Fix javadoc errors

java/hdf/hdf5lib/H5.java

@@ -92,7 +92,7 @@
  * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps
  * a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface.
  * <p>
- * For details of the HDF5 library, @see @ref RM
+ * For details of the HDF5 library, see also @ref RM
  * <hr>
  * <p>
  * <b>Mapping of arguments for Java</b>
@@ -132,7 +132,7 @@
  * <td>java.lang.String</td>
  * </tr>
  * <tr>
- * <td>void * <br />
+ * <td>void * <br>
  * (i.e., pointer to Any)</td>
  * <td>Special -- see @ref HDFARRAY</td>
  * </tr>
@@ -147,7 +147,7 @@
  * rather than just return <i>int</i> as in the C. Functions that return a value are declared
  * equivalent to the C function.
  * However, in most cases the Java method will raise an exception instead of returning an error code.
- * @see @ref ERRORS.
+ * See also @ref ERRORS.
  * <p>
  * Java does not support pass by reference of arguments, so arguments that are returned through <b>OUT</b>
  * parameters must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in
@@ -263,7 +263,7 @@
  *          @ref ERRORS hdf.hdf5lib.HDF5Exception<br />
  *          <a href="https://hdfgroup.org/HDF5/">HDF5</a>
  *
- * For details of the HDF5 library, @see @ref RM
+ * For details of the HDF5 library, see also @ref RM
  */
 
 /**
@@ -274,9 +274,9 @@
  * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps
  * a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface.
  *
- * @see H5, C-API
+ * @ref H5, C-API
  *
- * @see @ref H5_UG, User Guide
+ * @ref H5_UG, User Guide
  *
  */
 public class H5 implements java.io.Serializable {
@@ -832,9 +832,9 @@ private static String extractStringFromCharArray(MemorySegment charArray)
      * An HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary
      *data object. A primary data object may be a dataset, group, or committed datatype.
      *
-     * @see H5A, C-API
+     * @ref H5A, C-API
      *
-     * @see @ref H5A_UG, User Guide
+     * @ref H5A_UG, User Guide
      **/
 
     /**
@@ -3529,9 +3529,9 @@ public static int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type,
     /**
      * @defgroup JH5D Java Datasets (H5D) Interface
      *
-     * @see H5D, C-API
+     * @ref H5D, C-API
      *
-     * @see @ref H5D_UG, User Guide
+     * @ref H5D_UG, User Guide
      **/
 
     /**
@@ -5964,9 +5964,9 @@ public static void H5Drefresh(long dataset_id) throws HDF5LibraryException
      *
      * @defgroup JH5E Java Error (H5E) Interface
      *
-     * @see H5E, C-API
+     * @ref H5E, C-API
      *
-     * @see @ref H5E_UG, User Guide
+     * @ref H5E_UG, User Guide
      */
 
     /**
@@ -6578,9 +6578,9 @@ public static void H5Ewalk2(long stack_id, long direction, hdf.hdf5lib.callbacks
      *
      * @defgroup JH5ES Java Event Set (H5ES) Interface
      *
-     * @see H5ES, C-API
+     * @ref H5ES, C-API
      *
-     * @see @ref H5ES_UG, User Guide
+     * @ref H5ES_UG, User Guide
      */
 
     // /////// unimplemented ////////
@@ -6608,9 +6608,9 @@ public static void H5Ewalk2(long stack_id, long direction, hdf.hdf5lib.callbacks
      *
      * @defgroup JH5F Java File (H5F) Interface
      *
-     * @see H5F, C-API
+     * @ref H5F, C-API
      *
-     * @see @ref H5F_UG, User Guide
+     * @ref H5F_UG, User Guide
      */
 
