1 12 doxygen merge from 1.10 (#2094)

1 files changed, 132 insertions, 54 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index e701be3..ec9ba04 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -247,6 +247,10 @@ import hdf.hdf5lib.structs.H5O_token_t;
  * 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
+ *
+ * @see @ref H5_UG, User Guide
+ *
  */
 public class H5 implements java.io.Serializable {
     /**
@@ -585,6 +589,8 @@ public class H5 implements java.io.Serializable {
         throws HDF5LibraryException;
 
     /**
+     * @ingroup JH5
+     *
      * H5export_attribute is a utility function to save data in a file.
      *
      * @param file_export_name
@@ -2447,6 +2453,10 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5D Java Datasets (H5D) Interface
+     *
+     * @see H5D, C-API
+     *
+     * @see @ref H5D_UG, User Guide
      **/
 
     /**
@@ -4227,6 +4237,10 @@ public class H5 implements java.io.Serializable {
     /**
      *
      * @defgroup JH5E Java Error (H5E) Interface
+     *
+     * @see H5E, C-API
+     *
+     * @see @ref H5E_UG, User Guide
      */
 
     /**
@@ -4645,6 +4659,10 @@ public class H5 implements java.io.Serializable {
     /**
      *
      * @defgroup JH5F Java File (H5F) Interface
+     *
+     * @see H5F, C-API
+     *
+     * @see @ref H5F_UG, User Guide
      */
 
     /**
@@ -5389,6 +5407,10 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5G Java Group (H5G) Interface
+     *
+     * @see H5G, C-API
+     *
+     * @see @ref H5G_UG, User Guide
      **/
 
     /**
@@ -6000,6 +6022,10 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5I Java Identifier (H5I) Interface
+     *
+     * @see H5I, C-API
+     *
+     * @see @ref H5I_UG, User Guide
      **/
 
     /**
@@ -6265,6 +6291,10 @@ public class H5 implements java.io.Serializable {
     // //////////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5L Java Link (H5L) Interface
+     *
+     * @see H5L, C-API
+     *
+     * @see @ref H5L_UG, User Guide
      **/
 
     /**
@@ -6800,6 +6830,10 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5O Java Object (H5O) Interface
+     *
+     * @see H5O, C-API
+     *
+     * @see @ref H5O_UG, User Guide
      **/
 
     /**
@@ -7344,6 +7378,8 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Oincr_refcount(long object_id) throws HDF5LibraryException;
 
     /**
+     * @ingroup JH5O
+     *
      * H5Oopen_by_token opens a group, dataset, or named datatype using its object token within an HDF5 file.
      *
      * @param loc_id
@@ -7529,14 +7565,20 @@ public class H5 implements java.io.Serializable {
     /**
      * @ingroup JH5O
      *
-     * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying
-     * the object by location and relative name. Native HDF5-specific metadata includes things like object
-     * header information and object storage layout information.
+     * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying
+     * the object by an index position. Native HDF5-specific metadata includes things like object header
+     * information and object storage layout information.
      *
      * @param loc_id
-     *            IN: File or group identifier specifying location of group in which object is located
-     * @param name
-     *            IN: Relative name of group
+     *            IN: File or group identifier
+     * @param group_name
+     *            IN: Name of group, relative to loc_id, in which object is located
+     * @param idx_type
+     *            IN: Type of index by which objects are ordered
+     * @param order
+     *            IN: Order of iteration within index
+     * @param n
+     *            IN: Object to open
      * @param lapl_id
      *            IN: Access property list identifier for the link pointing to the object (Not currently used;
      *                pass as H5P_DEFAULT.)
@@ -7548,23 +7590,31 @@ public class H5 implements java.io.Serializable {
      * @exception NullPointerException
      *            name is null.
      **/
-    public static H5O_native_info_t H5Oget_native_info_by_name(long loc_id, String name, long lapl_id)
+    public static H5O_native_info_t H5Oget_native_info_by_idx(long loc_id, String group_name, int idx_type,
+                                                              int order, long n, long lapl_id)
         throws HDF5LibraryException, NullPointerException
     {
-        return H5Oget_native_info_by_name(loc_id, name, HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id);
+        return H5Oget_native_info_by_idx(loc_id, group_name, idx_type, order, n,
+                                         HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id);
     }
 
