Fixed: Some doxygen issues

git-svn-id: http://svn.sintef.no/trondheim/IFEM/trunk@2811 e10b68d5-8a6e-419e-a041-bce267b0401d

Doxyfile.in

@@ -566,7 +566,8 @@ WARN_LOGFILE           =
 
 INPUT                  = doc src \
 			 src/SIM src/ASM src/ASM/LR \
-			 src/Eig src/LinAlg src/Utility
+			 src/Eig src/LinAlg src/Utility \
+			 @PROJECT_BINARY_DIR@
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 

src/IFEM.h.in

@@ -21,15 +21,18 @@
 #include "SIMoptions.h"
 #include "ControlFIFO.h"
 
-
-#ifndef NDEBUG 
+#ifndef NDEBUG
 #include "ScopedLogger.h"
+//! \brief Macro for scope logging.
 #define SCOPED_LOG ScopedLogger no_conflict_logger(__PRETTY_FUNCTION__);
 #else
 #define SCOPED_LOG
 #endif
 
-/*! \brief Class holding global IFEM configuration */
+
+/*!
+  \brief Class holding global IFEM configuration.
+*/
 
 class IFEM
 {
@@ -40,19 +43,21 @@ public:
   //! \return The MPI process ID
   static int Init(int argc, char** argv);
 
+  //! \brief Applies command-line argument values to the general input options.
   static void applyCommandLineOptions(SIMoptions& opt);
+  //! \brief Returns a reference to the general input options
   static SIMoptions& getOptions() { return cmdOptions; }
 
-  //! \brief Register a fifo instruction callback
-  //! \brief callback The callback to register
+  //! \brief Registers a fifo instruction callback.
   static void registerCallback(ControlCallback& callback)
-  { 
+  {
     fifo.registerCallback(callback);
   }
 
-  //! \brief Poll the control fifo for instructions
+  //! \brief Polls the control fifo for instructions.
   static void pollControllerFifo() { fifo.poll(); }
-protected:
+
+private:
   static SIMoptions cmdOptions; //!< General input options
   static int argc;              //!< The number of command-line arguments
   static char** argv;           //!< The command-line arguments

src/Utility/HDF5Writer.h

@@ -52,28 +52,29 @@ public:
   //! \param[in] force If \e true, close even if \a keepopen was \e true
   virtual void closeFile(int level, bool force = false);
 
-  //! \brief Write a vector to file
+  //! \brief Writes a vector to file.
   //! \param[in] level The time level to write the vector at
   //! \param[in] entry The DataEntry describing the vector
   virtual void writeVector(int level, const DataEntry& entry);
 
-  //! \brief Read a vector from file
+  //! \brief Reads a vector from file.
   //! \param[in] level The time level to read the vector at
   //! \param[in] entry The DataEntry describing the vector
   virtual bool readVector(int level, const DataEntry& entry);
 
-  //! \brief Write data from a SIM to file
+  //! \brief Writes data from a SIM to file.
   //! \param[in] level The time level to write the data at
   //! \param[in] entry The DataEntry describing the vector
   //! \param[in] geometryUpdated Whether or not geometries should be written
   //! \param[in] prefix Field name prefix
-  //! \details If prefix is non-empty and we are asked to dump secondard
-  //!          solutions, we assume they come from different projections
+  //!
+  //! \details If prefix is non-empty and we are asked to dump secondary
+  //! solutions, we assume they come from different projections
   //! \sa SIMbase::project
   virtual void writeSIM(int level, const DataEntry& entry,
                         bool geometryUpdated, const std::string& prefix);
 
-  //! \brief Read data from a file into SIM
+  //! \brief Reads data from a file into a SIM.
   //! \param[in] level The time level to read the data at
   //! \param[in] entry The DataEntry describing the SIM
   virtual bool readSIM(int level, const DataEntry& entry);
@@ -83,7 +84,7 @@ public:
   //! \param[in] entry The DataEntry describing the vector
   virtual void writeNodalForces(int level, const DataEntry& entry);
 
-  //! \brief Write time stepping info to file (currently a dummy)
+  //! \brief Writes time stepping info to file.
   //! \param[in] level The time level to write the info at
   //! \param[in] order The temporal order
   //! \param[in] interval The number of time steps between each data dump
@@ -91,21 +92,11 @@ public:
   virtual bool writeTimeInfo(int level, int order, int interval,
                              const TimeStep& tp);
 
-  /* Not used, remove?
-  //! \brief Reads a vector field into a given SIM
-  //! \param[in] level The time level to read at
-  //! \param[in] name The name of the field
-  //! \param[in] vec The vector to read into
-  //! \param[in] sim The SIM this vector is associated with
-  //! \param[in] components The number of components in the field
-  bool readField(int level, const std::string& name,
-                 Vector& vec, SIMbase* sim, int components);
-  */
-
-  //! \brief Reads a text string
+  //! \brief Reads a text string.
   //! \param[in] name The name (path in HDF5 file) to the string
   //! \param[out] out The string to read data into
-  void readString(const std::string& name, std::string& out, bool close=true);
+  //! \param[in] close If \e false, keep the HDF5-file open after reading
+  void readString(const std::string& name, std::string& out, bool close = true);
 
   //! \brief Reads a double vector.
   //! \param[in] level The time level to read at
@@ -131,7 +122,7 @@ public:
   bool readDouble(int level, const std::string& group,
                   const std::string& name, double& data);
 
-  //! \brief Check if updated geometries exists in file at given time level
+  //! \brief Checks if updated geometries exist in file at given time level.
   //! \param[in] level The time level to check
   //! \param[in] basisName Check for a particular basis
   bool hasGeometries(int level, const std::string& basisName = "");
@@ -167,7 +158,7 @@ protected:
   //! \param[out] data The array to read data into
   void readArray(int group, const std::string& name, int& len, int*& data);
 
-  //! \brief Internal helper function. Check if a group exists in the HDF5 file
+  //! \brief Internal helper function. Checks if a group exists in the file.
   //! \param[in] parent The HDF5 group of the parent
   //! \param[in] group The name of the group to check for
   //! \return \e true if group exists, otherwise \e false