     /**
@@ -6714,17 +6714,11 @@ public static long H5Freopen(long file_id) throws HDF5LibraryException
      * @param flags
      *            File access flags. Possible values include:
      *            <ul>
-     *            <li>
-     *            @ref H5F_ACC_RDWR Allow read and write access to file.</li>
-     *            <li>
-     *            @ref H5F_ACC_RDONLY Allow read-only access to file.</li>
-     *            <li>
-     *            @ref H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously stored
-     *                               in the file.</li>
-     *            <li>
-     *            @ref H5F_ACC_EXCL Fail if file already exists.</li>
-     *            <li>
-     *            @ref H5P_DEFAULT Apply default file access and creation properties.</li>
+     *            <li>@ref H5F_ACC_RDWR Allow read and write access to file.</li>
+     *            <li>@ref H5F_ACC_RDONLY Allow read-only access to file.</li>
+     *            <li>@ref H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously
+     * stored in the file.</li> <li>@ref H5F_ACC_EXCL Fail if file already exists.</li> <li>@ref H5P_DEFAULT
+     * Apply default file access and creation properties.</li>
      *            </ul>
      *
      * @param create_id
@@ -7642,9 +7636,9 @@ public static void H5Fset_libver_bounds(long file_id, int low, int high) throws
     /**
      * @defgroup JH5G Java Group (H5G) Interface
      *
-     * @see H5G, C-API
+     * @ref H5G, C-API
      *
-     * @see @ref H5G_UG, User Guide
+     * @ref H5G_UG, User Guide
      **/
 
     /**
@@ -8640,9 +8634,9 @@ public static void H5Grefresh(long group_id) throws HDF5LibraryException
     /**
      * @defgroup JH5I Java Identifier (H5I) Interface
      *
-     * @see H5I, C-API
+     * @ref H5I, C-API
      *
-     * @see @ref H5I_UG, User Guide
+     * @ref H5I_UG, User Guide
      **/
 
     /**
@@ -9043,9 +9037,9 @@ public static void H5Idestroy_type(int type_id) throws HDF5LibraryException
     /**
      * @defgroup JH5L Java Link (H5L) Interface
      *
-     * @see H5L, C-API
+     * @ref H5L, C-API
      *
-     * @see @ref H5L_UG, User Guide
+     * @ref H5L_UG, User Guide
      **/
 
     /**
@@ -10005,9 +9999,9 @@ public static void H5Lunregister(int link_cls_id) throws HDF5LibraryException
     /**
      * @defgroup JH5O Java Object (H5O) Interface
      *
-     * @see H5O, C-API
+     * @ref H5O, C-API
      *
-     * @see @ref H5O_UG, User Guide
+     * @ref H5O_UG, User Guide
      **/
 
     /**
@@ -11314,9 +11308,9 @@ public static hdf.hdf5lib.structs.H5O_native_info_t H5Oget_native_info_by_name(l
     /**
      * @defgroup JH5P Java Property List (H5P) Interface
      *
-     * @see H5P, C-API
+     * @ref H5P, C-API
      *
-     * @see @ref H5P_UG, User Guide
+     * @ref H5P_UG, User Guide
      **/
 
     /**
@@ -12467,8 +12461,7 @@ public static int H5Pget_filter(long plist, int filter_number, int[] flags, long
      * H5Pget_filter2 returns information about a filter, specified by its filter number, in a filter
      * pipeline, specified by the property list with which it is associated.
      *
-     * @see public static int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[]
-     *      cd_values, int namelen, String[] name, int[] filter_config)
+     * @see #H5Pget_filter(long, int, int[], long[], int[], long, String[], int[])
      *
      **/
     private static int H5Pget_filter2(long plist, int filter_number, int[] flags, long[] cd_nelmts,
@@ -18070,9 +18063,9 @@ public static hdf.hdf5lib.structs.H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id
     /**
      * @defgroup JH5PL Java Plugin (H5PL) Interface
      *
-     * @see H5PL, C-API
+     * @ref H5PL, C-API
      *
-     * @see @ref H5PL_UG, User Guide
+     * @ref H5PL_UG, User Guide
      **/
 
