From bfae4648751129b1a8ce827f415b20b7c3943b1a Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Tue, 3 Nov 2020 16:56:16 -0600 Subject: HDFFV-10868 merge java changes from develop --- java/src/hdf/hdf5lib/H5.java | 4543 +++++++++++++++----- java/src/hdf/hdf5lib/HDF5Constants.java | 489 ++- java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java | 25 +- java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java | 22 +- java/src/hdf/hdf5lib/callbacks/H5D_append_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java | 24 +- java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java | 22 +- java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5L_iterate_cb.java | 25 +- java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java | 8 +- java/src/hdf/hdf5lib/callbacks/H5O_iterate_cb.java | 25 +- java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java | 8 +- .../hdf5lib/callbacks/H5P_cls_close_func_cb.java | 21 +- .../hdf5lib/callbacks/H5P_cls_close_func_t.java | 4 + .../hdf5lib/callbacks/H5P_cls_copy_func_cb.java | 22 +- .../hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java | 4 + .../hdf5lib/callbacks/H5P_cls_create_func_cb.java | 21 +- .../hdf5lib/callbacks/H5P_cls_create_func_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java | 22 +- java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java | 4 + .../hdf5lib/callbacks/H5P_prp_close_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_compare_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_copy_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_create_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_delete_func_cb.java | 23 +- .../hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java | 23 +- .../hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java | 23 +- java/src/hdf/hdf5lib/exceptions/HDF5Exception.java | 3 + .../hdf5lib/exceptions/HDF5ReferenceException.java | 6 + .../hdf/hdf5lib/structs/H5AC_cache_config_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5A_info_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5E_error2_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java | 2 +- java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java | 2 +- java/src/hdf/hdf5lib/structs/H5F_info2_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5G_info_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5L_info_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java | 25 +- java/src/hdf/hdf5lib/structs/H5O_info_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5_ih_info_t.java | 9 +- java/src/jni/h5Constants.c | 374 +- java/src/jni/h5sImp.c | 383 ++ java/src/jni/h5sImp.h | 59 + java/test/TestH5Sbasic.java | 138 + java/test/testfiles/JUnit-TestH5Sbasic.txt | 16 +- 47 files changed, 5436 insertions(+), 1082 deletions(-) diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 1242947..58c1e14 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -239,10 +239,14 @@ public class H5 implements java.io.Serializable { */ public final static int LIB_VERSION[] = { 1, 10, 8 }; + /** + * add system property to load library by path + */ public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib"; - // add system property to load library by name from library path, via - // System.loadLibrary() + /** + * add system property to load library by name from library path, via System.loadLibrary() + */ public final static String H5_LIBRARY_NAME_PROPERTY_KEY = "hdf.hdf5lib.H5.loadLibraryName"; private static String s_libraryName; private static boolean isLibraryLoaded = false; @@ -255,6 +259,9 @@ public class H5 implements java.io.Serializable { loadH5Lib(); } + /** + * load native library + */ public static void loadH5Lib() { // Make sure that the library is loaded only once if (isLibraryLoaded) @@ -466,6 +473,35 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native int H5get_libversion(int[] libversion) throws HDF5LibraryException; + /** + * H5set_free_list_limits + * Sets limits on the different kinds of free lists. Setting a value + * of -1 for a limit means no limit of that type. These limits are global + * for the entire library. Each "global" limit only applies to free lists + * of that type, so if an application sets a limit of 1 MB on each of the + * global lists, up to 3 MB of total storage might be allocated (1MB on + * each of regular, array and block type lists). + * + * The settings for block free lists are duplicated to factory free lists. + * Factory free list limits cannot be set independently currently. + * + * @param reg_global_lim + * The limit on all "regular" free list memory used + * @param reg_list_lim + * The limit on memory used in each "regular" free list + * @param arr_global_lim + * The limit on all "array" free list memory used + * @param arr_list_lim + * The limit on memory used in each "array" free list + * @param blk_global_lim + * The limit on all "block" free list memory used + * @param blk_list_lim + * The limit on memory used in each "block" free list + * @return a non-negative value if successful, along with the version information. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ public synchronized static native int H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim) throws HDF5LibraryException; @@ -1014,7 +1050,7 @@ public class H5 implements java.io.Serializable { /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with - * mem_type_id. The entire attribute is read into buf from the file. + * mem_type_id. The entire attribute is read into buffer from the file. * * @param attr_id * IN: Identifier of an attribute to read. @@ -1035,11 +1071,47 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Aread(attr_id, mem_type_id, obj, true); @@ -1139,211 +1211,1491 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of double from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of double to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of double from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of double to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_double(long attr_id, long mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_double(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of float from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of float to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of float from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of float to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_float(long attr_id, long mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_float(attr_id, mem_type_id, buf, true); } - public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Aread_int(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Aread_long(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Aread_short(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; - /** - * H5Arename changes the name of attribute that is attached to the object specified by loc_id. The attribute named - * old_attr_name is renamed new_attr_name. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of int from the file. * - * @param loc_id - * IN: Location or object identifier; may be dataset or group - * @param old_attr_name - * IN: Prior attribute name - * @param new_attr_name - * IN: New attribute name + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of int to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. * - * @return A non-negative value if successful; otherwise returns a negative value. + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * - data buffer is null. **/ - public synchronized static native int H5Arename(long loc_id, String old_attr_name, String new_attr_name) + public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; /** - * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name. - * The attribute named old_attr_name is renamed new_attr_name. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of int from the file. * - * @param loc_id - * IN: Location or object identifier; may be dataset or group - * @param obj_name - * IN: Name of object, relative to location, whose attribute is to be renamed - * @param old_attr_name - * IN: Prior attribute name - * @param new_attr_name - * IN: New attribute name - * @param lapl_id - * IN: Link access property list + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of int to store data read from the file. * - * @return A non-negative value if successful; otherwise returns a negative value. + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * - data buffer is null. **/ - public synchronized static native int H5Arename_by_name(long loc_id, String obj_name, String old_attr_name, - String new_attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Aread_int(attr_id, mem_type_id, buf, true); + } /** - * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with - * mem_type_id. The entire attribute is written from buf to the file. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of long from the file. * * @param attr_id - * IN: Identifier of an attribute to write. + * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param buf - * IN: Buffer with data to be written to the file. + * Buffer of long to store data read from the file. * @param isCriticalPinning - * IN: request lock on data reference. + * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * - data buffer is null. **/ - public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning) + public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; - public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf) + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of long from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of long to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException { - return H5Awrite(attr_id, mem_type_id, buf, true); - } - - public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj) - throws HDF5Exception, HDF5LibraryException, NullPointerException - { - return H5Awrite(attr_id, mem_type_id, obj, true); + return H5Aread_long(attr_id, mem_type_id, buf, true); } /** - * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with - * mem_type_id. The entire attribute is written from data object to the file. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of String from the file. * * @param attr_id - * IN: Identifier of an attribute to write. + * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). - * @param obj - * IN: Data object to be written. - * @param isCriticalPinning - * request lock on data reference. + * @param buf + * Buffer of String to store data read from the file. * * @return a non-negative value if successful * - * @exception HDF5Exception - * - Failure in the data conversion. * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - data object is null + * - data buffer is null. **/ - public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning) + public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of short from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of short to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of shortfrom the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of short to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Aread_short(attr_id, mem_type_id, buf, true); + } + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of variable-lenght from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of variable-lenght to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of String from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of String to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of variable-lenght strings from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of variable-lenght strings to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of string from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Arename changes the name of attribute that is attached to the object specified by loc_id. The attribute named + * old_attr_name is renamed new_attr_name. + * + * @param loc_id + * IN: Location or object identifier; may be dataset or group + * @param old_attr_name + * IN: Prior attribute name + * @param new_attr_name + * IN: New attribute name + * + * @return A non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - Name is null. + **/ + public synchronized static native int H5Arename(long loc_id, String old_attr_name, String new_attr_name) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name. + * The attribute named old_attr_name is renamed new_attr_name. + * + * @param loc_id + * IN: Location or object identifier; may be dataset or group + * @param obj_name + * IN: Name of object, relative to location, whose attribute is to be renamed + * @param old_attr_name + * IN: Prior attribute name + * @param new_attr_name + * IN: New attribute name + * @param lapl_id + * IN: Link access property list + * + * @return A non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - Name is null. + **/ + public synchronized static native int H5Arename_by_name(long loc_id, String obj_name, String old_attr_name, + String new_attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Awrite(attr_id, mem_type_id, buf, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * IN: Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { + return H5Awrite(attr_id, mem_type_id, obj, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from data object to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * IN: Data object to be written. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5Exception + * - Failure in the data conversion. + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data object is null + **/ + public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning) + throws HDF5Exception, HDF5LibraryException, NullPointerException + { + int status = -1; + boolean is1D = false; + + Class dataClass = obj.getClass(); + if (!dataClass.isArray()) { + throw (new HDF5JavaException("H5Dwrite: data is not an array")); + } + + String cname = dataClass.getName(); + is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); + char dname = cname.charAt(cname.lastIndexOf("[") + 1); + + if (is1D && (dname == 'B')) { + status = H5Awrite(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning); + } + else if (is1D && (dname == 'S')) { + status = H5Awrite_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning); + } + else if (is1D && (dname == 'I')) { + status = H5Awrite_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning); + } + else if (is1D && (dname == 'J')) { + status = H5Awrite_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning); + } + else if (is1D && (dname == 'F')) { + status = H5Awrite_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning); + } + else if (is1D && (dname == 'D')) { + status = H5Awrite_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning); + } + else if (is1D && (dataClass.getComponentType() == String.class)) { + log.trace("H5Dwrite_string type"); + status = H5Awrite_string(attr_id, mem_type_id, (String[]) obj); + } + else { + HDFArray theArray = new HDFArray(obj); + byte[] buf = theArray.byteify(); + + status = H5Awrite(attr_id, mem_type_id, buf); + buf = null; + theArray = null; + } + + return status; + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of double to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of double with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of double to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of double with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Awrite_double(attr_id, mem_type_id, buf, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of float to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of float with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of float to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of float with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Awrite_float(attr_id, mem_type_id, buf, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of int to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of int with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of int to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of int with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Awrite_int(attr_id, mem_type_id, buf, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of long to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of long with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of long to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of long with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Awrite_long(attr_id, mem_type_id, buf, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of short to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of short with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of short to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of short with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Awrite_short(attr_id, mem_type_id, buf, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of string to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of string with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of variable-lenght to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of variable-lenght with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from + * the application memory buffer buffer of variable-lenght strings into the file. + * + * ---- contributed by Rosetta Biosoftware + * + * @param attr_id + * Identifier of the attribute read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param buf + * Buffer of variable-lenght strings with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + + public synchronized static native int H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aget_create_plist retrieves a copy of the attribute creation property list identifier. + * + * @param attr_id + * IN: Identifier of an attribute. + * + * @return identifier for the attribute's creation property list if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Aget_create_plist(long attr_id) + throws HDF5LibraryException + { + long id = _H5Aget_create_plist(attr_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Aget_create_plist add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Aget_create_plist(long attr_id) throws HDF5LibraryException; + + /** + * H5Aiterate2 iterates over the attributes attached to a dataset, named datatype, or group, as + * specified by obj_id. For each attribute, user-provided data, op_data, with additional information + * as defined below, is passed to a user-defined function, op, which operates on that attribute. + * + * @param loc_id + * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. + * @param idx_type + * IN: The type of index specified by idx_type can be one of the following: + * H5_INDEX_NAME An alpha-numeric index by attribute name. + * H5_INDEX_CRT_ORDER An index by creation order. + * @param order + * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: + * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration + * incrementing the index position at each step. + * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration + * decrementing the index position at each step. + * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided + * as to the order, but HDF5 ensures that each element in the index will be + * visited if the iteration completes successfully. + * @param idx + * IN/OUT: Initial and returned offset within index. + * @param op + * IN: Callback function to operate on each value. + * @param op_data + * IN/OUT: Pointer to any user-efined data for use by operator function. + * + * @return returns the return value of the first operator that returns a positive value, or zero if all members were + * processed with no operator returning non-zero. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. + **/ + public synchronized static native int H5Aiterate(long loc_id, int idx_type, int order, long idx, + H5A_iterate_cb op, H5A_iterate_t op_data) throws HDF5LibraryException, NullPointerException; + + /** + * H5Aiterate_by_name iterates over the attributes attached to the dataset or group specified with loc_id + * and obj_name. For each attribute, user-provided data, op_data, with additional information as defined + * below, is passed to a user-defined function, op, which operates on that attribute. + * + * @param loc_id + * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. + * @param obj_name + * IN: Name of object, relative to location. + * @param idx_type + * IN: The type of index specified by idx_type can be one of the following: + * H5_INDEX_NAME An alpha-numeric index by attribute name. + * H5_INDEX_CRT_ORDER An index by creation order. + * @param order + * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: + * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration + * incrementing the index position at each step. + * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration + * decrementing the index position at each step. + * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided + * as to the order, but HDF5 ensures that each element in the index will be + * visited if the iteration completes successfully. + * @param idx + * IN/OUT: Initial and returned offset within index. + * @param op + * IN: Callback function to operate on each value. + * @param op_data + * IN/OUT: Pointer to any user-efined data for use by operator function. + * @param lapl_id + * IN: Link access property list + * + * @return returns the return value of the first operator that returns a positive value, or zero if all members were + * processed with no operator returning non-zero. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. + **/ + public synchronized static native int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, + int order, long idx, H5A_iterate_cb op, H5A_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException; + + // //////////////////////////////////////////////////////////// + // // + // H5AC: Cache Interface Functions // + // // + // //////////////////////////////////////////////////////////// + + // No public Functions + + // //////////////////////////////////////////////////////////// + // // + // H5B: B-link-tree Interface Functions // + // // + // //////////////////////////////////////////////////////////// + + // No public Functions + + // //////////////////////////////////////////////////////////// + // // + // H5B2: v2 B-tree Interface Functions // + // // + // //////////////////////////////////////////////////////////// + + // No public Functions + + // //////////////////////////////////////////////////////////// + // // + // H5C: Cache Interface Functions // + // // + // //////////////////////////////////////////////////////////// + + // No public Functions + + // //////////////////////////////////////////////////////////// + // // + // H5D: Datasets Interface Functions // + // // + // //////////////////////////////////////////////////////////// + + /** + * H5Dcopy copies the content of one dataset to another dataset. + * + * @param src_did + * the identifier of the source dataset + * @param dst_did + * the identifier of the destinaiton dataset + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ + public synchronized static native int H5Dcopy(long src_did, long dst_did) throws HDF5LibraryException; + + /** + * H5Dclose ends access to a dataset specified by dataset_id and releases resources used by it. + * + * @param dataset_id + * Identifier of the dataset to finish access to. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static int H5Dclose(long dataset_id) throws HDF5LibraryException { + if (dataset_id < 0) + return 0; // throw new HDF5LibraryException("Negative ID"); + + log.trace("OPEN_IDS: H5Dclose remove {}", dataset_id); + OPEN_IDS.remove(dataset_id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + return _H5Dclose(dataset_id); + } + + private synchronized static native int _H5Dclose(long dataset_id) throws HDF5LibraryException; + + /** + * H5Dcreate creates a new dataset named name at the location specified by loc_id. + * + * @param loc_id + * IN: Location identifier + * @param name + * IN: Dataset name + * @param type_id + * IN: Datatype identifier + * @param space_id + * IN: Dataspace identifier + * @param lcpl_id + * IN: Identifier of link creation property list. + * @param dcpl_id + * IN: Identifier of dataset creation property list. + * @param dapl_id + * IN: Identifier of dataset access property list. + * + * @return a dataset identifier + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public static long H5Dcreate(long loc_id, String name, long type_id, long space_id, long lcpl_id, long dcpl_id, + long dapl_id) throws HDF5LibraryException, NullPointerException { + long id = _H5Dcreate2(loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Dcreate add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + /** + * H5Dcreate2 creates a new dataset named name at the location specified by loc_id. + * + * @see public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int lcpl_id, int dcpl_id, + * int dapl_id) + **/ + private synchronized static native long _H5Dcreate2(long loc_id, String name, long type_id, long space_id, + long lcpl_id, long dcpl_id, long dapl_id) throws HDF5LibraryException, NullPointerException; + + /** + * H5Dcreate_anon creates a dataset in the file specified by loc_id. + * + * @param loc_id + * IN: Location identifier + * @param type_id + * IN: Datatype identifier + * @param space_id + * IN: Dataspace identifier + * @param dcpl_id + * IN: Identifier of dataset creation property list. + * @param dapl_id + * IN: Identifier of dataset access property list. + * + * @return a dataset identifier + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, long dapl_id) + throws HDF5LibraryException { + long id = _H5Dcreate_anon(loc_id, type_id, space_id, dcpl_id, dapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Dcreate_anon add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, + long dapl_id) throws HDF5LibraryException; + + /** + * H5Dfill explicitly fills the dataspace selection in memory, space_id, with the fill value specified in fill. + * + * @param fill + * IN: Pointer to the fill value to be used. + * @param fill_type + * IN: Fill value datatype identifier. + * @param buf + * IN/OUT: Pointer to the memory buffer containing the selection to be filled. + * @param buf_type + * IN: Datatype of dataspace elements to be filled. + * @param space_id + * IN: Dataspace describing memory buffer and containing the selection to be filled. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. + **/ + public synchronized static native void H5Dfill(byte[] fill, long fill_type, byte[] buf, long buf_type, long space_id) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Dget_access_plist returns an identifier for a copy of the dataset access property list for a dataset. + * + * @param dset_id + * IN: Identifier of the dataset to query. + * + * @return a dataset access property list identifier + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Dget_access_plist(long dset_id) throws HDF5LibraryException; + + /** + * H5Dget_create_plist returns an identifier for a copy of the dataset creation property list for a dataset. + * + * @param dataset_id + * Identifier of the dataset to query. + * @return a dataset creation property list identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Dget_create_plist(long dataset_id) throws HDF5LibraryException { + long id = _H5Dget_create_plist(dataset_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Dget_create_plist add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Dget_create_plist(long dataset_id) throws HDF5LibraryException; + + /** + * H5Dget_offset returns the address in the file of the dataset dset_id. + * + * @param dset_id + * IN: Identifier of the dataset in question + * + * @return the offset in bytes. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Dget_offset(long dset_id) throws HDF5LibraryException; + + /** + * H5Dget_space returns an identifier for a copy of the dataspace for a dataset. + * + * @param dataset_id + * Identifier of the dataset to query. + * + * @return a dataspace identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Dget_space(long dataset_id) throws HDF5LibraryException { + long id = _H5Dget_space(dataset_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Dget_space add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Dget_space(long dataset_id) throws HDF5LibraryException; + + /** + * H5Dget_space_status determines whether space has been allocated for the dataset dset_id. + * + * @param dset_id + * IN: Identifier of the dataset to query. + * + * @return the space allocation status + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Dget_space_status(long dset_id) throws HDF5LibraryException; + + /** + * H5Dget_storage_size returns the amount of storage that is required for the dataset. + * + * @param dataset_id + * Identifier of the dataset in question + * + * @return he amount of storage space allocated for the dataset. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Dget_storage_size(long dataset_id) throws HDF5LibraryException, + IllegalArgumentException; + + /** + * H5Dget_type returns an identifier for a copy of the datatype for a dataset. + * + * @param dataset_id + * Identifier of the dataset to query. + * + * @return a datatype identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Dget_type(long dataset_id) throws HDF5LibraryException { + long id = _H5Dget_type(dataset_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Dget_type add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Dget_type(long dataset_id) throws HDF5LibraryException; + + /** + * H5Diterate iterates over all the data elements in the memory buffer buf, executing the callback function operator + * once for each such data element. + * + * @param buf + * IN/OUT: Pointer to the memory containing the elements to iterate over. + * @param buf_type + * IN: Buffer datatype identifier. + * @param space_id + * IN: Dataspace describing memory buffer. + * @param op + * IN: Callback function to operate on each value. + * @param op_data + * IN/OUT: Pointer to any user-efined data for use by operator function. + * + * @return returns the return value of the first operator that returns a positive value, or zero if all members were + * processed with no operator returning non-zero. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. + **/ + public synchronized static native int H5Diterate(byte[] buf, long buf_type, long space_id, H5D_iterate_cb op, + H5D_iterate_t op_data) throws HDF5LibraryException, NullPointerException; + + /** + * H5Dopen opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. + * + * @param loc_id + * IN: Location identifier + * @param name + * IN: Dataset name + * @param dapl_id + * IN: Identifier of dataset access property list. + * + * @return a dataset identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException + { + long id = _H5Dopen2(loc_id, name, dapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Dopen add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + /** + * H5Dopen2 opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. + * + * @see public static int H5Dopen(int loc_id, String name, int dapl_id) + **/ + private synchronized static native long _H5Dopen2(long loc_id, String name, long dapl_id) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer buf. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param obj + * Buffer to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, + NullPointerException; + + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer buf. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, + long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); + } + + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer buf. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param obj + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, + long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException + { + return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); + } + + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * data object. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param obj + * Object to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5Exception + * - Failure in the data conversion. + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data object is null. + **/ + public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, + long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, + NullPointerException + { int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Dwrite: data is not an array")); + throw (new HDF5JavaException("H5Dread: data is not an array")); } String cname = dataClass.getName(); is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); char dname = cname.charAt(cname.lastIndexOf("[") + 1); + log.trace("H5Dread: cname={} is1D={} dname={}", cname, is1D, dname); if (is1D && (dname == 'B')) { - status = H5Awrite(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning); + log.trace("H5Dread_dname_B"); + status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, + isCriticalPinning); } else if (is1D && (dname == 'S')) { - status = H5Awrite_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning); + log.trace("H5Dread_dname_S"); + status = H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, + isCriticalPinning); } else if (is1D && (dname == 'I')) { - status = H5Awrite_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning); + log.trace("H5Dread_dname_I"); + status = H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, + isCriticalPinning); } else if (is1D && (dname == 'J')) { - status = H5Awrite_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning); + log.trace("H5Dread_dname_J"); + status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, + isCriticalPinning); } else if (is1D && (dname == 'F')) { - status = H5Awrite_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning); + log.trace("H5Dread_dname_F"); + status = H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, + isCriticalPinning); } else if (is1D && (dname == 'D')) { - status = H5Awrite_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning); + log.trace("H5Dread_dname_D"); + 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)) { + 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); } else if (is1D && (dataClass.getComponentType() == String.class)) { - log.trace("H5Dwrite_string type"); - status = H5Awrite_string(attr_id, mem_type_id, (String[]) obj); + log.trace("H5Dread_string type"); + status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (String[]) obj); } else { + // Create a data buffer to hold the data into a Java Array HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.byteify(); + byte[] buf = theArray.emptyBytes(); + log.trace("H5Dread_else"); - status = H5Awrite(attr_id, mem_type_id, buf); + // will raise exception if read fails + status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, + isCriticalPinning); + if (status >= 0) { + // convert the data into a Java Array + obj = theArray.arrayify(buf); + } + + // clean up these: assign 'null' as hint to gc() buf = null; theArray = null; } @@ -1351,548 +2703,537 @@ public class H5 implements java.io.Serializable { return status; } - public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Awrite_double(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Awrite_float(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Awrite_int(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Awrite_long(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Awrite_short(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; - /** - * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from - * the application memory buffer buf into the file. - * - * ---- contributed by Rosetta Biosoftware + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. * - * @param attr_id - * Identifier of the attribute read from. + * @param dataset_id + * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. * @param buf - * Buffer with data to be written to the file. + * Buffer of type double to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * - data buffer is null. **/ - - public synchronized static native int H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; /** - * H5Aget_create_plist retrieves a copy of the attribute creation property list identifier. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. * - * @param attr_id - * IN: Identifier of an attribute. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double to store data read from the file. * - * @return identifier for the attribute's creation property list if successful + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public static long H5Aget_create_plist(long attr_id) - throws HDF5LibraryException + public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { - long id = _H5Aget_create_plist(attr_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Aget_create_plist add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; + return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } - private synchronized static native long _H5Aget_create_plist(long attr_id) throws HDF5LibraryException; - - /** - * H5Aiterate2 iterates over the attributes attached to a dataset, named datatype, or group, as - * specified by obj_id. For each attribute, user-provided data, op_data, with additional information - * as defined below, is passed to a user-defined function, op, which operates on that attribute. - * - * @param loc_id - * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. - * @param idx_type - * IN: The type of index specified by idx_type can be one of the following: - * H5_INDEX_NAME An alpha-numeric index by attribute name. - * H5_INDEX_CRT_ORDER An index by creation order. - * @param order - * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: - * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration - * incrementing the index position at each step. - * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration - * decrementing the index position at each step. - * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided - * as to the order, but HDF5 ensures that each element in the index will be - * visited if the iteration completes successfully. - * @param idx - * IN/OUT: Initial and returned offset within index. - * @param op - * IN: Callback function to operate on each value. - * @param op_data - * IN/OUT: Pointer to any user-efined data for use by operator function. - * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. - **/ - public synchronized static native int H5Aiterate(long loc_id, int idx_type, int order, long idx, - H5A_iterate_cb op, H5A_iterate_t op_data) throws HDF5LibraryException, NullPointerException; - /** - * H5Aiterate_by_name iterates over the attributes attached to the dataset or group specified with loc_id - * and obj_name. For each attribute, user-provided data, op_data, with additional information as defined - * below, is passed to a user-defined function, op, which operates on that attribute. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. * - * @param loc_id - * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. - * @param obj_name - * IN: Name of object, relative to location. - * @param idx_type - * IN: The type of index specified by idx_type can be one of the following: - * H5_INDEX_NAME An alpha-numeric index by attribute name. - * H5_INDEX_CRT_ORDER An index by creation order. - * @param order - * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: - * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration - * incrementing the index position at each step. - * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration - * decrementing the index position at each step. - * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided - * as to the order, but HDF5 ensures that each element in the index will be - * visited if the iteration completes successfully. - * @param idx - * IN/OUT: Initial and returned offset within index. - * @param op - * IN: Callback function to operate on each value. - * @param op_data - * IN/OUT: Pointer to any user-efined data for use by operator function. - * @param lapl_id - * IN: Link access property list + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * - data buffer is null. **/ - public synchronized static native int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, - int order, long idx, H5A_iterate_cb op, H5A_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException; - - // //////////////////////////////////////////////////////////// - // // - // H5AC: Cache Interface Functions // - // // - // //////////////////////////////////////////////////////////// - - // No public Functions - - // //////////////////////////////////////////////////////////// - // // - // H5B: B-link-tree Interface Functions // - // // - // //////////////////////////////////////////////////////////// - - // No public Functions - - // //////////////////////////////////////////////////////////// - // // - // H5B2: v2 B-tree Interface Functions // - // // - // //////////////////////////////////////////////////////////// - - // No public Functions - - // //////////////////////////////////////////////////////////// - // // - // H5C: Cache Interface Functions // - // // - // //////////////////////////////////////////////////////////// - - // No public Functions - - // //////////////////////////////////////////////////////////// - // // - // H5D: Datasets Interface Functions // - // // - // //////////////////////////////////////////////////////////// + public synchronized static native int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; /** - * H5Dcopy copies the content of one dataset to another dataset. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. * - * @param src_did - * the identifier of the source dataset - * @param dst_did - * the identifier of the destinaiton dataset + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float to store data read from the file. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - */ - public synchronized static native int H5Dcopy(long src_did, long dst_did) throws HDF5LibraryException; + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); + } /** - * H5Dclose ends access to a dataset specified by dataset_id and releases resources used by it. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of int. * * @param dataset_id - * Identifier of the dataset to finish access to. + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public static int H5Dclose(long dataset_id) throws HDF5LibraryException { - if (dataset_id < 0) - return 0; // throw new HDF5LibraryException("Negative ID"); - - log.trace("OPEN_IDS: H5Dclose remove {}", dataset_id); - OPEN_IDS.remove(dataset_id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - return _H5Dclose(dataset_id); - } - - private synchronized static native int _H5Dclose(long dataset_id) throws HDF5LibraryException; + public synchronized static native int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, + NullPointerException; /** - * H5Dcreate creates a new dataset named name at the location specified by loc_id. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of int. * - * @param loc_id - * IN: Location identifier - * @param name - * IN: Dataset name - * @param type_id - * IN: Datatype identifier - * @param space_id - * IN: Dataspace identifier - * @param lcpl_id - * IN: Identifier of link creation property list. - * @param dcpl_id - * IN: Identifier of dataset creation property list. - * @param dapl_id - * IN: Identifier of dataset access property list. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int to store data read from the file. * - * @return a dataset identifier + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * - data buffer is null. **/ - public static long H5Dcreate(long loc_id, String name, long type_id, long space_id, long lcpl_id, long dcpl_id, - long dapl_id) throws HDF5LibraryException, NullPointerException { - long id = _H5Dcreate2(loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Dcreate add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; + public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } /** - * H5Dcreate2 creates a new dataset named name at the location specified by loc_id. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. * - * @see public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int lcpl_id, int dcpl_id, - * int dapl_id) + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - private synchronized static native long _H5Dcreate2(long loc_id, String name, long type_id, long space_id, - long lcpl_id, long dcpl_id, long dapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, + NullPointerException; /** - * H5Dcreate_anon creates a dataset in the file specified by loc_id. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. * - * @param loc_id - * IN: Location identifier - * @param type_id - * IN: Datatype identifier - * @param space_id - * IN: Dataspace identifier - * @param dcpl_id - * IN: Identifier of dataset creation property list. - * @param dapl_id - * IN: Identifier of dataset access property list. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long to store data read from the file. * - * @return a dataset identifier + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public static long H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, long dapl_id) - throws HDF5LibraryException { - long id = _H5Dcreate_anon(loc_id, type_id, space_id, dcpl_id, dapl_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Dcreate_anon add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; + public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } - private synchronized static native long _H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, - long dapl_id) throws HDF5LibraryException; - /** - * H5Dfill explicitly fills the dataspace selection in memory, space_id, with the fill value specified in fill. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of string. * - * @param fill - * IN: Pointer to the fill value to be used. - * @param fill_type - * IN: Fill value datatype identifier. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. * @param buf - * IN/OUT: Pointer to the memory buffer containing the selection to be filled. - * @param buf_type - * IN: Datatype of dataspace elements to be filled. - * @param space_id - * IN: Dataspace describing memory buffer and containing the selection to be filled. + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * - data buffer is null. **/ - public synchronized static native void H5Dfill(byte[] fill, long fill_type, byte[] buf, long buf_type, long space_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** - * H5Dget_access_plist returns an identifier for a copy of the dataset access property list for a dataset. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of short. * - * @param dset_id - * IN: Identifier of the dataset to query. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. * - * @return a dataset access property list identifier + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public synchronized static native long H5Dget_access_plist(long dset_id) throws HDF5LibraryException; + public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; /** - * H5Dget_create_plist returns an identifier for a copy of the dataset creation property list for a dataset. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of short. * * @param dataset_id - * Identifier of the dataset to query. - * @return a dataset creation property list identifier if successful + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short to store data read from the file. + * + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public static long H5Dget_create_plist(long dataset_id) throws HDF5LibraryException { - long id = _H5Dget_create_plist(dataset_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Dget_create_plist add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; + public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } - private synchronized static native long _H5Dget_create_plist(long dataset_id) throws HDF5LibraryException; - /** - * H5Dget_offset returns the address in the file of the dataset dset_id. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght. * - * @param dset_id - * IN: Identifier of the dataset in question + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-lenght to store data read from the file. * - * @return the offset in bytes. + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public synchronized static native long H5Dget_offset(long dset_id) throws HDF5LibraryException; + public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** - * H5Dget_space returns an identifier for a copy of the dataspace for a dataset. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of string. * * @param dataset_id - * Identifier of the dataset to query. + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string to store data read from the file. * - * @return a dataspace identifier if successful + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public static long H5Dget_space(long dataset_id) throws HDF5LibraryException { - long id = _H5Dget_space(dataset_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Dget_space add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; - } - - private synchronized static native long _H5Dget_space(long dataset_id) throws HDF5LibraryException; + public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** - * H5Dget_space_status determines whether space has been allocated for the dataset dset_id. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght strings. * - * @param dset_id - * IN: Identifier of the dataset to query. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-lenght strings to store data read from the file. * - * @return the space allocation status + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. **/ - public synchronized static native int H5Dget_space_status(long dset_id) throws HDF5LibraryException; + public synchronized static native int H5Dread_VLStrings(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** - * H5Dget_storage_size returns the amount of storage that is required for the dataset. - * - * @param dataset_id - * Identifier of the dataset in question + * H5Dset_extent sets the current dimensions of the chunked dataset dset_id to the sizes specified in size. * - * @return he amount of storage space allocated for the dataset. + * @param dset_id + * IN: Chunked dataset identifier. + * @param size + * IN: Array containing the new magnitude of each dimension of the dataset. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - size is null. **/ - public synchronized static native long H5Dget_storage_size(long dataset_id) throws HDF5LibraryException, - IllegalArgumentException; + public synchronized static native void H5Dset_extent(long dset_id, long size[]) throws HDF5LibraryException, + NullPointerException; /** - * H5Dget_type returns an identifier for a copy of the datatype for a dataset. + * H5Dvlen_get_buf_size determines the number of bytes required to store the VL data from the dataset, using the + * space_id for the selection in the dataset on disk and the type_id for the memory representation of the VL data in + * memory. * - * @param dataset_id - * Identifier of the dataset to query. + * @param dset_id + * IN: Identifier of the dataset read from. + * @param type_id + * IN: Identifier of the datatype. + * @param space_id + * IN: Identifier of the dataspace. * - * @return a datatype identifier if successful + * @return the size in bytes of the memory buffer required to store the VL data. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. **/ - public static long H5Dget_type(long dataset_id) throws HDF5LibraryException { - long id = _H5Dget_type(dataset_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Dget_type add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; - } - - private synchronized static native long _H5Dget_type(long dataset_id) throws HDF5LibraryException; + public synchronized static native long H5Dvlen_get_buf_size(long dset_id, long type_id, long space_id) + throws HDF5LibraryException; /** - * H5Diterate iterates over all the data elements in the memory buffer buf, executing the callback function operator - * once for each such data element. + * H5Dvlen_reclaim reclaims buffer used for VL data. * - * @param buf - * IN/OUT: Pointer to the memory containing the elements to iterate over. - * @param buf_type - * IN: Buffer datatype identifier. + * @param type_id + * Identifier of the datatype. * @param space_id - * IN: Dataspace describing memory buffer. - * @param op - * IN: Callback function to operate on each value. - * @param op_data - * IN/OUT: Pointer to any user-efined data for use by operator function. + * Identifier of the dataspace. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer with data to be reclaimed. * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @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 H5Diterate(byte[] buf, long buf_type, long space_id, H5D_iterate_cb op, - H5D_iterate_t op_data) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf) + throws HDF5LibraryException, NullPointerException; /** - * H5Dopen opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. * - * @param loc_id - * IN: Location identifier - * @param name - * IN: Dataset name - * @param dapl_id - * IN: Identifier of dataset access property list. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. * - * @return a dataset identifier if successful + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ - public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException - { - long id = _H5Dopen2(loc_id, name, dapl_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Dopen add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; - } + public synchronized static native int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, + NullPointerException; /** - * H5Dopen2 opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer with data to be written to the file. * - * @see public static int H5Dopen(int loc_id, String name, int dapl_id) + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. **/ - private synchronized static native long _H5Dopen2(long loc_id, String name, long dapl_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, + long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); + } /** - * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application - * memory buffer buf. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -1905,36 +3246,24 @@ public class H5 implements java.io.Serializable { * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param obj - * Buffer to store data read from the file. - * @param isCriticalPinning - * request lock on data reference. + * Buffer with data to be written to the file. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * - name is null. **/ - public synchronized static native int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; - - public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, + public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { - return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); + return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); } /** - * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application - * data object. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory data + * object into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -1947,7 +3276,7 @@ public class H5 implements java.io.Serializable { * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param obj - * Object to store data read from the file. + * Object with data to be written to the file. * @param isCriticalPinning * request lock on data reference. * @@ -1960,7 +3289,7 @@ public class H5 implements java.io.Serializable { * @exception NullPointerException * - data object is null. **/ - public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, + public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, NullPointerException { @@ -1969,69 +3298,49 @@ public class H5 implements java.io.Serializable { Class dataClass = obj.getClass(); if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Dread: data is not an array")); + throw (new HDF5JavaException("H5Dwrite: data is not an array")); } String cname = dataClass.getName(); is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); char dname = cname.charAt(cname.lastIndexOf("[") + 1); - log.trace("H5Dread: cname={} is1D={} dname={}", cname, is1D, dname); if (is1D && (dname == 'B')) { - log.trace("H5Dread_dname_B"); - status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, + status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { - log.trace("H5Dread_dname_S"); - status = H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, + status = H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { - log.trace("H5Dread_dname_I"); - status = H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, + status = H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { - log.trace("H5Dread_dname_J"); - status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, + status = H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, isCriticalPinning); } else if (is1D && (dname == 'F')) { - log.trace("H5Dread_dname_F"); - status = H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, + status = H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { - log.trace("H5Dread_dname_D"); - status = H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + status = H5Dwrite_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)) { - 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); - } else if (is1D && (dataClass.getComponentType() == String.class)) { - log.trace("H5Dread_string type"); - status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + log.trace("H5Dwrite_string type"); + status = H5Dwrite_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (String[]) obj); } else { - // Create a data buffer to hold the data into a Java Array HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.emptyBytes(); - log.trace("H5Dread_else"); + byte[] buf = theArray.byteify(); - // will raise exception if read fails - status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, + // will raise exception on error + status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, isCriticalPinning); - if (status >= 0) { - // convert the data into a Java Array - obj = theArray.arrayify(buf); - } // clean up these: assign 'null' as hint to gc() buf = null; @@ -2041,131 +3350,219 @@ public class H5 implements java.io.Serializable { return status; } - public synchronized static native int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public synchronized static native int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; - public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { - return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); + return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } - public synchronized static native int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public synchronized static native int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; - public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { - return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static native int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; - - public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static native int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; - - public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); + return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } - public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Dread_VLStrings(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; - /** - * H5Dset_extent sets the current dimensions of the chunked dataset dset_id to the sizes specified in size. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. * - * @param dset_id - * IN: Chunked dataset identifier. - * @param size - * IN: Array containing the new magnitude of each dimension of the dataset. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * - name is null. **/ - public synchronized static native void H5Dset_extent(long dset_id, long size[]) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, + NullPointerException; /** - * H5Dvlen_get_buf_size determines the number of bytes required to store the VL data from the dataset, using the - * space_id for the selection in the dataset on disk and the type_id for the memory representation of the VL data in - * memory. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. * - * @param dset_id - * IN: Identifier of the dataset read from. - * @param type_id - * IN: Identifier of the datatype. - * @param space_id - * IN: Identifier of the dataspace. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int with data to be written to the file. * - * @return the size in bytes of the memory buffer required to store the VL data. + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * - name is null. **/ - public synchronized static native long H5Dvlen_get_buf_size(long dset_id, long type_id, long space_id) - throws HDF5LibraryException; + public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); + } /** - * H5Dvlen_reclaim reclaims buffer used for VL data. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. * - * @param type_id - * Identifier of the datatype. - * @param space_id - * Identifier of the dataspace. + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf - * Buffer with data to be reclaimed. + * Buffer of long with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * - name is null. **/ - public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf) - throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, + NullPointerException; /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer - * buf into the file. + * into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -2178,9 +3575,7 @@ public class H5 implements java.io.Serializable { * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf - * Buffer with data to be written to the file. - * @param isCriticalPinning - * request lock on data reference. + * Buffer of long with data to be written to the file. * * @return a non-negative value if successful * @@ -2189,25 +3584,15 @@ public class H5 implements java.io.Serializable { * @exception NullPointerException * - name is null. **/ - public synchronized static native int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; - - public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException + public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { - return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); + return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } /** - * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory data - * object into the file. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -2219,134 +3604,103 @@ public class H5 implements java.io.Serializable { * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. - * @param obj - * Object with data to be written to the file. + * @param buf + * Buffer of short with data to be written to the file. * @param isCriticalPinning * request lock on data reference. * * @return a non-negative value if successful * - * @exception HDF5Exception - * - Failure in the data conversion. * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - data object is null. + * - name is null. **/ - public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, - NullPointerException - { - int status = -1; - boolean is1D = false; - - Class dataClass = obj.getClass(); - if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Dwrite: data is not an array")); - } - - String cname = dataClass.getName(); - is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); - char dname = cname.charAt(cname.lastIndexOf("[") + 1); - - if (is1D && (dname == 'B')) { - status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, - isCriticalPinning); - } - else if (is1D && (dname == 'S')) { - status = H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, - isCriticalPinning); - } - else if (is1D && (dname == 'I')) { - status = H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, - isCriticalPinning); - } - else if (is1D && (dname == 'J')) { - status = H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, - isCriticalPinning); - } - else if (is1D && (dname == 'F')) { - status = H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, - isCriticalPinning); - } - else if (is1D && (dname == 'D')) { - status = H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (double[]) obj, isCriticalPinning); - } - else if (is1D && (dataClass.getComponentType() == String.class)) { - log.trace("H5Dwrite_string type"); - status = H5Dwrite_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (String[]) obj); - } - else { - HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.byteify(); - - // will raise exception on error - status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, - isCriticalPinning); - - // clean up these: assign 'null' as hint to gc() - buf = null; - theArray = null; - } - - return status; - } - - public synchronized static native int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static native int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static native int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; - - public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - - public synchronized static native int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; - - public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - public synchronized static native int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-length with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5DwriteVL(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; @@ -2623,7 +3977,7 @@ public class H5 implements java.io.Serializable { /** - * H5Epush2 pushes a new error record onto the error stack specified by estack_id. + * H5Epush pushes a new error record onto the error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. @@ -2652,6 +4006,31 @@ public class H5 implements java.io.Serializable { { H5Epush2(stack_id, file, func, line, cls_id, maj_id, min_id, msg); } + /** + * H5Epush2 pushes a new error record onto the error stack specified by estack_id. + * + * @param stack_id + * IN: Error stack identifier. + * @param file + * IN: Name of the file in which the error was detected. + * @param func + * IN: Name of the function in which the error was detected. + * @param line + * IN: Line number within the file at which the error was detected. + * @param cls_id + * IN: Error class identifier. + * @param maj_id + * IN: Major error identifier. + * @param min_id + * IN: Minor error identifier. + * @param msg + * IN: Error description string. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - file, func, or msg is null. + **/ public synchronized static native void H5Epush2(long stack_id, String file, String func, int line, long cls_id, long maj_id, long min_id, String msg) throws HDF5LibraryException, NullPointerException; @@ -2709,6 +4088,24 @@ public class H5 implements java.io.Serializable { { H5Ewalk2(stack_id, direction, func, client_data); } + /** + * H5Ewalk2 walks the error stack specified by estack_id for the current thread and calls the + * function specified in func for each error along the way. + * + * @param stack_id + * IN: Error stack identifier. + * @param direction + * IN: Direction in which the error stack is to be walked. + * @param func + * IN: Function to be called for each error encountered. + * @param client_data + * IN: Data to be passed with func. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - func is null. + **/ public synchronized static native void H5Ewalk2(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException; @@ -2945,6 +4342,19 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Fget_create_plist(long file_id) throws HDF5LibraryException; + /** + * H5Fget_filesize retrieves the file size of the HDF5 file. This function + * is called after an existing file is opened in order + * to learn the true size of the underlying file. + * + * @param file_id + * IN: File identifier for a currently-open HDF5 file + * + * @return the file size of the HDF5 file + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Fget_filesize(long file_id) throws HDF5LibraryException; /** @@ -3560,40 +4970,121 @@ public class H5 implements java.io.Serializable { return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, objRef, HDF5Constants.H5_INDEX_NAME); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, - int[] ltype, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, ref, indx_type, -1); + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param objRef + * OUT: Reference number of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, + int[] ltype, long[] objRef, int indx_type) throws HDF5LibraryException, NullPointerException { + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, null, objRef, indx_type, -1); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, - int[] ltype, long[] fno, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, indx_type, -1); + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param fno + * OUT: File number + * @param objRef + * OUT: Reference number of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, + int[] ltype, long[] fno, long[] objRef, int indx_type) throws HDF5LibraryException, NullPointerException { + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, objRef, indx_type, -1); } - public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, - int[] ltype, long[] fno, long[] ref, int indx_type, int indx_order) throws HDF5LibraryException, + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param fno + * OUT: File number + * @param objRef + * OUT: Reference number of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * @param indx_order + * IN: Index order for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, + int[] ltype, long[] fno, long[] objRef, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException { - if (oname == null) { + if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_full(): name array is null"); } - if (otype == null) { + if (objTypes == null) { throw new NullPointerException("H5Gget_obj_info_full(): object type array is null"); } - if (oname.length == 0) { + if (objNames.length == 0) { throw new HDF5LibraryException("H5Gget_obj_info_full(): array size is zero"); } - if (oname.length != otype.length) { + if (objNames.length != objTypes.length) { throw new HDF5LibraryException("H5Gget_obj_info_full(): name and type array sizes are different"); } if (ltype == null) - ltype = new int[otype.length]; + ltype = new int[objTypes.length]; if (fno == null) - fno = new long[ref.length]; + fno = new long[objRef.length]; if (indx_type < 0) indx_type = HDF5Constants.H5_INDEX_NAME; @@ -3601,16 +5092,16 @@ public class H5 implements java.io.Serializable { if (indx_order < 0) indx_order = HDF5Constants.H5_ITER_INC; - log.trace("H5Gget_obj_info_full: oname_len={}", oname.length); - int status = H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, + log.trace("H5Gget_obj_info_full: objNames_len={}", objNames.length); + int status = H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, objRef, objNames.length, indx_type, indx_order); - for (int indx = 0; indx < oname.length; indx++) - log.trace("H5Gget_obj_info_full: oname={}", oname[indx]); + for (int indx = 0; indx < objNames.length; indx++) + log.trace("H5Gget_obj_info_full: objNames={}", objNames[indx]); return status; } - private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, - int[] ltype, long[] fno, long[] ref, int n, int indx_type, int indx_order) throws HDF5LibraryException, + private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, + int[] ltype, long[] fno, long[] objRef, int n, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException; /** @@ -3625,9 +5116,9 @@ public class H5 implements java.io.Serializable { * @param idx * IN: the index of the object to iterate. * @param oname - * the name of the object [OUT] + * OUT: the name of the object * @param type - * the type of the object [OUT] + * OUT: the type of the object * * @return non-negative if successful, -1 if not. * @@ -3828,13 +5319,40 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// + /** + * H5Iget_file_id obtains the file ID specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the file ID. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException; + /** + * H5Iget_name_long retrieves the name of an object specified by the identifier, obj_id. + * @deprecated + * + * @param obj_id + * IN: Identifier of the object. + * @param name + * OUT: Attribute name buffer. + * @param size + * IN: Maximum length of the name to retrieve. + * + * @return the length of the name retrieved. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ @Deprecated public synchronized static native long H5Iget_name_long(long obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException; /** - * H5Iget_name_str retrieves the name of an object specified by the identifier, obj_id. + * H5Iget_name retrieves the name of an object specified by the identifier, obj_id. * * @param obj_id * IN: Identifier of the object. @@ -3847,10 +5365,44 @@ public class H5 implements java.io.Serializable { public synchronized static native String H5Iget_name(long obj_id) throws HDF5LibraryException; + /** + * H5Iget_ref obtains the number of references outstanding specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Iget_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Idec_ref decrements the reference count specified by the identifier, obj_id. + * If the reference count for an ID reaches zero, the object will be closed. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Idec_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Iinc_ref increments the reference count specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Iinc_ref(long obj_id) throws HDF5LibraryException, NullPointerException; /** @@ -4944,11 +6496,13 @@ public class H5 implements java.io.Serializable { **/ public static long H5Oopen_by_addr(long loc_id, long addr) throws HDF5LibraryException { long id = _H5Oopen_by_addr(loc_id, addr); + if (id > 0) { log.trace("OPEN_IDS: H5Oopen_by_addr add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } + return id; } @@ -4981,7 +6535,7 @@ public class H5 implements java.io.Serializable { return id; } - public synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name, + private synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** @@ -5012,8 +6566,30 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException; + /** + * H5Odisable_mdc_flushes corks an object, keeping dirty entries associated with the object in the metadata cache. + * + * @param object_id + * IN: Identifier of the object to be corked. + **/ public synchronized static native void H5Odisable_mdc_flushes(long object_id); + /** + * H5Oenable_mdc_flushes uncorks an object, keeping dirty entries associated with the object in the metadata cache. + * + * @param object_id + * IN: Identifier of the object to be uncorked. + **/ public synchronized static native void H5Oenable_mdc_flushes(long object_id); + /** + * H5Oare_mdc_flushes_disabled retrieve the object's "cork" status. + * + * @param object_id + * IN: Identifier of the object to be flushed. + * + * @return the cork status + * TRUE if mdc flushes for the object is disabled + * FALSE if mdc flushes for the object is not disabled + **/ public synchronized static native boolean H5Oare_mdc_flushes_disabled(long object_id); // //////////////////////////////////////////////////////////// @@ -5160,6 +6736,7 @@ public class H5 implements java.io.Serializable { * IN: First property object to be compared * @param plid2 * IN: Second property object to be compared + * * @return positive value if equal; zero if unequal, a negative value if failed * * @exception HDF5LibraryException @@ -5167,6 +6744,19 @@ public class H5 implements java.io.Serializable { */ public synchronized static native int H5Pequal(long plid1, long plid2) throws HDF5LibraryException; + /** + * H5Pequal determines if two property lists or classes are equal + * + * @param plid1 + * IN: First property object to be compared + * @param plid2 + * IN: Second property object to be compared + * + * @return TRUE if equal, FALSE if unequal + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ public static boolean H5P_equal(long plid1, long plid2) throws HDF5LibraryException { if (H5Pequal(plid1, plid2) == 1) return true; @@ -5252,7 +6842,7 @@ public class H5 implements java.io.Serializable { return _H5Pclose_class(plid); } - public synchronized static native int _H5Pclose_class(long plid) throws HDF5LibraryException; + private synchronized static native int _H5Pclose_class(long plid) throws HDF5LibraryException; /** * H5Pclose terminates access to a property list. @@ -5299,6 +6889,40 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Pcopy(long plist) throws HDF5LibraryException; + // Define property list class callback function pointer types + // typedef herr_t (*H5P_cls_create_func_t)(hid_t prop_id, void *create_data); + // typedef herr_t (*H5P_cls_copy_func_t)(hid_t new_prop_id, hid_t old_prop_id, void *copy_data); + // typedef herr_t (*H5P_cls_close_func_t)(hid_t prop_id, void *close_data); + + // Define property list callback function pointer types + // typedef herr_t (*H5P_prp_cb1_t)(const char *name, size_t size, void *value); + // typedef herr_t (*H5P_prp_cb2_t)(hid_t prop_id, const char *name, size_t size, void *value); + // typedef H5P_prp_cb1_t H5P_prp_create_func_t; + // typedef H5P_prp_cb2_t H5P_prp_set_func_t; + // typedef H5P_prp_cb2_t H5P_prp_get_func_t; + // typedef herr_t (*H5P_prp_encode_func_t)(const void *value, void **buf, size_t *size); + // typedef herr_t (*H5P_prp_decode_func_t)(const void **buf, void *value); + // typedef H5P_prp_cb2_t H5P_prp_delete_func_t; + // typedef H5P_prp_cb1_t H5P_prp_copy_func_t; + // typedef int (*H5P_prp_compare_func_t)(const void *value1, const void *value2, size_t size); + // typedef H5P_prp_cb1_t H5P_prp_close_func_t; + + // Define property list iteration function type + // typedef herr_t (*H5P_iterate_t)(hid_t id, const char *name, void *iter_data); + + /** + * H5Pcreate_class_nocb creates an new property class with no callback functions. + * + * @param parent_class + * IN: Identifier of the parent property class. + * @param name + * IN: Name of the property class. + * + * @return a property list identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException { long id = _H5Pcreate_class_nocb(parent_class, name); if (id > 0) { @@ -5325,17 +6949,69 @@ public class H5 implements java.io.Serializable { // private synchronized static native long _H5Pcreate_class(long parent_class, String name, H5P_cls_create_func_cb create_op, H5P_cls_create_func_t create_data, // H5P_cls_copy_func_cb copy_op, H5P_cls_copy_func_t copy_data, H5P_cls_close_func_cb close_op, H5P_cls_close_func_t close_data) throws HDF5LibraryException; + /** + * H5Pregister2_nocb registers a property list with no callback functions. + * + * @param plist_class + * IN: Identifier of the property list. + * @param name + * IN: Name of the property. + * @param size + * IN: Size the property value. + * @param def_value + * IN: Defaul value of the property + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pregister2_nocb(long plist_class, String name, long size, byte[] def_value) throws HDF5LibraryException; // public synchronized static native void H5Pregister2(long plist_class, String name, long size, byte[] def_value, H5P_prp_create_func_cb prp_create, H5P_prp_set_func_cb prp_set, // H5P_prp_get_func_cb prp_get, H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; + /** + * H5Pinsert2_nocb inserts a property list with no callback functions. + * + * @param plist + * IN: Identifier of the property list. + * @param name + * IN: Name of the property. + * @param size + * IN: Size the property value. + * @param value + * IN: Defaul value of the property + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pinsert2_nocb(long plist, String name, long size, byte[] value) throws HDF5LibraryException; // public synchronized static native void H5Pinsert2(long plist, String name, long size, byte[] value, H5P_prp_set_func_cb prp_set, H5P_prp_get_func_cb prp_get, // H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; + /** + * H5Piterate iterates over the properties in a property list or class + * + * @param plist + * IN: ID of property object to iterate over + * @param idx + * IN/OUT: index of the property to begin with + * @param op + * IN: function to be called with each property iterated over. + * @param op_data + * IN: iteration data from user + * + * @return + * the return value of the last call to op if it was non-zero, + * zero if all properties have been processed + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - size is null. + * + **/ public synchronized static native int H5Piterate(long plist, int[] idx, H5P_iterate_cb op, H5P_iterate_t op_data) throws HDF5LibraryException; // /////// Object creation property list (OCPL) routines /////// @@ -5348,7 +7024,7 @@ public class H5 implements java.io.Serializable { * @param attributes * The maximun and minimum no. of attributes to be stored. * - * 
+     * 
      *      attributes[0] =  The maximum number of attributes to be stored in compact storage
      *      attributes[1] =  The minimum number of attributes to be stored in dense storage
      * 

