more doxygen fixes

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFilter.h

@@ -112,7 +112,7 @@ namespace OpenMS
       @brief Transfer the lower and upper bound values for the calculated concentrations
         based off of the AbsoluteQuantitationMethod
 
-      @param[in] quantitation_methods The absolute quantitation methods that has been determined for each component
+      @param[in] quantitation_method The absolute quantitation methods that has been determined for each component
       @param[in,out] filter_template A MRMFeatureQC class that will be used as a template to fill in the 
         MRMFeatureQC::ComponentQCs.calculated_concentration bounds based on the LLOQ and ULOQ values given in the quantitation_method.
     */
@@ -247,8 +247,8 @@ namespace OpenMS
     /**
       @brief Count the number of heavy/light labels and quantifying/detecting/identifying transitions
 
-      @param component component_group with subordinates
-      @param transitions transitions from a TargetedExperiment
+      @param component_group Component group with subordinates
+      @param transitions Transitions from a TargetedExperiment
 
       @return Map of labels/transition types and their corresponding number.
     */
@@ -277,7 +277,7 @@ namespace OpenMS
     /**
       @brief Set all members in MRMFeatureQC to zero 
 
-      @param[out] filter_zero A MRMFeatureQC object whose members have been set to 0
+      @param[out] filter_zeros A MRMFeatureQC object whose members have been set to 0
       @param[in] filter_template A MRMFeatureQC object that will be used as a template to fill in values
     */
     void zeroFilterValues(MRMFeatureQC& filter_zeros, const MRMFeatureQC& filter_template) const;

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h

@@ -61,7 +61,7 @@ namespace OpenMS
 
       @param ionseries the IonSeries from which to choose
       @param ionid the annotation string of the query fragment ion
-      @value std::pair<String, double> the annotation and product m/z of
+      @return std::pair<String, double> the annotation and product m/z of
       the queried fragment ion
 
     */
@@ -71,13 +71,13 @@ namespace OpenMS
       @brief Selects ion from IonSeries according to product m/z
 
       @param ionseries the IonSeries from which to choose
-      @param ProductMz the product m/z of the queried fragment ion
+      @param product_mz the product m/z of the queried fragment ion
       @param mz_threshold the m/z threshold for annotation of the fragment ion
-      @value std::pair<String, double> the annotation and product m/z of
+      @return std::pair<String, double> the annotation and product m/z of
       the queried fragment ion
 
     */
-    std::pair<String, double> annotateIon(const IonSeries& ionseries, const double ProductMZ, const double mz_threshold);
+    std::pair<String, double> annotateIon(const IonSeries& ionseries, const double product_mz, const double mz_threshold);
 
     /**
       @brief Annotates transition with CV terms
@@ -125,7 +125,7 @@ namespace OpenMS
       @param enable_specific_losses whether specific neutral losses should be considered
       @param enable_unspecific_losses whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered
       @param round_decPow round product m/z values to decimal power (default: -4)
-      @value IonSeries the theoretical fragment ion series
+      @return IonSeries the theoretical fragment ion series
     */
     IonSeries getIonSeries(const AASequence& sequence,
                            size_t precursor_charge,

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.h

@@ -64,8 +64,10 @@ namespace OpenMS
       only "TBDMS" is supported for now.
     */
     void isotopicCorrection(
-      const Feature& normalized_feature, Feature& corrected_feature,
-      const Matrix<double>& correction_matrix, const DerivatizationAgent& correction_matrix_agent);
+      const Feature& normalized_feature,
+      Feature& corrected_feature,
+      const Matrix<double>& correction_matrix,
+      const DerivatizationAgent& correction_matrix_agent);
 
     /**
       @brief This function performs an isotopic correction to account for unlabeled abundances coming from
@@ -74,16 +76,18 @@ namespace OpenMS
       The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes",
       Midani et al, doi:10.1016/j.ab.2016.12.011
      
-      @param  normalized_featuremap FeatureMap with normalized values for each component and unlabeled chemical formula for each component group.
-      @param[out] corrected_featuremap FeatureMap with corrected values for each component.
+      @param  measured_fm FeatureMap with normalized values for each component and unlabeled chemical formula for each component group.
+      @param[out] corrected_fm FeatureMap with corrected values for each component.
       @param  correction_matrix Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of
       naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent.
       @param  correction_matrix_agent name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied,
       only "TBDMS" is supported for now.
     */
     void isotopicCorrections(
-      const FeatureMap& normalized_featureMap, FeatureMap& corrected_featureMap,
-      const Matrix<double>& correction_matrix, const DerivatizationAgent& correction_matrix_agent);
+      const FeatureMap& measured_fm,
+      FeatureMap& corrected_fm,
+      const Matrix<double>& correction_matrix,
+      const DerivatizationAgent& correction_matrix_agent);
 
