Update java code with doxygen tags, add menu files. (#1972)

* Update java code with doxygen tags, add menu files.

* Add -Xdoclint:none to autotools javadoc command

* Committing clang-format changes

* Add fortran RM list descriptions

* delete empty file

* doc tag location changes

* Spelling corrections

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

5 files changed, 237 insertions, 5 deletions

diff --git a/doxygen/examples/ThreadSafeLibrary.html b/doxygen/examples/ThreadSafeLibrary.html
index ebb193e..68b46f5 100644
--- a/doxygen/examples/ThreadSafeLibrary.html
+++ b/doxygen/examples/ThreadSafeLibrary.html
@@ -20,9 +20,9 @@ The following code is placed at the beginning of H5private.h:
 </blockquote>
 
 <p>
-<code>H5_HAVE_THREADSAFE</code> is defined when the HDF-5 library is
+<code>H5_HAVE_THREADSAFE</code> is defined when the HDF5 library is
 compiled with the --enable-threadsafe configuration option. In general,
-code for the non-threadsafe version of HDF-5 library are placed within
+code for the non-threadsafe version of HDF5 library are placed within
 the <code>#else</code> part of the conditional compilation. The exception
 to this rule are the changes to the <code>FUNC_ENTER</code> (in
 H5private.h), <code>HRETURN</code> and <code>HRETURN_ERROR</code> (in
@@ -438,7 +438,7 @@ described in Appendix D and may be found in <code>H5TS.c</code>.
 
 <p>
 Except where stated, all tests involve 16 simultaneous threads that make
-use of HDF-5 API calls without any explicit synchronization typically
+use of HDF5 API calls without any explicit synchronization typically
 required in a non-threadsafe environment.
 </p>
 
@@ -453,7 +453,7 @@ dataset's named value.
 
 <p>
 The main thread would join with all 16 threads and attempt to match the
-resulting HDF-5 file with expected results - that each dataset contains
+resulting HDF5 file with expected results - that each dataset contains
 the correct value (0 for <i>zero</i>, 1 for <i>one</i> etc ...) and all
 datasets were correctly created.
 </p>
@@ -473,7 +473,7 @@ name.
 
