HDFFV-10876 Update h5dump and h5ls for new ref api.

12 files changed, 1274 insertions, 130 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 09fb223..01c18dc 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -1107,7 +1107,9 @@ public class H5 implements java.io.Serializable {
             log.trace("H5Aread_dname_D");
             status = H5Aread_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
         }
-        else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && (is1D && (dataClass.getComponentType() == String.class))) || H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+        else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
+                (is1D && (dataClass.getComponentType() == String.class))) ||
+                H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
             log.trace("H5Aread_reg_ref");
             status = H5Aread_reg_ref(attr_id, mem_type_id, (String[]) obj);
         }
@@ -2005,7 +2007,9 @@ public class H5 implements java.io.Serializable {
             status = H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
                     (double[]) obj, isCriticalPinning);
         }
-        else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && (is1D && (dataClass.getComponentType() == String.class))) || H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+        else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
+                (is1D && (dataClass.getComponentType() == String.class))) ||
+                H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
             log.trace("H5Dread_reg_ref");
             status = H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
                     (String[]) obj);
@@ -8095,6 +8099,325 @@ public class H5 implements java.io.Serializable {
 
     // ////////////////////////////////////////////////////////////
     // //
+    // H5R: HDF5 1.12 Reference API Functions //
+    // //
+    // ////////////////////////////////////////////////////////////
+
+    // Constructors //
+
+    /**
+     * H5Rcreate_object creates a reference pointing to the object named name located at loc id.
+     *
+     * @param loc_id
+     *            IN: Location identifier used to locate the object being pointed to.
+     * @param name
+     *            IN: Name of object at location loc_id.
+     *
+     * @return the reference (byte[]) if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native byte[] H5Rcreate_object(long loc_id, String name)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Rcreate_region creates the reference, pointing to the region represented by
+     * space id within the object named name located at loc id.
+     *
+     * @param loc_id
+     *            IN: Location identifier used to locate the object being pointed to.
+     * @param name
+     *            IN: Name of object at location loc_id.
+     * @param space_id
+     *            IN: Identifies the dataset region that a dataset region reference points to.
+     *
+     * @return the reference (byte[]) if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native byte[] H5Rcreate_region(long loc_id, String name, long space_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Rcreate_attr creates the reference, pointing to the attribute named attr name
+     * and attached to the object named name located at loc id.
+     *
+     * @param loc_id
+     *            IN: Location identifier used to locate the object being pointed to.
+     * @param name
+     *            IN: Name of object at location loc_id.
+     * @param attr_name
+     *            IN: Name of the attribute within the object.
+     *
+     * @return the reference (byte[]) if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Rdestroy destroys a reference and releases resources.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native void H5Rdestroy(byte[] ref_ptr)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    // Info //
+
+    /**
+     * H5Rget_type retrieves the type of a reference.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     *
+     * @return a valid reference type if successful; otherwise returns H5R UNKNOWN.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native int H5Rget_type(byte[] ref_ptr)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Requal determines whether two references point to the same object, region or attribute.
+     *
+     * @param ref1_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     * @param ref2_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     *
+     * @return true if equal, else false
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native boolean H5Requal(byte[] ref1_ptr, byte[] ref2_ptr)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Rcopy creates a copy of an existing reference.
+     *
+     * @param src_ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     *
+     * @return a valid copy of the reference (byte[]) if successful.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    // Dereference //
+
+    /**
+     * H5Ropen_object opens that object and returns an identifier.
+     * The object opened with this function should be closed when it is no longer needed
+     * so that resource leaks will not develop. Use the appropriate close function such
+     * as H5Oclose or H5Dclose for datasets.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     * @param rapl_id
+     *            IN: A reference access property list identifier for the reference. The access property
+     *                list can be used to access external files that the reference points
+     *                to (through a file access property list).
+     * @param oapl_id
+     *            IN: An object access property list identifier for the reference. The access property
+     *                property list must be of the same type as the object being referenced,
+     *                that is a group or dataset property list.
+     *
+     * @return a valid identifier if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Ropen region creates a copy of the dataspace of the dataset pointed to by a region reference,
+     * ref ptr, and defines a selection matching the selection pointed to by ref ptr within the dataspace copy.
+     * Use H5Sclose to release the dataspace identifier returned by this function when the identifier is no longer needed.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     * @param rapl_id
+     *            IN: A reference access property list identifier for the reference. The access property
+     *                list can be used to access external files that the reference points
+     *                to (through a file access property list).
+     * @param oapl_id
+     *            IN: An object access property list identifier for the reference. The access property
+     *                property list must be of the same type as the object being referenced,
+     *                that is a group or dataset property list.
+     *
+     * @return a valid dataspace identifier if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Ropen_attr opens the attribute attached to the object and returns an identifier.
+     * The attribute opened with this function should be closed with H5Aclose when it is no longer needed
+     * so that resource leaks will not develop.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     * @param rapl_id
+     *            IN: A reference access property list identifier for the reference. The access property
+     *                list can be used to access external files that the reference points
+     *                to (through a file access property list).
+     * @param aapl_id
+     *            IN: An attribute access property list identifier for the reference. The access property
+     *                property list must be of the same type as the object being referenced,
+     *                that is a group or dataset property list.
+     *
+     * @return a valid attribute identifier if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
+    public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    // Get type //
+
+    /**
+     * H5Rget obj type3 retrieves the type of the referenced object pointed to.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     * @param rapl_id
+     *            IN: A reference access property list identifier for the reference. The access property
+     *                list can be used to access external files that the reference points
+     *                to (through a file access property list).
+     *
+     * @return Returns the object type
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - array is null.
+     * @exception IllegalArgumentException
+     *                - array is invalid.
+     **/
+    public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    // Get name //
+
+    /**
+     * H5Rget_file_name retrieves the file name for the object, region or attribute reference pointed to.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     *
+     * @return Returns the file name of the reference
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - array is null.
+     * @exception IllegalArgumentException
+     *                - array is invalid.
+     **/
+    public synchronized static native String H5Rget_file_name(byte[] ref_ptr)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Rget_obj_name retrieves the object name for the object, region or attribute reference pointed to.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     * @param rapl_id
+     *            IN: A reference access property list identifier for the reference. The access property
+     *                list can be used to access external files that the reference points
+     *                to (through a file access property list).
+     *
+     * @return Returns the object name of the reference
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - array is null.
+     * @exception IllegalArgumentException
+     *                - array is invalid.
+     **/
+    public synchronized static native String H5Rget_obj_name(byte[] ref_ptr, long rapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Rget_attr_name retrieves the attribute name for the object, region or attribute reference pointed to.
+     *
+     * @param ref_ptr
+     *            IN: Reference to an object, region or attribute attached to an object.
+     *
+     * @return Returns the attribute name of the reference
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - array is null.
+     * @exception IllegalArgumentException
+     *                - array is invalid.
+     **/
+    public synchronized static native String H5Rget_attr_name(byte[] ref_ptr)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    // ////////////////////////////////////////////////////////////
+    // //
     // H5R: HDF5 1.8 Reference API Functions //
     // //
     // ////////////////////////////////////////////////////////////
@@ -10328,14 +10651,12 @@ public class H5 implements java.io.Serializable {
      * @param buf
      *            Buffer with data to be reclaimed.
      *
-     * @return a non-negative value if successful
-     *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      * @exception NullPointerException
      *                - buf is null.
      **/
-    public synchronized static native int H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
+    public synchronized static native void H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
             throws HDF5LibraryException, NullPointerException;
 
