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| author | Dana Robinson <43805+derobins@users.noreply.github.com> | 2022-04-21 05:24:35 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-04-21 05:24:35 (GMT) |
| commit | ec14985c8555bda02021568ea20295384a2cef7e (patch) | |
| tree | 491c1f08a68d92e400d939d96fefdc7bfef57ddc /java/src/hdf | |
| parent | bc62da7eb911727497475d1cc90991230f33fa3d (diff) | |
| download | hdf5-ec14985c8555bda02021568ea20295384a2cef7e.zip hdf5-ec14985c8555bda02021568ea20295384a2cef7e.tar.gz hdf5-ec14985c8555bda02021568ea20295384a2cef7e.tar.bz2 | |
VFD SWMR: Merges from develop (#1670)
* Cleans up SWMR test scripts (both legacy and VFD)
* Brings over format source changes for Java
* Normalization of HL, Fortran, C++, Java w/ develop
* Removes the STATIC flavor of FUNC_ENTER macros (#1622)
* Removes the STATIC flavor of FUNC_ENTER macros
* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)
* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.
This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.
* Committing clang-format changes
* Per discussion, use HD and add comments.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes unused definitions from module headers (#1624)
* Misc stuff from develop (includes some parallel things)
* Brings over SWMR test quiet mode changes from develop
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Diffstat (limited to 'java/src/hdf')
57 files changed, 3835 insertions, 3400 deletions
diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt index a26e117..0b716f7 100644 --- a/java/src/hdf/hdf5lib/CMakeLists.txt +++ b/java/src/hdf/hdf5lib/CMakeLists.txt @@ -132,6 +132,9 @@ SET_GLOBAL_VARIABLE (HDF5_JAVA_JARS ${${HDF5_JAVA_HDF5_LIB_TARGET}_JAR_FILE}) add_dependencies (${HDF5_JAVA_HDF5_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_TARGET}) set_target_properties (${HDF5_JAVA_HDF5_LIB_TARGET} PROPERTIES FOLDER libraries/java) +if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_JAVA_SRC_FORMAT ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVA_HDF_HDF5_SOURCES}) +endif () create_javadoc(hdf5_java_doc FILES ${HDF5_JAVADOC_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_SOURCES} diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 3180ede..9fac20c 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -11,47 +11,47 @@ * 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; import hdf.hdf5lib.callbacks.H5D_iterate_t; import hdf.hdf5lib.callbacks.H5E_walk_cb; import hdf.hdf5lib.callbacks.H5E_walk_t; -import hdf.hdf5lib.callbacks.H5L_iterate_t; import hdf.hdf5lib.callbacks.H5L_iterate_opdata_t; -import hdf.hdf5lib.callbacks.H5O_iterate_t; +import hdf.hdf5lib.callbacks.H5L_iterate_t; import hdf.hdf5lib.callbacks.H5O_iterate_opdata_t; +import hdf.hdf5lib.callbacks.H5O_iterate_t; import hdf.hdf5lib.callbacks.H5P_cls_close_func_cb; import hdf.hdf5lib.callbacks.H5P_cls_close_func_t; 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; @@ -61,8 +61,8 @@ import hdf.hdf5lib.structs.H5O_token_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> @@ -71,8 +71,8 @@ import hdf.hdf5lib.structs.H5O_token_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> @@ -112,17 +112,19 @@ import hdf.hdf5lib.structs.H5O_token_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: * @@ -143,53 +145,57 @@ import hdf.hdf5lib.structs.H5O_token_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; @@ -200,20 +206,22 @@ import hdf.hdf5lib.structs.H5O_token_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 1.13.2 <BR> @@ -222,7 +230,8 @@ import hdf.hdf5lib.structs.H5O_token_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 { /** * @@ -239,38 +248,36 @@ 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, 13, 2 }; + public final static int LIB_VERSION[] = {1, 13, 2}; /** - * 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 { @@ -311,7 +318,7 @@ public class H5 implements java.io.Serializable { } else { isLibraryLoaded = false; - throw (new UnsatisfiedLinkError("Invalid HDF5 library, " + filename)); + throw(new UnsatisfiedLinkError("Invalid HDF5 library, " + filename)); } } } @@ -320,7 +327,7 @@ 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; } @@ -369,18 +376,14 @@ 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. @@ -391,20 +394,21 @@ 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; @@ -414,35 +418,35 @@ 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(); @@ -452,13 +456,13 @@ 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. @@ -471,7 +475,7 @@ 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; @@ -502,10 +506,12 @@ 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. @@ -523,10 +529,11 @@ 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. @@ -544,10 +551,11 @@ 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. @@ -577,9 +585,10 @@ 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");; @@ -602,12 +611,13 @@ 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 @@ -625,12 +635,13 @@ 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); @@ -643,15 +654,16 @@ 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 @@ -673,13 +685,16 @@ 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); @@ -689,8 +704,9 @@ 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. @@ -703,12 +719,12 @@ 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. @@ -727,16 +743,17 @@ 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 @@ -750,12 +767,13 @@ 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. @@ -768,16 +786,16 @@ 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 . @@ -791,12 +809,13 @@ 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. @@ -807,7 +826,7 @@ 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; @@ -830,12 +849,14 @@ 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. @@ -852,12 +873,13 @@ 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. @@ -868,14 +890,13 @@ 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 @@ -893,12 +914,13 @@ 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. @@ -909,7 +931,7 @@ 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 { @@ -925,7 +947,8 @@ 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. @@ -933,7 +956,7 @@ 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; @@ -946,7 +969,7 @@ 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 { @@ -962,8 +985,8 @@ 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 @@ -975,12 +998,12 @@ 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) { @@ -992,11 +1015,11 @@ 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 @@ -1016,12 +1039,13 @@ 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) { @@ -1032,8 +1056,9 @@ 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 @@ -1052,12 +1077,12 @@ 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) { @@ -1069,7 +1094,8 @@ 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 @@ -1087,12 +1113,13 @@ 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 @@ -1108,11 +1135,12 @@ 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); } @@ -1131,11 +1159,12 @@ 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); } @@ -1156,66 +1185,67 @@ 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 @@ -1227,7 +1257,7 @@ public class H5 implements java.io.Serializable { } // clean up these: assign 'null' as hint to gc() - buf = null; + buf = null; theArray = null; } @@ -1250,12 +1280,13 @@ 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 @@ -1271,12 +1302,12 @@ 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); } @@ -1297,12 +1328,13 @@ 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 @@ -1318,12 +1350,12 @@ 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); } @@ -1344,12 +1376,13 @@ 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 @@ -1365,12 +1398,12 @@ 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); } @@ -1391,12 +1424,13 @@ 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 @@ -1412,12 +1446,12 @@ 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); } @@ -1436,12 +1470,12 @@ 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 @@ -1459,12 +1493,13 @@ 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 @@ -1480,12 +1515,12 @@ 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); } @@ -1504,12 +1539,12 @@ 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 @@ -1525,12 +1560,12 @@ 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 @@ -1546,12 +1581,12 @@ 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 @@ -1567,16 +1602,16 @@ 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 @@ -1588,16 +1623,16 @@ 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 @@ -1613,12 +1648,13 @@ 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 @@ -1636,12 +1672,13 @@ 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 @@ -1657,12 +1694,12 @@ 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); } @@ -1681,12 +1718,12 @@ 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); } @@ -1707,55 +1744,56 @@ 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; } @@ -1778,12 +1816,13 @@ 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 @@ -1799,12 +1838,12 @@ 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); } @@ -1825,12 +1864,13 @@ 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 @@ -1846,12 +1886,12 @@ 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); } @@ -1872,12 +1912,13 @@ 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 @@ -1893,12 +1934,12 @@ 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); } @@ -1919,12 +1960,13 @@ 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 @@ -1940,12 +1982,12 @@ 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); } @@ -1966,12 +2008,13 @@ 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 @@ -1987,12 +2030,12 @@ 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); } @@ -2011,12 +2054,12 @@ 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 @@ -2032,12 +2075,12 @@ 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 @@ -2055,13 +2098,13 @@ 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. @@ -2072,10 +2115,9 @@ 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) { @@ -2094,20 +2136,22 @@ 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 @@ -2115,16 +2159,17 @@ 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 @@ -2132,7 +2177,8 @@ 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 @@ -2140,14 +2186,15 @@ 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 @@ -2157,16 +2204,18 @@ 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; // //////////////////////////////////////////////////////////// // // @@ -2217,7 +2266,7 @@ 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; @@ -2230,9 +2279,10 @@ 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"); @@ -2265,12 +2315,13 @@ 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); @@ -2283,11 +2334,12 @@ 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. @@ -2306,10 +2358,11 @@ 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); @@ -2319,11 +2372,13 @@ 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. @@ -2337,12 +2392,13 @@ 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. @@ -2353,21 +2409,23 @@ 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); @@ -2388,7 +2446,7 @@ 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; @@ -2401,9 +2459,10 @@ 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); @@ -2424,7 +2483,7 @@ 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; @@ -2437,10 +2496,10 @@ 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. @@ -2451,9 +2510,10 @@ 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); @@ -2466,8 +2526,8 @@ 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. @@ -2480,19 +2540,21 @@ 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 @@ -2504,11 +2566,12 @@ 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) { @@ -2520,16 +2583,17 @@ 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. @@ -2549,17 +2613,18 @@ 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. @@ -2577,19 +2642,20 @@ 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. @@ -2607,19 +2673,20 @@ 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. @@ -2639,87 +2706,88 @@ 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; } @@ -2727,8 +2795,8 @@ 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. @@ -2748,17 +2816,18 @@ 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. @@ -2776,19 +2845,20 @@ 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. @@ -2808,17 +2878,18 @@ 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. @@ -2836,19 +2907,20 @@ 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. @@ -2868,17 +2940,18 @@ 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. @@ -2896,19 +2969,20 @@ 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. @@ -2928,17 +3002,18 @@ 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. @@ -2956,19 +3031,20 @@ 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. @@ -2986,16 +3062,18 @@ 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. @@ -3015,17 +3093,18 @@ 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. @@ -3043,19 +3122,20 @@ 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. @@ -3073,16 +3153,17 @@ 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. @@ -3100,16 +3181,17 @@ 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. @@ -3127,15 +3209,18 @@ 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. @@ -3143,17 +3228,17 @@ 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. @@ -3165,12 +3250,12 @@ 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. @@ -3187,19 +3272,20 @@ 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 - * - buf is null. + * buf is null. * * @deprecated As of HDF5 