 <p>
 The error stack implementation runs correctly if it reports 15 instances
-of the dataset name conflict error and finally generates a correct HDF-5
+of the dataset name conflict error and finally generates a correct HDF5
 containing that single dataset. Each thread should report its own stack
 of errors with a thread number associated with it.
 </p>
diff --git a/doxygen/examples/core_menu.md b/doxygen/examples/core_menu.md
new file mode 100644
index 0000000..1379f18
--- /dev/null
+++ b/doxygen/examples/core_menu.md
@@ -0,0 +1,61 @@
+<b>Core Library</b>
+
+- @ref H5A "Attributes (H5A)"
+<br />
+HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data object.
+
+- @ref H5D "Datasets (H5D)"
+<br />
+Manage HDF5 datasets, including the transfer of data between memory and disk and the description of dataset properties.
+
+- @ref H5S "Dataspaces (H5S)"
+<br />
+HDF5 dataspaces describe the shape of datasets in memory or in HDF5 files.
+
+- @ref H5T "Datatypes (H5T)"
+<br />
+HDF5 datatypes describe the element type of HDF5 datasets and attributes.
+
+- @ref H5E "Error Handling (H5E)"
+<br />
+HDF5 library error reporting.
+
+- @ref H5F "Files (H5F)"
+<br />
+Manage HDF5 files.
+
+- @ref H5Z "Filters (H5Z)"
+<br />
+Manage HDF5 user-defined filters
+
+- @ref H5G "Groups (H5G)"
+<br />
+Manage HDF5 groups.
+
+- @ref H5I "Identifiers (H5I)"
+<br />
+Manage identifiers defined by the HDF5 library.
+
+- @ref H5 "Library General (H5)"
+<br />
+Manage the life cycle of HDF5 library instances.
+
+- @ref H5L "Links (H5L)"
+<br />
+Manage HDF5 links and link types.
+
+- @ref H5O "Objects (H5O)"
+<br />
+Manage HDF5 objects (groups, datasets, datatype objects).
+
+- @ref H5P "Property Lists (H5P)"
+<br />
+HDF5 property lists are the main vehicle to configure the behavior of HDF5 API functions.
+
+- @ref H5PL "Dynamically-loaded Plugins (H5PL)"
+<br />
+Manage the loading behavior of HDF5 plugins.
+
+- @ref H5R "References (H5R)"
+<br />
+Manage HDF5 references (HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions).
diff --git a/doxygen/examples/fortran_menu.md b/doxygen/examples/fortran_menu.md
new file mode 100644
index 0000000..335a21a
--- /dev/null
+++ b/doxygen/examples/fortran_menu.md
@@ -0,0 +1,61 @@
+<b>Fortran Library</b>
+
+-  H5A "Attributes (H5A)"
+<br />
+HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data object.
+
+-  H5D "Datasets (H5D)"
+<br />
+Manage HDF5 datasets, including the transfer of data between memory and disk and the description of dataset properties.
+
+-  H5S "Dataspaces (H5S)"
+<br />
+HDF5 dataspaces describe the shape of datasets in memory or in HDF5 files.
+
+-  H5T "Datatypes (H5T)"
+<br />
+HDF5 datatypes describe the element type of HDF5 datasets and attributes.
+
+-  H5E "Error Handling (H5E)"
+<br />
+HDF5 library error reporting.
+
+-  H5F "Files (H5F)"
+<br />
+Manage HDF5 files.
+
+-  H5Z "Filters (H5Z)"
+<br />
+Manage HDF5 user-defined filters
+
+-  H5G "Groups (H5G)"
+<br />
+Manage HDF5 groups.
+
+-  H5I "Identifiers (H5I)"
+<br />
+Manage identifiers defined by the HDF5 library.
+
+-  H5 "Library General (H5)"
+<br />
+Manage the life cycle of HDF5 library instances.
+
+-  H5L "Links (H5L)"
+<br />
+Manage HDF5 links and link types.
+
+-  H5O "Objects (H5O)"
+<br />
+Manage HDF5 objects (groups, datasets, datatype objects).
+
+-  H5P "Property Lists (H5P)"
+<br />
+HDF5 property lists are the main vehicle to configure the behavior of HDF5 API functions.
+
+-  H5PL "Dynamically-loaded Plugins (H5PL)"
+<br />
+Manage the loading behavior of HDF5 plugins.
+
+-  H5R "References (H5R)"
+<br />
+Manage HDF5 references (HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions).
diff --git a/doxygen/examples/high_level_menu.md b/doxygen/examples/high_level_menu.md
new file mode 100644
index 0000000..9e6f696
--- /dev/null
+++ b/doxygen/examples/high_level_menu.md
@@ -0,0 +1,30 @@
+<b>High-level library</b>
+<br />
+The high-level HDF5 library includes several sets of convenience and standard-use APIs to 
+facilitate common HDF5 operations.
+
+- @ref H5LT "Lite (H5LT, H5LD)"
+<br />
+Functions to simplify creating and manipulating datasets, attributes and other features
+
+- @ref H5IM "Image (H5IM)"
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as images
+
+- @ref H5TB "Table (H5TB)"
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as tables
+
+- @ref H5PT "Packet Table (H5PT)"
+<br />
+Creating and manipulating HDF5 datasets to support append- and read-only operations on table data
+
+- @ref H5DS "Dimension Scale (H5DS)"
+<br />
+Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset
+
+- @ref H5DO "Optimizations (H5DO)"
+<br />
+Bypassing default HDF5 behavior in order to optimize for specific use cases
+
+- @ref H5LR "Extensions (H5LR, H5LT)"
diff --git a/doxygen/examples/java_menu.md b/doxygen/examples/java_menu.md
new file mode 100644
index 0000000..bec7d4e
--- /dev/null
+++ b/doxygen/examples/java_menu.md
@@ -0,0 +1,80 @@
+<b>Java Library</b>
+ @ref HDF5LIB
+ 
+- @ref JH5
+<br />
+This package is the Java interface for the HDF5 library.
+ 
+- @ref JH5A
+<br />
+This package is the Java interface for the HDF5 library attribute APIs.
+ 
+- @ref JH5D
+<br />
+This package is the Java interface for the HDF5 library dataset APIs.
+ 
+- @ref JH5S
+<br />
+This package is the Java interface for the HDF5 library dataspace APIs.
+ 
+- @ref JH5T
+<br />
+This package is the Java interface for the HDF5 library datatype APIs.
+ 
+- @ref JH5E
+<br />
+This package is the Java interface for the HDF5 library error APIs.
+ 
+- @ref JH5F
+<br />
+This package is the Java interface for the HDF5 library file APIs.
+ 
+- @ref JH5Z
+<br />
+This package is the Java interface for the HDF5 library filter APIs.
+ 
+- @ref JH5G
+<br />
+This package is the Java interface for the HDF5 library group APIs.
+ 
+- @ref JH5I
+<br />
+This package is the Java interface for the HDF5 library identifier APIs.
+ 
+- @ref JH5L
+<br />
+This package is the Java interface for the HDF5 library links APIs.
+ 
+- @ref JH5O
+<br />
+This package is the Java interface for the HDF5 library object APIs.
+ 
+- @ref JH5P
+<br />
+This package is the Java interface for the HDF5 library property list APIs.
+ 
+- @ref JH5PL
+<br />
+This package is the Java interface for the HDF5 library plugin APIs.
+ 
+- @ref JH5R
+<br />
+This package is the Java interface for the HDF5 library reference APIs.
+
+- @ref HDF5CONST
+<br />
+This class contains C constants and enumerated types of HDF5 library.
+
+- @ref HDFNATIVE
+<br />
+This class encapsulates native methods to deal with arrays of numbers,
+ * converting from numbers to bytes and bytes to numbers.
+
+- @ref HDFARRAY
+<br />
+This is a class for handling multidimensional arrays for HDF.
+
+- @ref ERRORS
+<br />
+The class HDF5Exception returns errors from the Java HDF5 Interface.
+ 
\ No newline at end of file