[svn-r8950] Purpose: Updated documentation

Description:
    Updated various function headers for the RM.
    Added DOXYGEN_SHOULD_SKIP_THIS to selectively un-display some
        info, that shouldn't be needed by application users.
    Added mainpage to the RM via the new file H5CppDoc.h

Platforms tested:
    SunOS 5.7 (arabica)
    Linux 2.4 (verbena)
    The new file will be added to windows project soon.

Misc. update:

26 files changed, 282 insertions, 129 deletions

diff --git a/c++/src/H5Attribute.cpp b/c++/src/H5Attribute.cpp
index 1e5e919..1b92a6f 100644
--- a/c++/src/H5Attribute.cpp
+++ b/c++/src/H5Attribute.cpp
@@ -258,14 +258,15 @@ string Attribute::getName() const
    return( attr_name ); 
 }
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 //--------------------------------------------------------------------------
-// Function:	Attribute::p_close (private)
-///\brief	Closes this attribute.
-///\exception	H5::AttributeIException
-///\note
-///		This function will be obsolete because its functionality
-///		is recently handled by the C library layer. - May, 2004
-// Programmer	Binh-Minh Ribler - 2000
+// Function:    Attribute::p_close (private)
+// Purpose:     Closes this attribute.
+// Exception    H5::AttributeIException
+// Description
+//              This function will be obsolete because its functionality
+//              is recently handled by the C library layer. - May, 2004
+// Programmer   Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void Attribute::p_close() const
 {
@@ -275,6 +276,7 @@ void Attribute::p_close() const
       throw AttributeIException(0, "H5Aclose failed");
    }
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:	Attribute destructor
diff --git a/c++/src/H5Attribute.h b/c++/src/H5Attribute.h
index 8b06a8b..8c15227 100644
--- a/c++/src/H5Attribute.h
+++ b/c++/src/H5Attribute.h
@@ -41,8 +41,10 @@ class H5_DLLCPP Attribute : public AbstractDs {
 	// do not inherit iterateAttrs from H5Object
 	int iterateAttrs() { return 0; }
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	// Used by the API to appropriately close an attribute
 	virtual void p_close() const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
         // Creates a copy of an existing attribute using the attribute id
         Attribute( const hid_t attr_id );
diff --git a/c++/src/H5CommonFG.cpp b/c++/src/H5CommonFG.cpp
index ee3e299..6d60c6d 100644
--- a/c++/src/H5CommonFG.cpp
+++ b/c++/src/H5CommonFG.cpp
@@ -757,7 +757,7 @@ hsize_t CommonFG::getNumObjs() const
 
 //--------------------------------------------------------------------------
 // Function:	CommonFG::getObjnameByIdx
-///\brief	Retrieves the name of an object in this group by giving the
+///\brief	Retrieves the name of an object in this group, given the
 ///		object's index.
 ///\param	idx  -     IN: Transient index of the object
 ///\param	name - IN/OUT: Retrieved name of the object
@@ -787,7 +787,7 @@ ssize_t CommonFG::getObjnameByIdx(hsize_t idx, string& name, size_t size) const
 
 //--------------------------------------------------------------------------
 // Function:	CommonFG::getObjTypeByIdx
-///\brief	Returns the type of an object in this group by giving the
+///\brief	Returns the type of an object in this group, given the
 ///		object's index.
 ///\param	idx - IN: Transient index of the object
 ///\return	Object type
diff --git a/c++/src/H5CommonFG.h b/c++/src/H5CommonFG.h
index 9a51015..cde7c89 100644
--- a/c++/src/H5CommonFG.h
+++ b/c++/src/H5CommonFG.h
@@ -53,7 +53,7 @@ class H5_DLLCPP CommonFG {
 	void unlink(const char* name) const;
 	void unlink(const string& name) const;
 
-	/// For subclasses to get the correct object id, i.e. file or group id.
+	/// For subclasses to return the correct object id, i.e. file or group id.
 	virtual hid_t getLocId() const = 0; 
 
 	// Renames an object at this location.
@@ -117,11 +117,11 @@ class H5_DLLCPP CommonFG {
 	// Returns the number of objects in this group.
 	hsize_t getNumObjs() const;
 
-	// Retrieves the name of an object in this group by giving the
+	// Retrieves the name of an object in this group, given the
 	// object's index.
 	ssize_t getObjnameByIdx(hsize_t idx, string& name, size_t size) const;
 