     /**
       @brief This function calculates the isotopic purity of the MDV using the following formula:
@@ -108,12 +112,12 @@ namespace OpenMS
       The formula is extracted from "High-resolution 13C metabolic flux analysis",
       Long et al, doi:10.1038/s41596-019-0204-0
 
-      @param[in,out]  normalized_featureMap FeatureMap with normalized values for each component and the number of heavy labeled e.g., carbons. Out is a FeatureMap with the calculated isotopic purity for the component group.
+      @param[in,out]  measured_fm FeatureMap with normalized values for each component and the number of heavy labeled e.g., carbons. Out is a FeatureMap with the calculated isotopic purity for the component group.
       @param[in]  experiment_data Vector of vectors of Experiment data in percent.
       @param[in]  isotopic_purity_name Vector of names of the isotopic purity tracer to be saved as a meta value.
     */
     void calculateIsotopicPurities(
-      FeatureMap& normalized_featureMap,
+      FeatureMap& measured_fm,
       const std::vector<std::vector<double>>& experiment_data,
       const std::vector<std::string>& isotopic_purity_name);
 
@@ -134,12 +138,12 @@ namespace OpenMS
        @brief This function calculates the accuracy of the MDVs as compared to the theoretical MDVs (only for 12C quality control experiments)
        using average deviation to the mean.
     
-       @param[in]  normalized_featuremap FeatureMap with normalized values for each component and the chemical formula of the component group. Out is a FeatureMap with the component group accuracy and accuracy for the error for each component.
+       @param[in]  normalized_fm FeatureMap with normalized values for each component and the chemical formula of the component group. Out is a FeatureMap with the component group accuracy and accuracy for the error for each component.
        @param[in]  feature_name Feature name to determine which features are needed to apply calculations on.
        @param[in]  fragment_isotopomer_theoretical_formulas A map of ProteinName/peptideRef to Empirical formula from which the theoretical values will be generated.
     */
     void calculateMDVAccuracies(
-      FeatureMap& normalized_featureMap,
+      FeatureMap& normalized_fm,
       const std::string& feature_name,
       const std::map<std::string, std::string>& fragment_isotopomer_theoretical_formulas);
 
@@ -164,14 +168,14 @@ namespace OpenMS
       either normalized to the highest mass intensity (norm_max) or normalized
       to the sum of all mass intensities (norm_sum)
      
-      @param[in]   measured_featuremap FeatureMap with measured intensity for each component.
-      @param[out]  normalized_featuremap FeatureMap with normalized values for each component.
+      @param[in]   measured_fm FeatureMap with measured intensity for each component.
+      @param[out]  normalized_fm FeatureMap with normalized values for each component.
       @param[in]   mass_intensity_type Mass intensity type (either norm_max or norm_sum).
       @param[in]   feature_name Feature name to determine which features are needed to apply calculations on.
     */
     void calculateMDVs(
-      const FeatureMap& measured_featureMap, 
-      FeatureMap& normalized_featureMap,
+      const FeatureMap& measured_fm, 
+      FeatureMap& normalized_fm,
       const MassIntensityType& mass_intensity_type, 
       const std::string& feature_name);
 

src/openms/include/OpenMS/ANALYSIS/TARGETED/MRMMapping.h

@@ -50,7 +50,7 @@ namespace OpenMS
       user can specify that the program should abort in such a case (see
       error_on_unmapped).
       
-      @Note If multiple mapping is enabled (see map_multiple_assays parameter)
+      @note If multiple mapping is enabled (see map_multiple_assays parameter)
       then each mapped assay will get its own chromatogram that contains the
       same raw data but different meta-annotation. This *can* be useful if the
       same transition is used to monitor multiple analytes but may also

src/openms/include/OpenMS/ANALYSIS/TARGETED/MetaboTargetedAssay.h

@@ -95,7 +95,7 @@ namespace OpenMS
     @return Vector of MetaboTargetedAssay
 
     @param spectra Input of MSExperiment with spectra information
-    @param feature_ms2_spectra_map FeatureMapping class with associated MS2 spectra
+    @param feature_ms2_index FeatureMapping class to associated MS2 spectra
     @param precursor_rt_tol Retention time tolerance of the precursor
     @param precursor_mz_distance Max m/z distance of the precursor entries of two spectra to be merged
     @param cosine_sim_threshold Cosine similarity threshold for the usage of SpectraMerger
@@ -172,8 +172,7 @@ namespace OpenMS
     /**
     @brief Resolve ambiguity groups based on occurrence in samples (e.g. at least in 20% of the samples) and if multiple possible identifications are reported within one ambiguity group use the one with the highest occurrence
 
