more doxygen fixes

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

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_;
-
   };
 }
 

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 <typename T>
@@ -163,9 +164,9 @@ namespace OpenMS
 
     @return True if @p elem is contained in @p container, false otherwise.
     */
-    static bool contains(const std::vector<String>& container, String elem, const CASE cs)
+    static bool contains(const std::vector<String>& 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 <T> 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 <typename T>

src/openms/include/OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h

@@ -206,18 +206,13 @@ namespace OpenMS
 
     */
     template <typename PeakTypeIterator, typename ConstPeakTypeIterator>
-#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")

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);
 

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);
     }