Refs #8632. More doxygen errors.

Fixing DataHandling, Kernel, MDAlgorithms, MDEvents and Nexus.

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus.h

@@ -73,7 +73,7 @@ namespace Mantid
       virtual const std::string category() const { return "DataHandling\\Nexus;Muon"; }
 
       /// Returns a confidence value that this algorithm can load a file
-      virtual int confidence(Kernel::NexusDescriptor &) const;
+      virtual int confidence(Kernel::NexusDescriptor &descriptor) const;
 
     protected:
 

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SetSampleMaterial.h

@@ -52,7 +52,6 @@ class DLLExport SetSampleMaterial : public Mantid::API::Algorithm
   virtual int version() const;
   /// Algorithm's category for identification
   virtual const std::string category() const;
-  /// @inheritdocs
   virtual std::map<std::string, std::string> validateInputs();
 
 private:

Code/Mantid/Framework/DataHandling/src/LoadAscii2.cpp

@@ -149,7 +149,6 @@ namespace Mantid
     * Check the start of the file for the first data set, then set the number of columns that hsould be expected thereafter
     * @param[in] line : The current line of data
     * @param[in] columns : the columns of values in the current line of data
-    * @param[in] lineNo : the current line number
     */
     void LoadAscii2::parseLine(const std::string & line, std::list<std::string> & columns)
     {
@@ -500,7 +499,6 @@ namespace Mantid
 
     /**
     * Check if the file has been found to incosistantly include spectra IDs
-    * @param[in] spectraSize : the number of spectra recorded so far
     */
     void LoadAscii2::inconsistantIDCheck() const
     {
@@ -554,6 +552,7 @@ namespace Mantid
     /**
     * Return true if the line is to be skipped.
     * @param[in] line :: The line to be checked
+    * @param[in] header :: Flag for if this is header material
     * @return True if the line should be skipped
     */
     bool LoadAscii2::skipLine(const std::string & line, bool header) const

Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp

@@ -139,10 +139,12 @@ class ProcessBankData : public Task
    * @param event_time_of_flight :: array with event TOFS
    * @param numEvents :: how many events in the arrays
    * @param startAt :: index of the first event from event_index
-   * @param event_index_ptr :: ptr to a vector of event index (length of # of pulses)
+   * @param event_index :: vector of event index (length of # of pulses)
    * @param thisBankPulseTimes :: ptr to the pulse times for this particular bank.
    * @param have_weight :: flag for handling simulated files
    * @param event_weight :: array with weights for events
+   * @param min_event_id ;: minimum detector ID to load
+   * @param max_event_id :: maximum detector ID to load
    * @return
    */
   ProcessBankData(LoadEventNexus * alg, std::string entry_name,
@@ -2611,7 +2613,7 @@ void LoadEventNexus::loadTimeOfFlightData(::NeXus::File& file, DataObjects::Even
  * 
  * @note: It does essentially the same thing of the method: LoadISISNexus2::loadSampleData
  * 
- * @param nexusfilename : path for the nexus file
+ * @param file : handle to the nexus file
  * @param WS : pointer to the workspace
  */
 void LoadEventNexus::loadSampleDataISIScompatibility(::NeXus::File& file, Mantid::API::MatrixWorkspace_sptr WS){

Code/Mantid/Framework/DataHandling/src/LoadFullprofResolution.cpp

@@ -304,6 +304,7 @@ namespace DataHandling
     * @param bankid :: [input] ID of the bank to get parsed
     * @param startlineindex :: [input] index of the first line of the bank in vector of lines
     * @param endlineindex :: [input] index of the last line of the bank in vector of lines
+    * @param profNumber :: [input] index of the profile number
     */
   void LoadFullprofResolution::parseResolutionStrings(map<string, double>& parammap, const vector<string>& lines,
                                                       int bankid, int startlineindex, int endlineindex, int profNumber)

Code/Mantid/Framework/DataHandling/src/LoadHelper.cpp

@@ -20,7 +20,7 @@ LoadHelper::~LoadHelper() {
 
 /**
  * Finds the path for the instrument name in the nexus file
- * Usually of the form: entry0/<NXinstrument class>/name
+ * Usually of the form: entry0/\<NXinstrument class\>/name
  */
 std::string LoadHelper::findInstrumentNexusPath(
 		const NeXus::NXEntry &firstEntry) {
@@ -81,6 +81,7 @@ double LoadHelper::calculateEnergy(double wavelength) {
 /**
  * Calculate TOF from distance
  *  @param distance :: distance in meters
+ *  @param wavelength :: wavelength to calculate TOF from
  *  @return tof in seconds
  */
 double LoadHelper::calculateTOF(double distance,double wavelength) {

