diff --git a/src/openms/include/OpenMS/CHEMISTRY/SimpleTSGXLMS.h b/src/openms/include/OpenMS/CHEMISTRY/SimpleTSGXLMS.h index 79d2106aae0..3365d707602 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/SimpleTSGXLMS.h +++ b/src/openms/include/OpenMS/CHEMISTRY/SimpleTSGXLMS.h @@ -21,17 +21,17 @@ namespace OpenMS class AASequence; /** - @brief Generates theoretical spectra for cross-linked peptides + @brief Generates theoretical spectra for cross-linked peptides - The spectra this class generates are vectors of SimplePeaks. - This class generates the same peak types as TheoreticalSpectrumGeneratorXLMS - and the interface is very similar, but it is simpler and faster. - SimplePeak only contains an mz value and a charge. No intensity values - or String annotations or other additional DataArrays are generated. + The spectra this class generates are vectors of SimplePeaks. + This class generates the same peak types as TheoreticalSpectrumGeneratorXLMS + and the interface is very similar, but it is simpler and faster. + SimplePeak only contains an mz value and a charge. No intensity values + or String annotations or other additional DataArrays are generated. @htmlinclude OpenMS_SimpleTSGXLMS.parameters - @ingroup Chemistry + @ingroup Chemistry */ class OPENMS_DLLAPI SimpleTSGXLMS : public DefaultParamHandler diff --git a/src/openms/include/OpenMS/CHEMISTRY/SpectrumAnnotator.h b/src/openms/include/OpenMS/CHEMISTRY/SpectrumAnnotator.h index 6ed377407e0..e375eae2423 100644 --- a/src/openms/include/OpenMS/CHEMISTRY/SpectrumAnnotator.h +++ b/src/openms/include/OpenMS/CHEMISTRY/SpectrumAnnotator.h @@ -66,7 +66,6 @@ namespace OpenMS The matches are added as DataArrays to the spectrum (Names: IonName and IonMatchError). The parameters of the TheoreticalSpectrumGenerator define the comprehensiveness of the available matching. The parameters of SpectrumAlignment define the matching tolerance. See the parameter section of this class for the available options. - @htmlinclude OpenMS_SpectrumAnnotator.parameters */ void annotateMatches(PeakSpectrum &spec, const PeptideHit& ph, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const; @@ -80,7 +79,6 @@ namespace OpenMS The ion match statistics are added as UserParams to either the PeptideIdentification (parameters of the matching) and PeptideHit. The parameters of the TheoreticalSpectrumGenerator define the comprehensiveness of the available matching. The parameters of SpectrumAlignment define the matching tolerance. See the parameter section of this class for the available statistics. - @htmlinclude OpenMS_SpectrumAnnotator.parameters */ void addIonMatchStatistics(PeptideIdentification& pi, MSSpectrum &spec, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const; @@ -103,7 +101,6 @@ namespace OpenMS static const boost::regex ct_regex_; static const boost::regex noloss_regex_; static const boost::regex seriesposition_regex_; - }; } diff --git a/src/openms/include/OpenMS/DATASTRUCTURES/ListUtils.h b/src/openms/include/OpenMS/DATASTRUCTURES/ListUtils.h index 07f02ba3d6f..3797c0877a5 100644 --- a/src/openms/include/OpenMS/DATASTRUCTURES/ListUtils.h +++ b/src/openms/include/OpenMS/DATASTRUCTURES/ListUtils.h @@ -86,6 +86,7 @@ namespace OpenMS @note The values get converted by boost::lexical_cast so a valid conversion from String to T needs to be available. @param str The string that should be split and converted to a list. + @param splitter The separator to look for in @p str @return A vector containing the elements of the string converted into type T. */ template @@ -163,9 +164,9 @@ namespace OpenMS @return True if @p elem is contained in @p container, false otherwise. */ - static bool contains(const std::vector& container, String elem, const CASE cs) + static bool contains(const std::vector& container, String elem, const CASE case_sensitive) { - if (cs == CASE::SENSITIVE) return contains(container, elem); + if (case_sensitive == CASE::SENSITIVE) return contains(container, elem); // case insensitive ... elem.toLower(); return find_if(container.begin(), container.end(), [&elem](String ce) { @@ -188,7 +189,7 @@ namespace OpenMS /** @brief Concatenates all elements of the @p container and puts the @p glue string between elements. - @param container The container to concatenate; must have begin() and end() iterator. + @param container The container to concatenate; must have begin() and end() iterator. @param glue The string to add in between elements. */ template diff --git a/src/openms/include/OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h b/src/openms/include/OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h index cb047dcca6a..5f0936e7c1e 100644 --- a/src/openms/include/OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h +++ b/src/openms/include/OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h @@ -206,18 +206,13 @@ namespace OpenMS */ template -#ifdef OPENMS_ASSERTIONS void raster(ConstPeakTypeIterator mz_raw_it, ConstPeakTypeIterator mz_raw_end, ConstPeakTypeIterator int_raw_it, ConstPeakTypeIterator int_raw_end, ConstPeakTypeIterator mz_resample_it, ConstPeakTypeIterator mz_resample_end, PeakTypeIterator int_resample_it, PeakTypeIterator int_resample_end) -#else - void raster(ConstPeakTypeIterator mz_raw_it, ConstPeakTypeIterator mz_raw_end, - ConstPeakTypeIterator int_raw_it, ConstPeakTypeIterator /* int_raw_end */, - PeakTypeIterator mz_resample_it, PeakTypeIterator mz_resample_end, - PeakTypeIterator int_resample_it, PeakTypeIterator /* int_resample_end */) -#endif { + (void*)&int_raw_end; // avoid 'unused parameter' compile error + (void*)&int_resample_end; // avoid 'unused parameter' compile error OPENMS_PRECONDITION(mz_resample_it != mz_resample_end, "Output iterators cannot be identical") // as we use +1 OPENMS_PRECONDITION(std::distance(mz_resample_it, mz_resample_end) == std::distance(int_resample_it, int_resample_end), "Resample m/z and intensity iterators need to cover the same distance") diff --git a/src/openms/include/OpenMS/FORMAT/MascotRemoteQuery.h b/src/openms/include/OpenMS/FORMAT/MascotRemoteQuery.h index fb179422a20..14effe2188f 100644 --- a/src/openms/include/OpenMS/FORMAT/MascotRemoteQuery.h +++ b/src/openms/include/OpenMS/FORMAT/MascotRemoteQuery.h @@ -122,7 +122,7 @@ private slots: /** @brief Remove host name information from an url, e.g., "http://www.google.de/search" -> "search" - @param The url that will be manipulated. + @param url The url that will be manipulated. */ void removeHostName_(QString& url); diff --git a/src/openms_gui/include/OpenMS/VISUAL/LayerDataBase.h b/src/openms_gui/include/OpenMS/VISUAL/LayerDataBase.h index 9a4107636cb..d289c2d59c2 100644 --- a/src/openms_gui/include/OpenMS/VISUAL/LayerDataBase.h +++ b/src/openms_gui/include/OpenMS/VISUAL/LayerDataBase.h @@ -225,8 +225,9 @@ namespace OpenMS * \param area Range to search in. Only dimensions used in the canvas are populated. * \return A proxy (e.g. scan + peak index in an MSExperiment) which points to the data */ - virtual PeakIndex findClosestDataPoint(const RangeAllType& /*area*/) const + virtual PeakIndex findClosestDataPoint(const RangeAllType& area) const { + (void*)&area; // allow doxygen to document the param throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION); } @@ -235,8 +236,9 @@ namespace OpenMS * \param area Range to search in. Only dimensions used in the canvas are populated. * \return A proxy (e.g. scan + peak index in an MSExperiment) which points to the data */ - virtual PeakIndex findHighestDataPoint(const RangeAllType& /*area*/) const + virtual PeakIndex findHighestDataPoint(const RangeAllType& area) const { + (void*)&area; // allow doxygen to document the param throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION); } @@ -257,8 +259,9 @@ namespace OpenMS * \param peak_index The datapoint * \return A string, e.g. "fwhm: 20, im: 3.3", depending on which float/string dataarrays are populated for the given datapoint */ - virtual String getDataArrayDescription(const PeakIndex& /*peak_index*/) + virtual String getDataArrayDescription(const PeakIndex& peak_index) { + (void*)&peak_index; // allow doxygen to document the param throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION); }