@@ -5438,16 +7114,61 @@ public class H5 implements java.io.Serializable {
      * @param ocpl_id
      *            IN: Object creation property list identifier
      *
-     * @param track_times
-     *            IN: TRUE or FALSE, specifying whether object times are to be tracked
+     * @param track_times
+     *            IN: TRUE or FALSE, specifying whether object times are to be tracked
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native void H5Pset_obj_track_times(long ocpl_id, boolean track_times)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pmodify_filter modifies the specified FILTER in the transient or permanent output filter pipeline
+     *              depending on whether PLIST is a dataset creation or dataset
+     *              transfer property list.  The FLAGS argument specifies certain
+     *              general properties of the filter and is documented below.
+     *              The CD_VALUES is an array of CD_NELMTS integers which are
+     *              auxiliary data for the filter.  The integer vlues will be
+     *              stored in the dataset object header as part of the filter
+     *              information.
+     *

+     *              The FLAGS argument is a bit vector of the following fields:
+     *

+     *              H5Z_FLAG_OPTIONAL(0x0001)
+     *              If this bit is set then the filter is optional.  If the
+     *              filter fails during an H5Dwrite() operation then the filter
+     *              is just excluded from the pipeline for the chunk for which it
+     *              failed; the filter will not participate in the pipeline
+     *              during an H5Dread() of the chunk.  If this bit is clear and
+     *              the filter fails then the entire I/O operation fails.
+     *              If this bit is set but encoding is disabled for a filter,
+     *              attempting to write will generate an error.
+     *

+     * Note:        This function currently supports only the permanent filter
+     *              pipeline.  That is, PLIST_ID must be a dataset creation
+     *              property list.
+     *
+     * @param plist
+     *            IN: Property list identifier.
+     * @param filter
+     *            IN: Filter to be modified to the pipeline.
+     * @param flags
+     *            IN: Bit vector specifying certain general properties of the filter.
+     * @param cd_nelmts
+     *            IN: Number of elements in cd_values
+     * @param cd_values
+     *            IN: Auxiliary data for the filter.
+     *
+     * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - name or an array is null.
      *
      **/
-    public synchronized static native void H5Pset_obj_track_times(long ocpl_id, boolean track_times)
-            throws HDF5LibraryException;
-
     public synchronized static native int H5Pmodify_filter(long plist, long filter, int flags, long cd_nelmts,
             int[] cd_values) throws HDF5LibraryException, NullPointerException;
 
@@ -5619,9 +7340,37 @@ public class H5 implements java.io.Serializable {
                     throws HDF5LibraryException, NullPointerException;
 
 
+    /**
+     * H5Pall_filters_avail query to verify that all the filters set
+     *                      in the dataset creation property list are available currently.
+     *
+     * @param dcpl_id
+     *            IN: Property list identifier.
+     *
+     * @return
+     *            TRUE if all filters available
+     *            FALSE if one or more filters not currently available.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native boolean H5Pall_filters_avail(long dcpl_id) throws HDF5LibraryException,
     NullPointerException;
 
+    /**
+     * H5Premove_filter deletes a filter from the dataset creation property list;
+     *                  deletes all filters if filter is H5Z_FILTER_NONE
+     *
+     * @param obj_id
+     *            IN: Property list identifier.
+     * @param filter
+     *            IN: Filter identifier.
+     *
+     * @return a non-negative value and the size of the user block; if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native int H5Premove_filter(long obj_id, long filter) throws HDF5LibraryException;
 
     /**
@@ -5639,6 +7388,18 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native int H5Pset_deflate(long plist, int level) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_fletcher32 sets Fletcher32 checksum of EDC for a dataset creation
+     *                   property list or group creation property list.
+     *
+     * @param plist
+     *            IN: Property list identifier.
+     *
+     * @return a non-negative value and the size of the user block; if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException,
     NullPointerException;
 
@@ -6109,11 +7870,35 @@ public class H5 implements java.io.Serializable {
      */
     public synchronized static native long H5Pget_driver(long plid) throws HDF5LibraryException;
 
-    public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pget_family_offset gets offset for family driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return the offset.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException;
 
-    public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pset_family_offset sets the offset for family driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param offset
+     *            IN: the offset value
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException;
 
     /**
      * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes
@@ -6164,9 +7949,8 @@ public class H5 implements java.io.Serializable {
             double rdcc_w0) throws HDF5LibraryException;
 
     /**
-     * H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list and
-     * loads it into the instance of H5AC_cache_config_t pointed to by the config_ptr parameter. This configuration is
-     * used when the file is opened.
+     * H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list.
+     *                   This configuration is used when the file is opened.
      *
      * @param plist_id
      *            IN: Identifier of the file access property list.
@@ -6178,6 +7962,19 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native H5AC_cache_config_t H5Pget_mdc_config(long plist_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_mdc_config sets the initial metadata cache configuration contained in a file access property list and
+     * loads it into the instance of H5AC_cache_config_t pointed to by the config_ptr parameter. This configuration is
+     * used when the file is opened.
+     *
+     * @param plist_id
+     *            IN: Identifier of the file access property list.
+     * @param config_ptr
+     *            IN: H5AC_cache_config_t, the initial metadata cache configuration.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native void H5Pset_mdc_config(long plist_id, H5AC_cache_config_t config_ptr)
             throws HDF5LibraryException;
 
@@ -6212,10 +8009,35 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_gc_references(long fapl_id, boolean gc_ref)
             throws HDF5LibraryException;
 
-    public synchronized static native int H5Pget_fclose_degree(long plist_id) throws HDF5LibraryException,
+    /**
+     * H5Pget_fclose_degree returns the degree for the file close behavior for a file access
+     * property list.
+     *
+     * @param fapl_id
+     *            IN File access property list
+     *
+     * @return the degree for the file close behavior
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pget_fclose_degree(long fapl_id) throws HDF5LibraryException,
     NullPointerException;
 
-    public synchronized static native int H5Pset_fclose_degree(long plist, int degree) throws HDF5LibraryException,
+    /**
+     * H5Pset_fclose_degree sets the degree for the file close behavior.
+     *
+     * @param fapl_id
+     *            IN File access property list
+     * @param degree
+     *            IN the degree for the file close behavior
+     *
+     * @return non-negative if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pset_fclose_degree(long fapl_id, int degree) throws HDF5LibraryException,
     NullPointerException;
 
     /**
@@ -6246,8 +8068,40 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException;
 
+    /**
+     * H5Pget_sieve_buf_size retrieves the current settings for the data sieve buffer size
+     *      property from a file access property list.
+     *
+     * @param fapl_id
+     *            IN: Identifier for property list to query.
+     *
+     * @return a non-negative value and the size of the user block; if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_sieve_buf_size Sets the maximum size of the data seive buffer used for file
+     *      drivers which are capable of using data sieving.  The data sieve
+     *      buffer is used when performing I/O on datasets in the file.  Using a
+     *      buffer which is large anough to hold several pieces of the dataset
+     *      being read in for hyperslab selections boosts performance by quite a
+     *      bit.
+     * 

+     *      The default value is set to 64KB, indicating that file I/O for raw data
+     *      reads and writes will occur in at least 64KB blocks. Setting the value to 0
+     *      with this function will turn off the data sieving
+     *
+     * @param fapl_id
+     *            IN: Identifier of property list to modify.
+     * @param size
+     *            IN: maximum size of the data seive buffer.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native void H5Pset_sieve_buf_size(long fapl_id, long size) throws HDF5LibraryException;
 
     /**
@@ -6586,6 +8440,25 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_chunk(long plist, int ndims, byte[] dim) throws HDF5LibraryException,
     NullPointerException, IllegalArgumentException;
 
+    /**
+     * H5Pset_chunk sets the size of the chunks used to store a chunked layout dataset.
+     *
+     * @param plist
+     *            IN: Identifier for property list to query.
+     * @param ndims
+     *            IN: The number of dimensions of each chunk.
+     * @param dim
+     *            IN: An array containing the size of each chunk.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5Exception
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - dims array is null.
+     * @exception IllegalArgumentException
+     *                - dims <=0
+     **/
     public synchronized static int H5Pset_chunk(long plist, int ndims, long[] dim) throws HDF5Exception,
     NullPointerException, IllegalArgumentException {
         if (dim == null) {
@@ -6821,9 +8694,37 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native int H5Pget_external_count(long plist) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_szip Sets up the use of the szip filter.
+     *
+     * @param plist
+     *            IN: Dataset creation property list identifier.
+     * @param options_mask
+     *            IN: Bit vector specifying certain general properties of the filter.
+     * @param pixels_per_block
+     *            IN: Number of pixels in blocks
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_szip(long plist, int options_mask, int pixels_per_block)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_shuffle Sets up the use of the shuffle filter.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_shuffle(long plist_id) throws HDF5LibraryException,
     NullPointerException;
 
@@ -6951,20 +8852,91 @@ public class H5 implements java.io.Serializable {
         return retVal;
     }
 
+    /**
+     * H5Pset_fill_value checks if the fill value is defined for a dataset creation property list.
+     *
+     * @param plist_id
+     *            IN: Property list identifier.
+     * @param status
+     *            IN: The fill value setting:
+     *                H5D_FILL_VALUE_UNDEFINED
+     *                H5D_FILL_VALUE_DEFAULT
+     *                H5D_FILL_VALUE_USER_DEFINED
+     *                H5D_FILL_VALUE_ERROR
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5Exception
+     *                - Error converting data array
+     **/
     public synchronized static native int H5Pfill_value_defined(long plist_id, int[] status)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_alloc_time Gets space allocation time for dataset during creation.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param alloc_time
+     *            OUT: allocation time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pget_alloc_time(long plist_id, int[] alloc_time)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_alloc_time Sets space allocation time for dataset during creation.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param alloc_time
+     *            IN: allocation time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_alloc_time(long plist_id, int alloc_time) throws HDF5LibraryException,
     NullPointerException;
 
-    public synchronized static native int H5Pget_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pset_fill_time Gets fill value writing time.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param fill_time
+     *            OUT: fill time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pget_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException;
 
-    public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pset_fill_time Sets the fill value writing time.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param fill_time
+     *            IN: fill time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException;
 
     /**
      * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
@@ -7264,6 +9236,20 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pget_buffer(long plist, byte[] tconv, byte[] bkg)
             throws HDF5LibraryException, IllegalArgumentException;
 
+    /**
+     * H5Pget_buffer_size gets type conversion and background buffer size, in bytes, if successful;
+     * otherwise 0 on failure.
+     *
+     * @param plist
+     *            Identifier for the dataset transfer property list.
+     *
+     * @return buffer size, in bytes, if successful; otherwise 0 on failure
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception IllegalArgumentException
+     *                - plist is invalid.
+     **/
     public synchronized static native long H5Pget_buffer_size(long plist)
             throws HDF5LibraryException, IllegalArgumentException;
 
@@ -7291,14 +9277,36 @@ public class H5 implements java.io.Serializable {
      * @exception IllegalArgumentException
      *                - plist is invalid.
      **/
-    public synchronized static native void H5Pset_buffer_size(long plist, long size) throws HDF5LibraryException,
-    IllegalArgumentException;
-
-    public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException,
-    NullPointerException;
-
-    public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException,
-    NullPointerException;
+    public synchronized static native void H5Pset_buffer_size(long plist, long size) throws HDF5LibraryException,
+    IllegalArgumentException;
+
+    /**
+     * H5Pget_edc_check gets the error-detecting algorithm in use.
+     *
+     * @param plist
+     *            Identifier for the dataset transfer property list.
+     *
+     * @return the error-detecting algorithm
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException;
+
+    /**
+     * H5Pset_edc_check sets the error-detecting algorithm.
+     *
+     * @param plist
+     *            Identifier for the dataset transfer property list.
+     * @param check
+     *            the error-detecting algorithm to use.
+     *
+     * @return non-negative if succeed
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException;
 