     /**
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index f5be38d..4aeeb98 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -407,11 +407,18 @@ public class HDF5Constants {
     public static final int H5PL_VOL_PLUGIN = H5PL_VOL_PLUGIN();
     public static final int H5PL_ALL_PLUGIN = H5PL_ALL_PLUGIN();
 
+    public static final int H5R_ATTR = H5R_ATTR();
     public static final int H5R_BADTYPE = H5R_BADTYPE();
     public static final int H5R_DATASET_REGION = H5R_DATASET_REGION();
+    public static final int H5R_DATASET_REGION1 = H5R_DATASET_REGION1();
+    public static final int H5R_DATASET_REGION2 = H5R_DATASET_REGION2();
     public static final int H5R_MAXTYPE = H5R_MAXTYPE();
+    public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
     public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
     public static final int H5R_OBJECT = H5R_OBJECT();
+    public static final int H5R_OBJECT1 = H5R_OBJECT1();
+    public static final int H5R_OBJECT2 = H5R_OBJECT2();
+
     public static final int H5S_ALL = H5S_ALL();
     public static final int H5S_MAX_RANK = H5S_MAX_RANK();
     public static final int H5S_NO_CLASS = H5S_NO_CLASS();
@@ -606,6 +613,7 @@ public class HDF5Constants {
     public static final long H5T_STD_I8LE = H5T_STD_I8LE();
     public static final long H5T_STD_REF_DSETREG = H5T_STD_REF_DSETREG();
     public static final long H5T_STD_REF_OBJ = H5T_STD_REF_OBJ();
+    public static final long H5T_STD_REF = H5T_STD_REF();
     public static final long H5T_STD_U16BE = H5T_STD_U16BE();
     public static final long H5T_STD_U16LE = H5T_STD_U16LE();
     public static final long H5T_STD_U32BE = H5T_STD_U32BE();
@@ -1420,16 +1428,28 @@ public class HDF5Constants {
 
     private static native final int H5PL_VOL_PLUGIN();
 
+    private static native final int H5R_ATTR();
+
     private static native final int H5R_BADTYPE();
 
     private static native final int H5R_DATASET_REGION();
 
+    private static native final int H5R_DATASET_REGION1();
+
+    private static native final int H5R_DATASET_REGION2();
+
     private static native final int H5R_MAXTYPE();
 
+    private static native final int H5R_REF_BUF_SIZE();
+
     private static native final int H5R_OBJ_REF_BUF_SIZE();
 
     private static native final int H5R_OBJECT();
 
+    private static native final int H5R_OBJECT1();
+
+    private static native final int H5R_OBJECT2();
+
     private static native final int H5S_ALL();
 
     private static native final int H5S_MAX_RANK();
@@ -1818,6 +1838,8 @@ public class HDF5Constants {
 
     private static native final long H5T_STD_REF_OBJ();
 
+    private static native final long H5T_STD_REF();
+
     private static native final long H5T_STD_U16BE();
 
     private static native final long H5T_STD_U16LE();
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 69adebd..05dc2ea 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -813,13 +813,25 @@ Java_hdf_hdf5lib_HDF5Constants_H5R_1BADTYPE(JNIEnv *env, jclass cls) { return H5
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5R_1MAXTYPE(JNIEnv *env, jclass cls) { return H5R_MAXTYPE; }
 JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5R_1REF_1BUF_1SIZE(JNIEnv *env, jclass cls) { return H5R_REF_BUF_SIZE; }
+JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5R_1OBJ_1REF_1BUF_1SIZE(JNIEnv *env, jclass cls) { return H5R_OBJ_REF_BUF_SIZE; }
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5R_1DSET_1REG_1REF_1BUF_1SIZE(JNIEnv *env, jclass cls) { return H5R_DSET_REG_REF_BUF_SIZE; }
 JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5R_1ATTR(JNIEnv *env, jclass cls) { return H5R_ATTR; }
+JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5R_1OBJECT(JNIEnv *env, jclass cls) { return H5R_OBJECT; }
 JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5R_1OBJECT1(JNIEnv *env, jclass cls) { return H5R_OBJECT1; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5R_1OBJECT2(JNIEnv *env, jclass cls) { return H5R_OBJECT2; }
+JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5R_1DATASET_1REGION(JNIEnv *env, jclass cls) { return H5R_DATASET_REGION; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5R_1DATASET_1REGION1(JNIEnv *env, jclass cls) { return H5R_DATASET_REGION1; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5R_1DATASET_1REGION2(JNIEnv *env, jclass cls) { return H5R_DATASET_REGION2; }
 
