diff options
Diffstat (limited to 'java/src/hdf/hdf5lib/H5.java')
| -rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 3202 |
1 files changed, 2934 insertions, 268 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 3d0b308..aef0ba1 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -241,10 +241,14 @@ public class H5 implements java.io.Serializable { */ public final static int LIB_VERSION[] = { 1, 13, 0 }; + /** + * 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; @@ -257,6 +261,9 @@ 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) @@ -468,6 +475,35 @@ 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; @@ -476,8 +512,8 @@ public class H5 implements java.io.Serializable { * * @param file_export_name * The file name to export data into. - * @param file_name - * The name of the HDF5 file containing the dataset. + * @param file_id + * The identifier of the HDF5 file containing the dataset. * @param object_path * The full path of the dataset to be exported. * @param binary_order @@ -489,10 +525,31 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native void H5export_dataset(String file_export_name, String file_name, + public synchronized static native void H5export_dataset(String file_export_name, long file_id, String object_path, int binary_order) throws HDF5LibraryException; /** + * H5export_attribute is a utility function to save data in a file. + * + * @param file_export_name + * The file name to export data into. + * @param dataset_id + * The identifier of the dataset containing the attribute. + * @param attribute_name + * The attribute to be exported. + * @param binary_order + * 99 - export data as text. + * 1 - export data as binary Native Order. + * 2 - export data as binary Little Endian. + * 3 - export data as binary Big Endian. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native void H5export_attribute(String file_export_name, long dataset_id, + String attribute_name, int binary_order) throws HDF5LibraryException; + + /** * H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled. * * @return true if hdf5 library implements threadsafe @@ -1016,7 +1073,7 @@ 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. @@ -1037,11 +1094,47 @@ 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); @@ -1141,63 +1234,343 @@ 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); } + /** + * 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 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 + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] 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 int 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 int 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_int(long attr_id, long mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_int(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 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. + * @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_long(long attr_id, long mem_type_id, long[] 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 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 H5Aread_long(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 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_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; @@ -1270,12 +1643,48 @@ public class H5 implements java.io.Serializable { 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 { @@ -1353,60 +1762,286 @@ public class H5 implements java.io.Serializable { 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 buf into the file. + * the application memory buffer buffer of variable-lenght strings into the file. * * ---- contributed by Rosetta Biosoftware * @@ -1415,7 +2050,7 @@ public class H5 implements java.io.Serializable { * @param mem_type_id * Identifier of the memory datatype. * @param buf - * Buffer with data to be written to the file. + * Buffer of variable-lenght strings with data to be written to the file. * * @return a non-negative value if successful * @@ -1922,12 +2557,60 @@ public class H5 implements java.io.Serializable { 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 { @@ -2043,65 +2726,411 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. + * + * @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 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 + * - data buffer is null. + **/ 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; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. + * + * @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 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_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); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. + * + * @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 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_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; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. + * + * @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. + * @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); } + /** + * 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 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 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; + /** + * 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 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 non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ 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); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. + * + * @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. + **/ 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; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. + * + * @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 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(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); } + /** + * 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 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 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_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; + /** + * 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 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 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_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; + /** + * 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 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 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); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght. + * + * @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 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 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; + /** + * 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 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 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_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; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght strings. + * + * @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 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_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; @@ -2170,7 +3199,7 @@ public class H5 implements java.io.Serializable { /** * 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. @@ -2198,12 +3227,60 @@ public class H5 implements java.io.Serializable { long file_space_id, long xfer_plist_id, byte[] 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 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(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); } + /** + * 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 obj + * 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 + * - 