1.12.0 in favor of H5Treclaim **/ @Deprecated - 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. @@ -3219,17 +3305,18 @@ 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. @@ -3247,19 +3334,20 @@ 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. @@ -3277,19 +3365,20 @@ 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. @@ -3309,67 +3398,68 @@ 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; } @@ -3377,8 +3467,8 @@ 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. @@ -3398,17 +3488,18 @@ 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. @@ -3426,19 +3517,21 @@ 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. @@ -3458,17 +3551,18 @@ 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. @@ -3486,19 +3580,20 @@ 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. @@ -3518,17 +3613,18 @@ 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. @@ -3546,19 +3642,20 @@ 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. @@ -3578,17 +3675,18 @@ 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. @@ -3606,19 +3704,20 @@ 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. @@ -3638,17 +3737,18 @@ 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. @@ -3666,19 +3766,20 @@ 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. @@ -3696,16 +3797,18 @@ 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. @@ -3723,16 +3826,17 @@ 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 * @@ -3752,48 +3856,52 @@ 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); // //////////////////////////////////////////////////////////// // // @@ -3802,58 +3910,57 @@ 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; @@ -3864,7 +3971,7 @@ 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; @@ -3875,7 +3982,7 @@ 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; @@ -3892,12 +3999,12 @@ 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. @@ -3905,7 +4012,7 @@ 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; @@ -3918,30 +4025,31 @@ 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; @@ -3956,13 +4064,14 @@ 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. @@ -3970,26 +4079,29 @@ 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. @@ -3997,11 +4109,10 @@ 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. * @@ -4023,14 +4134,14 @@ 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. @@ -4053,16 +4164,17 @@ 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. @@ -4074,12 +4186,12 @@ 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. @@ -4088,7 +4200,7 @@ 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; @@ -4106,13 +4218,14 @@ 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 @@ -4128,12 +4241,13 @@ 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 @@ -4176,9 +4290,10 @@ 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");; @@ -4203,12 +4318,13 @@ 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); @@ -4219,7 +4335,7 @@ 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. @@ -4227,11 +4343,13 @@ 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); @@ -4256,7 +4374,8 @@ 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> @@ -4264,22 +4383,23 @@ 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); @@ -4290,34 +4410,30 @@ 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; @@ -4330,9 +4446,10 @@ 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); @@ -4345,8 +4462,8 @@ 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 @@ -4354,9 +4471,10 @@ 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); @@ -4379,7 +4497,7 @@ 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; @@ -4392,7 +4510,7 @@ 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; @@ -4405,7 +4523,7 @@ 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; @@ -4418,13 +4536,13 @@ public class H5 implements java.io.Serializable { * @return the unique file number for the file. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5Fget_fileno(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. @@ -4432,7 +4550,7 @@ 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; @@ -4452,12 +4570,12 @@ 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. @@ -4468,7 +4586,7 @@ 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; @@ -4492,12 +4610,14 @@ 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 @@ -4511,12 +4631,13 @@ 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. @@ -4527,14 +4648,15 @@ 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. * * @deprecated As of HDF5 1.10.5 in favor of H5Fis_accessible. **/ @Deprecated - public synchronized static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException; + public synchronized static native boolean H5Fis_hdf5(String name) + throws HDF5LibraryException, NullPointerException; /** * H5Fis_accessible determines if the file can be opened with the given fapl. @@ -4547,15 +4669,16 @@ public class H5 implements java.io.Serializable { * @return true if file is accessible, 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_accessible(String name, long file_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native boolean H5Fis_accessible(String name, long file_id) + 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. @@ -4569,12 +4692,12 @@ 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. @@ -4587,24 +4710,25 @@ 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 @@ -4614,7 +4738,8 @@ 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; @@ -4626,19 +4751,20 @@ 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; @@ -4649,18 +4775,19 @@ 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; @@ -4676,12 +4803,13 @@ 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. @@ -4692,11 +4820,10 @@ 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. @@ -4704,14 +4831,13 @@ 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. @@ -4724,17 +4850,18 @@ 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], @@ -4814,11 +4941,10 @@ 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*/); @@ -4845,9 +4971,10 @@ 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");; @@ -4871,18 +4998,19 @@ 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); @@ -4893,7 +5021,8 @@ 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. @@ -4903,15 +5032,16 @@ 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); @@ -4922,11 +5052,11 @@ 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. @@ -4934,13 +5064,13 @@ 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. @@ -4948,12 +5078,13 @@ 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. @@ -4971,16 +5102,18 @@ 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. @@ -4992,15 +5125,16 @@ 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 @@ -5016,21 +5150,25 @@ 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, - H5O_token_t[] tokens) throws HDF5LibraryException, NullPointerException { + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, + int[] objTypes, H5O_token_t[] tokens) + 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, tokens, HDF5Constants.H5_INDEX_NAME); + return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, tokens, + 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 @@ -5050,17 +5188,21 @@ 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, H5O_token_t[] tokens, 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, H5O_token_t[] tokens, + int indx_type) + throws HDF5LibraryException, NullPointerException + { return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, null, tokens, 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 @@ -5082,17 +5224,21 @@ 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, H5O_token_t[] tokens, 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, + H5O_token_t[] tokens, int indx_type) + throws HDF5LibraryException, NullPointerException + { return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, tokens, 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 @@ -5116,13 +5262,15 @@ 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, H5O_token_t[] tokens, 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, + H5O_token_t[] tokens, int indx_type, int indx_order) + throws HDF5LibraryException, NullPointerException + { if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_full(): name array is null"); } @@ -5152,21 +5300,22 @@ 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, tokens, objNames.length, indx_type, - indx_order); + int status = H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, tokens, + objNames.length, indx_type, indx_order); for (int indx = 0; indx < 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, H5O_token_t[] tokens, 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, + H5O_token_t[] tokens, 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. @@ -5182,19 +5331,21 @@ 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; } @@ -5204,8 +5355,8 @@ 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 @@ -5223,12 +5374,14 @@ 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, - H5O_token_t[] objToken, long objMax) throws HDF5LibraryException, NullPointerException { + public synchronized static int H5Gget_obj_info_max(long loc_id, String[] objNames, int[] objTypes, + int[] lnkTypes, H5O_token_t[] objToken, long objMax) + throws HDF5LibraryException, NullPointerException + { if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_max(): name array is null"); } @@ -5256,12 +5409,15 @@ public class H5 implements java.io.Serializable { return H5Gget_obj_info_max(loc_id, objNames, objTypes, lnkTypes, objToken, objMax, objNames.length); } - private synchronized static native int H5Gget_obj_info_max(long loc_id, String[] oname, int[] otype, int[] ltype, - H5O_token_t[] tokens, 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, H5O_token_t[] tokens, 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. @@ -5271,18 +5427,19 @@ 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); @@ -5304,12 +5461,13 @@ 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); @@ -5320,7 +5478,7 @@ 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 @@ -5330,7 +5488,7 @@ 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; @@ -5344,7 +5502,7 @@ 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; @@ -5387,7 +5545,7 @@ 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; @@ -5405,11 +5563,11 @@ 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. * @@ -5419,10 +5577,9 @@ 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. @@ -5433,13 +5590,14 @@ 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. @@ -5447,9 +5605,10 @@ 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. @@ -5460,9 +5619,10 @@ 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. @@ -5473,13 +5633,13 @@ 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 @@ -5487,13 +5647,13 @@ 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 @@ -5502,13 +5662,13 @@ 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 @@ -5516,7 +5676,7 @@ 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; @@ -5529,7 +5689,7 @@ 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; @@ -5542,7 +5702,7 @@ 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; @@ -5555,11 +5715,10 @@ 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. * @@ -5569,9 +5728,10 @@ 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 @@ -5581,7 +5741,7 @@ 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; @@ -5604,7 +5764,6 @@ public class H5 implements java.io.Serializable { // typedef herr_t (*H5I_iterate_func_t)(hid_t id, void *udata); // herr_t H5Iiterate(H5I_type_t type, H5I_iterate_func_t op, void *op_data); - // ////////////////////////////////////////////////////////////////// // H5L: Link Interface Functions // // ////////////////////////////////////////////////////////////////// @@ -5626,16 +5785,17 @@ 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. @@ -5651,12 +5811,14 @@ 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. @@ -5675,12 +5837,13 @@ 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. @@ -5697,12 +5860,13 @@ 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. @@ -5715,15 +5879,16 @@ 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 @@ -5739,12 +5904,13 @@ 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. @@ -5759,12 +5925,12 @@ 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. @@ -5779,16 +5945,16 @@ 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 @@ -5806,16 +5972,18 @@ 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 @@ -5833,12 +6001,13 @@ 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 @@ -5856,12 +6025,13 @@ 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. @@ -5886,12 +6056,14 @@ 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. @@ -5909,14 +6081,15 @@ 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_t op, - H5L_iterate_opdata_t op_data) throws HDF5LibraryException; + public synchronized static native int H5Literate(long grp_id, int idx_type, int order, long idx, + H5L_iterate_t op, H5L_iterate_opdata_t op_data) + throws HDF5LibraryException; /** * H5Literate_by_name iterates through links in a group. @@ -5938,17 +6111,18 @@ 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_t op, H5L_iterate_opdata_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_t op, + H5L_iterate_opdata_t op_data, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lmove renames a link within an HDF5 file. @@ -5967,12 +6141,13 @@ 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. @@ -5988,14 +6163,14 @@ 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_t op, - H5L_iterate_opdata_t op_data) throws HDF5LibraryException; + H5L_iterate_opdata_t op_data) throws HDF5LibraryException; /** * H5Lvisit_by_name