-	// Returns the type of an object in this group by giving the
+	// Returns the type of an object in this group, given the
 	// object's index.
 	H5G_obj_t getObjTypeByIdx(hsize_t idx) const;
 	H5G_obj_t getObjTypeByIdx(hsize_t idx, string& type_name) const;
diff --git a/c++/src/H5CppDoc.h b/c++/src/H5CppDoc.h
new file mode 100644
index 0000000..5ecd87a
--- /dev/null
+++ b/c++/src/H5CppDoc.h
@@ -0,0 +1,70 @@
+// C++ informative line for the emacs editor: -*- C++ -*-
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+  * Copyright by the Board of Trustees of the University of Illinois.         *
+  * All rights reserved.                                                      *
+  *                                                                           *
+  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+  * terms governing use, modification, and redistribution, is contained in    *
+  * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+  * of the source code distribution tree; Copyright.html can be found at the  *
+  * root level of an installed copy of the electronic HDF5 document set and   *
+  * is linked from the top-level documents page.  It can also be found at     *
+  * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
+  * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
+  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef _H5CPPDOC_H
+#define _H5CPPDOC_H
+
+//-------------------------------------------------------------------------
+// The following section will be used to generate the 'Mainpage' 
+// and the 'Examples' for the RM.
+// ------------------------------------------------------------------------
+
+/*! \mainpage notitle
+ *
+ * \section intro_sec Introduction
+ *
+ * The C++ API provides C++ wrappers for the HDF5 C library.
+ * It is assumed that the user has knowledge of the HDF5 file format 
+ * and its components.  If you are not familiar with HDF5 file format,
+ * and would like to find out more, please refer to the HDF5 documentation
+ * at http://hdf.ncsa.uiuc.edu/HDF5/doc/H5.intro.html
+ *
+ * Because the HDF5 library maps very well to 
+ * the object oriented design approach, classes in the C++ API can 
+ * closely represent the interfaces of the HDF5 APIs, as followed:
+ * 
+ * \verbatim
+ 	HDF5 C APIs				C++ Classes
+ 	-----------				-----------
+ 	Attribute Interface (H5A)		Attribute
+ 	Datasets Interface (H5D)		DataSet
+ 	Error Interface (H5E)			Exception
+ 	File Interface (H5F)			H5File
+ 	Group Interface (H5G)			Group
+ 	Identifier Interface (H5I)		IdComponent
+ 	Property List Interface (H5P)		PropList
+ 	Reference Interface (H5R)		Reference
+ 	Dataspace Interface (H5S)		DataSpace
+ 	Datatype Interface (H5T)		DataType
+ 	Filters and Compression Interface (H5Z)	FilterCompress (not done)
+  \endverbatim
+ * \section install_sec Installation
+ *
+ * Please refer to the file release_docs/INSTALL
+ * under the top directory for information about installing, building,
+ * and testing the C++ API.
+ *
+ *  
+ */
+
+///\par Dataset example:
+///   This example shows how to create datasets.
+///\example     create.cpp
+
+///\par Another example:
+///   This example shows how to write datasets.
+///\example     writedata.cpp
+
+#endif
diff --git a/c++/src/H5DataSet.cpp b/c++/src/H5DataSet.cpp
index 5b38621..f344308 100644
--- a/c++/src/H5DataSet.cpp
+++ b/c++/src/H5DataSet.cpp
@@ -480,13 +480,14 @@ DataSpace DataSet::getRegion(void *ref, H5R_type_t ref_type) const
    return(dataspace);
 }
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 //--------------------------------------------------------------------------
 // Function:    DataSet::p_close (private)
-///\brief       Closes this dataset.
-///\exception   H5::DataSetIException
-///\note
-///             This function will be obsolete because its functionality
-///             is recently handled by the C library layer.
+// Purpose:     Closes this dataset.
+// Exception    H5::DataSetIException
+// Description
+//              This function will be obsolete because its functionality
+//              is recently handled by the C library layer. - May, 2004
 // Programmer   Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataSet::p_close() const
@@ -497,6 +498,7 @@ void DataSet::p_close() const
       throw DataSetIException(0, "H5Dclose failed");
    }
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:	DataSet destructor
diff --git a/c++/src/H5DataSet.h b/c++/src/H5DataSet.h
index c12a539..85aa974 100644
--- a/c++/src/H5DataSet.h
+++ b/c++/src/H5DataSet.h
@@ -82,8 +82,10 @@ class H5_DLLCPP DataSet : public AbstractDs {
 	// Creates a copy of an existing DataSet using its id.
 	DataSet(const hid_t existing_id);
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	// Used by the API to appropriately close a dataset.
 	virtual void p_close() const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	// Default constructor.
 	DataSet();
diff --git a/c++/src/H5DataSpace.cpp b/c++/src/H5DataSpace.cpp
index 9f35f13..8b6f508 100644
--- a/c++/src/H5DataSpace.cpp
+++ b/c++/src/H5DataSpace.cpp
@@ -37,14 +37,14 @@ const DataSpace DataSpace::ALL( H5S_ALL );
 
 //--------------------------------------------------------------------------
 // Function:	DataSpace default constructor
-///\brief	Default constructor: Creates a stub datatype
+///\brief	Default constructor: creates a stub dataspace instance.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 DataSpace::DataSpace() : IdComponent() {}
 