     /**
      * H5Pget_btree_ratio Get the B-tree split ratios for a dataset transfer property list.
@@ -7343,9 +9351,46 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_btree_ratios(long plist_id, double left, double middle, double right)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pget_hyper_vector_size reads values previously set with H5Pset_hyper_vector_size.
+     *
+     * @param dxpl_id
+     *            IN: Dataset transfer property list identifier.
+     * @param vector_size
+     *            OUT:  hyper vector size.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pget_hyper_vector_size(long dxpl_id, long[] vector_size)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_hyper_vector_size sets the number of
+     *              "I/O vectors" (offset and length pairs) which are to be
+     *              accumulated in memory before being issued to the lower levels
+     *              of the library for reading or writing the actual data.
+     *              Increasing the number should give better performance, but use
+     *              more memory during hyperslab I/O.  The vector size must be
+     *              greater than 1.
+     *,p.
+     *              The default is to use 1024 vectors for I/O during hyperslab
+     *              reading/writing.
+     *
+     * @param dxpl_id
+     *            IN: Dataset transfer property list identifier.
+     * @param vector_size
+     *            IN: hyper vestor size.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_hyper_vector_size(long dxpl_id, long vector_size)
             throws HDF5LibraryException, NullPointerException;
 
@@ -7543,8 +9588,32 @@ public class H5 implements java.io.Serializable {
 
     // /////// String creation property list (STRCPL) routines ///////
 
+    /**
+     * H5Pget_char_encoding gets the character encoding of the string.
+     *
+     * @param plist_id
+     *            IN: the property list identifier
+     *
+     * @return Returns the character encoding of the string.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_char_encoding sets the character encoding of the string.
+     *
+     * @param plist_id
+     *            IN: the property list identifier
+     * @param encoding
+     *            IN: the character encoding of the string
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding)
             throws HDF5LibraryException;
 
@@ -7732,7 +9801,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options)
             throws HDF5LibraryException;
 
-    // /////// Other/Older property list routines ///////
+    // /////// file drivers property list routines ///////
 
     /**
      * H5Pget_version retrieves the version information of various objects for a file creation property list.
@@ -7759,25 +9828,57 @@ public class H5 implements java.io.Serializable {
      *
      * @deprecated As of HDF5 1.10.0 in favor of H5Fget_info.
      **/
+    @Deprecated
     public synchronized static native int H5Pget_version(long plist, int[] version_info) throws HDF5LibraryException,
     NullPointerException, IllegalArgumentException;
 
     // /////// file drivers property list routines ///////
 
+    /**
+     * H5Pget_fapl_core retrieve H5FD_CORE I/O settings.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param increment
+     *            OUT: how much to grow the memory each time
+     * @param backing_store
+     *            OUT: write to file name on flush setting
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_core modifies the file access property list to use the H5FD_CORE driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param increment
+     *            IN: how much to grow the memory each time
+     * @param backing_store
+     *            IN: write to file name on flush setting
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_core(long fapl_id, long increment, boolean backing_store)
             throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Pget_fapl_direct Retrieve direct I/O settings.
+     * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_direct.
      *
      * @param fapl_id
      *            IN: File access property list identifier
      * @param info
-     *            OUT: Returned property list information info[0] = alignment Required memory alignment boundary info[1]
-     *            = block_size File system block size info[2] = cbuf_size Copy buffer size
+     *            OUT: Returned property list information
+     *                 info[0] = increment -how much to grow the memory each time
+     *                 info[1] = backing_store - write to file name on flush setting
      *
      * @return a non-negative value if successful; otherwise returns a negative value.
      *
@@ -7808,14 +9909,72 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_fapl_direct(long fapl_id, long alignment, long block_size,
             long cbuf_size) throws HDF5LibraryException;
 
+    /**
+     * H5Pget_fapl_family Returns information about the family file access property list.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param memb_size
+     *            OUT: the size in bytes of each file member (used only when creating a new file)
+     * @param memb_fapl_id
+     *            OUT: the file access property list to be used for each family member
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pget_fapl_family(long fapl_id, long[] memb_size, long[] memb_fapl_id)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_family Sets up use of the direct I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param memb_size
+     *            IN: the size in bytes of each file member (used only when creating a new file)
+     * @param memb_fapl_id
+     *            IN: the file access property list to be used for each family member
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_family(long fapl_id, long memb_size, long memb_fapl_id)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_hdfs Modify the file access property list to use the H5FD_HDFS driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param fapl_conf
+     *            IN: the properties of the hdfs driver
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_hdfs(long fapl_id, H5FD_hdfs_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pget_fapl_hdfs gets the properties hdfs I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return the properties of the hdfs driver.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native H5FD_hdfs_fapl_t H5Pget_fapl_hdfs(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
     /**
@@ -7893,17 +10052,99 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_fapl_log(long fapl_id, String logfile, long flags, long buf_size)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_sec2 Sets up use of the sec2 I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_sec2(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_split Sets up use of the split I/O driver. Makes the multi driver act like the
+     *        old split driver which stored meta data in one file and raw
+     *        data in another file
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param meta_ext
+     *            IN: meta filename extension
+     * @param meta_plist_id
+     *            IN: File access property list identifier for metadata
+     * @param raw_ext
+     *            IN: raw data filename extension
+     * @param raw_plist_id
+     *            IN: File access property list identifier raw data
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native void H5Pset_fapl_split(long fapl_id, String meta_ext, long meta_plist_id,
             String raw_ext, long raw_plist_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_stdio Sets up use of the stdio I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_stdio(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_windows Sets up use of the windows I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_windows(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_ros3 Modify the file access property list to use the H5FD_ROS3 driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param fapl_conf
+     *            IN: the properties of the ros3 driver
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_ros3(long fapl_id, H5FD_ros3_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pget_fapl_ros3 gets the properties of the ros3 I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return the properties of the ros3 driver.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
     // /////// unimplemented ////////
@@ -8286,29 +10527,109 @@ public class H5 implements java.io.Serializable {
     // //
     // ////////////////////////////////////////////////////////////
 
+    /**************** Operations on dataspaces ********************/
+
     /**
-     * H5Sclose releases a dataspace.
+     * H5Screate creates a new dataspace of a particular type.
+     *
+     * @param type
+     *            IN: The type of dataspace to be created.
+     *
+     * @return a dataspace identifier
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public static long H5Screate(int type) throws HDF5LibraryException {
+        long id = _H5Screate(type);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Screate add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Screate(int type) throws HDF5LibraryException;
+
+    /**
+     * H5Screate_simple creates a new simple data space and opens it for access.
+     *
+     * @param rank
+     *            IN: Number of dimensions of dataspace.
+     * @param dims
+     *            IN: An array of the size of each dimension.
+     * @param maxdims
+     *            IN: An array of the maximum size of each dimension.
+     *
+     * @return a dataspace identifier
+     *
+     * @exception HDF5Exception
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - dims or maxdims is null.
+     **/
+    public static long H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception,
+            NullPointerException {
+        long id = _H5Screate_simple(rank, dims, maxdims);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Screate_simple add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Screate_simple(int rank, long[] dims, long[] maxdims)
+            throws HDF5Exception, NullPointerException;
+
+    /**
+     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
      *
      * @param space_id
-     *            Identifier of dataspace to release.
+     *            Dataspace identifier.
+     * @param rank
+     *            Rank, or dimensionality, of the dataspace.
+     * @param current_size
+     *            Array containing current size of dataspace.
+     * @param maximum_size
+     *            Array containing maximum size of dataspace.
+     *
+     * @return a dataspace identifier if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size,
+            long[] maximum_size) throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
+     *
+     * @param space_id
+     *            Dataspace identifier.
+     * @param rank
+     *            Rank, or dimensionality, of the dataspace.
+     * @param current_size
+     *            Array containing current size of dataspace.
+     * @param maximum_size
+     *            Array containing maximum size of dataspace.
      *
-     * @return a non-negative value if successful
+     * @return a dataspace identifier if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public static int H5Sclose(long space_id) throws HDF5LibraryException {
-        if (space_id < 0)
-            return 0; // throw new HDF5LibraryException("Negative ID");;
+    public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size,
+            byte[] maximum_size) throws HDF5LibraryException, NullPointerException {
+        ByteBuffer csbb = ByteBuffer.wrap(current_size);
+        long[] lacs = (csbb.asLongBuffer()).array();
+        ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size);
+        long[] lamaxs = (maxsbb.asLongBuffer()).array();
 
-        log.trace("OPEN_IDS: H5Sclose remove {}", space_id);
-        OPEN_IDS.remove(space_id);
-        log.trace("OPEN_IDS: {}", OPEN_IDS.size());
-        return _H5Sclose(space_id);
+        return H5Sset_extent_simple(space_id, rank, lacs, lamaxs);
     }
 
-    private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException;
-
     /**
      * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id.
      *
@@ -8332,58 +10653,40 @@ public class H5 implements java.io.Serializable {
     private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Screate creates a new dataspace of a particular type.
+     * H5Sclose releases a dataspace.
      *
-     * @param type
-     *            IN: The type of dataspace to be created.
+     * @param space_id
+     *            Identifier of dataspace to release.
      *
-     * @return a dataspace identifier
+     * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public static long H5Screate(int type) throws HDF5LibraryException {
-        long id = _H5Screate(type);
-        if (id > 0) {
-            log.trace("OPEN_IDS: H5Screate add {}", id);
-            OPEN_IDS.add(id);
-            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
-        }
-        return id;
+    public static int H5Sclose(long space_id) throws HDF5LibraryException {
+        if (space_id < 0)
+            return 0; // throw new HDF5LibraryException("Negative ID");;
+
+        log.trace("OPEN_IDS: H5Sclose remove {}", space_id);
+        OPEN_IDS.remove(space_id);
+        log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        return _H5Sclose(space_id);
     }
 
-    private synchronized static native long _H5Screate(int type) throws HDF5LibraryException;
+    private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Screate_simple creates a new simple data space and opens it for access.
+     * H5Sencode converts a data space description into binary form in a buffer.
      *
-     * @param rank
-     *            IN: Number of dimensions of dataspace.
-     * @param dims
-     *            IN: An array of the size of each dimension.
-     * @param maxdims
-     *            IN: An array of the maximum size of each dimension.
+     * @param obj_id
+     *            IN: Identifier of the object to be encoded.
      *
-     * @return a dataspace identifier
+     * @return the buffer for the object to be encoded into.
      *
-     * @exception HDF5Exception
+     * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     * @exception NullPointerException
-     *                - dims or maxdims is null.
      **/
-    public static long H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception,
-            NullPointerException {
-        long id = _H5Screate_simple(rank, dims, maxdims);
-        if (id > 0) {
-            log.trace("OPEN_IDS: H5Screate_simple add {}", id);
-            OPEN_IDS.add(id);
-            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
-        }
-        return id;
-    }
-
-    private synchronized static native long _H5Screate_simple(int rank, long[] dims, long[] maxdims)
-            throws HDF5Exception, NullPointerException;
+    public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException;
 
     /**
      * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it.
@@ -8401,154 +10704,137 @@ public class H5 implements java.io.Serializable {
     public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sencode converts a data space description into binary form in a buffer.
+     * H5Sget_simple_extent_npoints determines the number of elements in a dataspace.
      *
-     * @param obj_id
-     *            IN: Identifier of the object to be encoded.
+     * @param space_id
+     *            ID of the dataspace object to query
+     * @return the number of elements in the dataspace if successful
      *
-     * @return the buffer for the object to be encoded into.
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException;
+
+    /**
+     * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace.
+     *
+     * @param space_id
+     *            IN: Identifier of the dataspace
+     *
+     * @return the number of dimensions in the dataspace if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException;
+    public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the
-     * dataspace.
+     * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims
+     * and maxdims parameters.
      *
-     * @param dest_space_id
-     *            IN: The identifier for the dataspace from which the extent is copied.
-     * @param source_space_id
-     *            IN: The identifier for the dataspace to which the extent is copied.
+     * @param space_id
+     *            IN: Identifier of the dataspace object to query
+     * @param dims
+     *            OUT: Pointer to array to store the size of each dimension.
+     * @param maxdims
+     *            OUT: Pointer to array to store the maximum size of each dimension.
      *
-     * @return a non-negative value if successful
+     * @return the number of dimensions in the dataspace if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - dims or maxdims is null.
      **/
-    public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id)
-            throws HDF5LibraryException;
+    public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims)
+            throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal.
+     * H5Sis_simple determines whether a dataspace is a simple dataspace.
      *
-     * @param first_space_id
-     *            IN: The identifier for the first dataspace.
-     * @param second_space_id
-     *            IN: The identifier for the seconddataspace.
+     * @param space_id
+     *            Identifier of the dataspace to query
      *
-     * @return true if successful, else false
+     * @return true if is a simple dataspace
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id)
-            throws HDF5LibraryException;
+    public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places
-     * them into user-supplied buffers.
-     * 

-     * The start and end buffers must be large enough to hold the dataspace rank number of coordinates.
+     * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
-     * @param start
-     *            coordinates of lowest corner of bounding box.
-     * @param end
-     *            coordinates of highest corner of bounding box.
+     * @param space_id
+     *            Dataspace identifier.
      *
-     * @return a non-negative value if successful,with start and end initialized.
+     * @return a dataspace class name if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     * @exception NullPointerException
-     *                - start or end is null.
      **/
-    public synchronized static native int H5Sget_select_bounds(long spaceid, long[] start, long[] end)
-            throws HDF5LibraryException, NullPointerException;
+    public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection.
+     * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
+     * @param space_id
+     *            The identifier for the dataspace from which the extent is to be removed.
      *
      * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException;
+    public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point
-     * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per
-     * point.
+     * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the
+     * dataspace.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
-     * @param startpoint
-     *            first point to retrieve
-     * @param numpoints
-     *            number of points to retrieve
-     * @param buf
-     *            returns points startblock to startblock+num-1, each points is rank longs.
+     * @param dest_space_id
+     *            IN: The identifier for the dataspace from which the extent is copied.
+     * @param source_space_id
+     *            IN: The identifier for the dataspace to which the extent is copied.
      *
      * @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 H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints,
-            long[] buf) throws HDF5LibraryException, NullPointerException;
+    public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id)
+            throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same
-     * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows:
-     *
-     * 
-     *    <"start" coordinate>, immediately followed by
-     *    <"opposite" corner coordinate>, followed by
-     *   the next "start" and "opposite" coordinates,
-     *   etc.
-     *   until all of the selected blocks have been listed.
-     * 

+     * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
-     * @param startblock
-     *            first block to retrieve
-     * @param numblocks
-     *            number of blocks to retrieve
-     * @param buf
-     *            returns blocks startblock to startblock+num-1, each block is rank * 2 (corners) longs.
+     * @param first_space_id
+     *            IN: The identifier for the first dataspace.
+     * @param second_space_id
+     *            IN: The identifier for the seconddataspace.
      *
-     * @return a non-negative value if successful
+     * @return true if successful, else false
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     * @exception NullPointerException
-     *                - buf is null.
      **/
-    public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks,
-            long[] buf) throws HDF5LibraryException, NullPointerException;
+    public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id)
+            throws HDF5LibraryException;
+
+    /***************** Operations on dataspace selections *****************/
 
     /**
-     * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection.
+     * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
+     * @param space_id
+     *            IN: Identifier of the dataspace object to query
      *
-     * @return a non-negative value if successful
+     * @return the dataspace selection type if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException;
+    public synchronized static native int H5Sget_select_type(long space_id) throws HDF5LibraryException;
 
     /**
      * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace.
@@ -8564,89 +10850,123 @@ public class H5 implements java.io.Serializable {
     public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id.
+     * H5Sselect_copy copies all the selection information (including offset) from the source
+     * dataspace to the destination dataspace.
+     * @param dst_id              ID of the destination dataspace
+     * @param src_id              ID of the source dataspace
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Sselect_copy(long dst_id, long src_id) throws HDF5LibraryException;
+
+    /**
+     * H5Sselect_valid verifies that the selection for the dataspace.
      *
      * @param space_id
-     *            IN: Identifier of the dataspace object to query
+     *            The identifier for the dataspace in which the selection is being reset.
      *
-     * @return the dataspace selection type if successful
+     * @return true if the selection is contained within the extent and FALSE if it is not or is an error.
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native int H5Sget_select_type(long space_id) throws HDF5LibraryException;
+    public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims
-     * and maxdims parameters.
+     * H5Sselect_adjust moves a selection by subtracting an offset from it.
      *
      * @param space_id
-     *            IN: Identifier of the dataspace object to query
-     * @param dims
-     *            OUT: Pointer to array to store the size of each dimension.
-     * @param maxdims
-     *            OUT: Pointer to array to store the maximum size of each dimension.
-     *
-     * @return the number of dimensions in the dataspace if successful
+     *            ID of dataspace to adjust
+     * @param offset
+     *            Offset to subtract
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      * @exception NullPointerException
-     *                - dims or maxdims is null.
+     *                - offset is null.
      **/
-    public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims)
-            throws HDF5LibraryException, NullPointerException;
+     public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset)
+             throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace.
+     * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places
+     * them into user-supplied buffers.
+     * 

+     * The start and end buffers must be large enough to hold the dataspace rank number of coordinates.
      *
      * @param space_id
-     *            IN: Identifier of the dataspace
+     *            Identifier of dataspace to release.
+     * @param start
+     *            coordinates of lowest corner of bounding box.
+     * @param end
+     *            coordinates of highest corner of bounding box.
      *
-     * @return the number of dimensions in the dataspace if successful
+     * @return a non-negative value if successful,with start and end initialized.
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - start or end is null.
      **/
-    public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException;
+    public synchronized static native int H5Sget_select_bounds(long space_id, long[] start, long[] end)
+            throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sget_simple_extent_npoints determines the number of elements in a dataspace.
+     * H5Sselect_shape_same checks to see if the current selection in the dataspaces are the same
+     * dimensionality and shape.
+     * This is primarily used for reading the entire selection in one swoop.
      *
-     * @param space_id
-     *            ID of the dataspace object to query
-     * @return the number of elements in the dataspace if successful
+     * @param   space1_id         ID of 1st Dataspace pointer to compare
+     * @param   space2_id         ID of 2nd Dataspace pointer to compare
+     *
+     * @return true if the selection is the same dimensionality and shape;
+     *         false otherwise
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException;
+    public synchronized static native boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace.
+     * H5Sselect_intersect_block checks to see if the current selection in the
+     * dataspace intersects with the block given.
      *
      * @param space_id
-     *            Dataspace identifier.
+     *             ID of dataspace pointer to compare
+     * @param start
+     *             Starting coordinate of block
+     * @param end
+     *             Opposite ("ending") coordinate of block
      *
-     * @return a dataspace class name if successful
+     * @return a TRUE  if the current selection in the dataspace intersects with the block given
+     *           FALSE otherwise
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - offset is null.
      **/
-    public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException;
+     public synchronized static native boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end)
+             throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sis_simple determines whether a dataspace is a simple dataspace.
+     * H5Soffset_simple sets the offset of a simple dataspace space_id.
      *
      * @param space_id
-     *            Identifier of the dataspace to query
+     *            IN: The identifier for the dataspace object to reset.
+     * @param offset
+     *            IN: The offset at which to position the selection.
      *
-     * @return true if is a simple dataspace
+     * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - offset array is null.
      **/
-    public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException;
+    public synchronized static native int H5Soffset_simple(long space_id, byte[] offset) throws HDF5LibraryException,
+            NullPointerException;
 
     /**
      * H5Soffset_simple sets the offset of a simple dataspace space_id.
@@ -8663,9 +10983,6 @@ public class H5 implements java.io.Serializable {
      * @exception NullPointerException
      *                - offset array is null.
      **/
-    public synchronized static native int H5Soffset_simple(long space_id, byte[] offset) throws HDF5LibraryException,
-            NullPointerException;
-
     public synchronized static int H5Soffset_simple(long space_id, long[] offset) throws HDF5Exception,
             NullPointerException {
         if (offset == null) {
@@ -8696,6 +11013,18 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Sselect_all(long space_id) throws HDF5LibraryException;
 
     /**
+     * H5Sselect_none resets the selection region for the dataspace space_id to include no elements.
+     *
+     * @param space_id
+     *            IN: The identifier of the dataspace to be reset.
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException;
+
+    /**
      * H5Sselect_elements selects array elements to be included in the selection for the space_id dataspace.
      *
      * @param space_id
@@ -8753,6 +11082,43 @@ public class H5 implements java.io.Serializable {
     }
 
     /**
+     * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection.
+     *
+     * @param spaceid
+     *            Identifier of dataspace to release.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException;
+
+    /**
+     * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point
+     * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per
+     * point.
+     *
+     * @param spaceid
+     *            Identifier of dataspace to release.
+     * @param startpoint
+     *            first point to retrieve
+     * @param numpoints
+     *            number of points to retrieve
+     * @param buf
+     *            returns points startblock to startblock+num-1, each points is rank longs.
+     *
+     * @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 H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints,
+            long[] buf) throws HDF5LibraryException, NullPointerException;
+
+    /**
      * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified
      * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace.
      *
@@ -8792,76 +11158,118 @@ public class H5 implements java.io.Serializable {
         return H5Sselect_hyperslab(space_id, op, lastart, lastride, lacount, lablock);
     }
 
-    public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride,
-            long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
-
     /**
-     * H5Sselect_none resets the selection region for the dataspace space_id to include no elements.
+     * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified
+     * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace.
      *
      * @param space_id
-     *            IN: The identifier of the dataspace to be reset.
+     *            IN: Identifier of dataspace selection to modify
+     * @param op
+     *            IN: Operation to perform on current selection.
+     * @param start
+     *            IN: Offset of start of hyperslab
+     * @param stride
+     *            IN: Hyperslab stride.
+     * @param count
+     *            IN: Number of blocks included in hyperslab.
+     * @param block
+     *            IN: Size of block in hyperslab.
+     *
      * @return a non-negative value 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 int H5Sselect_none(long space_id) throws HDF5LibraryException;
+    public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride,
+            long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
 