Code/Mantid/Framework/DataHandling/src/LoadLog.cpp

@@ -541,6 +541,7 @@ namespace Mantid
     /**
      * Count the number of columns in the first line of the text file
      * @param logFileStream :: stream to the file
+     * @param logFileName :: name for the log file
      */
     int LoadLog::countNumberColumns(std::ifstream& logFileStream, const std::string& logFileName)
     {

Code/Mantid/Framework/DataHandling/src/LoadMcStas.cpp

@@ -211,8 +211,8 @@ namespace DataHandling
 
 	/**
 	 * Return the confidence with with this algorithm can load the file
-	 * @param descriptor A descriptor for the file
-	 * @param descriptor A descriptor for the file
+   * @param eventEntries map of the file entries that have events
+   * @param outputGroup pointer to the workspace group
 	 * @param nxFile Reads data from inside first first top entry
 	 */
 	void LoadMcStas::readEventData(const std::map<std::string, std::string>& eventEntries, WorkspaceGroup_sptr& outputGroup, ::NeXus::File& nxFile)
@@ -389,7 +389,9 @@ namespace DataHandling
 
 	/**
 	 * Return the confidence with with this algorithm can load the file
-	 * @param descriptor A descriptor for the file
+   * @param histogramEntries map of the file entries that have histogram
+   * @param outputGroup pointer to the workspace group
+   * @param nxFile Reads data from inside first first top entry
 	 * @returns An integer specifying the confidence level. 0 indicates it will not be used
 	 */
 	void LoadMcStas::readHistogramData(const std::map<std::string, std::string>& histogramEntries, WorkspaceGroup_sptr& outputGroup, ::NeXus::File& nxFile)

Code/Mantid/Framework/DataHandling/src/LoadMuonNexus.cpp

@@ -169,8 +169,9 @@ namespace Mantid
      * @param descriptor A descriptor for the file
      * @returns An integer specifying the confidence level. 0 indicates it will not be used
      */
-    int LoadMuonNexus::confidence(Kernel::NexusDescriptor &) const
+    int LoadMuonNexus::confidence(Kernel::NexusDescriptor &descriptor) const
     {
+      UNUSED_ARG(descriptor);
       return 0; // Not to be used but LoadMuonNexus2, which inherits from this will
     }
 

Code/Mantid/Framework/DataHandling/src/LoadNexusProcessed.cpp

@@ -339,7 +339,7 @@ bool LoadNexusProcessed::checkForCommonNameStem(NXRoot & root, std::vector<std::
  * Load the workspace name, if the attribute exists
  *
  * @param root :: Root of NeXus file
- * @param entr_name :: Entry in NeXus file to look at
+ * @param entry_name :: Entry in NeXus file to look at
  * @return The workspace name. If none found an empty string is returned.
  */
 std::string LoadNexusProcessed::loadWorkspaceName(NXRoot & root, const std::string& entry_name)

Code/Mantid/Framework/DataHandling/src/LoadTOFRawNexus.cpp

@@ -316,6 +316,7 @@ void LoadTOFRawNexus::countPixels(const std::string &nexusfilename, const std::s
  * @param entry_name :: NXentry name
  * @param bankName :: NXdata bank name
  * @param WS :: workspace to modify
+ * @param id_to_wi :: det ID to workspace index mapping
  */
 void LoadTOFRawNexus::loadBank(const std::string &nexusfilename, const std::string & entry_name,
     const std::string &bankName, API::MatrixWorkspace_sptr WS, const detid2index_map& id_to_wi)

Code/Mantid/Framework/DataHandling/src/SaveSPE.cpp

@@ -124,7 +124,7 @@ namespace Mantid
     }
 
     /** Write the data to the SPE file
-    *  @param outFile :: the file object to write to
+    *  @param outSPEFile :: the file object to write to
     *  @param inputWS :: the workspace to be saved
     */
     void SaveSPE::writeSPEFile(FILE * outSPEFile, const API::MatrixWorkspace_const_sptr &inputWS)