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) throws HDF5Exception, HDF5LibraryException, NullPointerException { @@ -2299,59 +3376,357 @@ public class H5 implements java.io.Serializable { return status; } + /** + * 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; + /** + * 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 H5Dwrite_double(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 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; + /** + * 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 H5Dwrite_float(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 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 + * - name is null. + **/ 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; + /** + * 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 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 + * - name is null. + **/ 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); } + /** + * 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 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 + * - name is null. + **/ 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 + * 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 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 + * - name is null. + **/ 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); } + /** + * 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. + * @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_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; @@ -2628,7 +4003,7 @@ 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. @@ -2657,6 +4032,31 @@ 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; @@ -2714,6 +4114,24 @@ 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; @@ -2950,6 +4368,19 @@ 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; /** @@ -3598,37 +5029,118 @@ public class H5 implements java.io.Serializable { return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, tokens, HDF5Constants.H5_INDEX_NAME); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, + /** + * 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 tokens + * OUT: Object token 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, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, tokens, indx_type, -1); + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, null, tokens, indx_type, -1); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, + /** + * 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 tokens + * OUT: Object token 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, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, indx_type, -1); + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, tokens, indx_type, -1); } - public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, + /** + * 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 tokens + * OUT: Object token 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, H5O_token_t[] tokens, 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[tokens.length]; @@ -3639,15 +5151,15 @@ 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, tokens, 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, tokens, 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, + private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, H5O_token_t[] tokens, int n, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException; @@ -3663,9 +5175,9 @@ 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. * @@ -3866,13 +5378,40 @@ 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. @@ -3885,10 +5424,44 @@ 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; /** @@ -5179,7 +6752,7 @@ 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; /** @@ -5210,8 +6783,30 @@ 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); // /////// unimplemented //////// @@ -5364,6 +6959,7 @@ 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 @@ -5371,6 +6967,19 @@ 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; @@ -5456,7 +7065,7 @@ 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. @@ -5524,6 +7133,19 @@ public class H5 implements java.io.Serializable { // 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) { @@ -5550,17 +7172,69 @@ 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 /////// @@ -5573,7 +7247,7 @@ public class H5 implements java.io.Serializable { * @param attributes * The maximun and minimum no. of attributes to be stored. * - * <pre> + * <pre> * 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 * </pre> @@ -5673,6 +7347,51 @@ public class H5 implements java.io.Serializable { 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. + *<p> + * The FLAGS argument is a bit vector of the following fields: + *<p> + * 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. + *<p> + * 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 int H5Pmodify_filter(long plist, long filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException; @@ -5844,9 +7563,37 @@ 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; /** @@ -5864,6 +7611,18 @@ 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; @@ -6334,11 +8093,35 @@ 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 @@ -6389,9 +8172,8 @@ 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. @@ -6403,6 +8185,19 @@ 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; @@ -6437,10 +8232,35 @@ 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; /** @@ -6471,8 +8291,40 @@ 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. + * <p> + * 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; /** @@ -6687,6 +8539,55 @@ public class H5 implements java.io.Serializable { public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close) throws HDF5LibraryException; + /** + * H5Pget_use_file_locking retrieves whether we are using file locking. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return indication if file locking is used. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native boolean H5Pget_use_file_locking(long fapl_id) + throws HDF5LibraryException; + + /** + * H5Pget_use_file_locking retrieves whether we ignore file locks when they are disabled. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return indication if file locking is ignored. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native boolean H5Pget_ignore_disabled_file_locking(long fapl_id) + throws HDF5LibraryException; + + /** + * H5Pset_file_locking sets parameters related to file locking. + * + * @param fapl_id + * IN: File access property list identifier + * + * @param use_file_locking + * IN: Whether the library will use file locking when opening files (mainly for SWMR semantics). + * + * @param ignore_when_disabled + * IN: Whether file locking will be ignored when disabled on a file system (useful for Lustre). + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native void H5Pset_file_locking(long fapl_id, boolean use_file_locking, boolean ignore_when_disabled) + throws HDF5LibraryException; + // ///// unimplemented ///// // herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info); // herr_t H5Pget_vol_id(hid_t plist_id, hid_t *vol_id); @@ -6767,6 +8668,25 @@ 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) { @@ -7002,9 +8922,37 @@ 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; @@ -7132,20 +9080,91 @@ 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. @@ -7445,6 +9464,20 @@ 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; @@ -7475,11 +9508,33 @@ public class H5 implements java.io.Serializable { 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; + /** + * 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; - public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException, - NullPointerException; + /** + * 