param_.remove("log"); - vis_param_.remove("no_progress"); - vis_param_.remove("debug"); - //load data into editor - editor_->load(vis_param_); + single_tool_param_ = arg_param_.copy(getTool() + ":1:", true); setInputOutputCombo_(arg_param_); + + updateGUIParamFromSingleToolParam_(); + } void ToolsDialog::storeINI_() @@ -385,7 +413,10 @@ namespace OpenMS filename_.append(".ini"); } editor_->store(); - arg_param_.insert(getTool() + ":1:", vis_param_); + mergeGUIParamIntoSingleToolParam_(); + applyThreadsToSingleToolParam_(); + + arg_param_.insert(getTool() + ":1:", single_tool_param_); try { ParamXMLFile paramFile; @@ -408,7 +439,8 @@ namespace OpenMS { tool_desc_->clear(); arg_param_.clear(); - vis_param_.clear(); + single_tool_param_.clear(); + gui_param_.clear(); editor_->clear(); input_combo_->clear(); output_combo_->clear(); @@ -443,11 +475,17 @@ namespace OpenMS String ToolsDialog::getExtension() { + // no explicit output selected (e.g. tools with optional output such as FileInfo) + if (output_combo_->currentText() == "