Code/Mantid/Framework/Kernel/inc/MantidKernel/BoundedValidator.h

@@ -60,6 +60,7 @@ class DLLExport BoundedValidator : public TypedValidator<TYPE>
   /** Constructor
    * @param lowerBound :: The lower bounding value
    * @param upperBound :: The upper bounding value
+   * @param exclusive :: make bounds exclusive (default inclusive)
    */
   BoundedValidator(const TYPE lowerBound, const TYPE upperBound, bool exclusive=false)
   : TypedValidator<TYPE>(),

Code/Mantid/Framework/Kernel/src/FileDescriptor.cpp

@@ -16,7 +16,7 @@ namespace Mantid
      * first nbytes of the file and returns false if a non-ascii character is found.
      * If the file is shorter than nbytes then it checks until the end of the stream.
      * @param filename A string pointing to an existing file
-     * @param bytes The number of bytes of the file to check (Default=256)
+     * @param nbytes The number of bytes of the file to check (Default=256)
      * @returns True if the file is considered ASCII, false otherwise
      * @throws std::invalid_argument if the file cannot be opened
      * @throws std::runtime_error if an error is occurred while reading the stream
@@ -39,7 +39,7 @@ namespace Mantid
      * the result up to that point
      * The stream is reset to the position is was at when entering the function
      * @param data An input stream opened in binary mode
-     * @param bytes The number of bytes of the file to check (Default=256)
+     * @param nbytes The number of bytes of the file to check (Default=256)
      * @returns True if the stream is considered ASCII, false otherwise
      */
     bool FileDescriptor::isAscii(std::istream & data, const size_t nbytes)

Code/Mantid/Framework/Kernel/src/FileValidator.cpp

@@ -28,6 +28,7 @@ Logger& FileValidator::g_log = Logger::get("FileValidator");
 /** Constructor
  *  @param extensions :: The permitted file extensions (e.g. .RAW)
  *  @param testFileExists :: Flag indicating whether to test for existence of file (default: yes)
+ *  @param testCanWrite :: Flag to check if file writing permissible.
  */
 FileValidator::FileValidator(const std::vector<std::string>& extensions, bool testFileExists,
                              bool testCanWrite) :

Code/Mantid/Framework/Kernel/src/Logger.cpp

@@ -450,8 +450,8 @@ namespace Kernel
 
    /**
    * Log a given message at a given priority
-   * @param message :: The message to log
    * @param priority :: The priority level
+   * @return :: the stream
    */
   std::ostream& Logger::getLogStream(Logger::Priority priority)
   {

Code/Mantid/Framework/Kernel/src/NeutronAtom.cpp

@@ -663,7 +663,7 @@ NeutronAtom operator*(const NeutronAtom& left, const double right)
 }
 
 /**
- * This calls @link operator*(const NeutronAtom&, const double)
+ * This calls @link operator*(const NeutronAtom&, const double) @endlink
  * with the parameters reversed.
  */
 NeutronAtom operator*(const double left, const NeutronAtom& right)

Code/Mantid/Framework/Kernel/src/NexusDescriptor.cpp

@@ -220,7 +220,6 @@ namespace Mantid
      * @param file An open NeXus File object
      * @param rootPath The current path that is open in the file
      * @param className The class of the current open path
-     * @param tmap [Out] An output map filled with mappings of type->path
      * @param pmap [Out] An output map filled with mappings of path->type
      * @param level An integer defining the current level in the file
      */

Code/Mantid/Framework/Kernel/src/UnitConversion.cpp

@@ -62,13 +62,7 @@ namespace Mantid
 
     /**
      * Convert a single value between the given units (overload for Unit objects)
-     * @param srcUnit :: The starting unit
-     * @param destUnit :: The destination unit
-     * @param srcValue :: The value to convert
-     * @param l1 ::       The source-sample distance (in metres)
-     * @param l2 ::       The sample-detector distance (in metres)
      * @param twoTheta :: The scattering angle (in radians)
-     * @param emode ::    The energy mode enumeration
      * @param efixed ::   Value of fixed energy: EI (emode=1) or EF (emode=2) (in meV)
      * @return The value converted to the destination unit
      */

Code/Mantid/Framework/MDAlgorithms/src/IntegratePeaksMD.cpp

@@ -649,7 +649,7 @@ namespace MDAlgorithms
 
   /** Calculate if this Q is on a detector
    *
-   * @param QLabFrame. The Peak center.
+   * @param QLabFrame: The Peak center.
    * @param r: Peak radius.
    */
   bool IntegratePeaksMD::detectorQ(Mantid::Kernel::V3D QLabFrame, double r)