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5S_1ALL(JNIEnv *env, jclass cls) { return H5S_ALL; }
@@ -1211,6 +1223,8 @@ Java_hdf_hdf5lib_HDF5Constants_H5T_1STD_1REF_1DSETREG(JNIEnv *env, jclass cls) {
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5T_1STD_1REF_1OBJ(JNIEnv *env, jclass cls) { return H5T_STD_REF_OBJ; }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5T_1STD_1REF(JNIEnv *env, jclass cls) { return H5T_STD_REF; }
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U16BE(JNIEnv *env, jclass cls) { return H5T_STD_U16BE; }
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U16LE(JNIEnv *env, jclass cls) { return H5T_STD_U16LE; }
diff --git a/java/src/jni/h5pFAPLImp.c b/java/src/jni/h5pFAPLImp.c
index 006707a..a627e65 100644
--- a/java/src/jni/h5pFAPLImp.c
+++ b/java/src/jni/h5pFAPLImp.c
@@ -425,6 +425,8 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1hdfs
 
     CALL_CONSTRUCTOR(ENVONLY, "hdf/hdf5lib/structs/H5FD_hdfs_fapl_t", "(Ljava/lang/String;ILjava/lang/String;Ljava/lang/String;I)V", args, ret_obj);
 #else
+    UNUSED(fapl_id);
+
     H5_UNIMPLEMENTED(ENVONLY, "H5Pget_fapl_hdfs: not implemented");
 #endif /* H5_HAVE_LIBHDFS */
 
@@ -532,6 +534,9 @@ Java_hdf_hdf5lib_H5_H5Pset_1fapl_1hdfs
     if (H5Pset_fapl_hdfs((hid_t)fapl_id, &instance) < 0)
             H5_LIBRARY_ERROR(ENVONLY);
 #else
+    UNUSED(fapl_id);
+    UNUSED(fapl_config);
+
     H5_UNIMPLEMENTED(ENVONLY, "H5Pset_fapl_hdfs: not implemented");
 #endif /* H5_HAVE_LIBHDFS */
 
@@ -841,6 +846,8 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1ros3
 
     CALL_CONSTRUCTOR(ENVONLY, "hdf/hdf5lib/structs/H5FD_ros3_fapl_t", "(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V", args, ret_obj);
 #else
+    UNUSED(fapl_id);
+
     H5_UNIMPLEMENTED(ENVONLY, "H5Pget_fapl_ros3: not implemented");
 #endif /* H5_HAVE_ROS3_VFD */
 
@@ -939,6 +946,9 @@ Java_hdf_hdf5lib_H5_H5Pset_1fapl_1ros3
     if (H5Pset_fapl_ros3((hid_t)fapl_id, &instance) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 #else
+    UNUSED(fapl_id);
+    UNUSED(fapl_config);
+
     H5_UNIMPLEMENTED(ENVONLY, "H5Pset_fapl_ros3: not implemented");
 #endif /* H5_HAVE_ROS3_VFD */
 
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index 1a77fd3..f7dcb30 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -26,10 +26,599 @@ extern "C" {
 #include "h5jni.h"
 #include "h5rImp.h"
 