recursively visits all links starting from a specified group. @@ -6015,17 +6190,18 @@ 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_t op, H5L_iterate_opdata_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_t op, + H5L_iterate_opdata_t op_data, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Lis_registered tests whether a user-defined link class is currently registered, @@ -6035,21 +6211,23 @@ 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; @@ -6093,9 +6271,10 @@ 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");; @@ -6108,8 +6287,8 @@ 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 @@ -6125,12 +6304,13 @@ 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. @@ -6141,9 +6321,10 @@ 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. @@ -6154,12 +6335,13 @@ 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. @@ -6174,12 +6356,12 @@ 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. @@ -6194,15 +6376,16 @@ 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. @@ -6213,12 +6396,12 @@ 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); } @@ -6233,38 +6416,41 @@ 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_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 @@ -6273,18 +6459,19 @@ 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; /** * H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position. @@ -6300,19 +6487,22 @@ 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); } /** @@ -6331,22 +6521,25 @@ 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_native_info retrieves the native HDF5-specific metadata for an HDF5 object specified by an identifier. - * Native HDF5-specific metadata includes things like object header information and object storage layout information. + * H5Oget_native_info retrieves the native HDF5-specific metadata for an HDF5 object specified by an + * identifier. Native HDF5-specific metadata includes things like object header information and object + * storage layout information. * * @param loc_id * IN: Identifier for target object @@ -6354,18 +6547,20 @@ 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_native_info_t H5Oget_native_info(long loc_id) throws HDF5LibraryException, - NullPointerException { + public static H5O_native_info_t H5Oget_native_info(long loc_id) + throws HDF5LibraryException, NullPointerException + { return H5Oget_native_info(loc_id, HDF5Constants.H5O_NATIVE_INFO_ALL); } /** - * H5Oget_native_info retrieves the native HDF5-specific metadata for an HDF5 object specified by an identifier. - * Native HDF5-specific metadata includes things like object header information and object storage layout information. + * H5Oget_native_info retrieves the native HDF5-specific metadata for an HDF5 object specified by an + * identifier. Native HDF5-specific metadata includes things like object header information and object + * storage layout information. * * @param loc_id * IN: Identifier for target object @@ -6375,42 +6570,43 @@ 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_native_info_t H5Oget_native_info(long loc_id, int fields) throws HDF5LibraryException, - NullPointerException; + public synchronized static native H5O_native_info_t H5Oget_native_info(long loc_id, int fields) + throws HDF5LibraryException, NullPointerException; /** - * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object - * by location and relative name. Native HDF5-specific metadata includes things like object header information and - * object storage layout information. + * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying + * the object by location and relative name. Native HDF5-specific metadata includes things like object + * header information and object storage layout information. * * @param loc_id * IN: File or group identifier 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_native_info_t H5Oget_native_info_by_name(long loc_id, String name, long lapl_id) - throws HDF5LibraryException, NullPointerException { + throws HDF5LibraryException, NullPointerException + { return H5Oget_native_info_by_name(loc_id, name, HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id); } /** - * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object - * by location and relative name. Native HDF5-specific metadata includes things like object header information and - * object storage layout information. + * H5Oget_native_info_by_name retrieves the native HDF5-specific metadata for an HDF5 object, identifying + * the object by location and relative name. Native HDF5-specific metadata includes things like object + * header information and object storage layout information. * * @param loc_id * IN: File or group identifier specifying location of group in which object is located @@ -6419,23 +6615,24 @@ 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_native_info_t H5Oget_native_info_by_name(long loc_id, String name, int fields, long lapl_id) - throws HDF5LibraryException, NullPointerException; + public synchronized static native H5O_native_info_t H5Oget_native_info_by_name(long loc_id, String name, + int fields, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** - * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object - * by an index position. Native HDF5-specific metadata includes things like object header information and - * object storage layout information. + * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying + * the object by an index position. Native HDF5-specific metadata includes things like object header + * information and object storage layout information. * * @param loc_id * IN: File or group identifier @@ -6448,25 +6645,28 @@ 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_native_info_t H5Oget_native_info_by_idx(long loc_id, String group_name, int idx_type, - int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException { - return H5Oget_native_info_by_idx(loc_id, group_name, idx_type, order, n, HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id); + int order, long n, long lapl_id) + throws HDF5LibraryException, NullPointerException + { + return H5Oget_native_info_by_idx(loc_id, group_name, idx_type, order, n, + HDF5Constants.H5O_NATIVE_INFO_ALL, lapl_id); } /** - * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying the object - * by an index position. Native HDF5-specific metadata includes things like object header information and - * object storage layout information. + * H5Oget_native_info_by_idx retrieves the native HDF5-specific metadata for an HDF5 object, identifying + * the object by an index position. Native HDF5-specific metadata includes things like object header + * information and object storage layout information. * * @param loc_id * IN: File or group identifier @@ -6481,18 +6681,19 @@ 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_native_info_t H5Oget_native_info_by_idx(long loc_id, String group_name, int idx_type, - int order, long n, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static native H5O_native_info_t H5Oget_native_info_by_idx( + long loc_id, String group_name, int idx_type, int order, long n, int fields, long lapl_id) + throws HDF5LibraryException, NullPointerException; /** * H5Olink creates a new hard link to an object in an HDF5 file. @@ -6509,12 +6710,13 @@ 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. @@ -6529,11 +6731,13 @@ 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); @@ -6544,7 +6748,7 @@ 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. @@ -6558,18 +6762,20 @@ 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_t op, H5O_iterate_opdata_t op_data) - throws HDF5LibraryException, NullPointerException { + public static int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_t op, + H5O_iterate_opdata_t op_data) throws HDF5LibraryException, NullPointerException + { return H5Ovisit(obj_id, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL); } @@ -6585,20 +6791,22 @@ 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_t op, - H5O_iterate_opdata_t op_data, int fields) throws HDF5LibraryException, NullPointerException; + H5O_iterate_opdata_t op_data, int fields) + throws HDF5LibraryException, NullPointerException; /** * H5Ovisit_by_name recursively visits all objects starting from a specified object. @@ -6614,21 +6822,25 @@ 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_t op, H5O_iterate_opdata_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_t op, H5O_iterate_opdata_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); } /** @@ -6645,23 +6857,25 @@ 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_t op, H5O_iterate_opdata_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_t op, + H5O_iterate_opdata_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. @@ -6677,41 +6891,50 @@ 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_token opens a group, dataset, or named datatype using its object token within an HDF5 file. * - * @param loc_id IN: File or group identifier - * @param token IN: Object's token in the file + * @param loc_id + * IN: File or group identifier + * @param token + * IN: Object's token 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_token(long loc_id, H5O_token_t token) throws HDF5LibraryException { + public static long H5Oopen_by_token(long loc_id, H5O_token_t token) throws HDF5LibraryException + { long id = _H5Oopen_by_token(loc_id, token); if (id > 0) { @@ -6724,25 +6947,34 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Oopen_by_token(long loc_id, H5O_token_t token) - 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); @@ -6752,51 +6984,54 @@ 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 + * ncluding 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. * @@ -6804,10 +7039,10 @@ 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); // /////// unimplemented //////// // herr_t H5Otoken_cmp(hid_t loc_id, const H5O_token_t *token1, const H5O_token_t *token2, @@ -6831,7 +7066,7 @@ 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; @@ -6844,9 +7079,10 @@ 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); @@ -6868,7 +7104,7 @@ 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; @@ -6884,9 +7120,10 @@ 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 @@ -6895,10 +7132,11 @@ 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; @@ -6912,7 +7150,7 @@ 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; @@ -6924,7 +7162,7 @@ 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; @@ -6936,7 +7174,7 @@ 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; @@ -6948,7 +7186,7 @@ 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; @@ -6963,7 +7201,7 @@ 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; @@ -6978,9 +7216,10 @@ 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; @@ -6996,7 +7235,7 @@ 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; @@ -7012,10 +7251,10 @@ 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 @@ -7027,7 +7266,7 @@ 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; @@ -7041,7 +7280,7 @@ 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; @@ -7053,9 +7292,10 @@ 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");; @@ -7075,9 +7315,10 @@ 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");; @@ -7098,9 +7339,10 @@ 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); @@ -7144,11 +7386,12 @@ 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()); @@ -7156,21 +7399,27 @@ 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. @@ -7187,10 +7436,13 @@ 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. @@ -7205,37 +7457,39 @@ 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 /////// @@ -7243,7 +7497,7 @@ 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. * @@ -7255,13 +7509,13 @@ 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 @@ -7277,14 +7531,16 @@ 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 @@ -7292,14 +7548,15 @@ 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 @@ -7309,15 +7566,15 @@ 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 @@ -7325,14 +7582,15 @@ 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 @@ -7341,11 +7599,11 @@ 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 @@ -7387,16 +7645,18 @@ 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. @@ -7412,14 +7672,14 @@ 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. @@ -7427,18 +7687,19 @@ 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 @@ -7455,44 +7716,49 @@ 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. @@ -7514,24 +7780,26 @@ 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. @@ -7553,15 +7821,15 @@ 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 @@ -7575,10 +7843,10 @@ 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; @@ -7592,9 +7860,10 @@ 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. @@ -7607,7 +7876,7 @@ 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; @@ -7621,10 +7890,10 @@ 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 /////// @@ -7639,12 +7908,12 @@ 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. @@ -7657,13 +7926,13 @@ 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. @@ -7677,14 +7946,14 @@ 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. @@ -7699,13 +7968,14 @@ 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. @@ -7720,14 +7990,14 @@ 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. @@ -7742,9 +8012,10 @@ 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. @@ -7757,15 +8028,16 @@ 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. @@ -7775,46 +8047,47 @@ 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. @@ -7834,15 +8107,16 @@ 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 @@ -7859,13 +8133,14 @@ 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. @@ -7876,20 +8151,21 @@ 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. @@ -7897,24 +8173,28 @@ 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 @@ -7924,7 +8204,8 @@ 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 @@ -7932,20 +8213,23 @@ 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 @@ -7957,16 +8241,18 @@ 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 @@ -7974,16 +8260,17 @@ 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 @@ -7991,54 +8278,55 @@ 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. @@ -8052,18 +8340,18 @@ 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. @@ -8075,21 +8363,21 @@ 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; @@ -8102,7 +8390,7 @@ 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; @@ -8118,14 +8406,15 @@ 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. @@ -8141,16 +8430,17 @@ 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. @@ -8166,14 +8456,15 @@ 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. @@ -8181,14 +8472,15 @@ 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. @@ -8196,14 +8488,14 @@ 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 @@ -8211,13 +8503,13 @@ 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 @@ -8227,10 +8519,10 @@ 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 @@ -8242,10 +8534,10 @@ 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. @@ -8258,10 +8550,10 @@ 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. @@ -8272,7 +8564,7 @@ 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; @@ -8286,14 +8578,15 @@ 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. @@ -8301,7 +8594,7 @@ 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; @@ -8323,12 +8616,14 @@ 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. @@ -8336,13 +8631,14 @@ 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. @@ -8352,14 +8648,14 @@ 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 @@ -8374,17 +8670,17 @@ 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 @@ -8397,13 +8693,13 @@ 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. @@ -8414,13 +8710,15 @@ 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 @@ -8428,11 +8726,11 @@ 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. @@ -8447,13 +8745,14 @@ 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. @@ -8463,19 +8762,21 @@ 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 @@ -8483,18 +8784,20 @@ 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 @@ -8502,15 +8805,15 @@ 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 @@ -8518,14 +8821,14 @@ 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 @@ -8533,11 +8836,11 @@ 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. @@ -8548,11 +8851,11 @@ 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. @@ -8563,11 +8866,11 @@ 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. @@ -8576,17 +8879,19 @@ 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; // ///// unimplemented ///// // herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info); @@ -8601,11 +8906,11 @@ 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; @@ -8620,7 +8925,7 @@ 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; @@ -8637,14 +8942,14 @@ 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. @@ -8659,14 +8964,14 @@ 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. @@ -8681,24 +8986,25 @@ 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; } @@ -8711,28 +9017,35 @@ 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. @@ -8740,15 +9053,17 @@ 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. @@ -8758,15 +9073,17 @@ 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. @@ -8776,15 +9093,17 @@ 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. @@ -8794,15 +9113,17 @@ 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. @@ -8812,41 +9133,44 @@ 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. @@ -8871,20 +9195,21 @@ 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. @@ -8894,20 +9219,20 @@ 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. @@ -8918,7 +9243,7 @@ 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; @@ -8935,11 +9260,11 @@ 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. @@ -8950,11 +9275,11 @@ 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. @@ -8965,7 +9290,7 @@ 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; @@ -8983,13 +9308,13 @@ 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. @@ -9004,10 +9329,10 @@ 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. @@ -9022,11 +9347,13 @@ 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) { @@ -9049,10 +9376,10 @@ 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. @@ -9067,15 +9394,17 @@ 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; } @@ -9095,10 +9424,10 @@ 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. @@ -9111,11 +9440,11 @@ 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. @@ -9128,11 +9457,11 @@ 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. @@ -9145,10 +9474,11 @@ 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. @@ -9161,10 +9491,11 @@ 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. @@ -9177,12 +9508,13 @@ 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 @@ -9190,13 +9522,14 @@ 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 @@ -9204,33 +9537,32 @@ 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. @@ -9242,16 +9574,17 @@ 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. @@ -9263,10 +9596,11 @@ 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, @@ -9278,9 +9612,10 @@ 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, @@ -9292,26 +9627,28 @@ 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 @@ -9325,9 +9662,11 @@ 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. @@ -9338,11 +9677,10 @@ 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. @@ -9353,13 +9691,13 @@ 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. @@ -9370,11 +9708,10 @@ 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. @@ -9385,24 +9722,25 @@ 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 @@ -9411,18 +9749,19 @@ 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 @@ -9435,17 +9774,17 @@ 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. @@ -9457,12 +9796,12 @@ 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; @@ -9474,26 +9813,27 @@ 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. @@ -9501,12 +9841,12 @@ 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. @@ -9517,7 +9857,7 @@ 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; @@ -9532,7 +9872,7 @@ 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; @@ -9551,16 +9891,17 @@ 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 @@ -9574,10 +9915,10 @@ 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. @@ -9590,11 +9931,11 @@ 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 @@ -9604,7 +9945,7 @@ 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. * @@ -9616,17 +9957,17 @@ 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 @@ -9634,14 +9975,15 @@ 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 @@ -9651,11 +9993,12 @@ 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 /////// @@ -9668,10 +10011,11 @@ 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. @@ -9684,11 +10028,11 @@ 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. @@ -9696,7 +10040,8 @@ 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 @@ -9706,13 +10051,13 @@ 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. @@ -9727,13 +10072,14 @@ 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. @@ -9741,7 +10087,8 @@ 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 @@ -9751,13 +10098,13 @@ 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. @@ -9772,17 +10119,18 @@ 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 @@ -9790,14 +10138,15 @@ 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 @@ -9808,11 +10157,11 @@ 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 /////// @@ -9825,7 +10174,7 @@ 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; @@ -9839,18 +10188,18 @@ 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 @@ -9858,15 +10207,15 @@ 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 @@ -9876,13 +10225,13 @@ 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. @@ -9892,17 +10241,17 @@ 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. @@ -9915,17 +10264,17 @@ 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 @@ -9933,10 +10282,11 @@ 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); @@ -9949,7 +10299,8 @@ 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 @@ -9959,14 +10310,15 @@ 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 @@ -9974,13 +10326,14 @@ 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 @@ -9990,13 +10343,13 @@ 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 /////// @@ -10009,7 +10362,7 @@ 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; @@ -10023,11 +10376,11 @@ 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; + throws HDF5LibraryException; // /////// file drivers property list routines /////// @@ -10042,11 +10395,12 @@ 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. @@ -10061,11 +10415,12 @@ 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. @@ -10080,10 +10435,11 @@ 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. @@ -10100,11 +10456,11 @@ 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. @@ -10119,11 +10475,12 @@ 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. @@ -10138,11 +10495,11 @@ 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. @@ -10155,10 +10512,11 @@ 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. @@ -10169,10 +10527,11 @@ 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. @@ -10186,19 +10545,21 @@ 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. @@ -10212,25 +10573,27 @@ 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. @@ -10242,12 +10605,13 @@ 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. @@ -10258,10 +10622,11 @@ 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 @@ -10280,11 +10645,12 @@ 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. @@ -10295,10 +10661,11 @@ 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. @@ -10309,10 +10676,11 @@ 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. @@ -10325,10 +10693,11 @@ 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. @@ -10339,10 +10708,11 @@ 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 //////// @@ -10373,32 +10743,35 @@ 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 // @@ -10444,9 +10817,10 @@ 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.. @@ -10458,7 +10832,7 @@ 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; @@ -10469,7 +10843,7 @@ 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; @@ -10480,7 +10854,7 @@ 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; @@ -10493,9 +10867,10 @@ 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. @@ -10506,9 +10881,10 @@ 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. @@ -10517,7 +10893,7 @@ 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; @@ -10530,7 +10906,7 @@ 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; @@ -10540,7 +10916,7 @@ 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; @@ -10565,14 +10941,14 @@ 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 native byte[] H5Rcreate_object(long loc_id, String name, long access_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rcreate_region creates the reference, pointing to the region represented by @@ -10590,14 +10966,15 @@ 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 native byte[] H5Rcreate_region(long loc_id, String name, long space_id, long access_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + public synchronized static native byte[] H5Rcreate_region(long loc_id, String name, long space_id, + long access_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rcreate_attr creates the reference, pointing to the attribute named attr name @@ -10615,14 +10992,15 @@ 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 native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name, long access_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + public synchronized static native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name, + long access_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rdestroy destroys a reference and releases resources. @@ -10631,14 +11009,14 @@ public class H5 implements java.io.Serializable { * IN: Reference to an object, region or attribute attached to an object. * * @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 void H5Rdestroy(byte[] ref_ptr) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // Info // @@ -10651,14 +11029,14 @@ public class H5 implements java.io.Serializable { * @return a valid reference type if successful; otherwise returns H5R UNKNOWN. * * @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 H5Rget_type(byte[] ref_ptr) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Requal determines whether two references point to the same object, region or attribute. @@ -10671,14 +11049,14 @@ public class H5 implements java.io.Serializable { * @return true if equal, else false * * @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 boolean H5Requal(byte[] ref1_ptr, byte[] ref2_ptr) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rcopy creates a copy of an existing reference. @@ -10689,14 +11067,14 @@ public class H5 implements java.io.Serializable { * @return a valid copy of 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 native byte[] H5Rcopy(byte[] src_ref_ptr) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // Dereference // @@ -10720,14 +11098,15 @@ 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 - * - an input array is null. + * an input array is null. * @exception IllegalArgumentException - * - an input array is invalid. + * an input array is invalid. **/ public static long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { long id = _H5Ropen_object(ref_ptr, rapl_id, oapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Ropen_object add {}", id); @@ -10738,12 +11117,13 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Ropen region creates a copy of the dataspace of the dataset pointed to by a region reference, - * ref ptr, and defines a selection matching the selection pointed to by ref ptr within the dataspace copy. - * Use H5Sclose to release the dataspace identifier returned by this function when the identifier is no longer needed. + * ref ptr, and defines a selection matching the selection pointed to by ref ptr within the dataspace + * copy. Use H5Sclose to release the dataspace identifier returned by this function when the identifier is + * no longer needed. * * @param ref_ptr * IN: Reference to an object, region or attribute attached to an object. @@ -10759,14 +11139,15 @@ 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 NullPointerException - * - an input array is null. + * an input array is null. * @exception IllegalArgumentException - * - an input array is invalid. + * an input array is invalid. **/ public static long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { long id = _H5Ropen_region(ref_ptr, rapl_id, oapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Ropen_region add {}", id); @@ -10777,7 +11158,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Ropen_attr opens the attribute attached to the object and returns an identifier. @@ -10798,14 +11179,15 @@ public class H5 implements java.io.Serializable { * @return a valid attribute identifier 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 static long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + throws HDF5LibraryException, NullPointerException, IllegalArgumentException + { long id = _H5Ropen_attr(ref_ptr, rapl_id, aapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Ropen_attr add {}", id); @@ -10816,7 +11198,7 @@ public class H5 implements java.io.Serializable { } private synchronized static native long _H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // Get type // @@ -10833,14 +11215,14 @@ 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. + * array is null. * @exception IllegalArgumentException - * - array is invalid. + * array is invalid. **/ public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // Get name // @@ -10853,14 +11235,14 @@ public class H5 implements java.io.Serializable { * @return Returns the file name of the reference * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - array is null. + * array is null. * @exception IllegalArgumentException - * - array is invalid. + * array is invalid. **/ public synchronized static native String H5Rget_file_name(byte[] ref_ptr) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_obj_name retrieves the object name for the object, region or attribute reference pointed to. @@ -10875,14 +11257,14 @@ public class H5 implements java.io.Serializable { * @return Returns the object name of the reference * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - array is null. + * array is null. * @exception IllegalArgumentException - * - array is invalid. + * array is invalid. **/ public synchronized static native String H5Rget_obj_name(byte[] ref_ptr, long rapl_id) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_attr_name retrieves the attribute name for the object, region or attribute reference pointed to. @@ -10893,14 +11275,14 @@ public class H5 implements java.io.Serializable { * @return Returns the attribute name of the reference * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. * @exception NullPointerException - * - array is null. + * array is null. * @exception IllegalArgumentException - * - array is invalid. + * array is invalid. **/ public synchronized static native String H5Rget_attr_name(byte[] ref_ptr) - throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // //////////////////////////////////////////////////////////// // // @@ -10908,12 +11290,13 @@ 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. @@ -10927,14 +11310,15 @@ 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) { @@ -10963,14 +11347,15 @@ 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); @@ -10980,8 +11365,9 @@ 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. @@ -10997,23 +11383,25 @@ 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. @@ -11025,26 +11413,27 @@ 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. + * array is null. * @exception IllegalArgumentException - * - array is invalid. + * 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. @@ -11056,14 +11445,15 @@ 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. + * output array is null. * @exception IllegalArgumentException - * - output array is invalid. + * output 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); @@ -11074,7 +11464,7 @@ 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; // //////////////////////////////////////////////////////////// // // @@ -11093,9 +11483,10 @@ 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); @@ -11120,12 +11511,13 @@ 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); @@ -11136,7 +11528,7 @@ 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. @@ -11153,10 +11545,11 @@ 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. @@ -11173,14 +11566,16 @@ 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); } @@ -11193,9 +11588,10 @@ 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); @@ -11216,9 +11612,10 @@ 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");; @@ -11239,9 +11636,10 @@ 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. @@ -11252,11 +11650,12 @@ 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 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. @@ -11266,9 +11665,10 @@ public class H5 implements java.io.Serializable { * @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. @@ -11279,13 +11679,14 @@ 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 @@ -11297,12 +11698,13 @@ 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. @@ -11313,7 +11715,7 @@ 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; @@ -11326,9 +11728,10 @@ 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. @@ -11339,13 +11742,13 @@ 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. @@ -11355,13 +11758,14 @@ 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. @@ -11371,10 +11775,10 @@ 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 *****************/ @@ -11387,7 +11791,7 @@ 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; @@ -11400,20 +11804,24 @@ 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. @@ -11424,7 +11832,7 @@ 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; @@ -11437,18 +11845,17 @@ 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. @@ -11460,50 +11867,54 @@ 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. @@ -11516,12 +11927,12 @@ 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. @@ -11534,22 +11945,22 @@ 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; } @@ -11563,7 +11974,7 @@ 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; @@ -11575,7 +11986,7 @@ 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_none(long space_id) throws HDF5LibraryException; @@ -11594,10 +12005,11 @@ 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. @@ -11614,24 +12026,25 @@ 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; } @@ -11645,14 +12058,15 @@ 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. @@ -11666,16 +12080,18 @@ 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 @@ -11693,29 +12109,32 @@ 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 @@ -11733,15 +12152,15 @@ 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, @@ -11767,14 +12186,15 @@ 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 @@ -11782,16 +12202,17 @@ public class H5 implements java.io.Serializable { * 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 @@ -11799,18 +12220,19 @@ 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 @@ -11822,50 +12244,56 @@ 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 @@ -11882,17 +12310,19 @@ 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 @@ -11904,30 +12334,30 @@ public class H5 implements java.io.Serializable { * @param dst_space_id * Selection that is mapped to src_space_id * @param src_intersect_space_id - * Selection whose intersection with src_space_id is projected to dst_space_id to obtain the result + * 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; - - - // /////// unimplemented //////// - ///// Operations on dataspace selections ///// - - // - ///// Operations on dataspace selection iterators ///// - //public synchronized static native H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned flags); - //public synchronized static native H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size_t *nseq, - // size_t *nbytes, hsize_t *off, size_t *len); - //public synchronized static native H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id); - //public synchronized static native H5Ssel_iter_close(hid_t sel_iter_id); + public synchronized static native long + H5Sselect_project_intersection(long src_space_id, long dst_space_id, long src_intersect_space_id) + throws HDF5LibraryException; + // /////// unimplemented //////// + ///// Operations on dataspace selections ///// + // + ///// Operations on dataspace selection iterators ///// + // public synchronized static native H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned + // flags); public synchronized static native H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, + // size_t maxbytes, size_t *nseq, + // size_t *nbytes, hsize_t *off, size_t *len); + // public synchronized static native H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id); + // public synchronized static native H5Ssel_iter_close(hid_t sel_iter_id); // //////////////////////////////////////////////////////////// // // @@ -11948,12 +12378,13 @@ 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); @@ -11964,7 +12395,7 @@ 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. @@ -11975,9 +12406,10 @@ 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");; @@ -12006,16 +12438,17 @@ 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. @@ -12027,14 +12460,14 @@ 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. @@ -12042,13 +12475,13 @@ 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. @@ -12056,9 +12489,10 @@ 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. @@ -12077,12 +12511,13 @@ 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); @@ -12090,15 +12525,16 @@ 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); @@ -12121,9 +12557,10 @@ 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); @@ -12144,11 +12581,12 @@ 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); @@ -12158,11 +12596,12 @@ 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. @@ -12172,9 +12611,10 @@ 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. @@ -12182,36 +12622,38 @@ 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. - // * - // * @return the buffer for the object to be encoded into. - // * - // * @exception HDF5LibraryException - Error from the HDF-5 Library. - // **/ + // * H5Tencode converts a data type description into binary form in a buffer. + // * + // * @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. + // **/ // public synchronized static native byte[] H5Tencode(int obj_id) // 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. @@ -12219,9 +12661,10 @@ 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); @@ -12244,12 +12687,12 @@ 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. @@ -12264,12 +12707,13 @@ 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); } @@ -12286,21 +12730,23 @@ 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. @@ -12312,17 +12758,18 @@ 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. @@ -12336,20 +12783,22 @@ 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. @@ -12359,13 +12808,14 @@ 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. @@ -12377,17 +12827,18 @@ 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. @@ -12400,9 +12851,10 @@ 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. @@ -12415,11 +12867,13 @@ 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); } @@ -12434,12 +12888,12 @@ 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. @@ -12450,7 +12904,7 @@ 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; @@ -12463,7 +12917,7 @@ 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; @@ -12476,7 +12930,8 @@ 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"; @@ -12492,7 +12947,7 @@ 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"; @@ -12507,8 +12962,8 @@ 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. @@ -12516,9 +12971,10 @@ 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); @@ -12539,7 +12995,7 @@ 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; @@ -12554,7 +13010,7 @@ 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; @@ -12567,7 +13023,7 @@ 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; @@ -12582,10 +13038,11 @@ 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; } @@ -12598,7 +13055,7 @@ 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; @@ -12611,12 +13068,13 @@ 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. @@ -12631,17 +13089,18 @@ 