diff options
Diffstat (limited to 'java/src/hdf/hdf5lib/H5.java')
-rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 5325 |
1 files changed, 2891 insertions, 2434 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 2537123..443fb25 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -11,13 +11,13 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - package hdf.hdf5lib; import java.io.File; import java.nio.ByteBuffer; import java.util.Collection; import java.util.LinkedHashSet; + import hdf.hdf5lib.callbacks.H5A_iterate_cb; import hdf.hdf5lib.callbacks.H5A_iterate_t; import hdf.hdf5lib.callbacks.H5D_iterate_cb; @@ -34,24 +34,24 @@ import hdf.hdf5lib.callbacks.H5P_cls_copy_func_cb; import hdf.hdf5lib.callbacks.H5P_cls_copy_func_t; import hdf.hdf5lib.callbacks.H5P_cls_create_func_cb; import hdf.hdf5lib.callbacks.H5P_cls_create_func_t; -import hdf.hdf5lib.callbacks.H5P_prp_set_func_cb; -import hdf.hdf5lib.callbacks.H5P_prp_get_func_cb; -import hdf.hdf5lib.callbacks.H5P_prp_delete_func_cb; -import hdf.hdf5lib.callbacks.H5P_prp_copy_func_cb; -import hdf.hdf5lib.callbacks.H5P_prp_compare_func_cb; -import hdf.hdf5lib.callbacks.H5P_prp_close_func_cb; -import hdf.hdf5lib.callbacks.H5P_prp_create_func_cb; import hdf.hdf5lib.callbacks.H5P_iterate_cb; import hdf.hdf5lib.callbacks.H5P_iterate_t; +import hdf.hdf5lib.callbacks.H5P_prp_close_func_cb; +import hdf.hdf5lib.callbacks.H5P_prp_compare_func_cb; +import hdf.hdf5lib.callbacks.H5P_prp_copy_func_cb; +import hdf.hdf5lib.callbacks.H5P_prp_create_func_cb; +import hdf.hdf5lib.callbacks.H5P_prp_delete_func_cb; +import hdf.hdf5lib.callbacks.H5P_prp_get_func_cb; +import hdf.hdf5lib.callbacks.H5P_prp_set_func_cb; import hdf.hdf5lib.exceptions.HDF5Exception; import hdf.hdf5lib.exceptions.HDF5JavaException; import hdf.hdf5lib.exceptions.HDF5LibraryException; import hdf.hdf5lib.structs.H5AC_cache_config_t; import hdf.hdf5lib.structs.H5A_info_t; import hdf.hdf5lib.structs.H5E_error2_t; -import hdf.hdf5lib.structs.H5F_info2_t; import hdf.hdf5lib.structs.H5FD_hdfs_fapl_t; import hdf.hdf5lib.structs.H5FD_ros3_fapl_t; +import hdf.hdf5lib.structs.H5F_info2_t; import hdf.hdf5lib.structs.H5G_info_t; import hdf.hdf5lib.structs.H5L_info_t; import hdf.hdf5lib.structs.H5O_info_t; @@ -59,8 +59,8 @@ import hdf.hdf5lib.structs.H5O_info_t; /** * This class is the Java interface for the HDF5 library. * <p> - * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps a single - * HDF5 entry point, generally with the arguments and return codes analogous to the C interface. + * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps + * a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface. * <p> * For details of the HDF5 library, see the HDF5 Documentation at: * <a href="http://hdfgroup.org/HDF5/">http://hdfgroup.org/HDF5/</a> @@ -69,8 +69,8 @@ import hdf.hdf5lib.structs.H5O_info_t; * <b>Mapping of arguments for Java</b> * * <p> - * In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF - * Reference Manual. + * In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in + * the HDF Reference Manual. * * <table border=1> * <caption><b>HDF-5 C types to Java types</b> </caption> @@ -110,17 +110,19 @@ import hdf.hdf5lib.structs.H5O_info_t; * </table> * <b>General Rules for Passing Arguments and Results</b> * <p> - * In general, arguments passed <b>IN</b> to Java are the analogous basic types, as above. The exception is for arrays, - * which are discussed below. + * In general, arguments passed <b>IN</b> to Java are the analogous basic types, as above. The exception is + * for arrays, which are discussed below. * <p> - * The <i>return value</i> of Java methods is also the analogous type, as above. A major exception to that rule is that - * all HDF functions that return SUCCEED/FAIL are declared <i>boolean</i> in the Java version, rather than <i>int</i> as - * in the C. Functions that return a value or else FAIL are declared the equivalent to the C function. However, in most - * cases the Java method will raise an exception instead of returning an error code. See <a href="#ERRORS">Errors and - * Exceptions</a> below. + * The <i>return value</i> of Java methods is also the analogous type, as above. A major exception to that + * rule is that all HDF functions that return SUCCEED/FAIL are declared <i>boolean</i> in the Java version, + * rather than <i>int</i> as in the C. Functions that return a value or else FAIL are declared the + * equivalent to the C function. + * However, in most cases the Java method will raise an exception instead of returning an error code. + * See <a href="#ERRORS">Errors and Exceptions</a> below. * <p> - * Java does not support pass by reference of arguments, so arguments that are returned through <b>OUT</b> parameters - * must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in arrays. + * Java does not support pass by reference of arguments, so arguments that are returned through <b>OUT</b> + * parameters must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in + * arrays. * <p> * For instance, a function that returns two integers is declared: * @@ -141,53 +143,57 @@ import hdf.hdf5lib.structs.H5O_info_t; * </pre> * * <p> - * All the routines where this convention is used will have specific documentation of the details, given below. + * All the routines where this convention is used will have specific documentation of the details, given + * below. * <p> * <b>Arrays</b> * <p> - * HDF5 needs to read and write multi-dimensional arrays of any number type (and records). The HDF5 API describes the - * layout of the source and destination, and the data for the array passed as a block of bytes, for instance, + * HDF5 needs to read and write multi-dimensional arrays of any number type (and records). The HDF5 API + * describes the layout of the source and destination, and the data for the array passed as a block of + * bytes, for instance, * * <pre> - * herr_t H5Dread(long fid, long filetype, long memtype, long memspace, - * void * data); + * herr_t H5Dread(long fid, long filetype, long memtype, long memspace, void * data); * </pre> * * <p> - * where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of bytes that is the - * data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype of the array on - * disk (source) and in memory (destination). + * where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of bytes that + * is the data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype + * of the array ondisk (source) and in memory (destination). * <p> - * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, multidimensional - * arrays are definitely <i>not</i> laid out contiguously in memory. It would be infeasible to declare a separate - * routine for every combination of number type and dimensionality. For that reason, the - * <a href="./hdf.hdf5lib.HDFArray.html"><b>HDFArray</b></a> class is used to discover the type, shape, and size of the - * data array at run time, and to convert to and from a contiguous array of bytes in synchronized static native C order. + * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, + * multidimensional arrays are definitely <i>not</i> laid out contiguously in memory. It would be infeasible + * to declare a separate routine for every combination of number type and dimensionality. For that reason, the + * <a href="./hdf.hdf5lib.HDFArray.html"><b>HDFArray</b></a> class is used to discover the type, shape, and + * size of the data array at run time, and to convert to and from a contiguous array of bytes in synchronized + * static native C order. * <p> - * The upshot is that any Java array of numbers (either primitive or sub-classes of type <b>Number</b>) can be passed as - * an ``Object'', and the Java API will translate to and from the appropriate packed array of bytes needed by the C - * library. So the function above would be declared: + * The upshot is that any Java array of numbers (either primitive or sub-classes of type <b>Number</b>) can be + * passed as an ``Object'', and the Java API will translate to and from the appropriate packed array of bytes + * needed by the C library. So the function above would be declared: * * <pre> - * public synchronized static native int H5Dread(long fid, long filetype, long memtype, long memspace, Object data); + * public synchronized static native int H5Dread(long fid, long filetype, long memtype, long memspace, + * Object data); * </pre> * OPEN_IDS.addElement(id); - * and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or int[][][], or - * Double[][]. + * and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or + * int[][][], or Double[][]. * <p> * <b>HDF-5 Constants</b> * <p> - * The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs - * via the class <a href="./hdf.hdf5lib.HDF5Constants.html"> <b>HDF5Constants</b></a>. For example, the parameters for - * the h5open() call include two numeric values, <b><i>HDFConstants.H5F_ACC_RDWR</i></b> and - * <b><i>HDF5Constants.H5P_DEFAULT</i></b>. As would be expected, these numbers correspond to the C constants + * The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java + * programs via the class <a href="./hdf.hdf5lib.HDF5Constants.html"> <b>HDF5Constants</b></a>. For example, + * the parameters for the h5open() call include two numeric values, <b><i>HDFConstants.H5F_ACC_RDWR</i></b> + * and <b><i>HDF5Constants.H5P_DEFAULT</i></b>. + * As would be expected, these numbers correspond to the C constants * <b><i>H5F_ACC_RDWR</i></b> and <b><i>H5P_DEFAULT</i></b>. * <p> - * The HDF-5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and "hsize_t". - * These values are determined at run time by the HDF-5 C library. To support these parameters, the Java class - * <a href="./hdf.hdf5lib.HDF5CDataTypes.html"> <b>HDF5CDataTypes</b></a> looks up the values when initiated. The values - * can be accessed as public variables of the Java class, such as: + * The HDF-5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and + * "hsize_t". These values are determined at run time by the HDF-5 C library. To support these parameters, + * the Java class <a href="./hdf.hdf5lib.HDF5CDataTypes.html"> <b>HDF5CDataTypes</b></a> looks up the values + * when initiated. The values can be accessed as public variables of the Java class, such as: * * <pre> * long data_type = HDF5CDataTypes.JH5T_NATIVE_INT; @@ -198,20 +204,22 @@ import hdf.hdf5lib.structs.H5O_info_t; * <p> * <b>Error handling and Exceptions</b> * <p> - * The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is omitted from the - * JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural - * for Java programming. + * The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is omitted + * from the JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, + * but is very natural for Java programming. * <p> * The exceptions of the JHI5 are organized as sub-classes of the class - * <a href="./hdf.hdf5lib.exceptions.HDF5Exception.html"> <b>HDF5Exception</b></a>. There are two subclasses of - * <b>HDF5Exception</b>, <a href="./hdf.hdf5lib.exceptions.HDF5LibraryException.html"> <b>HDF5LibraryException</b></a> - * and <a href="./hdf.hdf5lib.exceptions.HDF5JavaException.html"> <b>HDF5JavaException</b></a>. The sub-classes of the - * former represent errors from the HDF-5 C library, while sub-classes of the latter represent errors in the JHI5 - * wrapper and support code. + * <a href="./hdf.hdf5lib.exceptions.HDF5Exception.html"> <b>HDF5Exception</b></a>. There are two subclasses + * of + * <b>HDF5Exception</b>, <a href="./hdf.hdf5lib.exceptions.HDF5LibraryException.html"> + <b>HDF5LibraryException</b></a> + * and <a href="./hdf.hdf5lib.exceptions.HDF5JavaException.html"> <b>HDF5JavaException</b></a>. The + * sub-classes of the former represent errors from the HDF-5 C library, while sub-classes of the latter + * represent errors in the JHI5 wrapper and support code. * <p> - * The super-class <b><i>HDF5LibraryException</i></b> implements the method '<b><i>printStackTrace()</i></b>', which - * prints out the HDF-5 error stack, as described in the HDF-5 C API <i><b>H5Eprint()</b>.</i> This may be used by Java - * exception handlers to print out the HDF-5 error stack. + * The super-class <b><i>HDF5LibraryException</i></b> implements the method '<b><i>printStackTrace()</i></b>', + * which prints out the HDF-5 error stack, as described in the HDF-5 C API <i><b>H5Eprint()</b>.</i> This may + * be used by Java exception handlers to print out the HDF-5 error stack. * <hr> * * @version HDF5 1.10.9 <BR> @@ -220,7 +228,8 @@ import hdf.hdf5lib.structs.H5O_info_t; * <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR> * <a href ="./hdf.hdf5lib.HDF5Exception.html"> hdf.hdf5lib.HDF5Exception</a><BR> * <a href="http://hdfgroup.org/HDF5/"> http://hdfgroup.org/HDF5"</a> - **/ + * + */ public class H5 implements java.io.Serializable { /** * @@ -237,38 +246,36 @@ public class H5 implements java.io.Serializable { * * Make sure to update the versions number when a different library is used. */ - public final static int LIB_VERSION[] = { 1, 10, 9 }; + public final static int LIB_VERSION[] = {1, 10, 9}; /** - * add system property to load library by path - */ + * 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; - private final static boolean IS_CRITICAL_PINNING = true; - // change from Vector to LinkedHashSet - jp 6-Oct-2014 + private final static boolean IS_CRITICAL_PINNING = true; private final static LinkedHashSet<Long> OPEN_IDS = new LinkedHashSet<Long>(); - static { - loadH5Lib(); - } + static { loadH5Lib(); } /** - * load native library - */ - public static void loadH5Lib() { + * load native library + */ + public static void loadH5Lib() + { // Make sure that the library is loaded only once if (isLibraryLoaded) return; // first try loading library by name from user supplied library path - s_libraryName = System.getProperty(H5_LIBRARY_NAME_PROPERTY_KEY, null); + s_libraryName = System.getProperty(H5_LIBRARY_NAME_PROPERTY_KEY, null); String mappedName = null; if ((s_libraryName != null) && (s_libraryName.length() > 0)) { try { @@ -309,7 +316,7 @@ public class H5 implements java.io.Serializable { } else { isLibraryLoaded = false; - throw (new UnsatisfiedLinkError("Invalid HDF5 library, " + filename)); + throw(new UnsatisfiedLinkError("Invalid HDF5 library, " + filename)); } } } @@ -318,7 +325,7 @@ public class H5 implements java.io.Serializable { if (!isLibraryLoaded) { try { s_libraryName = "hdf5_java"; - mappedName = System.mapLibraryName(s_libraryName); + mappedName = System.mapLibraryName(s_libraryName); System.loadLibrary("hdf5_java"); isLibraryLoaded = true; } @@ -367,18 +374,14 @@ public class H5 implements java.io.Serializable { * * @return Returns a count of open IDs */ - public final static int getOpenIDCount() { - return OPEN_IDS.size(); - } + public final static int getOpenIDCount() { return OPEN_IDS.size(); } /** * Get the open IDs * * @return Returns a collection of open IDs */ - public final static Collection<Long> getOpenIDs() { - return OPEN_IDS; - } + public final static Collection<Long> getOpenIDs() { return OPEN_IDS; } /** * H5check_version verifies that the arguments match the version numbers compiled into the library. @@ -389,20 +392,21 @@ public class H5 implements java.io.Serializable { * The minor version of the library. * @param relnum * The release number of the library. - * @return a non-negative value if successful. Upon failure (when the versions do not match), this function causes - * the application to abort (i.e., crash) + * @return a non-negative value if successful. Upon failure (when the versions do not match), this + * function causes the application to abort (i.e., crash) * - * See C API function: herr_t H5check_version() + * See C API function: herr_t H5check_version() **/ public synchronized static native int H5check_version(int majnum, int minnum, int relnum); /** - * H5close flushes all data to disk, closes all file identifiers, and cleans up all memory used by the library. + * H5close flushes all data to disk, closes all file identifiers, and cleans up all memory used by the + * library. * * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5close() throws HDF5LibraryException; @@ -412,35 +416,35 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5open() throws HDF5LibraryException; /** - * H5dont_atexit indicates to the library that an atexit() cleanup routine should not be installed. In order to be - * effective, this routine must be called before any other HDF function calls, and must be called each time the - * library is loaded/linked into the application (the first time and after it's been unloaded). - * <P> - * This is called by the static initializer, so this should never need to be explicitly called by a Java program. + * H5dont_atexit indicates to the library that an atexit() cleanup routine should not be installed. In + * order to be effective, this routine must be called before any other HDF function calls, and must be + * called each time the library is loaded/linked into the application (the first time and after it's been + * unloaded). <P> This is called by the static initializer, so this should never need to be explicitly + * called by a Java program. * * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ private synchronized static native int H5dont_atexit() throws HDF5LibraryException; /** - * Turn off error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This - * behavior may be disabled by calling H5error_off(). + * Turn off error handling. By default, the C library prints the error stack of the HDF-5 C library on + * stdout. This behavior may be disabled by calling H5error_off(). * * @return a non-negative value if successful */ public synchronized static native int H5error_off(); /** - * Turn on error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This - * behavior may be re-enabled by calling H5error_on(). + * Turn on error handling. By default, the C library prints the error stack of the HDF-5 C library on + * stdout. This behavior may be re-enabled by calling H5error_on(). */ public synchronized static native void H5error_on(); @@ -450,13 +454,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5garbage_collect() throws HDF5LibraryException; /** - * H5get_libversion retrieves the major, minor, and release numbers of the version of the HDF library which is - * linked to the application. + * H5get_libversion retrieves the major, minor, and release numbers of the version of the HDF library + * which is linked to the application. * * @param libversion * The version information of the HDF library. @@ -469,7 +473,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful, along with the version information. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5get_libversion(int[] libversion) throws HDF5LibraryException; @@ -500,10 +504,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful, along with the version information. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - */ + * 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; + int arr_global_lim, int arr_list_lim, + int blk_global_lim, int blk_list_lim) + throws HDF5LibraryException; /** * H5export_dataset is a utility function to save data in a file. @@ -521,10 +527,11 @@ public class H5 implements java.io.Serializable { * 3 - export data as binary Big Endian. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5export_dataset(String file_export_name, long file_id, - String object_path, int binary_order) throws HDF5LibraryException; + String object_path, int binary_order) + throws HDF5LibraryException; /** * H5export_attribute is a utility function to save data in a file. @@ -542,10 +549,11 @@ public class H5 implements java.io.Serializable { * 3 - export data as binary Big Endian. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + String attribute_name, int binary_order) + throws HDF5LibraryException; /** * H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled. @@ -575,9 +583,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Aclose(long attr_id) throws HDF5LibraryException { + public static int H5Aclose(long attr_id) throws HDF5LibraryException + { if (attr_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -600,12 +609,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Acopy(long src_aid, long dst_aid) throws HDF5LibraryException; /** - * H5Acreate creates an attribute, attr_name, which is attached to the object specified by the identifier loc_id. + * H5Acreate creates an attribute, attr_name, which is attached to the object specified by the identifier + * loc_id. * * @param loc_id * IN: Location or object identifier; may be dataset or group @@ -623,12 +633,13 @@ public class H5 implements java.io.Serializable { * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * Name is null. **/ - public static long H5Acreate(long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long aapl_id) - throws HDF5LibraryException, NullPointerException { + public static long H5Acreate(long loc_id, String attr_name, long type_id, long space_id, long acpl_id, + long aapl_id) throws HDF5LibraryException, NullPointerException + { long id = _H5Acreate2(loc_id, attr_name, type_id, space_id, acpl_id, aapl_id); if (id > 0) { log.trace("OPEN_IDS: H5A create add {}", id); @@ -641,15 +652,16 @@ public class H5 implements java.io.Serializable { /** * H5Acreate2 an attribute, attr_name, which is attached to the object specified by the identifier loc_id. * - * @see public static long H5Acreate( long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long - * aapl_id ) + * @see public static long H5Acreate( long loc_id, String attr_name, long type_id, long space_id, long + * acpl_id, long aapl_id ) **/ - private synchronized static native long _H5Acreate2(long loc_id, String attr_name, long type_id, long space_id, - long acpl_id, long aapl_id) throws HDF5LibraryException, NullPointerException; + private synchronized static native long _H5Acreate2(long loc_id, String attr_name, long type_id, + long space_id, long acpl_id, long aapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Acreate_by_name creates an attribute, attr_name, which is attached to the object specified by loc_id and - * obj_name. + * H5Acreate_by_name creates an attribute, attr_name, which is attached to the object specified by loc_id + * and obj_name. * * @param loc_id * IN: Location or object identifier; may be dataset or group @@ -671,13 +683,16 @@ public class H5 implements java.io.Serializable { * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Acreate_by_name(long loc_id, String obj_name, String attr_name, long type_id, long space_id, - long acpl_id, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException { - long id = _H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id); + public static long H5Acreate_by_name(long loc_id, String obj_name, String attr_name, long type_id, + long space_id, long acpl_id, long aapl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException + { + long id = + _H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Acreate_by_name add {}", id); OPEN_IDS.add(id); @@ -687,8 +702,9 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Acreate_by_name(long loc_id, String obj_name, String attr_name, - long type_id, long space_id, long acpl_id, long aapl_id, long lapl_id) throws HDF5LibraryException, - NullPointerException; + long type_id, long space_id, long acpl_id, + long aapl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Adelete removes the attribute specified by its name, name, from a dataset, group, or named datatype. @@ -701,12 +717,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native int H5Adelete(long loc_id, String name) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Adelete(long loc_id, String name) + throws HDF5LibraryException, NullPointerException; /** * H5Adelete_by_idx removes an attribute, specified by its location in an index, from an object. @@ -725,16 +741,17 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - obj_name is null. + * obj_name is null. **/ - public synchronized static native void H5Adelete_by_idx(long loc_id, String obj_name, int idx_type, int order, - long n, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Adelete_by_idx(long loc_id, String obj_name, int idx_type, + int order, long n, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Adelete_by_name removes the attribute attr_name from an object specified by location and name, loc_id and - * obj_name, respectively. + * H5Adelete_by_name removes the attribute attr_name from an object specified by location and name, loc_id + * and obj_name, respectively. * * @param loc_id * IN: Location or object identifier; may be dataset or group @@ -748,12 +765,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native int H5Adelete_by_name(long loc_id, String obj_name, String attr_name, long lapl_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Adelete_by_name(long loc_id, String obj_name, String attr_name, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Aexists determines whether the attribute attr_name exists on the object specified by obj_id. @@ -766,16 +784,16 @@ public class H5 implements java.io.Serializable { * @return boolean true if an attribute with a given name exists. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - attr_name is null. + * attr_name is null. **/ - public synchronized static native boolean H5Aexists(long obj_id, String attr_name) throws HDF5LibraryException, - NullPointerException; + public synchronized static native boolean H5Aexists(long obj_id, String attr_name) + throws HDF5LibraryException, NullPointerException; /** - * H5Aexists_by_name determines whether the attribute attr_name exists on an object. That object is specified by its - * location and name, loc_id and obj_name, respectively. + * H5Aexists_by_name determines whether the attribute attr_name exists on an object. That object is + * specified by its location and name, loc_id and obj_name, respectively. * * @param loc_id * IN: Location of object to which attribute is attached . @@ -789,12 +807,13 @@ public class H5 implements java.io.Serializable { * @return boolean true if an attribute with a given name exists, otherwise returns false. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native boolean H5Aexists_by_name(long loc_id, String obj_name, String attr_name, - long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native boolean H5Aexists_by_name(long loc_id, String obj_name, + String attr_name, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Aget_info retrieves attribute information, by attribute identifier. @@ -805,7 +824,7 @@ public class H5 implements java.io.Serializable { * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native H5A_info_t H5Aget_info(long attr_id) throws HDF5LibraryException; @@ -828,12 +847,14 @@ public class H5 implements java.io.Serializable { * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - obj_name is null. + * obj_name is null. **/ - public synchronized static native H5A_info_t H5Aget_info_by_idx(long loc_id, String obj_name, int idx_type, - int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5A_info_t H5Aget_info_by_idx(long loc_id, String obj_name, + int idx_type, int order, long n, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Aget_info_by_name Retrieves attribute information, by attribute name. @@ -850,12 +871,13 @@ public class H5 implements java.io.Serializable { * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - obj_name is null. + * obj_name is null. **/ - public synchronized static native H5A_info_t H5Aget_info_by_name(long loc_id, String obj_name, String attr_name, - long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5A_info_t H5Aget_info_by_name(long loc_id, String obj_name, + String attr_name, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Aget_name retrieves the name of an attribute specified by the identifier, attr_id. @@ -866,14 +888,13 @@ public class H5 implements java.io.Serializable { * @return String for Attribute name. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native String H5Aget_name(long attr_id) - throws HDF5LibraryException; + public synchronized static native String H5Aget_name(long attr_id) throws HDF5LibraryException; /** - * H5Aget_name_by_idx retrieves the name of an attribute that is attached to an object, which is specified by its - * location and name, loc_id and obj_name, respectively. + * H5Aget_name_by_idx retrieves the name of an attribute that is attached to an object, which is specified + * by its location and name, loc_id and obj_name, respectively. * * @param attr_id * IN: Attribute identifier @@ -891,12 +912,13 @@ public class H5 implements java.io.Serializable { * @return String for Attribute name. * * @exception HDF5LibraryException - * - Error from the HDF5 Library. + * Error from the HDF5 Library. * @exception NullPointerException - * - obj_name is null. + * obj_name is null. **/ - public synchronized static native String H5Aget_name_by_idx(long attr_id, String obj_name, int idx_type, int order, - long n, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native String H5Aget_name_by_idx(long attr_id, String obj_name, int idx_type, + int order, long n, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Aget_space retrieves a copy of the dataspace for an attribute. @@ -907,7 +929,7 @@ public class H5 implements java.io.Serializable { * @return attribute dataspace identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public static long H5Aget_space(long attr_id) throws HDF5LibraryException { @@ -923,7 +945,8 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Aget_space(long attr_id) throws HDF5LibraryException; /** - * H5Aget_storage_size returns the amount of storage that is required for the specified attribute, attr_id. + * H5Aget_storage_size returns the amount of storage that is required for the specified attribute, + * attr_id. * * @param attr_id * IN: Identifier of the attribute to query. @@ -931,7 +954,7 @@ public class H5 implements java.io.Serializable { * @return the amount of storage size allocated for the attribute; otherwise returns 0 (zero) * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Aget_storage_size(long attr_id) throws HDF5LibraryException; @@ -944,7 +967,7 @@ public class H5 implements java.io.Serializable { * @return a datatype identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public static long H5Aget_type(long attr_id) throws HDF5LibraryException { @@ -960,8 +983,8 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Aget_type(long attr_id) throws HDF5LibraryException; /** - * H5Aopen opens an existing attribute, attr_name, that is attached to an object specified an object identifier, - * object_id. + * H5Aopen opens an existing attribute, attr_name, that is attached to an object specified an object + * identifier, object_id. * * @param obj_id * IN: Identifier for object to which attribute is attached @@ -973,12 +996,12 @@ public class H5 implements java.io.Serializable { * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * Name is null. **/ public static long H5Aopen(long obj_id, String attr_name, long aapl_id) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { long id = _H5Aopen(obj_id, attr_name, aapl_id); if (id > 0) { @@ -990,11 +1013,11 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Aopen(long obj_id, String attr_name, long aapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Aopen_by_idx opens an existing attribute that is attached to an object specified by location and name, loc_id - * and obj_name, respectively + * H5Aopen_by_idx opens an existing attribute that is attached to an object specified by location and + * name, loc_id and obj_name, respectively * * @param loc_id * IN: Location of object to which attribute is attached @@ -1014,12 +1037,13 @@ public class H5 implements java.io.Serializable { * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * Name is null. **/ - public static long H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long aapl_id, - long lapl_id) throws HDF5LibraryException, NullPointerException + public static long H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, + long aapl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException { long id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id); if (id > 0) { @@ -1030,8 +1054,9 @@ public class H5 implements java.io.Serializable { return id; } - private synchronized static native long _H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, - long n, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; + private synchronized static native long _H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, + int order, long n, long aapl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Aopen_by_name Opens an attribute for an object by object name and attribute name @@ -1050,12 +1075,12 @@ public class H5 implements java.io.Serializable { * @return Returns an attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - obj_name is null. + * obj_name is null. **/ - public static long H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, long lapl_id) - throws HDF5LibraryException, NullPointerException + public static long H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, + long lapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id); if (id > 0) { @@ -1067,7 +1092,8 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Aopen_by_name(long loc_id, String obj_name, String attr_name, - long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; + long aapl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with @@ -1085,12 +1111,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ - public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + 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 @@ -1106,11 +1133,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ - public synchronized static int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException + 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); } @@ -1129,11 +1157,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ - public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException + 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); } @@ -1154,66 +1183,67 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Failure in the data conversion. + * Failure in the data conversion. * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. See public synchronized static native int H5Aread( ) + * data buffer is null. See public synchronized static native int H5Aread( ) **/ - public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning) - throws HDF5Exception, HDF5LibraryException, NullPointerException + public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj, + boolean isCriticalPinning) + throws HDF5Exception, HDF5LibraryException, NullPointerException { - int status = -1; + int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Aread: data is not an array")); + throw(new HDF5JavaException("H5Aread: data is not an array")); } String cname = dataClass.getName(); - is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); - char dname = cname.charAt(cname.lastIndexOf("[") + 1); + is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); + char dname = cname.charAt(cname.lastIndexOf("[") + 1); log.trace("H5Aread: cname={} is1D={} dname={}", cname, is1D, dname); if (is1D && (dname == 'B')) { log.trace("H5Aread_dname_B"); - status = H5Aread(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning); + status = H5Aread(attr_id, mem_type_id, (byte[])obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { log.trace("H5Aread_dname_S"); - status = H5Aread_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning); + status = H5Aread_short(attr_id, mem_type_id, (short[])obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { log.trace("H5Aread_dname_I"); - status = H5Aread_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning); + status = H5Aread_int(attr_id, mem_type_id, (int[])obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { log.trace("H5Aread_dname_J"); - status = H5Aread_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning); + status = H5Aread_long(attr_id, mem_type_id, (long[])obj, isCriticalPinning); } else if (is1D && (dname == 'F')) { log.trace("H5Aread_dname_F"); - status = H5Aread_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning); + status = H5Aread_float(attr_id, mem_type_id, (float[])obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { log.trace("H5Aread_dname_D"); - status = H5Aread_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning); + status = H5Aread_double(attr_id, mem_type_id, (double[])obj, isCriticalPinning); } else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && - (is1D && (dataClass.getComponentType() == String.class))) || - H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) { + (is1D && (dataClass.getComponentType() == String.class))) || + H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) { log.trace("H5Aread_reg_ref"); - status = H5Aread_reg_ref(attr_id, mem_type_id, (String[]) obj); + status = H5Aread_reg_ref(attr_id, mem_type_id, (String[])obj); } else if (is1D && (dataClass.getComponentType() == String.class)) { log.trace("H5Aread_string type"); - status = H5Aread_string(attr_id, mem_type_id, (String[]) obj); + status = H5Aread_string(attr_id, mem_type_id, (String[])obj); } else { // Create a data buffer to hold the data into a Java Array HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.emptyBytes(); + byte[] buf = theArray.emptyBytes(); log.trace("H5Aread_else"); // This will raise an exception if there is an error @@ -1225,7 +1255,7 @@ public class H5 implements java.io.Serializable { } // clean up these: assign 'null' as hint to gc() - buf = null; + buf = null; theArray = null; } @@ -1248,12 +1278,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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 @@ -1269,12 +1300,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static int H5Aread_double(long attr_id, long mem_type_id, double[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Aread_double(attr_id, mem_type_id, buf, true); } @@ -1295,12 +1326,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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 @@ -1316,12 +1348,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static int H5Aread_float(long attr_id, long mem_type_id, float[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Aread_float(attr_id, mem_type_id, buf, true); } @@ -1342,12 +1374,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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 @@ -1363,12 +1396,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Aread_int(attr_id, mem_type_id, buf, true); } @@ -1389,12 +1422,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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 @@ -1410,12 +1444,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Aread_long(attr_id, mem_type_id, buf, true); } @@ -1434,12 +1468,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with @@ -1457,12 +1491,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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 @@ -1478,12 +1513,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Aread_short(attr_id, mem_type_id, buf, true); } @@ -1502,12 +1537,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with @@ -1523,12 +1558,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with @@ -1544,12 +1579,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with @@ -1565,16 +1600,16 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Arename changes the name of attribute that is attached to the object specified by loc_id. The attribute named - * old_attr_name is renamed new_attr_name. + * H5Arename changes the name of attribute that is attached to the object specified by loc_id. The + *attribute named old_attr_name is renamed new_attr_name. * * @param loc_id * IN: Location or object identifier; may be dataset or group @@ -1586,16 +1621,16 @@ public class H5 implements java.io.Serializable { * @return A non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * Name is null. **/ public synchronized static native int H5Arename(long loc_id, String old_attr_name, String new_attr_name) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name. - * The attribute named old_attr_name is renamed new_attr_name. + * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and + * obj_name. The attribute named old_attr_name is renamed new_attr_name. * * @param loc_id * IN: Location or object identifier; may be dataset or group @@ -1611,12 +1646,13 @@ public class H5 implements java.io.Serializable { * @return A non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * Name is null. **/ - public synchronized static native int H5Arename_by_name(long loc_id, String obj_name, String old_attr_name, - String new_attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native int + H5Arename_by_name(long loc_id, String obj_name, String old_attr_name, String new_attr_name, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with @@ -1634,12 +1670,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ - public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + 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 @@ -1655,12 +1692,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Awrite(attr_id, mem_type_id, buf, true); } @@ -1679,12 +1716,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj) - throws HDF5Exception, HDF5LibraryException, NullPointerException + throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Awrite(attr_id, mem_type_id, obj, true); } @@ -1705,55 +1742,56 