     /**
-     * H5Sselect_valid verifies that the selection for the dataspace.
+     * H5Scombine_hyperslab combines a hyperslab selection with the current selection for a dataspace,
+     * creating a new dataspace to return the generated selection.
+     * If the current selection is not a hyperslab, it is freed and the hyperslab
+     * parameters passed in are combined with the H5S_SEL_ALL hyperslab (ie. a
+     * selection composing the entire current extent).  If STRIDE or BLOCK is
+     * NULL, they are assumed to be set to all '1'.
      *
      * @param space_id
-     *            The identifier for the dataspace in which the selection is being reset.
+     *            IN: Dataspace ID of selection to use
+     * @param op
+     *            IN: Operation to perform on current selection.
+     * @param start
+     *            IN: Offset of start of hyperslab
+     * @param stride
+     *            IN: Hyperslab stride.
+     * @param count
+     *            IN: Number of blocks included in hyperslab.
+     * @param block
+     *            IN: Size of block in hyperslab.
      *
-     * @return true if the selection is contained within the extent and FALSE if it is not or is an error.
+     * @return a dataspace ID on success / H5I_INVALID_HID on failure
+     *
+     * @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 H5Scombine_hyperslab(long space_id, int op, long[] start, long[] stride,
+            long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+    /**
+     * H5Smodify_select refine an existing hyperslab selection with an operation, using a second
+     * hyperslab.  The first selection is modified to contain the result of
+     * space1 operated on by space2.
+     *
+     * @param space1_id
+     *               ID of the destination dataspace
+     * @param op
+     *               Operation to perform on current selection.
+     * @param space2_id
+     *               ID of the source dataspace
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException;
+    public synchronized static native void H5Smodify_select(long space1_id, int op, long space2_id) throws HDF5LibraryException;
 
     /**
-     * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE.
+     * H5Scombine_select combines two existing hyperslab selections with an operation, returning
+     * a new dataspace with the resulting selection.  The dataspace extent from
+     * space1 is copied for the dataspace extent of the newly created dataspace.
      *
-     * @param space_id
-     *            The identifier for the dataspace from which the extent is to be removed.
+     * @param space1_id
+     *               ID of the first dataspace
+     * @param op
+     *               Operation to perform on current selection.
+     * @param space2_id
+     *               ID of the second dataspace
      *
-     * @return a non-negative value if successful
+     * @return a dataspace ID on success / H5I_INVALID_HID on failure
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException;
+    public synchronized static native long H5Scombine_select(long space1_id, int op, long space2_id) throws HDF5LibraryException;
 
     /**
-     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
+     * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified
+     * by space_id.
      *
      * @param space_id
-     *            Dataspace identifier.
-     * @param rank
-     *            Rank, or dimensionality, of the dataspace.
-     * @param current_size
-     *            Array containing current size of dataspace.
-     * @param maximum_size
-     *            Array containing maximum size of dataspace.
+     *            IN: Identifier of dataspace selection to query
      *
-     * @return a dataspace identifier if successful
+     * @return a TRUE/FALSE for hyperslab selection if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size,
-            long[] maximum_size) throws HDF5LibraryException, NullPointerException;
-
-    public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size,
-            byte[] maximum_size) throws HDF5LibraryException, NullPointerException {
-        ByteBuffer csbb = ByteBuffer.wrap(current_size);
-        long[] lacs = (csbb.asLongBuffer()).array();
-        ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size);
-        long[] lamaxs = (maxsbb.asLongBuffer()).array();
-
-        return H5Sset_extent_simple(space_id, rank, lacs, lamaxs);
-    }
+     public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException;
 
     /**
      * H5Sget_regular_hyperslab determines if a hyperslab selection is regular for the dataspace specified
@@ -8887,32 +11295,71 @@ public class H5 implements java.io.Serializable {
      **/
      public synchronized static native void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
+     /**
+      * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection.
+      *
+      * @param spaceid
+      *            Identifier of dataspace to release.
+      *
+      * @return a non-negative value if successful
+      *
+      * @exception HDF5LibraryException
+      *                - Error from the HDF-5 Library.
+      **/
+     public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException;
+
     /**
-     * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified
-     * by space_id.
+     * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same
+     * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows:
      *
-     * @param space_id
-     *            IN: Identifier of dataspace selection to query
+     * 
+     *    <"start" coordinate>, immediately followed by
+     *    <"opposite" corner coordinate>, followed by
+     *   the next "start" and "opposite" coordinates,
+     *   etc.
+     *   until all of the selected blocks have been listed.
+     * 

      *
-     * @return a TRUE/FALSE for hyperslab selection if successful
+     * @param spaceid
+     *            Identifier of dataspace to release.
+     * @param startblock
+     *            first block to retrieve
+     * @param numblocks
+     *            number of blocks to retrieve
+     * @param buf
+     *            returns blocks startblock to startblock+num-1, each block is rank * 2 (corners) longs.
+     *
+     * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - buf is null.
      **/
-     public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException;
+    public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks,
+            long[] buf) throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Sselect_project_intersection projects the intersection of the selections of src_space_id and
+     * src_intersect_space_id within the selection of src_space_id as a
+     * selection within the selection of dst_space_id.
+     *
+     * @param src_space_id
+     *          Selection that is mapped to dst_space_id, and intersected with src_intersect_space_id
+     * @param dst_space_id
+     *          Selection that is mapped to src_space_id
+     * @param src_intersect_space_id
+     *          Selection whose intersection with src_space_id is projected to dst_space_id to obtain the result
+     *
+     * @return a dataspace with a selection equal to the intersection of
+     *         src_intersect_space_id and src_space_id projected from src_space to dst_space on success
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Sselect_project_intersection(long src_space_id, long dst_space_id,
+            long src_intersect_space_id) throws HDF5LibraryException;
 
-    // /////// unimplemented ////////
-    // #ifdef NEW_HYPERSLAB_API
-    //  hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
-    //                                  const hsize_t start[],
-    //                                  const hsize_t _stride[],
-    //                                  const hsize_t count[],
-    //                                  const hsize_t _block[]);
-    // herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
-    //                                  hid_t space2_id);
-    // hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
-    //                                  hid_t space2_id);
-    // #endif /* NEW_HYPERSLAB_API */
 
 
 
@@ -9260,6 +11707,23 @@ public class H5 implements java.io.Serializable {
         return H5Tenum_insert_int(type, name, value);
     }
 
+    /**
+     * H5Tenum_insert inserts a new enumeration datatype member into an enumeration datatype.
+     *
+     * @param type
+     *            IN: Identifier of datatype.
+     * @param name
+     *            IN: The name of the member
+     * @param value
+     *            IN: The value of the member, data of the correct type
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - name is null.
+     **/
     public static int H5Tenum_insert(long type, String name, int value) throws HDF5LibraryException,
             NullPointerException {
         int[] val = { value };
@@ -10395,11 +12859,44 @@ public class H5 implements java.io.Serializable {
     // //
     // ////////////////////////////////////////////////////////////
 
-    public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException, NullPointerException;
+    /**
+     * H5Zfilter_avail checks if a filter is available.
+     *
+     * @param filter
+     *            IN: filter number.
+     *
+     * @return a non-negative(TRUE/FALSE) value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException;
 
+    /**
+     * H5Zget_filter_info gets information about a pipeline data filter.
+     *
+     * @param filter
+     *            IN: filter number.
+     *
+     * @return the filter information flags
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native int H5Zget_filter_info(int filter) throws HDF5LibraryException;
 
-    public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException;
+    /**
+     * H5Zunregister unregisters a filter.
+     *
+     * @param filter
+     *            IN: filter number.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException;
 
     // /////// unimplemented ////////
 
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 3f8e5d1..42b103d 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -35,10 +35,15 @@ public class HDF5Constants {
 
     public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX();
 
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_MAX_PIXELS_PER_BLOCK = H5_SZIP_MAX_PIXELS_PER_BLOCK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_NN_OPTION_MASK = H5_SZIP_NN_OPTION_MASK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_EC_OPTION_MASK = H5_SZIP_EC_OPTION_MASK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_ALLOW_K13_OPTION_MASK = H5_SZIP_ALLOW_K13_OPTION_MASK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_CHIP_OPTION_MASK = H5_SZIP_CHIP_OPTION_MASK();
     public static final int H5_INDEX_UNKNOWN = H5_INDEX_UNKNOWN();
     public static final int H5_INDEX_NAME = H5_INDEX_NAME();
@@ -90,108 +95,353 @@ public class HDF5Constants {
     public static final int H5D_VDS_LAST_AVAILABLE = H5D_VDS_LAST_AVAILABLE();
     public static final int H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS = H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS();
 
+    /** Different kinds of error information - H5E_type_t */
     public static final int H5E_MAJOR = H5E_MAJOR();
+    /** Different kinds of error information - H5E_type_t */
     public static final int H5E_MINOR = H5E_MINOR();
+    /** Minor error codes - Object header related errors - Alignment error */
     public static final long H5E_ALIGNMENT = H5E_ALIGNMENT();
+    /** Minor error codes - Resource errors - Object already exists */
     public static final long H5E_ALREADYEXISTS = H5E_ALREADYEXISTS();
+    /** Minor error codes - Function entry/exit interface - Object already initialized */
     public static final long H5E_ALREADYINIT = H5E_ALREADYINIT();
+    /** Major error codes - Invalid arguments to routine */
     public static final long H5E_ARGS = H5E_ARGS();
+    /** Major error codes - Object atom */
     public static final long H5E_ATOM = H5E_ATOM();
+    /** Major error codes - Attribute */
     public static final long H5E_ATTR = H5E_ATTR();
+    /** Minor error codes - Object atom related errors - Unable to find atom information (already closed?) */
     public static final long H5E_BADATOM = H5E_BADATOM();
+    /** Minor error codes - File accessibility errors - Bad file ID accessed */
     public static final long H5E_BADFILE = H5E_BADFILE();
+    /** Minor error codes - Object atom related errors - Unable to find ID group information */
     public static final long H5E_BADGROUP = H5E_BADGROUP();
+    /** Minor error codes - Object header related errors - Iteration failed */
+    public static final long H5E_BADITER = H5E_BADITER();
+    /** Minor error codes - Object header related errors - Unrecognized message */
     public static final long H5E_BADMESG = H5E_BADMESG();
+    /** Minor error codes - Argument errors - Out of range */
     public static final long H5E_BADRANGE = H5E_BADRANGE();
+    /** Minor error codes - Dataspace errors - Invalid selection */
     public static final long H5E_BADSELECT = H5E_BADSELECT();
+    /** Datatype conversion errors - Bad size for object */
     public static final long H5E_BADSIZE = H5E_BADSIZE();
+    /** Minor error codes - Argument errors - Inappropriate type */
     public static final long H5E_BADTYPE = H5E_BADTYPE();
+    /** Minor error codes - Argument errors - Bad value */
     public static final long H5E_BADVALUE = H5E_BADVALUE();
+    /** Major error codes - B-Tree node */
     public static final long H5E_BTREE = H5E_BTREE();
+    /** Major error codes - Object cache */
     public static final long H5E_CACHE = H5E_CACHE();
+    /** I/O pipeline errors - Callback failed */
     public static final long H5E_CALLBACK = H5E_CALLBACK();
+    /** I/O pipeline errors - Error from filter 'can apply' callback */
     public static final long H5E_CANAPPLY = H5E_CANAPPLY();
-    // public static final long H5E_CANTALLOC = H5E_CANTALLOC();
+    /** Minor error codes - Resource errors - Can't allocate space */
+    public static final long H5E_CANTALLOC = H5E_CANTALLOC();
+    /** Minor error codes - Dataspace errors - Can't append object */
+    public static final long H5E_CANTAPPEND = H5E_CANTAPPEND();
+    /** Minor error codes - Heap errors - Can't attach object */
+    public static final long H5E_CANTATTACH = H5E_CANTATTACH();
+    /** Minor error codes - Cache related errors - Unable to mark metadata as clean */
+    public static final long H5E_CANTCLEAN = H5E_CANTCLEAN();
+    /** Minor error codes - Dataspace errors - Can't clip hyperslab region */
     public static final long H5E_CANTCLIP = H5E_CANTCLIP();
+    /** Minor error codes - File accessibility errors - Unable to close file */
     public static final long H5E_CANTCLOSEFILE = H5E_CANTCLOSEFILE();
+    /** Minor error codes - Group related errors - Can't close object */
+    public static final long H5E_CANTCLOSEOBJ = H5E_CANTCLOSEOBJ();
+    /** Minor error codes - Dataspace errors - Can't compare objects */
+    public static final long H5E_CANTCOMPARE = H5E_CANTCOMPARE();
+    /** Minor error codes - Heap errors - Can't compute value */
+    public static final long H5E_CANTCOMPUTE = H5E_CANTCOMPUTE();
+    /** Datatype conversion errors - Can't convert datatypes */
     public static final long H5E_CANTCONVERT = H5E_CANTCONVERT();
+    /** Minor error codes - Resource errors - Unable to copy object */
     public static final long H5E_CANTCOPY = H5E_CANTCOPY();
+    /** Minor error codes - Cache related errors - Unable to cork an object */
+    public static final long H5E_CANTCORK = H5E_CANTCORK();
+    /** Minor error codes - Dataspace errors - Can't count elements */
     public static final long H5E_CANTCOUNT = H5E_CANTCOUNT();
+    /** Minor error codes - File accessibility errors - Unable to create file */
     public static final long H5E_CANTCREATE = H5E_CANTCREATE();
+    /** Minor error codes - Object atom related errors - Unable to decrement reference count */
     public static final long H5E_CANTDEC = H5E_CANTDEC();
+    /** Minor error codes - B-tree related errors - Unable to decode value */
     public static final long H5E_CANTDECODE = H5E_CANTDECODE();
+    /** Minor error codes - Object header related errors - Can't delete message */
     public static final long H5E_CANTDELETE = H5E_CANTDELETE();
+    /** Minor error codes - Cache related errors - Unable to create a flush dependency */
+    public static final long H5E_CANTDEPEND = H5E_CANTDEPEND();
+    /** Minor error codes - Cache related errors - Unable to mark metadata as dirty */
+    public static final long H5E_CANTDIRTY = H5E_CANTDIRTY();
+    /** Minor error codes - B-tree related errors - Unable to encode value */
     public static final long H5E_CANTENCODE = H5E_CANTENCODE();
+    /** Minor error codes - Cache related errors - Unable to expunge a metadata cache entry */
+    public static final long H5E_CANTEXPUNGE = H5E_CANTEXPUNGE();
+    /** Minor error codes - Heap errors - Can't extend heap's space */
+    public static final long H5E_CANTEXTEND = H5E_CANTEXTEND();
+    /** I/O pipeline errors - Filter operation failed */
+    public static final long H5E_CANTFILTER = H5E_CANTFILTER();
+    /** Minor error codes - Cache related errors - Unable to flush data from cache */
     public static final long H5E_CANTFLUSH = H5E_CANTFLUSH();
+    /** Minor error codes - Resource errors - Unable to free object */
     public static final long H5E_CANTFREE = H5E_CANTFREE();
+    /** Minor error codes - Parallel MPI - Can't gather data */
+    public static final long H5E_CANTGATHER = H5E_CANTGATHER();
+    /** Minor error codes - Resource errors - Unable to garbage collect */
+    public static final long H5E_CANTGC = H5E_CANTGC();
+    /** Minor error codes - Property list errors - Can't get value */
     public static final long H5E_CANTGET = H5E_CANTGET();
+    /** Minor error codes - Resource errors - Unable to compute size */
+    public static final long H5E_CANTGETSIZE = H5E_CANTGETSIZE();
+    /** Minor error codes - Object atom related errors - Unable to increment reference count */
     public static final long H5E_CANTINC = H5E_CANTINC();
+    /** Minor error codes - Function entry/exit interface - Unable to initialize object */
     public static final long H5E_CANTINIT = H5E_CANTINIT();
+    /** Minor error codes - Cache related errors - Unable to insert metadata into cache */
+    public static final long H5E_CANTINS = H5E_CANTINS();
+    /** Minor error codes - B-tree related errors - Unable to insert object */
     public static final long H5E_CANTINSERT = H5E_CANTINSERT();
+    /** Minor error codes - B-tree related errors - Unable to list node */
     public static final long H5E_CANTLIST = H5E_CANTLIST();
+    /** Minor error codes - Cache related errors - Unable to load metadata into cache */
     public static final long H5E_CANTLOAD = H5E_CANTLOAD();
+    /** Minor error codes - Resource errors - Unable to lock object */
     public static final long H5E_CANTLOCK = H5E_CANTLOCK();
+    /** Minor error codes - File accessibility errors  Unable to lock file */
+    public static final long H5E_CANTLOCKFILE = H5E_CANTLOCKFILE();
+    /** Minor error codes - Cache related errors - Unable to mark a pinned entry as clean */
+    public static final long H5E_CANTMARKCLEAN = H5E_CANTMARKCLEAN();
+    /** Minor error codes - Cache related errors - Unable to mark a pinned entry as dirty */
+    public static final long H5E_CANTMARKDIRTY = H5E_CANTMARKDIRTY();
+    /** Minor error codes - Cache related errors - Unable to mark an entry as unserialized */
+    public static final long H5E_CANTMARKSERIALIZED = H5E_CANTMARKSERIALIZED();
+    /** Minor error codes - Cache related errors - Unable to mark an entry as serialized */
+    public static final long H5E_CANTMARKUNSERIALIZED = H5E_CANTMARKUNSERIALIZED();
+    /** Minor error codes - Free space errors - Can't merge objects */
+    public static final long H5E_CANTMERGE = H5E_CANTMERGE();
+    /** Minor error codes - B-tree related errors - Unable to modify record */
+    public static final long H5E_CANTMODIFY = H5E_CANTMODIFY();
+    /** Minor error codes - Link related errors - Can't move object */
+    public static final long H5E_CANTMOVE = H5E_CANTMOVE();
+    /** Minor error codes - Dataspace errors - Can't move to next iterator location */
     public static final long H5E_CANTNEXT = H5E_CANTNEXT();
+    /** Minor error codes - Cache related errors - Unable to notify object about action */
+    public static final long H5E_CANTNOTIFY = H5E_CANTNOTIFY();
+    /** Minor error codes - File accessibility errors - Unable to open file */
     public static final long H5E_CANTOPENFILE = H5E_CANTOPENFILE();
+    /** Minor error codes - Group related errors - Can't open object */
     public static final long H5E_CANTOPENOBJ = H5E_CANTOPENOBJ();
-    // public static final long H5E_CANTRECV = H5E_CANTRECV();
+    /** Minor error codes - Heap errors - Can't operate on object */
+    public static final long H5E_CANTOPERATE = H5E_CANTOPERATE();
+    /** Minor error codes - Object header related errors - Can't pack messages */
+    public static final long H5E_CANTPACK = H5E_CANTPACK();
+    /** Minor error codes - Cache related errors - Unable to pin cache entry */
+    public static final long H5E_CANTPIN = H5E_CANTPIN();
+    /** Minor error codes - Cache related errors - Unable to protect metadata */
+    public static final long H5E_CANTPROTECT = H5E_CANTPROTECT();
+    /** Minor error codes - Parallel MPI - Can't receive data */
+    public static final long H5E_CANTRECV = H5E_CANTRECV();
+    /** Minor error codes - B-tree related errors - Unable to redistribute records */
+    public static final long H5E_CANTREDISTRIBUTE = H5E_CANTREDISTRIBUTE();
+    /** Minor error codes - Object atom related errors - Unable to register new atom */
     public static final long H5E_CANTREGISTER = H5E_CANTREGISTER();
+    /** Minor error codes - Function entry/exit interface - Unable to release object */
     public static final long H5E_CANTRELEASE = H5E_CANTRELEASE();
+    /** Minor error codes - B-tree related errors - Unable to remove object */
+    public static final long H5E_CANTREMOVE = H5E_CANTREMOVE();
+    /** Minor error codes - Object header related errors - Unable to rename object */
+    public static final long H5E_CANTRENAME = H5E_CANTRENAME();
+    /** Minor error codes - Object header related errors - Can't reset object */
+    public static final long H5E_CANTRESET = H5E_CANTRESET();
+    /** Minor error codes - Cache related errors - Unable to resize a metadata cache entry */
+    public static final long H5E_CANTRESIZE = H5E_CANTRESIZE();
+    /** Minor error codes - Heap errors - Can't restore condition */
+    public static final long H5E_CANTRESTORE = H5E_CANTRESTORE();
+    /** Minor error codes - Free space errors - Can't revive object */
+    public static final long H5E_CANTREVIVE = H5E_CANTREVIVE();
+    /** Minor error codes - Free space errors - Can't shrink container */
+    public static final long H5E_CANTSHRINK = H5E_CANTSHRINK();
+    /** Minor error codes - Dataspace errors - Can't select hyperslab */
     public static final long H5E_CANTSELECT = H5E_CANTSELECT();
+    /** Minor error codes - Cache related errors - Unable to serialize data from cache */
+    public static final long H5E_CANTSERIALIZE = H5E_CANTSERIALIZE();
+    /** Minor error codes - Property list errors - Can't set value */
     public static final long H5E_CANTSET = H5E_CANTSET();
+    /** Minor error codes - Link related errors - Can't sort objects */
+    public static final long H5E_CANTSORT = H5E_CANTSORT();
+    /** Minor error codes - B-tree related errors - Unable to split node */
     public static final long H5E_CANTSPLIT = H5E_CANTSPLIT();
+    /** Minor error codes - B-tree related errors - Unable to swap records */
+    public static final long H5E_CANTSWAP = H5E_CANTSWAP();
+    /** Minor error codes - Cache related errors - Unable to tag metadata in the cache */
+    public static final long H5E_CANTTAG = H5E_CANTTAG();
+    /** Minor error codes - Cache related errors - Unable to uncork an object */
+    public static final long H5E_CANTUNCORK = H5E_CANTUNCORK();
+    /** Minor error codes - Cache related errors - Unable to destroy a flush dependency */
+    public static final long H5E_CANTUNDEPEND = H5E_CANTUNDEPEND();
+    /** Minor error codes - Resource errors - Unable to unlock object */
     public static final long H5E_CANTUNLOCK = H5E_CANTUNLOCK();
+    /** Minor error codes - File accessibility errors  Unable to unlock file */
+    public static final long H5E_CANTUNLOCKFILE = H5E_CANTUNLOCKFILE();
+    /** Minor error codes - Cache related errors - Unable to un-pin cache entry */
+    public static final long H5E_CANTUNPIN = H5E_CANTUNPIN();
+    /** Minor error codes - Cache related errors - Unable to unprotect metadata */
+    public static final long H5E_CANTUNPROTECT = H5E_CANTUNPROTECT();
+    /** Minor error codes - Cache related errors - Unable to mark metadata as unserialized */
+    public static final long H5E_CANTUNSERIALIZE = H5E_CANTUNSERIALIZE();
+    /** Minor error codes - Heap errors - Can't update object */
+    public static final long H5E_CANTUPDATE = H5E_CANTUPDATE();
+    /** Generic low-level file I/O errors - Close failed */
     public static final long H5E_CLOSEERROR = H5E_CLOSEERROR();
+    /** Minor error codes - Group related errors - Name component is too long */
     public static final long H5E_COMPLEN = H5E_COMPLEN();
+    /** Major error codes - API Context */
+    public static final long H5E_CONTEXT = H5E_CONTEXT();
+    /** Major error codes - Dataset */
     public static final long H5E_DATASET = H5E_DATASET();
+    /** Major error codes - Dataspace */
     public static final long H5E_DATASPACE = H5E_DATASPACE();
+    /** Major error codes - Datatype */
     public static final long H5E_DATATYPE = H5E_DATATYPE();
+    /** Value for the default error stack */
     public static final long H5E_DEFAULT = H5E_DEFAULT();
+    /** Minor error codes - Property list errors - Duplicate class name in parent class */
     public static final long H5E_DUPCLASS = H5E_DUPCLASS();
+    /** Major error codes - Extensible Array */
+    public static final long H5E_EARRAY = H5E_EARRAY();
+    /** Major error codes - External file list */
     public static final long H5E_EFL = H5E_EFL();
+    /** Major error codes - Error API */
+    public static final long H5E_ERROR = H5E_ERROR();
+    /** Minor error codes - B-tree related errors - Object already exists */
     public static final long H5E_EXISTS = H5E_EXISTS();
+    /** Major error codes - Fixed Array */
+    public static final long H5E_FARRAY = H5E_FARRAY();
+    /** Generic low-level file I/O errors - File control (fcntl) failed */
     public static final long H5E_FCNTL = H5E_FCNTL();
+    /** Major error codes - File accessibility */
     public static final long H5E_FILE = H5E_FILE();
+    /** Minor error codes - File accessibility errors - File already exists */
     public static final long H5E_FILEEXISTS = H5E_FILEEXISTS();
+    /** Minor error codes - File accessibility errors - File already open */
     public static final long H5E_FILEOPEN = H5E_FILEOPEN();
+    /** Major error codes - Free Space Manager */
+    public static final long H5E_FSPACE = H5E_FSPACE();
+    /** Major error codes - Function entry/exit */
     public static final long H5E_FUNC = H5E_FUNC();
+    /** Major error codes - Heap */
     public static final long H5E_HEAP = H5E_HEAP();
+    /** Minor error codes - Dataspace errors - Internal states are inconsistent */
+    public static final long H5E_INCONSISTENTSTATE = H5E_INCONSISTENTSTATE();
+    /** Major error codes - Internal error (too specific to document in detail) */
     public static final long H5E_INTERNAL = H5E_INTERNAL();
+    /** Major error codes - Low-level I/O */
     public static final long H5E_IO = H5E_IO();
+    /** Major error codes - Links */
     public static final long H5E_LINK = H5E_LINK();
+    /** Minor error codes - Object header related errors - Bad object header link count */
     public static final long H5E_LINKCOUNT = H5E_LINKCOUNT();
+    /** Minor error codes - Cache related errors - Failure in the cache logging framework */
+    public static final long H5E_LOGGING = H5E_LOGGING();
+    /** Minor error codes - File accessibility errors - File mount error */
     public static final long H5E_MOUNT = H5E_MOUNT();
+    /** Minor error codes - Parallel MPI - Some MPI function failed */
     public static final long H5E_MPI = H5E_MPI();
+    /** Minor error codes - Parallel MPI - MPI Error String */
     public static final long H5E_MPIERRSTR = H5E_MPIERRSTR();
+    /** Minor error codes - Link related errors - Too many soft links in path */
+    public static final long H5E_NLINKS = H5E_NLINKS();
+    /** Minor error codes - Parallel MPI - Can't perform independent IO */
+    public static final long H5E_NO_INDEPENDENT = H5E_NO_INDEPENDENT();
+    /** I/O pipeline errors - Filter present but encoding disabled */
+    public static final long H5E_NOENCODER = H5E_NOENCODER();
+    /** I/O pipeline errors - Requested filter is not available */
     public static final long H5E_NOFILTER = H5E_NOFILTER();
+    /** Minor error codes - Object atom related errors - Out of IDs for group */
     public static final long H5E_NOIDS = H5E_NOIDS();
+    /** Major error codes - No error */
     public static final long H5E_NONE_MAJOR = H5E_NONE_MAJOR();
+    /** No error */
     public static final long H5E_NONE_MINOR = H5E_NONE_MINOR();
+    /** Minor error codes - Resource errors - No space available for allocation */
     public static final long H5E_NOSPACE = H5E_NOSPACE();
+    /** Minor error codes - Cache related errors - Metadata not currently cached */
     public static final long H5E_NOTCACHED = H5E_NOTCACHED();
+    /** Minor error codes - B-tree related errors - Object not found */
     public static final long H5E_NOTFOUND = H5E_NOTFOUND();
+    /** Minor error codes - File accessibility errors - Not an HDF5 file */
     public static final long H5E_NOTHDF5 = H5E_NOTHDF5();
+    /** Minor error codes - Link related errors - Link class not registered */
+    public static final long H5E_NOTREGISTERED = H5E_NOTREGISTERED();
+    /** Minor error codes - Resource errors - Object is already open */
+    public static final long H5E_OBJOPEN = H5E_OBJOPEN();
+    /** Major error codes - Object header */
     public static final long H5E_OHDR = H5E_OHDR();
+    /** Minor error codes - Plugin errors - Can't open directory or file */
+    public static final long H5E_OPENERROR = H5E_OPENERROR();
+    /** Generic low-level file I/O errors - Address overflowed */
     public static final long H5E_OVERFLOW = H5E_OVERFLOW();
+    /** Major error codes - Page Buffering */
+    public static final long H5E_PAGEBUF = H5E_PAGEBUF();
+    /** Minor error codes - Group related errors - Problem with path to object */
+    public static final long H5E_PATH = H5E_PATH();
+    /** Major error codes - Data filters */
     public static final long H5E_PLINE = H5E_PLINE();
+    /** Major error codes - Property lists */
     public static final long H5E_PLIST = H5E_PLIST();
+    /** Major error codes - Plugin for dynamically loaded library */
+    public static final long H5E_PLUGIN = H5E_PLUGIN();
+    /** Minor error codes - Cache related errors - Protected metadata error */
     public static final long H5E_PROTECT = H5E_PROTECT();
+    /** Generic low-level file I/O errors - Read failed */
     public static final long H5E_READERROR = H5E_READERROR();
+    /** Major error codes - References */
     public static final long H5E_REFERENCE = H5E_REFERENCE();
+    /** Major error codes - Resource unavailable */
     public static final long H5E_RESOURCE = H5E_RESOURCE();
+    /** Major error codes - Reference Counted Strings */
     public static final long H5E_RS = H5E_RS();
+    /** Generic low-level file I/O errors - Seek failed */
     public static final long H5E_SEEKERROR = H5E_SEEKERROR();
+    /** Minor error codes - Property list errors - Disallowed operation */
+    public static final long H5E_SETDISALLOWED = H5E_SETDISALLOWED();
+    /** I/O pipeline errors - Error from filter 'set local' callback */
     public static final long H5E_SETLOCAL = H5E_SETLOCAL();
+    /** Major error codes - Skip Lists */
+    public static final long H5E_SLIST = H5E_SLIST();
+    /** Major error codes - Shared Object Header Messages */
+    public static final long H5E_SOHM = H5E_SOHM();
+    /** Major error codes - Data storage */
     public static final long H5E_STORAGE = H5E_STORAGE();
+    /** Major error codes - Symbol table */
     public static final long H5E_SYM = H5E_SYM();
+    /** Minor error codes - System level errors - System error message */
+    public static final long H5E_SYSERRSTR = H5E_SYSERRSTR();
+    /** Minor error codes - Cache related errors - Internal error detected */
+    public static final long H5E_SYSTEM = H5E_SYSTEM();
+    /** Minor error codes - Link related errors - Link traversal failure */
+    public static final long H5E_TRAVERSE = H5E_TRAVERSE();
+    /** Minor error codes - File accessibility errors - File has been truncated */
     public static final long H5E_TRUNCATED = H5E_TRUNCATED();
+    /** Major error codes - Ternary Search Trees */
     public static final long H5E_TST = H5E_TST();
+    /** Minor error codes - Argument errors - Information is uinitialized */
     public static final long H5E_UNINITIALIZED = H5E_UNINITIALIZED();
+    /** Minor error codes - Argument errors - Feature is unsupported */
     public static final long H5E_UNSUPPORTED = H5E_UNSUPPORTED();
+    /** Minor error codes - Object header related errors - Wrong version number */
     public static final long H5E_VERSION = H5E_VERSION();
+    /** Major error codes - Virtual File Layer */
     public static final long H5E_VFL = H5E_VFL();
+    /** Error stack traversal direction - begin at API function, end deep */
     public static final long H5E_WALK_DOWNWARD = H5E_WALK_DOWNWARD();
+    /** Error stack traversal direction - begin deep, end at API function */
     public static final long H5E_WALK_UPWARD = H5E_WALK_UPWARD();
+    /** Generic low-level file I/O errors - Write failed */
     public static final long H5E_WRITEERROR = H5E_WRITEERROR();
 