     /**
@@ -18360,9 +18353,9 @@ public static int H5PLsize() throws HDF5LibraryException
     /**
      * @defgroup JH5R Java Reference (H5R) Interface
      *
-     * @see H5R, C-API
+     * @ref H5R, C-API
      *
-     * @see @ref H5R_UG, User Guide
+     * @ref H5R_UG, User Guide
      * @deprecated As of HDF5 1.12.0 in favor of H5Rcreate_object(), H5Rcreate_region() and H5Rcreate_attr()
      **/
     @Deprecated
@@ -18642,7 +18635,7 @@ public static int H5Rget_obj_type(long loc_id, int ref_type, byte ref[])
      *
      * H5Rget_obj_type2 Retrieves the type of object that an object reference points to.
      *
-     * @see public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[])
+     * @see #H5Rget_obj_type(long, int, byte[])
      **/
     private static int H5Rget_obj_type2(long loc_id, int ref_type, byte ref[], int[] obj_type)
         throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
@@ -19309,7 +19302,7 @@ public static String H5Rget_attr_name(byte[] ref_ptr)
      *
      * @see H5S, C-API
      *
-     * @see @ref H5S_UG, User Guide
+     * @ref H5S_UG, User Guide
      **/
 
     /**
@@ -20783,7 +20776,7 @@ public static long H5Sselect_project_intersection(long src_space_id, long dst_sp
      *
      * @see H5T, C-API
      *
-     * @see @ref H5T_UG, User Guide
+     * @ref H5T_UG, User Guide
      **/
 
     /**
@@ -23229,7 +23222,7 @@ public static void H5Trefresh(long dtype_id) throws HDF5LibraryException
      *
      * @see H5VL, C-API
      *
-     * @see @ref H5VL_UG, User Guide
+     * @ref H5VL_UG, User Guide
      **/
 
     /**
@@ -23568,7 +23561,7 @@ public static boolean H5VLcmp_connector_cls(long conn_id1, long conn_id2) throws
      *
      * @see H5Z, C-API
      *
-     * @see @ref H5Z_UG, User Guide
+     * @ref H5Z_UG, User Guide
      **/
 
     /**

java/hdf/hdf5lib/HDF5Constants.java

@@ -33,7 +33,7 @@
  * <P>
  * <B>Do not edit this file!</b>
  *
- * @see @ref HDF5LIB
+ * @ref HDF5LIB
  */
 public class HDF5Constants {
 

java/hdf/hdf5lib/HDFArray.java

@@ -25,14 +25,16 @@
 import hdf.hdf5lib.exceptions.HDF5JavaException;
 
 /**
- * \page HDFARRAY Java Array Conversion This is a class for handling multidimensional arrays for HDF.
+ * \page HDFARRAY Java Array Conversion
+ * This is a class for handling multidimensional arrays for HDF.
  * <p>
  * The purpose is to allow the storage and retrieval of arbitrary array types containing scientific data.
  * <p>
  * The methods support the conversion of an array to and from Java to a one-dimensional array of bytes
- * suitable for I/O by the C library. <p> This class heavily uses the
+ * suitable for I/O by the C library. <p> This class heavily uses the HDFNativeData class to convert between
+ * Java and C representations.
  *
- * @ref HDFNATIVE class to convert between Java and C representations.
+ * See also @ref HDFNATIVE
  */
 
 public class HDFArray {

java/hdf/hdf5lib/HDFNativeData.java

@@ -30,7 +30,7 @@
  * Variant interfaces convert a section of an array, and also can convert to
  * sub-classes of Java <b>Number</b>.
  * <P>
- * @see @ref HDFARRAY.
+ * @ref HDFARRAY.
  */
 
 public class HDFNativeData {

java/hdf/hdf5lib/callbacks/H5A_iterate_cb.java

@@ -28,9 +28,9 @@ public interface H5A_iterate_cb extends org.hdfgroup.javahdf5.H5A_operator2_t.Fu
      *
      *  application callback for each attribute
      *
-     *  @param loc_id    the ID for the group or dataset being iterated over
-     *  @param name      the name of the current attribute about the object
-     *  @param info      the attribute's "info" struct
+     *  @param location_id  the ID for the group or dataset being iterated over
+     *  @param attr_name    the name of the current attribute about the object
+     *  @param ainfo        the attribute's "info" struct
      *  @param op_data   the operator data passed in to H5Aiterate
      *
      *  @return operation status

