Fix doxygen missing references (#5205)

java/src/Makefile.am

@@ -41,7 +41,7 @@ CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$$CLASSPATH
 AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation
 
 hdf5_java_JAVA =  \
-	${pkgpath}/callbacks/Callbacks.java \
+	${pkgpath}/callbacks/H5Callbacks.java \
 	${pkgpath}/callbacks/H5A_iterate_cb.java \
 	${pkgpath}/callbacks/H5A_iterate_t.java \
 	${pkgpath}/callbacks/H5D_append_cb.java \

java/src/hdf/hdf5lib/CMakeLists.txt

@@ -10,7 +10,7 @@ SET_GLOBAL_VARIABLE (HDF5_JAVA_SOURCE_PACKAGES
 )
 
 set (HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES
-    callbacks/Callbacks.java
+    callbacks/H5Callbacks.java
     callbacks/H5A_iterate_cb.java
     callbacks/H5A_iterate_t.java
     callbacks/H5D_append_cb.java

java/src/hdf/hdf5lib/H5.java

@@ -5348,7 +5348,7 @@ public class H5 implements java.io.Serializable {
     //    herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
     // #endif /* H5_HAVE_PARALLEL */
 
-    // /**
+    // /*
     // * H5Fget_vfd_handle returns a pointer to the file handle from the
     // low-level file driver
     // * currently being used by the HDF5 library for file I/O.
@@ -5365,7 +5365,7 @@ public class H5 implements java.io.Serializable {
     // H5Fget_vfd_handle(int file_id, int fapl)
     //             throws HDF5LibraryException;
 
-    // /**
+    // /*
     // * H5Fget_mdc_config loads the current metadata cache configuration into
     // * the instance of H5AC_cache_config_t pointed to by the config_ptr
     // parameter.
@@ -5382,7 +5382,7 @@ public class H5 implements java.io.Serializable {
     // public synchronized static native void H5Fget_mdc_config(int file_id, H5AC_cache_config_t config_ptr)
     //             throws HDF5LibraryException, NullPointerException;
 
-    // /**
+    // /*
     // * H5Fset_mdc_config attempts to configure the file's metadata cache
     // according to the configuration supplied.
     // *
@@ -10028,7 +10028,7 @@ public class H5 implements java.io.Serializable {
         throws HDF5LibraryException, IllegalArgumentException;
 
     //    /////  unimplemented /////
-    //    /**
+    //    /*
     //     * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache.
     //     *
     //     * @param fapl_id
@@ -10043,7 +10043,7 @@ public class H5 implements java.io.Serializable {
     //    public synchronized static native int H5Pget_vds_file_cache_size(long fapl_id) throws
     //    HDF5LibraryException;
     //
-    //    /**
+    //    /*
     //     * H5Pset_vds_file_cache_size sets the number of files that can be held open in an vds link open
     //     * file cache.
     //     *
@@ -10075,10 +10075,9 @@ public class H5 implements java.io.Serializable {
      * @param size
      *            OUT: the offset value and the size of the external file data.
      *
-     *            <pre>
-     *      size[0] = offset // a location to return an offset value
-     *      size[1] = size // a location to return the size of
-     *                // the external file data.
+     * <pre>
+     *    size[0] = offset // a location to return an offset value
+     *    size[1] = size // a location to return the size of the external file data.
      * </pre>
      *
      * @return a non-negative value if successful
@@ -13929,7 +13928,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Tencode(long obj_id, byte[] buf, long nalloc)
         throws HDF5LibraryException, NullPointerException;
 
-    // /**
+    // /*
     //  * @ingroup JH5T
     //  *
     //  * H5Tencode converts a data type description into binary form in a buffer.

java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java

@@ -18,7 +18,7 @@ import hdf.hdf5lib.structs.H5A_info_t;
  * Information class for link callback for H5Aiterate.
  *
  */
-public interface H5A_iterate_cb extends Callbacks {
+public interface H5A_iterate_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5Callbacks.java