 //--------------------------------------------------------------------------
 // Function:	DataSpace overloaded constructor
-///\brief	Creates a dataspace given a dataspace type.
+///\brief	Creates a new dataspace given a dataspace type.
 ///\param	type - IN: Type of the dataspace to be created, which 
 ///		currently can be either \c H5S_SCALAR or \c H5S_SIMPLE
 ///\exception	H5::DataSpaceIException
@@ -61,7 +61,7 @@ DataSpace::DataSpace( H5S_class_t type ) : IdComponent()
 
 //--------------------------------------------------------------------------
 // Function:	DataSpace overloaded constructor
-///\brief	Creates a new simple dataspace and opens it for access.
+///\brief	Creates a new simple dataspace.
 ///\param	rank - IN: Number of dimensions of dataspace. 
 ///\param	dims - IN: An array of the size of each dimension. 
 ///\param	maxdims - IN: An array of the maximum size of each dimension. 
@@ -124,7 +124,7 @@ void DataSpace::copy( const DataSpace& like_space )
 
 //--------------------------------------------------------------------------
 // Function:	DataSpace::operator=
-///\brief	Assignment operator
+///\brief	Assignment operator.
 ///\param	rhs - IN: Reference to the existing dataspace
 ///\return	Reference to DataSpace instance
 ///\exception	H5::DataSpaceIException
@@ -142,7 +142,7 @@ DataSpace& DataSpace::operator=( const DataSpace& rhs )
 //--------------------------------------------------------------------------
 // Function:	DataSpace::isSimple
 ///\brief	Determines whether this dataspace is a simple dataspace.
-///\return	true if the dataspace is a simple dataspace, and false, 
+///\return	\c true if the dataspace is a simple dataspace, and \c false, 
 ///		otherwise
 ///\exception	H5::DataSpaceIException
 // Programmer	Binh-Minh Ribler - 2000
@@ -266,7 +266,7 @@ H5S_class_t DataSpace::getSimpleExtentType () const
 //--------------------------------------------------------------------------
 // Function:	DataSpace::extentCopy
 ///\brief	Copies the extent of a dataspace.
-///\param	dest_space  - IN: DataSpace to copy from
+///\param	dest_space  - IN: Dataspace to copy from
 ///\exception	H5::DataSpaceIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
@@ -497,8 +497,8 @@ void DataSpace::selectNone () const
 // Function:	DataSpace::selectValid
 ///\brief	Verifies that the selection is within the extent of the 
 ///		dataspace.
-///\return	true if the selection is within the extent of the
-///		dataspace, and false, otherwise
+///\return	\c true if the selection is within the extent of the
+///		dataspace, and \c false, otherwise
 ///\exception	H5::DataSpaceIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
@@ -527,8 +527,8 @@ bool DataSpace::selectValid () const
 ///\exception	H5::DataSpaceIException
 ///\par Description
 ///		For more information, please refer to the C layer Reference
-///		Manual at:
-/// http:
+///		Manual at: 
+/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5S.html#Dataspace-SelectHyperslab
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataSpace::selectHyperslab( H5S_seloper_t op, const hsize_t *count, const hssize_t *start, const hsize_t *stride, const hsize_t *block ) const
@@ -542,7 +542,16 @@ void DataSpace::selectHyperslab( H5S_seloper_t op, const hsize_t *count, const h
    }
 }
 
-// Closes the dataspace if it is not a constant
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+//--------------------------------------------------------------------------
+// Function:	DataSpace::p_close (private)
+// Purpose:	Closes the dataspace if it is not a constant.
+// Exception	H5::DataSpaceIException
+// Description
+//		This function will be obsolete because its functionality
+//		is recently handled by the C library layer. - May, 2004
+// Programmer	Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
 void DataSpace::p_close() const
 {
    hid_t space_id = id;
@@ -555,6 +564,7 @@ void DataSpace::p_close() const
       }
    }
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:	DataSpace destructor
diff --git a/c++/src/H5DataSpace.h b/c++/src/H5DataSpace.h
index 4378f40..c56b7a5 100644
--- a/c++/src/H5DataSpace.h
+++ b/c++/src/H5DataSpace.h
@@ -103,8 +103,10 @@ class H5_DLLCPP DataSpace : public IdComponent {
 	// or uses a default id to create a default dataspace object
 	DataSpace( const hid_t space_id );
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	// Used by the API to close the dataspace 
 	void p_close() const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	// Default constructor
 	DataSpace();
diff --git a/c++/src/H5DataType.cpp b/c++/src/H5DataType.cpp
index d1cb1ee..1f01aa2 100644
--- a/c++/src/H5DataType.cpp
+++ b/c++/src/H5DataType.cpp
@@ -613,8 +613,16 @@ DataSpace DataType::getRegion(void *ref, H5R_type_t ref_type) const
    return(dataspace);
 }
 