+
+/* H5R: HDF5 1.12 Reference API Functions */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcreate_object
+ * Signature: (JLjava/lang/String;)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcreate_1object
+  (JNIEnv *env, jclass clss, jlong loc_id, jstring name)
+{
+    const char *refName = NULL;
+    jboolean    isCopy;
+    jbyteArray  ref = NULL;
+    jbyte      *refBuf = NULL;
+    herr_t      status = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == name)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rcreate_object: name is NULL");
+
+    PIN_JAVA_STRING(ENVONLY, name, refName, NULL, "H5Rcreate_object: reference name not pinned");
+
+    if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Rcreate_object: failed to allocate reference buffer");
+
+    if ((status = H5Rcreate_object((hid_t)loc_id, refName, (const H5R_ref_t *)refBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+    ENVPTR->SetByteArrayRegion(ENVONLY, ref, 0, (jsize)H5R_REF_BUF_SIZE, (jbyte *)refBuf);
+    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (refName)
+        UNPIN_JAVA_STRING(ENVONLY, name, refName);
+    if (refBuf)
+        HDfree(refBuf);
+
+    return ref;
+} /* end Java_hdf_hdf5lib_H5_H5Rcreate_1object */
+
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcreate_region
+ * Signature: (JLjava/lang/String;J)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcreate_1region
+  (JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong space_id)
+{
+    const char *refName = NULL;
+    jboolean    isCopy;
+    jbyteArray  ref = NULL;
+    jbyte      *refBuf = NULL;
+    herr_t      status = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == name)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rcreate_region: name is NULL");
+
+    PIN_JAVA_STRING(ENVONLY, name, refName, NULL, "H5Rcreate_region: reference name not pinned");
+
+    if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Rcreate_region: failed to allocate reference buffer");
+
+    if ((status = H5Rcreate_region((hid_t)loc_id, refName, space_id, (const H5R_ref_t *)refBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+    ENVPTR->SetByteArrayRegion(ENVONLY, ref, 0, (jsize)H5R_REF_BUF_SIZE, (jbyte *)refBuf);
+    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (refName)
+        UNPIN_JAVA_STRING(ENVONLY, name, refName);
+    if (refBuf)
+        HDfree(refBuf);
+
+    return ref;
+} /* end Java_hdf_hdf5lib_H5_H5Rcreate_1region */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcreate_attr
+ * Signature: (JLjava/lang/String;Ljava/lang/String;)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcreate_1attr
+  (JNIEnv *env, jclass clss, jlong loc_id, jstring name, jstring attr_name)
+{
+    const char *refName = NULL;
+    const char *attrName = NULL;
+    jboolean    isCopy;
+    jbyteArray  ref = NULL;
+    jbyte      *refBuf = NULL;
+    herr_t      status = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == name)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rcreate_attr: name is NULL");
+    if (NULL == attr_name)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rcreate_attr: attribute name is NULL");
+
+    PIN_JAVA_STRING(ENVONLY, attr_name, attrName, NULL, "H5Rcreate_attr: attribute name not pinned");
+
+    PIN_JAVA_STRING(ENVONLY, name, refName, NULL, "H5Rcreate_attr: reference name not pinned");
+
+    if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Rcreate_attr: failed to allocate reference buffer");
+
+    if ((status = H5Rcreate_attr((hid_t)loc_id, refName, attrName, (const H5R_ref_t *)refBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+    ENVPTR->SetByteArrayRegion(ENVONLY, ref, 0, (jsize)H5R_REF_BUF_SIZE, (jbyte *)refBuf);
+    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (attrName)
+        UNPIN_JAVA_STRING(ENVONLY, attr_name, attrName);
+    if (refName)
+        UNPIN_JAVA_STRING(ENVONLY, name, refName);
+    if (refBuf)
+        HDfree(refBuf);
+
+    return ref;
+} /* end Java_hdf_hdf5lib_H5_H5Rcreate_1attr */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rdestroy
+ * Signature: ([B)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Rdestroy
+  (JNIEnv *env, jclass clss, jbyteArray ref)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jsize       refBufLen;
+    herr_t      status = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rdestroy: reference is NULL");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rdestroy: reference array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rdestroy: reference buffer not pinned");
+
+    if ((status = H5Rdestroy((const H5R_ref_t *)refBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (status < 0) ? JNI_ABORT : 0);
+} /* end Java_hdf_hdf5lib_H5_H5Rdestroy */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_type
+ * Signature: ([B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1type
+  (JNIEnv *env, jclass clss, jbyteArray ref)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jsize       refBufLen;
+    H5R_type_t  ref_type;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rget_type: reference is NULL");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rget_type: reference array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_type: reference buffer not pinned");
+
+    if ((ref_type = H5Rget_type((const H5R_ref_t *)refBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (ref_type < 0) ? JNI_ABORT : 0);
+
+    return (jint)ref_type;
+} /* end Java_hdf_hdf5lib_H5_H5Rget_1type */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Requal
+ * Signature: ([B[B)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Requal
+  (JNIEnv *env, jclass clss, jbyteArray ref1, jbyteArray ref2)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf1 = NULL;
+    jbyte      *refBuf2 = NULL;
+    jsize       refBufLen;
+    htri_t      bval = JNI_FALSE;
+    herr_t      status = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == ref1)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Requal: reference1 is NULL");
+
+    if (NULL == ref2)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Requal: reference2 is NULL");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref1)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Requal: reference1 array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, ref1, refBuf1, &isCopy, "H5Requal: reference1 buffer not pinned");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref2)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Requal: reference2 array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, ref2, refBuf2, &isCopy, "H5Requal: reference2 buffer not pinned");
+
+    if ((bval = H5Requal((const H5R_ref_t *)refBuf1, (const H5R_ref_t *)refBuf2)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+    status = bval;
+
+    bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
+
+done:
+    if (refBuf2)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref2, refBuf2, (status < 0) ? JNI_ABORT : 0);
+    if (refBuf1)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref1, refBuf1, (status < 0) ? JNI_ABORT : 0);
+
+    return (jboolean)bval;
+} /* end Java_hdf_hdf5lib_H5_H5Requal */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcopy
+ * Signature: ([B)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcopy
+  (JNIEnv *env, jclass clss, jbyteArray src_ref)
+{
+    jboolean    isCopy;
+    jbyte      *src_refBuf = NULL;
+    jsize       refBufLen;
+    jbyteArray  dst_ref = NULL;
+    jbyte      *dst_refBuf = NULL;
+    herr_t      status = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == src_ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rcopy: src reference is NULL");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, src_ref)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Rcopy: src reference array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, src_ref, src_refBuf, &isCopy, "H5Rcopy: src reference buffer not pinned");
+