-    @return Map of pair (mz, rt) and vector of ambiguities for this mz,rt combination (MetaboTargetedAssay)
-
+    @param[in,out] map_mta_filter Map of pair (mz, rt) and vector of ambiguities for this mz,rt combination (MetaboTargetedAssay)
     @param total_occurrence_filter Value which has to be reached for the ambiguity group to be reported (e.g. in 20 % of the samples)
     @param in_files_size Number of files which were processed in the vector of MetaboTargetedAssay (e.g. initially 5 different files in the vector<MetaboTargetedAssay>)
     */
@@ -199,8 +198,7 @@ namespace OpenMS
     /**
     @brief Filter one ambiguity group based on occurrence in samples (e.g. at least in 20% of the samples)
 
-    @return Vector of MetaboTargetedAssay
-
+    @param[in,out] mta Either cleared or left untouched
     @param total_occurrence_filter Value which has to be reached for the ambiguity group to be reported (e.g. in 20 % of the samples)
     @param in_files_size Number of files which were processed in the vector of MetaboTargetedAssay (e.g. initially 5 different files in the vector<MetaboTargetedAssay>)
     */
@@ -209,7 +207,7 @@ namespace OpenMS
     /**
     @brief Filter one ambiguity group with multiple possible identifications to use the one with the highest occurrence
 
-    @return Vector of MetaboTargetedAssay
+    @param mta Vector of MetaboTargetedAssay
     */
     static void filterBasedOnMolFormAdductOccurrence_(std::vector<MetaboTargetedAssay>& mta);
 

src/openms/include/OpenMS/ANALYSIS/XLMS/OpenPepXLAlgorithm.h

@@ -108,6 +108,7 @@ namespace OpenMS
      * @brief Performs the main function of this class, the search for cross-linked peptides
 
      @param unprocessed_spectra The input PeakMap of experimental spectra
+     @param cfeatures Consensus features linking light and heavy mass pairs; e.g. created by FeatureFinderMultiplex
      @param fasta_db The protein database containing targets and decoys
      @param protein_ids A result vector containing search settings. Should contain one PeptideIdentification.
      @param peptide_ids A result vector containing cross-link spectrum matches as PeptideIdentifications and PeptideHits. Should be empty.

src/openms/include/OpenMS/CHEMISTRY/ModificationsDB.h

@@ -109,7 +109,7 @@ namespace OpenMS
 
        @return The matching modification given the constraints. Returns nullptr
        if no modification exists that fulfills the criteria. If multiple
-       modifications are found, the @multiple_matches flag will be set.
+       modifications are found, the @p multiple_matches flag will be set.
     */
     const ResidueModification* searchModificationsFast(const String& mod_name,
                                                        bool& multiple_matches,
@@ -195,9 +195,10 @@ namespace OpenMS
         will choose the _first_ match which defaults to the first matching
         UniMod entry.
 
-        @param residue The residue at which the modifications occurs
         @param mass The monoisotopic mass of the residue including the mass of the modification
         @param max_error The maximal mass error in the modification search
+        @param residue The residue at which the modifications occurs
+        @param term_spec Only modifications with matching term specificity are considered.
 
         @return A pointer to the best matching modification (or NULL if none was found)
 

src/openms/include/OpenMS/CHEMISTRY/NASequence.h

@@ -505,7 +505,7 @@ namespace OpenMS
 
        @param str_it Current position in the string to be parsed
        @param str Full input string
-       @param aas Current AASequence object (will be modified with the correct ribo added)
+       @param nas Current AASequence object (will be modified with the correct ribo added)
 
        @return Position at which to continue parsing
     */

src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataAggregatingConsumer.h

@@ -62,9 +62,9 @@ namespace OpenMS
 
       void setExpectedSize(Size, Size) override {}
 
-      void consumeSpectrum(SpectrumType & s) override;
+      void consumeSpectrum(SpectrumType& s) override;
 
-      void consumeChromatogram(ChromatogramType & c) override;
+      void consumeChromatogram(ChromatogramType& c) override;
 
       void setExperimentalSettings(const OpenMS::ExperimentalSettings&) override {}
 

src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataSqlConsumer.h

@@ -45,7 +45,7 @@ namespace OpenMS
 
         Opens the SQLite file and writes the tables.
 