-// This private function calls the C API H5Tclose to close this datatype.
-// Used by H5Object::p_reset.
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+//--------------------------------------------------------------------------
+// Function:    DataType::p_close (private)
+// Purpose:     Closes the datatype if it is not a predefined type.
+// Exception    H5::DataTypeIException
+// Description
+//              This function will be obsolete because its functionality
+//              is recently handled by the C library layer. - May, 2004
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
 void DataType::p_close() const
 {
    // If this datatype is not a predefined type, call H5Tclose on it.
@@ -627,6 +635,7 @@ void DataType::p_close() const
       }
    }
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:    DataType destructor
diff --git a/c++/src/H5DataType.h b/c++/src/H5DataType.h
index d0141f8..6ac6418 100644
--- a/c++/src/H5DataType.h
+++ b/c++/src/H5DataType.h
@@ -105,8 +105,11 @@ class H5_DLLCPP DataType : public H5Object {
 
 	// Retrieves a dataspace with the region pointed to selected.
 	DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
+	
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	// Used by the API to appropriately close a datatype
         void p_close() const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	// Creates a copy of an existing DataType using its id 
 	DataType( const hid_t type_id, bool predtype = false );
diff --git a/c++/src/H5DcreatProp.cpp b/c++/src/H5DcreatProp.cpp
index d2a74f4..b263fa5 100644
--- a/c++/src/H5DcreatProp.cpp
+++ b/c++/src/H5DcreatProp.cpp
@@ -245,9 +245,9 @@ H5D_fill_value_t DSetCreatPropList::isFillValueDefined()
 ///             during a \c DataSet::read() of the chunk.  If this bit is clear
 ///             and the filter fails then the entire I/O operation fails.
 //--------------------------------------------------------------------------
-void DSetCreatPropList::setFilter( H5Z_filter_t filter, unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[] ) const
+void DSetCreatPropList::setFilter( H5Z_filter_t filter_id, unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[] ) const
 {
-   herr_t ret_value = H5Pset_filter( id, filter, flags, cd_nelmts, cd_values );
+   herr_t ret_value = H5Pset_filter( id, filter_id, flags, cd_nelmts, cd_values );
    if( ret_value < 0 )
    {
       throw PropListIException("DSetCreatPropList::setFilter",
diff --git a/c++/src/H5DxferProp.cpp b/c++/src/H5DxferProp.cpp
index 1f9ade3..5ed6c82 100644
--- a/c++/src/H5DxferProp.cpp
+++ b/c++/src/H5DxferProp.cpp
@@ -265,9 +265,9 @@ void DSetMemXferPropList::getBtreeRatios( double& left, double& middle, double&
 //--------------------------------------------------------------------------
 // Function:	DSetMemXferPropList::setVlenMemManager
 ///\brief	Sets the memory manager for variable-length datatype allocation.
-///\param       alloc      - IN: User's allocate routine
+///\param       alloc_func - IN: User's allocate routine
 ///\param	alloc_info - IN: User's allocation parameters
-///\param	free       - IN: User's free routine
+///\param	free_func  - IN: User's free routine
 ///\param	free_info  - IN: User's free parameters
 ///\exception	H5::PropListIException
 // Programmer:	Binh-Minh Ribler - 2000
@@ -298,9 +298,9 @@ void DSetMemXferPropList::setVlenMemManager() const
 //--------------------------------------------------------------------------
 // Function:	DSetMemXferPropList::getVlenMemManager
 ///\brief	Gets the memory manager for variable-length datatype allocation 
-///\param       alloc      - OUT: User's allocate routine
+///\param       alloc_func - OUT: User's allocate routine
 ///\param	alloc_info - OUT: User's allocation parameters
-///\param	free       - OUT: User's free routine
+///\param	free_func  - OUT: User's free routine
 ///\param	free_info  - OUT: User's free parameters
 ///\exception	H5::PropListIException
 // Programmer:	Binh-Minh Ribler - 2000
diff --git a/c++/src/H5Exception.cpp b/c++/src/H5Exception.cpp
index 196205c..767385d 100644
--- a/c++/src/H5Exception.cpp
+++ b/c++/src/H5Exception.cpp
@@ -33,8 +33,8 @@ Exception::Exception() : detail_message(""), func_name("") {}
 
 //--------------------------------------------------------------------------
 // Function:	Exception overloaded constructor
-///\brief	Creates an exception with a function name where the failure
-///		occurs and an optional detailed message
+///\brief	Creates an exception with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 ///\exception	H5::DataTypeIException
@@ -64,11 +64,11 @@ Exception::Exception( const Exception& orig )
 ///		will be returned.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-string Exception::getMajorString( H5E_major_t major_num ) const
+string Exception::getMajorString(H5E_major_t err_major) const
 {
    // calls the C API routine to get the major string - Note: in the
    // failure case, the string "Invalid major error number" will be returned.
-   string major_str( H5Eget_major( major_num ));
+   string major_str(H5Eget_major(err_major));
    return( major_str );
 }
 