+    if (NULL == (dst_refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Rcreate_attr: failed to allocate dst reference buffer");
+
+    if ((status = H5Rcopy((const H5R_ref_t *)src_refBuf, (const H5R_ref_t *)dst_refBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (dst_ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+    ENVPTR->SetByteArrayRegion(ENVONLY, dst_ref, 0, (jsize)H5R_REF_BUF_SIZE, (jbyte *)dst_refBuf);
+    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (src_refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, src_ref, src_refBuf, (status < 0) ? JNI_ABORT : 0);
+    if (dst_refBuf)
+        HDfree(dst_refBuf);
+
+    return dst_ref;
+} /* end Java_hdf_hdf5lib_H5_H5Rcopy */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Ropen_object
+ * Signature: ([BJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Ropen_1object
+  (JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jsize       refBufLen;
+    hid_t     retVal = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Ropen_object: reference is NULL");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Ropen_object: reference array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Ropen_object: reference buffer not pinned");
+
+    if ((retVal = H5Ropen_object((const H5R_ref_t *)refBuf, (hid_t)rapl_id, (hid_t)oapl_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (retVal < 0) ? JNI_ABORT : 0);
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Ropen_1object */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Ropen_region
+ * Signature: ([BJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Ropen_1region
+  (JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jsize       refBufLen;
+    hid_t       retVal = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Ropen_region: reference is NULL");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Ropen_region: reference array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Ropen_region: reference buffer not pinned");
+
+    if ((retVal = H5Ropen_region((const H5R_ref_t *)refBuf, (hid_t)rapl_id, (hid_t)oapl_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (retVal < 0) ? JNI_ABORT : 0);
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Ropen_1region */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Ropen_attr
+ * Signature: ([BJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Ropen_1attr
+  (JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jsize       refBufLen;
+    hid_t       retVal = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Ropen_attr: reference is NULL");
+
+    if ((refBufLen = ENVPTR->GetArrayLength(ENVONLY, ref)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Ropen_attr: reference array length < 0");
+    }
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Ropen_attr: reference buffer not pinned");
+
+    if ((retVal = H5Ropen_attr((const H5R_ref_t *)refBuf, (hid_t)rapl_id, (hid_t)aapl_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (retVal < 0) ? JNI_ABORT : 0);
+
+    return (jlong)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Ropen_1attr */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_obj_type3
+ * Signature: ([BJ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1obj_1type3
+  (JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id)
+{
+    H5O_type_t  object_info;
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    int         retVal = -1;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rget_obj_type3: reference buffer is NULL");
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_obj_type3: reference buffer not pinned");
+
+    if ((retVal = H5Rget_obj_type3((const H5R_ref_t *)refBuf, (hid_t)rapl_id, &object_info)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (retVal >= 0)
+        retVal = object_info;
+
+done:
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (retVal < 0) ? JNI_ABORT : 0);
+
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Rget_1obj_1type3 */
+
 /*
- * Pointer to the JNI's Virtual Machine; used for callback functions.
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_file_name
+ * Signature: ([B)Ljava/lang/String;
  */
-/* extern JavaVM *jvm; */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1file_1name
+  (JNIEnv *env, jclass clss, jbyteArray ref)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jstring     str = NULL;
+    ssize_t     buf_size;
+    ssize_t     check_size;
+    char       *namePtr = NULL;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rget_file_name: reference buffer is NULL");
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_file_name: reference buffer not pinned");
+
+    /* Get the length of the name */
+    if ((buf_size = H5Rget_file_name((const H5R_ref_t *)refBuf, NULL, 0)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Rget_file_name: malloc failed");
+
+    if ((check_size = H5Rget_file_name((const H5R_ref_t *)refBuf, namePtr, (size_t)buf_size + 1)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+    namePtr[buf_size] = '\0';
+
+    if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, namePtr)))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (namePtr)
+        HDfree(namePtr);
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (check_size < 0) ? JNI_ABORT : 0);
+
+    return str;
+} /* end Java_hdf_hdf5lib_H5_H5Rget_1file_1name */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_obj_name
+ * Signature: ([BJ)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1obj_1name
+  (JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jstring     str = NULL;
+    ssize_t     buf_size;
+    ssize_t     check_size;
+    char       *namePtr = NULL;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rget_obj_name: reference buffer is NULL");
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_obj_name: reference buffer not pinned");
+
+    /* Get the length of the name */
+    if ((buf_size = H5Rget_obj_name((const H5R_ref_t *)refBuf, (hid_t)rapl_id, NULL, 0)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Rget_obj_name: malloc failed");
+
+    if ((check_size = H5Rget_obj_name((const H5R_ref_t *)refBuf, (hid_t)rapl_id, namePtr, (size_t)buf_size + 1)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+    namePtr[buf_size] = '\0';
+
+    if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, namePtr)))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (namePtr)
+        HDfree(namePtr);
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (check_size < 0) ? JNI_ABORT : 0);
+
+    return str;
+} /* end Java_hdf_hdf5lib_H5_H5Rget_1obj_1name */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_attr_name
+ * Signature: ([B)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1attr_1name
+  (JNIEnv *env, jclass clss, jbyteArray ref)
+{
+    jboolean    isCopy;
+    jbyte      *refBuf = NULL;
+    jstring     str = NULL;
+    ssize_t     buf_size;
+    ssize_t     check_size;
+    char       *namePtr = NULL;
+
+    UNUSED(clss);
+
+    if (NULL == ref)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Rget_attr_name: reference buffer is NULL");
+
+    PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_attr_name: reference buffer not pinned");
+
+    /* Get the length of the name */
+    if ((buf_size = H5Rget_attr_name((const H5R_ref_t *)refBuf, NULL, 0)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Rget_attr_name: malloc failed");
+
+    if ((check_size = H5Rget_attr_name((const H5R_ref_t *)refBuf, namePtr, (size_t)buf_size + 1)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+    namePtr[buf_size] = '\0';
+
+    if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, namePtr)))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (namePtr)
+        HDfree(namePtr);
+    if (refBuf)
+        UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (check_size < 0) ? JNI_ABORT : 0);
+
+    return str;
+} /* end Java_hdf_hdf5lib_H5_H5Rget_1attr_1name */
+
+/* H5R: HDF5 1.8 Reference API Functions */
 
