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void | registerOptionsAndFlags_ () override |
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map< String, String > | mapMzML2Ids_ (StringList &in, StringList &in_ids) |
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map< String, String > | mapId2MzMLs_ (const map< String, String > &m2i) |
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ExitCodes | centroidAndCorrectPrecursors_ (const String &mz_file, MSExperiment &ms_centroided) |
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void | recalibrateMasses_ (MSExperiment &ms_centroided, vector< PeptideIdentification > &peptide_ids, const String &id_file_abs_path) |
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double | estimateMedianChromatographicFWHM_ (MSExperiment &ms_centroided) |
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void | calculateSeeds_ (const MSExperiment &ms_centroided, FeatureMap &seeds, double median_fwhm) |
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double | align_ (vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations) |
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void | transform_ (vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations) |
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void | link_ (vector< FeatureMap > &feature_maps, double median_fwhm, double max_alignment_diff, ConsensusMap &consensus_fraction) |
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double | alignAndLink_ (vector< FeatureMap > &feature_maps, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, const double median_fwhm) |
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map< pair< String, UInt >, vector< int > > | getPeptideOccurrence_ (const ConsensusMap &cons) |
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multimap< Size, PeptideIdentification > | transferIDsBetweenSameFraction_ (const ConsensusMap &consensus_fraction, Size min_occurrence=3) |
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ExitCodes | quantifyFraction_ (const pair< unsigned int, std::vector< String > > &ms_files, const map< String, String > &mzfile2idfile, double median_fwhm, const multimap< Size, PeptideIdentification > &transfered_ids, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, double &max_alignment_diff, set< String > &fixed_modifications, set< String > &variable_modifications) |
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ExitCodes | main_ (int, const char **) override |
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