@@ -13,11 +13,11 @@
 package hdf.hdf5lib.callbacks;
 
 /**
- * @page CALLBACKS HDF5 Java Callbacks Interface
+ * @page CALLBACKS HDF5 Java H5Callbacks Interface
  * All callback definitions must derive from this interface.  Any
  * derived interfaces must define a single public method  named "callback".
  * You are responsible for deregistering your callback (if necessary)
- * in its {@link Object#finalize} method.  If native code attempts to call
+ * in its Object finalize method.  If native code attempts to call
  * a callback which has been GC'd, you will likely crash the VM.  If
  * there is no method to deregister the callback (e.g. <code>atexit</code>
  * in the C library), you must ensure that you always keep a live reference
@@ -28,7 +28,7 @@ package hdf.hdf5lib.callbacks;
  * exceptions thrown will be passed to the default callback exception
  * handler.
  *
- * @defgroup JCALLBK HDF5 Library Java Callbacks
+ * @defgroup JCALLBK HDF5 Library Java H5Callbacks
  */
-public interface Callbacks {
+public interface H5Callbacks {
 }

java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pset/get_append_flush.
  *
  */
-public interface H5D_append_cb extends Callbacks {
+public interface H5D_append_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Diterate.
  *
  */
-public interface H5D_iterate_cb extends Callbacks {
+public interface H5D_iterate_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java

@@ -18,7 +18,7 @@ import hdf.hdf5lib.structs.H5E_error2_t;
  * Information class for link callback for H5Ewalk.
  *
  */
-public interface H5E_walk_cb extends Callbacks {
+public interface H5E_walk_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java

@@ -18,7 +18,7 @@ import hdf.hdf5lib.structs.H5L_info_t;
  * Information class for link callback for H5Lvisit/H5Lvisit_by_name.
  *
  */
-public interface H5L_iterate_t extends Callbacks {
+public interface H5L_iterate_t extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java

@@ -18,7 +18,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * Information class for link callback for H5Ovisit/H5Ovisit_by_name.
  *
  */
-public interface H5O_iterate_t extends Callbacks {
+public interface H5O_iterate_t extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pcreate_class.
  *
  */
-public interface H5P_cls_close_func_cb extends Callbacks {
+public interface H5P_cls_close_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pcreate_class
  *
  */
-public interface H5P_cls_copy_func_cb extends Callbacks {
+public interface H5P_cls_copy_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pcreate_class.
  *
  */
-public interface H5P_cls_create_func_cb extends Callbacks {
+public interface H5P_cls_create_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Piterate.
  *
  */
-public interface H5P_iterate_cb extends Callbacks {
+public interface H5P_iterate_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_close_func_cb extends Callbacks {
+public interface H5P_prp_close_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_compare_func_cb extends Callbacks {
+public interface H5P_prp_compare_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_copy_func_cb extends Callbacks {
+public interface H5P_prp_copy_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_create_func_cb extends Callbacks {
+public interface H5P_prp_create_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_delete_func_cb extends Callbacks {
+public interface H5P_prp_delete_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_get_func_cb extends Callbacks {
+public interface H5P_prp_get_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java

@@ -16,7 +16,7 @@ package hdf.hdf5lib.callbacks;
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_set_func_cb extends Callbacks {
+public interface H5P_prp_set_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

java/src/hdf/hdf5lib/callbacks/package-info.java

@@ -11,8 +11,8 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /**
- * @page CALLBACKS_UG HDF5 Java Callbacks Interface
- * All callback definitions must derive from the Callbacks interface.  Any
+ * @page CALLBACKS_UG HDF5 Java H5Callbacks Interface
+ * All callback definitions must derive from the H5Callbacks interface.  Any
  * derived interfaces must define a single public method named "callback".
  * You are responsible for deregistering your callback (if necessary)
  * in its {@link Object#finalize} method.  If native code attempts to call