 /*
  * Class:     hdf_hdf5lib_H5
diff --git a/java/src/jni/h5rImp.h b/java/src/jni/h5rImp.h
index e28329b..7749f91 100644
--- a/java/src/jni/h5rImp.h
+++ b/java/src/jni/h5rImp.h
@@ -21,6 +21,136 @@
 extern "C" {
 #endif /* __cplusplus */
 
+/* H5R: HDF5 1.12 Reference API Functions */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcreate_object
+ * Signature: (JLjava/lang/String;)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcreate_1object
+  (JNIEnv *, jclass, jlong, jstring);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcreate_region
+ * Signature: (JLjava/lang/String;J)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcreate_1region
+  (JNIEnv *, jclass, jlong, jstring, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcreate_attr
+ * Signature: (JLjava/lang/String;Ljava/lang/String;)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcreate_1attr
+  (JNIEnv *, jclass, jlong, jstring, jstring);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rdestroy
+ * Signature: ([B)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Rdestroy
+  (JNIEnv *, jclass, jbyteArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_type
+ * Signature: ([B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1type
+  (JNIEnv *, jclass, jbyteArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Requal
+ * Signature: ([B[B)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Requal
+  (JNIEnv *, jclass, jbyteArray, jbyteArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rcopy
+ * Signature: ([B)[B
+ */
+JNIEXPORT jbyteArray JNICALL
+Java_hdf_hdf5lib_H5_H5Rcopy
+  (JNIEnv *, jclass, jbyteArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Ropen_object
+ * Signature: ([BJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Ropen_1object
+  (JNIEnv *, jclass, jbyteArray, jlong, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Ropen_region
+ * Signature: ([BJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Ropen_1region
+  (JNIEnv *, jclass, jbyteArray, jlong, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Ropen_attr
+ * Signature: ([BJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Ropen_1attr
+  (JNIEnv *, jclass, jbyteArray, jlong, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_obj_type3
+ * Signature: ([BJ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1obj_1type3
+  (JNIEnv *, jclass, jbyteArray, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_file_name
+ * Signature: ([B)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1file_1name
+  (JNIEnv *, jclass, jbyteArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_obj_name
+ * Signature: ([BJ)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1obj_1name
+  (JNIEnv *, jclass, jbyteArray, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Rget_attr_name
+ * Signature: ([B)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Rget_1attr_1name
+  (JNIEnv *, jclass, jbyteArray);
+
+/* H5R: HDF5 1.8 Reference API Functions */
+
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Rcreate
diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c
index eedd42e..c703e90 100644
--- a/java/src/jni/h5sImp.c
+++ b/java/src/jni/h5sImp.c
@@ -162,9 +162,9 @@ done:
 } /* end Java_hdf_hdf5lib_H5__1H5Scopy */
 
 #ifdef notdef
-// 10/28/99 -- added code to copy the array -- this is not used,
-// but serves as a reminder in case we try to implement this in
-// the future....
+/* 10/28/99 -- added code to copy the array -- this is not used,
+ * but serves as a reminder in case we try to implement this in
+ */ the future....
 /*
  *  Note:  the argument coord is actually long coord[][], which has been
  *         flattened by the caller.
diff --git a/java/src/jni/h5sImp.h b/java/src/jni/h5sImp.h
index 141e504..87661e3 100644
--- a/java/src/jni/h5sImp.h
+++ b/java/src/jni/h5sImp.h
@@ -49,9 +49,9 @@ Java_hdf_hdf5lib_H5__1H5Scopy
 (JNIEnv *, jclass, jlong);
 
 #ifdef notdef
-// 10/28/99 -- added code to copy the array -- this is not used,
-// but serves as a reminder in case we try to implement this in
-// the future....
+/* 10/28/99 -- added code to copy the array -- this is not used,
+ * but serves as a reminder in case we try to implement this in
+ */ the future....
 /*
  *  Note:  the argument coord is actually long coord[][], which has been
  *         flattened by the caller.
diff --git a/java/src/jni/h5tImp.c b/java/src/jni/h5tImp.c
index 3302b7d..1adff3c 100644
--- a/java/src/jni/h5tImp.c
+++ b/java/src/jni/h5tImp.c
@@ -981,9 +981,9 @@ done:
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Treclaim
- * Signature: (JJJ[B)I
+ * Signature: (JJJ[B)V
  */
-JNIEXPORT jint JNICALL
+JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Treclaim
     (JNIEnv *env, jclass clss, jlong type_id, jlong space_id,
           jlong xfer_plist_id, jbyteArray buf)
@@ -1005,8 +1005,6 @@ Java_hdf_hdf5lib_H5_H5Treclaim
 done:
     if (pinBuf)
         UNPIN_BYTE_ARRAY(ENVONLY, buf, pinBuf, (status < 0) ? JNI_ABORT : 0);
-
-    return (jint)status;
 } /* end Java_hdf_hdf5lib_H5_H5Treclaim */
 
 /*
diff --git a/java/src/jni/h5tImp.h b/java/src/jni/h5tImp.h
index a63969b..78e4561 100644
--- a/java/src/jni/h5tImp.h
+++ b/java/src/jni/h5tImp.h
@@ -402,9 +402,9 @@ Java_hdf_hdf5lib_H5_H5Tpack
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Treclaim
- * Signature: (JJJ[B)I
+ * Signature: (JJJ[B)V
  */
-JNIEXPORT jint JNICALL
+JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Treclaim
   (JNIEnv*, jclass, jlong, jlong, jlong, jbyteArray);
 
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 700f75f..cd54f8b 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -71,6 +71,12 @@ static int     render_bin_output_region_data_points(FILE *stream, hid_t region_s
 static int     render_bin_output_region_points(FILE *stream, hid_t region_space,
             hid_t region_id, hid_t container);
 
+/* Strings for output */
+#define H5_TOOLS_GROUP           "GROUP"
+#define H5_TOOLS_DATASET         "DATASET"
+#define H5_TOOLS_DATATYPE        "DATATYPE"
+#define H5_TOOLS_ATTRIBUTE       "ATTRIBUTE"
+
 /** frees memory held by array of strings */
 void
 h5str_array_free
@@ -625,6 +631,64 @@ done:
     return retVal;
 } /* end h5str_convert */
 