-        @param filename The filename of the SQLite database
+        @param sql_filename The filename of the SQLite database
         @param run_id Unique identifier which links the sqMass and OSW file
         @param buffer_size How large the internal buffer size should be (defaults to 500 spectra / chromatograms)
         @param full_meta Whether to write the full meta-data in the SQLite header

src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataStoringConsumer.h

@@ -37,9 +37,9 @@ namespace OpenMS
 
     void setExpectedSize(Size s_size, Size c_size) override;
 
-    void consumeSpectrum(SpectrumType & s) override;
+    void consumeSpectrum(SpectrumType& s) override;
 
-    void consumeChromatogram(ChromatogramType & c) override;
+    void consumeChromatogram(ChromatogramType& c) override;
 
     const PeakMap& getData() const;
 

src/openms/include/OpenMS/FORMAT/FileHandler.h

@@ -329,7 +329,8 @@ namespace OpenMS
       @param filename the file name of the file to write.
       @param map The MSQuantifications to store.
       @param allowed_types A vector of supported filetypes. If empty we try to guess based on the filename. If that fails we throw UnableToCreateFile. If there is only one allowed type, check whether it agrees with the filename, and throw UnableToCreateFile if they disagree.
-
+      @param log Progress logging mode
+      
       @exception Exception::UnableToCreateFile is thrown if the file could not be written
     */
     void storeQuantifications(const String& filename, const MSQuantifications& map, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);

src/openms/include/OpenMS/FORMAT/MSPGenericFile.h

@@ -92,7 +92,7 @@ namespace OpenMS
       @throw MissingInformation If the spectrum doesn't have a name or Num Peaks info is missing
       @throw ParseError If Num Peaks' value doesn't match with the number of raw peaks parsed
 
-      @param[in/out] spectrum The spectrum to be added
+      @param[in,out] spectrum The spectrum to be added
       @param[out] library The spectrum is added into this `MSExperiment` library
     */
     void addSpectrumToLibrary(

src/openms/include/OpenMS/FORMAT/MzMLFile.h

@@ -114,6 +114,7 @@ namespace OpenMS
       @param filename_in Filename of input mzML file to transform
       @param consumer Consumer class to operate on the input filename (implementing a transformation)
       @param skip_full_count Whether to skip computing the correct number of spectra and chromatograms in the input file
+      @param skip_first_pass Skip first file parsing pass, which hands only meta-data (number of spectra/chroms and experimental settings) to the consumer
     */
     void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count = false, bool skip_first_pass = false);
 
@@ -130,6 +131,7 @@ namespace OpenMS
       @param consumer Consumer class to operate on the input filename (implementing a transformation)
       @param map Map to store the resulting spectra and chromatograms
       @param skip_full_count Whether to skip computing the correct number of spectra and chromatograms in the input file
+      @param skip_first_pass Skip first file parsing pass, which hands only meta-data (number of spectra/chroms and experimental settings) to the consumer
     */
     void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, PeakMap& map, bool skip_full_count = false, bool skip_first_pass = false);
 

src/openms/include/OpenMS/FORMAT/MzTab.h

@@ -543,7 +543,7 @@ namespace OpenMS
       * @param[in] first_run_inference_only Is all protein inference information (groups and scores) stored in the first run?
       * @param[in] export_empty_pep_ids		Export spectra without PSMs as well?
       * @param[in] export_all_psms		Instead of just the best PSM per spectrum, should other PSMs be exported as well?
-      *
+      * @param[in] title The title for the metadata section
       * @return mzTab object
     */
     static MzTab exportIdentificationsToMzTab(
@@ -567,10 +567,13 @@ namespace OpenMS
 	 *
 	 * @param consensus_map		data structure of the linked peptide features
 	 * @param filename		input consensusXML file name
+   * @param first_run_inference_only Is all protein inference information (groups and scores) stored in the first run?
 	 * @param export_unidentified_features		Should not identified peptide features be exported?
 	 * @param export_unassigned_ids		Should unassigned identifications be exported?
 	 * @param export_subfeatures		The position of the consensus feature will always be exported. Should the individual subfeatures be exported as well?
+   * @param export_empty_pep_ids		Export spectra without PSMs as well?
 	 * @param export_all_psms		Instead of just the best PSM per spectrum, should other PSMs be exported as well?
+   * @param title The title for the metadata section
 	 *
 	 * @return mzTab object
 	 */

src/openms/include/OpenMS/INTERFACES/IMSDataConsumer.h

@@ -57,7 +57,7 @@ namespace Interfaces
 
         @param s The spectrum to be consumed
       */
-      virtual void consumeSpectrum(SpectrumType & s) = 0;
+      virtual void consumeSpectrum(SpectrumType& s) = 0;
 
       /**
         @brief Consume a chromatogram
@@ -66,9 +66,9 @@ namespace Interfaces
 
         @note The implementation might not allow to consume spectra and chromatograms in any order
 
-        @param s The chromatogram to be consumed
+        @param c The chromatogram to be consumed
       */
-      virtual void consumeChromatogram(ChromatogramType &) = 0;
+      virtual void consumeChromatogram(ChromatogramType& c) = 0;
 
       /**
         @brief Set expected size of spectra and chromatograms to be consumed.