     public static final int H5F_ACC_CREAT = H5F_ACC_CREAT();
@@ -390,6 +640,7 @@ public class HDF5Constants {
 
     public static final int H5PL_TYPE_ERROR = H5PL_TYPE_ERROR();
     public static final int H5PL_TYPE_FILTER = H5PL_TYPE_FILTER();
+    public static final int H5PL_TYPE_NONE = H5PL_TYPE_NONE();
     public static final int H5PL_FILTER_PLUGIN = H5PL_FILTER_PLUGIN();
     public static final int H5PL_ALL_PLUGIN = H5PL_ALL_PLUGIN();
 
@@ -398,29 +649,54 @@ public class HDF5Constants {
     public static final int H5R_MAXTYPE = H5R_MAXTYPE();
     public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
     public static final int H5R_OBJECT = H5R_OBJECT();
+
+    /** Define atomic datatypes */
     public static final int H5S_ALL = H5S_ALL();
+    /** Define user-level maximum number of dimensions */
     public static final int H5S_MAX_RANK = H5S_MAX_RANK();
+    /** Different types of dataspaces - error */
     public static final int H5S_NO_CLASS = H5S_NO_CLASS();
+    /** Different types of dataspaces - null dataspace */
     public static final int H5S_NULL = H5S_NULL();
+    /** Different types of dataspaces - scalar variable */
     public static final int H5S_SCALAR = H5S_SCALAR();
+    /** Enumerated type for the type of selection - Entire extent selected */
     public static final int H5S_SEL_ALL = H5S_SEL_ALL();
+    /** Enumerated type for the type of selection - Error */
     public static final int H5S_SEL_ERROR = H5S_SEL_ERROR();
+    /** Enumerated type for the type of selection - Hyperslab selected */
     public static final int H5S_SEL_HYPERSLABS = H5S_SEL_HYPERSLABS();
+    /** Enumerated type for the type of selection - LAST */
     public static final int H5S_SEL_N = H5S_SEL_N();
+    /** Enumerated type for the type of selection - Nothing selected */
     public static final int H5S_SEL_NONE = H5S_SEL_NONE();
+    /** Enumerated type for the type of selection - Points / elements selected */
     public static final int H5S_SEL_POINTS = H5S_SEL_POINTS();
+    /** Different ways of combining selections - Binary "and" operation for hyperslabs */
     public static final int H5S_SELECT_AND = H5S_SELECT_AND();
+    /** Different ways of combining selections - Append elements to end of point selection */
     public static final int H5S_SELECT_APPEND = H5S_SELECT_APPEND();
+    /** Different ways of combining selections - Invalid upper bound on selection operations */
     public static final int H5S_SELECT_INVALID = H5S_SELECT_INVALID();
+    /** Different ways of combining selections - error */
     public static final int H5S_SELECT_NOOP = H5S_SELECT_NOOP();
+    /** Different ways of combining selections - Binary "not" operation for hyperslabs */
     public static final int H5S_SELECT_NOTA = H5S_SELECT_NOTA();
+    /** Different ways of combining selections - Binary "not" operation for hyperslabs */
     public static final int H5S_SELECT_NOTB = H5S_SELECT_NOTB();
+    /** Different ways of combining selections - Binary "or" operation for hyperslabs */
     public static final int H5S_SELECT_OR = H5S_SELECT_OR();
+    /** Different ways of combining selections - Prepend elements to beginning of point selection */
     public static final int H5S_SELECT_PREPEND = H5S_SELECT_PREPEND();
+    /** Different ways of combining selections - Select "set" operation */
     public static final int H5S_SELECT_SET = H5S_SELECT_SET();
+    /** Different ways of combining selections - Binary "xor" operation for hyperslabs */
     public static final int H5S_SELECT_XOR = H5S_SELECT_XOR();
+    /** Different types of dataspaces - simple dataspace */
     public static final int H5S_SIMPLE = H5S_SIMPLE();
+    /** Define atomic datatypes */
     public static final int H5S_UNLIMITED = H5S_UNLIMITED();
+
     public static final long H5T_ALPHA_B16 = H5T_ALPHA_B16();
     public static final long H5T_ALPHA_B32 = H5T_ALPHA_B32();
     public static final long H5T_ALPHA_B64 = H5T_ALPHA_B64();
@@ -626,48 +902,97 @@ public class HDF5Constants {
     public static final long H5T_VARIABLE = H5T_VARIABLE();
     public static final int H5T_VLEN = H5T_VLEN();
     public static final int H5T_VL_T = H5T_VL_T();
+
+    /** Return values for filter callback function */
     public static final int H5Z_CB_CONT = H5Z_CB_CONT();
+    /** Return values for filter callback function */
     public static final int H5Z_CB_ERROR = H5Z_CB_ERROR();
+    /** Return values for filter callback function */
     public static final int H5Z_CB_FAIL = H5Z_CB_FAIL();
+    /** Return values for filter callback function */
     public static final int H5Z_CB_NO = H5Z_CB_NO();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_DISABLE_EDC = H5Z_DISABLE_EDC();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_ENABLE_EDC = H5Z_ENABLE_EDC();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_ERROR_EDC = H5Z_ERROR_EDC();
+    /** Filter IDs - deflation like gzip */
     public static final int H5Z_FILTER_DEFLATE = H5Z_FILTER_DEFLATE();
+    /** Filter IDs - no filter */
     public static final int H5Z_FILTER_ERROR = H5Z_FILTER_ERROR();
+    /** Filter IDs - fletcher32 checksum of EDC */
     public static final int H5Z_FILTER_FLETCHER32 = H5Z_FILTER_FLETCHER32();
+    /** Filter IDs - maximum filter id */
     public static final int H5Z_FILTER_MAX = H5Z_FILTER_MAX();
+    /** Filter IDs - nbit compression */
     public static final int H5Z_FILTER_NBIT = H5Z_FILTER_NBIT();
+    /** Filter IDs - reserved indefinitely */
     public static final int H5Z_FILTER_NONE = H5Z_FILTER_NONE();
+    /** Filter IDs - filter ids below this value are reserved for library use */
     public static final int H5Z_FILTER_RESERVED = H5Z_FILTER_RESERVED();
+    /** Filter IDs - scale+offset compression */
     public static final int H5Z_FILTER_SCALEOFFSET = H5Z_FILTER_SCALEOFFSET();
+    /** Filter IDs - shuffle the data */
     public static final int H5Z_FILTER_SHUFFLE = H5Z_FILTER_SHUFFLE();
+    /** Filter IDs - szip compression */
     public static final int H5Z_FILTER_SZIP = H5Z_FILTER_SZIP();
+    /** Flags for filter definition (stored)
+     * definition flag mask */
     public static final int H5Z_FLAG_DEFMASK = H5Z_FLAG_DEFMASK();
+    /** Additional flags for filter invocation (not stored)
+     * invocation flag mask */
     public static final int H5Z_FLAG_INVMASK = H5Z_FLAG_INVMASK();
+    /** Flags for filter definition (stored)
+     * filter is mandatory */
     public static final int H5Z_FLAG_MANDATORY = H5Z_FLAG_MANDATORY();
+    /** Flags for filter definition (stored)
+     * filter is optional */
     public static final int H5Z_FLAG_OPTIONAL = H5Z_FLAG_OPTIONAL();
+    /** Additional flags for filter invocation (not stored)
+     * reverse direction; read */
     public static final int H5Z_FLAG_REVERSE = H5Z_FLAG_REVERSE();
+    /** Additional flags for filter invocation (not stored)
+     * skip EDC filters for read */
     public static final int H5Z_FLAG_SKIP_EDC = H5Z_FLAG_SKIP_EDC();
+    /** Symbol to remove all filters in H5Premove_filter */
+    public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL();
+    /** Maximum number of filters allowed in a pipeline */
     public static final int H5Z_MAX_NFILTERS = H5Z_MAX_NFILTERS();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_NO_EDC = H5Z_NO_EDC();
+    /** Bit flags for H5Zget_filter_info */
     public static final int H5Z_FILTER_CONFIG_ENCODE_ENABLED = H5Z_FILTER_CONFIG_ENCODE_ENABLED();
+    /** Bit flags for H5Zget_filter_info */
     public static final int H5Z_FILTER_CONFIG_DECODE_ENABLED = H5Z_FILTER_CONFIG_DECODE_ENABLED();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_INT_MINBITS_DEFAULT = H5Z_SO_INT_MINBITS_DEFAULT();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_FLOAT_DSCALE = H5Z_SO_FLOAT_DSCALE();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_FLOAT_ESCALE = H5Z_SO_FLOAT_ESCALE();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_INT = H5Z_SO_INT();
+    /** shuffle filter - Number of parameters that users can set */
     public static final int H5Z_SHUFFLE_USER_NPARMS = H5Z_SHUFFLE_USER_NPARMS();
+    /** shuffle filter - Total number of parameters for filter */
     public static final int H5Z_SHUFFLE_TOTAL_NPARMS = H5Z_SHUFFLE_TOTAL_NPARMS();
+    /** szip filter - Number of parameters that users can set */
     public static final int H5Z_SZIP_USER_NPARMS = H5Z_SZIP_USER_NPARMS();
+    /** szip filter - Total number of parameters for filter */
     public static final int H5Z_SZIP_TOTAL_NPARMS = H5Z_SZIP_TOTAL_NPARMS();
+    /** szip filter - "User" parameter for option mask */
     public static final int H5Z_SZIP_PARM_MASK = H5Z_SZIP_PARM_MASK();
+    /** szip filter - "User" parameter for pixels-per-block */
     public static final int H5Z_SZIP_PARM_PPB = H5Z_SZIP_PARM_PPB();
+    /** szip filter - "Local" parameter for bits-per-pixel */
     public static final int H5Z_SZIP_PARM_BPP = H5Z_SZIP_PARM_BPP();
+    /** szip filter - "Local" parameter for pixels-per-scanline */
     public static final int H5Z_SZIP_PARM_PPS = H5Z_SZIP_PARM_PPS();
+    /** nbit filter - Number of parameters that users can set */
     public static final int H5Z_NBIT_USER_NPARMS = H5Z_NBIT_USER_NPARMS();
+    /** scale offset filter - Number of parameters that users can set */
     public static final int H5Z_SCALEOFFSET_USER_NPARMS = H5Z_SCALEOFFSET_USER_NPARMS();
-    public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL();
 
     // /////////////////////////////////////////////////////////////////////////
     // List of private native variables to get constant values from C //
@@ -802,6 +1127,8 @@ public class HDF5Constants {
 
     private static native final long H5E_BADGROUP();
 
+    private static native final long H5E_BADITER();
+
     private static native final long H5E_BADMESG();
 
     private static native final long H5E_BADRANGE();
@@ -822,15 +1149,30 @@ public class HDF5Constants {
 
     private static native final long H5E_CANAPPLY();
 
-    // private static native final long H5E_CANTALLOC();
+    private static native final long H5E_CANTALLOC();
+
+    private static native final long H5E_CANTAPPEND();
+
+    private static native final long H5E_CANTATTACH();
+
+    private static native final long H5E_CANTCLEAN();
+
     private static native final long H5E_CANTCLIP();
 
     private static native final long H5E_CANTCLOSEFILE();
 
+    private static native final long H5E_CANTCLOSEOBJ();
+
+    private static native final long H5E_CANTCOMPARE();
+
+    private static native final long H5E_CANTCOMPUTE();
+
     private static native final long H5E_CANTCONVERT();
 
     private static native final long H5E_CANTCOPY();
 
+    private static native final long H5E_CANTCORK();
+
     private static native final long H5E_CANTCOUNT();
 
     private static native final long H5E_CANTCREATE();
@@ -841,18 +1183,36 @@ public class HDF5Constants {
 
     private static native final long H5E_CANTDELETE();
 
+    private static native final long H5E_CANTDEPEND();
+
+    private static native final long H5E_CANTDIRTY();
+
     private static native final long H5E_CANTENCODE();
 
+    private static native final long H5E_CANTEXPUNGE();
+
+    private static native final long H5E_CANTEXTEND();
+
+    private static native final long H5E_CANTFILTER();
+
     private static native final long H5E_CANTFLUSH();
 
     private static native final long H5E_CANTFREE();
 
+    private static native final long H5E_CANTGATHER();
+
+    private static native final long H5E_CANTGC();
+
     private static native final long H5E_CANTGET();
 
+    private static native final long H5E_CANTGETSIZE();
+
     private static native final long H5E_CANTINC();
 
     private static native final long H5E_CANTINIT();
 
+    private static native final long H5E_CANTINS();
+
     private static native final long H5E_CANTINSERT();
 
     private static native final long H5E_CANTLIST();
@@ -861,29 +1221,96 @@ public class HDF5Constants {
 
     private static native final long H5E_CANTLOCK();
 