java/hdf/hdf5lib/callbacks/H5D_iterate_cb.java

@@ -28,11 +28,11 @@ public interface H5D_iterate_cb extends org.hdfgroup.javahdf5.H5D_operator_t.Fun
      *
      *  application callback for each dataset element
      *
-     *  @param elem      the pointer to the element in memory containing the current point
-     *  @param elem_type the datatype ID for the elements stored in elem
-     *  @param ndim      the number of dimensions for POINT array
-     *  @param point     the array containing the location of the element within the original dataspace
-     *  @param op_data   the operator data passed in to H5Diterate
+     *  @param elem            the pointer to the element in memory containing the current point
+     *  @param type_id         the datatype ID for the elements stored in elem
+     *  @param ndim            the number of dimensions for POINT array
+     *  @param point           the array containing the location of the element within the original dataspace
+     *  @param operator_data   the operator data passed in to H5Diterate
      *
      *  @return operation status
      *      A. Zero causes the iterator to continue, returning zero when all

java/hdf/hdf5lib/callbacks/H5E_walk_cb.java

@@ -28,9 +28,9 @@ public interface H5E_walk_cb extends H5E_walk2_t.Function {
      *
      *  application callback for each error stack element
      *
-     *  @param nidx      the index of the current error stack element
-     *  @param info      the error stack "info" struct
-     *  @param op_data   the operator data passed in to H5Ewalk
+     *  @param n             the index of the current error stack element
+     *  @param err_desc      the error stack "info" struct
+     *  @param client_data   the operator data passed in to H5Ewalk
      *
      *  @return operation status
      *      A. Zero causes the iterator to continue, returning zero when all

java/hdf/hdf5lib/callbacks/H5L_iterate_t.java

@@ -28,7 +28,7 @@ public interface H5L_iterate_t extends H5L_iterate2_t.Function {
      *
      *  application callback for each group
      *
-     *  @param loc_id    the ID for the group being iterated over
+     *  @param group     the ID for the group being iterated over
      *  @param name      the name of the current link
      *  @param info      the link's "info" struct
      *  @param op_data   the operator data passed in to H5Literate

java/hdf/hdf5lib/callbacks/H5O_iterate_t.java

@@ -28,7 +28,7 @@ public interface H5O_iterate_t extends H5O_iterate2_t.Function {
      *
      *  application callback for each group
      *
-     *  @param loc_id    the ID for the group or dataset being iterated over
+     *  @param obj       the ID for the group or dataset being iterated over
      *  @param name      the name of the current object
      *  @param info      the object's "info" struct
      *  @param op_data   the operator data passed in to H5Oiterate

java/hdf/hdf5lib/callbacks/H5P_iterate_cb.java

@@ -28,9 +28,9 @@ public interface H5P_iterate_cb extends org.hdfgroup.javahdf5.H5P_iterate_t.Func
      *
      *  application callback for each property list
      *
-     *  @param plist     the ID for the property list being iterated over
-     *  @param name      the name of the current property list
-     *  @param op_data   the operator data passed in to H5Piterate
+     *  @param id         the ID for the property list being iterated over
+     *  @param name       the name of the current property list
+     *  @param iter_data  the operator data passed in to H5Piterate
      *
      *  @return operation status
      *      A. Zero causes the iterator to continue, returning zero when all

java/hdf/hdf5lib/exceptions/HDF5LibraryException.java

@@ -37,7 +37,7 @@
  * this class, and by default the 'detailedMessage' is set according to the
  * minor error code from the HDF5 Library.
  * <p>
- * For major and minor error codes, @see <b>@ref H5E</b> in the HDF5 library.
+ * For major and minor error codes, see @ref H5E in the HDF5 library.
  *
  * @defgroup JERRLIB HDF5 Library JNI Exception Interface
  *