+/*-------------------------------------------------------------------------
+ * Function:    h5str_sprint_reference
+ *
+ * Purpose: Object reference -- show the name of the referenced object.
+ *
+ * Return:  Nothing
+ *-------------------------------------------------------------------------
+ */
+void
+h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_p)
+{
+    ssize_t      buf_size, status;
+    char *ref_name = NULL;
+    const H5R_ref_t *ref_vp = (H5R_ref_t *)ref_p;
+
+    UNUSED(container);
+
+    if (!h5str_append(out_str, " "))
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+    buf_size = H5Rget_file_name(ref_vp, NULL, 0);
+    if (buf_size) {
+        ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
+        status = H5Rget_file_name(ref_vp, ref_name, buf_size + 1);
+        ref_name[buf_size] = '\0';
+        if (!h5str_append(out_str, ref_name))
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+        HDfree(ref_name);
+        ref_name = NULL;
+    }
+
+    buf_size = H5Rget_obj_name(ref_vp, H5P_DEFAULT, NULL, 0);
+    if (buf_size) {
+        ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
+        status = H5Rget_obj_name(ref_vp, H5P_DEFAULT, ref_name, buf_size + 1);
+        ref_name[buf_size] = '\0';
+        if (!h5str_append(out_str, ref_name))
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+        HDfree(ref_name);
+        ref_name = NULL;
+    }
+
+    if (H5Rget_type(ref_vp) == H5R_ATTR) {
+        buf_size = H5Rget_attr_name(ref_vp, NULL, 0);
+        if (buf_size) {
+            ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1);
+            status = H5Rget_attr_name(ref_vp, ref_name, buf_size + 1);
+            ref_name[buf_size] = '\0';
+            if (!h5str_append(out_str, ref_name))
+                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+            HDfree(ref_name);
+            ref_name = NULL;
+        }
+    }
+done:
+    if (ref_name)
+        HDfree(ref_name);
+}
+
 /*
  * Prints the value of a data point into a string.
  *
@@ -984,96 +1048,89 @@ h5str_sprintf
                 break;
             }
 
-            if (H5R_DSET_REG_REF_BUF_SIZE == typeSize) {
-                H5S_sel_type region_type = H5S_SEL_ERROR;
-                hid_t        region_obj = H5I_INVALID_HID;
-                hid_t        region = H5I_INVALID_HID;
-                char         ref_name[1024];
-
-                /*
-                 * Dataset region reference --
-                 * show the type and the referenced object
-                 */
-
-                /* Get name of the dataset the region reference points to using H5Rget_name */
-                if ((region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, cptr)) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
-
-                if ((region = H5Rget_region(container, H5R_DATASET_REGION, cptr)) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
-
-                if (expand_data) {
-                    if (H5S_SEL_ERROR == (region_type = H5Sget_select_type(region)))
-                        H5_LIBRARY_ERROR(ENVONLY);
-
-                    if (H5S_SEL_POINTS == region_type) {
-                        if (h5str_dump_region_points_data(ENVONLY, out_str, region, region_obj) < 0)
-                            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                    }
-                    else {
-                        if (h5str_dump_region_blocks_data(ENVONLY, out_str, region, region_obj) < 0)
-                            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                    }
-                }
-                else {
-                    if (H5Rget_name(region_obj, H5R_DATASET_REGION, cptr, (char *)ref_name, 1024) < 0)
-                        H5_LIBRARY_ERROR(ENVONLY);
-
-                    if (!h5str_append(out_str, ref_name))
-                        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-                    if (H5S_SEL_ERROR == (region_type = H5Sget_select_type(region)))
-                        H5_LIBRARY_ERROR(ENVONLY);
-
-                    if (H5S_SEL_POINTS == region_type) {
-                        if (!h5str_append(out_str, " REGION_TYPE POINT"))
-                            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-                        if (h5str_dump_region_points(ENVONLY, out_str, region, region_obj) < 0)
+            if (H5Tequal(tid, H5T_STD_REF)) {
+                H5O_type_t obj_type;   /* Object type */
+                H5R_type_t ref_type;   /* Reference type */
+                const H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
+
+                ref_type = H5Rget_type(ref_vp);
+                H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type);
+                switch (ref_type) {
+                    case H5R_OBJECT1:
+                        switch (obj_type) {
+                            case H5O_TYPE_GROUP:
+                                if (!h5str_append(out_str, H5_TOOLS_GROUP))
+                                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                                break;
+
+                            case H5O_TYPE_DATASET:
+                                if (!h5str_append(out_str, H5_TOOLS_DATASET))
+                                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                                break;
+
+                            case H5O_TYPE_NAMED_DATATYPE:
+                                if (!h5str_append(out_str, H5_TOOLS_DATATYPE))
+                                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                                break;
+
+                            case H5O_TYPE_MAP:
+                            case H5O_TYPE_UNKNOWN:
+                            case H5O_TYPE_NTYPES:
+                            default:
+                                break;
+                        } /* end switch */
+                        break;
+                    case H5R_DATASET_REGION1:
+                        if (!h5str_append(out_str, H5_TOOLS_DATASET))
                             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                    }
-                    else {
-                        if (!h5str_append(out_str, " REGION_TYPE BLOCK"))
+                        h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+                        break;
+                    case H5R_OBJECT2:
+                        switch (obj_type) {
+                            case H5O_TYPE_GROUP:
+                                if (!h5str_append(out_str, H5_TOOLS_GROUP))
+                                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                                break;
+
+                            case H5O_TYPE_DATASET:
+                                if (!h5str_append(out_str, H5_TOOLS_DATASET))
+                                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                                break;
+
+                            case H5O_TYPE_NAMED_DATATYPE:
+                                if (!h5str_append(out_str, H5_TOOLS_DATATYPE))
+                                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                                break;
+
+                            case H5O_TYPE_MAP:
+                            case H5O_TYPE_UNKNOWN:
+                            case H5O_TYPE_NTYPES:
+                            default:
+                                break;
+                        } /* end switch */
+                        h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+                        break;
+                    case H5R_DATASET_REGION2:
+                        if (!h5str_append(out_str, H5_TOOLS_DATASET))
                             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-                        if (h5str_dump_region_blocks(ENVONLY, out_str, region, region_obj) < 0)
+                        h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+                        break;
+                    case H5R_ATTR:
+                        if (!h5str_append(out_str, H5_TOOLS_ATTRIBUTE))
                             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                    }
-                }
-
-                if (H5Sclose(region) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
-                region = H5I_INVALID_HID;
-
-                if (H5Dclose(region_obj) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
-                region_obj = H5I_INVALID_HID;
+                        h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr);
+                        break;
+                    default:
+                        break;
+                } /* end switch */
             }
-            else if (H5R_OBJ_REF_BUF_SIZE == typeSize) {
-                H5O_info_t oi;
-                hid_t      obj = H5I_INVALID_HID;
-
-                /*
-                 * Object references -- show the type and OID of the referenced
-                 * object.
-                 */
-
-                if (NULL == (this_str = (char *) HDmalloc(64)))
-                    H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
-
-                if ((obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, cptr)) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
-
-                if (H5Oget_info2(obj, &oi, H5O_INFO_ALL) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
-
-                /* Print object data and close object */
-                if (HDsprintf(this_str, "%u-%lu", (unsigned) oi.type, oi.addr) < 0)
-                    H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure");
-
-                if (H5Oclose(obj) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
-                obj = H5I_INVALID_HID;
+            else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
+                /* (H5R_DSET_REG_REF_BUF_SIZE == typeSize) */
+                H5_LIBRARY_ERROR(ENVONLY);
+            }
+            else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
+                /* (H5R_OBJ_REF_BUF_SIZE == typeSize) */
+                H5_LIBRARY_ERROR(ENVONLY);
             }
 