+    private static native final long H5E_CANTLOCKFILE();
+
+    private static native final long H5E_CANTMARKCLEAN();
+
+    private static native final long H5E_CANTMARKDIRTY();
+
+    private static native final long H5E_CANTMARKSERIALIZED();
+
+    private static native final long H5E_CANTMARKUNSERIALIZED();
+
+    private static native final long H5E_CANTMERGE();
+
+    private static native final long H5E_CANTMOVE();
+
+    private static native final long H5E_CANTMODIFY();
+
     private static native final long H5E_CANTNEXT();
 
+    private static native final long H5E_CANTNOTIFY();
+
     private static native final long H5E_CANTOPENFILE();
 
     private static native final long H5E_CANTOPENOBJ();
 
-    // private static native final long H5E_CANTRECV();
+    private static native final long H5E_CANTOPERATE();
+
+    private static native final long H5E_CANTPACK();
+
+    private static native final long H5E_CANTPIN();
+
+    private static native final long H5E_CANTPROTECT();
+
+    private static native final long H5E_CANTRECV();
+
+    private static native final long H5E_CANTREDISTRIBUTE();
+
     private static native final long H5E_CANTREGISTER();
 
     private static native final long H5E_CANTRELEASE();
 
+    private static native final long H5E_CANTREMOVE();
+
+    private static native final long H5E_CANTRENAME();
+
+    private static native final long H5E_CANTRESET();
+
+    private static native final long H5E_CANTRESIZE();
+
+    private static native final long H5E_CANTRESTORE();
+
+    private static native final long H5E_CANTREVIVE();
+
+    private static native final long H5E_CANTSHRINK();
+
     private static native final long H5E_CANTSELECT();
 
     private static native final long H5E_CANTSET();
 
+    private static native final long H5E_CANTSERIALIZE();
+
+    private static native final long H5E_CANTSORT();
+
     private static native final long H5E_CANTSPLIT();
 
+    private static native final long H5E_CANTSWAP();
+
+    private static native final long H5E_CANTTAG();
+
+    private static native final long H5E_CANTUNCORK();
+
+    private static native final long H5E_CANTUNDEPEND();
+
     private static native final long H5E_CANTUNLOCK();
 
+    private static native final long H5E_CANTUNLOCKFILE();
+
+    private static native final long H5E_CANTUNPIN();
+
+    private static native final long H5E_CANTUNPROTECT();
+
+    private static native final long H5E_CANTUNSERIALIZE();
+
+    private static native final long H5E_CANTUPDATE();
+
     private static native final long H5E_CLOSEERROR();
 
     private static native final long H5E_COMPLEN();
 
+    private static native final long H5E_CONTEXT();
+
     private static native final long H5E_DATASET();
 
     private static native final long H5E_DATASPACE();
@@ -894,10 +1321,16 @@ public class HDF5Constants {
 
     private static native final long H5E_DUPCLASS();
 
+    private static native final long H5E_EARRAY();
+
     private static native final long H5E_EFL();
 
+    private static native final long H5E_ERROR();
+
     private static native final long H5E_EXISTS();
 
+    private static native final long H5E_FARRAY();
+
     private static native final long H5E_FCNTL();
 
     private static native final long H5E_FILE();
@@ -906,10 +1339,14 @@ public class HDF5Constants {
 
     private static native final long H5E_FILEOPEN();
 
+    private static native final long H5E_FSPACE();
+
     private static native final long H5E_FUNC();
 
     private static native final long H5E_HEAP();
 
+    private static native final long H5E_INCONSISTENTSTATE();
+
     private static native final long H5E_INTERNAL();
 
     private static native final long H5E_IO();
@@ -918,6 +1355,8 @@ public class HDF5Constants {
 
     private static native final long H5E_LINKCOUNT();
 
+    private static native final long H5E_LOGGING();
+
     private static native final int H5E_MAJOR();
 
     private static native final int H5E_MINOR();
@@ -928,6 +1367,12 @@ public class HDF5Constants {
 
     private static native final long H5E_MPIERRSTR();
 
+    private static native final long H5E_NLINKS();
+
+    private static native final long H5E_NO_INDEPENDENT();
+
+    private static native final long H5E_NOENCODER();
+
     private static native final long H5E_NOFILTER();
 
     private static native final long H5E_NOIDS();
@@ -944,14 +1389,26 @@ public class HDF5Constants {
 
     private static native final long H5E_NOTHDF5();
 
+    private static native final long H5E_NOTREGISTERED();
+
+    private static native final long H5E_OBJOPEN();
+
     private static native final long H5E_OHDR();
 
+    private static native final long H5E_OPENERROR();
+
     private static native final long H5E_OVERFLOW();
 
+    private static native final long H5E_PAGEBUF();
+
+    private static native final long H5E_PATH();
+
     private static native final long H5E_PLINE();
 
     private static native final long H5E_PLIST();
 
+    private static native final long H5E_PLUGIN();
+
     private static native final long H5E_PROTECT();
 
     private static native final long H5E_READERROR();
@@ -964,12 +1421,24 @@ public class HDF5Constants {
 
     private static native final long H5E_SEEKERROR();
 
+    private static native final long H5E_SETDISALLOWED();
+
     private static native final long H5E_SETLOCAL();
 
+    private static native final long H5E_SLIST();
+
+    private static native final long H5E_SOHM();
+
     private static native final long H5E_STORAGE();
 
     private static native final long H5E_SYM();
 
+    private static native final long H5E_SYSERRSTR();
+
+    private static native final long H5E_SYSTEM();
+
+    private static native final long H5E_TRAVERSE();
+
     private static native final long H5E_TRUNCATED();
 
     private static native final long H5E_TST();
@@ -988,6 +1457,14 @@ public class HDF5Constants {
 
     private static native final long H5E_WRITEERROR();
 
+    private static native final int H5ES_STATUS_IN_PROGRESS();
+
+    private static native final int H5ES_STATUS_SUCCEED();
+
+    private static native final int H5ES_STATUS_FAIL();
+
+    private static native final int H5ES_STATUS_CANCELED();
+
     private static native final int H5F_ACC_CREAT();
 
     private static native final int H5F_ACC_EXCL();
@@ -1364,6 +1841,8 @@ public class HDF5Constants {
 
     private static native final int H5PL_TYPE_FILTER();
 
+    private static native final int H5PL_TYPE_NONE();
+
     private static native final int H5PL_FILTER_PLUGIN();
 
     private static native final int H5PL_ALL_PLUGIN();
diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
index 988c8fb..69c9709 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
@@ -15,7 +15,28 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5A_info_t;
 
-//Information class for link callback(for H5Aiterate)
+/**
+ * Information class for link callback for H5Aiterate.
+ *
+ */
 public interface H5A_iterate_cb extends Callbacks {
-    int callback(long group, String name, H5A_info_t info, H5A_iterate_t op_data);
+    /**
+     *  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 op_data   the operator data passed in to H5Aiterate
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
+    int callback(long loc_id, String name, H5A_info_t info, H5A_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java
index 51d67d5..bdc96fa 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Aiterate.
+ *
+ */
 public interface H5A_iterate_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java
index ead8f73..8ad336f 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pset/get_append_flush)
+/**
+ * Information class for link callback for H5Pset/get_append_flush.
+ *
+ */
 public interface H5D_append_cb extends Callbacks {
+    /**
+     *  application callback for each dataset access property list
+     *
+     *  @param dataset_id    the ID for the dataset being iterated over
+     *  @param cur_dims      the dimension sizes for determining boundary
+     *  @param op_data       the operator data passed in to H5Pset/get_append_flush
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long dataset_id, long[] cur_dims, H5D_append_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java
index 8bf6410..795ed1e 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Dappend.
+ *
+ */
 public interface H5D_append_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
index a911a1c..ca10342 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
@@ -13,7 +13,29 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Diterate)
+/**
+ * Information class for link callback for H5Diterate.
+ *
+ */
 public interface H5D_iterate_cb extends Callbacks {
+    /**
+     *  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
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(byte[] elem, long elem_type, int ndim, long[] point, H5D_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java
index d049711..43fc159 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Diterate.
+ *
+ */
 public interface H5D_iterate_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
index afc04ae..e5914c1 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
@@ -15,7 +15,27 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5E_error2_t;
 
-//Information class for link callback(for H5Ewalk)
+/**
+ * Information class for link callback for H5Ewalk.
+ *
+ */
 public interface H5E_walk_cb extends Callbacks {
+    /**
+     *  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
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(int nidx, H5E_error2_t info, H5E_walk_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java
index 0be8977..3ff09ec 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Ewalk.
+ *
+ */
 public interface H5E_walk_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_cb.java
index ec71911..c472a3e 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_cb.java
@@ -15,7 +15,28 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5L_info_t;
 
-//Information class for link callback(for H5Lvisit/H5Lvisit_by_name)
+/**
+ * Information class for link callback for H5Lvisit/H5Lvisit_by_name.
+ *
+ */
 public interface H5L_iterate_cb extends Callbacks {
-    int callback(long group, String name, H5L_info_t info, H5L_iterate_t op_data);
+    /**
+     *  application callback for each group
+     *
+     *  @param loc_id    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
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
+    int callback(long loc_id, String name, H5L_info_t info, H5L_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
index 28ffb8a..916632d 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
@@ -13,8 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Lvisit/H5Lvisit_by_name.
+ *
+ */
 public interface H5L_iterate_t {
-/**    public ArrayList iterdata = new ArrayList();
-  * Any derived interfaces must define the single public variable as above.
-  */
+
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_cb.java
index 89cf206..ef90dae 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_cb.java
@@ -15,7 +15,28 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5O_info_t;
 
-//Information class for link callback(for H5Ovisit/H5Ovisit_by_name)
+/**
+ * Information class for link callback for H5Ovisit/H5Ovisit_by_name.
+ *
+ */
 public interface H5O_iterate_cb extends Callbacks {
-    int callback(long group, String name, H5O_info_t info, H5O_iterate_t op_data);
+    /**
+     *  application callback for each group
+     *
+     *  @param loc_id    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
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
+    int callback(long loc_id, String name, H5O_info_t info, H5O_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
index 1491b09..2c3984c 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
@@ -13,8 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Ovisit/H5Ovisit_by_name.
+ *
+ */
 public interface H5O_iterate_t {
-/**    public ArrayList iterdata = new ArrayList();
-  * Any derived interfaces must define the single public variable as above.
-  */
+
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java
index e77d386..78a87ad 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java
@@ -13,7 +13,26 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pcreate_class)
+/**
+ * Information class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_close_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id     the ID for the property list class being iterated over
+     *  @param close_data  the function to call when a property list is closed
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, H5P_cls_close_func_t close_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java
index 0d5ad9e..709ee494 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_close_func_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java
index 139f877..878bbd3 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pcreate_class)
+/**
+ * Information class for link callback for H5Pcreate_class
+ *
+ */
 public interface H5P_cls_copy_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param new_prop_id   the ID for the property list copy
+     *  @param old_prop_id   the ID for the property list class being copied
+     *  @param copy_data     the function to call when each property list in this class is copied
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long new_prop_id, long old_prop_id, H5P_cls_copy_func_t copy_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java
index 12c2601..b3e7f09 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_copy_func_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java
index e64ec6f..88d0aa6 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java
@@ -13,7 +13,26 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pcreate_class)
+/**
+ * Information class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_create_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id       the ID for the property list class being iterated over
+     *  @param create_data   the function to call when each property list in this class is created
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, H5P_cls_create_func_t create_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java
index 73646f1..8e259cc 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_create_func_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
index 5ecb88d..60e1884 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Piterate)
+/**
+ * Information class for link callback for H5Piterate.
+ *
+ */
 public interface H5P_iterate_cb extends Callbacks {
+    /**
+     *  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
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long plist, String name, H5P_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java
index 2e320b4..4c5d222 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Piterate.
+ *
+ */
 public interface H5P_iterate_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java
index 103fe5f..40569bc 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_close_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param name    the name of the property being closed
+     *  @param size    the size of the property value
+     *  @param value   the value of the property being closed
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(String name, long size, byte[] value);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java
index 46477b9..cc466a6 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_compare_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param value1  the value of the first property being compared
+     *  @param value2  the value of the second property being compared
+     *  @param size    the size of the property value
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(byte[] value1, byte[] value2, long size);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java
index 57994bb5..59e4bb8 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_copy_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param name      the name of the property being copied
+     *  @param size      the size of the property value
+     *  @param value     the value of the property being copied
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(String name, long size, byte[] value);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java
index 8791c22..5c6df7a 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_create_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param name      the name of the property list being created
+     *  @param size      the size of the property value
+     *  @param value     the initial value for the property being created
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(String name, long size, byte[] value);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java
index 46cd097..5206d4f 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java
@@ -13,7 +13,28 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_delete_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id   the ID of the property list the property is deleted from
+     *  @param name      the name of the property being deleted
+     *  @param size      the size of the property value
+     *  @param value     the value of the property being deleted
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, String name, long size, byte[] value);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java
index 04599a0..8f44497 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java
@@ -13,7 +13,28 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_get_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id   the ID for the property list being queried
+     *  @param name      the name of the property being queried
+     *  @param size      the size of the property value
+     *  @param value     the value being retrieved for the property
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, String name, long size, byte[] value);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java
index 6ac750f..2a2d3a1 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java
@@ -13,7 +13,28 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_set_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id   the ID for the property list being modified
+     *  @param name      the name of the property being modified
+     *  @param size      the size of the property value
+     *  @param value     the value being set for the property
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, String name, long size, byte[] value);
 }
diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
index 1e4b5fd..70fdd11 100644
--- a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
+++ b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
@@ -31,6 +31,9 @@ package hdf.hdf5lib.exceptions;
  *
  */
 public class HDF5Exception extends RuntimeException {
+    /**
+     *  the specified detail message of this exception
+     */
     protected String detailMessage;
 
     /**
diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java
index ea4a89a..fea5b6d 100644
--- a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java
+++ b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java
@@ -13,6 +13,12 @@
 
 package hdf.hdf5lib.exceptions;
 
+/**
+ * The class HDF5LibraryException returns errors raised by the HDF5 library.
+ * 

+ * This sub-class represents HDF-5 major error code H5E_REFERENCE
+ */
+
 public class HDF5ReferenceException extends HDF5LibraryException {
     /**
      * Constructs an HDF5ReferenceException with no specified
diff --git a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
index 20863dc..a118d05 100644
--- a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for H5Pget_mdc_config/H5Pset_mdc_config
+/**
+ * Information struct for H5Pget_mdc_config/H5Pset_mdc_config
+ *
+ */
 public class H5AC_cache_config_t implements Serializable{
     private static final long serialVersionUID = -6748085696476149972L;
     // general configuration fields:
diff --git a/java/src/hdf/hdf5lib/structs/H5A_info_t.java b/java/src/hdf/hdf5lib/structs/H5A_info_t.java
index a46a495..cd7a397 100644
--- a/java/src/hdf/hdf5lib/structs/H5A_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5A_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name)
+/**
+ * Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name)
+ *
+ */
 public class H5A_info_t implements Serializable{
     private static final long serialVersionUID = 2791443594041667613L;
     public boolean corder_valid; // Indicate if creation order is valid
diff --git a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java
index 257ad05..083537f 100644
--- a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for Attribute (For H5Ewalk)
+/**
+ * Information struct for Attribute (For H5Ewalk)
+ *
+ */
 public class H5E_error2_t implements Serializable{
     private static final long serialVersionUID = 279144359041667613L;
 
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
index 9fcff2e..26690ec 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
@@ -16,7 +16,7 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-/*
+/**
  * Java representation of the HDFS VFD file access property list (fapl)
  * structure.
  *
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
index a899e10..735cc7e 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
@@ -16,7 +16,7 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-/*
+/**
  * Java representation of the ROS3 VFD file access property list (fapl)
  * structure.
  *
diff --git a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java
index 4664b5b..836b683 100644
--- a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for object (for H5Fget_info)
+/**
+ * Information struct for object (for H5Fget_info)
+ *
+ */
 public class H5F_info2_t implements Serializable{
     private static final long serialVersionUID = 4691681162544054518L;
     public int         super_version;    // Superblock version #
diff --git a/java/src/hdf/hdf5lib/structs/H5G_info_t.java b/java/src/hdf/hdf5lib/structs/H5G_info_t.java
index 56c876e..9a5c72e 100644
--- a/java/src/hdf/hdf5lib/structs/H5G_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5G_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+/**
+ * Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+ *
+ */
 public class H5G_info_t implements Serializable{
     private static final long serialVersionUID = -3746463015312132912L;
     public int storage_type; // Type of storage for links in group
diff --git a/java/src/hdf/hdf5lib/structs/H5L_info_t.java b/java/src/hdf/hdf5lib/structs/H5L_info_t.java
index 3bbb189..a595708 100644
--- a/java/src/hdf/hdf5lib/structs/H5L_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5L_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for link (for H5Lget_info/H5Lget_info_by_idx)
+/**
+ * Information struct for link (for H5Lget_info/H5Lget_info_by_idx)
+ *
+ */
 public class H5L_info_t implements Serializable{
     private static final long serialVersionUID = -4754320605310155033L;
     public int     type;
diff --git a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java
index 73aaa47..df76638 100644
--- a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-// Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+/**
+ * Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+ *
+ */
 public class H5O_hdr_info_t implements Serializable {
     private static final long serialVersionUID = 7883826382952577189L;
     public int version;       /* Version number of header format in file */
@@ -56,25 +59,25 @@ public class H5O_hdr_info_t implements Serializable {
         H5O_hdr_info_t info = (H5O_hdr_info_t) o;
 
         if (this.version != info.version)
-        	return false;
+            return false;
         if (this.nmesgs != info.nmesgs)
-        	return false;
+            return false;
         if (this.nchunks != info.nchunks)
-        	return false;
+            return false;
         if (this.flags != info.flags)
-        	return false;
+            return false;
         if (this.space_total != info.space_total)
-        	return false;
+            return false;
         if (this.space_meta != info.space_meta)
-        	return false;
+            return false;
         if (this.space_mesg != info.space_mesg)
-        	return false;
+            return false;
         if (this.space_free != info.space_free)
-        	return false;
+            return false;
         if (this.mesg_present != info.mesg_present)
-        	return false;
+            return false;
         if (this.mesg_shared != info.mesg_shared)
-        	return false;
+            return false;
 
         return true;
     }
diff --git a/java/src/hdf/hdf5lib/structs/H5O_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_info_t.java
index 5dd078f..8dedeca 100644
--- a/java/src/hdf/hdf5lib/structs/H5O_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5O_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-// Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+/**
+ * Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+ *
+ */
 public class H5O_info_t implements Serializable {
     private static final long serialVersionUID = 4691681163544054518L;
     public long   fileno;     /* File number that object is located in */
diff --git a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
index 7159f02..1c3ab80 100644
--- a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+/**
+ * Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+ *
+ */
 public class H5_ih_info_t implements Serializable {
     private static final long serialVersionUID = -142238015615462707L;
     public long     index_size;     /* btree and/or list */
@@ -38,9 +41,9 @@ public class H5_ih_info_t implements Serializable {
         H5_ih_info_t info = (H5_ih_info_t) o;
 
         if (this.index_size != info.index_size)
-        	return false;
+            return false;
         if (this.heap_size != info.heap_size)
-        	return false;
+            return false;
 