Code/Mantid/Framework/MDAlgorithms/src/IntegratePeaksMD2.cpp

@@ -638,7 +638,7 @@ namespace MDAlgorithms
 
   /** Calculate if this Q is on a detector
    *
-   * @param QLabFrame. The Peak center.
+   * @param QLabFrame: The Peak center.
    * @param r: Peak radius.
    */
   bool IntegratePeaksMD2::detectorQ(Mantid::Kernel::V3D QLabFrame, double r)

Code/Mantid/Framework/MDEvents/inc/MantidMDEvents/ConvToMDBase.h

@@ -59,7 +59,7 @@ namespace MDEvents
      ConvToMDBase();
 
     ///method which initates all main class variables 
-    virtual size_t initialize(const MDWSDescription &WSD, boost::shared_ptr<MDEventWSWrapper> inWSWrapper, bool IgnoreZeros);
+    virtual size_t initialize(const MDWSDescription &WSD, boost::shared_ptr<MDEventWSWrapper> inWSWrapper, bool ignoreZeros);
     /// method which starts the conversion procedure
     virtual void runConversion(API::Progress *)=0;
     /// virtual destructor

Code/Mantid/Framework/MDEvents/inc/MantidMDEvents/MDGridBox.h

@@ -40,7 +40,7 @@ namespace MDEvents
   {
   public:
 
-    MDGridBox(boost::shared_ptr<Mantid::API::BoxController> &bc, const uint32_t depth,const std::vector<Mantid::Geometry::MDDimensionExtents<coord_t> > & extentsVector);
+    MDGridBox(boost::shared_ptr<API::BoxController> &bc, const uint32_t depth,const std::vector<Mantid::Geometry::MDDimensionExtents<coord_t> > & extentsVector);
     MDGridBox(Mantid::API::BoxController *const bc, const uint32_t depth,const std::vector<Mantid::Geometry::MDDimensionExtents<coord_t> > & extentsVector);
 
     MDGridBox(MDBox<MDE, nd> * box);

Code/Mantid/Framework/MDEvents/src/CoordTransformDistance.cpp

@@ -24,6 +24,7 @@ namespace MDEvents
    * @param center :: array of size[inD], with the coordinates at the center
    * @param dimensionsUsed :: bool array of size[inD] where True is set for those dimensions that are considered when
    *        calculating distance.
+   * @param outD :: # of output dimensions
    * @return
    */
   CoordTransformDistance::CoordTransformDistance(const size_t inD, const coord_t * center, const bool * dimensionsUsed, const size_t outD)

Code/Mantid/Framework/MDEvents/src/MDBox.cpp

@@ -614,6 +614,7 @@ namespace MDEvents
    * @param length :: length below which to integrate
    * @param[out] signal :: set to the integrated signal
    * @param[out] errorSquared :: set to the integrated squared error.
+   * @param[out] signal_fit :: evaluation parameter on fit
    */
   TMDE(
   void MDBox)::integrateCylinder(Mantid::API::CoordTransform & radiusTransform, const coord_t radius, const coord_t length, signal_t & signal, signal_t & errorSquared, std::vector<signal_t> & signal_fit) const

Code/Mantid/Framework/MDEvents/src/MDGridBox.cpp

@@ -1316,9 +1316,11 @@ GCC_DIAG_OFF(array-bounds)
    *
    * @param radiusTransform :: nd-to-1 coordinate transformation that converts from these
    *        dimensions to the distance (squared) from the center of the sphere.
-   * @param radiusSquared :: radius^2 below which to integrate
+   * @param radius :: radius below which to integrate
+   * @param length :: length below which to integrate
    * @param signal [out] :: set to the integrated signal
    * @param errorSquared [out] :: set to the integrated squared error.
+   * @param[out] signal_fit :: evaluation parameter on fit
    */
   TMDE(
   void MDGridBox)::integrateCylinder(Mantid::API::CoordTransform & radiusTransform, const coord_t radius, const coord_t length, signal_t & signal, signal_t & errorSquared, std::vector<signal_t> & signal_fit) const

Code/Mantid/Framework/Nexus/src/NexusFileIO.cpp

@@ -150,6 +150,7 @@ using namespace DataObjects;
        The URLs are not correct as they do not exist presently, but follow the format for other
        Nexus specs.
        @param title :: title field.
+       @param wsName :: workspace name.
   */
   int NexusFileIO::writeNexusProcessedHeader( const std::string& title, const std::string& wsName) const
   {