     /**
      * @ingroup JH5O
      *
-     * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying
-     * the object by location and relative name. Native HDF5-specific metadata includes things like object
-     * header information and object storage layout information.
+     * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying
+     * the object by an index position. Native HDF5-specific metadata includes things like object header
+     * information and object storage layout information.
      *
      * @param loc_id
-     *            IN: File or group identifier specifying location of group in which object is located
-     * @param name
-     *            IN: Relative name of group
+     *            IN: File or group identifier
+     * @param group_name
+     *            IN: Name of group, relative to loc_id, in which object is located
+     * @param idx_type
+     *            IN: Type of index by which objects are ordered
+     * @param order
+     *            IN: Order of iteration within index
+     * @param n
+     *            IN: Object to open
      * @param fields
      *            IN: Object fields to select
      * @param lapl_id
@@ -7578,27 +7628,21 @@ public class H5 implements java.io.Serializable {
      * @exception NullPointerException
      *            name is null.
      **/
-    public synchronized static native H5O_native_info_t H5Oget_native_info_by_name(long loc_id, String name,
-                                                                                   int fields, long lapl_id)
+    public synchronized static native H5O_native_info_t H5Oget_native_info_by_idx(
+        long loc_id, String group_name, int idx_type, int order, long n, int fields, long lapl_id)
         throws HDF5LibraryException, NullPointerException;
 
     /**
      * @ingroup JH5O
      *
-     * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying
-     * the object by an index position. Native HDF5-specific metadata includes things like object header
-     * information and object storage layout information.
+     * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying
+     * the object by location and relative name. Native HDF5-specific metadata includes things like object
+     * header information and object storage layout information.
      *
      * @param loc_id
-     *            IN: File or group identifier
-     * @param group_name
-     *            IN: Name of group, relative to loc_id, in which object is located
-     * @param idx_type
-     *            IN: Type of index by which objects are ordered
-     * @param order
-     *            IN: Order of iteration within index
-     * @param n
-     *            IN: Object to open
+     *            IN: File or group identifier specifying location of group in which object is located
+     * @param name
+     *            IN: Relative name of group
      * @param lapl_id
      *            IN: Access property list identifier for the link pointing to the object (Not currently used;
      *                pass as H5P_DEFAULT.)
@@ -7610,31 +7654,23 @@ public class H5 implements java.io.Serializable {
      * @exception NullPointerException
      *            name is null.
      **/
-    public static H5O_native_info_t H5Oget_native_info_by_idx(long loc_id, String group_name, int idx_type,
-                                                              int order, long n, long lapl_id)
+    public static H5O_native_info_t H5Oget_native_info_by_name(long loc_id, String name, long lapl_id)
         throws HDF5LibraryException, NullPointerException
     {
-        return H5Oget_native_info_by_idx(loc_id, group_name, idx_type, order, n,
-                                         HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id);
+        return H5Oget_native_info_by_name(loc_id, name, HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id);
     }
 
     /**
      * @ingroup JH5O
      *
-     * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying
-     * the object by an index position. Native HDF5-specific metadata includes things like object header
-     * information and object storage layout information.
+     * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying
+     * the object by location and relative name. Native HDF5-specific metadata includes things like object
+     * header information and object storage layout information.
      *
      * @param loc_id
-     *            IN: File or group identifier
-     * @param group_name
-     *            IN: Name of group, relative to loc_id, in which object is located
-     * @param idx_type
-     *            IN: Type of index by which objects are ordered
-     * @param order
-     *            IN: Order of iteration within index
-     * @param n
-     *            IN: Object to open
+     *            IN: File or group identifier specifying location of group in which object is located
+     * @param name
+     *            IN: Relative name of group
      * @param fields
      *            IN: Object fields to select
      * @param lapl_id
@@ -7648,8 +7684,8 @@ public class H5 implements java.io.Serializable {
      * @exception NullPointerException
      *            name is null.
      **/
-    public synchronized static native H5O_native_info_t H5Oget_native_info_by_idx(
-        long loc_id, String group_name, int idx_type, int order, long n, int fields, long lapl_id)
+    public synchronized static native H5O_native_info_t H5Oget_native_info_by_name(long loc_id, String name,
+                                                                                   int fields, long lapl_id)
         throws HDF5LibraryException, NullPointerException;
 
     // /////// unimplemented ////////
@@ -7665,6 +7701,13 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
 