         return true;
     }
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 3c8fc68..c0dcbb8 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -355,6 +355,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1BADGROUP(JNIEnv *env, jclass cls)
     return H5E_BADGROUP;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1BADITER(JNIEnv *env, jclass cls)
+{
+    return H5E_BADITER;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1BADMESG(JNIEnv *env, jclass cls)
 {
     return H5E_BADMESG;
@@ -404,8 +409,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANAPPLY(JNIEnv *env, jclass cls)
 {
     return H5E_CANAPPLY;
 }
-/*JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls) { return H5E_CANTALLOC; }*/
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTALLOC;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTAPPEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTAPPEND;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTATTACH(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTATTACH;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLEAN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCLEAN;
+}
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLIP(JNIEnv *env, jclass cls)
 {
@@ -417,6 +440,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEFILE(JNIEnv *env, jclass cls)
     return H5E_CANTCLOSEFILE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEOBJ(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCLOSEOBJ;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPARE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCOMPARE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPUTE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCOMPUTE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCONVERT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTCONVERT;
@@ -427,6 +465,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOPY(JNIEnv *env, jclass cls)
     return H5E_CANTCOPY;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCORK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCORK;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOUNT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTCOUNT;
@@ -452,11 +495,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDELETE(JNIEnv *env, jclass cls)
     return H5E_CANTDELETE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDEPEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTDEPEND;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDIRTY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTDIRTY;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFILTER(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTFILTER;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTENCODE(JNIEnv *env, jclass cls)
 {
     return H5E_CANTENCODE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXPUNGE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTEXPUNGE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXTEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTEXTEND;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFLUSH(JNIEnv *env, jclass cls)
 {
     return H5E_CANTFLUSH;
@@ -467,11 +535,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFREE(JNIEnv *env, jclass cls)
     return H5E_CANTFREE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGATHER(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTGATHER;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGC(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTGC;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGET(JNIEnv *env, jclass cls)
 {
     return H5E_CANTGET;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGETSIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTGETSIZE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINC(JNIEnv *env, jclass cls)
 {
     return H5E_CANTINC;
@@ -482,6 +565,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINIT(JNIEnv *env, jclass cls)
     return H5E_CANTINIT;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINS(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTINS;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINSERT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTINSERT;
@@ -502,11 +590,56 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCK(JNIEnv *env, jclass cls)
     return H5E_CANTLOCK;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCKFILE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTLOCKFILE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKCLEAN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKCLEAN;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKDIRTY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKDIRTY;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKSERIALIZED(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKSERIALIZED;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKUNSERIALIZED(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKUNSERIALIZED;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMERGE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMERGE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMODIFY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMODIFY;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMOVE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMOVE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNEXT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTNEXT;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNOTIFY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTNOTIFY;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENFILE(JNIEnv *env, jclass cls)
 {
     return H5E_CANTOPENFILE;
@@ -516,8 +649,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENOBJ(JNIEnv *env, jclass cls)
 {
     return H5E_CANTOPENOBJ;
 }
-/*JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls) { return H5E_CANTRECV; }*/
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPERATE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTOPERATE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPACK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTPACK;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPIN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTPIN;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPROTECT(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTPROTECT;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRECV;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREDISTRIBUTE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTREDISTRIBUTE;
+}
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREGISTER(JNIEnv *env, jclass cls)
 {
@@ -529,6 +690,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRELEASE(JNIEnv *env, jclass cls)
     return H5E_CANTRELEASE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREMOVE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTREMOVE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRENAME(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRENAME;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESET(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRESET;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRESIZE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESTORE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRESTORE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREVIVE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTREVIVE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSHRINK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSHRINK;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSELECT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTSELECT;
@@ -539,16 +735,71 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSET(JNIEnv *env, jclass cls)
     return H5E_CANTSET;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSERIALIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSERIALIZE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSORT(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSORT;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSPLIT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTSPLIT;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSWAP(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSWAP;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTTAG(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTTAG;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNCORK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNCORK;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNDEPEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNDEPEND;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCK(JNIEnv *env, jclass cls)
 {
     return H5E_CANTUNLOCK;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCKFILE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNLOCKFILE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPIN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNPIN;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPROTECT(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNPROTECT;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNSERIALIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNSERIALIZE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUPDATE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUPDATE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CLOSEERROR(JNIEnv *env, jclass cls)
 {
     return H5E_CLOSEERROR;
@@ -559,6 +810,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1COMPLEN(JNIEnv *env, jclass cls)
     return H5E_COMPLEN;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CONTEXT(JNIEnv *env, jclass cls)
+{
+    return H5E_CONTEXT;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1DATASET(JNIEnv *env, jclass cls)
 {
     return H5E_DATASET;
@@ -584,16 +840,31 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1DUPCLASS(JNIEnv *env, jclass cls)
     return H5E_DUPCLASS;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1EARRAY(JNIEnv *env, jclass cls)
+{
+    return H5E_EARRAY;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1EFL(JNIEnv *env, jclass cls)
 {
     return H5E_EFL;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1ERROR(JNIEnv *env, jclass cls)
+{
+    return H5E_ERROR;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1EXISTS(JNIEnv *env, jclass cls)
 {
     return H5E_EXISTS;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1FARRAY(JNIEnv *env, jclass cls)
+{
+    return H5E_FARRAY;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1FCNTL(JNIEnv *env, jclass cls)
 {
     return H5E_FCNTL;
@@ -614,6 +885,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1FILEOPEN(JNIEnv *env, jclass cls)
     return H5E_FILEOPEN;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1FSPACE(JNIEnv *env, jclass cls)
+{
+    return H5E_FSPACE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1FUNC(JNIEnv *env, jclass cls)
 {
     return H5E_FUNC;
@@ -624,6 +900,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1HEAP(JNIEnv *env, jclass cls)
     return H5E_HEAP;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1INCONSISTENTSTATE(JNIEnv *env, jclass cls)
+{
+    return H5E_INCONSISTENTSTATE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1INTERNAL(JNIEnv *env, jclass cls)
 {
     return H5E_INTERNAL;
@@ -643,6 +924,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1LINKCOUNT(JNIEnv *env, jclass cls)
 {
     return H5E_LINKCOUNT;
 }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1LOGGING(JNIEnv *env, jclass cls)
+{
+    return H5E_LOGGING;
+}
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1MAJOR(JNIEnv *env, jclass cls)
 {
@@ -669,6 +955,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1MPIERRSTR(JNIEnv *env, jclass cls)
     return H5E_MPIERRSTR;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NLINKS(JNIEnv *env, jclass cls)
+{
+    return H5E_NLINKS;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NO_1INDEPENDENT(JNIEnv *env, jclass cls)
+{
+    return H5E_NO_INDEPENDENT;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NOENCODER(JNIEnv *env, jclass cls)
+{
+    return H5E_NOENCODER;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1NOFILTER(JNIEnv *env, jclass cls)
 {
     return H5E_NOFILTER;
@@ -709,16 +1010,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTHDF5(JNIEnv *env, jclass cls)
     return H5E_NOTHDF5;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTREGISTERED(JNIEnv *env, jclass cls)
+{
+    return H5E_NOTREGISTERED;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1OBJOPEN(JNIEnv *env, jclass cls)
+{
+    return H5E_OBJOPEN;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1OHDR(JNIEnv *env, jclass cls)
 {
     return H5E_OHDR;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1OPENERROR(JNIEnv *env, jclass cls)
+{
+    return H5E_OPENERROR;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1OVERFLOW(JNIEnv *env, jclass cls)
 {
     return H5E_OVERFLOW;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1PAGEBUF(JNIEnv *env, jclass cls)
+{
+    return H5E_PAGEBUF;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1PATH(JNIEnv *env, jclass cls)
+{
+    return H5E_PATH;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1PLINE(JNIEnv *env, jclass cls)
 {
     return H5E_PLINE;
@@ -729,6 +1055,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1PLIST(JNIEnv *env, jclass cls)
     return H5E_PLIST;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1PLUGIN(JNIEnv *env, jclass cls)
+{
+    return H5E_PLUGIN;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1PROTECT(JNIEnv *env, jclass cls)
 {
     return H5E_PROTECT;
@@ -759,11 +1090,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SEEKERROR(JNIEnv *env, jclass cls)
     return H5E_SEEKERROR;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SETDISALLOWED(JNIEnv *env, jclass cls)
+{
+    return H5E_SETDISALLOWED;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1SETLOCAL(JNIEnv *env, jclass cls)
 {
     return H5E_SETLOCAL;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SLIST(JNIEnv *env, jclass cls)
+{
+    return H5E_SLIST;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SOHM(JNIEnv *env, jclass cls)
+{
+    return H5E_SOHM;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1STORAGE(JNIEnv *env, jclass cls)
 {
     return H5E_STORAGE;
@@ -774,6 +1120,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SYM(JNIEnv *env, jclass cls)
     return H5E_SYM;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSERRSTR(JNIEnv *env, jclass cls)
+{
+    return H5E_SYSERRSTR;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSTEM(JNIEnv *env, jclass cls)
+{
+    return H5E_SYSTEM;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1TRAVERSE(JNIEnv *env, jclass cls)
+{
+    return H5E_TRAVERSE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1TRUNCATED(JNIEnv *env, jclass cls)
 {
     return H5E_TRUNCATED;
@@ -1798,6 +2159,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5PL_1TYPE_1FILTER(JNIEnv *env, jclass cls)
     return H5PL_TYPE_FILTER;
 }
 JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5PL_1TYPE_1NONE(JNIEnv *env, jclass cls)
+{
+    return H5PL_TYPE_NONE;
+}
+JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5PL_1FILTER_1PLUGIN(JNIEnv *env, jclass cls)
 {
     return H5PL_FILTER_PLUGIN;
diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c
index d23f6cc..95be74d 100644
--- a/java/src/jni/h5sImp.c
+++ b/java/src/jni/h5sImp.c
@@ -1340,6 +1340,389 @@ done:
     return;
 } /* end Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_copy
+ * Signature: (JJ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *env, jclass clss, jlong dst_id, jlong src_id)
+{
+    herr_t    status = FAIL;
+
+    UNUSED(clss);
+
+    if ((status = H5Sselect_copy((hid_t)dst_id, (hid_t)src_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1copy */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_shape_same
+ * Signature: (JJ)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *env, jclass clss, jlong space1_id, jlong space2_id)
+{
+    htri_t bval = JNI_FALSE;
+
+    UNUSED(clss);
+
+    if ((bval = H5Sselect_shape_same((hid_t)space1_id, (hid_t)space2_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
+
+done:
+    return (jboolean)bval;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_adjust
+ * Signature: (J[J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *env, jclass clss, jlong space_id, jlongArray offset)
+{
+    jboolean  isCopy;
+    hssize_t *offst       = NULL;
+    jlong *   offsetP     = NULL;
+    jsize     offset_rank = -1;
+    int       i, rank = -1;
+    herr_t    status = FAIL;
+
+    UNUSED(clss);
+
+    if (space_id < 0)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: invalid dataspace ID");
+
+    if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == offset) {
+        offsetP = NULL;
+        offst   = (hssize_t *)offsetP;
+    }
+    else {
+        if ((offset_rank = ENVPTR->GetArrayLength(ENVONLY, offset)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset length < 0");
+        }
+
+        if (offset_rank != rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset rank doesn't match dataspace rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, offset, offsetP, &isCopy, "H5Sselect_adjust: offset not pinned");
+
+        if (NULL == (offst = (hssize_t *)HDmalloc((size_t)offset_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_adjust: failed to allocate offset buffer");
+    }
+
+    if ((status = H5Sselect_adjust(space_id, (hssize_t *)offst)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    for (i = 0; i < offset_rank; i++) {
+        offsetP[i] = (jlong)offst[i];
+    } /* end for */
+
+done:
+    if (offst)
+        HDfree(offst);
+    if (offsetP)
+        UNPIN_LONG_ARRAY(ENVONLY, offset, offsetP, (status < 0) ? JNI_ABORT : 0);
+
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1adjust */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_intersect_block
+ * Signature: (J[J[J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *env, jclass clss, jlong space_id, jlongArray start,
+                                                jlongArray end)
+{
+    htri_t   bval = JNI_FALSE;
+    jboolean isCopy;
+    hsize_t *strt = NULL, *nd = NULL;
+    jlong *  startP = NULL, *endP = NULL;
+    jsize    start_rank = -1, end_rank = -1;
+    int      i, rank                   = -1;
+
+    UNUSED(clss);
+
+    if (space_id < 0)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: invalid dataspace ID");
+
+    if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == start) {
+        startP = NULL;
+        strt   = (hsize_t *)startP;
+    }
+    else {
+        if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: start length < 0");
+        }
+
+        if (start_rank != rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY,
+                                  "H5Sselect_intersect_block: start rank doesn't match dataspace rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Sselect_intersect_block: start not pinned");
+
+        if (NULL == (strt = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate start buffer");
+    }
+
+    if (NULL == end) {
+        endP = NULL;
+        nd   = (hsize_t *)endP;
+    }
+    else {
+        if ((end_rank = ENVPTR->GetArrayLength(ENVONLY, end)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: end array length < 0");
+        }
+
+        if (end_rank != rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY,
+                                  "H5Sselect_intersect_block: end rank doesn't match dataspace rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, end, endP, &isCopy, "H5Sselect_intersect_block: end not pinned");
+
+        if (NULL == (nd = (hsize_t *)HDmalloc((size_t)end_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate end buffer");
+    }
+
+    if ((bval = H5Sselect_intersect_block(space_id, (hsize_t *)strt, (hsize_t *)nd)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
+
+    for (i = 0; i < start_rank; i++) {
+        startP[i] = (jlong)strt[i];
+        endP[i]   = (jlong)nd[i];
+    } /* end for */
+
+done:
+    if (strt)
+        HDfree(strt);
+    if (startP)
+        UNPIN_LONG_ARRAY(ENVONLY, start, startP, (bval < 0) ? JNI_ABORT : 0);
+    if (nd)
+        HDfree(nd);
+    if (endP)
+        UNPIN_LONG_ARRAY(ENVONLY, end, endP, (bval < 0) ? JNI_ABORT : 0);
+
+    return (jboolean)bval;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_project_intersection
+ * Signature: (JJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *env, jclass clss, jlong src_space_id,
+                                                     jlong dst_space_id, jlong src_intersect_space_id)
+{
+    hid_t sid = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if ((sid = H5Sselect_project_intersection(src_space_id, dst_space_id, src_intersect_space_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+
+    return (jlong)sid;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_hyperslab
+ * Signature: (JI[J[J[J[J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_id, jint op, jlongArray start,
+                                          jlongArray stride, jlongArray count, jlongArray block)
+{
+    jboolean isCopy;
+    hsize_t *strt = NULL, *strd = NULL, *cnt = NULL, *blk = NULL;
+    hsize_t *lp     = NULL;
+    jlong *  startP = NULL, *strideP = NULL, *countP = NULL, *blockP = NULL;
+    jlong *  jlp = NULL;
+    jsize    start_rank, stride_rank, count_rank, block_rank;
+    int      i;
+    hid_t    sid = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if (NULL == start)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start is NULL");
+    if (NULL == count)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count is NULL");
+
+    if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start array length < 0");
+    }
+    if ((count_rank = ENVPTR->GetArrayLength(ENVONLY, count)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count array length < 0");
+    }
+
+    if (start_rank != count_rank)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count and start have different rank!");
+
+    PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Scombine_hyperslab: start not pinned");
+
+    if (NULL == (strt = lp = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t))))
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate start buffer");
+
+    jlp = (jlong *)startP;
+    for (i = 0; i < start_rank; i++) {
+        *lp = (hsize_t)*jlp;
+        lp++;
+        jlp++;
+    } /* end if */
+
+    PIN_LONG_ARRAY(ENVONLY, count, countP, &isCopy, "H5Scombine_hyperslab: count not pinned");
+
+    if (NULL == (cnt = lp = (hsize_t *)HDmalloc((size_t)count_rank * sizeof(hsize_t))))
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate count buffer");
+
+    jlp = (jlong *)countP;
+    for (i = 0; i < count_rank; i++) {
+        *lp = (hsize_t)*jlp;
+        lp++;
+        jlp++;
+    } /* end if */
+
+    if (NULL == stride) {
+        strideP = NULL;
+        strd    = (hsize_t *)strideP;
+    }
+    else {
+        if ((stride_rank = ENVPTR->GetArrayLength(ENVONLY, stride)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride array length < 0");
+        }
+
+        if (stride_rank != start_rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride and start have different rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, stride, strideP, &isCopy, "H5Scombine_hyperslab: stride not pinned");
+
+        if (NULL == (strd = lp = (hsize_t *)HDmalloc((size_t)stride_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate stride buffer");
+
+        jlp = (jlong *)strideP;
+        for (i = 0; i < stride_rank; i++) {
+            *lp = (hsize_t)*jlp;
+            lp++;
+            jlp++;
+        } /* end if */
+    }
+
+    if (NULL == block) {
+        blockP = NULL;
+        blk    = (hsize_t *)blockP;
+    }
+    else {
+        if ((block_rank = ENVPTR->GetArrayLength(ENVONLY, block)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block array length < 0");
+        }
+
+        if (block_rank != start_rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block and start have different rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, block, blockP, &isCopy, "H5Scombine_hyperslab: block not pinned");
+
+        if (NULL == (blk = lp = (hsize_t *)HDmalloc((size_t)block_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate block buffer");
+
+        jlp = (jlong *)blockP;
+        for (i = 0; i < block_rank; i++) {
+            *lp = (hsize_t)*jlp;
+            lp++;
+            jlp++;
+        } /* end for */
+    }
+
+    if ((sid = H5Scombine_hyperslab(space_id, (H5S_seloper_t)op, (const hsize_t *)strt, (const hsize_t *)strd,
+                                    (const hsize_t *)cnt, (const hsize_t *)blk)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (blk)
+        HDfree(blk);
+    if (blockP)
+        UNPIN_LONG_ARRAY(ENVONLY, block, blockP, JNI_ABORT);
+    if (strd)
+        HDfree(strd);
+    if (strideP)
+        UNPIN_LONG_ARRAY(ENVONLY, stride, strideP, JNI_ABORT);
+    if (cnt)
+        HDfree(cnt);
+    if (countP)
+        UNPIN_LONG_ARRAY(ENVONLY, count, countP, JNI_ABORT);
+    if (strt)
+        HDfree(strt);
+    if (startP)
+        UNPIN_LONG_ARRAY(ENVONLY, start, startP, JNI_ABORT);
+
+    return (jlong)sid;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1hyperslab */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Smodify_select
+ * Signature: (JIJ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id)
+{
+    herr_t    status = FAIL;
+
+    UNUSED(clss);
+
+    if ((status = H5Smodify_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Smodify_1select */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_select
+ * Signature: (JIJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id)
+{
+    hid_t sid = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if ((sid = H5Scombine_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+
+    return (jlong)sid;
+} /* end Java_hdf_hdf5lib_H5_H5Scombine_1select */
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5sImp.h b/java/src/jni/h5sImp.h
index ee28b39..83255c1 100644
--- a/java/src/jni/h5sImp.h
+++ b/java/src/jni/h5sImp.h
@@ -259,6 +259,65 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sis_1regular_1hyperslab(JNIEnv
 JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab(JNIEnv *, jclass, jlong, jlongArray,
                                                                       jlongArray, jlongArray, jlongArray);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_copy
+ * Signature: (JJ)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *, jclass, jlong, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_shape_same
+ * Signature: (JJ)Z
+ */
+JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *, jclass, jlong, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_adjust
+ * Signature: (J[J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *, jclass, jlong, jlongArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_intersect_block
+ * Signature: (J[J[J)Z
+ */
+JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *, jclass, jlong,
+                                                                           jlongArray, jlongArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_project_intersection
+ * Signature: (JJJ)J
+ */
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *, jclass, jlong, jlong,
+                                                                             jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_hyperslab
+ * Signature: (JI[J[J[J[J)J
+ */
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *, jclass, jlong, jint, jlongArray,
+                                                                  jlongArray, jlongArray, jlongArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Smodify_select
+ * Signature: (JIJ)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *, jclass, jlong, jint, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_select
+ * Signature: (JIJ)J
+ */
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *, jclass, jlong, jint, jlong);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/test/TestH5Sbasic.java b/java/test/TestH5Sbasic.java
index 2173647..9874584 100644
--- a/java/test/TestH5Sbasic.java
+++ b/java/test/TestH5Sbasic.java
@@ -242,4 +242,142 @@ public class TestH5Sbasic {
         H5.H5Sdecode(null);
     }
 
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sget_regular_hyperslab_invalid() throws Throwable {
+        long q_start[] = new long[2];
+        long q_stride[] = new long[2];
+        long q_count[] = new long[2];
+        long q_block[] = new long[2];
+
+        H5.H5Sget_regular_hyperslab(-1, q_start, q_stride, q_count, q_block);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Sselect_copy_invalid() throws Throwable {
+        H5.H5Sselect_copy(-1, -1);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException.class)
+    public void testH5Sselect_shape_same_invalid() throws Throwable {
+        H5.H5Sselect_shape_same(-1, -1);
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_adjust_invalid() throws Throwable {
+        long offset[][] = {{0,1},{2,4},{5,6}};
+        H5.H5Sselect_adjust(-1, offset);
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_adjust_rank_offset() throws Throwable {
+        long sid = -1;
+        long offset[][] = {{0,1},{2,4},{5,6}};
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Sselect_adjust(sid, offset);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_intersect_block_invalid() throws Throwable {
+        long start[] = new long[2];
+        long end[] = new long[2];
+        H5.H5Sselect_intersect_block(-1, start, end);
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_intersect_block_rank_start() throws Throwable {
+        long sid = -1;
+        long start[] = new long[2];
+        long end[] = null;
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Sselect_intersect_block(sid, start, end);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_intersect_block_rank_end() throws Throwable {
+        long sid = -1;
+        long start[] = null;
+        long end[] = new long[2];
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Sselect_intersect_block(sid, start, end);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException.class)
+    public void testH5Sselect_project_intersection_invalid() throws Throwable {
+        H5.H5Sselect_project_intersection(-1, -1, -1);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Scombine_hyperslab_invalid() throws Throwable {
+        long start[] = new long[2];
+        long count[] = new long[2];
+        H5.H5Scombine_hyperslab(-1, 0, start, null, count, null);
+    }
+
+    @Test(expected = NullPointerException.class)
+    public void testH5Scombine_hyperslab_null_start() throws Throwable {
+        long sid = -1;
+        long start[] = null;
+        long stride[] = null;
+        long count[] = new long[2];
+        long block[] = null;
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Scombine_hyperslab(sid, 0, start, stride, count, block);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = NullPointerException.class)
+    public void testH5Scombine_hyperslab_null_count() throws Throwable {
+        long sid = -1;
+        long start[] = new long[2];
+        long stride[] = null;
+        long count[] = null;
+        long block[] = null;
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Scombine_hyperslab(sid, 0, start, stride, count, block);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Smodify_select_invalid() throws Throwable {
+        H5.H5Smodify_select(-1, 0, -1);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Scombine_select_invalid() throws Throwable {
+        H5.H5Scombine_select(-1, 0, -1);
+    }
+
 }
diff --git a/java/test/testfiles/JUnit-TestH5Sbasic.txt b/java/test/testfiles/JUnit-TestH5Sbasic.txt
index 707878e..3422442 100644
--- a/java/test/testfiles/JUnit-TestH5Sbasic.txt
+++ b/java/test/testfiles/JUnit-TestH5Sbasic.txt
@@ -5,18 +5,32 @@ JUnit version 4.11
 .testH5Sdecode_null
 .testH5Screate_simple_dims_exceed
 .testH5Screate_simple_unlimted_1d
+.testH5Sselect_intersect_block_rank_start
+.testH5Sget_regular_hyperslab_invalid
+.testH5Sselect_adjust_rank_offset
 .testH5Screate_simple_dims_invalid
 .testH5Screate_scalar
 .testH5Screate_simple
+.testH5Sselect_project_intersection_invalid
 .testH5Screate_simple_rank_invalid
 .testH5Sget_simple_extent_type_invalid
+.testH5Scombine_hyperslab_invalid
+.testH5Scombine_hyperslab_null_count
+.testH5Scombine_hyperslab_null_start
 .testH5Sencode_invalid
 .testH5Screate_null
 .testH5Screate_simple_extent
 .testH5Screate_invalid
+.testH5Sselect_intersect_block_invalid
+.testH5Sselect_adjust_invalid
 .testH5Screate_simple_unlimted
+.testH5Sselect_shape_same_invalid
+.testH5Smodify_select_invalid
+.testH5Scombine_select_invalid
+.testH5Sselect_copy_invalid
+.testH5Sselect_intersect_block_rank_end
 
 Time:  XXXX
 
-OK (16 tests)
+OK (30 tests)
 
-- 
cgit v0.12


From 2bdad92a26662256704deed7974ea81a0635a6b9 Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Thu, 5 Nov 2020 11:30:04 -0600
Subject: HDFFV-10868 add release note

---
 release_docs/RELEASE.txt | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 654d2c0..9942c19 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -86,7 +86,14 @@ New Features
 
     Java Library:
     ----------------
-    - 
+    - Added new H5S functions.
+
+      H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust,
+      H5Sselect_intersect_block, H5Sselect_project_intersection,
+      H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select
+      wrapper functions added.
+
+      (ADB - 2020/10/27, HDFFV-10868)
 
     Tools:
     ------
-- 
cgit v0.12