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. @@ -7524,9 +9579,46 @@ 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; @@ -7724,8 +9816,32 @@ 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; @@ -7915,20 +10031,51 @@ public class H5 implements java.io.Serializable { // /////// 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. * @@ -7959,14 +10106,72 @@ 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; /** @@ -8044,17 +10249,99 @@ 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 //////// @@ -8762,50 +11049,7 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// - /** - * H5Sclose releases a dataspace. - * - * @param space_id - * Identifier of dataspace to release. - * - * @return a non-negative value 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");; - - 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 int _H5Sclose(long space_id) throws HDF5LibraryException; - - /** - * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id. - * - * @param space_id - * Identifier of dataspace to copy. - * @return a dataspace identifier if successful - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - **/ - public static long H5Scopy(long space_id) throws HDF5LibraryException { - long id = _H5Scopy(space_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Scopy add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; - } - - private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException; + /**************** Operations on dataspaces ********************/ /** * H5Screate creates a new dataspace of a particular type. @@ -8862,19 +11106,96 @@ public class H5 implements java.io.Serializable { throws HDF5Exception, NullPointerException; /** - * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. + * H5Sset_extent_simple sets or resets the size of an existing dataspace. * - * @param buf - * IN: Buffer for the data space object to be decoded. + * @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 new object handle + * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. **/ - public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; + 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 dataspace identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + 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); + } + + /** + * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id. + * + * @param space_id + * Identifier of dataspace to copy. + * @return a dataspace identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Scopy(long space_id) throws HDF5LibraryException { + long id = _H5Scopy(space_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Scopy add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException; + + /** + * H5Sclose releases a dataspace. + * + * @param space_id + * Identifier of dataspace to release. + * + * @return a non-negative value 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");; + + 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 int _H5Sclose(long space_id) throws HDF5LibraryException; /** * H5Sencode converts a data space description into binary form in a buffer. @@ -8890,154 +11211,139 @@ public class H5 implements java.io.Serializable { public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException; /** - * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the - * dataspace. + * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. * - * @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 buf + * IN: Buffer for the data space object to be decoded. * - * @return a non-negative value if successful + * @return a new object handle * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. **/ - public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) - throws HDF5LibraryException; + public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; /** - * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. + * H5Sget_simple_extent_npoints determines the number of elements in a 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 + * ID of the dataspace object to query + * @return the number of elements in the dataspace if successful * - * @return true if successful, else false + * @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 boolean H5Sextent_equal(long first_space_id, long second_space_id) - throws HDF5LibraryException; + public synchronized static native int H5Sget_simple_extent_ndims(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. - * <P> - * The start and end buffers must be large enough to hold the dataspace rank number of coordinates. + * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims + * and maxdims parameters. * - * @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 + * 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,with start and end initialized. + * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - start or end is null. + * - dims or maxdims is null. **/ - public synchronized static native int H5Sget_select_bounds(long spaceid, long[] start, long[] end) + public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims) throws HDF5LibraryException, NullPointerException; /** - * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection. + * H5Sis_simple determines whether a dataspace is a simple dataspace. * - * @param spaceid - * Identifier of dataspace to release. + * @param space_id + * Identifier of the dataspace to query * - * @return a non-negative value if successful + * @return true if is a simple dataspace * * @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 boolean H5Sis_simple(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. + * H5Sget_simple_extent_type queries a dataspace to determine the current class of a 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 <i>rank</i> longs. + * @param space_id + * Dataspace identifier. * - * @return a non-negative value if successful + * @return a dataspace class name 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 H5Sget_simple_extent_type(long 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: - * - * <pre> - * <"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. - * </pre> + * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. * - * @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 <i>rank</i> * 2 (corners) longs. + * @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. - * @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 int H5Sset_extent_none(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection. + * 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 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. **/ - public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException; + public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) + throws HDF5LibraryException; /** - * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace. + * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. * - * @param space_id - * IN: Identifier of the dataspace object to query + * @param first_space_id + * IN: The identifier for the first dataspace. + * @param second_space_id + * IN: The identifier for the seconddataspace. * - * @return the number of elements in the selection if successful + * @return true if successful, else false * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id) + throws HDF5LibraryException; + + /***************** Operations on dataspace selections *****************/ /** * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id. @@ -9053,76 +11359,118 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Sget_select_type(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. + * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace. * * @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 + * @return the number of elements in the selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - dims or maxdims 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 long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. + * 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 + * The identifier for the dataspace in which the selection is being reset. * - * @return the number of dimensions in the dataspace 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_simple_extent_ndims(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. + * H5Sselect_adjust moves a selection by subtracting an offset from it. * * @param space_id - * ID of the dataspace object to query - * @return the number of elements 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 + * - offset is null. **/ - public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException; + public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset) + throws HDF5LibraryException, NullPointerException; /** - * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. + * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places + * them into user-supplied buffers. + * <P> + * The start and end buffers must be large enough to hold the dataspace rank number of coordinates. * * @param space_id - * Dataspace identifier. + * Identifier of dataspace to release. + * @param start + * coordinates of lowest corner of bounding box. + * @param end + * coordinates of highest corner of bounding box. * - * @return a dataspace class name 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_type(long space_id) throws HDF5LibraryException; + public synchronized static native int H5Sget_select_bounds(long space_id, long[] start, long[] end) + throws HDF5LibraryException, NullPointerException; /** - * H5Sis_simple determines whether a dataspace is a simple 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 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 boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException; + + /** + * H5Sselect_intersect_block checks to see if the current selection in the + * dataspace intersects with the block given. * * @param space_id - * Identifier of the dataspace to query + * ID of dataspace pointer to compare + * @param start + * Starting coordinate of block + * @param end + * Opposite ("ending") coordinate of block * - * @return true if is a simple dataspace + * @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 boolean H5Sis_simple(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end) + throws HDF5LibraryException, NullPointerException; /** * H5Soffset_simple sets the offset of a simple dataspace space_id. @@ -9142,6 +11490,21 @@ public class H5 implements java.io.Serializable { 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. + * + * @param space_id + * IN: The identifier for the dataspace object to reset. + * @param offset + * IN: The offset at which to position the selection. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - offset array is null. + **/ public synchronized static int H5Soffset_simple(long space_id, long[] offset) throws HDF5Exception, NullPointerException { if (offset == null) { @@ -9172,6 +11535,18 @@ 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 @@ -9229,6 +11604,43 @@ 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 <i>rank</i> 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. * @@ -9268,76 +11680,118 @@ 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 @@ -9363,33 +11817,82 @@ 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 + * <pre> + * <"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. + * </pre> * - * @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 <i>rank</i> * 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; - // /////// 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 */ - // herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id); + /** + * 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 //////// + ///// Operations on dataspace selections ///// + + // + ///// Operations on dataspace selection iterators ///// + //public synchronized static native H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned flags); + //public synchronized static native H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size_t *nseq, + // size_t *nbytes, hsize_t *off, size_t *len); + //public synchronized static native H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id); + //public synchronized static native H5Ssel_iter_close(hid_t sel_iter_id); @@ -9737,6 +12240,23 @@ 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 }; @@ -10893,15 +13413,128 @@ public class H5 implements java.io.Serializable { // //////////////////////////////////////////////////////////// /// VOL Connector Functionality + /** + * H5VLregister_connector_by_name registers a new VOL connector as a member of the virtual object layer class. + * + * @param connector_name + * IN: name of the connector. + * @param vipl_id + * IN: VOL initialization property list which must be + * created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT). + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id); + /** + * H5VLregister_connector_by_value registers a new VOL connector as a member of the virtual object layer class. + * + * @param connector_value + * IN: value of the connector. + * @param vipl_id + * IN: VOL initialization property list which must be + * created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT). + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id); + /** + * H5VLis_connector_registered_by_name tests whether a VOL class has been registered. + * + * @param name + * IN: name of the connector. + * + * @return true if a VOL connector with that name has been registered + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native boolean H5VLis_connector_registered_by_name(String name); + /** + * H5VLis_connector_registered_by_value tests whether a VOL class has been registered. + * + * @param connector_value + * IN: value of the connector. + * + * @return true if a VOL connector with that value has been registered + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value); + /** + * H5VLget_connector_id retrieves the ID for a registered VOL connector for a given object. + * + * @param object_id + * IN: Identifier of the object. + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLget_connector_id(long object_id); + /** + * H5VLget_connector_id_by_name retrieves the ID for a registered VOL connector. + * + * @param name + * IN: name of the connector. + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLget_connector_id_by_name(String name); + /** + * H5VLget_connector_id_by_value retrieves the ID for a registered VOL connector. + * + * @param connector_value + * IN: value of the connector. + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLget_connector_id_by_value(int connector_value); + /** + * H5VLget_connector_name returns the connector name for the VOL associated with the + * object or file ID. + * + * @param object_id + * IN: Identifier of the object. + * + * @return the connector name + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native String H5VLget_connector_name(long object_id); + /** + * H5VLclose closes a VOL connector ID. + * + * @param connector_id + * IN: Identifier of the connector. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5VLclose(long connector_id); + /** + * H5VLunregister_connector removes a VOL connector ID from the library. + * + * @param connector_id + * IN: Identifier of the connector. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5VLunregister_connector(long connector_id); // /////// unimplemented //////// @@ -10914,11 +13547,44 @@ 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 //////// |