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Failure in the data conversion. + * Failure in the data conversion. * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data object is null + * data object is null **/ - public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning) - throws HDF5Exception, HDF5LibraryException, NullPointerException + public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, + boolean isCriticalPinning) + throws HDF5Exception, HDF5LibraryException, NullPointerException { - int status = -1; + int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Dwrite: data is not an array")); + throw(new HDF5JavaException("H5Dwrite: data is not an array")); } String cname = dataClass.getName(); - is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); - char dname = cname.charAt(cname.lastIndexOf("[") + 1); + is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); + char dname = cname.charAt(cname.lastIndexOf("[") + 1); if (is1D && (dname == 'B')) { - status = H5Awrite(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning); + status = H5Awrite(attr_id, mem_type_id, (byte[])obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { - status = H5Awrite_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning); + status = H5Awrite_short(attr_id, mem_type_id, (short[])obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { - status = H5Awrite_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning); + status = H5Awrite_int(attr_id, mem_type_id, (int[])obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { - status = H5Awrite_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning); + status = H5Awrite_long(attr_id, mem_type_id, (long[])obj, isCriticalPinning); } else if (is1D && (dname == 'F')) { - status = H5Awrite_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning); + status = H5Awrite_float(attr_id, mem_type_id, (float[])obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { - status = H5Awrite_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning); + status = H5Awrite_double(attr_id, mem_type_id, (double[])obj, isCriticalPinning); } else if (is1D && (dataClass.getComponentType() == String.class)) { log.trace("H5Dwrite_string type"); - status = H5Awrite_string(attr_id, mem_type_id, (String[]) obj); + status = H5Awrite_string(attr_id, mem_type_id, (String[])obj); } else { HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.byteify(); + byte[] buf = theArray.byteify(); - status = H5Awrite(attr_id, mem_type_id, buf); - buf = null; + status = H5Awrite(attr_id, mem_type_id, buf); + buf = null; theArray = null; } @@ -1776,12 +1814,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ - public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + 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 @@ -1797,12 +1836,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Awrite_double(attr_id, mem_type_id, buf, true); } @@ -1823,12 +1862,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ - public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + 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 @@ -1844,12 +1884,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Awrite_float(attr_id, mem_type_id, buf, true); } @@ -1870,12 +1910,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ - public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + 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 @@ -1891,12 +1932,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Awrite_int(attr_id, mem_type_id, buf, true); } @@ -1917,12 +1958,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ - public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + 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 @@ -1938,12 +1980,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Awrite_long(attr_id, mem_type_id, buf, true); } @@ -1964,12 +2006,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ - public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + 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 @@ -1985,12 +2028,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf) - throws HDF5LibraryException, NullPointerException + throws HDF5LibraryException, NullPointerException { return H5Awrite_short(attr_id, mem_type_id, buf, true); } @@ -2009,12 +2052,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with @@ -2030,12 +2073,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * data is null. **/ public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from @@ -2053,13 +2096,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native int H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Aget_create_plist retrieves a copy of the attribute creation property list identifier. @@ -2070,10 +2113,9 @@ public class H5 implements java.io.Serializable { * @return identifier for the attribute's creation property list if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Aget_create_plist(long attr_id) - throws HDF5LibraryException + public static long H5Aget_create_plist(long attr_id) throws HDF5LibraryException { long id = _H5Aget_create_plist(attr_id); if (id > 0) { @@ -2092,20 +2134,22 @@ public class H5 implements java.io.Serializable { * as defined below, is passed to a user-defined function, op, which operates on that attribute. * * @param loc_id - * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. + * IN: Identifier for object to which attributes are attached; may be group, dataset, or named + * datatype. * @param idx_type * IN: The type of index specified by idx_type can be one of the following: * H5_INDEX_NAME An alphanumeric index by attribute name. * H5_INDEX_CRT_ORDER An index by creation order. * @param order - * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: + * IN: The order in which the index is to be traversed, as specified by order, can be one of + * the following: * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration * incrementing the index position at each step. - * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration - * decrementing the index position at each step. - * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided - * as to the order, but HDF5 ensures that each element in the index will be - * visited if the iteration completes successfully. + * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up + * iteration decrementing the index position at each step. + * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is + * provided as to the order, but HDF5 ensures that each element in + * the index will be visited if the iteration completes successfully. * @param idx * IN/OUT: Initial and returned offset within index. * @param op @@ -2113,16 +2157,17 @@ public class H5 implements java.io.Serializable { * @param op_data * IN/OUT: Pointer to any user-efined data for use by operator function. * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public synchronized static native int H5Aiterate(long loc_id, int idx_type, int order, long idx, - H5A_iterate_cb op, H5A_iterate_t op_data) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Aiterate(long loc_id, int idx_type, int order, long idx, + H5A_iterate_cb op, H5A_iterate_t op_data) + throws HDF5LibraryException, NullPointerException; /** * H5Aiterate_by_name iterates over the attributes attached to the dataset or group specified with loc_id @@ -2130,7 +2175,8 @@ public class H5 implements java.io.Serializable { * below, is passed to a user-defined function, op, which operates on that attribute. * * @param loc_id - * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. + * IN: Identifier for object to which attributes are attached; may be group, dataset, or named + * datatype. * @param obj_name * IN: Name of object, relative to location. * @param idx_type @@ -2138,14 +2184,15 @@ public class H5 implements java.io.Serializable { * H5_INDEX_NAME An alphanumeric index by attribute name. * H5_INDEX_CRT_ORDER An index by creation order. * @param order - * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: - * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration - * incrementing the index position at each step. - * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration - * decrementing the index position at each step. - * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided - * as to the order, but HDF5 ensures that each element in the index will be - * visited if the iteration completes successfully. + * IN: The order in which the index is to be traversed, as specified by order, can be one of + * the following: + * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down + * iteration incrementing the index position at each step. + * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration + * decrementing the index position at each step. + * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided + * as to the order, but HDF5 ensures that each element in the index will be + * visited if the iteration completes successfully. * @param idx * IN/OUT: Initial and returned offset within index. * @param op @@ -2155,16 +2202,18 @@ public class H5 implements java.io.Serializable { * @param lapl_id * IN: Link access property list * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public synchronized static native int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, - int order, long idx, H5A_iterate_cb op, H5A_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, + int order, long idx, H5A_iterate_cb op, + H5A_iterate_t op_data, long lapl_id) + throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // @@ -2215,7 +2264,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Dcopy(long src_did, long dst_did) throws HDF5LibraryException; @@ -2228,9 +2277,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Dclose(long dataset_id) throws HDF5LibraryException { + public static int H5Dclose(long dataset_id) throws HDF5LibraryException + { if (dataset_id < 0) return 0; // throw new HDF5LibraryException("Negative ID"); @@ -2263,12 +2313,13 @@ public class H5 implements java.io.Serializable { * @return a dataset identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Dcreate(long loc_id, String name, long type_id, long space_id, long lcpl_id, long dcpl_id, - long dapl_id) throws HDF5LibraryException, NullPointerException { + public static long H5Dcreate(long loc_id, String name, long type_id, long space_id, long lcpl_id, + long dcpl_id, long dapl_id) throws HDF5LibraryException, NullPointerException + { long id = _H5Dcreate2(loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Dcreate add {}", id); @@ -2281,11 +2332,12 @@ public class H5 implements java.io.Serializable { /** * H5Dcreate2 creates a new dataset named name at the location specified by loc_id. * - * @see public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int lcpl_id, int dcpl_id, - * int dapl_id) + * @see public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int lcpl_id, int + * dcpl_id, int dapl_id) **/ private synchronized static native long _H5Dcreate2(long loc_id, String name, long type_id, long space_id, - long lcpl_id, long dcpl_id, long dapl_id) throws HDF5LibraryException, NullPointerException; + long lcpl_id, long dcpl_id, long dapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Dcreate_anon creates a dataset in the file specified by loc_id. @@ -2304,10 +2356,11 @@ public class H5 implements java.io.Serializable { * @return a dataset identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public static long H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, long dapl_id) - throws HDF5LibraryException { + throws HDF5LibraryException + { long id = _H5Dcreate_anon(loc_id, type_id, space_id, dcpl_id, dapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Dcreate_anon add {}", id); @@ -2317,11 +2370,13 @@ public class H5 implements java.io.Serializable { return id; } - private synchronized static native long _H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, - long dapl_id) throws HDF5LibraryException; + private synchronized static native long _H5Dcreate_anon(long loc_id, long type_id, long space_id, + long dcpl_id, long dapl_id) + throws HDF5LibraryException; /** - * H5Dfill explicitly fills the dataspace selection in memory, space_id, with the fill value specified in fill. + * H5Dfill explicitly fills the dataspace selection in memory, space_id, with the fill value specified in + * fill. * * @param fill * IN: Pointer to the fill value to be used. @@ -2335,12 +2390,13 @@ public class H5 implements java.io.Serializable { * IN: Dataspace describing memory buffer and containing the selection to be filled. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public synchronized static native void H5Dfill(byte[] fill, long fill_type, byte[] buf, long buf_type, long space_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Dfill(byte[] fill, long fill_type, byte[] buf, long buf_type, + long space_id) + throws HDF5LibraryException, NullPointerException; /** * H5Dget_access_plist returns an identifier for a copy of the dataset access property list for a dataset. @@ -2351,21 +2407,23 @@ public class H5 implements java.io.Serializable { * @return a dataset access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Dget_access_plist(long dset_id) throws HDF5LibraryException; /** - * H5Dget_create_plist returns an identifier for a copy of the dataset creation property list for a dataset. + * H5Dget_create_plist returns an identifier for a copy of the dataset creation property list for a + * dataset. * * @param dataset_id * Identifier of the dataset to query. * @return a dataset creation property list identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Dget_create_plist(long dataset_id) throws HDF5LibraryException { + public static long H5Dget_create_plist(long dataset_id) throws HDF5LibraryException + { long id = _H5Dget_create_plist(dataset_id); if (id > 0) { log.trace("OPEN_IDS: H5Dget_create_plist add {}", id); @@ -2386,7 +2444,7 @@ public class H5 implements java.io.Serializable { * @return the offset in bytes. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Dget_offset(long dset_id) throws HDF5LibraryException; @@ -2399,9 +2457,10 @@ public class H5 implements java.io.Serializable { * @return a dataspace identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Dget_space(long dataset_id) throws HDF5LibraryException { + public static long H5Dget_space(long dataset_id) throws HDF5LibraryException + { long id = _H5Dget_space(dataset_id); if (id > 0) { log.trace("OPEN_IDS: H5Dget_space add {}", id); @@ -2422,7 +2481,7 @@ public class H5 implements java.io.Serializable { * @return the space allocation status * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Dget_space_status(long dset_id) throws HDF5LibraryException; @@ -2435,10 +2494,10 @@ public class H5 implements java.io.Serializable { * @return he amount of storage space allocated for the dataset. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5Dget_storage_size(long dataset_id) throws HDF5LibraryException, - IllegalArgumentException; + public synchronized static native long H5Dget_storage_size(long dataset_id) + throws HDF5LibraryException, IllegalArgumentException; /** * H5Dget_type returns an identifier for a copy of the datatype for a dataset. @@ -2449,9 +2508,10 @@ public class H5 implements java.io.Serializable { * @return a datatype identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Dget_type(long dataset_id) throws HDF5LibraryException { + public static long H5Dget_type(long dataset_id) throws HDF5LibraryException + { long id = _H5Dget_type(dataset_id); if (id > 0) { log.trace("OPEN_IDS: H5Dget_type add {}", id); @@ -2464,8 +2524,8 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Dget_type(long dataset_id) throws HDF5LibraryException; /** - * H5Diterate iterates over all the data elements in the memory buffer buf, executing the callback function operator - * once for each such data element. + * H5Diterate iterates over all the data elements in the memory buffer buf, executing the callback + * function operator once for each such data element. * * @param buf * IN/OUT: Pointer to the memory containing the elements to iterate over. @@ -2478,19 +2538,21 @@ public class H5 implements java.io.Serializable { * @param op_data * IN/OUT: Pointer to any user-efined data for use by operator function. * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public synchronized static native int H5Diterate(byte[] buf, long buf_type, long space_id, H5D_iterate_cb op, - H5D_iterate_t op_data) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Diterate(byte[] buf, long buf_type, long space_id, + H5D_iterate_cb op, H5D_iterate_t op_data) + throws HDF5LibraryException, NullPointerException; /** - * H5Dopen opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. + * H5Dopen opens the existing dataset specified by a location identifier and name, loc_id and name, + * respectively. * * @param loc_id * IN: Location identifier @@ -2502,11 +2564,12 @@ public class H5 implements java.io.Serializable { * @return a dataset identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException + public static long H5Dopen(long loc_id, String name, long dapl_id) + throws HDF5LibraryException, NullPointerException { long id = _H5Dopen2(loc_id, name, dapl_id); if (id > 0) { @@ -2518,16 +2581,17 @@ public class H5 implements java.io.Serializable { } /** - * H5Dopen2 opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. + * H5Dopen2 opens the existing dataset specified by a location identifier and name, loc_id and name, + * respectively. * * @see public static int H5Dopen(int loc_id, String name, int dapl_id) **/ private synchronized static native long _H5Dopen2(long loc_id, String name, long dapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application - * memory buffer buf. + * 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. @@ -2547,17 +2611,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * data buffer is null. **/ public synchronized static native int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; + 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. + * 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. @@ -2575,19 +2640,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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 + 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. + * 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. @@ -2605,19 +2671,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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 + public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, Object obj) + throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); } /** - * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application - * data object. + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the + * application data object. * * @param dataset_id * Identifier of the dataset read from. @@ -2637,87 +2704,88 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Failure in the data conversion. + * Failure in the data conversion. * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data object is null. + * data object is null. **/ - public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, - NullPointerException + public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, Object obj, + boolean isCriticalPinning) + throws HDF5Exception, HDF5LibraryException, NullPointerException { - int status = -1; + int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Dread: data is not an array")); + throw(new HDF5JavaException("H5Dread: data is not an array")); } String cname = dataClass.getName(); - is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); - char dname = cname.charAt(cname.lastIndexOf("[") + 1); + is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); + char dname = cname.charAt(cname.lastIndexOf("[") + 1); log.trace("H5Dread: cname={} is1D={} dname={}", cname, is1D, dname); if (is1D && (dname == 'B')) { log.trace("H5Dread_dname_B"); - status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, - isCriticalPinning); + status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[])obj, + isCriticalPinning); } else if (is1D && (dname == 'S')) { log.trace("H5Dread_dname_S"); - status = H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, - isCriticalPinning); + status = H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (short[])obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { log.trace("H5Dread_dname_I"); - status = H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, - isCriticalPinning); + status = H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (int[])obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { log.trace("H5Dread_dname_J"); - status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, - isCriticalPinning); + status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (long[])obj, isCriticalPinning); } else if (is1D && (dname == 'F')) { log.trace("H5Dread_dname_F"); - status = H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, - isCriticalPinning); + status = H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (float[])obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { log.trace("H5Dread_dname_D"); status = H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (double[]) obj, isCriticalPinning); + (double[])obj, isCriticalPinning); } else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && - (is1D && (dataClass.getComponentType() == String.class))) || - H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) { + (is1D && (dataClass.getComponentType() == String.class))) || + H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) { log.trace("H5Dread_reg_ref"); status = H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (String[]) obj); + (String[])obj); } else if (is1D && (dataClass.getComponentType() == String.class)) { log.trace("H5Dread_string type"); status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (String[]) obj); + (String[])obj); } else { // Create a data buffer to hold the data into a Java Array HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.emptyBytes(); + byte[] buf = theArray.emptyBytes(); log.trace("H5Dread_else"); // will raise exception if read fails status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, - isCriticalPinning); + isCriticalPinning); if (status >= 0) { // convert the data into a Java Array obj = theArray.arrayify(buf); } // clean up these: assign 'null' as hint to gc() - buf = null; + buf = null; theArray = null; } @@ -2725,8 +2793,8 @@ public class H5 implements java.io.Serializable { } /** - * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application - * memory buffer of type double. + * 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. @@ -2746,17 +2814,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -2774,19 +2843,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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 + 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. + * 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. @@ -2806,17 +2876,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -2834,19 +2905,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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 + 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. + * 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. @@ -2866,17 +2938,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -2894,19 +2967,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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 + 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. + * 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. @@ -2926,17 +3000,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -2954,19 +3029,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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 + 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. + * 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. @@ -2984,16 +3060,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -3013,17 +3091,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -3041,19 +3120,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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 + 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. + * 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. @@ -3071,16 +3151,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -3098,16 +3179,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + 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. + * 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. @@ -3125,15 +3207,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data buffer is null. + * 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; + public synchronized static native int H5Dread_VLStrings(long dataset_id, long mem_type_id, + long mem_space_id, long file_space_id, + long xfer_plist_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; /** - * H5Dset_extent sets the current dimensions of the chunked dataset dset_id to the sizes specified in size. + * H5Dset_extent sets the current dimensions of the chunked dataset dset_id to the sizes specified in + * size. * * @param dset_id * IN: Chunked dataset identifier. @@ -3141,17 +3226,17 @@ public class H5 implements java.io.Serializable { * IN: Array containing the new magnitude of each dimension of the dataset. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. **/ - public synchronized static native void H5Dset_extent(long dset_id, long size[]) throws HDF5LibraryException, - NullPointerException; + public synchronized static native void H5Dset_extent(long dset_id, long size[]) + throws HDF5LibraryException, NullPointerException; /** - * H5Dvlen_get_buf_size determines the number of bytes required to store the VL data from the dataset, using the - * space_id for the selection in the dataset on disk and the type_id for the memory representation of the VL data in - * memory. + * H5Dvlen_get_buf_size determines the number of bytes required to store the VL data from the dataset, + * using the space_id for the selection in the dataset on disk and the type_id for the memory + * representation of the VL data in memory. * * @param dset_id * IN: Identifier of the dataset read from. @@ -3163,12 +3248,12 @@ public class H5 implements java.io.Serializable { * @return the size in bytes of the memory buffer required to store the VL data. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ public synchronized static native long H5Dvlen_get_buf_size(long dset_id, long type_id, long space_id) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Dvlen_reclaim reclaims buffer used for VL data. @@ -3185,16 +3270,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf) - throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, + byte[] buf) + throws HDF5LibraryException, NullPointerException; /** - * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer - * into the file. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application + * memory buffer into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -3214,17 +3300,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; + 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. + * 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. @@ -3242,19 +3329,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException + public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, byte[] buf) + throws HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } /** - * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer - * into the file. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application + * memory buffer into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -3272,19 +3360,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException + public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, Object obj) + throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); } /** - * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory data - * object into the file. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application + * memory data object into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -3304,67 +3393,68 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Failure in the data conversion. + * Failure in the data conversion. * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - data object is null. + * data object is null. **/ - public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, - NullPointerException + public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, Object obj, + boolean isCriticalPinning) + throws HDF5Exception, HDF5LibraryException, NullPointerException { - int status = -1; + int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Dwrite: data is not an array")); + throw(new HDF5JavaException("H5Dwrite: data is not an array")); } String cname = dataClass.getName(); - is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); - char dname = cname.charAt(cname.lastIndexOf("[") + 1); + is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); + char dname = cname.charAt(cname.lastIndexOf("[") + 1); if (is1D && (dname == 'B')) { - status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, - isCriticalPinning); + status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (byte[])obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { - status = H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, - isCriticalPinning); + status = H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (short[])obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { - status = H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, - isCriticalPinning); + status = H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (int[])obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { - status = H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, - isCriticalPinning); + status = H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (long[])obj, isCriticalPinning); } else if (is1D && (dname == 'F')) { - status = H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, - isCriticalPinning); + status = H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, + (float[])obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { status = H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (double[]) obj, isCriticalPinning); + (double[])obj, isCriticalPinning); } else if (is1D && (dataClass.getComponentType() == String.class)) { log.trace("H5Dwrite_string type"); status = H5Dwrite_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (String[]) obj); + (String[])obj); } else { HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.byteify(); + byte[] buf = theArray.byteify(); // will raise exception on error status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, - isCriticalPinning); + isCriticalPinning); // clean up these: assign 'null' as hint to gc() - buf = null; + buf = null; theArray = null; } @@ -3372,8 +3462,8 @@ public class H5 implements java.io.Serializable { } /** - * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer - * into the file. + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application + * memory buffer into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -3393,17 +3483,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; + public synchronized static 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. + * 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. @@ -3421,19 +3512,21 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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 + 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); + 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. + * 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. @@ -3453,17 +3546,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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; + 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. + * 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. @@ -3481,19 +3575,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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 + 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. + * 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. @@ -3513,17 +3608,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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; + 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. + * 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. @@ -3541,19 +3637,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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 + 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. + * 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. @@ -3573,17 +3670,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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; + 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. + * 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. @@ -3601,19 +3699,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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 + 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. + * 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. @@ -3633,17 +3732,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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; + 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. + * 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. @@ -3661,19 +3761,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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 + 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. + * 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. @@ -3691,16 +3792,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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; + 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. + * 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. @@ -3718,16 +3821,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * 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; + long file_space_id, long xfer_plist_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; /** - * H5Dwrite_VLStrings writes a (partial) variable length String dataset, specified by its identifier dataset_id, from - * the application memory buffer buf into the file. + * H5Dwrite_VLStrings writes a (partial) variable length String dataset, specified by its identifier + * dataset_id, from the application memory buffer buf into the file. * * ---- contributed by Rosetta Biosoftware * @@ -3747,48 +3851,52 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native int H5Dwrite_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; + public synchronized static native int H5Dwrite_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; /** - * H5Dflush causes all buffers associated with a dataset to be immediately flushed to disk without removing the - * data from the cache. + * H5Dflush causes all buffers associated with a dataset to be immediately flushed to disk without + * removing the data from the cache. * * @param dset_id * IN: Identifier of the dataset to be flushed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Dflush(long dset_id) throws HDF5LibraryException; /** - * H5Drefresh causes all buffers associated with a dataset to be cleared and immediately re-loaded with updated - * contents from disk. This function essentially closes the dataset, evicts all metadata associated with it - * from the cache, and then re-opens the dataset. The reopened dataset is automatically re-registered with the same ID. + * H5Drefresh causes all buffers associated with a dataset to be cleared and immediately re-loaded with + * updated contents from disk. This function essentially closes the dataset, evicts all metadata + * associated with it from the cache, and then re-opens the dataset. The reopened dataset is automatically + * re-registered with the same ID. * * @param dset_id * IN: Identifier of the dataset to be refreshed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Drefresh(long dset_id) throws HDF5LibraryException; // /////// unimplemented //////// - // herr_t H5Ddebug(hid_t dset_id); - // herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes); - // herr_t H5Dformat_convert(hid_t dset_id); - // herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type); + // herr_t H5Ddebug(hid_t dset_id); + // herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes); + // herr_t H5Dformat_convert(hid_t dset_id); + // herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type); // herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, // size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data); - // herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void *dst_buf); + // herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void + // *dst_buf); // //////////////////////////////////////////////////////////// // // @@ -3797,58 +3905,57 @@ public class H5 implements java.io.Serializable { // //////////////////////////////////////////////////////////// /** - * H5Eauto_is_v2 determines whether the error auto reporting function for an error stack conforms to the H5E_auto2_t - * typedef or the H5E_auto1_t typedef. + * H5Eauto_is_v2 determines whether the error auto reporting function for an error stack conforms to the + * H5E_auto2_t typedef or the H5E_auto1_t typedef. * * @param stack_id * IN: Error stack identifier. * - * @return boolean true if the error stack conforms to H5E_auto2_t and false if it conforms to H5E_auto1_t. + * @return boolean true if the error stack conforms to H5E_auto2_t and false if it conforms to + * H5E_auto1_t. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Eauto_is_v2(long stack_id) throws HDF5LibraryException; /** - * H5Eclear clears the error stack for the current thread. H5Eclear can fail if there are problems initializing the - * library. - * <p> - * This may be used by exception handlers to assure that the error condition in the HDF-5 library has been reset. + * H5Eclear clears the error stack for the current thread. H5Eclear can fail if there are problems + * initializing the library. <p> This may be used by exception handlers to assure that the error condition + * in the HDF-5 library has been reset. * * @return Returns a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Eclear() throws HDF5LibraryException { + public static int H5Eclear() throws HDF5LibraryException + { H5Eclear2(HDF5Constants.H5E_DEFAULT); return 0; } /** - * H5Eclear clears the error stack specified by estack_id, or, if estack_id is set to H5E_DEFAULT, the error stack - * for the current thread. + * H5Eclear clears the error stack specified by estack_id, or, if estack_id is set to H5E_DEFAULT, the + * error stack for the current thread. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static void H5Eclear(long stack_id) throws HDF5LibraryException { - H5Eclear2(stack_id); - } + public static void H5Eclear(long stack_id) throws HDF5LibraryException { H5Eclear2(stack_id); } /** - * H5Eclear2 clears the error stack specified by estack_id, or, if estack_id is set to H5E_DEFAULT, the error stack - * for the current thread. + * H5Eclear2 clears the error stack specified by estack_id, or, if estack_id is set to H5E_DEFAULT, the + * error stack for the current thread. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Eclear2(long stack_id) throws HDF5LibraryException; @@ -3859,7 +3966,7 @@ public class H5 implements java.io.Serializable { * IN: Error message identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_msg(long err_id) throws HDF5LibraryException; @@ -3870,7 +3977,7 @@ public class H5 implements java.io.Serializable { * IN: Error stack identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_stack(long stack_id) throws HDF5LibraryException; @@ -3887,12 +3994,12 @@ public class H5 implements java.io.Serializable { * @return a message identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - msg is null. + * msg is null. **/ public synchronized static native long H5Ecreate_msg(long cls_id, int msg_type, String msg) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Ecreate_stack creates a new empty error stack and returns the new stack's identifier. @@ -3900,7 +4007,7 @@ public class H5 implements java.io.Serializable { * @return an error stack identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Ecreate_stack() throws HDF5LibraryException; @@ -3913,30 +4020,31 @@ public class H5 implements java.io.Serializable { * @return the name of the error class * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native String H5Eget_class_name(long class_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Eget_current_stack copies the current error stack and returns an error stack identifier for the new copy. + * H5Eget_current_stack copies the current error stack and returns an error stack identifier for the new + * copy. * * @return an error stack identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Eget_current_stack() throws HDF5LibraryException; /** - * H5Eset_current_stack replaces the content of the current error stack with a copy of the content of the error - * stack specified by estack_id. + * H5Eset_current_stack replaces the content of the current error stack with a copy of the content of the + * error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Eset_current_stack(long stack_id) throws HDF5LibraryException; @@ -3951,13 +4059,14 @@ public class H5 implements java.io.Serializable { * @return the error message * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native String H5Eget_msg(long msg_id, int[] type_list) throws HDF5LibraryException; + public synchronized static native String H5Eget_msg(long msg_id, int[] type_list) + throws HDF5LibraryException; /** - * H5Eget_num retrieves the number of error records in the error stack specified by estack_id (including major, - * minor messages and description). + * H5Eget_num retrieves the number of error records in the error stack specified by estack_id (including + * major, minor messages and description). * * @param stack_id * IN: Error stack identifier. @@ -3965,26 +4074,29 @@ public class H5 implements java.io.Serializable { * @return the number of error messages * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5Eget_num(long stack_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Eget_num(long stack_id) + throws HDF5LibraryException, NullPointerException; /** * H5Eprint2 prints the error stack specified by estack_id on the specified stream, stream. * * @param stack_id - * IN: Error stack identifier.If the identifier is H5E_DEFAULT, the current error stack will be printed. + * IN: Error stack identifier.If the identifier is H5E_DEFAULT, the current error stack will be + * printed. * @param stream * IN: File pointer, or stderr if null. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Eprint2(long stack_id, Object stream) throws HDF5LibraryException; + public synchronized static native void H5Eprint2(long stack_id, Object stream) + throws HDF5LibraryException; /** - * H5Epop deletes the number of error records specified in count from the top of the error stack specified by - * estack_id (including major, minor messages and description). + * H5Epop deletes the number of error records specified in count from the top of the error stack specified + * by estack_id (including major, minor messages and description). * * @param stack_id * IN: Error stack identifier. @@ -3992,11 +4104,10 @@ public class H5 implements java.io.Serializable { * IN: Version of the client library or application to which the error class belongs. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Epop(long stack_id, long count) throws HDF5LibraryException; - /** * H5Epush pushes a new error record onto the error stack specified by estack_id. * @@ -4018,14 +4129,14 @@ public class H5 implements java.io.Serializable { * IN: Error description string. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - file, func, or msg is null. - **/ - public static void H5Epush(long stack_id, String file, String func, int line, - long cls_id, long maj_id, long min_id, String msg) throws HDF5LibraryException, NullPointerException + * file, func, or msg is null. + **/ + public static void H5Epush(long stack_id, String file, String func, int line, long cls_id, long maj_id, + long min_id, String msg) throws HDF5LibraryException, NullPointerException { - H5Epush2(stack_id, file, func, line, cls_id, maj_id, min_id, msg); + 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. @@ -4048,16 +4159,17 @@ public class H5 implements java.io.Serializable { * IN: Error description string. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - file, func, or msg is null. - **/ + * 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; + long cls_id, long maj_id, long min_id, String msg) + throws HDF5LibraryException, NullPointerException; /** - * H5Eregister_class registers a client library or application program to the HDF5 error API so that the client - * library or application program can report errors together with HDF5 library. + * H5Eregister_class registers a client library or application program to the HDF5 error API so that the + * client library or application program can report errors together with HDF5 library. * * @param cls_name * IN: Name of the error class. @@ -4069,12 +4181,12 @@ public class H5 implements java.io.Serializable { * @return a class identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native long H5Eregister_class(String cls_name, String lib_name, String version) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Eunregister_class removes the error class specified by class_id. @@ -4083,7 +4195,7 @@ public class H5 implements java.io.Serializable { * IN: Error class identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Eunregister_class(long class_id) throws HDF5LibraryException; @@ -4101,13 +4213,14 @@ public class H5 implements java.io.Serializable { * IN: Data to be passed with func. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - func is null. + * func is null. **/ - public static void H5Ewalk(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException + public static void H5Ewalk(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) + throws HDF5LibraryException, NullPointerException { - H5Ewalk2(stack_id, direction, func, client_data); + H5Ewalk2(stack_id, direction, func, client_data); } /** * H5Ewalk2 walks the error stack specified by estack_id for the current thread and calls the @@ -4123,12 +4236,13 @@ public class H5 implements java.io.Serializable { * IN: Data to be passed with func. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - func is null. + * 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; + public synchronized static native void H5Ewalk2(long stack_id, long direction, H5E_walk_cb func, + H5E_walk_t client_data) + throws HDF5LibraryException, NullPointerException; // /////// unimplemented //////// // public interface H5E_auto2_t extends Callback @@ -4171,9 +4285,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Fclose(long file_id) throws HDF5LibraryException { + public static int H5Fclose(long file_id) throws HDF5LibraryException + { if (file_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -4198,12 +4313,13 @@ public class H5 implements java.io.Serializable { * @return a file identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Fopen(String name, int flags, long access_id) throws HDF5LibraryException, - NullPointerException { + public static long H5Fopen(String name, int flags, long access_id) + throws HDF5LibraryException, NullPointerException + { long id = _H5Fopen(name, flags, access_id); if (id > 0) { log.trace("OPEN_IDS: H5Fopen add {}", id); @@ -4214,7 +4330,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Fopen(String name, int flags, long access_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Freopen reopens an HDF5 file. @@ -4222,11 +4338,13 @@ public class H5 implements java.io.Serializable { * @param file_id * Identifier of a file to terminate and reopen access to. * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. * @return a new file identifier if successful + * + * @exception HDF5LibraryException + * Error from the HDF-5 Library. **/ - public static long H5Freopen(long file_id) throws HDF5LibraryException { + public static long H5Freopen(long file_id) throws HDF5LibraryException + { long id = _H5Freopen(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Freopen add {}", id); @@ -4251,7 +4369,8 @@ public class H5 implements java.io.Serializable { * <LI> * H5F_ACC_RDONLY Allow read-only access to file.</LI> * <LI> - * H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously stored in the file.</LI> + * H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously stored in the + * file.</LI> * <LI> * H5F_ACC_EXCL Fail if file already exists.</LI> * <LI> @@ -4259,22 +4378,23 @@ public class H5 implements java.io.Serializable { * </UL> * * @param create_id - * File creation property list identifier, used when modifying default file meta-data. Use H5P_DEFAULT - * for default access properties. + * File creation property list identifier, used when modifying default file meta-data. Use + * H5P_DEFAULT for default access properties. * @param access_id - * File access property list identifier. If parallel file access is desired, this is a collective call - * according to the communicator stored in the access_id (not supported in Java). Use H5P_DEFAULT for - * default access properties. + * File access property list identifier. If parallel file access is desired, this is a + * collective call according to the communicator stored in the access_id (not supported + * in Java). Use H5P_DEFAULT for default access properties. * * @return a file identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Fcreate(String name, int flags, long create_id, long access_id) throws HDF5LibraryException, - NullPointerException { + public static long H5Fcreate(String name, int flags, long create_id, long access_id) + throws HDF5LibraryException, NullPointerException + { long id = _H5Fcreate(name, flags, create_id, access_id); if (id > 0) { log.trace("OPEN_IDS: H5Fcreate add {}", id); @@ -4285,34 +4405,30 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Fcreate(String name, int flags, long create_id, long access_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Fflush causes all buffers associated with a file or object to be immediately flushed (written) to disk without - * removing the data from the (memory) cache. - * <P> - * After this call completes, the file (or object) is in a consistent state and all data written to date is assured - * to be permanent. + * H5Fflush causes all buffers associated with a file or object to be immediately flushed (written) to + * disk without removing the data from the (memory) cache. <P> After this call completes, the file (or + * object) is in a consistent state and all data written to date is assured to be permanent. * * @param object_id - * Identifier of object used to identify the file. <b>object_id</b> can be any object associated with the - * file, including the file itself, a dataset, a group, an attribute, or a named data type. + * Identifier of object used to identify the file. <b>object_id</b> can be any object + * associated with the file, including the file itself, a dataset, a group, an attribute, + * or a named data type. * @param scope - * specifies the scope of the flushing action, in the case that the HDF-5 file is not a single physical - * file. - * <P> - * Valid values are: + * specifies the scope of the flushing action, in the case that the HDF-5 file is not a single + * physical file. + * <P> Valid values are: * <UL> - * <LI> - * H5F_SCOPE_GLOBAL Flushes the entire virtual file.</LI> - * <LI> - * H5F_SCOPE_LOCAL Flushes only the specified file.</LI> + * <LI> H5F_SCOPE_GLOBAL Flushes the entire virtual file.</LI> + * <LI> H5F_SCOPE_LOCAL Flushes only the specified file.</LI> * </UL> * * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Fflush(long object_id, int scope) throws HDF5LibraryException; @@ -4325,9 +4441,10 @@ public class H5 implements java.io.Serializable { * @return a file access property list identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Fget_access_plist(long file_id) throws HDF5LibraryException { + public static long H5Fget_access_plist(long file_id) throws HDF5LibraryException + { long id = _H5Fget_access_plist(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Fget_access_plist add {}", id); @@ -4340,8 +4457,8 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Fget_access_plist(long file_id) throws HDF5LibraryException; /** - * H5Fget_create_plist returns a file creation property list identifier identifying the creation properties used to - * create this file. + * H5Fget_create_plist returns a file creation property list identifier identifying the creation + * properties used to create this file. * * @param file_id * Identifier of the file to get creation property list @@ -4349,9 +4466,10 @@ public class H5 implements java.io.Serializable { * @return a file creation property list identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Fget_create_plist(long file_id) throws HDF5LibraryException { + public static long H5Fget_create_plist(long file_id) throws HDF5LibraryException + { long id = _H5Fget_create_plist(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Fget_create_plist add {}", id); @@ -4374,7 +4492,7 @@ public class H5 implements java.io.Serializable { * @return the file size of the HDF5 file * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Fget_filesize(long file_id) throws HDF5LibraryException; @@ -4387,7 +4505,7 @@ public class H5 implements java.io.Serializable { * @return the amount of free space in the file * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Fget_freespace(long file_id) throws HDF5LibraryException; @@ -4400,13 +4518,13 @@ public class H5 implements java.io.Serializable { * @return the intended access mode flag, as originally passed with H5Fopen. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Fget_intent(long file_id) throws HDF5LibraryException; /** - * H5Fget_mdc_hit_rate queries the metadata cache of the target file to obtain its hit rate (cache hits / (cache - * hits + cache misses)) since the last time hit rate statistics were reset. + * H5Fget_mdc_hit_rate queries the metadata cache of the target file to obtain its hit rate (cache hits / + * (cache hits + cache misses)) since the last time hit rate statistics were reset. * * @param file_id * IN: Identifier of the target file. @@ -4414,7 +4532,7 @@ public class H5 implements java.io.Serializable { * @return the double in which the hit rate is returned. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native double H5Fget_mdc_hit_rate(long file_id) throws HDF5LibraryException; @@ -4434,12 +4552,12 @@ public class H5 implements java.io.Serializable { * @return current number of entries in the cache * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - metadata_cache is null. + * metadata_cache is null. **/ public synchronized static native int H5Fget_mdc_size(long file_id, long[] metadata_cache) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Fget_name retrieves the name of the file to which the object obj_id belongs. @@ -4450,7 +4568,7 @@ public class H5 implements java.io.Serializable { * @return the filename. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native String H5Fget_name(long obj_id) throws HDF5LibraryException; @@ -4474,12 +4592,14 @@ public class H5 implements java.io.Serializable { * @return the number of open objects. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5Fget_obj_count(long file_id, int types) throws HDF5LibraryException; + public synchronized static native long H5Fget_obj_count(long file_id, int types) + throws HDF5LibraryException; /** - * H5Fget_obj_ids returns the list of identifiers for all open HDF5 objects fitting the specified criteria. + * H5Fget_obj_ids returns the list of identifiers for all open HDF5 objects fitting the specified + * criteria. * * @param file_id * IN: File identifier for a currently-open HDF5 file @@ -4493,12 +4613,13 @@ public class H5 implements java.io.Serializable { * @return the number of objects placed into obj_id_list. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - obj_id_list is null. + * obj_id_list is null. **/ - public synchronized static native long H5Fget_obj_ids(long file_id, int types, long max_objs, long[] obj_id_list) - throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Fget_obj_ids(long file_id, int types, long max_objs, + long[] obj_id_list) + throws HDF5LibraryException, NullPointerException; /** * H5Fis_hdf5 determines whether a file is in the HDF5 format. @@ -4509,15 +4630,16 @@ public class H5 implements java.io.Serializable { * @return true if is HDF-5, false if not. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException; + public synchronized static native boolean H5Fis_hdf5(String name) + throws HDF5LibraryException, NullPointerException; /** - * H5Fmount mounts the file specified by child_id onto the group specified by loc_id and name using the mount - * properties plist_id. + * H5Fmount mounts the file specified by child_id onto the group specified by loc_id and name using the + * mount properties plist_id. * * @param loc_id * The identifier for the group onto which the file specified by child_id is to be mounted. @@ -4531,12 +4653,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native int H5Fmount(long loc_id, String name, long child_id, long plist_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * Given a mount point, H5Funmount disassociates the mount point's file from the file mounted there. @@ -4549,24 +4671,25 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native int H5Funmount(long loc_id, String name) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Funmount(long loc_id, String name) + throws HDF5LibraryException, NullPointerException; /** - * H5Freset_mdc_hit_rate_stats resets the hit rate statistics counters in the metadata cache associated with the - * specified file. + * H5Freset_mdc_hit_rate_stats resets the hit rate statistics counters in the metadata cache associated + * with the specified file. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Freset_mdc_hit_rate_stats(long file_id) throws HDF5LibraryException; + public synchronized static native void H5Freset_mdc_hit_rate_stats(long file_id) + throws HDF5LibraryException; /** * H5Fget_info returns global information for the file associated with the @@ -4576,7 +4699,8 @@ public class H5 implements java.io.Serializable { * * @return A buffer(H5F_info2_t) for current "global" information about file * - * @exception HDF5LibraryException - Error from the HDF-5 Library. + * @exception HDF5LibraryException + * Error from the HDF-5 Library. **/ public synchronized static native H5F_info2_t H5Fget_info(long obj_id) throws HDF5LibraryException; @@ -4588,19 +4712,20 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the target file. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Fclear_elink_file_cache(long file_id) throws HDF5LibraryException; + public synchronized static native void H5Fclear_elink_file_cache(long file_id) + throws HDF5LibraryException; /** - * H5Fstart_swmr_write will activate SWMR writing mode for a file associated with file_id. This routine will - * prepare and ensure the file is safe for SWMR writing. + * H5Fstart_swmr_write will activate SWMR writing mode for a file associated with file_id. This routine + * will prepare and ensure the file is safe for SWMR writing. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Fstart_swmr_write(long file_id) throws HDF5LibraryException; @@ -4611,18 +4736,19 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the target file. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Fstart_mdc_logging(long file_id) throws HDF5LibraryException; /** - * H5Fstop_mdc_logging stops logging metadata cache events if logging was previously enabled and is currently ongoing. + * H5Fstop_mdc_logging stops logging metadata cache events if logging was previously enabled and is + * currently ongoing. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Fstop_mdc_logging(long file_id) throws HDF5LibraryException; @@ -4638,12 +4764,13 @@ public class H5 implements java.io.Serializable { * mdc_logging_status[1] = is_currently_logging, whether events are currently being logged * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - mdc_logging_status is null. + * mdc_logging_status is null. **/ - public synchronized static native void H5Fget_mdc_logging_status(long file_id, boolean[] mdc_logging_status) - throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Fget_mdc_logging_status(long file_id, + boolean[] mdc_logging_status) + throws HDF5LibraryException, NullPointerException; /** * H5Fget_dset_no_attrs_hint gets the file-level setting to create minimized dataset object headers. @@ -4654,11 +4781,10 @@ public class H5 implements java.io.Serializable { * @return true if the file-level is set to create minimized dataset object headers, false if not. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Fget_dset_no_attrs_hint(long file_id) - throws HDF5LibraryException; - + throws HDF5LibraryException; /** * H5Fset_dset_no_attrs_hint sets the file-level setting to create minimized dataset object headers. @@ -4666,14 +4792,13 @@ public class H5 implements java.io.Serializable { * @param file_id * IN: Identifier of the target file. * @param minimize - * the minimize hint setting + * the minimize hint setting * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Fset_dset_no_attrs_hint(long file_id, boolean minimize) - throws HDF5LibraryException; - + throws HDF5LibraryException; /** * H5Fset_libver_bounds sets a different low and high bounds while a file is open. @@ -4686,17 +4811,18 @@ public class H5 implements java.io.Serializable { * IN: The latest version of the library that will be used for writing objects. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Fset_libver_bounds(long file_id, int low, int high) - throws HDF5LibraryException; + throws HDF5LibraryException; // /////// unimplemented //////// // herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa); // herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment); // ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len); // herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info); - // ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/); + // ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t + // *sect_info/*out*/); // herr_t H5Fformat_convert(hid_t fid); // herr_t H5Freset_page_buffering_stats(hid_t file_id); // herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], @@ -4776,11 +4902,10 @@ public class H5 implements java.io.Serializable { // herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa); // haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type); // herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle); - // herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/); - // herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf); - // herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing); - // herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing); - // herr_t H5FDlock(H5FD_t *file, hbool_t rw); + // herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void + // *buf/*out*/); herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t + // size, const void *buf); herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing); herr_t + // H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing); herr_t H5FDlock(H5FD_t *file, hbool_t rw); // herr_t H5FDunlock(H5FD_t *file); // herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/); @@ -4807,9 +4932,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Gclose(long group_id) throws HDF5LibraryException { + public static int H5Gclose(long group_id) throws HDF5LibraryException + { if (group_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -4833,18 +4959,19 @@ public class H5 implements java.io.Serializable { * @param gcpl_id * IN: Identifier of group creation property list. * @param gapl_id - * IN: Identifier of group access property list. (No group access properties have been implemented at - * this time; use H5P_DEFAULT.) + * IN: Identifier of group access property list. (No group access properties have been + *implemented at this time; use H5P_DEFAULT.) * * @return a valid group identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public static long H5Gcreate(long loc_id, String name, long lcpl_id, long gcpl_id, long gapl_id) - throws HDF5LibraryException, NullPointerException { + throws HDF5LibraryException, NullPointerException + { long id = _H5Gcreate2(loc_id, name, lcpl_id, gcpl_id, gapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Gcreate add {}", id); @@ -4855,7 +4982,8 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Gcreate2(long loc_id, String name, long lcpl_id, long gcpl_id, - long gapl_id) throws HDF5LibraryException, NullPointerException; + long gapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Gcreate_anon creates a new empty group in the file specified by loc_id. @@ -4865,15 +4993,16 @@ public class H5 implements java.io.Serializable { * @param gcpl_id * IN: Identifier of group creation property list. * @param gapl_id - * IN: Identifier of group access property list. (No group access properties have been implemented at - * this time; use H5P_DEFAULT.) + * IN: Identifier of group access property list. (No group access properties have been + * implemented at this time; use H5P_DEFAULT.) * * @return a valid group identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Gcreate_anon(long loc_id, long gcpl_id, long gapl_id) throws HDF5LibraryException { + public static long H5Gcreate_anon(long loc_id, long gcpl_id, long gapl_id) throws HDF5LibraryException + { long id = _H5Gcreate_anon(loc_id, gcpl_id, gapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Gcreate_anon add {}", id); @@ -4884,11 +5013,11 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Gcreate_anon(long loc_id, long gcpl_id, long gapl_id) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Gget_create_plist returns an identifier for the group creation property list associated with the group - * specified by group_id. + * H5Gget_create_plist returns an identifier for the group creation property list associated with the + * group specified by group_id. * * @param group_id * IN: Identifier of the group. @@ -4896,13 +5025,13 @@ public class H5 implements java.io.Serializable { * @return an identifier for the group's creation property list * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Gget_create_plist(long group_id) throws HDF5LibraryException; /** - * H5Gget_info retrieves information about the group specified by group_id. The information is returned in the - * group_info struct. + * H5Gget_info retrieves information about the group specified by group_id. The information is returned in + * the group_info struct. * * @param group_id * IN: Identifier of the group. @@ -4910,12 +5039,13 @@ public class H5 implements java.io.Serializable { * @return a structure in which group information is returned * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native H5G_info_t H5Gget_info(long group_id) throws HDF5LibraryException; /** - * H5Gget_info_by_idx retrieves information about a group, according to the group's position within an index. + * H5Gget_info_by_idx retrieves information about a group, according to the group's position within an + * index. * * @param group_id * IN: File or group identifier. @@ -4933,16 +5063,18 @@ public class H5 implements java.io.Serializable { * @return a structure in which group information is returned * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native H5G_info_t H5Gget_info_by_idx(long group_id, String group_name, int idx_type, - int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5G_info_t H5Gget_info_by_idx(long group_id, String group_name, + int idx_type, int order, long n, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Gget_info_by_name retrieves information about the group group_name located in the file or group specified by - * loc_id. + * H5Gget_info_by_name retrieves information about the group group_name located in the file or group + * specified by loc_id. * * @param group_id * IN: File or group identifier. @@ -4954,15 +5086,16 @@ public class H5 implements java.io.Serializable { * @return a structure in which group information is returned * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native H5G_info_t H5Gget_info_by_name(long group_id, String name, long lapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * 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 @@ -4978,21 +5111,25 @@ public class H5 implements java.io.Serializable { * @return the number of items found * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. */ - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, - long[] objRef) throws HDF5LibraryException, NullPointerException { + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, + int[] objTypes, long[] objRef) + throws HDF5LibraryException, NullPointerException + { if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_all(): name array is null"); } - return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, objRef, HDF5Constants.H5_INDEX_NAME); + return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, objRef, + HDF5Constants.H5_INDEX_NAME); } /** - * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * 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 @@ -5012,17 +5149,21 @@ public class H5 implements java.io.Serializable { * @return the number of items found * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. */ - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, - int[] ltype, long[] objRef, int indx_type) throws HDF5LibraryException, NullPointerException { + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, + int[] objTypes, int[] ltype, long[] objRef, + int indx_type) + throws HDF5LibraryException, NullPointerException + { return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, null, objRef, indx_type, -1); } /** - * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * 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 @@ -5044,17 +5185,21 @@ public class H5 implements java.io.Serializable { * @return the number of items found * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. */ - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, - int[] ltype, long[] fno, long[] objRef, int indx_type) throws HDF5LibraryException, NullPointerException { + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, + int[] objTypes, int[] ltype, long[] fno, long[] objRef, + int indx_type) + throws HDF5LibraryException, NullPointerException + { return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, objRef, indx_type, -1); } /** - * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * 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 @@ -5078,13 +5223,15 @@ public class H5 implements java.io.Serializable { * @return the number of items found * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. */ - public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, - int[] ltype, long[] fno, long[] objRef, int indx_type, int indx_order) throws HDF5LibraryException, - NullPointerException { + public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, + int[] objTypes, int[] ltype, long[] fno, + long[] objRef, int indx_type, int indx_order) + throws HDF5LibraryException, NullPointerException + { if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_full(): name array is null"); } @@ -5114,21 +5261,22 @@ public class H5 implements java.io.Serializable { indx_order = HDF5Constants.H5_ITER_INC; log.trace("H5Gget_obj_info_full: objNames_len={}", objNames.length); - int status = H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, objRef, objNames.length, indx_type, - indx_order); + int status = H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, objRef, + objNames.length, indx_type, indx_order); for (int indx = 0; indx < 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[] objNames, int[] objTypes, - int[] ltype, long[] fno, long[] objRef, int n, int indx_type, int indx_order) throws HDF5LibraryException, - NullPointerException; + private synchronized static native int + H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, + long[] objRef, int n, int indx_type, int indx_order) + throws HDF5LibraryException, NullPointerException; /** - * H5Gget_obj_info_idx report the name and type of object with index 'idx' in a Group. The 'idx' corresponds to the - * index maintained by H5Giterate. Each link is returned, so objects with multiple links will be counted once for - * each link. + * H5Gget_obj_info_idx report the name and type of object with index 'idx' in a Group. The 'idx' + * corresponds to the index maintained by H5Giterate. Each link is returned, so objects with multiple + * links will be counted once for each link. * * @param loc_id * IN: file or group ID. @@ -5144,19 +5292,21 @@ public class H5 implements java.io.Serializable { * @return non-negative if successful, -1 if not. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. */ - public synchronized static int H5Gget_obj_info_idx(long loc_id, String name, int idx, String[] oname, int[] type) - throws HDF5LibraryException, NullPointerException { + public synchronized static int H5Gget_obj_info_idx(long loc_id, String name, int idx, String[] oname, + int[] type) + throws HDF5LibraryException, NullPointerException + { String n[] = new String[1]; - n[0] = new String(""); - oname[0] = H5Lget_name_by_idx(loc_id, name, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, idx, - HDF5Constants.H5P_DEFAULT); - H5L_info_t info = H5Lget_info_by_idx(loc_id, name, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, idx, - HDF5Constants.H5P_DEFAULT); - type[0] = info.type; + n[0] = new String(""); + oname[0] = H5Lget_name_by_idx(loc_id, name, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, + idx, HDF5Constants.H5P_DEFAULT); + H5L_info_t info = H5Lget_info_by_idx(loc_id, name, HDF5Constants.H5_INDEX_NAME, + HDF5Constants.H5_ITER_INC, idx, HDF5Constants.H5P_DEFAULT); + type[0] = info.type; return 0; } @@ -5166,8 +5316,8 @@ public class H5 implements java.io.Serializable { * a lot of time to finish if the number of objects is more than 10,000 */ /** - * retrieves information of all objects (recurvisely) under the group (name) located in the file or group specified - * by loc_id up to maximum specified by objMax. + * retrieves information of all objects (recurvisely) under the group (name) located in the file or group + * specified by loc_id up to maximum specified by objMax. * * @param loc_id * IN: File or group identifier @@ -5185,12 +5335,14 @@ public class H5 implements java.io.Serializable { * @return the number of items found * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. */ - public synchronized static int H5Gget_obj_info_max(long loc_id, String[] objNames, int[] objTypes, int[] lnkTypes, - long[] objRef, long objMax) throws HDF5LibraryException, NullPointerException { + public synchronized static int H5Gget_obj_info_max(long loc_id, String[] objNames, int[] objTypes, + int[] lnkTypes, long[] objRef, long objMax) + throws HDF5LibraryException, NullPointerException + { if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_max(): name array is null"); } @@ -5218,12 +5370,14 @@ public class H5 implements java.io.Serializable { return H5Gget_obj_info_max(loc_id, objNames, objTypes, lnkTypes, objRef, objMax, objNames.length); } - private synchronized static native int H5Gget_obj_info_max(long loc_id, String[] oname, int[] otype, int[] ltype, - long[] ref, long amax, int n) throws HDF5LibraryException, NullPointerException; + private synchronized static native int H5Gget_obj_info_max(long loc_id, String[] oname, int[] otype, + int[] ltype, long[] ref, long amax, int n) + throws HDF5LibraryException, NullPointerException; /** - * H5Gn_members report the number of objects in a Group. The 'objects' include everything that will be visited by - * H5Giterate. Each link is returned, so objects with multiple links will be counted once for each link. + * H5Gn_members report the number of objects in a Group. The 'objects' include everything that will be + * visited by H5Giterate. Each link is returned, so objects with multiple links will be counted once for + * each link. * * @param loc_id * file or group ID. @@ -5233,18 +5387,19 @@ public class H5 implements java.io.Serializable { * @return the number of members in the group or -1 if error. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. */ - public synchronized static long H5Gn_members(long loc_id, String name) throws HDF5LibraryException, - NullPointerException { + public synchronized static long H5Gn_members(long loc_id, String name) + throws HDF5LibraryException, NullPointerException + { long grp_id = H5Gopen(loc_id, name, HDF5Constants.H5P_DEFAULT); - long n = -1; + long n = -1; try { H5G_info_t info = H5.H5Gget_info(grp_id); - n = info.nlinks; + n = info.nlinks; } finally { H5Gclose(grp_id); @@ -5266,12 +5421,13 @@ public class H5 implements java.io.Serializable { * @return a valid group identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Gopen(long loc_id, String name, long gapl_id) throws HDF5LibraryException, - NullPointerException { + public static long H5Gopen(long loc_id, String name, long gapl_id) + throws HDF5LibraryException, NullPointerException + { long id = _H5Gopen2(loc_id, name, gapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Gopen add {}", id); @@ -5282,7 +5438,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Gopen2(long loc_id, String name, long gapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Gflush causes all buffers associated with a group to be immediately flushed to disk without @@ -5292,7 +5448,7 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the group to be flushed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Gflush(long group_id) throws HDF5LibraryException; @@ -5306,7 +5462,7 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the group to be refreshed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Grefresh(long group_id) throws HDF5LibraryException; @@ -5349,7 +5505,7 @@ public class H5 implements java.io.Serializable { * @return the file ID. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException; @@ -5367,11 +5523,11 @@ public class H5 implements java.io.Serializable { * @return the length of the name retrieved. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + throws HDF5LibraryException, NullPointerException; /** * H5Iget_name retrieves the name of an object specified by the identifier, obj_id. * @@ -5381,10 +5537,9 @@ public class H5 implements java.io.Serializable { * @return String for Attribute name. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native String H5Iget_name(long obj_id) - throws HDF5LibraryException; + 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. @@ -5395,13 +5550,14 @@ public class H5 implements java.io.Serializable { * @return the reference count. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Iget_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + 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. + * If the reference count for an ID reaches zero, the object will be closed. * * @param obj_id * IN: Identifier of the object. @@ -5409,9 +5565,10 @@ public class H5 implements java.io.Serializable { * @return the reference count. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Idec_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + 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. @@ -5422,9 +5579,10 @@ public class H5 implements java.io.Serializable { * @return the reference count. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Iinc_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Iinc_ref(long obj_id) + throws HDF5LibraryException, NullPointerException; /** * H5Iget_type retrieves the type of the object identified by obj_id. @@ -5435,13 +5593,13 @@ public class H5 implements java.io.Serializable { * @return the object type if successful; otherwise H5I_BADID. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Iget_type(long obj_id) throws HDF5LibraryException; /** - * H5Iget_type_ref retrieves the reference count on an ID type. The reference count is used by the library to - * indicate when an ID type can be destroyed. + * H5Iget_type_ref retrieves the reference count on an ID type. The reference count is used by the library + * to indicate when an ID type can be destroyed. * * @param type_id * IN: The identifier of the type whose reference count is to be retrieved @@ -5449,13 +5607,13 @@ public class H5 implements java.io.Serializable { * @return The current reference count on success, negative on failure. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Iget_type_ref(long type_id) throws HDF5LibraryException; /** - * H5Idec_type_ref decrements the reference count on an identifier type. The reference count is used by the - * library to indicate when an identifier type can be destroyed. If the reference count reaches zero, + * H5Idec_type_ref decrements the reference count on an identifier type. The reference count is used by + * the library to indicate when an identifier type can be destroyed. If the reference count reaches zero, * this function will destroy it. * * @param type_id @@ -5464,13 +5622,13 @@ public class H5 implements java.io.Serializable { * @return The current reference count on success, negative on failure. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Idec_type_ref(long type_id) throws HDF5LibraryException; /** - * H5Iinc_type_ref increments the reference count on an ID type. The reference count is used by the library - * to indicate when an ID type can be destroyed. + * H5Iinc_type_ref increments the reference count on an ID type. The reference count is used by the + * library to indicate when an ID type can be destroyed. * * @param type_id * IN: The identifier of the type whose reference count is to be incremented @@ -5478,7 +5636,7 @@ public class H5 implements java.io.Serializable { * @return The current reference count on success, negative on failure. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Iinc_type_ref(long type_id) throws HDF5LibraryException; @@ -5491,7 +5649,7 @@ public class H5 implements java.io.Serializable { * @return Number of identifiers of the specified identifier type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Inmembers(long type_id) throws HDF5LibraryException; @@ -5504,7 +5662,7 @@ public class H5 implements java.io.Serializable { * @return a boolean, true if the specified identifier id is valid * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Iis_valid(long obj_id) throws HDF5LibraryException; @@ -5517,11 +5675,10 @@ public class H5 implements java.io.Serializable { * @return a boolean, true if the specified identifier type exists * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Itype_exists(int type_id) throws HDF5LibraryException; - /** * H5Iclear_type deletes all identifiers of the type identified by the argument type. * @@ -5531,9 +5688,10 @@ public class H5 implements java.io.Serializable { * IN: Whether or not to force deletion of all identifiers * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Iclear_type(int type_id, boolean force) throws HDF5LibraryException; + public synchronized static native void H5Iclear_type(int type_id, boolean force) + throws HDF5LibraryException; /** * H5Idestroy_type deletes an entire identifier type. All identifiers of this type are destroyed @@ -5543,7 +5701,7 @@ public class H5 implements java.io.Serializable { * IN: Identifier of identifier type which is to be destroyed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Idestroy_type(int type_id) throws HDF5LibraryException; @@ -5580,16 +5738,17 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native void H5Lcopy(long src_loc, String src_name, long dst_loc, String dst_name, - long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Lcopy(long src_loc, String src_name, long dst_loc, + String dst_name, long lcpl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Lcreate_external creates a new soft link to an external object, which is an object in a different HDF5 file - * from the location of the link. + * H5Lcreate_external creates a new soft link to an external object, which is an object in a different + * HDF5 file from the location of the link. * * @param file_name * IN: Name of the target file containing the target object. @@ -5605,12 +5764,14 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native void H5Lcreate_external(String file_name, String obj_name, long link_loc_id, - String link_name, long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Lcreate_external(String file_name, String obj_name, + long link_loc_id, String link_name, + long lcpl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_hard creates a new hard link to a pre-existing object in an HDF5 file. @@ -5629,12 +5790,13 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - cur_name or dst_name is null. + * cur_name or dst_name is null. **/ - public synchronized static native void H5Lcreate_hard(long cur_loc, String cur_name, long dst_loc, String dst_name, - long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Lcreate_hard(long cur_loc, String cur_name, long dst_loc, + String dst_name, long lcpl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_soft creates a new soft link to an object in an HDF5 file. @@ -5651,12 +5813,13 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - link_name is null. + * link_name is null. **/ - public synchronized static native void H5Lcreate_soft(String link_target, long link_loc_id, String link_name, - long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Lcreate_soft(String link_target, long link_loc_id, + String link_name, long lcpl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Ldelete removes the link specified from a group. @@ -5669,15 +5832,16 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native void H5Ldelete(long loc_id, String name, long lapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Ldelete_by_idx removes the nth link in a group according to the specified order and in the specified index. + * H5Ldelete_by_idx removes the nth link in a group according to the specified order and in the specified + * index. * * @param loc_id * IN: File or group identifier specifying location of subject group @@ -5693,12 +5857,13 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - group_name is null. + * group_name is null. **/ - public synchronized static native void H5Ldelete_by_idx(long loc_id, String group_name, int idx_type, int order, - long n, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Ldelete_by_idx(long loc_id, String group_name, int idx_type, + int order, long n, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lexists checks if a link with a particular name exists in a group. @@ -5713,12 +5878,12 @@ public class H5 implements java.io.Serializable { * @return a boolean, true if the name exists, otherwise false. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native boolean H5Lexists(long loc_id, String name, long lapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Lget_info returns information about the specified link. @@ -5733,16 +5898,16 @@ public class H5 implements java.io.Serializable { * @return a buffer(H5L_info_t) for the link information. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native H5L_info_t H5Lget_info(long loc_id, String name, long lapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Lget_info_by_idx opens a named datatype at the location specified by loc_id and return an identifier for the - * datatype. + * H5Lget_info_by_idx opens a named datatype at the location specified by loc_id and return an identifier + * for the datatype. * * @param loc_id * IN: File or group identifier specifying location of subject group @@ -5760,16 +5925,18 @@ public class H5 implements java.io.Serializable { * @return a buffer(H5L_info_t) for the link information. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - group_name is null. + * group_name is null. **/ - public synchronized static native H5L_info_t H5Lget_info_by_idx(long loc_id, String group_name, int idx_type, - int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5L_info_t H5Lget_info_by_idx(long loc_id, String group_name, + int idx_type, int order, long n, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Lget_name_by_idx retrieves name of the nth link in a group, according to the order within a specified field or - * index. + * H5Lget_name_by_idx retrieves name of the nth link in a group, according to the order within a specified + * field or index. * * @param loc_id * IN: File or group identifier specifying location of subject group @@ -5787,12 +5954,13 @@ public class H5 implements java.io.Serializable { * @return a String for the link name. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - group_name is null. + * group_name is null. **/ public synchronized static native String H5Lget_name_by_idx(long loc_id, String group_name, int idx_type, - int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; + int order, long n, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lget_value returns the link value of a symbolic link. Note that this function is a combination @@ -5810,12 +5978,13 @@ public class H5 implements java.io.Serializable { * @return the link type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native int H5Lget_value(long loc_id, String name, String[] link_value, long lapl_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Lget_value(long loc_id, String name, String[] link_value, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lget_value_by_idx retrieves value of the nth link in a group, according to the order within an index. @@ -5840,12 +6009,14 @@ public class H5 implements java.io.Serializable { * @return the link type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - group_name is null. + * group_name is null. **/ - public synchronized static native int H5Lget_value_by_idx(long loc_id, String group_name, int idx_type, int order, - long n, String[] link_value, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Lget_value_by_idx(long loc_id, String group_name, int idx_type, + int order, long n, String[] link_value, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Literate iterates through links in a group. @@ -5863,14 +6034,15 @@ public class H5 implements java.io.Serializable { * @param op_data * IN: User-defined pointer to data required by the application for its processing of the link * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Literate(long grp_id, int idx_type, int order, long idx, H5L_iterate_cb op, - H5L_iterate_t op_data) throws HDF5LibraryException; + public synchronized static native int H5Literate(long grp_id, int idx_type, int order, long idx, + H5L_iterate_cb op, H5L_iterate_t op_data) + throws HDF5LibraryException; /** * H5Literate_by_name iterates through links in a group. @@ -5892,17 +6064,18 @@ public class H5 implements java.io.Serializable { * @param lapl_id * IN: Link access property list identifier * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - group_name is null. + * group_name is null. **/ - public synchronized static native int H5Literate_by_name(long grp_id, String group_name, int idx_type, int order, - long idx, H5L_iterate_cb op, H5L_iterate_t op_data, long lapl_id) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Literate_by_name(long grp_id, String group_name, int idx_type, + int order, long idx, H5L_iterate_cb op, + H5L_iterate_t op_data, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lmove renames a link within an HDF5 file. @@ -5921,12 +6094,13 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier to be associated with the new link. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native void H5Lmove(long src_loc, String src_name, long dst_loc, String dst_name, - long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Lmove(long src_loc, String src_name, long dst_loc, + String dst_name, long lcpl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lvisit recursively visits all links starting from a specified group. @@ -5942,14 +6116,14 @@ public class H5 implements java.io.Serializable { * @param op_data * IN: User-defined pointer to data required by the application for its processing of the link * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Lvisit(long grp_id, int idx_type, int order, H5L_iterate_cb op, - H5L_iterate_t op_data) throws HDF5LibraryException; + H5L_iterate_t op_data) throws HDF5LibraryException; /** * H5Lvisit_by_name recursively visits all links starting from a specified group. @@ -5969,17 +6143,18 @@ public class H5 implements java.io.Serializable { * @param lapl_id * IN: link access property * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - group_name is null. + * group_name is null. **/ - public synchronized static native int H5Lvisit_by_name(long loc_id, String group_name, int idx_type, int order, - H5L_iterate_cb op, H5L_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException; - + public synchronized static native int H5Lvisit_by_name(long loc_id, String group_name, int idx_type, + int order, H5L_iterate_cb op, + H5L_iterate_t op_data, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lis_registered tests whether a user-defined link class is currently registered, @@ -5989,21 +6164,23 @@ public class H5 implements java.io.Serializable { * IN: User-defined link class identifier * * @return Returns a positive value if the link class has been registered and zero if it is unregistered. - * Otherwise returns a negative value; this may mean that the identifier is not a valid user-defined class identifier. + * Otherwise returns a negative value; this may mean that the identifier is not a valid + * user-defined class identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Lis_registered(int link_cls_id) throws HDF5LibraryException; /** - * H5Lunregister unregisters a class of user-defined links, preventing them from being traversed, queried, moved, etc. + * H5Lunregister unregisters a class of user-defined links, preventing them from being traversed, queried, + * moved, etc. * * @param link_cls_id * IN: User-defined link class identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Lunregister(int link_cls_id) throws HDF5LibraryException; @@ -6047,9 +6224,10 @@ public class H5 implements java.io.Serializable { * @return non-negative on success * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Oclose(long object_id) throws HDF5LibraryException { + public static int H5Oclose(long object_id) throws HDF5LibraryException + { if (object_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -6062,8 +6240,8 @@ public class H5 implements java.io.Serializable { private synchronized static native int _H5Oclose(long object_id) throws HDF5LibraryException; /** - * H5Ocopy copies the group, dataset or named datatype specified from the file or group specified by source location - * to the destination location. + * H5Ocopy copies the group, dataset or named datatype specified from the file or group specified by + * source location to the destination location. * * @param src_loc_id * IN: Object identifier indicating the location of the source object to be copied @@ -6079,12 +6257,13 @@ public class H5 implements java.io.Serializable { * IN: Link creation property list for the new hard link * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native void H5Ocopy(long src_loc_id, String src_name, long dst_loc_id, String dst_name, - long ocpypl_id, long lcpl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Ocopy(long src_loc_id, String src_name, long dst_loc_id, + String dst_name, long ocpypl_id, long lcpl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Oget_comment retrieves the comment for the specified object. @@ -6095,9 +6274,10 @@ public class H5 implements java.io.Serializable { * @return the comment * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native String H5Oget_comment(long obj_id) throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native String H5Oget_comment(long obj_id) + throws HDF5LibraryException, IllegalArgumentException; /** * H5Oset_comment sets the comment for the specified object. @@ -6108,12 +6288,13 @@ public class H5 implements java.io.Serializable { * IN: The new comment. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * * @deprecated As of HDF5 1.8 in favor of object attributes. **/ @Deprecated - public synchronized static native void H5Oset_comment(long obj_id, String comment) throws HDF5LibraryException; + public synchronized static native void H5Oset_comment(long obj_id, String comment) + throws HDF5LibraryException; /** * H5Oget_comment_by_name retrieves the comment for an object. @@ -6128,12 +6309,12 @@ public class H5 implements java.io.Serializable { * @return the comment * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native String H5Oget_comment_by_name(long loc_id, String name, long lapl_id) - throws HDF5LibraryException, IllegalArgumentException, NullPointerException; + throws HDF5LibraryException, IllegalArgumentException, NullPointerException; /** * H5Oset_comment_by_name sets the comment for the specified object. @@ -6148,15 +6329,16 @@ public class H5 implements java.io.Serializable { * IN: Link access property list identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. * * @deprecated As of HDF5 1.8 in favor of object attributes. **/ @Deprecated - public synchronized static native void H5Oset_comment_by_name(long loc_id, String name, String comment, long lapl_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Oset_comment_by_name(long loc_id, String name, String comment, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Oget_info retrieves the metadata for an object specified by an identifier. @@ -6167,12 +6349,12 @@ public class H5 implements java.io.Serializable { * @return object information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static H5O_info_t H5Oget_info(long loc_id) throws HDF5LibraryException, - NullPointerException { + public static H5O_info_t H5Oget_info(long loc_id) throws HDF5LibraryException, NullPointerException + { return H5Oget_info(loc_id, HDF5Constants.H5O_INFO_ALL); } @@ -6187,12 +6369,12 @@ public class H5 implements java.io.Serializable { * @return object information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native H5O_info_t H5Oget_info(long loc_id, int fields) throws HDF5LibraryException, - NullPointerException; + public synchronized static native H5O_info_t H5Oget_info(long loc_id, int fields) + throws HDF5LibraryException, NullPointerException; /** * H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position. @@ -6208,19 +6390,22 @@ public class H5 implements java.io.Serializable { * @param n * IN: Object to open * @param lapl_id - * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as - * H5P_DEFAULT.) + * IN: Access property list identifier for the link pointing to the object (Not currently used; + * pass as H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static H5O_info_t H5Oget_info_by_idx(long loc_id, String group_name, int idx_type, - int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException { - return H5Oget_info_by_idx(loc_id, group_name, idx_type, order, n, HDF5Constants.H5O_INFO_ALL, lapl_id); + public static H5O_info_t H5Oget_info_by_idx(long loc_id, String group_name, int idx_type, int order, + long n, long lapl_id) + throws HDF5LibraryException, NullPointerException + { + return H5Oget_info_by_idx(loc_id, group_name, idx_type, order, n, HDF5Constants.H5O_INFO_ALL, + lapl_id); } /** @@ -6239,44 +6424,49 @@ public class H5 implements java.io.Serializable { * @param fields * IN: Object fields to select * @param lapl_id - * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as - * H5P_DEFAULT.) + * IN: Access property list identifier for the link pointing to the object (Not currently used; + * pass as H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native H5O_info_t H5Oget_info_by_idx(long loc_id, String group_name, int idx_type, - int order, long n, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5O_info_t H5Oget_info_by_idx(long loc_id, String group_name, + int idx_type, int order, long n, + int fields, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name. + * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and + *relative name. * * @param loc_id * IN: File or group identifier specifying location of group in which object is located * @param name * IN: Relative name of group * @param lapl_id - * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as - * H5P_DEFAULT.) + * IN: Access property list identifier for the link pointing to the object (Not currently used; + * pass as H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public static H5O_info_t H5Oget_info_by_name(long loc_id, String name, long lapl_id) - throws HDF5LibraryException, NullPointerException { + throws HDF5LibraryException, NullPointerException + { return H5Oget_info_by_name(loc_id, name, HDF5Constants.H5O_INFO_ALL, lapl_id); } /** - * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name. + * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and + * relative name. * * @param loc_id * IN: File or group identifier specifying location of group in which object is located @@ -6285,18 +6475,19 @@ public class H5 implements java.io.Serializable { * @param fields * IN: Object fields to select * @param lapl_id - * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as - * H5P_DEFAULT.) + * IN: Access property list identifier for the link pointing to the object (Not currently used; + * pass as H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native H5O_info_t H5Oget_info_by_name(long loc_id, String name, int fields, long lapl_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static native H5O_info_t H5Oget_info_by_name(long loc_id, String name, int fields, + long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Olink creates a new hard link to an object in an HDF5 file. @@ -6313,12 +6504,13 @@ public class H5 implements java.io.Serializable { * IN: Access property list identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native void H5Olink(long obj_id, long new_loc_id, String new_name, long lcpl_id, - long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Olink(long obj_id, long new_loc_id, String new_name, + long lcpl_id, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Oopen opens a group, dataset, or named datatype specified by a location and a path name. @@ -6333,11 +6525,13 @@ public class H5 implements java.io.Serializable { * @return an object identifier for the opened object * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Oopen(long loc_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException { + public static long H5Oopen(long loc_id, String name, long lapl_id) + throws HDF5LibraryException, NullPointerException + { long id = _H5Oopen(loc_id, name, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Oopen add {}", id); @@ -6348,7 +6542,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Oopen(long loc_id, String name, long lapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Ovisit recursively visits all objects accessible from a specified object. @@ -6362,18 +6556,20 @@ public class H5 implements java.io.Serializable { * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data - * IN: User-defined pointer to data required by the application for its processing of the object + * IN: User-defined pointer to data required by the application for its processing of the + * object * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public static int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data) - throws HDF5LibraryException, NullPointerException { + throws HDF5LibraryException, NullPointerException + { return H5Ovisit(obj_id, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL); } @@ -6389,20 +6585,22 @@ public class H5 implements java.io.Serializable { * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data - * IN: User-defined pointer to data required by the application for its processing of the object + * IN: User-defined pointer to data required by the application for its processing of the + * object * @param fields * IN: Object fields to select * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_cb op, - H5O_iterate_t op_data, int fields) throws HDF5LibraryException, NullPointerException; + H5O_iterate_t op_data, int fields) + throws HDF5LibraryException, NullPointerException; /** * H5Ovisit_by_name recursively visits all objects starting from a specified object. @@ -6418,21 +6616,25 @@ public class H5 implements java.io.Serializable { * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data - * IN: User-defined pointer to data required by the application for its processing of the object + * IN: User-defined pointer to data required by the application for its processing of the + * object * @param lapl_id * IN: Link access property list identifier * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public static int H5Ovisit_by_name(long loc_id, String obj_name, int idx_type, int order, - H5O_iterate_cb op, H5O_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException { - return H5Ovisit_by_name(loc_id, obj_name, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL, lapl_id); + H5O_iterate_cb op, H5O_iterate_t op_data, long lapl_id) + throws HDF5LibraryException, NullPointerException + { + return H5Ovisit_by_name(loc_id, obj_name, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL, + lapl_id); } /** @@ -6449,23 +6651,25 @@ public class H5 implements java.io.Serializable { * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data - * IN: User-defined pointer to data required by the application for its processing of the object + * IN: User-defined pointer to data required by the application for its processing of the + * object * @param fields * IN: Object fields to select * @param lapl_id * IN: Link access property list identifier * - * @return returns the return value of the first operator that returns a positive value, or zero if all members were - * processed with no operator returning non-zero. + * @return returns the return value of the first operator that returns a positive value, or zero if all + * members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native int H5Ovisit_by_name(long loc_id, String obj_name, int idx_type, int order, - H5O_iterate_cb op, H5O_iterate_t op_data, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException; - + public synchronized static native int H5Ovisit_by_name(long loc_id, String obj_name, int idx_type, + int order, H5O_iterate_cb op, + H5O_iterate_t op_data, int fields, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Oexists_by_name is used by an application to check that an existing link resolves to an object. @@ -6481,41 +6685,50 @@ public class H5 implements java.io.Serializable { * @return Returns TRUE or FALSE if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public synchronized static native boolean H5Oexists_by_name(long loc_id, String obj_name, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native boolean H5Oexists_by_name(long loc_id, String obj_name, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Odecr_refcount decrements the hard link reference count for an object. * - * @param object_id IN: Object identifier + * @param object_id + * IN: Object identifier * - * @exception HDF5LibraryException - Error from the HDF-5 Library. + * @exception HDF5LibraryException + * Error from the HDF-5 Library. **/ public synchronized static native void H5Odecr_refcount(long object_id) throws HDF5LibraryException; /** * H5Oincr_refcount increments the hard link reference count for an object. * - * @param object_id IN: Object identifier + * @param object_id + * IN: Object identifier * - * @exception HDF5LibraryException - Error from the HDF-5 Library. + * @exception HDF5LibraryException + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Oincr_refcount(long object_id) throws HDF5LibraryException; + public synchronized static native void H5Oincr_refcount(long object_id) throws HDF5LibraryException; /** * H5Oopen_by_addr opens a group, dataset, or named datatype using its address within an HDF5 file. * - * @param loc_id IN: File or group identifier - * @param addr IN: Object's address in the file + * @param loc_id + * IN: File or group identifier + * @param addr + * IN: Object's address in the file * * @return an object identifier for the opened object * - * @exception HDF5LibraryException - Error from the HDF-5 Library. + * @exception HDF5LibraryException + * Error from the HDF-5 Library. **/ - public static long H5Oopen_by_addr(long loc_id, long addr) throws HDF5LibraryException { + public static long H5Oopen_by_addr(long loc_id, long addr) throws HDF5LibraryException + { long id = _H5Oopen_by_addr(loc_id, addr); if (id > 0) { @@ -6528,25 +6741,34 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Oopen_by_addr(long loc_id, long addr) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Oopen_by_idx opens the nth object in the group specified. * - * @param loc_id IN: File or group identifier - * @param group_name IN: Name of group, relative to loc_id, in which object is located - * @param idx_type IN: Type of index by which objects are ordered - * @param order IN: Order of iteration within index - * @param n IN: Object to open - * @param lapl_id IN: Access property list identifier for the link pointing to the object + * @param loc_id + * IN: File or group identifier + * @param group_name + * IN: Name of group, relative to loc_id, in which object is located + * @param idx_type + * IN: Type of index by which objects are ordered + * @param order + * IN: Order of iteration within index + * @param n + * IN: Object to open + * @param lapl_id + * IN: Access property list identifier for the link pointing to the object * * @return an object identifier for the opened object * - * @exception HDF5LibraryException - Error from the HDF-5 Library. - * @exception NullPointerException - group_name is null. + * @exception HDF5LibraryException + * Error from the HDF-5 Library. + * @exception NullPointerException + * group_name is null. **/ - public static long H5Oopen_by_idx(long loc_id, String group_name, - int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException { + public static long H5Oopen_by_idx(long loc_id, String group_name, int idx_type, int order, long n, + long lapl_id) throws HDF5LibraryException, NullPointerException + { long id = _H5Oopen_by_idx(loc_id, group_name, idx_type, order, n, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Oopen_by_idx add {}", id); @@ -6556,51 +6778,54 @@ public class H5 implements java.io.Serializable { return id; } - 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; + 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; /** - * H5Oflush causes all buffers associated with an object to be immediately flushed to disk without removing - * the data from the cache. object_id can be any named object associated with an HDF5 file including a - * dataset, a group, or a committed datatype. + * H5Oflush causes all buffers associated with an object to be immediately flushed to disk without + * removing the data from the cache. object_id can be any named object associated with an HDF5 file + * including a dataset, a group, or a committed datatype. * * @param object_id * IN: Identifier of the object to be flushed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Oflush(long object_id) throws HDF5LibraryException; /** * H5Orefresh causes all buffers associated with an object to be cleared and immediately re-loaded with * updated contents from disk. This function essentially closes the object, evicts all metadata associated - * with it from the cache, and then re-opens the object. The reopened object is automatically re-registered - * with the same ID. object_id can be any named object associated with an HDF5 file including a - * dataset, a group, or a committed datatype. + * with it from the cache, and then re-opens the object. The reopened object is automatically + * re-registered with the same ID. object_id can be any named object associated with an HDF5 file + * including a dataset, a group, or a committed datatype. * * @param object_id * IN: Identifier of the object to be refreshed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ 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. + * 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); + 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. + * 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); + public synchronized static native void H5Oenable_mdc_flushes(long object_id); /** * H5Oare_mdc_flushes_disabled retrieve the object's "cork" status. * @@ -6608,10 +6833,10 @@ public class H5 implements java.io.Serializable { * 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 + * 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); + public synchronized static native boolean H5Oare_mdc_flushes_disabled(long object_id); // //////////////////////////////////////////////////////////// // // @@ -6629,7 +6854,7 @@ public class H5 implements java.io.Serializable { * @return name of a property list if successful; null if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native String H5Pget_class_name(long plid) throws HDF5LibraryException; @@ -6642,9 +6867,10 @@ public class H5 implements java.io.Serializable { * @return a property list identifier (plist) if successful; otherwise Fail (-1). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Pcreate(long type) throws HDF5LibraryException { + public static long H5Pcreate(long type) throws HDF5LibraryException + { long id = _H5Pcreate(type); if (id > 0) { log.trace("OPEN_IDS: H5Pcreate add {}", id); @@ -6666,7 +6892,7 @@ public class H5 implements java.io.Serializable { * @return value for a property if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Pget(long plid, String name) throws HDF5LibraryException; @@ -6682,9 +6908,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ - public synchronized static native int H5Pset(long plid, String name, int value) throws HDF5LibraryException; + public synchronized static native int H5Pset(long plid, String name, int value) + throws HDF5LibraryException; /** * H5Pexist determines whether a property exists within a property list or class @@ -6693,10 +6920,11 @@ public class H5 implements java.io.Serializable { * IN: Identifier for the property to query * @param name * IN: Name of property to check for - * @return a true value if the property exists in the property object; false if the property does not exist; + * @return a true value if the property exists in the property object; false if the property does not + * exist; * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native boolean H5Pexist(long plid, String name) throws HDF5LibraryException; @@ -6710,7 +6938,7 @@ public class H5 implements java.io.Serializable { * @return size of a property's value if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native long H5Pget_size(long plid, String name) throws HDF5LibraryException; @@ -6722,7 +6950,7 @@ public class H5 implements java.io.Serializable { * @return number of properties if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native long H5Pget_nprops(long plid) throws HDF5LibraryException; @@ -6734,7 +6962,7 @@ public class H5 implements java.io.Serializable { * @return a property list class if successful. Otherwise returns H5P_ROOT (-1). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Pget_class(long plist) throws HDF5LibraryException; @@ -6746,7 +6974,7 @@ public class H5 implements java.io.Serializable { * @return a valid parent class object identifier if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native long H5Pget_class_parent(long plid) throws HDF5LibraryException; @@ -6761,7 +6989,7 @@ public class H5 implements java.io.Serializable { * @return positive value if equal; zero if unequal, a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Pequal(long plid1, long plid2) throws HDF5LibraryException; @@ -6776,9 +7004,10 @@ public class H5 implements java.io.Serializable { * @return TRUE if equal, FALSE if unequal * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ - public static boolean H5P_equal(long plid1, long plid2) throws HDF5LibraryException { + public static boolean H5P_equal(long plid1, long plid2) throws HDF5LibraryException + { if (H5Pequal(plid1, plid2) == 1) return true; return false; @@ -6794,7 +7023,7 @@ public class H5 implements java.io.Serializable { * @return a positive value if equal; zero if unequal; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Pisa_class(long plist, long pclass) throws HDF5LibraryException; @@ -6810,10 +7039,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Pcopy_prop(long dst_id, long src_id, String name) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Premove removes a property from a property list @@ -6825,7 +7054,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Premove(long plid, String name) throws HDF5LibraryException; @@ -6839,7 +7068,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native int H5Punregister(long plid, String name) throws HDF5LibraryException; @@ -6851,9 +7080,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ - public static int H5Pclose_class(long plid) throws HDF5LibraryException { + public static int H5Pclose_class(long plid) throws HDF5LibraryException + { if (plid < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -6873,9 +7103,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Pclose(long plist) throws HDF5LibraryException { + public static int H5Pclose(long plist) throws HDF5LibraryException + { if (plist < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -6896,9 +7127,10 @@ public class H5 implements java.io.Serializable { * @return a property list identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Pcopy(long plist) throws HDF5LibraryException { + public static long H5Pcopy(long plist) throws HDF5LibraryException + { long id = _H5Pcopy(plist); if (id > 0) { log.trace("OPEN_IDS: H5Pcopy add {}", id); @@ -6942,11 +7174,12 @@ public class H5 implements java.io.Serializable { * @return a property list identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException { + public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException + { long id = _H5Pcreate_class_nocb(parent_class, name); - if (id > 0) { + if (id > 0) { log.trace("OPEN_IDS: H5Pcreate_class_nocb add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); @@ -6954,21 +7187,27 @@ public class H5 implements java.io.Serializable { return id; } - private synchronized static native long _H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException; - -// public static 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 { -// long id = _H5Pcreate_class(parent_class, name, create_op, create_data, copy_op, copy_data, close_op, close_data); -// if (id > 0) { -// log.trace("OPEN_IDS: H5Pcreate_class add {}", id); -// OPEN_IDS.add(id); -// log.trace("OPEN_IDS: {}", OPEN_IDS.size()); -// } -// return id; -// } -// -// 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; + private synchronized static native long _H5Pcreate_class_nocb(long parent_class, String name) + throws HDF5LibraryException; + + // public static 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 { + // long id = _H5Pcreate_class(parent_class, name, create_op, create_data, copy_op, copy_data, + // close_op, close_data); + // if (id > 0) { + // log.trace("OPEN_IDS: H5Pcreate_class add {}", id); + // OPEN_IDS.add(id); + // log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + // } + // return id; + // } + // + // 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. @@ -6985,10 +7224,13 @@ public class H5 implements java.io.Serializable { * @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_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; + // 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. @@ -7003,37 +7245,39 @@ public class H5 implements java.io.Serializable { * IN: Default value of the property * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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_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; + // 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 + * IN: ID of property object to iterate over * @param idx - * IN/OUT: index of the property to begin with + * IN/OUT: index of the property to begin with * @param op - * IN: function to be called with each property iterated over. + * IN: function to be called with each property iterated over. * @param op_data - * IN: iteration data from user + * 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 + * @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. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * **/ - public synchronized static native int H5Piterate(long plist, int[] idx, H5P_iterate_cb op, H5P_iterate_t op_data) throws HDF5LibraryException; + 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 /////// @@ -7041,7 +7285,7 @@ public class H5 implements java.io.Serializable { * H5Pget_attr_phase_change retrieves attribute storage phase change thresholds. * * @param ocpl_id - * IN: : Object (dataset or group) creation property list identifier + * IN: Object (dataset or group) creation property list identifier * @param attributes * The maximum and minimum no. of attributes to be stored. * @@ -7053,13 +7297,13 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * **/ public synchronized static native int H5Pget_attr_phase_change(long ocpl_id, int[] attributes) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_attr_phase_change sets threshold values for attribute storage on an object. These @@ -7075,14 +7319,16 @@ public class H5 implements java.io.Serializable { * IN: Minimum number of attributes to be stored in dense storage (Default: 6) * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native void H5Pset_attr_phase_change(long ocpl_id, int max_compact, int min_dense) - throws HDF5LibraryException; + public synchronized static native void H5Pset_attr_phase_change(long ocpl_id, int max_compact, + int min_dense) + throws HDF5LibraryException; /** - * H5Pget_attr_creation_order retrieves the settings for tracking and indexing attribute creation order on an object + * H5Pget_attr_creation_order retrieves the settings for tracking and indexing attribute creation order on + * an object. * * @param ocpl_id * IN: Object (group or dataset) creation property list identifier @@ -7090,14 +7336,15 @@ public class H5 implements java.io.Serializable { * @return Flags specifying whether to track and index attribute creation order * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pget_attr_creation_order(long ocpl_id) throws HDF5LibraryException; + public synchronized static native int H5Pget_attr_creation_order(long ocpl_id) + throws HDF5LibraryException; /** - * H5Pset_attr_creation_order sets flags specifying whether to track and index attribute creation order on an - * object. + * H5Pset_attr_creation_order sets flags specifying whether to track and index attribute creation order on + * an object. * * @param ocpl_id * IN: Object creation property list identifier @@ -7107,15 +7354,15 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_attr_creation_order(long ocpl_id, int crt_order_flags) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Pget_obj_track_times queries the object creation property list, ocpl_id, to determine whether object times are - * being recorded. + * H5Pget_obj_track_times queries the object creation property list, ocpl_id, to determine whether object + * times are being recorded. * * @param ocpl_id * IN: Object creation property list identifier @@ -7123,14 +7370,15 @@ public class H5 implements java.io.Serializable { * @return TRUE or FALSE, specifying whether object times are being recorded * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native boolean H5Pget_obj_track_times(long ocpl_id) throws HDF5LibraryException; + public synchronized static native boolean H5Pget_obj_track_times(long ocpl_id) + throws HDF5LibraryException; /** - * H5Pset_obj_track_times sets a property in the object creation property list, ocpl_id, that governs the recording - * of times associated with an object. + * H5Pset_obj_track_times sets a property in the object creation property list, ocpl_id, that governs the + * recording of times associated with an object. * * @param ocpl_id * IN: Object creation property list identifier @@ -7139,11 +7387,11 @@ public class H5 implements java.io.Serializable { * IN: TRUE or FALSE, specifying whether object times are to be tracked * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_obj_track_times(long ocpl_id, boolean track_times) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Pmodify_filter modifies the specified FILTER in the transient or permanent output filter pipeline @@ -7185,16 +7433,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name or an array is null. + * 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; + int[] cd_values) + throws HDF5LibraryException, NullPointerException; /** - * H5Pset_filter adds the specified filter and corresponding properties to the end of an output filter pipeline. + * H5Pset_filter adds the specified filter and corresponding properties to the end of an output filter + * pipeline. * * @param plist * IN: Property list identifier. @@ -7210,14 +7460,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_filter(long plist, int filter, int flags, long cd_nelmts, - int[] cd_values) throws HDF5LibraryException; + int[] cd_values) throws HDF5LibraryException; /** - * H5Pget_nfilters returns the number of filters defined in the filter pipeline associated with the property list - * plist. + * H5Pget_nfilters returns the number of filters defined in the filter pipeline associated with the + * property list plist. * * @param plist * IN: Property list identifier. @@ -7225,18 +7475,19 @@ public class H5 implements java.io.Serializable { * @return the number of filters in the pipeline if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_nfilters(long plist) throws HDF5LibraryException; /** - * H5Pget_filter returns information about a filter, specified by its filter number, in a filter pipeline, specified - * by the property list with which it is associated. + * H5Pget_filter returns information about a filter, specified by its filter number, in a filter pipeline, + * specified by the property list with which it is associated. * * @param plist * IN: Property list identifier. * @param filter_number - * IN: Sequence number within the filter pipeline of the filter for which information is sought. + * IN: Sequence number within the filter pipeline of the filter for which information is + * sought. * @param flags * OUT: Bit vector specifying certain general properties of the filter. * @param cd_nelmts @@ -7253,44 +7504,49 @@ public class H5 implements java.io.Serializable { * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR (-1). * * @exception ArrayIndexOutOfBoundsException - * Fatal error on Copyback + * Fatal error on Copyback * @exception ArrayStoreException - * Fatal error on Copyback + * Fatal error on Copyback * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name or an array is null. + * name or an array is null. * **/ - public static int H5Pget_filter(long plist, int filter_number, int[] flags, long[] cd_nelmts, int[] cd_values, - long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, - ArrayStoreException, HDF5LibraryException, NullPointerException { - return H5Pget_filter2(plist, filter_number, flags, cd_nelmts, cd_values, namelen, name, filter_config); + public static int H5Pget_filter(long plist, int filter_number, int[] flags, long[] cd_nelmts, + int[] cd_values, long namelen, String[] name, int[] filter_config) + throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException + { + return H5Pget_filter2(plist, filter_number, flags, cd_nelmts, cd_values, namelen, name, + filter_config); } /** - * H5Pget_filter2 returns information about a filter, specified by its filter number, in a filter pipeline, - * specified by the property list with which it is associated. + * H5Pget_filter2 returns information about a filter, specified by its filter number, in a filter + * pipeline, specified by the property list with which it is associated. * - * @see public static int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] cd_values, - * int namelen, String[] name, int[] filter_config) + * @see public static int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] + * cd_values, int namelen, String[] name, int[] filter_config) * **/ - private synchronized static native int H5Pget_filter2(long plist, int filter_number, int[] flags, long[] cd_nelmts, - int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, - ArrayStoreException, HDF5LibraryException, NullPointerException; + private synchronized static native int H5Pget_filter2(long plist, int filter_number, int[] flags, + long[] cd_nelmts, int[] cd_values, long namelen, + String[] name, int[] filter_config) + throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, + NullPointerException; /** - * H5Pget_filter_by_id returns information about the filter specified in filter_id, a filter identifier. plist_id - * must be a dataset or group creation property list and filter_id must be in the associated filter pipeline. The - * filter_id and flags parameters are used in the same manner as described in the discussion of H5Pset_filter. Aside - * from the fact that they are used for output, the parameters cd_nelmts and cd_values[] are used in the same manner - * as described in the discussion of H5Pset_filter. On input, the cd_nelmts parameter indicates the number of - * entries in the cd_values[] array allocated by the calling program; on exit it contains the number of values - * defined by the filter. On input, the namelen parameter indicates the number of characters allocated for the - * filter name by the calling program in the array name[]. On exit name[] contains the name of the filter with one - * character of the name in each element of the array. If the filter specified in filter_id is not set for the - * property list, an error will be returned and H5Pget_filter_by_id1 will fail. + * H5Pget_filter_by_id returns information about the filter specified in filter_id, a filter identifier. + * plist_id must be a dataset or group creation property list and filter_id must be in the associated + * filter pipeline. The filter_id and flags parameters are used in the same manner as described in the + * discussion of H5Pset_filter. Aside from the fact that they are used for output, the parameters + * cd_nelmts and cd_values[] are used in the same manner as described in the discussion of H5Pset_filter. + * On input, the cd_nelmts parameter indicates the number of entries in the cd_values[] array allocated by + * the calling program; on exit it contains the number of values defined by the filter. On input, the + * namelen parameter indicates the number of characters allocated for the filter name by the calling + * program in the array name[]. On exit name[] contains the name of the filter with one character of the + * name in each element of the array. If the filter specified in filter_id is not set for the property + * list, an error will be returned and H5Pget_filter_by_id1 will fail. * * @param plist_id * IN: Property list identifier. @@ -7312,24 +7568,26 @@ public class H5 implements java.io.Serializable { * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR (-1). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception ArrayIndexOutOfBoundsException - * Fatal error on Copyback + * Fatal error on Copyback * @exception ArrayStoreException - * Fatal error on Copyback + * Fatal error on Copyback * @exception NullPointerException - * - name or an array is null. + * name or an array is null. * **/ public static int H5Pget_filter_by_id(long plist_id, long filter_id, int[] flags, long[] cd_nelmts, - int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, - ArrayStoreException, HDF5LibraryException, NullPointerException { - return H5Pget_filter_by_id2(plist_id, filter_id, flags, cd_nelmts, cd_values, namelen, name, filter_config); + int[] cd_values, long namelen, String[] name, int[] filter_config) + throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException + { + return H5Pget_filter_by_id2(plist_id, filter_id, flags, cd_nelmts, cd_values, namelen, name, + filter_config); } /** - * H5Pget_filter_by_id2 returns information about a filter, specified by its filter id, in a filter pipeline, - * specified by the property list with which it is associated. + * H5Pget_filter_by_id2 returns information about a filter, specified by its filter id, in a filter + * pipeline, specified by the property list with which it is associated. * * @param plist_id * IN: Property list identifier. @@ -7351,15 +7609,15 @@ public class H5 implements java.io.Serializable { * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR (-1). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name or an array is null. + * name or an array is null. * **/ - public synchronized static native int H5Pget_filter_by_id2(long plist_id, long filter_id, int[] flags, - long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) - throws HDF5LibraryException, NullPointerException; - + public synchronized static native int + H5Pget_filter_by_id2(long plist_id, long filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, + long namelen, String[] name, int[] filter_config) + throws HDF5LibraryException, NullPointerException; /** * H5Pall_filters_avail query to verify that all the filters set @@ -7373,10 +7631,10 @@ public class H5 implements java.io.Serializable { * FALSE if one or more filters not currently available. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Pall_filters_avail(long dcpl_id) throws HDF5LibraryException, - NullPointerException; + 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; @@ -7390,9 +7648,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Premove_filter(long obj_id, long filter) throws HDF5LibraryException; + public synchronized static native int H5Premove_filter(long obj_id, long filter) + throws HDF5LibraryException; /** * H5Pset_deflate sets the compression method for a dataset. @@ -7405,7 +7664,7 @@ public class H5 implements java.io.Serializable { * @return non-negative if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_deflate(long plist, int level) throws HDF5LibraryException; @@ -7419,10 +7678,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Pset_fletcher32(long plist) + throws HDF5LibraryException, NullPointerException; // /////// File creation property list (FCPL) routines /////// @@ -7437,12 +7696,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. **/ - public synchronized static native int H5Pget_userblock(long plist, long[] size) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Pget_userblock(long plist, long[] size) + throws HDF5LibraryException, NullPointerException; /** * H5Pset_userblock sets the user block size of a file creation property list. @@ -7455,13 +7714,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_userblock(long plist, long size) throws HDF5LibraryException; /** - * H5Pget_sizes retrieves the size of the offsets and lengths used in an HDF5 file. This function is only valid for - * file creation property lists. + * H5Pget_sizes retrieves the size of the offsets and lengths used in an HDF5 file. This function is only + * valid for file creation property lists. * * @param plist * IN: Identifier of property list to query. @@ -7475,14 +7734,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value with the sizes initialized; if successful; * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * @exception IllegalArgumentException - * - size is invalid. + * size is invalid. **/ - public synchronized static native int H5Pget_sizes(long plist, long[] size) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + public synchronized static native int H5Pget_sizes(long plist, long[] size) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_sizes sets the byte size of the offsets and lengths used to address objects in an HDF5 file. @@ -7497,13 +7756,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_sizes(long plist, int sizeof_addr, int sizeof_size) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Pget_sym_k retrieves the size of the symbol table B-tree 1/2 rank and the symbol table leaf node 1/2 size. + * H5Pget_sym_k retrieves the size of the symbol table B-tree 1/2 rank and the symbol table leaf node 1/2 + * size. * * @param plist * IN: Property list to query. @@ -7518,14 +7778,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * @exception IllegalArgumentException - * - size is invalid. + * size is invalid. **/ - public synchronized static native int H5Pget_sym_k(long plist, int[] size) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + public synchronized static native int H5Pget_sym_k(long plist, int[] size) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_sym_k sets the size of parameters used to control the symbol table nodes. @@ -7540,9 +7800,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Pset_sym_k(long plist, int ik, int lk) throws HDF5LibraryException; + public synchronized static native int H5Pset_sym_k(long plist, int ik, int lk) + throws HDF5LibraryException; /** * H5Pget_istore_k queries the 1/2 rank of an indexed storage B-tree. @@ -7555,15 +7816,16 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - ik array is null. + * ik array is null. **/ - public synchronized static native int H5Pget_istore_k(long plist, int[] ik) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Pget_istore_k(long plist, int[] ik) + throws HDF5LibraryException, NullPointerException; /** - * H5Pset_istore_k sets the size of the parameter used to control the B-trees for indexing chunked datasets. + * H5Pset_istore_k sets the size of the parameter used to control the B-trees for indexing chunked + * datasets. * * @param plist * IN: Identifier of property list to query. @@ -7573,46 +7835,47 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_istore_k(long plist, int ik) throws HDF5LibraryException; /** - * H5Pget_shared_mesg_nindexes retrieves number of shared object header message indexes in file creation property - * list. + * H5Pget_shared_mesg_nindexes retrieves number of shared object header message indexes in file creation + * property list. * * @param fcpl_id * IN: : File creation property list identifier * - * @return nindexes, the number of shared object header message indexes available in files created with this - * property list + * @return nindexes, the number of shared object header message indexes available in files created with + * this property list * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pget_shared_mesg_nindexes(long fcpl_id) throws HDF5LibraryException; + public synchronized static native int H5Pget_shared_mesg_nindexes(long fcpl_id) + throws HDF5LibraryException; /** - * H5Pset_shared_mesg_nindexes sets the number of shared object header message indexes in the specified file - * creation property list. + * H5Pset_shared_mesg_nindexes sets the number of shared object header message indexes in the specified + * file creation property list. * * @param plist_id * IN: File creation property list * @param nindexes - * IN: Number of shared object header message indexes to be available in files created with this property - * list + * IN: Number of shared object header message indexes to be available in files created with + * this property list * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid value of nindexes + * Invalid value of nindexes * **/ public synchronized static native int H5Pset_shared_mesg_nindexes(long plist_id, int nindexes) - throws HDF5LibraryException, IllegalArgumentException; + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_shared_mesg_index Retrieves the configuration settings for a shared message index. @@ -7632,15 +7895,16 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - mesg_info is null. + * mesg_info is null. * @exception IllegalArgumentException - * - Invalid value of nindexes + * Invalid value of nindexes * **/ - public synchronized static native int H5Pget_shared_mesg_index(long fcpl_id, int index_num, int[] mesg_info) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + public synchronized static native int H5Pget_shared_mesg_index(long fcpl_id, int index_num, + int[] mesg_info) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_shared_mesg_index Configures the specified shared object header message index @@ -7657,13 +7921,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid value of nindexes + * Invalid value of nindexes * **/ - public synchronized static native int H5Pset_shared_mesg_index(long fcpl_id, int index_num, int mesg_type_flags, - int min_mesg_size) throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native int H5Pset_shared_mesg_index(long fcpl_id, int index_num, + int mesg_type_flags, int min_mesg_size) + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_shared_mesg_phase_change retrieves shared object header message phase change information. @@ -7674,20 +7939,21 @@ public class H5 implements java.io.Serializable { * The threshold values for storage of shared object header message indexes in a file. * * <pre> - * size[0] = Threshold above which storage of a shared object header message index shifts from list to B-tree - * size[1] = Threshold below which storage of a shared object header message index reverts to list format + * size[0] = Threshold above which storage of a shared object header message index shifts from list + * to B-tree size[1] = Threshold below which storage of a shared object header message index reverts + * to list format * </pre> * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * **/ public synchronized static native int H5Pget_shared_mesg_phase_change(long fcpl_id, int[] size) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_shared_mesg_phase_change sets shared object header message storage phase change thresholds. @@ -7695,24 +7961,28 @@ public class H5 implements java.io.Serializable { * @param fcpl_id * IN: File creation property list identifier * @param max_list - * IN: Threshold above which storage of a shared object header message index shifts from list to B-tree + * IN: Threshold above which storage of a shared object header message index shifts from list + * to B-tree * @param min_btree - * IN: Threshold below which storage of a shared object header message index reverts to list format + * IN: Threshold below which storage of a shared object header message index reverts to list + * format * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid values of max_list and min_btree. + * Invalid values of max_list and min_btree. * **/ - public synchronized static native int H5Pset_shared_mesg_phase_change(long fcpl_id, int max_list, int min_btree) - throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native int H5Pset_shared_mesg_phase_change(long fcpl_id, int max_list, + int min_btree) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pset_file_space_strategy sets the file space management strategy for the file associated with fcpl_id to strategy. - * There are four strategies that applications can select and they are described in the Parameters section. + * H5Pset_file_space_strategy sets the file space management strategy for the file associated with fcpl_id + * to strategy. There are four strategies that applications can select and they are described in the + * Parameters section. * * @param fcpl_id * IN: File creation property list identifier @@ -7722,7 +7992,8 @@ public class H5 implements java.io.Serializable { * Mechanisms: free-space managers, aggregators, and virtual file drivers * This is the library default when not set. * H5F_FSPACE_STRATEGY_PAGE - * Mechanisms: free-space managers with embedded paged aggregation and virtual file drivers + * Mechanisms: free-space managers with embedded paged aggregation and virtual file + * drivers * H5F_FSPACE_STRATEGY_AGGR * Mechanisms: aggregators and virtual file drivers * H5F_FSPACE_STRATEGY_NONE @@ -7730,20 +8001,23 @@ public class H5 implements java.io.Serializable { * @param persist * IN: True to persist free-space. * @param threshold - * IN: The free-space section threshold. The library default is 1, which is to track all free-space sections. - * Passing a value of zero (0) indicates that the value of threshold is not to be modified. + * IN: The free-space section threshold. The library default is 1, which is to track all + * free-space sections. Passing a value of zero (0) indicates that the value of threshold + * is not to be modified. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid values of max_list and min_btree. + * Invalid values of max_list and min_btree. * **/ - public synchronized static native void H5Pset_file_space_strategy(long fcpl_id, int strategy, boolean persist, long threshold) - throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native void H5Pset_file_space_strategy(long fcpl_id, int strategy, + boolean persist, long threshold) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_file_space_strategy provides the means for applications to manage the HDF5 file's file space strategy for their specific needs. + * H5Pget_file_space_strategy provides the means for applications to manage the HDF5 file's file space + * strategy for their specific needs. * * @param fcpl_id * IN: File creation property list identifier @@ -7755,16 +8029,18 @@ public class H5 implements java.io.Serializable { * @return the current free-space strategy. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid values of max_list and min_btree. + * Invalid values of max_list and min_btree. * **/ - public synchronized static native int H5Pget_file_space_strategy(long fcpl_id, boolean[] persist, long[] threshold) - throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native int H5Pget_file_space_strategy(long fcpl_id, boolean[] persist, + long[] threshold) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_file_space_strategy_persist provides the means for applications to manage the HDF5 file's file space strategy for their specific needs. + * H5Pget_file_space_strategy_persist provides the means for applications to manage the HDF5 file's file + * space strategy for their specific needs. * * @param fcpl_id * IN: File creation property list identifier @@ -7772,16 +8048,17 @@ public class H5 implements java.io.Serializable { * @return the current free-space persistence. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid values of max_list and min_btree. + * Invalid values of max_list and min_btree. * **/ public synchronized static native boolean H5Pget_file_space_strategy_persist(long fcpl_id) - throws HDF5LibraryException, IllegalArgumentException; + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_file_space_strategy_threshold provides the means for applications to manage the HDF5 file's file space strategy for their specific needs. + * H5Pget_file_space_strategy_threshold provides the means for applications to manage the HDF5 file's file + * space strategy for their specific needs. * * @param fcpl_id * IN: File creation property list identifier @@ -7789,54 +8066,55 @@ public class H5 implements java.io.Serializable { * @return the current free-space section threshold. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid values of max_list and min_btree. - * - **/ - public synchronized static native long H5Pget_file_space_strategy_threshold(long fcpl_id) - throws HDF5LibraryException, IllegalArgumentException; - - /** - * H5Pset_file_space_page_size retrieves the file space page size for aggregating small metadata or raw data. - * - * @param fcpl_id - * IN: File creation property list identifier - * @param page_size - * IN: the file space page size. - * - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - * @exception IllegalArgumentException - * - Invalid values of max_list and min_btree. - * - **/ - public synchronized static native void H5Pset_file_space_page_size(long fcpl_id, long page_size) - throws HDF5LibraryException, IllegalArgumentException; - - /** - * H5Pget_file_space_page_size Sets the file space page size for paged aggregation. - * - * @param fcpl_id - * IN: File creation property list identifier - * - * @return the current file space page size. - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - * @exception IllegalArgumentException - * - Invalid values of max_list and min_btree. - * - **/ - public synchronized static native long H5Pget_file_space_page_size(long fcpl_id) - throws HDF5LibraryException, IllegalArgumentException; + * Invalid values of max_list and min_btree. + * + **/ + public synchronized static native long H5Pget_file_space_strategy_threshold(long fcpl_id) + throws HDF5LibraryException, IllegalArgumentException; + /** + * H5Pset_file_space_page_size retrieves the file space page size for aggregating small metadata or raw + * data. + * + * @param fcpl_id + * IN: File creation property list identifier + * @param page_size + * IN: the file space page size. + * + * + * @exception HDF5LibraryException + * Error from the HDF-5 Library. + * @exception IllegalArgumentException + * Invalid values of max_list and min_btree. + * + **/ + public synchronized static native void H5Pset_file_space_page_size(long fcpl_id, long page_size) + throws HDF5LibraryException, IllegalArgumentException; + + /** + * H5Pget_file_space_page_size Sets the file space page size for paged aggregation. + * + * @param fcpl_id + * IN: File creation property list identifier + * + * @return the current file space page size. + * + * @exception HDF5LibraryException + * Error from the HDF-5 Library. + * @exception IllegalArgumentException + * Invalid values of max_list and min_btree. + * + **/ + public synchronized static native long H5Pget_file_space_page_size(long fcpl_id) + throws HDF5LibraryException, IllegalArgumentException; // /////// File access property list (FAPL) routines /////// /** - * H5Pget_alignment retrieves the current settings for alignment properties from a file access property list. + * H5Pget_alignment retrieves the current settings for alignment properties from a file access property + * list. * * @param plist * IN: Identifier of a file access property list. @@ -7850,18 +8128,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - alignment array is null. + * alignment array is null. * @exception IllegalArgumentException - * - alignment array is invalid. + * alignment array is invalid. **/ - public synchronized static native int H5Pget_alignment(long plist, long[] alignment) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + public synchronized static native int H5Pget_alignment(long plist, long[] alignment) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * H5Pset_alignment sets the alignment properties of a file access property list so that any file object >= - * THRESHOLD bytes will be aligned on an address which is a multiple of ALIGNMENT. + * H5Pset_alignment sets the alignment properties of a file access property list so that any file object + * >= THRESHOLD bytes will be aligned on an address which is a multiple of ALIGNMENT. * * @param plist * IN: Identifier for a file access property list. @@ -7873,21 +8151,21 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_alignment(long plist, long threshold, long alignment) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Pget_driver returns the identifier of the low-level file driver associated with the file access property list - * or data transfer property list plid. + * H5Pget_driver returns the identifier of the low-level file driver associated with the file access + * property list or data transfer property list plid. * * @param plid * IN: File access or data transfer property list identifier. * @return a valid low-level driver identifier if successful; a negative value if failed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. */ public synchronized static native long H5Pget_driver(long plid) throws HDF5LibraryException; @@ -7900,7 +8178,7 @@ public class H5 implements java.io.Serializable { * @return the offset. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException; @@ -7916,14 +8194,15 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException; + 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 - * and the RDCC_W0 value in the raw data chunk cache. + * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible + * number of bytes and the RDCC_W0 value in the raw data chunk cache. * * @param plist * IN: Identifier of the file access property list. @@ -7939,16 +8218,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an array is null. + * an array is null. **/ public synchronized static native int H5Pget_cache(long plist, int[] mdc_nelmts, long[] rdcc_nelmts, - long[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException; + long[] rdcc_nbytes, double[] rdcc_w0) + throws HDF5LibraryException, NullPointerException; /** - * H5Pset_cache sets the number of elements (objects) in the meta data cache and the total number of bytes in the - * raw data chunk cache. + * H5Pset_cache sets the number of elements (objects) in the meta data cache and the total number of bytes + * in the raw data chunk cache. * * @param plist * IN: Identifier of the file access property list. @@ -7964,14 +8244,15 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Pset_cache(long plist, int mdc_nelmts, long rdcc_nelmts, long rdcc_nbytes, - double rdcc_w0) throws HDF5LibraryException; + public synchronized static native int H5Pset_cache(long plist, int mdc_nelmts, long rdcc_nelmts, + long rdcc_nbytes, double rdcc_w0) + throws HDF5LibraryException; /** - * 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. + * 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. @@ -7979,14 +8260,15 @@ public class H5 implements java.io.Serializable { * @return A buffer(H5AC_cache_config_t) for the current metadata cache configuration information * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native H5AC_cache_config_t H5Pget_mdc_config(long plist_id) throws HDF5LibraryException; + 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. + * 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. @@ -7994,14 +8276,14 @@ public class H5 implements java.io.Serializable { * IN: H5AC_cache_config_t, the initial metadata cache configuration. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + throws HDF5LibraryException; /** - * H5Pget_gc_references Returns the current setting for the garbage collection references property from a file access - * property list. + * H5Pget_gc_references Returns the current setting for the garbage collection references property from a + * file access property list. * * @param fapl_id * IN File access property list @@ -8009,13 +8291,13 @@ public class H5 implements java.io.Serializable { * @return GC is on (true) or off (false) * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Pget_gc_references(long fapl_id) throws HDF5LibraryException; /** - * H5Pset_gc_references Sets the flag for garbage collecting references for the file. Default value for garbage - * collecting references is off. + * H5Pset_gc_references Sets the flag for garbage collecting references for the file. Default value for + * garbage collecting references is off. * * @param fapl_id * IN File access property list @@ -8025,10 +8307,10 @@ public class H5 implements java.io.Serializable { * @return non-negative if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_gc_references(long fapl_id, boolean gc_ref) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Pget_fclose_degree returns the degree for the file close behavior for a file access @@ -8040,10 +8322,10 @@ public class H5 implements java.io.Serializable { * @return the degree for the file close behavior * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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 H5Pget_fclose_degree(long fapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Pset_fclose_degree sets the degree for the file close behavior. @@ -8056,10 +8338,10 @@ public class H5 implements java.io.Serializable { * @return non-negative if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Pset_fclose_degree(long fapl_id, int degree) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Pset_fclose_degree(long fapl_id, int degree) + throws HDF5LibraryException, NullPointerException; /** * H5Pget_meta_block_size the current metadata block size setting. @@ -8070,7 +8352,7 @@ public class H5 implements java.io.Serializable { * @return the minimum size, in bytes, of metadata block allocations. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_meta_block_size(long fapl_id) throws HDF5LibraryException; @@ -8084,14 +8366,15 @@ public class H5 implements java.io.Serializable { * IN: Minimum size, in bytes, of metadata block allocations. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException; + 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. + * property from a file access property list. * * @param fapl_id * IN: Identifier for property list to query. @@ -8099,7 +8382,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException; @@ -8121,12 +8404,14 @@ public class H5 implements java.io.Serializable { * IN: maximum size of the data seive buffer. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Pset_sieve_buf_size(long fapl_id, long size) throws HDF5LibraryException; + public synchronized static native void H5Pset_sieve_buf_size(long fapl_id, long size) + throws HDF5LibraryException; /** - * H5Pget_small_data_block_size retrieves the size of a block of small data in a file creation property list. + * H5Pget_small_data_block_size retrieves the size of a block of small data in a file creation property + * list. * * @param plist * IN: Identifier for property list to query. @@ -8134,13 +8419,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5Pget_small_data_block_size(long plist) throws HDF5LibraryException; + public synchronized static native long H5Pget_small_data_block_size(long plist) + throws HDF5LibraryException; /** - * H5Pset_small_data_block_size reserves blocks of size bytes for the contiguous storage of the raw data portion of - * small datasets. + * H5Pset_small_data_block_size reserves blocks of size bytes for the contiguous storage of the raw data + * portion of small datasets. * * @param plist * IN: Identifier of property list to modify. @@ -8150,14 +8436,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_small_data_block_size(long plist, long size) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Pget_libver_bounds retrieves the lower and upper bounds on the HDF5 Library versions that indirectly determine - * the object formats versions used when creating objects in the file. + * H5Pget_libver_bounds retrieves the lower and upper bounds on the HDF5 Library versions that indirectly + * determine the object formats versions used when creating objects in the file. * * @param fapl_id * IN: File access property list identifier @@ -8172,17 +8458,17 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * **/ - public synchronized static native int H5Pget_libver_bounds(long fapl_id, int[] libver) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Pget_libver_bounds(long fapl_id, int[] libver) + throws HDF5LibraryException, NullPointerException; /** - * H5Pset_libver_bounds Sets bounds on library versions, and indirectly format versions, to be used when creating - * objects + * H5Pset_libver_bounds Sets bounds on library versions, and indirectly format versions, to be used when + * creating objects * * @param fapl_id * IN: File access property list identifier @@ -8195,13 +8481,13 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Argument is Illegal + * Argument is Illegal * **/ public synchronized static native int H5Pset_libver_bounds(long fapl_id, int low, int high) - throws HDF5LibraryException, IllegalArgumentException; + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_elink_file_cache_size retrieves the size of the external link open file cache. @@ -8212,13 +8498,15 @@ public class H5 implements java.io.Serializable { * @return External link open file cache size in number of files. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pget_elink_file_cache_size(long fapl_id) throws HDF5LibraryException; + public synchronized static native int H5Pget_elink_file_cache_size(long fapl_id) + throws HDF5LibraryException; /** - * H5Pset_elink_file_cache_size sets the number of files that can be held open in an external link open file cache. + * H5Pset_elink_file_cache_size sets the number of files that can be held open in an external link open + * file cache. * * @param fapl_id * IN: File access property list identifier @@ -8226,11 +8514,11 @@ public class H5 implements java.io.Serializable { * IN: External link open file cache size in number of files. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_elink_file_cache_size(long fapl_id, int efc_size) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Pset_mdc_log_options sets metadata cache logging options. @@ -8245,13 +8533,14 @@ public class H5 implements java.io.Serializable { * IN: Whether the logging begins as soon as the file is opened or created. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - location is null. + * location is null. * **/ - public synchronized static native void H5Pset_mdc_log_options(long fapl_id, boolean is_enabled, String location, boolean start_on_access) - throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Pset_mdc_log_options(long fapl_id, boolean is_enabled, + String location, boolean start_on_access) + throws HDF5LibraryException, NullPointerException; /** * H5Pget_mdc_log_options gets metadata cache logging options. @@ -8261,19 +8550,21 @@ public class H5 implements java.io.Serializable { * @param mdc_log_options * the options * mdc_logging_options[0] = is_enabled, whether logging is enabled - * mdc_logging_options[1] = start_on_access, whether the logging begins as soon as the file is opened or created + * mdc_logging_options[1] = start_on_access, whether the logging begins as soon as the file is + * opened or created * * @return the location of log in UTF-8/ASCII (file path/name) (On Windows, this must be ASCII). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native String H5Pget_mdc_log_options(long fapl_id, boolean[] mdc_log_options) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Pget_metadata_read_attempts retrieves the number of read attempts that is set in the file access property list plist_id. + * H5Pget_metadata_read_attempts retrieves the number of read attempts that is set in the file access + * property list plist_id. * * @param plist_id * IN: File access property list identifier @@ -8281,18 +8572,20 @@ public class H5 implements java.io.Serializable { * @return The number of read attempts. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native long H5Pget_metadata_read_attempts(long plist_id) throws HDF5LibraryException; + public synchronized static native long H5Pget_metadata_read_attempts(long plist_id) + throws HDF5LibraryException; /** - * H5Pset_metadata_read_attempts sets the number of reads that the library will try when reading checksummed - * metadata in an HDF5 file opened with SWMR access. When reading such metadata, the library will compare the - * checksum computed for the metadata just read with the checksum stored within the piece of checksum. When - * performing SWMR operations on a file, the checksum check might fail when the library reads data on a system - * that is not atomic. To remedy such situations, the library will repeatedly read the piece of metadata until - * the check passes or finally fails the read when the allowed number of attempts is reached. + * H5Pset_metadata_read_attempts sets the number of reads that the library will try when reading + * checksummed metadata in an HDF5 file opened with SWMR access. When reading such metadata, the library + * will compare the checksum computed for the metadata just read with the checksum stored within the piece + * of checksum. When performing SWMR operations on a file, the checksum check might fail when the library + * reads data on a system that is not atomic. To remedy such situations, the library will repeatedly read + * the piece of metadata until the check passes or finally fails the read when the allowed number of + * attempts is reached. * * @param plist_id * IN: File access property list identifier @@ -8300,15 +8593,15 @@ public class H5 implements java.io.Serializable { * IN: The number of read attempts which is a value greater than 0. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_metadata_read_attempts(long plist_id, long attempts) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Pget_evict_on_close retrieves the file access property list setting that determines whether an HDF5 object - * will be evicted from the library's metadata cache when it is closed. + * H5Pget_evict_on_close retrieves the file access property list setting that determines whether an HDF5 + * object will be evicted from the library's metadata cache when it is closed. * * @param fapl_id * IN: File access property list identifier @@ -8316,14 +8609,14 @@ public class H5 implements java.io.Serializable { * @return indication if the object will be evicted on close. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native boolean H5Pget_evict_on_close(long fapl_id) - throws HDF5LibraryException; + public synchronized static native boolean H5Pget_evict_on_close(long fapl_id) throws HDF5LibraryException; /** - * H5Pset_evict_on_close controls the library's behavior of evicting metadata associated with a closed object. + * H5Pset_evict_on_close controls the library's behavior of evicting metadata associated with a closed + * object. * * @param fapl_id * IN: File access property list identifier @@ -8331,11 +8624,11 @@ public class H5 implements java.io.Serializable { * IN: Whether the HDF5 object should be evicted on close. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Pget_use_file_locking retrieves whether we are using file locking. @@ -8346,11 +8639,11 @@ public class H5 implements java.io.Serializable { * @return indication if file locking is used. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_use_file_locking(long fapl_id) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Pget_use_file_locking retrieves whether we ignore file locks when they are disabled. @@ -8361,11 +8654,11 @@ public class H5 implements java.io.Serializable { * @return indication if file locking is ignored. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_ignore_disabled_file_locking(long fapl_id) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Pset_file_locking sets parameters related to file locking. @@ -8374,17 +8667,19 @@ public class H5 implements java.io.Serializable { * 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). + * 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. + * 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; + public synchronized static native void H5Pset_file_locking(long fapl_id, boolean use_file_locking, + boolean ignore_when_disabled) + throws HDF5LibraryException; // Dataset creation property list (DCPL) routines // @@ -8394,11 +8689,11 @@ public class H5 implements java.io.Serializable { * @param plist * IN: Identifier for property list to query. * - * @return the layout type of a dataset creation property list if successful. Otherwise returns H5D_LAYOUT_ERROR - * (-1). + * @return the layout type of a dataset creation property list if successful. Otherwise returns + * H5D_LAYOUT_ERROR (-1). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_layout(long plist) throws HDF5LibraryException; @@ -8413,7 +8708,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_layout(long plist, int layout) throws HDF5LibraryException; @@ -8430,14 +8725,14 @@ public class H5 implements java.io.Serializable { * @return chunk dimensionality successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dims array is null. + * dims array is null. * @exception IllegalArgumentException - * - max_ndims <=0 + * max_ndims <=0 **/ public synchronized static native int H5Pget_chunk(long plist, int max_ndims, long[] dims) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_chunk sets the size of the chunks used to store a chunked layout dataset. @@ -8452,14 +8747,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dims array is null. + * dims array is null. * @exception IllegalArgumentException - * - dims <=0 + * dims <=0 **/ - public synchronized static native int H5Pset_chunk(long plist, int ndims, byte[] dim) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + 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. @@ -8474,24 +8769,25 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dims array is null. + * dims array is null. * @exception IllegalArgumentException - * - dims <=0 + * dims <=0 **/ - public synchronized static int H5Pset_chunk(long plist, int ndims, long[] dim) throws HDF5Exception, - NullPointerException, IllegalArgumentException { + public synchronized static int H5Pset_chunk(long plist, int ndims, long[] dim) + throws HDF5Exception, NullPointerException, IllegalArgumentException + { if (dim == null) { return -1; } HDFArray theArray = new HDFArray(dim); - byte[] thedims = theArray.byteify(); + byte[] thedims = theArray.byteify(); int retVal = H5Pset_chunk(plist, ndims, thedims); - thedims = null; + thedims = null; theArray = null; return retVal; } @@ -8504,28 +8800,35 @@ public class H5 implements java.io.Serializable { * and the name of the dataset, src_dset_name. * * @param dcpl_id - * IN: The identifier of the dataset creation property list that will be used when creating the virtual dataset. + * IN: The identifier of the dataset creation property list that will be used when creating the + * virtual dataset. * @param vspace_id - * IN: The dataspace identifier with the selection within the virtual dataset applied, possibly an unlimited selection. + * IN: The dataspace identifier with the selection within the virtual dataset applied, possibly + * an unlimited selection. * @param src_file_name - * IN: The name of the HDF5 file where the source dataset is located. The file might not exist yet. The name can be specified using a C-style printf statement. + * IN: The name of the HDF5 file where the source dataset is located. The file might not exist + * yet. The name can be specified using a C-style printf statement. * @param src_dset_name - * IN: The path to the HDF5 dataset in the file specified by src_file_name. The dataset might not exist yet. The dataset name can be specified using a C-style printf statement. + * IN: The path to the HDF5 dataset in the file specified by src_file_name. The dataset might + * not exist yet. The dataset name can be specified using a C-style printf statement. * @param src_space_id - * IN: The source dataset dataspace identifier with a selection applied, possibly an unlimited selection. + * IN: The source dataset dataspace identifier with a selection applied, possibly an unlimited + * selection. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an name string is null. + * an name string is null. * @exception IllegalArgumentException - * - An id is <=0 + * an id is <=0 **/ - public synchronized static native void H5Pset_virtual(long dcpl_id, long vspace_id, String src_file_name, String src_dset_name, long src_space_id) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + public synchronized static native void H5Pset_virtual(long dcpl_id, long vspace_id, String src_file_name, + String src_dset_name, long src_space_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * H5Pget_virtual_count gets the number of mappings for a virtual dataset that has the creation property list specified by dcpl_id. + * H5Pget_virtual_count gets the number of mappings for a virtual dataset that has the creation property + * list specified by dcpl_id. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. @@ -8533,15 +8836,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative number of mappings if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - An id is <=0 + * An id is <=0 **/ - public synchronized static native long H5Pget_virtual_count(long dcpl_id) throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native long H5Pget_virtual_count(long dcpl_id) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_virtual_vspace takes the dataset creation property list for the virtual dataset, dcpl_id, and the mapping index, index, - * and returns a dataspace identifier for the selection within the virtual dataset used in the mapping. + * H5Pget_virtual_vspace takes the dataset creation property list for the virtual dataset, dcpl_id, and + * the mapping index, index, and returns a dataspace identifier for the selection within the virtual + * dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. @@ -8551,15 +8856,17 @@ public class H5 implements java.io.Serializable { * @return a valid dataspace identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - An id is <=0 + * An id is <=0 **/ - public synchronized static native long H5Pget_virtual_vspace(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native long H5Pget_virtual_vspace(long dcpl_id, long index) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_virtual_srcspace takes the dataset creation property list for the virtual dataset, dcpl_id, and the mapping index, index, - * and returns a dataspace identifier for the selection within the source dataset used in the mapping. + * H5Pget_virtual_srcspace takes the dataset creation property list for the virtual dataset, dcpl_id, and + * the mapping index, index, and returns a dataspace identifier for the selection within the source + * dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. @@ -8569,15 +8876,17 @@ public class H5 implements java.io.Serializable { * @return a valid dataspace identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - An id is <=0 + * An id is <=0 **/ - public synchronized static native long H5Pget_virtual_srcspace(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native long H5Pget_virtual_srcspace(long dcpl_id, long index) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_virtual_filename takes the dataset creation property list for the virtual dataset, dcpl_id, the mapping index, index, - * the size of the filename for a source dataset, size, and retrieves the name of the file for a source dataset used in the mapping. + * H5Pget_virtual_filename takes the dataset creation property list for the virtual dataset, dcpl_id, the + * mapping index, index, the size of the filename for a source dataset, size, and retrieves the name of + * the file for a source dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. @@ -8587,15 +8896,17 @@ public class H5 implements java.io.Serializable { * @return the name of the file containing the source dataset if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - An id is <=0 + * An id is <=0 **/ - public synchronized static native String H5Pget_virtual_filename(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native String H5Pget_virtual_filename(long dcpl_id, long index) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_virtual_dsetname takes the dataset creation property list for the virtual dataset, dcpl_id, the mapping index, index, the - * size of the dataset name for a source dataset, size, and retrieves the name of the source dataset used in the mapping. + * H5Pget_virtual_dsetname takes the dataset creation property list for the virtual dataset, dcpl_id, the + * mapping index, index, the size of the dataset name for a source dataset, size, and retrieves the name + * of the source dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. @@ -8605,41 +8916,44 @@ public class H5 implements java.io.Serializable { * @return the name of the source dataset if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - An id is <=0 - **/ - public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; - -// ///// unimplemented ///// -// /** -// * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache. -// * -// * @param fapl_id -// * IN: File access property list identifier -// * -// * @return VDS link open file cache size in number of files. -// * -// * @exception HDF5LibraryException -// * - Error from the HDF-5 Library. -// * -// **/ -// public synchronized static native int H5Pget_vds_file_cache_size(long fapl_id) throws HDF5LibraryException; -// -// /** -// * H5Pset_vds_file_cache_size sets the number of files that can be held open in an vds link open file cache. -// * -// * @param fapl_id -// * IN: File access property list identifier -// * @param efc_size -// * IN: VDS link open file cache size in number of files. -// * -// * @exception HDF5LibraryException -// * - Error from the HDF-5 Library. -// * -// **/ -// public synchronized static native void H5Pset_vds_file_cache_size(long fapl_id, int efc_size) -// throws HDF5LibraryException; + * An id is <=0 + **/ + public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, long index) + throws HDF5LibraryException, IllegalArgumentException; + + // ///// unimplemented ///// + // /** + // * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache. + // * + // * @param fapl_id + // * IN: File access property list identifier + // * + // * @return VDS link open file cache size in number of files. + // * + // * @exception HDF5LibraryException + // * Error from the HDF-5 Library. + // * + // **/ + // public synchronized static native int H5Pget_vds_file_cache_size(long fapl_id) throws + // HDF5LibraryException; + // + // /** + // * H5Pset_vds_file_cache_size sets the number of files that can be held open in an vds link open + // * file cache. + // * + // * @param fapl_id + // * IN: File access property list identifier + // * @param efc_size + // * IN: VDS link open file cache size in number of files. + // * + // * @exception HDF5LibraryException + // * Error from the HDF-5 Library. + // * + // **/ + // public synchronized static native void H5Pset_vds_file_cache_size(long fapl_id, int efc_size) + // throws HDF5LibraryException; /** * H5Pget_external returns information about an external file. @@ -8664,20 +8978,21 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception ArrayIndexOutOfBoundsException - * Fatal error on Copyback + * Fatal error on Copyback * @exception ArrayStoreException - * Fatal error on Copyback + * Fatal error on Copyback * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name or size is null. + * name or size is null. * @exception IllegalArgumentException - * - name_size <= 0 . + * name_size <= 0 . * **/ public synchronized static native int H5Pget_external(long plist, int idx, long name_size, String[] name, - long[] size) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, - NullPointerException, IllegalArgumentException; + long[] size) + throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, + NullPointerException, IllegalArgumentException; /** * H5Pset_external adds an external file to the list of external files. @@ -8687,20 +9002,20 @@ public class H5 implements java.io.Serializable { * @param name * IN: Name of an external file. * @param offset - * IN: Offset, in bytes, from the beginning of the file to the location in the file where the data - * starts. + * IN: Offset, in bytes, from the beginning of the file to the location in the file where the + * data starts. * @param size * IN: Number of bytes reserved in the file for the data. * * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native int H5Pset_external(long plist, String name, long offset, long size) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pget_external_count returns the number of external files for the specified dataset. @@ -8711,7 +9026,7 @@ public class H5 implements java.io.Serializable { * @return the number of external files if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_external_count(long plist) throws HDF5LibraryException; @@ -8728,11 +9043,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_shuffle Sets up the use of the shuffle filter. @@ -8743,11 +9058,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_shuffle(long plist_id) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Pset_shuffle(long plist_id) + throws HDF5LibraryException, NullPointerException; /** * H5Pset_nbit Sets up the use of the N-Bit filter. @@ -8758,7 +9073,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_nbit(long plist_id) throws HDF5LibraryException; @@ -8776,13 +9091,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid arguments + * Invalid arguments * **/ public synchronized static native int H5Pset_scaleoffset(long plist_id, int scale_type, int scale_factor) - throws HDF5LibraryException, IllegalArgumentException; + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_fill_value queries the fill value property of a dataset creation property list. @@ -8797,10 +9112,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Error converting data array. + * Error converting data array. **/ public synchronized static native int H5Pget_fill_value(long plist_id, long type_id, byte[] value) - throws HDF5Exception; + throws HDF5Exception; /** * H5Pget_fill_value queries the fill value property of a dataset creation property list. @@ -8815,16 +9130,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Error converting data array. + * Error converting data array. **/ - public synchronized static int H5Pget_fill_value(long plist_id, long type_id, Object obj) throws HDF5Exception { + public synchronized static int H5Pget_fill_value(long plist_id, long type_id, Object obj) + throws HDF5Exception + { HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.emptyBytes(); + byte[] buf = theArray.emptyBytes(); int status = H5Pget_fill_value(plist_id, type_id, buf); - if (status >= 0) { + if (status >= 0) obj = theArray.arrayify(buf); - } return status; } @@ -8842,10 +9158,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Error converting data array + * Error converting data array **/ public synchronized static native int H5Pset_fill_value(long plist_id, long type_id, byte[] value) - throws HDF5Exception; + throws HDF5Exception; /** * H5Pset_fill_value sets the fill value for a dataset creation property list. @@ -8860,15 +9176,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Error converting data array + * Error converting data array **/ - public synchronized static int H5Pset_fill_value(long plist_id, long type_id, Object obj) throws HDF5Exception { + public synchronized static int H5Pset_fill_value(long plist_id, long type_id, Object obj) + throws HDF5Exception + { HDFArray theArray = new HDFArray(obj); - byte[] buf = theArray.byteify(); + byte[] buf = theArray.byteify(); int retVal = H5Pset_fill_value(plist_id, type_id, buf); - buf = null; + buf = null; theArray = null; return retVal; } @@ -8888,10 +9206,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Error converting data array + * Error converting data array **/ public synchronized static native int H5Pfill_value_defined(long plist_id, int[] status) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_alloc_time Gets space allocation time for dataset during creation. @@ -8904,11 +9222,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_alloc_time(long plist_id, int[] alloc_time) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_alloc_time Sets space allocation time for dataset during creation. @@ -8921,11 +9239,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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 H5Pset_alloc_time(long plist_id, int alloc_time) + throws HDF5LibraryException, NullPointerException; /** * H5Pset_fill_time Gets fill value writing time. @@ -8938,10 +9256,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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 H5Pget_fill_time(long plist_id, int[] fill_time) + throws HDF5LibraryException; /** * H5Pset_fill_time Sets the fill value writing time. @@ -8954,10 +9273,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_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; /** * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list. @@ -8970,12 +9290,13 @@ public class H5 implements java.io.Serializable { * 0 - Disables option; partial edge chunks will be compressed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library + * Error from the HDF-5 Library **/ - public synchronized static native void H5Pset_chunk_opts(long dcpl_id, int opts) throws HDF5LibraryException; + public synchronized static native void H5Pset_chunk_opts(long dcpl_id, int opts) + throws HDF5LibraryException; /** - * H5Pget_chunk_opts retrieves the edge chunk option setting stored in the dataset creation property list . + * H5Pget_chunk_opts retrieves the edge chunk option setting stored in the dataset creation property list * * @param dcpl_id * IN: Dataset creation property list @@ -8983,13 +9304,14 @@ public class H5 implements java.io.Serializable { * @return The edge chunk option setting. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library - **/ + * Error from the HDF-5 Library + * + */ public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException; /** * H5Pget_dset_no_attrs_hint accesses the flag for whether or not datasets created by the given dcpl - * will be created with a "minimized" object header. + * will be created with a "minimized" object header. * * @param dcpl_id * IN: Dataset creation property list @@ -8997,33 +9319,32 @@ public class H5 implements java.io.Serializable { * @return true if the given dcpl is set to create minimized dataset object headers, false if not. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Pget_dset_no_attrs_hint(long dcpl_id) - throws HDF5LibraryException; - + throws HDF5LibraryException; /** * H5Pset_dset_no_attrs_hint sets the dcpl to minimize (or explicitly to not minimized) dataset object - * headers upon creation. + * headers upon creation. * * @param dcpl_id * IN: Dataset creation property list * * @param minimize - * the minimize hint setting + * IN: the minimize hint setting * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Pset_dset_no_attrs_hint(long dcpl_id, boolean minimize) - throws HDF5LibraryException; + throws HDF5LibraryException; // /////// Dataset access property list (DAPL) routines /////// /** - * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes - * and the RDCC_W0 value in the raw data chunk cache on a per-datset basis. + * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible + * number of bytes and the RDCC_W0 value in the raw data chunk cache on a per-datset basis. * * @param dapl_id * IN: Identifier of the dataset access property list. @@ -9035,16 +9356,17 @@ public class H5 implements java.io.Serializable { * IN/OUT: Preemption policy. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an array is null. + * an array is null. **/ - public synchronized static native void H5Pget_chunk_cache(long dapl_id, long[] rdcc_nslots, long[] rdcc_nbytes, - double[] rdcc_w0) throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Pget_chunk_cache(long dapl_id, long[] rdcc_nslots, + long[] rdcc_nbytes, double[] rdcc_w0) + throws HDF5LibraryException, NullPointerException; /** - * H5Pset_chunk_cache sets the number of elements (objects) in the meta data cache and the total number of bytes in - * the raw data chunk cache on a per-datset basis. + * H5Pset_chunk_cache sets the number of elements (objects) in the meta data cache and the total number of + * bytes in the raw data chunk cache on a per-datset basis. * * @param dapl_id * IN: Identifier of the dataset access property list. @@ -9056,10 +9378,11 @@ public class H5 implements java.io.Serializable { * IN: Preemption policy. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Pset_chunk_cache(long dapl_id, long rdcc_nslots, long rdcc_nbytes, - double rdcc_w0) throws HDF5LibraryException; + public synchronized static native void H5Pset_chunk_cache(long dapl_id, long rdcc_nslots, + long rdcc_nbytes, double rdcc_w0) + throws HDF5LibraryException; /** * H5Pset_virtual_view takes the access property list for the virtual dataset, dapl_id, and the flag, @@ -9071,9 +9394,10 @@ public class H5 implements java.io.Serializable { * IN: Flag specifying the extent of the data to be included in the view. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library + * Error from the HDF-5 Library **/ - public synchronized static native void H5Pset_virtual_view(long dapl_id, int view) throws HDF5LibraryException; + public synchronized static native void H5Pset_virtual_view(long dapl_id, int view) + throws HDF5LibraryException; /** * H5Pget_virtual_view takes the virtual dataset access property list, dapl_id, and retrieves the flag, @@ -9085,26 +9409,28 @@ public class H5 implements java.io.Serializable { * @return The flag specifying the view of the virtual dataset. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library - **/ + * Error from the HDF-5 Library + * + */ public synchronized static native int H5Pget_virtual_view(long dapl_id) throws HDF5LibraryException; /** - * H5Pset_virtual_printf_gap sets the access property list for the virtual dataset, dapl_id, to instruct the - * library to stop looking for the mapped data stored in the files and/or datasets with the printf-style names - * after not finding gap_size files and/or datasets. The found source files and datasets will determine the - * extent of the unlimited virtual dataset with the printf-style mappings. + * H5Pset_virtual_printf_gap sets the access property list for the virtual dataset, dapl_id, to instruct + * the library to stop looking for the mapped data stored in the files and/or datasets with the + * printf-style names after not finding gap_size files and/or datasets. The found source files and + * datasets will determine the extent of the unlimited virtual dataset with the printf-style mappings. * * @param dapl_id * IN: Dataset access property list identifier for the virtual dataset * @param gap_size * IN: Maximum number of files and/or datasets allowed to be missing for determining - * the extent of an unlimited virtual dataset with printf-style mappings. + * the extent of an unlimited virtual dataset with printf-style mappings. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library + * Error from the HDF-5 Library **/ - public synchronized static native void H5Pset_virtual_printf_gap(long dapl_id, long gap_size) throws HDF5LibraryException; + public synchronized static native void H5Pset_virtual_printf_gap(long dapl_id, long gap_size) + throws HDF5LibraryException; /** * H5Pget_virtual_printf_gap returns the maximum number of missing printf-style files and/or datasets for @@ -9118,9 +9444,11 @@ public class H5 implements java.io.Serializable { * the extent of an unlimited virtual dataset with printf-style mappings. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library - **/ - public synchronized static native long H5Pget_virtual_printf_gap(long dapl_id) throws HDF5LibraryException; + * Error from the HDF-5 Library + * + */ + public synchronized static native long H5Pget_virtual_printf_gap(long dapl_id) + throws HDF5LibraryException; /** * H5Pget_virtual_prefix Retrieves prefix applied to virtual file paths. @@ -9131,11 +9459,10 @@ public class H5 implements java.io.Serializable { * @return the prefix to be applied to virtual file paths. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native String H5Pget_virtual_prefix(long dapl_id) - throws HDF5LibraryException; + public synchronized static native String H5Pget_virtual_prefix(long dapl_id) throws HDF5LibraryException; /** * H5Pset_virtual_prefix Sets prefix to be applied to virtual file paths. @@ -9146,13 +9473,13 @@ public class H5 implements java.io.Serializable { * IN: Prefix to be applied to virtual file paths * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - prefix is null. + * prefix is null. * **/ public synchronized static native void H5Pset_virtual_prefix(long dapl_id, String prefix) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pget_efile_prefix Retrieves prefix applied to external file paths. @@ -9163,11 +9490,10 @@ public class H5 implements java.io.Serializable { * @return the prefix to be applied to external file paths. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native String H5Pget_efile_prefix(long dapl_id) - throws HDF5LibraryException; + public synchronized static native String H5Pget_efile_prefix(long dapl_id) throws HDF5LibraryException; /** * H5Pset_efile_prefix Sets prefix to be applied to external file paths. @@ -9178,24 +9504,25 @@ public class H5 implements java.io.Serializable { * IN: Prefix to be applied to external file paths * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - prefix is null. + * prefix is null. * **/ public synchronized static native void H5Pset_efile_prefix(long dapl_id, String prefix) - throws HDF5LibraryException, NullPointerException; - - // public synchronized static native void H5Pset_append_flush(long plist_id, int ndims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException; + throws HDF5LibraryException, NullPointerException; - // public synchronized static native void H5Pget_append_flush(long plist_id, int dims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException; + // public synchronized static native void H5Pset_append_flush(long plist_id, int ndims, long[] boundary, + // H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException; + // public synchronized static native void H5Pget_append_flush(long plist_id, int dims, long[] boundary, + // H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException; // /////// Dataset xfer property list (DXPL) routines /////// /** - * H5Pget_data_transform retrieves the data transform expression previously set in the dataset transfer property - * list plist_id by H5Pset_data_transform. + * H5Pget_data_transform retrieves the data transform expression previously set in the dataset transfer + * property list plist_id by H5Pset_data_transform. * * @param plist_id * IN: Identifier of the property list or class @@ -9204,18 +9531,19 @@ public class H5 implements java.io.Serializable { * @param expression * OUT: A data transform expression * - * @return The size of the transform expression if successful; 0(zero) if no transform expression exists. Otherwise - * returns a negative value. + * @return The size of the transform expression if successful; 0(zero) if no transform expression exists. + * Otherwise returns a negative value. * * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Size is <= 0. + * Size is <= 0. * **/ - public synchronized static native long H5Pget_data_transform(long plist_id, String[] expression, long size) - throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native long H5Pget_data_transform(long plist_id, String[] expression, + long size) + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_data_transform sets a data transform expression @@ -9228,17 +9556,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative valule if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - expression is null. + * expression is null. * **/ public synchronized static native int H5Pset_data_transform(long plist_id, String expression) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * HH5Pget_buffer gets type conversion and background buffers. Returns buffer size, in bytes, if successful; - * otherwise 0 on failure. + * HH5Pget_buffer gets type conversion and background buffers. Returns buffer size, in bytes, if + * successful; otherwise 0 on failure. * * @param plist * Identifier for the dataset transfer property list. @@ -9250,12 +9578,12 @@ public class H5 implements java.io.Serializable { * @return buffer size, in bytes, if successful; otherwise 0 on failure * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - plist is invalid. + * plist is invalid. **/ public synchronized static native int H5Pget_buffer(long plist, byte[] tconv, byte[] bkg) - throws HDF5LibraryException, IllegalArgumentException; + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_buffer_size gets type conversion and background buffer size, in bytes, if successful; @@ -9267,26 +9595,27 @@ public class H5 implements java.io.Serializable { * @return buffer size, in bytes, if successful; otherwise 0 on failure * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - plist is invalid. + * plist is invalid. **/ public synchronized static native long H5Pget_buffer_size(long plist) - throws HDF5LibraryException, IllegalArgumentException; + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_buffer sets type conversion and background buffers. status to TRUE or FALSE. * - * Given a dataset transfer property list, H5Pset_buffer sets the maximum size for the type conversion buffer and - * background buffer and optionally supplies pointers to application-allocated buffers. If the buffer size is - * smaller than the entire amount of data being transferred between the application and the file, and a type - * conversion buffer or background buffer is required, then strip mining will be used. + * Given a dataset transfer property list, H5Pset_buffer sets the maximum size for the type conversion + * buffer and background buffer and optionally supplies pointers to application-allocated buffers. If the + * buffer size is smaller than the entire amount of data being transferred between the application and the + * file, and a type conversion buffer or background buffer is required, then strip mining will be used. * - * Note that there are minimum size requirements for the buffer. Strip mining can only break the data up along the - * first dimension, so the buffer must be large enough to accommodate a complete slice that encompasses all of the - * remaining dimensions. For example, when strip mining a 100x200x300 hyperslab of a simple data space, the buffer - * must be large enough to hold 1x200x300 data elements. When strip mining a 100x200x300x150 hyperslab of a simple - * data space, the buffer must be large enough to hold 1x200x300x150 data elements. + * Note that there are minimum size requirements for the buffer. Strip mining can only break the data up + * along the first dimension, so the buffer must be large enough to accommodate a complete slice that + * encompasses all of the remaining dimensions. For example, when strip mining a 100x200x300 hyperslab of + * a simple data space, the buffer must be large enough to hold 1x200x300 data elements. When strip mining + * a 100x200x300x150 hyperslab of a simple data space, the buffer must be large enough to hold + * 1x200x300x150 data elements. * * @param plist * Identifier for the dataset transfer property list. @@ -9294,12 +9623,12 @@ public class H5 implements java.io.Serializable { * Size, in bytes, of the type conversion and background buffers. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - plist is invalid. + * plist is invalid. **/ - public synchronized static native void H5Pset_buffer_size(long plist, long size) throws HDF5LibraryException, - IllegalArgumentException; + public synchronized static native void H5Pset_buffer_size(long plist, long size) + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_edc_check gets the error-detecting algorithm in use. @@ -9310,7 +9639,7 @@ public class H5 implements java.io.Serializable { * @return the error-detecting algorithm * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException; @@ -9325,7 +9654,7 @@ public class H5 implements java.io.Serializable { * @return non-negative if succeed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException; @@ -9344,16 +9673,17 @@ public class H5 implements java.io.Serializable { * @return non-negative if succeed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an input array is null. + * an input array is null. **/ public synchronized static native int H5Pget_btree_ratios(long plist_id, double[] left, double[] middle, - double[] right) throws HDF5LibraryException, NullPointerException; + double[] right) + throws HDF5LibraryException, NullPointerException; /** - * H5Pset_btree_ratio Sets B-tree split ratios for a dataset transfer property list. The split ratios determine what - * percent of children go in the first node when a node splits. + * H5Pset_btree_ratio Sets B-tree split ratios for a dataset transfer property list. The split ratios + * determine what percent of children go in the first node when a node splits. * * @param plist_id * IN Dataset transfer property list @@ -9367,10 +9697,10 @@ public class H5 implements java.io.Serializable { * @return non-negative if succeed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Pset_btree_ratios(long plist_id, double left, double middle, double right) - throws HDF5LibraryException; + 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. @@ -9383,11 +9713,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_hyper_vector_size(long dxpl_id, long[] vector_size) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_hyper_vector_size sets the number of @@ -9397,7 +9727,7 @@ public class H5 implements java.io.Serializable { * Increasing the number should give better performance, but use * more memory during hyperslab I/O. The vector size must be * greater than 1. - *,p. + *<p> * The default is to use 1024 vectors for I/O during hyperslab * reading/writing. * @@ -9409,17 +9739,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_hyper_vector_size(long dxpl_id, long vector_size) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; // /////// Link creation property list (LCPL) routines /////// /** - * H5Pget_create_intermediate_group determines whether property is set to enable creating missing intermediate - * groups. + * H5Pget_create_intermediate_group determines whether property is set to enable creating missing + * intermediate groups. * * @param lcpl_id * IN: Link creation property list identifier @@ -9427,14 +9757,15 @@ public class H5 implements java.io.Serializable { * @return Boolean true or false * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_create_intermediate_group(long lcpl_id) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Pset_create_intermediate_group specifies in property list whether to create missing intermediate groups + * H5Pset_create_intermediate_group specifies in property list whether to create missing intermediate + * groups * * @param lcpl_id * IN: Link creation property list identifier @@ -9444,11 +9775,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative valule if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_create_intermediate_group(long lcpl_id, boolean crt_intermed_group) - throws HDF5LibraryException; + public synchronized static native int H5Pset_create_intermediate_group(long lcpl_id, + boolean crt_intermed_group) + throws HDF5LibraryException; // /////// Group creation property list (GCPL) routines /////// @@ -9461,10 +9793,11 @@ public class H5 implements java.io.Serializable { * @return size_hint, the anticipated size of local heap * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native long H5Pget_local_heap_size_hint(long gcpl_id) throws HDF5LibraryException; + public synchronized static native long H5Pget_local_heap_size_hint(long gcpl_id) + throws HDF5LibraryException; /** * H5Pset_local_heap_size_hint Specifies the anticipated maximum size of a local heap. @@ -9477,11 +9810,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_local_heap_size_hint(long gcpl_id, long size_hint) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Pget_link_phase_change Queries the settings for conversion between compact and dense groups. @@ -9489,7 +9822,8 @@ public class H5 implements java.io.Serializable { * @param gcpl_id * IN: Group creation property list identifier * @param links - * The max. no. of compact links & the min. no. of dense links, which are used for storing groups + * The max. no. of compact links & the min. no. of dense links, which are used for storing + * groups * * <pre> * links[0] = The maximum number of links for compact storage @@ -9499,13 +9833,13 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * **/ public synchronized static native int H5Pget_link_phase_change(long gcpl_id, int[] links) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_link_phase_change Sets the parameters for conversion between compact and dense groups. @@ -9520,13 +9854,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid values of max_compact and min_dense. + * Invalid values of max_compact and min_dense. * **/ - public synchronized static native int H5Pset_link_phase_change(long gcpl_id, int max_compact, int min_dense) - throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native int H5Pset_link_phase_change(long gcpl_id, int max_compact, + int min_dense) + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_est_link_info Queries data required to estimate required local heap or object header size. @@ -9534,7 +9869,8 @@ public class H5 implements java.io.Serializable { * @param gcpl_id * IN: Group creation property list identifier * @param link_info - * Estimated number of links to be inserted into group And the estimated average length of link names + * Estimated number of links to be inserted into group And the estimated average length of link + * names * * <pre> * link_info[0] = Estimated number of links to be inserted into group @@ -9544,13 +9880,13 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - link_info is null. + * link_info is null. * **/ public synchronized static native int H5Pget_est_link_info(long gcpl_id, int[] link_info) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_est_link_info Sets estimated number of links and length of link names in a group. @@ -9565,17 +9901,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid values to est_num_entries and est_name_len. + * Invalid values to est_num_entries and est_name_len. * **/ - public synchronized static native int H5Pset_est_link_info(long gcpl_id, int est_num_entries, int est_name_len) - throws HDF5LibraryException, IllegalArgumentException; + public synchronized static native int H5Pset_est_link_info(long gcpl_id, int est_num_entries, + int est_name_len) + throws HDF5LibraryException, IllegalArgumentException; /** - * H5Pget_link_creation_order queries the group creation property list, gcpl_id, and returns a flag indicating - * whether link creation order is tracked and/or indexed in a group. + * H5Pget_link_creation_order queries the group creation property list, gcpl_id, and returns a flag + * indicating whether link creation order is tracked and/or indexed in a group. * * @param gcpl_id * IN: Group creation property list identifier @@ -9583,14 +9920,15 @@ public class H5 implements java.io.Serializable { * @return crt_order_flags -Creation order flag(s) * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pget_link_creation_order(long gcpl_id) throws HDF5LibraryException; + public synchronized static native int H5Pget_link_creation_order(long gcpl_id) + throws HDF5LibraryException; /** - * H5Pset_link_creation_order Sets flags in a group creation property list, gcpl_id, for tracking and/or indexing - * links on creation order. + * H5Pset_link_creation_order Sets flags in a group creation property list, gcpl_id, for tracking and/or + * indexing links on creation order. * * @param gcpl_id * IN: Group creation property list identifier @@ -9601,11 +9939,11 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_link_creation_order(long gcpl_id, int crt_order_flags) - throws HDF5LibraryException; + throws HDF5LibraryException; // /////// String creation property list (STRCPL) routines /////// @@ -9618,7 +9956,7 @@ public class H5 implements java.io.Serializable { * @return Returns the character encoding of the string. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException; @@ -9632,18 +9970,18 @@ public class H5 implements java.io.Serializable { * IN: the character encoding of the string * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding) - throws HDF5LibraryException; + throws HDF5LibraryException; // /////// Link access property list (LAPL) routines /////// /** - * H5Pget_nlinks retrieves the maximum number of soft or user-defined link traversals allowed, nlinks, before the - * library assumes it has found a cycle and aborts the traversal. This value is retrieved from the link access - * property list lapl_id. + * H5Pget_nlinks retrieves the maximum number of soft or user-defined link traversals allowed, nlinks, + * before the library assumes it has found a cycle and aborts the traversal. This value is retrieved from + * the link access property list lapl_id. * * @param lapl_id * IN: File access property list identifier @@ -9651,15 +9989,15 @@ public class H5 implements java.io.Serializable { * @return Returns a Maximum number of links to traverse. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_nlinks(long lapl_id) throws HDF5LibraryException; /** - * H5Pset_nlinks sets the maximum number of soft or user-defined link traversals allowed, nlinks, before the library - * assumes it has found a cycle and aborts the traversal. This value is set in the link access property list - * lapl_id. + * H5Pset_nlinks sets the maximum number of soft or user-defined link traversals allowed, nlinks, before + * the library assumes it has found a cycle and aborts the traversal. This value is set in the link access + * property list lapl_id. * * @param lapl_id * IN: File access property list identifier @@ -9669,13 +10007,13 @@ public class H5 implements java.io.Serializable { * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Argument is Illegal + * Argument is Illegal * **/ - public synchronized static native int H5Pset_nlinks(long lapl_id, long nlinks) throws HDF5LibraryException, - IllegalArgumentException; + public synchronized static native int H5Pset_nlinks(long lapl_id, long nlinks) + throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_elink_prefix Retrieves prefix applied to external link paths. @@ -9685,17 +10023,17 @@ public class H5 implements java.io.Serializable { * @param prefix * OUT: Prefix applied to external link paths * - * @return If successful, returns a non-negative value specifying the size in bytes of the prefix without the NULL - * terminator; otherwise returns a negative value. + * @return If successful, returns a non-negative value specifying the size in bytes of the prefix without + * the NULL terminator; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - prefix is null. + * prefix is null. * **/ public synchronized static native long H5Pget_elink_prefix(long lapl_id, String[] prefix) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_elink_prefix Sets prefix to be applied to external link paths. @@ -9708,17 +10046,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - prefix is null. + * prefix is null. * **/ - public synchronized static native int H5Pset_elink_prefix(long lapl_id, String prefix) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Pset_elink_prefix(long lapl_id, String prefix) + throws HDF5LibraryException, NullPointerException; /** - * H5Pget_elink_fapl Retrieves the file access property list identifier associated with the link access property - * list. + * H5Pget_elink_fapl Retrieves the file access property list identifier associated with the link access + * property list. * * @param lapl_id * IN: Link access property list identifier @@ -9726,10 +10064,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public static long H5Pget_elink_fapl(long lapl_id) throws HDF5LibraryException { + public static long H5Pget_elink_fapl(long lapl_id) throws HDF5LibraryException + { long id = _H5Pget_elink_fapl(lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Pget_elink_fapl add {}", id); @@ -9742,7 +10081,8 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Pget_elink_fapl(long lapl_id) throws HDF5LibraryException; /** - * H5Pset_elink_fapl sets a file access property list for use in accessing a file pointed to by an external link. + * H5Pset_elink_fapl sets a file access property list for use in accessing a file pointed to by an + * external link. * * @param lapl_id * IN: Link access property list identifier @@ -9752,14 +10092,15 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_elink_fapl(long lapl_id, long fapl_id) throws HDF5LibraryException; + public synchronized static native int H5Pset_elink_fapl(long lapl_id, long fapl_id) + throws HDF5LibraryException; /** - * H5Pget_elink_acc_flags retrieves the external link traversal file access flag from the specified link access - * property list. + * H5Pget_elink_acc_flags retrieves the external link traversal file access flag from the specified link + * access property list. * * @param lapl_id * IN: Link access property list identifier @@ -9767,13 +10108,14 @@ public class H5 implements java.io.Serializable { * @return File access flag for link traversal. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_elink_acc_flags(long lapl_id) throws HDF5LibraryException; /** - * H5Pset_elink_acc_flags Sets the external link traversal file access flag in a link access property list. + * H5Pset_elink_acc_flags Sets the external link traversal file access flag in a link access property + * list. * * @param lapl_id * IN: Link access property list identifier @@ -9783,13 +10125,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception IllegalArgumentException - * - Invalid Flag values. + * Invalid Flag values. * **/ - public synchronized static native int H5Pset_elink_acc_flags(long lapl_id, int flags) throws HDF5LibraryException, - IllegalArgumentException; + public synchronized static native int H5Pset_elink_acc_flags(long lapl_id, int flags) + throws HDF5LibraryException, IllegalArgumentException; // /////// Object copy property list (OCPYPL) routines /////// @@ -9802,7 +10144,7 @@ public class H5 implements java.io.Serializable { * @return Copy option(s) set in the object copy property list * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_copy_object(long ocp_plist_id) throws HDF5LibraryException; @@ -9816,13 +10158,11 @@ public class H5 implements java.io.Serializable { * IN: Copy option(s) to be set * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options) - throws HDF5LibraryException; - - // /////// file drivers property list routines /////// + throws HDF5LibraryException; /** * H5Pget_version retrieves the version information of various objects for a file creation property list. @@ -9832,7 +10172,7 @@ public class H5 implements java.io.Serializable { * @param version_info * OUT: version information. * - * <pre> + * <pre> * version_info[0] = boot // boot block version number * version_info[1] = freelist // global freelist version * version_info[2] = stab // symbol tabl version number @@ -9841,17 +10181,17 @@ public class H5 implements java.io.Serializable { * @return a non-negative value, with the values of version_info initialized, if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - version_info is null. + * version_info is null. * @exception IllegalArgumentException - * - version_info is illegal. + * version_info is illegal. * * @deprecated As of HDF5 1.10.0 in favor of H5Fget_info. **/ @Deprecated - public synchronized static native int H5Pget_version(long plist, int[] version_info) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + public synchronized static native int H5Pget_version(long plist, int[] version_info) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // /////// file drivers property list routines /////// @@ -9866,11 +10206,12 @@ public class H5 implements java.io.Serializable { * OUT: write to file name on flush setting * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + 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. @@ -9885,11 +10226,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + public synchronized static native int H5Pset_fapl_core(long fapl_id, long increment, + boolean backing_store) + throws HDF5LibraryException, NullPointerException; /** * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_direct. @@ -9904,10 +10246,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pget_fapl_direct(long fapl_id, long[] info) throws HDF5LibraryException; + public synchronized static native int H5Pget_fapl_direct(long fapl_id, long[] info) + throws HDF5LibraryException; /** * H5Pset_fapl_direct Sets up use of the direct I/O driver. @@ -9924,11 +10267,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_fapl_direct(long fapl_id, long alignment, long block_size, - long cbuf_size) throws HDF5LibraryException; + long cbuf_size) throws HDF5LibraryException; /** * H5Pget_fapl_family Returns information about the family file access property list. @@ -9943,11 +10286,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + 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. @@ -9962,11 +10306,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + throws HDF5LibraryException, NullPointerException; /** * H5Pset_fapl_hdfs Modify the file access property list to use the H5FD_HDFS driver. @@ -9979,10 +10323,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + 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. @@ -9993,10 +10338,11 @@ public class H5 implements java.io.Serializable { * @return the properties of the hdfs driver. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native H5FD_hdfs_fapl_t H5Pget_fapl_hdfs(long fapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5FD_hdfs_fapl_t H5Pget_fapl_hdfs(long fapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Pget_fapl_multi Sets up use of the multi I/O driver. @@ -10010,19 +10356,21 @@ public class H5 implements java.io.Serializable { * @param memb_name * IN: Name generator for names of member files. * @param memb_addr - * IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of - * data storage begins. + * IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each + * type of data storage begins. * * @return a boolean value; Allows read-only access to incomplete file sets when TRUE. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an array is null. + * an array is null. * **/ - public synchronized static native boolean H5Pget_fapl_multi(long fapl_id, int[] memb_map, long[] memb_fapl, - String[] memb_name, long[] memb_addr) throws HDF5LibraryException, NullPointerException; + public synchronized static native boolean H5Pget_fapl_multi(long fapl_id, int[] memb_map, + long[] memb_fapl, String[] memb_name, + long[] memb_addr) + throws HDF5LibraryException, NullPointerException; /** * H5Pset_fapl_multi Sets up use of the multi I/O driver. @@ -10036,25 +10384,27 @@ public class H5 implements java.io.Serializable { * @param memb_name * IN: Name generator for names of member files. * @param memb_addr - * IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of - * data storage begins. + * IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each + * type of data storage begins. * @param relax * IN: Allows read-only access to incomplete file sets when TRUE. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an array is null. + * an array is null. * **/ public synchronized static native void H5Pset_fapl_multi(long fapl_id, int[] memb_map, long[] memb_fapl, - String[] memb_name, long[] memb_addr, boolean relax) throws HDF5LibraryException, NullPointerException; - + String[] memb_name, long[] memb_addr, + boolean relax) + throws HDF5LibraryException, NullPointerException; /** - * H5Pset_fapl_log Sets up the logging virtual file driver (H5FD_LOG) for use. H5Pset_fapl_log modifies the file - * access property list to use the logging driver, H5FD_LOG. The logging virtual file driver (VFD) is a clone of the - * standard SEC2 (H5FD_SEC2) driver with additional facilities for logging VFD metrics and activity to a file. + * H5Pset_fapl_log Sets up the logging virtual file driver (H5FD_LOG) for use. H5Pset_fapl_log modifies + * the file access property list to use the logging driver, H5FD_LOG. The logging virtual file driver + * (VFD) is a clone of the standard SEC2 (H5FD_SEC2) driver with additional facilities for logging VFD + * metrics and activity to a file. * * @param fapl_id * IN: File access property list identifier. @@ -10066,12 +10416,13 @@ public class H5 implements java.io.Serializable { * IN: The size of the logging buffers, in bytes. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - logfile is null. + * logfile is null. **/ - public synchronized static native void H5Pset_fapl_log(long fapl_id, String logfile, long flags, long buf_size) - throws HDF5LibraryException, NullPointerException; + 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. @@ -10082,10 +10433,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_fapl_sec2(long fapl_id) throws HDF5LibraryException, NullPointerException; + 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 @@ -10104,11 +10456,12 @@ public class H5 implements java.io.Serializable { * IN: File access property list identifier raw data * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + 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. @@ -10119,10 +10472,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_fapl_stdio(long fapl_id) throws HDF5LibraryException, NullPointerException; + 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. @@ -10133,10 +10487,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native int H5Pset_fapl_windows(long fapl_id) throws HDF5LibraryException, NullPointerException; + 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. @@ -10149,10 +10504,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + 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. @@ -10163,10 +10519,11 @@ public class H5 implements java.io.Serializable { * @return the properties of the ros3 driver. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * **/ - public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id) + throws HDF5LibraryException, NullPointerException; // /////// unimplemented //////// @@ -10197,32 +10554,35 @@ public class H5 implements java.io.Serializable { // #endif /* H5_HAVE_PARALLEL */ // herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr); // herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/); - // herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per); - // herr_t H5Pget_page_buffer_size(hid_t fapl_id, size_t *buf_size, unsigned *min_meta_perc, unsigned *min_raw_perc); - // herr_t H5Pset_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t func, void *user_data); + // herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned + // min_raw_per); + // herr_t H5Pget_page_buffer_size(hid_t fapl_id, size_t *buf_size, unsigned *min_meta_perc, unsigned + // *min_raw_perc); herr_t H5Pset_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t func, void *user_data); // herr_t H5Pget_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t *func, void **user_data); // Dataset creation property list (DCPL) routines // // Dataset access property list (DAPL) routines // - // herr_t H5Pset_append_flush (hid_t dapl_id, int ndims, const hsize_t boundary[], H5D_append_cb_t func, void *user_data); - // herr_t H5Pget_append_flush(hid_t dapl_id, int ndims, hsize_t boundary[], H5D_append_cb_t *func, void **user_data) + // herr_t H5Pset_append_flush (hid_t dapl_id, int ndims, const hsize_t boundary[], H5D_append_cb_t func, + // void *user_data); herr_t H5Pget_append_flush(hid_t dapl_id, int ndims, hsize_t boundary[], + // H5D_append_cb_t *func, void **user_data) // Dataset xfer property list (DXPL) routines // // herr_t H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg); // herr_t H5Pset_preserve(hid_t plist_id, hbool_t status); // int H5Pget_preserve(hid_t plist_id); // herr_t H5Pset_filter_callback(hid_t plist, H5Z_filter_func_t func, void *op_data) - // herr_t H5Pget_vlen_mem_manager(hid_t plist, H5MM_allocate_t *alloc, void **alloc_info, H5MM_free_t *free, void + // herr_t H5Pget_vlen_mem_manager(hid_t plist, H5MM_allocate_t *alloc, void **alloc_info, H5MM_free_t + // *free, void // **free_info ) - // herr_t H5Pset_vlen_mem_manager(hid_t plist, H5MM_allocate_t alloc, void *alloc_info, H5MM_free_t free, void - // *free_info ) - // herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data) + // herr_t H5Pset_vlen_mem_manager(hid_t plist, H5MM_allocate_t alloc, void *alloc_info, H5MM_free_t free, + // void *free_info ) herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data) // herr_t H5Pset_type_conv_cb( hid_t plist, H5T_conv_except_func_t func, void *op_data) // #ifdef H5_HAVE_PARALLEL - // herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode); - // herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode); - // herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause); + // herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t + // *actual_chunk_opt_mode); herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t + // *actual_io_mode); herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t + // *local_no_collective_cause, uint32_t *global_no_collective_cause); // #endif /* H5_HAVE_PARALLEL */ // Link creation property list (LCPL) routines // @@ -10268,9 +10628,10 @@ public class H5 implements java.io.Serializable { * * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5PLset_loading_state(int plugin_flags) throws HDF5LibraryException; + public synchronized static native void H5PLset_loading_state(int plugin_flags) + throws HDF5LibraryException; /** * H5PLget_loading_state retrieves the state of the dynamic plugins flag, plugin_flags.. @@ -10282,7 +10643,7 @@ public class H5 implements java.io.Serializable { * If the value of plugin_flags is 0 (zero), all dynamic plugins are disabled. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5PLget_loading_state() throws HDF5LibraryException; @@ -10293,7 +10654,7 @@ public class H5 implements java.io.Serializable { * IN: Path for location of filter plugin libraries. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5PLappend(String plugin_path) throws HDF5LibraryException; @@ -10304,7 +10665,7 @@ public class H5 implements java.io.Serializable { * IN: Path for location of filter plugin libraries. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5PLprepend(String plugin_path) throws HDF5LibraryException; @@ -10317,9 +10678,10 @@ public class H5 implements java.io.Serializable { * IN: The table index (0-based). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5PLreplace(String plugin_path, int index) throws HDF5LibraryException; + public synchronized static native void H5PLreplace(String plugin_path, int index) + throws HDF5LibraryException; /** * H5PLinsert inserts the plugin path at the specified index. @@ -10330,9 +10692,10 @@ public class H5 implements java.io.Serializable { * IN: The table index (0-based). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5PLinsert(String plugin_path, int index) throws HDF5LibraryException; + public synchronized static native void H5PLinsert(String plugin_path, int index) + throws HDF5LibraryException; /** * H5PLremove removes the plugin path at the specified index. @@ -10341,7 +10704,7 @@ public class H5 implements java.io.Serializable { * IN: The table index (0-based). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5PLremove(int index) throws HDF5LibraryException; @@ -10354,7 +10717,7 @@ public class H5 implements java.io.Serializable { * @return the current path at the index in plugin path table * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native String H5PLget(int index) throws HDF5LibraryException; @@ -10364,7 +10727,7 @@ public class H5 implements java.io.Serializable { * @return the current number of paths in the plugin path table * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5PLsize() throws HDF5LibraryException; @@ -10374,12 +10737,13 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// - private synchronized static native int H5Rcreate(byte[] ref, long loc_id, String name, int ref_type, long space_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + private synchronized static native int H5Rcreate(byte[] ref, long loc_id, String name, int ref_type, + long space_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * H5Rcreate creates the reference, ref, of the type specified in ref_type, pointing to the object name located at - * loc_id. + * H5Rcreate creates the reference, ref, of the type specified in ref_type, pointing to the object name + * located at loc_id. * * @param loc_id * IN: Location identifier used to locate the object being pointed to. @@ -10393,19 +10757,20 @@ public class H5 implements java.io.Serializable { * @return the reference (byte[]) if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an input array is null. + * an input array is null. * @exception IllegalArgumentException - * - an input array is invalid. + * an input array is invalid. **/ public synchronized static byte[] H5Rcreate(long loc_id, String name, int ref_type, long space_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { /* These sizes are correct for HDF5.1.2 */ int ref_size = 8; - if (ref_type == HDF5Constants.H5R_DATASET_REGION) { + if (ref_type == HDF5Constants.H5R_DATASET_REGION) ref_size = 12; - } + byte rbuf[] = new byte[ref_size]; /* will raise an exception if fails */ @@ -10429,14 +10794,15 @@ public class H5 implements java.io.Serializable { * @return valid identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - output array is null. + * output array is null. * @exception IllegalArgumentException - * - output array is invalid. + * output array is invalid. **/ public static long H5Rdereference(long dataset, long access_list, int ref_type, byte[] ref) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { long id = _H5Rdereference(dataset, access_list, ref_type, ref); if (id > 0) { log.trace("OPEN_IDS: H5Rdereference add {}", id); @@ -10446,8 +10812,9 @@ public class H5 implements java.io.Serializable { return id; } - private synchronized static native long _H5Rdereference(long dataset, long access_list, int ref_type, byte[] ref) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + private synchronized static native long _H5Rdereference(long dataset, long access_list, int ref_type, + byte[] ref) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_name retrieves a name for the object identified by ref. @@ -10463,23 +10830,23 @@ public class H5 implements java.io.Serializable { * @param size * IN: The size of the name buffer. * - * @return Returns the length of the name if successful, returning 0 (zero) if no name is associated with the - * identifier. Otherwise returns a negative value. - * + * @return Returns the length of the name if successful, returning 0 (zero) if no name is associated with + * the identifier. Otherwise returns a negative value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - size is null. + * size is null. * @exception IllegalArgumentException - * - Argument is illegal. - * + * Argument is illegal. **/ - public synchronized static native long H5Rget_name(long loc_id, int ref_type, byte[] ref, String[] name, long size) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + public synchronized static native long H5Rget_name(long loc_id, int ref_type, byte[] ref, String[] name, + long size) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * H5Rget_obj_type Given a reference to an object ref, H5Rget_obj_type returns the type of the object pointed to. + * H5Rget_obj_type Given a reference to an object ref, H5Rget_obj_type returns the type of the object + * pointed to. * * @param loc_id * IN: loc_id of the reference object. @@ -10491,26 +10858,27 @@ public class H5 implements java.io.Serializable { * @return Returns the object type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - array is null. + * an input array is null. * @exception IllegalArgumentException - * - array is invalid. + * an input array is invalid. **/ public synchronized static native int H5Rget_obj_type(long loc_id, int ref_type, byte ref[]) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_obj_type2 Retrieves the type of object that an object reference points to. * * @see public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[]) **/ - private synchronized static native int H5Rget_obj_type2(long loc_id, int ref_type, byte ref[], int[] obj_type) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + private synchronized static native int H5Rget_obj_type2(long loc_id, int ref_type, byte ref[], + int[] obj_type) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * Given a reference to an object ref, H5Rget_region creates a copy of the dataspace of the dataset pointed to and - * defines a selection in the copy which is the region pointed to. + * Given a reference to an object ref, H5Rget_region creates a copy of the dataspace of the dataset + * pointed to and defines a selection in the copy which is the region pointed to. * * @param loc_id * IN: loc_id of the reference object. @@ -10522,14 +10890,15 @@ public class H5 implements java.io.Serializable { * @return a valid identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - output array is null. + * an input array is null. * @exception IllegalArgumentException - * - output array is invalid. + * an input array is invalid. **/ - public static long H5Rget_region(long loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException { + public static long H5Rget_region(long loc_id, int ref_type, byte[] ref) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { long id = _H5Rget_region(loc_id, ref_type, ref); if (id > 0) { log.trace("OPEN_IDS: H5Rget_region add {}", id); @@ -10540,7 +10909,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Rget_region(long loc_id, int ref_type, byte[] ref) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // //////////////////////////////////////////////////////////// // // @@ -10559,9 +10928,10 @@ public class H5 implements java.io.Serializable { * @return a dataspace identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Screate(int type) throws HDF5LibraryException { + public static long H5Screate(int type) throws HDF5LibraryException + { long id = _H5Screate(type); if (id > 0) { log.trace("OPEN_IDS: H5Screate add {}", id); @@ -10586,12 +10956,13 @@ public class H5 implements java.io.Serializable { * @return a dataspace identifier * * @exception HDF5Exception - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dims or maxdims is null. + * dims or maxdims is null. **/ - public static long H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception, - NullPointerException { + public static long H5Screate_simple(int rank, long[] dims, long[] maxdims) + throws HDF5Exception, NullPointerException + { long id = _H5Screate_simple(rank, dims, maxdims); if (id > 0) { log.trace("OPEN_IDS: H5Screate_simple add {}", id); @@ -10602,7 +10973,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Screate_simple(int rank, long[] dims, long[] maxdims) - throws HDF5Exception, NullPointerException; + throws HDF5Exception, NullPointerException; /** * H5Sset_extent_simple sets or resets the size of an existing dataspace. @@ -10619,10 +10990,11 @@ public class H5 implements java.io.Serializable { * @return a dataspace identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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; + long[] maximum_size) + throws HDF5LibraryException, NullPointerException; /** * H5Sset_extent_simple sets or resets the size of an existing dataspace. @@ -10639,14 +11011,16 @@ public class H5 implements java.io.Serializable { * @return a dataspace identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * 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(); + 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(); + long[] lamaxs = (maxsbb.asLongBuffer()).array(); return H5Sset_extent_simple(space_id, rank, lacs, lamaxs); } @@ -10659,9 +11033,10 @@ public class H5 implements java.io.Serializable { * @return a dataspace identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Scopy(long space_id) throws HDF5LibraryException { + public static long H5Scopy(long space_id) throws HDF5LibraryException + { long id = _H5Scopy(space_id); if (id > 0) { log.trace("OPEN_IDS: H5Scopy add {}", id); @@ -10682,9 +11057,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Sclose(long space_id) throws HDF5LibraryException { + public static int H5Sclose(long space_id) throws HDF5LibraryException + { if (space_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -10705,9 +11081,10 @@ public class H5 implements java.io.Serializable { * @return the buffer for the object to be encoded into. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native byte[] H5Sencode(long obj_id) + throws HDF5LibraryException, NullPointerException; /** * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. @@ -10718,23 +11095,26 @@ public class H5 implements java.io.Serializable { * @return a new object handle * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Sdecode(byte[] buf) + throws HDF5LibraryException, NullPointerException; /** * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. * * @param space_id * ID of the dataspace object to query + * * @return the number of elements in the dataspace if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException; + 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. @@ -10745,13 +11125,14 @@ public class H5 implements java.io.Serializable { * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException; + public synchronized static native int H5Sget_simple_extent_ndims(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_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through + * the dims and maxdims parameters. * * @param space_id * IN: Identifier of the dataspace object to query @@ -10763,12 +11144,13 @@ public class H5 implements java.io.Serializable { * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dims or maxdims is null. + * 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 int H5Sget_simple_extent_dims(long space_id, long[] dims, + long[] maxdims) + throws HDF5LibraryException, NullPointerException; /** * H5Sis_simple determines whether a dataspace is a simple dataspace. @@ -10779,7 +11161,7 @@ public class H5 implements java.io.Serializable { * @return true if is a simple dataspace * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException; @@ -10792,9 +11174,10 @@ public class H5 implements java.io.Serializable { * @return a dataspace class name if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException; + public synchronized static native int H5Sget_simple_extent_type(long space_id) + throws HDF5LibraryException; /** * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. @@ -10805,13 +11188,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException; /** - * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the - * dataspace. + * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type + * of the dataspace. * * @param dest_space_id * IN: The identifier for the dataspace from which the extent is copied. @@ -10821,13 +11204,14 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) - throws HDF5LibraryException; + throws HDF5LibraryException; /** - * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. + * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, + * are equal. * * @param first_space_id * IN: The identifier for the first dataspace. @@ -10837,10 +11221,10 @@ public class H5 implements java.io.Serializable { * @return true if successful, else false * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id) - throws HDF5LibraryException; + throws HDF5LibraryException; /***************** Operations on dataspace selections *****************/ @@ -10853,7 +11237,7 @@ public class H5 implements java.io.Serializable { * @return the dataspace selection type if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Sget_select_type(long space_id) throws HDF5LibraryException; @@ -10866,20 +11250,24 @@ public class H5 implements java.io.Serializable { * @return the number of elements in the selection if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; /** * 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 + * + * @param dst_id + * ID of the destination dataspace + * @param src_id + * ID of the source dataspace * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Sselect_copy(long dst_id, long src_id) throws HDF5LibraryException; + public synchronized static native void H5Sselect_copy(long dst_id, long src_id) + throws HDF5LibraryException; /** * H5Sselect_valid verifies that the selection for the dataspace. @@ -10890,7 +11278,7 @@ public class H5 implements java.io.Serializable { * @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. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException; @@ -10903,18 +11291,17 @@ public class H5 implements java.io.Serializable { * Offset to subtract * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - offset is null. + * offset is null. **/ - public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset) - throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset) + throws HDF5LibraryException, NullPointerException; /** - * 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_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 * Identifier of dataspace to release. @@ -10926,50 +11313,54 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful,with start and end initialized. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - start or end is null. + * start or end is null. **/ public synchronized static native int H5Sget_select_bounds(long space_id, long[] start, long[] end) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * 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 + * @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. + * Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException; + 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 - * ID of dataspace pointer to compare + * ID of dataspace pointer to compare * @param start - * Starting coordinate of block + * Starting coordinate of block * @param end - * Opposite ("ending") coordinate of block + * Opposite ("ending") coordinate of block * * @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. + * Error from the HDF-5 Library. * @exception NullPointerException - * - offset is null. + * offset is null. **/ - public synchronized static native boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end) - throws HDF5LibraryException, NullPointerException; + 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. @@ -10982,12 +11373,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - offset array is null. + * offset array is null. **/ - public synchronized static native int H5Soffset_simple(long space_id, byte[] offset) throws HDF5LibraryException, - NullPointerException; + 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. @@ -11000,22 +11391,22 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - offset array is null. + * offset array is null. **/ - public synchronized static int H5Soffset_simple(long space_id, long[] offset) throws HDF5Exception, - NullPointerException { - if (offset == null) { + public synchronized static int H5Soffset_simple(long space_id, long[] offset) + throws HDF5Exception, NullPointerException + { + if (offset == null) return -1; - } HDFArray theArray = new HDFArray(offset); - byte[] theArr = theArray.byteify(); + byte[] theArr = theArray.byteify(); int retVal = H5Soffset_simple(space_id, theArr); - theArr = null; + theArr = null; theArray = null; return retVal; } @@ -11029,7 +11420,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Sselect_all(long space_id) throws HDF5LibraryException; @@ -11038,10 +11429,11 @@ public class H5 implements java.io.Serializable { * * @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. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException; @@ -11060,10 +11452,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - private synchronized static native int H5Sselect_elements(long space_id, int op, int num_elements, byte[] coord) - throws HDF5LibraryException, NullPointerException; + private synchronized static native int H5Sselect_elements(long space_id, int op, int num_elements, + byte[] coord) + throws HDF5LibraryException, NullPointerException; /** * H5Sselect_elements selects array elements to be included in the selection for the space_id dataspace. @@ -11080,24 +11473,25 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5Exception - * - Error in the data conversion + * Error in the data conversion * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - cord array is + * cord array is **/ - public synchronized static int H5Sselect_elements(long space_id, int op, int num_elements, long[][] coord2D) - throws HDF5Exception, HDF5LibraryException, NullPointerException { - if (coord2D == null) { + public synchronized static int H5Sselect_elements(long space_id, int op, int num_elements, + long[][] coord2D) + throws HDF5Exception, HDF5LibraryException, NullPointerException + { + if (coord2D == null) return -1; - } HDFArray theArray = new HDFArray(coord2D); - byte[] coord = theArray.byteify(); + byte[] coord = theArray.byteify(); int retVal = H5Sselect_elements(space_id, op, num_elements, coord); - coord = null; + coord = null; theArray = null; return retVal; } @@ -11111,14 +11505,15 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException; + 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. + * 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. @@ -11132,16 +11527,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * 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_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. + * 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: Identifier of dataspace selection to modify @@ -11159,29 +11556,32 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an input array is null. + * an input array is null. * @exception IllegalArgumentException - * - an input array is invalid. + * an input array is invalid. **/ public synchronized static int H5Sselect_hyperslab(long space_id, int op, byte[] start, byte[] stride, - byte[] count, byte[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { - ByteBuffer startbb = ByteBuffer.wrap(start); - long[] lastart = (startbb.asLongBuffer()).array(); + byte[] count, byte[] block) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { + ByteBuffer startbb = ByteBuffer.wrap(start); + long[] lastart = (startbb.asLongBuffer()).array(); ByteBuffer stridebb = ByteBuffer.wrap(stride); - long[] lastride = (stridebb.asLongBuffer()).array(); - ByteBuffer countbb = ByteBuffer.wrap(count); - long[] lacount = (countbb.asLongBuffer()).array(); - ByteBuffer blockbb = ByteBuffer.wrap(block); - long[] lablock = (blockbb.asLongBuffer()).array(); + long[] lastride = (stridebb.asLongBuffer()).array(); + ByteBuffer countbb = ByteBuffer.wrap(count); + long[] lacount = (countbb.asLongBuffer()).array(); + ByteBuffer blockbb = ByteBuffer.wrap(block); + long[] lablock = (blockbb.asLongBuffer()).array(); return H5Sselect_hyperslab(space_id, op, lastart, lastride, lacount, lablock); } /** - * 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. + * 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: Identifier of dataspace selection to modify @@ -11199,15 +11599,15 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an input array is null. + * an input array is null. * @exception IllegalArgumentException - * - an input array is invalid. + * an input array is invalid. **/ - public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride, - long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; - + public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, + long[] stride, long[] count, long[] block) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Scombine_hyperslab combines a hyperslab selection with the current selection for a dataspace, @@ -11233,31 +11633,33 @@ public class H5 implements java.io.Serializable { * @return a dataspace ID on success / H5I_INVALID_HID on failure * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an input array is null. + * an input array is null. * @exception IllegalArgumentException - * - an input array is invalid. + * 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; + 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 + * hyperslab. The first selection is modified to contain the result of * space1 operated on by space2. * * @param space1_id - * ID of the destination dataspace + * ID of the destination dataspace * @param op - * Operation to perform on current selection. + * Operation to perform on current selection. * @param space2_id - * ID of the source dataspace + * ID of the source dataspace * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Smodify_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; + public synchronized static native void H5Smodify_select(long space1_id, int op, long space2_id) + throws HDF5LibraryException; /** * H5Scombine_select combines two existing hyperslab selections with an operation, returning @@ -11265,18 +11667,19 @@ public class H5 implements java.io.Serializable { * space1 is copied for the dataspace extent of the newly created dataspace. * * @param space1_id - * ID of the first dataspace + * ID of the first dataspace * @param op - * Operation to perform on current selection. + * Operation to perform on current selection. * @param space2_id - * ID of the second dataspace + * ID of the second dataspace * * @return a dataspace ID on success / H5I_INVALID_HID on failure * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5Scombine_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; + public synchronized static native long H5Scombine_select(long space1_id, int op, long space2_id) + throws HDF5LibraryException; /** * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified @@ -11288,50 +11691,56 @@ public class H5 implements java.io.Serializable { * @return a TRUE/FALSE for hyperslab selection if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException; + 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 - * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace. + * 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: Identifier of dataspace selection to modify * @param start - * OUT: Offset of start of hyperslab + * OUT: Offset of start of hyperslab * @param stride - * OUT: Hyperslab stride. + * OUT: Hyperslab stride. * @param count - * OUT: Number of blocks included in hyperslab. + * OUT: Number of blocks included in hyperslab. * @param block - * OUT: Size of block in hyperslab. + * OUT: Size of block in hyperslab. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - an output array is null. + * an output array is null. * @exception IllegalArgumentException - * - an output array is invalid. + * an output array is invalid. **/ - public synchronized static native void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + 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; + /** + * 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; /** * 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: + * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as + * follows: * * <pre> * <"start" coordinate>, immediately followed by @@ -11348,17 +11757,19 @@ public class H5 implements java.io.Serializable { * @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. + * 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. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * 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 H5Sget_select_hyper_blocklist(long spaceid, long startblock, + long numblocks, long[] buf) + throws HDF5LibraryException, NullPointerException; /** * H5Sselect_project_intersection projects the intersection of the selections of src_space_id and @@ -11366,23 +11777,22 @@ public class H5 implements java.io.Serializable { * 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 + * 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 + * 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 + * 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. + * 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; - - - + long src_intersect_space_id) + throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // @@ -11403,12 +11813,13 @@ public class H5 implements java.io.Serializable { * @return a valid datatype identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dim is null. + * dim is null. **/ - public static long H5Tarray_create(long base_id, int ndims, long[] dim) throws HDF5LibraryException, - NullPointerException { + public static long H5Tarray_create(long base_id, int ndims, long[] dim) + throws HDF5LibraryException, NullPointerException + { long id = _H5Tarray_create2(base_id, ndims, dim); if (id > 0) { log.trace("OPEN_IDS: H5Tarray_create add {}", id); @@ -11419,7 +11830,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Tarray_create2(long base_id, int ndims, long[] dim) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Tclose releases a datatype. @@ -11430,9 +11841,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Tclose(long type_id) throws HDF5LibraryException { + public static int H5Tclose(long type_id) throws HDF5LibraryException + { if (type_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; @@ -11461,16 +11873,17 @@ public class H5 implements java.io.Serializable { * IN: Datatype access property list. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native void H5Tcommit(long loc_id, String name, long type_id, long lcpl_id, - long tcpl_id, long tapl_id) throws HDF5LibraryException, NullPointerException; + long tcpl_id, long tapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Tcommit_anon commits a transient datatype (not immutable) to a file, turning it into a named datatype with the - * specified creation and property lists. + * H5Tcommit_anon commits a transient datatype (not immutable) to a file, turning it into a named datatype + * with the specified creation and property lists. * * @param loc_id * IN: Location identifier. @@ -11482,14 +11895,14 @@ public class H5 implements java.io.Serializable { * IN: Datatype access property list. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Tcommit_anon(long loc_id, long type_id, long tcpl_id, long tapl_id) - throws HDF5LibraryException; + public synchronized static native void H5Tcommit_anon(long loc_id, long type_id, long tcpl_id, + long tapl_id) throws HDF5LibraryException; /** - * H5Tcommitted queries a type to determine whether the type specified by the type identifier is a named type or a - * transient type. + * H5Tcommitted queries a type to determine whether the type specified by the type identifier is a named + * type or a transient type. * * @param type_id * IN: Identifier of datatype. @@ -11497,13 +11910,13 @@ public class H5 implements java.io.Serializable { * @return true the datatype has been committed * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tcommitted(long type_id) throws HDF5LibraryException; /** - * H5Tcompiler_conv finds out whether the library's conversion function from type src_id to type dst_id is a - * compiler (hard) conversion. + * H5Tcompiler_conv finds out whether the library's conversion function from type src_id to type dst_id is + *a compiler (hard) conversion. * * @param src_id * IN: Identifier of source datatype. @@ -11511,12 +11924,13 @@ public class H5 implements java.io.Serializable { * IN: Identifier of destination datatype. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Tcompiler_conv(long src_id, long dst_id) throws HDF5LibraryException; + public synchronized static native void H5Tcompiler_conv(long src_id, long dst_id) + throws HDF5LibraryException; /** - ** H5Tconvert converts nelmts elements from the type specified by the src_id identifier to type dst_id. + * H5Tconvert converts nelmts elements from the type specified by the src_id identifier to type dst_id. * * @param src_id * IN: Identifier of source datatype. @@ -11532,12 +11946,13 @@ public class H5 implements java.io.Serializable { * IN: Dataset transfer property list identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ public synchronized static native void H5Tconvert(long src_id, long dst_id, long nelmts, byte[] buf, - byte[] background, long plist_id) throws HDF5LibraryException, NullPointerException; + byte[] background, long plist_id) + throws HDF5LibraryException, NullPointerException; // int H5Tconvert(int src_id, int dst_id, long nelmts, Pointer buf, Pointer background, int plist_id); @@ -11545,15 +11960,16 @@ public class H5 implements java.io.Serializable { * H5Tcopy copies an existing datatype. The returned type is always transient and unlocked. * * @param type_id - * IN: Identifier of datatype to copy. Can be a datatype identifier, a predefined datatype (defined in - * H5Tpublic.h), or a dataset Identifier. + * IN: Identifier of datatype to copy. Can be a datatype identifier, a predefined datatype + * (defined in H5Tpublic.h), or a dataset Identifier. * * @return a datatype identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tcopy(long type_id) throws HDF5LibraryException { + public static long H5Tcopy(long type_id) throws HDF5LibraryException + { long id = _H5Tcopy(type_id); if (id > 0) { log.trace("OPEN_IDS: H5Tcopy add {}", id); @@ -11576,9 +11992,10 @@ public class H5 implements java.io.Serializable { * @return datatype identifier * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tcreate(int tclass, long size) throws HDF5LibraryException { + public static long H5Tcreate(int tclass, long size) throws HDF5LibraryException + { long id = _H5Tcreate(tclass, size); if (id > 0) { log.trace("OPEN_IDS: H5Tcreate add {}", id); @@ -11599,11 +12016,12 @@ public class H5 implements java.io.Serializable { * @return a new object handle * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public static long H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException { + public static long H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException + { long id = _H5Tdecode(buf); if (id > 0) { log.trace("OPEN_IDS: H5Tdecode add {}", id); @@ -11613,11 +12031,12 @@ public class H5 implements java.io.Serializable { return id; } - private synchronized static native long _H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; + private synchronized static native long _H5Tdecode(byte[] buf) + throws HDF5LibraryException, NullPointerException; /** - * H5Tdetect_class determines whether the datatype specified in dtype_id contains any datatypes of the datatype - * class specified in dtype_class. + * H5Tdetect_class determines whether the datatype specified in dtype_id contains any datatypes of the + * datatype class specified in dtype_class. * * @param type_id * IN: Identifier of datatype to query. @@ -11627,9 +12046,10 @@ public class H5 implements java.io.Serializable { * @return true if the datatype specified in dtype_id contains any datatypes of the datatype class * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Tdetect_class(long type_id, int cls) throws HDF5LibraryException; + public synchronized static native boolean H5Tdetect_class(long type_id, int cls) + throws HDF5LibraryException; /** * H5Tencode converts a data type description into binary form in a buffer. @@ -11637,36 +12057,38 @@ public class H5 implements java.io.Serializable { * @param obj_id * IN: Identifier of the object to be encoded. * @param buf - * OUT: Buffer for the object to be encoded into. If the provided buffer is NULL, only the size of buffer - * needed is returned. + * OUT: Buffer for the object to be encoded into. If the provided buffer is NULL, only the size + * of buffer needed is returned. * @param nalloc * IN: The size of the allocated buffer. * * @return the size needed for the allocated buffer. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - buf is null. + * buf is null. **/ - public synchronized static native int H5Tencode(long obj_id, byte[] buf, long nalloc) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Tencode(long obj_id, byte[] buf, long nalloc) + throws HDF5LibraryException, NullPointerException; // /** // * H5Tencode converts a data type description into binary form in a buffer. // * - // * @param obj_id IN: Identifier of the object to be encoded. + // * @param obj_id + // * IN: Identifier of the object to be encoded. // * // * @return the buffer for the object to be encoded into. // * - // * @exception HDF5LibraryException - Error from the HDF-5 Library. + // * @exception HDF5LibraryException + // * Error from the HDF-5 Library. // **/ // public synchronized static native byte[] H5Tencode(int obj_id) - // throws HDF5LibraryException; + // throws HDF5LibraryException; /** - * H5Tenum_create creates a new enumeration datatype based on the specified base datatype, parent_id, which must be - * an integer type. + * H5Tenum_create creates a new enumeration datatype based on the specified base datatype, parent_id, + * which must be an integer type. * * @param base_id * IN: Identifier of the parent datatype to release. @@ -11674,9 +12096,10 @@ public class H5 implements java.io.Serializable { * @return the datatype identifier for the new enumeration datatype * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tenum_create(long base_id) throws HDF5LibraryException { + public static long H5Tenum_create(long base_id) throws HDF5LibraryException + { long id = _H5Tenum_create(base_id); if (id > 0) { log.trace("OPEN_IDS: H5Tenum_create add {}", id); @@ -11699,12 +12122,12 @@ public class H5 implements java.io.Serializable { * IN: The value of the member, data of the correct type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native void H5Tenum_insert(long type, String name, byte[] value) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Tenum_insert inserts a new enumeration datatype member into an enumeration datatype. @@ -11719,12 +12142,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static int H5Tenum_insert(long type, String name, int[] value) throws HDF5LibraryException, - NullPointerException { + public static int H5Tenum_insert(long type, String name, int[] value) + throws HDF5LibraryException, NullPointerException + { return H5Tenum_insert_int(type, name, value); } @@ -11741,21 +12165,23 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static int H5Tenum_insert(long type, String name, int value) throws HDF5LibraryException, - NullPointerException { - int[] val = { value }; + public static int H5Tenum_insert(long type, String name, int value) + throws HDF5LibraryException, NullPointerException + { + int[] val = {value}; return H5Tenum_insert_int(type, name, val); } private synchronized static native int H5Tenum_insert_int(long type, String name, int[] value) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the enumeration datatype type. + * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the enumeration + * datatype type. * * @param type * IN: Identifier of datatype. @@ -11767,17 +12193,18 @@ public class H5 implements java.io.Serializable { * @return the symbol name. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - value is null. + * value is null. **/ public synchronized static native String H5Tenum_nameof(long type, byte[] value, long size) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; // int H5Tenum_nameof(int type, Pointer value, Buffer name/* out */, long size); /** - * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the enumeration datatype type. + * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the enumeration + * datatype type. * * @param type * IN: Identifier of datatype. @@ -11791,20 +12218,22 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static int H5Tenum_nameof(long type, int[] value, String[] name, int size) throws HDF5LibraryException, - NullPointerException { + public static int H5Tenum_nameof(long type, int[] value, String[] name, int size) + throws HDF5LibraryException, NullPointerException + { return H5Tenum_nameof_int(type, value, name, size); } private synchronized static native int H5Tenum_nameof_int(long type, int[] value, String[] name, int size) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration datatype type. + * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration datatype + * type. * * @param type * IN: Identifier of datatype. @@ -11814,13 +12243,14 @@ public class H5 implements java.io.Serializable { * OUT: The value of the member * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Tenum_valueof(long type, String name, byte[] value) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration datatype type. + * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration datatype + * type. * * @param type * IN: Identifier of datatype. @@ -11832,17 +12262,18 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static int H5Tenum_valueof(long type, String name, int[] value) throws HDF5LibraryException, - NullPointerException { + public static int H5Tenum_valueof(long type, String name, int[] value) + throws HDF5LibraryException, NullPointerException + { return H5Tenum_valueof_int(type, name, value); } private synchronized static native int H5Tenum_valueof_int(long type, String name, int[] value) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Tequal determines whether two datatype identifiers refer to the same datatype. @@ -11855,9 +12286,10 @@ public class H5 implements java.io.Serializable { * @return true if the datatype identifiers refer to the same datatype, else false. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Tequal(long type_id1, long type_id2) throws HDF5LibraryException; + public synchronized static native boolean H5Tequal(long type_id1, long type_id2) + throws HDF5LibraryException; /** * H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object. @@ -11870,11 +12302,13 @@ public class H5 implements java.io.Serializable { * @return the non-negative number of dimensions of the array type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dims is null. + * dims is null. **/ - public static int H5Tget_array_dims(long type_id, long[] dims) throws HDF5LibraryException, NullPointerException { + public static int H5Tget_array_dims(long type_id, long[] dims) + throws HDF5LibraryException, NullPointerException + { return H5Tget_array_dims2(type_id, dims); } @@ -11889,12 +12323,12 @@ public class H5 implements java.io.Serializable { * @return the non-negative number of dimensions of the array type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - dims is null. + * dims is null. **/ - public synchronized static native int H5Tget_array_dims2(long type_id, long[] dims) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Tget_array_dims2(long type_id, long[] dims) + throws HDF5LibraryException, NullPointerException; /** * H5Tget_array_ndims returns the rank, the number of dimensions, of an array datatype object. @@ -11905,7 +12339,7 @@ public class H5 implements java.io.Serializable { * @return the rank of the array * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_array_ndims(long type_id) throws HDF5LibraryException; @@ -11918,7 +12352,7 @@ public class H5 implements java.io.Serializable { * @return datatype class identifier if successful; otherwise H5T_NO_CLASS(-1). * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_class(long type_id) throws HDF5LibraryException; @@ -11931,7 +12365,8 @@ public class H5 implements java.io.Serializable { * @return class name if successful; otherwise H5T_NO_CLASS. * **/ - public static String H5Tget_class_name(long class_id) { + public static String H5Tget_class_name(long class_id) + { String retValue = null; if (HDF5Constants.H5T_INTEGER == class_id) /* integer types */ retValue = "H5T_INTEGER"; @@ -11947,7 +12382,7 @@ public class H5 implements java.io.Serializable { retValue = "H5T_OPAQUE"; else if (HDF5Constants.H5T_COMPOUND == class_id) /* compound types */ retValue = "H5T_COMPOUND"; - else if (HDF5Constants.H5T_REFERENCE == class_id)/* reference types */ + else if (HDF5Constants.H5T_REFERENCE == class_id) /* reference types */ retValue = "H5T_REFERENCE"; else if (HDF5Constants.H5T_ENUM == class_id) /* enumeration types */ retValue = "H5T_ENUM"; @@ -11962,8 +12397,8 @@ public class H5 implements java.io.Serializable { } /** - * H5Tget_create_plist returns a property list identifier for the datatype creation property list associated with - * the datatype specified by type_id. + * H5Tget_create_plist returns a property list identifier for the datatype creation property list + * associated with the datatype specified by type_id. * * @param type_id * IN: Identifier of datatype. @@ -11971,9 +12406,10 @@ public class H5 implements java.io.Serializable { * @return a datatype property list identifier. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tget_create_plist(long type_id) throws HDF5LibraryException { + public static long H5Tget_create_plist(long type_id) throws HDF5LibraryException + { long id = _H5Tget_create_plist(type_id); if (id > 0) { log.trace("OPEN_IDS: _H5Tget_create_plist add {}", id); @@ -11994,7 +12430,7 @@ public class H5 implements java.io.Serializable { * @return a valid character set type if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_cset(long type_id) throws HDF5LibraryException; @@ -12009,7 +12445,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_cset(long type_id, int cset) throws HDF5LibraryException; @@ -12022,7 +12458,7 @@ public class H5 implements java.io.Serializable { * @return the bias if successful; otherwise 0. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_ebias(long type_id) throws HDF5LibraryException; @@ -12037,10 +12473,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Tset_ebias(long type_id, int ebias) throws HDF5LibraryException { - H5Tset_ebias(type_id, (long) ebias); + public static int H5Tset_ebias(long type_id, int ebias) throws HDF5LibraryException + { + H5Tset_ebias(type_id, (long)ebias); return 0; } @@ -12053,7 +12490,7 @@ public class H5 implements java.io.Serializable { * @return the bias * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_ebias_long(long type_id) throws HDF5LibraryException; @@ -12066,12 +12503,13 @@ public class H5 implements java.io.Serializable { * IN: Exponent bias value. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_ebias(long type_id, long ebias) throws HDF5LibraryException; /** - * H5Tget_fields retrieves information about the locations of the various bit fields of a floating point datatype. + * H5Tget_fields retrieves information about the locations of the various bit fields of a floating point + * datatype. * * @param type_id * IN: Identifier of datatype to query. @@ -12086,24 +12524,25 @@ public class H5 implements java.io.Serializable { * </ul> * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - fields is null. + * fields is null. * @exception IllegalArgumentException - * - fields array is invalid. + * fields array is invalid. **/ - public synchronized static native void H5Tget_fields(long type_id, long[] fields) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + public synchronized static native void H5Tget_fields(long type_id, long[] fields) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * H5Tget_fields retrieves information about the locations of the various bit fields of a floating point datatype. + * H5Tget_fields retrieves information about the locations of the various bit fields of a floating point + * datatype. * * @param type_id * IN: Identifier of datatype to query. * @param fields * OUT: location of size and bit-position. * - * <pre> + * <pre> * fields[0] = spos OUT: location to return size of in bits. * fields[1] = epos OUT: location to return exponent bit-position. * fields[2] = esize OUT: location to return size of exponent in bits. @@ -12114,19 +12553,20 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - fields is null. + * fields is null. * @exception IllegalArgumentException - * - fields array is invalid. + * fields array is invalid. **/ - public static int H5Tget_fields(long type_id, int[] fields) throws HDF5LibraryException, NullPointerException, - IllegalArgumentException { + public static int H5Tget_fields(long type_id, int[] fields) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { return H5Tget_fields_int(type_id, fields); } - private synchronized static native int H5Tget_fields_int(long type_id, int[] fields) throws HDF5LibraryException, - NullPointerException, IllegalArgumentException; + private synchronized static native int H5Tget_fields_int(long type_id, int[] fields) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Tset_fields sets the locations and sizes of the various floating point bit fields. @@ -12145,10 +12585,10 @@ public class H5 implements java.io.Serializable { * IN: Size of mantissa in bits. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Tset_fields(long type_id, long spos, long epos, long esize, long mpos, - long msize) throws HDF5LibraryException; + public synchronized static native void H5Tset_fields(long type_id, long spos, long epos, long esize, + long mpos, long msize) throws HDF5LibraryException; /** * H5Tset_fields sets the locations and sizes of the various floating point bit fields. @@ -12169,11 +12609,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public static int H5Tset_fields(long type_id, int spos, int epos, int esize, int mpos, int msize) - throws HDF5LibraryException { - H5Tset_fields(type_id, (long) spos, (long) epos, (long) esize, (long) mpos, (long) msize); + throws HDF5LibraryException + { + H5Tset_fields(type_id, (long)spos, (long)epos, (long)esize, (long)mpos, (long)msize); return 0; } @@ -12186,14 +12627,14 @@ public class H5 implements java.io.Serializable { * @return a valid padding type if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_inpad(long type_id) throws HDF5LibraryException; /** - * If any internal bits of a floating point type are unused (that is, those significant bits which are not part of - * the sign, exponent, or mantissa), then H5Tset_inpad will be filled according to the value of the padding value - * property inpad. + * If any internal bits of a floating point type are unused (that is, those significant bits which are not + * part of the sign, exponent, or mantissa), then H5Tset_inpad will be filled according to the value of the + * padding value property inpad. * * @param type_id * IN: Identifier of datatype to modify. @@ -12203,7 +12644,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_inpad(long type_id, int inpad) throws HDF5LibraryException; @@ -12218,9 +12659,10 @@ public class H5 implements java.io.Serializable { * @return the class of the datatype of the field if successful; * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Tget_member_class(long type_id, int membno) throws HDF5LibraryException; + public synchronized static native int H5Tget_member_class(long type_id, int membno) + throws HDF5LibraryException; /** * H5Tget_member_index retrieves the index of a field of a compound datatype. @@ -12233,12 +12675,14 @@ public class H5 implements java.io.Serializable { * @return if field is defined, the index; else negative. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Tget_member_index(long type_id, String field_name) throws HDF5LibraryException; + public synchronized static native int H5Tget_member_index(long type_id, String field_name) + throws HDF5LibraryException; /** - * H5Tget_member_name retrieves the name of a field of a compound datatype or an element of an enumeration datatype. + * H5Tget_member_name retrieves the name of a field of a compound datatype or an element of an enumeration + * datatype. * * @param type_id * IN: Identifier of datatype to query. @@ -12248,13 +12692,15 @@ public class H5 implements java.io.Serializable { * @return a valid pointer to the name if successful; otherwise null. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native String H5Tget_member_name(long type_id, int field_idx) throws HDF5LibraryException; + public synchronized static native String H5Tget_member_name(long type_id, int field_idx) + throws HDF5LibraryException; /** - * H5Tget_member_offset returns the byte offset of the specified member of the compound datatype. This is the byte - * offset in the HDF-5 file/library, NOT the offset of any Java object which might be mapped to this data item. + * H5Tget_member_offset returns the byte offset of the specified member of the compound datatype. This is + * the byte offset in the HDF-5 file/library, NOT the offset of any Java object which might be mapped to + * this data item. * * @param type_id * IN: Identifier of datatype to query. @@ -12276,9 +12722,10 @@ public class H5 implements java.io.Serializable { * @return the identifier of a copy of the datatype of the field if successful; * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tget_member_type(long type_id, int field_idx) throws HDF5LibraryException { + public static long H5Tget_member_type(long type_id, int field_idx) throws HDF5LibraryException + { long id = _H5Tget_member_type(type_id, field_idx); if (id > 0) { log.trace("OPEN_IDS: H5Tget_member_type add {}", id); @@ -12289,7 +12736,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Tget_member_type(long type_id, int field_idx) - throws HDF5LibraryException; + throws HDF5LibraryException; /** * H5Tget_member_value returns the value of the enumeration datatype member memb_no. @@ -12302,12 +12749,12 @@ public class H5 implements java.io.Serializable { * OUT: The value of the member * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - value is null. + * value is null. **/ public synchronized static native void H5Tget_member_value(long type_id, int membno, byte[] value) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Tget_member_value returns the value of the enumeration datatype member memb_no. @@ -12322,30 +12769,33 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - value is null. + * value is null. **/ - public static int H5Tget_member_value(long type_id, int membno, int[] value) throws HDF5LibraryException, - NullPointerException { + public static int H5Tget_member_value(long type_id, int membno, int[] value) + throws HDF5LibraryException, NullPointerException + { return H5Tget_member_value_int(type_id, membno, value); } private synchronized static native int H5Tget_member_value_int(long type_id, int membno, int[] value) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Tget_native_type returns the equivalent native datatype for the datatype specified in type_id. * * @param type_id - * IN: Identifier of datatype to query. Direction of search is assumed to be in ascending order. + * IN: Identifier of datatype to query. Direction of search is assumed to be in ascending + * order. * * @return the native datatype identifier for the specified dataset datatype. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static long H5Tget_native_type(long type_id) throws HDF5LibraryException { + public synchronized static long H5Tget_native_type(long type_id) throws HDF5LibraryException + { return H5Tget_native_type(type_id, HDF5Constants.H5T_DIR_ASCEND); } @@ -12360,9 +12810,10 @@ public class H5 implements java.io.Serializable { * @return the native datatype identifier for the specified dataset datatype. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tget_native_type(long type_id, int direction) throws HDF5LibraryException { + public static long H5Tget_native_type(long type_id, int direction) throws HDF5LibraryException + { long id = _H5Tget_native_type(type_id, direction); if (id > 0) { log.trace("OPEN_IDS: H5Tget_native_type add {}", id); @@ -12372,7 +12823,8 @@ public class H5 implements java.io.Serializable { return id; } - private synchronized static native long _H5Tget_native_type(long tid, int direction) throws HDF5LibraryException; + private synchronized static native long _H5Tget_native_type(long tid, int direction) + throws HDF5LibraryException; /** * H5Tget_nmembers retrieves the number of fields a compound datatype has. @@ -12383,7 +12835,7 @@ public class H5 implements java.io.Serializable { * @return number of members datatype has if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_nmembers(long type_id) throws HDF5LibraryException; @@ -12396,7 +12848,7 @@ public class H5 implements java.io.Serializable { * @return a valid normalization type if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_norm(long type_id) throws HDF5LibraryException; @@ -12411,7 +12863,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_norm(long type_id, int norm) throws HDF5LibraryException; @@ -12424,7 +12876,7 @@ public class H5 implements java.io.Serializable { * @return a positive offset value if successful; otherwise 0. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_offset(long type_id) throws HDF5LibraryException; @@ -12439,10 +12891,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Tset_offset(long type_id, int offset) throws HDF5LibraryException { - H5Tset_offset(type_id, (long) offset); + public static int H5Tset_offset(long type_id, int offset) throws HDF5LibraryException + { + H5Tset_offset(type_id, (long)offset); return 0; } @@ -12455,9 +12908,10 @@ public class H5 implements java.io.Serializable { * IN: Offset of first significant bit. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Tset_offset(long type_id, long offset) throws HDF5LibraryException; + public synchronized static native void H5Tset_offset(long type_id, long offset) + throws HDF5LibraryException; /** * H5Tget_order returns the byte order of an atomic datatype. @@ -12468,7 +12922,7 @@ public class H5 implements java.io.Serializable { * @return a byte order constant if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_order(long type_id) throws HDF5LibraryException; @@ -12483,7 +12937,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_order(long type_id, int order) throws HDF5LibraryException; @@ -12495,7 +12949,7 @@ public class H5 implements java.io.Serializable { * @param pad * OUT: locations to return least-significant and most-significant bit padding type. * - * <pre> + * <pre> * pad[0] = lsb // least-significant bit padding type * pad[1] = msb // most-significant bit padding type * </pre> @@ -12503,12 +12957,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - pad is null. + * pad is null. **/ - public synchronized static native int H5Tget_pad(long type_id, int[] pad) throws HDF5LibraryException, - NullPointerException; + public synchronized static native int H5Tget_pad(long type_id, int[] pad) + throws HDF5LibraryException, NullPointerException; /** * H5Tset_pad sets the least and most-significant bits padding types. @@ -12523,9 +12977,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native int H5Tset_pad(long type_id, int lsb, int msb) throws HDF5LibraryException; + public synchronized static native int H5Tset_pad(long type_id, int lsb, int msb) + throws HDF5LibraryException; /** * H5Tget_precision returns the precision of an atomic datatype. @@ -12536,7 +12991,7 @@ public class H5 implements java.io.Serializable { * @return the number of significant bits if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_precision(long type_id) throws HDF5LibraryException; @@ -12551,10 +13006,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static int H5Tset_precision(long type_id, int precision) throws HDF5LibraryException { - H5Tset_precision(type_id, (long) precision); + public static int H5Tset_precision(long type_id, int precision) throws HDF5LibraryException + { + H5Tset_precision(type_id, (long)precision); return 0; } @@ -12567,7 +13023,7 @@ public class H5 implements java.io.Serializable { * @return the number of significant bits if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_precision_long(long type_id) throws HDF5LibraryException; @@ -12580,9 +13036,10 @@ public class H5 implements java.io.Serializable { * IN: Number of bits of precision for datatype. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5Tset_precision(long type_id, long precision) throws HDF5LibraryException; + public synchronized static native void H5Tset_precision(long type_id, long precision) + throws HDF5LibraryException; /** * H5Tget_sign retrieves the sign type for an integer type. @@ -12593,7 +13050,7 @@ public class H5 implements java.io.Serializable { * @return a valid sign type if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_sign(long type_id) throws HDF5LibraryException; @@ -12608,7 +13065,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_sign(long type_id, int sign) throws HDF5LibraryException; @@ -12621,13 +13078,13 @@ public class H5 implements java.io.Serializable { * @return the size of the datatype in bytes * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_size(long type_id) throws HDF5LibraryException; /** - * H5Tset_size sets the total size in bytes, size, for an atomic datatype (this operation is not permitted on - * compound datatypes). + * H5Tset_size sets the total size in bytes, size, for an atomic datatype (this operation is not permitted + * on compound datatypes). * * @param type_id * IN: Identifier of datatype to change size. @@ -12637,7 +13094,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_size(long type_id, long size) throws HDF5LibraryException; @@ -12650,7 +13107,7 @@ public class H5 implements java.io.Serializable { * @return a valid string padding type if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_strpad(long type_id) throws HDF5LibraryException; @@ -12665,7 +13122,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_strpad(long type_id, int strpad) throws HDF5LibraryException; @@ -12678,9 +13135,10 @@ public class H5 implements java.io.Serializable { * @return the parent type * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tget_super(long type) throws HDF5LibraryException { + public static long H5Tget_super(long type) throws HDF5LibraryException + { long id = _H5Tget_super(type); if (id > 0) { log.trace("OPEN_IDS: H5Tget_super add {}", id); @@ -12701,7 +13159,7 @@ public class H5 implements java.io.Serializable { * @return the tag * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native String H5Tget_tag(long type) throws HDF5LibraryException; @@ -12716,7 +13174,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_tag(long type, String tag) throws HDF5LibraryException; @@ -12735,12 +13193,12 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ public synchronized static native int H5Tinsert(long type_id, String name, long offset, long field_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** * H5Tis_variable_str determines whether the datatype identified in type_id is a variable-length string. @@ -12751,12 +13209,13 @@ public class H5 implements java.io.Serializable { * @return true if type_id is a variable-length string. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tis_variable_str(long type_id) throws HDF5LibraryException; /** - * H5Tlock locks the datatype specified by the type_id identifier, making it read-only and non-destrucible. + * H5Tlock locks the datatype specified by the type_id identifier, making it read-only and + * non-destrucible. * * @param type_id * IN: Identifier of datatype to lock. @@ -12764,12 +13223,13 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tlock(long type_id) throws HDF5LibraryException; /** - * H5Topen opens a named datatype at the location specified by loc_id and return an identifier for the datatype. + * H5Topen opens a named datatype at the location specified by loc_id and return an identifier for the + * datatype. * * @param loc_id * IN: A file, group, or datatype identifier. @@ -12781,12 +13241,13 @@ public class H5 implements java.io.Serializable { * @return a named datatype identifier if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - name is null. + * name is null. **/ - public static long H5Topen(long loc_id, String name, long tapl_id) throws HDF5LibraryException, - NullPointerException { + public static long H5Topen(long loc_id, String name, long tapl_id) + throws HDF5LibraryException, NullPointerException + { long id = _H5Topen2(loc_id, name, tapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Topen add {}", id); @@ -12797,14 +13258,12 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Topen2(long loc_id, String name, long tapl_id) - throws HDF5LibraryException, NullPointerException; + throws HDF5LibraryException, NullPointerException; /** - * H5Tpack recursively removes padding from within a compound datatype to make it more efficient (space-wise) to - * store that data. - * <P> - * <b>WARNING:</b> This call only affects the C-data, even if it succeeds, there may be no visible effect on Java - * objects. + * H5Tpack recursively removes padding from within a compound datatype to make it more efficient + * (space-wise) to store that data. <P> <b>WARNING:</b> This call only affects the C-data, even if it + * succeeds, there may be no visible effect on Java objects. * * @param type_id * IN: Identifier of datatype to modify. @@ -12812,7 +13271,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Tpack(long type_id) throws HDF5LibraryException; @@ -12825,9 +13284,10 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public static long H5Tvlen_create(long base_id) throws HDF5LibraryException { + public static long H5Tvlen_create(long base_id) throws HDF5LibraryException + { long id = _H5Tvlen_create(base_id); if (id > 0) { log.trace("OPEN_IDS: H5Tvlen_create add {}", id); @@ -12847,7 +13307,7 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the committed datatype to be flushed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Tflush(long dtype_id) throws HDF5LibraryException; @@ -12861,7 +13321,7 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the committed datatype to be refreshed. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5Trefresh(long dtype_id) throws HDF5LibraryException; @@ -12873,9 +13333,8 @@ public class H5 implements java.io.Serializable { // H5T_conv_t func) // throws HDF5LibraryException, NullPointerException; - // public synchronized static native int H5Tunregister(H5T_pers_t pers, String name, int src_id, int dst_id, - // H5T_conv_t func) - // throws HDF5LibraryException, NullPointerException; + // public synchronized static native int H5Tunregister(H5T_pers_t pers, String name, int src_id, int + // dst_id, H5T_conv_t func) throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // @@ -12892,7 +13351,7 @@ public class H5 implements java.io.Serializable { * @return a non-negative(TRUE/FALSE) value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException; @@ -12905,7 +13364,7 @@ public class H5 implements java.io.Serializable { * @return the filter information flags * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Zget_filter_info(int filter) throws HDF5LibraryException; @@ -12918,13 +13377,11 @@ public class H5 implements java.io.Serializable { * @return a non-negative value if successful * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException; // /////// unimplemented //////// // herr_t H5Zregister(const void *cls); - } - |