@@ -82,11 +82,11 @@ string Exception::getMajorString( H5E_major_t major_num ) const
 ///		will be returned.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-string Exception::getMinorString( H5E_minor_t minor_num ) const
+string Exception::getMinorString(H5E_minor_t err_minor) const
 {
    // calls the C API routine to get the minor string - Note: in the
    // failure case, the string "Invalid minor error number" will be returned.
-   string minor_str( H5Eget_minor( minor_num ));
+   string minor_str(H5Eget_minor(err_minor));
    return( minor_str );
 }
 
@@ -285,7 +285,7 @@ void Exception::printError( FILE* stream ) const
 Exception::~Exception() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	FileIException
+// Subclass:	FileIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -295,8 +295,8 @@ Exception::~Exception() {}
 FileIException::FileIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	FileIException overloaded constructor
-///\brief	Creates a FileIException with a function name where the failure 
-///		occurs and an optional detailed message.
+///\brief	Creates a FileIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -308,7 +308,7 @@ FileIException::FileIException(const string func_name, const string message) : E
 FileIException::~FileIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	GroupIException
+// Subclass:	GroupIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -318,8 +318,8 @@ FileIException::~FileIException() {}
 GroupIException::GroupIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	GroupIException overloaded constructor
-///\brief	Creates a GroupIException with a function name where the 
-///		failure occurs and an optional detailed message.
+///\brief	Creates a GroupIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -331,7 +331,7 @@ GroupIException::GroupIException(const string func_name, const string message) :
 GroupIException::~GroupIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	DataSpaceIException
+// Subclass:	DataSpaceIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -341,8 +341,8 @@ GroupIException::~GroupIException() {}
 DataSpaceIException::DataSpaceIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	DataSpaceIException overloaded constructor
-///\brief	Creates a DataSpaceIException with a function name where 
-///		the failure occurs and an optional detailed message.
+///\brief	Creates a DataSpaceIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -354,7 +354,7 @@ DataSpaceIException::DataSpaceIException(const string func_name, const string me
 DataSpaceIException::~DataSpaceIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	DataTypeIException
+// Subclass:	DataTypeIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -364,8 +364,8 @@ DataSpaceIException::~DataSpaceIException() {}
 DataTypeIException::DataTypeIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	DataTypeIException overloaded constructor
-///\brief	Creates a DataTypeIException with a function name where the 
-///		failure occurs and an optional detailed message.
+///\brief	Creates a DataTypeIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -377,7 +377,7 @@ DataTypeIException::DataTypeIException(const string func_name, const string mess
 DataTypeIException::~DataTypeIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	PropListIException
+// Subclass:	PropListIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -387,8 +387,8 @@ DataTypeIException::~DataTypeIException() {}
 PropListIException::PropListIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	PropListIException overloaded constructor
-///\brief	Creates a PropListIException with a function name where 
-///		the failure occurs and an optional detailed message.
+///\brief	Creates a PropListIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -400,7 +400,7 @@ PropListIException::PropListIException(const string func_name, const string mess
 PropListIException::~PropListIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	DataSetIException
+// Subclass:	DataSetIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -410,8 +410,8 @@ PropListIException::~PropListIException() {}
 DataSetIException::DataSetIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	DataSetIException overloaded constructor
-///\brief	Creates a DataSetIException with a function name where 
-///		the failure occurs and an optional detailed message.
+///\brief	Creates a DataSetIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -423,7 +423,7 @@ DataSetIException::DataSetIException(const string func_name, const string messag
 DataSetIException::~DataSetIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	AttributeIException
+// Subclass:	AttributeIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -433,8 +433,8 @@ DataSetIException::~DataSetIException() {}
 AttributeIException::AttributeIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	AttributeIException overloaded constructor
-///\brief	Creates a AttributeIException with a function name where 
-///		the failure occurs and an optional detailed message.
+///\brief	Creates an AttributeIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -446,7 +446,7 @@ AttributeIException::AttributeIException(const string func_name, const string me
 AttributeIException::~AttributeIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	ReferenceException
+// Subclass:	ReferenceException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -456,8 +456,8 @@ AttributeIException::~AttributeIException() {}
 ReferenceException::ReferenceException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	ReferenceException overloaded constructor
-///\brief	Creates a ReferenceException with a function name where 
-///		the failure occurs and an optional detailed message.
+///\brief	Creates a ReferenceException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -469,7 +469,7 @@ ReferenceException::ReferenceException(const string func_name, const string mess
 ReferenceException::~ReferenceException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	LibraryIException
+// Subclass:	LibraryIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -479,8 +479,8 @@ ReferenceException::~ReferenceException() {}
 LibraryIException::LibraryIException():Exception(){}
 //--------------------------------------------------------------------------
 // Function:	LibraryIException overloaded constructor
-///\brief	Creates a LibraryIException with a function name where 
-///		the failure occurs and an optional detailed message.
+///\brief	Creates a LibraryIException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
@@ -492,7 +492,7 @@ LibraryIException::LibraryIException(const string func_name, const string messag
 LibraryIException::~LibraryIException() {}
 