     // /////// Generic property list routines ///////
+    /**
+     * @defgroup JH5P Java Property List (H5P) Interface
+     *
+     * @see H5P, C-API
+     *
+     * @see @ref H5P_UG, User Guide
+     **/
 
     /**
      * @ingroup JH5P
@@ -11768,6 +11811,10 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5PL Java Plugin (H5PL) Interface
+     *
+     * @see H5PL, C-API
+     *
+     * @see @ref H5PL_UG, User Guide
      **/
 
     /**
@@ -11921,6 +11968,10 @@ public class H5 implements java.io.Serializable {
 
     /**
      * @defgroup JH5R Java Reference (H5R) Interface
+     *
+     * @see H5R, C-API
+     *
+     * @see @ref H5R_UG, User Guide
      **/
 
     private synchronized static native int H5Rcreate(byte[] ref, long loc_id, String name, int ref_type,
@@ -11956,9 +12007,9 @@ public class H5 implements java.io.Serializable {
     {
         /* These sizes are correct for HDF5.1.2 */
         int ref_size = 8;
-        if (ref_type == HDF5Constants.H5R_DATASET_REGION) {
+        if (ref_type == HDF5Constants.H5R_DATASET_REGION)
             ref_size = 12;
-        }
+
         byte rbuf[] = new byte[ref_size];
 
         /* will raise an exception if fails */
@@ -12025,14 +12076,12 @@ public class H5 implements java.io.Serializable {
      * @return Returns the length of the name if successful, returning 0 (zero) if no name is associated with
      *         the identifier. Otherwise returns a negative value.
      *
-     *
      * @exception HDF5LibraryException
      *            Error from the HDF5 Library.
      * @exception NullPointerException
      *            size is null.
      * @exception IllegalArgumentException
      *            Argument is illegal.
-     *
      **/
     public synchronized static native long H5Rget_name(long loc_id, int ref_type, byte[] ref, String[] name,
                                                        long size)
@@ -12081,9 +12130,9 @@ public class H5 implements java.io.Serializable {
      * @exception HDF5LibraryException
      *            Error from the HDF5 Library.
      * @exception NullPointerException
-     *            array is null.
+     *            an input array is null.
      * @exception IllegalArgumentException
-     *            array is invalid.
+     *            an input array is invalid.
      **/
     public synchronized static native int H5Rget_obj_type(long loc_id, int ref_type, byte ref[])
         throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
@@ -12117,9 +12166,9 @@ public class H5 implements java.io.Serializable {
      * @exception HDF5LibraryException
      *            Error from the HDF5 Library.
      * @exception NullPointerException
-     *            output array is null.
+     *            an input array is null.
      * @exception IllegalArgumentException
-     *            output array is invalid.
+     *            an input array is invalid.
      **/
     public static long H5Rget_region(long loc_id, int ref_type, byte[] ref)
         throws HDF5LibraryException, NullPointerException, IllegalArgumentException
@@ -12525,6 +12574,14 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5S Java Dataspace (H5S) Interface
+     *
+     * @see H5S, C-API
+     *
+     * @see @ref H5S_UG, User Guide
+     **/
+
+    /**
+     * @defgroup JH5S Java Dataspace (H5S) Interface
      **/
 
     /**************** Operations on dataspaces ********************/
@@ -13507,6 +13564,14 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5T Java Datatype (H5T) Interface
+     *
+     * @see H5T, C-API
+     *
+     * @see @ref H5T_UG, User Guide
+     **/
+
+    /**
+     * @defgroup JH5T Java Datatype (H5T) Interface
      **/
 
     /**
@@ -15233,6 +15298,15 @@ public class H5 implements java.io.Serializable {
     // H5VL: VOL Interface Functions //
     // //
     // ////////////////////////////////////////////////////////////
+
+    /**
+     * @defgroup JH5VL Java VOL Connector (H5VL) Interface
+     *
+     * @see H5VL, C-API
+     *
+     * @see @ref H5VL_UG, User Guide
+     **/
+
     /**
      * @defgroup JH5VL Java VOL Connector (H5VL) Interface
      **/
@@ -15401,6 +15475,10 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
     /**
      * @defgroup JH5Z Java Filter (H5Z) Interface
+     *
+     * @see H5Z, C-API
+     *
+     * @see @ref H5Z_UG, User Guide
      **/
 
     /**