             break;
@@ -2204,20 +2261,28 @@ h5str_render_bin_output
 
         case H5T_REFERENCE:
         {
-            if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
+            if (H5Tequal(tid, H5T_STD_REF)) {
+                hid_t   region_id = H5I_INVALID_HID;
+                hid_t   region_space = H5I_INVALID_HID;
                 H5S_sel_type region_type;
-                hid_t        region_id, region_space;
 
                 /* Region data */
                 for (block_index = 0; block_index < block_nelmts; block_index++) {
                     mem = ((unsigned char*)_mem) + block_index * size;
-
-                    if ((region_id = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, mem)) < 0)
+                    if((region_id = H5Ropen_object((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0)
                         continue;
-
-                    if ((region_space = H5Rget_region(container, H5R_DATASET_REGION, mem)) < 0) {
+                    else {
+                        if((region_space = H5Ropen_region((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+                            if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) {
+                                region_type = H5Sget_select_type(region_space);
+                                if (region_type == H5S_SEL_POINTS)
+                                    ret_value = render_bin_output_region_points(stream, region_space, region_id, container);
+                                else
+                                    ret_value = render_bin_output_region_blocks(stream, region_space, region_id, container);
+                            }
+                            H5Sclose(region_space);
+                        } /* end if (region_space >= 0) */
                         H5Dclose(region_id);
-                        continue;
                     }
 
                     if ((region_type = H5Sget_select_type(region_space)) < 0) {
@@ -2225,19 +2290,13 @@ h5str_render_bin_output
                         H5Dclose(region_id);
                         continue;
                     }
-
-                    if (region_type == H5S_SEL_POINTS)
-                        ret_value = render_bin_output_region_points(stream, region_space, region_id, container);
-                    else
-                        ret_value = render_bin_output_region_blocks(stream, region_space, region_id, container);
-
-                    H5Sclose(region_space);
-                    H5Dclose(region_id);
-
                     if (ret_value < 0)
                         break;
                 }
             }
+            else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
+                ;
+            }
             else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
                 ;
             }
@@ -3091,15 +3150,15 @@ done:
 } /* end Java_hdf_hdf5lib_H5_H5Dcopy */
 
 /*
-/////////////////////////////////////////////////////////////////////////////////
-//
-//
-// Add these methods so that we don't need to call H5Gget_objtype_by_idx
-// in a loop to get information for all the objects in a group, which takes
-// a lot of time to finish if the number of objects is more than 10,000
-//
-/////////////////////////////////////////////////////////////////////////////////
-*/
+ * /////////////////////////////////////////////////////////////////////////////////
+ * //
+ * //
+ * // Add these methods so that we don't need to call H5Gget_objtype_by_idx
+ * // in a loop to get information for all the objects in a group, which takes
+ * // a lot of time to finish if the number of objects is more than 10,000
+ * //
+ * /////////////////////////////////////////////////////////////////////////////////
+ */
 
 #ifdef __cplusplus
     herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data);
diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h
index e5f0d0b..c26cd5d 100644
--- a/java/src/jni/h5util.h
+++ b/java/src/jni/h5util.h
@@ -40,6 +40,7 @@ extern void    h5str_free(h5str_t *str);
 extern void    h5str_resize(h5str_t *str, size_t new_len);
 extern char*   h5str_append(h5str_t *str, const char* cstr);
 extern size_t  h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf, size_t out_buf_offset);
+extern void    h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_p);
 extern size_t  h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, size_t in_buf_len, int expand_data);
 extern void    h5str_array_free(char **strs, size_t len);
 extern int     h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order);