 //--------------------------------------------------------------------------
-// Subclasses:	IdComponentException
+// Subclass:	IdComponentException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 //--------------------------------------------------------------------------
@@ -502,8 +502,8 @@ LibraryIException::~LibraryIException() {}
 IdComponentException::IdComponentException(): Exception() {}
 //--------------------------------------------------------------------------
 // Function:	IdComponentException overloaded constructor
-///\brief	Creates a IdComponentException with a function name where 
-///		the failure occurs and an optional detailed message.
+///\brief	Creates a IdComponentException with the name of the function, 
+///		in which the failure occurs, and an optional detailed message.
 ///\param	func_name - IN: Name of the function where failure occurs
 ///\param	message   - IN: Message on the failure
 //--------------------------------------------------------------------------
diff --git a/c++/src/H5File.cpp b/c++/src/H5File.cpp
index 79ddf93..e176146 100644
--- a/c++/src/H5File.cpp
+++ b/c++/src/H5File.cpp
@@ -519,13 +519,14 @@ hid_t H5File::getLocId() const
    return( getId() );
 }
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 //--------------------------------------------------------------------------
 // Function:    H5File::p_close (private)
-///\brief       Closes this H5 file.
-///\exception   H5::FileIException
-///\note
-///             This function will be obsolete because its functionality
-///             is recently handled by the C library layer.
+// Purpose:     Closes this HDF5 file.
+// Exception    H5::FileIException
+// Description
+//              This function will be obsolete because its functionality
+//              is recently handled by the C library layer. - May, 2004
 // Programmer   Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void H5File::p_close() const
@@ -536,6 +537,7 @@ void H5File::p_close() const
       throw FileIException(0, "H5Fclose failed");
    }
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:	H5File::throwException
diff --git a/c++/src/H5File.h b/c++/src/H5File.h
index 2e0eeec..6493a3b 100644
--- a/c++/src/H5File.h
+++ b/c++/src/H5File.h
@@ -90,8 +90,10 @@ class H5_DLLCPP H5File : public IdComponent, public CommonFG {
 	// Throw file exception.
 	virtual void throwException(const string func_name, const string msg) const;
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	// Used by the API to appropriately close a file.
 	void p_close() const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	// H5File destructor.
 	virtual ~H5File();
diff --git a/c++/src/H5Group.cpp b/c++/src/H5Group.cpp
index 8827630..398d181 100644
--- a/c++/src/H5Group.cpp
+++ b/c++/src/H5Group.cpp
@@ -142,7 +142,17 @@ DataSpace Group::getRegion(void *ref, H5R_type_t ref_type) const
    DataSpace dataspace(p_get_region(ref, ref_type));
    return(dataspace);
 }
-// Calls the C API H5Gclose to close this group.  Used by IdComponent::reset
+
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+//--------------------------------------------------------------------------
+// Function:    Group::p_close (private)
+// Purpose:     Closes this group.
+// Exception    H5::GroupIException
+// Description
+//              This function will be obsolete because its functionality
+//              is recently handled by the C library layer. - May, 2004
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
 void Group::p_close() const
 {
    herr_t ret_value = H5Gclose( id );
@@ -151,10 +161,11 @@ void Group::p_close() const
       throw GroupIException(0, "H5Gclose failed");
    }
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:	Group::throwException
-///\brief	Throws group exception - initially implemented for CommonFG
+///\brief	Throws H5::GroupIException.
 ///\param	func_name - Name of the function where failure occurs
 ///\param	msg       - Message describing the failure
 ///\exception	H5::GroupIException
diff --git a/c++/src/H5Group.h b/c++/src/H5Group.h
index df299c3..6ed2a4a 100644
--- a/c++/src/H5Group.h
+++ b/c++/src/H5Group.h
@@ -28,26 +28,28 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
 	// Copy constructor: makes a copy of the original object
 	Group( const Group& original );
 
-	// Creates a reference to a named Hdf5 object in this object.
-	void* Reference(const char* name) const;
-
 	// Creates a reference to a named Hdf5 object or to a dataset region
 	// in this object.
 	void* Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) const;
 
+	// Creates a reference to a named Hdf5 object in this object.
+	void* Reference(const char* name) const;
+
 	// Retrieves the type of object that an object reference points to.
 	H5G_obj_t getObjType(void *ref, H5R_type_t ref_type) const;
 
 	// Retrieves a dataspace with the region pointed to selected.
 	DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
-	// for CommonFG to get the file id
+	// for CommonFG to get the file id.
 	virtual hid_t getLocId() const;
 
-        // Throw group exception
+        // Throw group exception.
         virtual void throwException(const string func_name, const string msg) const;
 
-	// Used by the API to appropriately close a group
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+	// Used by the API to appropriately close a group - will be obsolete.
 	void p_close() const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	// Destructor
 	virtual ~Group();
diff --git a/c++/src/H5IdComponent.cpp b/c++/src/H5IdComponent.cpp
index e8b85c0..cf5ae95 100644
--- a/c++/src/H5IdComponent.cpp
+++ b/c++/src/H5IdComponent.cpp
@@ -84,8 +84,16 @@ void IdComponent::decRefCount() { ref_count->decrement(); }
 //--------------------------------------------------------------------------
 int IdComponent::getCounter() { return( ref_count->getCounter()); }
 
-// Decrements the reference counter then determines if there are no more
-// reference to this object
+//--------------------------------------------------------------------------
+// Function:	IdComponent::noReference
+///\brief	Determines whether this object has any references.
+///\return      \c true if there is no reference, and \c false, otherwise.
+///\note	This function will be obsolete in the next release.
+// Description
+//		Decrements the reference counter then determines if there 
+//		are no more reference to this object.
+// Programmer	Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
 bool IdComponent::noReference()
 {
    if( ref_count->getCounter() > 0 )
@@ -173,6 +181,42 @@ void IdComponent::reset ()
 }
 
 //--------------------------------------------------------------------------
+// Function:	IdComponent destructor
+///\brief	Noop destructor.
+// Programmer	Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+IdComponent::~IdComponent() {
+
+/* uncomment this block and complete it when deciding to use dontAtExit 
+   unless the atexit/global destructor problem is fixed, then 
+   remove it- BMR 11/14/00
+
+   if( id == NOTATEXIT )
+   {
+      // Call H5Library::close to clean up - temporary solution to avoid the
+      // trouble of atexit/global destructors
+      try {
+         if( H5Library::need_cleanup == true )
+         {
+            H5Library::close();
+            H5Library::need_cleanup = false; // reset the boolean just in case
+         }
+      }
+      // catch failure caused by the H5Library operations
+      catch( LibraryIException error )
+      {
+         error.printError();
+      }
+   }
+*/
+}
+
+//
+// Implementation of protected functions
+// 
+
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+//--------------------------------------------------------------------------
 // Function:	IdComponent::p_get_file_name
 // Purpose:	Gets the name of the file, in which this object belongs.
 // Exception:	H5::IdComponentException
@@ -212,41 +256,6 @@ string IdComponent::p_get_file_name() const
 }
 
 //--------------------------------------------------------------------------
-// Function:	IdComponent destructor
-///\brief	Noop destructor.
-// Programmer	Binh-Minh Ribler - 2000
-//--------------------------------------------------------------------------
-IdComponent::~IdComponent() {
-
-/* uncomment this block and complete it when deciding to use dontAtExit 
-   unless the atexit/global destructor problem is fixed, then 
-   remove it- BMR 11/14/00
-
-   if( id == NOTATEXIT )
-   {
-      // Call H5Library::close to clean up - temporary solution to avoid the
-      // trouble of atexit/global destructors
-      try {
-         if( H5Library::need_cleanup == true )
-         {
-            H5Library::close();
-            H5Library::need_cleanup = false; // reset the boolean just in case
-         }
-      }
-      // catch failure caused by the H5Library operations
-      catch( LibraryIException error )
-      {
-         error.printError();
-      }
-   }
-*/
-}
-
-//
-// Implementation of protected functions for HDF5 Reference Interface.
-// 
-
-//--------------------------------------------------------------------------
 // Function:	IdComponent::p_reference (protected)
 // Purpose	Creates a reference to an HDF5 object or a dataset region.
 // Parameters
@@ -315,6 +324,7 @@ hid_t IdComponent::p_get_region(void *ref, H5R_type_t ref_type) const
    }
    return(space_id);
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 #ifndef H5_NO_NAMESPACE
 }
diff --git a/c++/src/H5IdComponent.h b/c++/src/H5IdComponent.h
index 12dc97f..bea8cd4 100644
--- a/c++/src/H5IdComponent.h
+++ b/c++/src/H5IdComponent.h
@@ -29,10 +29,6 @@ class H5_DLLCPP IdComponent {
 	// before setting new id to control reference count
 	void setId( hid_t new_id );
 
-	// Pure virtual function so appropriate close function can
-	// be called by subclasses' for the corresponding object
-	virtual void p_close() const = 0;
-
 	// Creates an object to hold an HDF5 identifier
 	IdComponent( const hid_t h5_id );
 
@@ -59,12 +55,20 @@ class H5_DLLCPP IdComponent {
 	IdComponent& operator=( const IdComponent& rhs );
 
 	void reset();
-	void resetId();
+
+	// Pure virtual function so appropriate close function can
+	// be called by subclasses' for the corresponding object
+	// This function will be obsolete because its functionality
+	// is recently handled by the C library layer.
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+	virtual void p_close() const = 0;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	// Destructor
 	virtual ~IdComponent();
 
    protected:
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	hid_t id;	// HDF5 object id
 	RefCounter* ref_count; // used to keep track of the
 	                              // number of copies of an object
@@ -90,6 +94,7 @@ class H5_DLLCPP IdComponent {
 
         // Retrieves a dataspace with the region pointed to selected.
         hid_t p_get_region(void *ref, H5R_type_t ref_type) const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 }; // end class IdComponent
 
diff --git a/c++/src/H5Library.cpp b/c++/src/H5Library.cpp
index a449dc2..fa36e0f 100644
--- a/c++/src/H5Library.cpp
+++ b/c++/src/H5Library.cpp
@@ -14,6 +14,7 @@
 
 #include <string>
 
+#include "H5CppDoc.h"	// included only for Doxygen to generate part of RM 
 #include "H5Include.h"
 #include "H5Exception.h"
 #include "H5Library.h"
@@ -22,8 +23,10 @@
 namespace H5 {
 #endif
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 // This static variable will be set to true when dontAtExit is called
 bool H5Library::need_cleanup = false;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:	H5Library::open
diff --git a/c++/src/H5Library.h b/c++/src/H5Library.h
index 34b816b..9dac9a8 100644
--- a/c++/src/H5Library.h
+++ b/c++/src/H5Library.h
@@ -28,7 +28,9 @@ namespace H5 {
 
 class H5_DLLCPP H5Library {
    public:
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	static bool need_cleanup; // indicates if H5close should be called
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	// Initializes the HDF5 library. 
 	static void open(); 
diff --git a/c++/src/H5Object.h b/c++/src/H5Object.h
index 1ba8929..b99764c 100644
--- a/c++/src/H5Object.h
+++ b/c++/src/H5Object.h
@@ -34,6 +34,7 @@ typedef void (*attr_operator_t)( H5Object& loc/*in*/,
 				 const string attr_name/*in*/, 
 				 void *operator_data/*in,out*/);
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 class UserData4Aiterate { // user data for attribute iteration
    public:
 	unsigned int* idx;
@@ -41,6 +42,7 @@ class UserData4Aiterate { // user data for attribute iteration
 	void* opData;
 	H5Object* object;
 };
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 // The above part is being moved into Iterator, but not completed
 
diff --git a/c++/src/H5PropList.cpp b/c++/src/H5PropList.cpp
index df56c69..30bb0f1 100644
--- a/c++/src/H5PropList.cpp
+++ b/c++/src/H5PropList.cpp
@@ -155,7 +155,16 @@ void PropList::copyProp( PropList& dest, PropList& src, const string& name ) con
    copyProp( dest, src, name.c_str());
 }
 
-// Closes the property list if it is not a default one
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+//--------------------------------------------------------------------------
+// Function:	PropList::p_close (private)
+// Purpose:	Closes the property list if it is not a default one.
+// Exception	H5::PropListIException
+// Description
+//		This function will be obsolete because its functionality
+//		is recently handled by the C library layer. - May, 2004
+// Programmer	Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
 void PropList::p_close() const
 {
    if( id != H5P_NO_CLASS ) // not a constant, should call H5Pclose
@@ -167,6 +176,7 @@ void PropList::p_close() const
       }
    }
 }
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 //--------------------------------------------------------------------------
 // Function:    PropList::getClass
diff --git a/c++/src/H5PropList.h b/c++/src/H5PropList.h
index 1c7d934..438b0ee 100644
--- a/c++/src/H5PropList.h
+++ b/c++/src/H5PropList.h
@@ -83,8 +83,10 @@ class H5_DLLCPP PropList : public IdComponent {
 
 	PropList getClassParent() const;
 
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
 	// Used by the API to close the property list
 	void p_close() const;
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 
 	virtual ~PropList();
 };
diff --git a/c++/src/H5RefCounter.cpp b/c++/src/H5RefCounter.cpp
index 896d06a..1a0eff4 100644
--- a/c++/src/H5RefCounter.cpp
+++ b/c++/src/H5RefCounter.cpp
@@ -62,10 +62,10 @@ void RefCounter::decrement()
 ///		that uses this counter.
 ///\return	true if there are no more reference to the object
 ///             that uses this counter, and false, otherwise.
+///\note	This function will be obsolete in the next release.
 // Description
 //		Decrements the reference counter then determines if there 
 //		are no more reference to the object that uses this counter.
-///\note	This function will be obsolete in the next release.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 bool RefCounter::noReference()