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. @@ -12659,19 +13118,20 @@ 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. @@ -12690,10 +13150,10 @@ 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. @@ -12714,11 +13174,12 @@ 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; } @@ -12731,14 +13192,14 @@ 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. @@ -12748,7 +13209,7 @@ 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; @@ -12763,9 +13224,10 @@ 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. @@ -12778,12 +13240,14 @@ 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. @@ -12793,13 +13257,15 @@ 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. @@ -12821,9 +13287,10 @@ 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); @@ -12834,7 +13301,7 @@ 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. @@ -12847,12 +13314,12 @@ 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. @@ -12867,30 +13334,33 @@ 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); } @@ -12905,9 +13375,10 @@ 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); @@ -12917,7 +13388,8 @@ 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. @@ -12928,7 +13400,7 @@ 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; @@ -12941,7 +13413,7 @@ 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; @@ -12956,7 +13428,7 @@ 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; @@ -12969,7 +13441,7 @@ 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; @@ -12984,10 +13456,11 @@ 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; } @@ -13000,9 +13473,10 @@ 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. @@ -13013,7 +13487,7 @@ 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; @@ -13028,7 +13502,7 @@ 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; @@ -13048,12 +13522,12 @@ 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. @@ -13068,9 +13542,10 @@ 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. @@ -13081,7 +13556,7 @@ 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; @@ -13096,10 +13571,11 @@ 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; } @@ -13112,7 +13588,7 @@ 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; @@ -13125,9 +13601,10 @@ 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. @@ -13138,7 +13615,7 @@ 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; @@ -13153,7 +13630,7 @@ 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; @@ -13166,13 +13643,13 @@ 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. @@ -13182,7 +13659,7 @@ 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; @@ -13195,7 +13672,7 @@ 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; @@ -13210,7 +13687,7 @@ 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; @@ -13223,9 +13700,10 @@ 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); @@ -13246,7 +13724,7 @@ 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; @@ -13261,7 +13739,7 @@ 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; @@ -13280,12 +13758,12 @@ 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. @@ -13296,12 +13774,13 @@ 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. @@ -13309,12 +13788,13 @@ 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. @@ -13326,12 +13806,13 @@ 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); @@ -13342,14 +13823,12 @@ 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. @@ -13357,7 +13836,7 @@ 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; @@ -13374,12 +13853,13 @@ public class H5 implements java.io.Serializable { * Buffer with data to be reclaimed. * * @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 H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf) - throws HDF5LibraryException, NullPointerException; + public synchronized static native void H5Treclaim(long type_id, long space_id, long xfer_plist_id, + byte[] buf) + throws HDF5LibraryException, NullPointerException; /** * H5Tvlen_create creates a new variable-length (VL) dataype. @@ -13390,9 +13870,10 @@ 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); @@ -13412,7 +13893,7 @@ 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; @@ -13426,7 +13907,7 @@ 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; @@ -13438,9 +13919,8 @@ 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; // //////////////////////////////////////////////////////////// // // @@ -13450,7 +13930,8 @@ public class H5 implements java.io.Serializable { /// VOL Connector Functionality /** - * H5VLregister_connector_by_name registers a new VOL connector as a member of the virtual object layer class. + * H5VLregister_connector_by_name registers a new VOL connector as a member of the virtual object layer + * class. * * @param connector_name * IN: name of the connector. @@ -13461,11 +13942,13 @@ public class H5 implements java.io.Serializable { * @return a VOL connector ID * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id) throws HDF5LibraryException; + public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id) + throws HDF5LibraryException; /** - * H5VLregister_connector_by_value registers a new VOL connector as a member of the virtual object layer class. + * H5VLregister_connector_by_value registers a new VOL connector as a member of the virtual object layer + * class. * * @param connector_value * IN: value of the connector. @@ -13476,9 +13959,10 @@ public class H5 implements java.io.Serializable { * @return a VOL connector ID * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id) throws HDF5LibraryException; + public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id) + throws HDF5LibraryException; /** * H5VLis_connector_registered_by_name tests whether a VOL class has been registered. * @@ -13488,9 +13972,10 @@ public class H5 implements java.io.Serializable { * @return true if a VOL connector with that name has been registered * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native boolean H5VLis_connector_registered_by_name(String name) throws HDF5LibraryException; + public synchronized static native boolean H5VLis_connector_registered_by_name(String name) + throws HDF5LibraryException; /** * H5VLis_connector_registered_by_value tests whether a VOL class has been registered. * @@ -13500,9 +13985,10 @@ public class H5 implements java.io.Serializable { * @return true if a VOL connector with that value has been registered * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value) throws HDF5LibraryException; + public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value) + throws HDF5LibraryException; /** * H5VLget_connector_id retrieves the ID for a registered VOL connector for a given object. * @@ -13512,7 +13998,7 @@ public class H5 implements java.io.Serializable { * @return a VOL connector ID * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native long H5VLget_connector_id(long object_id) throws HDF5LibraryException; /** @@ -13524,9 +14010,10 @@ public class H5 implements java.io.Serializable { * @return a VOL connector ID * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5VLget_connector_id_by_name(String name) throws HDF5LibraryException; + public synchronized static native long H5VLget_connector_id_by_name(String name) + throws HDF5LibraryException; /** * H5VLget_connector_id_by_value retrieves the ID for a registered VOL connector. * @@ -13536,12 +14023,13 @@ public class H5 implements java.io.Serializable { * @return a VOL connector ID * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native long H5VLget_connector_id_by_value(int connector_value) throws HDF5LibraryException; + public synchronized static native long H5VLget_connector_id_by_value(int connector_value) + throws HDF5LibraryException; /** * H5VLget_connector_name returns the connector name for the VOL associated with the - * object or file ID. + * object or file ID. * * @param object_id * IN: Identifier of the object. @@ -13549,9 +14037,10 @@ public class H5 implements java.io.Serializable { * @return the connector name * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native String H5VLget_connector_name(long object_id) throws HDF5LibraryException; + public synchronized static native String H5VLget_connector_name(long object_id) + throws HDF5LibraryException; /** * H5VLclose closes a VOL connector ID. * @@ -13559,7 +14048,7 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the connector. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ public synchronized static native void H5VLclose(long connector_id) throws HDF5LibraryException; /** @@ -13569,14 +14058,14 @@ public class H5 implements java.io.Serializable { * IN: Identifier of the connector. * * @exception HDF5LibraryException - * - Error from the HDF-5 Library. + * Error from the HDF-5 Library. **/ - public synchronized static native void H5VLunregister_connector(long connector_id) throws HDF5LibraryException; + public synchronized static native void H5VLunregister_connector(long connector_id) + throws HDF5LibraryException; // /////// unimplemented //////// // hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id); - // //////////////////////////////////////////////////////////// // // // H5Z: Filter Interface Functions // @@ -13592,7 +14081,7 @@ 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; @@ -13605,7 +14094,7 @@ 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; @@ -13618,13 +14107,11 @@ 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); - } - diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java index 4125907..cbdf463 100644 --- a/java/src/hdf/hdf5lib/HDF5Constants.java +++ b/java/src/hdf/hdf5lib/HDF5Constants.java @@ -11,7 +11,6 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - package hdf.hdf5lib; import hdf.hdf5lib.structs.H5O_token_t; @@ -27,15 +26,13 @@ import hdf.hdf5lib.structs.H5O_token_t; * <b>See also:</b> hdf.hdf5lib.HDF5Library */ public class HDF5Constants { - static { - H5.loadH5Lib(); - } + static { H5.loadH5Lib(); } // ///////////////////////////////////////////////////////////////////////// // Get the HDF5 constants from the library // // ///////////////////////////////////////////////////////////////////////// - //public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX(); + // public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX(); /** Special parameters for szip compression */ public static final int H5_SZIP_MAX_PIXELS_PER_BLOCK = H5_SZIP_MAX_PIXELS_PER_BLOCK(); @@ -70,9 +67,11 @@ public class HDF5Constants { /** */ public static final int H5AC_MAX_TRACE_FILE_NAME_LEN = H5AC_MAX_TRACE_FILE_NAME_LEN(); /** */ - public static final int H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY = H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY(); + public static final int H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY = + H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY(); /** */ - public static final int H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED = H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED(); + public static final int H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED = + H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED(); /** */ public static final int H5C_incr_off = H5C_incr_off(); /** */ @@ -681,22 +680,22 @@ public class HDF5Constants { /** */ public static final long H5FD_MEM_DEFAULT_OHDR_SIZE = H5FD_MEM_DEFAULT_OHDR_SIZE(); -// public static final int H5G_DATASET = H5G_DATASET(); -// public static final int H5G_GROUP = H5G_GROUP(); -// public static final int H5G_LINK = H5G_LINK(); -// public static final int H5G_UDLINK = H5G_UDLINK(); -// public static final int H5G_LINK_ERROR = H5G_LINK_ERROR(); -// public static final int H5G_LINK_HARD = H5G_LINK_HARD(); -// public static final int H5G_LINK_SOFT = H5G_LINK_SOFT(); -// public static final int H5G_NLIBTYPES = H5G_NLIBTYPES(); -// public static final int H5G_NTYPES = H5G_NTYPES(); -// public static final int H5G_NUSERTYPES = H5G_NUSERTYPES(); -// public static final int H5G_RESERVED_5 = H5G_RESERVED_5(); -// public static final int H5G_RESERVED_6 = H5G_RESERVED_6(); -// public static final int H5G_RESERVED_7 = H5G_RESERVED_7(); -// public static final int H5G_SAME_LOC = H5G_SAME_LOC(); -// public static final int H5G_TYPE = H5G_TYPE(); -// public static final int H5G_UNKNOWN = H5G_UNKNOWN(); + // public static final int H5G_DATASET = H5G_DATASET(); + // public static final int H5G_GROUP = H5G_GROUP(); + // public static final int H5G_LINK = H5G_LINK(); + // public static final int H5G_UDLINK = H5G_UDLINK(); + // public static final int H5G_LINK_ERROR = H5G_LINK_ERROR(); + // public static final int H5G_LINK_HARD = H5G_LINK_HARD(); + // public static final int H5G_LINK_SOFT = H5G_LINK_SOFT(); + // public static final int H5G_NLIBTYPES = H5G_NLIBTYPES(); + // public static final int H5G_NTYPES = H5G_NTYPES(); + // public static final int H5G_NUSERTYPES = H5G_NUSERTYPES(); + // public static final int H5G_RESERVED_5 = H5G_RESERVED_5(); + // public static final int H5G_RESERVED_6 = H5G_RESERVED_6(); + // public static final int H5G_RESERVED_7 = H5G_RESERVED_7(); + // public static final int H5G_SAME_LOC = H5G_SAME_LOC(); + // public static final int H5G_TYPE = H5G_TYPE(); + // public static final int H5G_UNKNOWN = H5G_UNKNOWN(); /** */ public static final int H5G_STORAGE_TYPE_UNKNOWN = H5G_STORAGE_TYPE_UNKNOWN(); @@ -756,7 +755,7 @@ public class HDF5Constants { /** */ public static final int H5O_COPY_SHALLOW_HIERARCHY_FLAG = H5O_COPY_SHALLOW_HIERARCHY_FLAG(); /** */ - public static final int H5O_COPY_EXPAND_SOFT_LINK_FLAG = H5O_COPY_EXPAND_SOFT_LINK_FLAG(); + public static final int H5O_COPY_EXPAND_SOFT_LINK_FLAG = H5O_COPY_EXPAND_SOFT_LINK_FLAG(); /** */ public static final int H5O_COPY_EXPAND_EXT_LINK_FLAG = H5O_COPY_EXPAND_EXT_LINK_FLAG(); /** */ @@ -1438,23 +1437,35 @@ public class HDF5Constants { public static final int H5Z_FILTER_SHUFFLE = H5Z_FILTER_SHUFFLE(); /** Filter IDs - szip compression */ public static final int H5Z_FILTER_SZIP = H5Z_FILTER_SZIP(); - /** Flags for filter definition (stored) - * definition flag mask */ + /** + * Flags for filter definition (stored) + * definition flag mask + */ public static final int H5Z_FLAG_DEFMASK = H5Z_FLAG_DEFMASK(); - /** Additional flags for filter invocation (not stored) - * invocation flag mask */ + /** + * Additional flags for filter invocation (not stored) + * invocation flag mask + */ public static final int H5Z_FLAG_INVMASK = H5Z_FLAG_INVMASK(); - /** Flags for filter definition (stored) - * filter is mandatory */ + /** + * Flags for filter definition (stored) + * filter is mandatory + */ public static final int H5Z_FLAG_MANDATORY = H5Z_FLAG_MANDATORY(); - /** Flags for filter definition (stored) - * filter is optional */ + /** + * Flags for filter definition (stored) + * filter is optional + */ public static final int H5Z_FLAG_OPTIONAL = H5Z_FLAG_OPTIONAL(); - /** Additional flags for filter invocation (not stored) - * reverse direction; read */ + /** + * Additional flags for filter invocation (not stored) + * reverse direction; read + */ public static final int H5Z_FLAG_REVERSE = H5Z_FLAG_REVERSE(); - /** Additional flags for filter invocation (not stored) - * skip EDC filters for read */ + /** + * Additional flags for filter invocation (not stored) + * skip EDC filters for read + */ public static final int H5Z_FLAG_SKIP_EDC = H5Z_FLAG_SKIP_EDC(); /** Symbol to remove all filters in H5Premove_filter */ public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL(); @@ -2953,5 +2964,4 @@ public class HDF5Constants { private static native final int H5Z_SCALEOFFSET_USER_NPARMS(); private static native final int H5Z_FILTER_ALL(); - } diff --git a/java/src/hdf/hdf5lib/HDF5GroupInfo.java b/java/src/hdf/hdf5lib/HDF5GroupInfo.java index 4c31af7..220cfb6 100644 --- a/java/src/hdf/hdf5lib/HDF5GroupInfo.java +++ b/java/src/hdf/hdf5lib/HDF5GroupInfo.java @@ -11,7 +11,6 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - package hdf.hdf5lib; /** @@ -41,14 +40,17 @@ public class HDF5GroupInfo { long mtime; int linklen; - /** Container for the information reported about an HDF5 Object - * from the H5Gget_obj_info() method */ - public HDF5GroupInfo() { - fileno = new long[2]; - objno = new long[2]; - nlink = -1; - type = -1; - mtime = 0; + /** + * Container for the information reported about an HDF5 Object + * from the H5Gget_obj_info() method + */ + public HDF5GroupInfo() + { + fileno = new long[2]; + objno = new long[2]; + nlink = -1; + type = -1; + mtime = 0; linklen = 0; } @@ -68,84 +70,79 @@ public class HDF5GroupInfo { * @param len * Length of link **/ - public void setGroupInfo(long[] fn, long[] on, int nl, int t, long mt, - int len) { - fileno = fn; - objno = on; - nlink = nl; - type = t; - mtime = mt; + public void setGroupInfo(long[] fn, long[] on, int nl, int t, long mt, int len) + { + fileno = fn; + objno = on; + nlink = nl; + type = t; + mtime = mt; linklen = len; } /** Resets all the group information to defaults. */ - public void reset() { + public void reset() + { fileno[0] = 0; fileno[1] = 0; - objno[0] = 0; - objno[1] = 0; - nlink = -1; - type = -1; - mtime = 0; - linklen = 0; + objno[0] = 0; + objno[1] = 0; + nlink = -1; + type = -1; + mtime = 0; + linklen = 0; } - /** fileno accessors + /** + * fileno accessors * @return the file number if successful */ - public long[] getFileno() { - return fileno; - } + public long[] getFileno() { return fileno; } - /** accessors + /** + * accessors * @return the object number if successful */ - public long[] getObjno() { - return objno; - } + public long[] getObjno() { return objno; } - /** accessors + /** + * accessors * @return type of group if successful */ - public int getType() { - return type; - } + public int getType() { return type; } - /** accessors + /** + * accessors * @return the number of links in the group if successful */ - public int getNlink() { - return nlink; - } + public int getNlink() { return nlink; } - /** accessors + /** + * accessors * @return the modified time value if successful */ - public long getMtime() { - return mtime; - } + public long getMtime() { return mtime; } - /** accessors + /** + * accessors * @return a length of link name if successful */ - public int getLinklen() { - return linklen; - } + public int getLinklen() { return linklen; } /** * The fileno and objno fields contain four values which uniquely identify * an object among those HDF5 files. */ @Override - public boolean equals(Object obj) { + public boolean equals(Object obj) + { if (!(obj instanceof HDF5GroupInfo)) { return false; } - HDF5GroupInfo target = (HDF5GroupInfo) obj; - if ((fileno[0] == target.fileno[0]) && (fileno[1] == target.fileno[1]) - && (objno[0] == target.objno[0]) - && (objno[1] == target.objno[1])) { + HDF5GroupInfo target = (HDF5GroupInfo)obj; + if ((fileno[0] == target.fileno[0]) && (fileno[1] == target.fileno[1]) && + (objno[0] == target.objno[0]) && (objno[1] == target.objno[1])) { return true; } else { @@ -158,9 +155,7 @@ public class HDF5GroupInfo { * * @return the object id */ - public long getOID() { - return objno[0]; - } + public long getOID() { return objno[0]; } /** * /** Converts this object to a String representation. @@ -168,9 +163,10 @@ public class HDF5GroupInfo { * @return a string representation of this object */ @Override - public String toString() { + public String toString() + { String fileStr = "fileno=null"; - String objStr = "objno=null"; + String objStr = "objno=null"; if (fileno != null) { fileStr = "fileno[0]=" + fileno[0] + ",fileno[1]=" + fileno[1]; @@ -180,9 +176,7 @@ public class HDF5GroupInfo { objStr = "objno[0]=" + objno[0] + ",objno[1]=" + objno[1]; } - return getClass().getName() + "[" + fileStr + "," + objStr + ",type=" - + type + ",nlink=" + nlink + ",mtime=" + mtime + ",linklen=" - + linklen + "]"; + return getClass().getName() + "[" + fileStr + "," + objStr + ",type=" + type + ",nlink=" + nlink + + ",mtime=" + mtime + ",linklen=" + linklen + "]"; } - } diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java index 21e2b02..8525fb0 100644 --- a/java/src/hdf/hdf5lib/HDFArray.java +++ b/java/src/hdf/hdf5lib/HDFArray.java @@ -13,36 +13,34 @@ package hdf.hdf5lib; +import java.util.Arrays; + import hdf.hdf5lib.exceptions.HDF5Exception; import hdf.hdf5lib.exceptions.HDF5JavaException; -import java.util.Arrays; /** * This is a class for handling multidimensional arrays for HDF. * <p> * The purpose is to allow the storage and retrieval of arbitrary array types containing scientific data. * <p> - * The methods support the conversion of an array to and from Java to a one-dimensional array of bytes suitable for I/O - * by the C library. - * <p> - * This class heavily uses the <a href="./hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a> class to convert between - * Java and C representations. + * The methods support the conversion of an array to and from Java to a one-dimensional array of bytes + * suitable for I/O by the C library. <p> This class heavily uses the <a + * href="./hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a> class to convert between Java and C + * representations. */ public class HDFArray { - private Object _theArray = null; + private Object _theArray = null; private ArrayDescriptor _desc = null; - private byte[] _barray = null; + private byte[] _barray = null; // public HDFArray() {} /** - * The input must be a Java Array (possibly multidimensional) of primitive numbers or sub-classes of Number. - * <p> - * The input is analysed to determine the number of dimensions and size of each dimension, as well as the type of - * the elements. - * <p> - * The description is saved in private variables, and used to convert data. + * The input must be a Java Array (possibly multidimensional) of primitive numbers or sub-classes of + * Number. <p> The input is analysed to determine the number of dimensions and size of each dimension, as + * well as the type of the elements. <p> The description is saved in private variables, and used to + * convert data. * * @param anArray * The array object. @@ -58,25 +56,26 @@ public class HDFArray { if (tc.isArray() == false) { /* exception: not an array */ HDF5JavaException ex = new HDF5JavaException("HDFArray: not an array?: "); - throw (ex); + throw(ex); } _theArray = anArray; - _desc = new ArrayDescriptor(_theArray); + _desc = new ArrayDescriptor(_theArray); /* extra error checking -- probably not needed */ if (_desc == null) { - HDF5JavaException ex = new HDF5JavaException("HDFArray: internal error: array description failed?: "); - throw (ex); + HDF5JavaException ex = + new HDF5JavaException("HDFArray: internal error: array description failed?: "); + throw(ex); } } /** * Allocate a one-dimensional array of bytes sufficient to store the array. * - * @return A one-D array of bytes, filled with zeroes. The bytes are sufficient to hold the data of the Array passed - * to the constructor. + * @return A one-D array of bytes, filled with zeroes. The bytes are sufficient to hold the data of the + * Array passed to the constructor. * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * Allocation failed. + * Allocation failed. */ public byte[] emptyBytes() throws HDF5JavaException @@ -84,14 +83,14 @@ public class HDFArray { byte[] b = null; if ((ArrayDescriptor.dims == 1) && (ArrayDescriptor.NT == 'B')) { - b = (byte[]) _theArray; + b = (byte[])_theArray; } else { b = new byte[ArrayDescriptor.totalSize]; } if (b == null) { HDF5JavaException ex = new HDF5JavaException("HDFArray: emptyBytes: allocation failed"); - throw (ex); + throw(ex); } return (b); } @@ -112,14 +111,14 @@ public class HDFArray { if (_theArray == null) { /* exception: not an array */ HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify not an array?: "); - throw (ex); + throw(ex); } if (ArrayDescriptor.dims == 1) { /* special case */ if (ArrayDescriptor.NT == 'B') { /* really special case! */ - _barray = (byte[]) _theArray; + _barray = (byte[])_theArray; return _barray; } else { @@ -128,54 +127,56 @@ public class HDFArray { byte[] therow; if (ArrayDescriptor.NT == 'I') { - therow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[1], (int[]) _theArray); + therow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[1], (int[])_theArray); } else if (ArrayDescriptor.NT == 'S') { - therow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[1], (short[]) _theArray); + therow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[1], (short[])_theArray); } else if (ArrayDescriptor.NT == 'F') { - therow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[1], (float[]) _theArray); + therow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[1], (float[])_theArray); } else if (ArrayDescriptor.NT == 'J') { - therow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[1], (long[]) _theArray); + therow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[1], (long[])_theArray); } else if (ArrayDescriptor.NT == 'D') { - therow = HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[1], (double[]) _theArray); + therow = + HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[1], (double[])_theArray); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { - therow = ByteObjToByte((Byte[]) _theArray); + therow = ByteObjToByte((Byte[])_theArray); } else if (ArrayDescriptor.className.equals("java.lang.Integer")) { - therow = IntegerToByte((Integer[]) _theArray); + therow = IntegerToByte((Integer[])_theArray); } else if (ArrayDescriptor.className.equals("java.lang.Short")) { - therow = ShortToByte((Short[]) _theArray); + therow = ShortToByte((Short[])_theArray); } else if (ArrayDescriptor.className.equals("java.lang.Float")) { - therow = FloatObjToByte((Float[]) _theArray); + therow = FloatObjToByte((Float[])_theArray); } else if (ArrayDescriptor.className.equals("java.lang.Double")) { - therow = DoubleObjToByte((Double[]) _theArray); + therow = DoubleObjToByte((Double[])_theArray); } else if (ArrayDescriptor.className.equals("java.lang.Long")) { - therow = LongObjToByte((Long[]) _theArray); + therow = LongObjToByte((Long[])_theArray); } else { HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown type of Object?"); - throw (ex); + throw(ex); } } else { HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown type of data?"); - throw (ex); + throw(ex); } - System.arraycopy(therow, 0, _barray, 0, (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize)); + System.arraycopy(therow, 0, _barray, 0, + (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize)); return _barray; } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); - throw (ex); + throw(ex); } } } @@ -185,15 +186,15 @@ public class HDFArray { } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); - throw (ex); + throw(ex); } Object oo = _theArray; - int n = 0; /* the current byte */ + int n = 0; /* the current byte */ int index = 0; int i; while (n < ArrayDescriptor.totalSize) { - oo = ArrayDescriptor.objs[0]; + oo = ArrayDescriptor.objs[0]; index = n / ArrayDescriptor.bytetoindex[0]; index %= ArrayDescriptor.dimlen[0]; for (i = 0; i < (ArrayDescriptor.dims); i++) { @@ -209,9 +210,9 @@ public class HDFArray { if (index > (ArrayDescriptor.dimlen[i] - 1)) { throw new java.lang.IndexOutOfBoundsException("HDFArray: byteify index OOB?"); } - oo = java.lang.reflect.Array.get(oo, index); + oo = java.lang.reflect.Array.get(oo, index); ArrayDescriptor.currentindex[i] = index; - ArrayDescriptor.objs[i] = oo; + ArrayDescriptor.objs[i] = oo; } } @@ -220,85 +221,90 @@ public class HDFArray { try { if (ArrayDescriptor.NT == 'J') { arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + (long[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'I') { arow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (int[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + (int[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'S') { arow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + (short[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'B') { - arow = (byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]; + arow = (byte[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]; } else if (ArrayDescriptor.NT == 'F') { /* 32 bit float */ arow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + (float[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'D') { /* 64 bit float */ - arow = HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = + HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (double[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { - arow = ByteObjToByte((Byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = ByteObjToByte((Byte[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Integer")) { - arow = IntegerToByte((Integer[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = IntegerToByte((Integer[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Short")) { - arow = ShortToByte((Short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = ShortToByte((Short[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Float")) { - arow = FloatObjToByte((Float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = FloatObjToByte((Float[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Double")) { - arow = DoubleObjToByte((Double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = DoubleObjToByte((Double[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Long")) { - arow = LongObjToByte((Long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = LongObjToByte((Long[])ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else { - HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify Object type not implemented?"); - throw (ex); + HDF5JavaException ex = + new HDF5JavaException("HDFArray: byteify Object type not implemented?"); + throw(ex); } } else { - HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify unknown type not implemented?"); - throw (ex); + HDF5JavaException ex = + new HDF5JavaException("HDFArray: byteify unknown type not implemented?"); + throw(ex); } System.arraycopy(arow, 0, _barray, n, - (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize)); + (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize)); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); - throw (ex); + throw(ex); } } /* assert: the whole array is completed--currentindex should == len - 1 */ /* error checks */ if (n < ArrayDescriptor.totalSize) { - throw new java.lang.InternalError(new String("HDFArray::byteify: Panic didn't complete all input data: n= " - + n + " size = " + ArrayDescriptor.totalSize)); + throw new java.lang.InternalError( + new String("HDFArray::byteify: Panic didn't complete all input data: n= " + n + + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i < ArrayDescriptor.dims; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { - throw new java.lang.InternalError(new String( - "Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + " ?)")); + throw new java.lang.InternalError(new String("Panic didn't complete all data: currentindex[" + + i + "] = " + ArrayDescriptor.currentindex[i] + + " (should be " + + (ArrayDescriptor.dimlen[i] - 1) + " ?)")); } } return _barray; } /** - * Given a one-dimensional array of bytes representing numbers, convert it to a java array of the shape and size - * passed to the constructor. + * Given a one-dimensional array of bytes representing numbers, convert it to a java array of the shape + * and size passed to the constructor. * * @param bytes * The bytes to construct the Array. @@ -312,13 +318,13 @@ public class HDFArray { if (_theArray == null) { /* exception: not an array */ HDF5JavaException ex = new HDF5JavaException("arrayify: not an array?: "); - throw (ex); + throw(ex); } if (java.lang.reflect.Array.getLength(bytes) != ArrayDescriptor.totalSize) { /* exception: array not right size */ HDF5JavaException ex = new HDF5JavaException("arrayify: array is wrong size?: "); - throw (ex); + throw(ex); } _barray = bytes; /* hope that the bytes are correct.... */ @@ -387,74 +393,77 @@ public class HDFArray { return _theArray; } else { - HDF5JavaException ex = new HDF5JavaException("arrayify: Object type not implemented yet..."); - throw (ex); + HDF5JavaException ex = + new HDF5JavaException("arrayify: Object type not implemented yet..."); + throw(ex); } } else { - HDF5JavaException ex = new HDF5JavaException("arrayify: unknown type not implemented yet..."); - throw (ex); + HDF5JavaException ex = + new HDF5JavaException("arrayify: unknown type not implemented yet..."); + throw(ex); } } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException("HDFArray: arrayify array too big?"); - throw (ex); + throw(ex); } } /* Assert dims >= 2 */ Object oo = _theArray; - int n = 0; /* the current byte */ - int m = 0; /* the current array index */ + int n = 0; /* the current byte */ + int m = 0; /* the current array index */ int index = 0; int i; Object flattenedArray = null; switch (ArrayDescriptor.NT) { case 'J': - flattenedArray = (Object) HDFNativeData.byteToLong(_barray); + flattenedArray = (Object)HDFNativeData.byteToLong(_barray); break; case 'S': - flattenedArray = (Object) HDFNativeData.byteToShort(_barray); + flattenedArray = (Object)HDFNativeData.byteToShort(_barray); break; case 'I': - flattenedArray = (Object) HDFNativeData.byteToInt(_barray); + flattenedArray = (Object)HDFNativeData.byteToInt(_barray); break; case 'F': - flattenedArray = (Object) HDFNativeData.byteToFloat(_barray); + flattenedArray = (Object)HDFNativeData.byteToFloat(_barray); break; case 'D': - flattenedArray = (Object) HDFNativeData.byteToDouble(_barray); + flattenedArray = (Object)HDFNativeData.byteToDouble(_barray); break; case 'B': - flattenedArray = (Object) _barray; + flattenedArray = (Object)_barray; break; - case 'L': - { - if (ArrayDescriptor.className.equals("java.lang.Byte")) - flattenedArray = (Object) ByteToByteObj(_barray); - else if (ArrayDescriptor.className.equals("java.lang.Short")) - flattenedArray = (Object) ByteToShort(_barray); - else if (ArrayDescriptor.className.equals("java.lang.Integer")) - flattenedArray = (Object) ByteToInteger(_barray); - else if (ArrayDescriptor.className.equals("java.lang.Long")) - flattenedArray = (Object) ByteToLongObj(_barray); - else if (ArrayDescriptor.className.equals("java.lang.Float")) - flattenedArray = (Object) ByteToFloatObj(_barray); - else if (ArrayDescriptor.className.equals("java.lang.Double")) - flattenedArray = (Object) ByteToDoubleObj(_barray); - else { - HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); - throw (ex); - } - } // end of statement for arrays of boxed objects + case 'L': { + if (ArrayDescriptor.className.equals("java.lang.Byte")) + flattenedArray = (Object)ByteToByteObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Short")) + flattenedArray = (Object)ByteToShort(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Integer")) + flattenedArray = (Object)ByteToInteger(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Long")) + flattenedArray = (Object)ByteToLongObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Float")) + flattenedArray = (Object)ByteToFloatObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Double")) + flattenedArray = (Object)ByteToDoubleObj(_barray); + else { + HDF5JavaException ex = + new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); + throw(ex); + } + } // end of statement for arrays of boxed objects default: - HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown or unsupported type: " + ArrayDescriptor.NT); - throw (ex); + HDF5JavaException ex = + new HDF5JavaException("HDFArray: unknown or unsupported type: " + ArrayDescriptor.NT); + throw(ex); } // end of switch statement for arrays of primitives while (n < ArrayDescriptor.totalSize) { - oo = ArrayDescriptor.objs[0]; + oo = ArrayDescriptor.objs[0]; index = n / ArrayDescriptor.bytetoindex[0]; index %= ArrayDescriptor.dimlen[0]; for (i = 0; i < (ArrayDescriptor.dims); i++) { @@ -471,86 +480,88 @@ public class HDFArray { System.out.println("out of bounds?"); return null; } - oo = java.lang.reflect.Array.get(oo, index); + oo = java.lang.reflect.Array.get(oo, index); ArrayDescriptor.currentindex[i] = index; - ArrayDescriptor.objs[i] = oo; + ArrayDescriptor.objs[i] = oo; } } /* array-ify */ try { Object arow = null; - int mm = m + ArrayDescriptor.dimlen[ArrayDescriptor.dims]; + int mm = m + ArrayDescriptor.dimlen[ArrayDescriptor.dims]; switch (ArrayDescriptor.NT) { case 'B': - arow = (Object) Arrays.copyOfRange((byte[]) flattenedArray, m, mm); + arow = (Object)Arrays.copyOfRange((byte[])flattenedArray, m, mm); break; case 'S': - arow = (Object) Arrays.copyOfRange((short[]) flattenedArray, m, mm); + arow = (Object)Arrays.copyOfRange((short[])flattenedArray, m, mm); break; case 'I': - arow = (Object) Arrays.copyOfRange((int[]) flattenedArray, m, mm); + arow = (Object)Arrays.copyOfRange((int[])flattenedArray, m, mm); break; case 'J': - arow = (Object) Arrays.copyOfRange((long[]) flattenedArray, m, mm); + arow = (Object)Arrays.copyOfRange((long[])flattenedArray, m, mm); break; case 'F': - arow = (Object) Arrays.copyOfRange((float[]) flattenedArray, m, mm); + arow = (Object)Arrays.copyOfRange((float[])flattenedArray, m, mm); break; case 'D': - arow = (Object) Arrays.copyOfRange((double[]) flattenedArray, m, mm); + arow = (Object)Arrays.copyOfRange((double[])flattenedArray, m, mm); break; - case 'L': - { - if (ArrayDescriptor.className.equals("java.lang.Byte")) - arow = (Object) Arrays.copyOfRange((Byte[]) flattenedArray, m, mm); - else if (ArrayDescriptor.className.equals("java.lang.Short")) - arow = (Object) Arrays.copyOfRange((Short[]) flattenedArray, m, mm); - else if (ArrayDescriptor.className.equals("java.lang.Integer")) - arow = (Object) Arrays.copyOfRange((Integer[]) flattenedArray, m, mm); - else if (ArrayDescriptor.className.equals("java.lang.Long")) - arow = (Object) Arrays.copyOfRange((Long[]) flattenedArray, m, mm); - else if (ArrayDescriptor.className.equals("java.lang.Float")) - arow = (Object) Arrays.copyOfRange((Float[]) flattenedArray, m, mm); - else if (ArrayDescriptor.className.equals("java.lang.Double")) - arow = (Object) Arrays.copyOfRange((Double[]) flattenedArray, m, mm); - else { - HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); - throw (ex); - } - } // end of statement for arrays of boxed numerics + case 'L': { + if (ArrayDescriptor.className.equals("java.lang.Byte")) + arow = (Object)Arrays.copyOfRange((Byte[])flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Short")) + arow = (Object)Arrays.copyOfRange((Short[])flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Integer")) + arow = (Object)Arrays.copyOfRange((Integer[])flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Long")) + arow = (Object)Arrays.copyOfRange((Long[])flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Float")) + arow = (Object)Arrays.copyOfRange((Float[])flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Double")) + arow = (Object)Arrays.copyOfRange((Double[])flattenedArray, m, mm); + else { + HDF5JavaException ex = + new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); + throw(ex); + } + } // end of statement for arrays of boxed numerics } // end of switch statement for arrays of primitives java.lang.reflect.Array.set(ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); + (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; m = mm; } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException("HDFArray: arrayify array too big?"); - throw (ex); + throw(ex); } } /* assert: the whole array is completed--currentindex should == len - 1 */ /* error checks */ if (n < ArrayDescriptor.totalSize) { - throw new java.lang.InternalError(new String("HDFArray::arrayify Panic didn't complete all input data: n= " - + n + " size = " + ArrayDescriptor.totalSize)); + throw new java.lang.InternalError( + new String("HDFArray::arrayify Panic didn't complete all input data: n= " + n + + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i <= ArrayDescriptor.dims - 2; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { throw new java.lang.InternalError( - new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " - + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i] - 1) - + "?")); + new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + + "] = " + ArrayDescriptor.currentindex[i] + " (should be " + + (ArrayDescriptor.dimlen[i] - 1) + "?")); } } - if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) { - throw new java.lang.InternalError( - new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " - + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i]) + "?")); + if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != + ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) { + throw new java.lang.InternalError(new String( + "HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i]) + "?")); } return _theArray; @@ -559,7 +570,7 @@ public class HDFArray { private byte[] IntegerToByte(Integer in[]) { int nelems = java.lang.reflect.Array.getLength(in); - int[] out = new int[nelems]; + int[] out = new int[nelems]; for (int i = 0; i < nelems; i++) { out[i] = in[i].intValue(); @@ -569,8 +580,8 @@ public class HDFArray { private Integer[] ByteToInteger(byte[] bin) { - int in[] = HDFNativeData.byteToInt(bin); - int nelems = java.lang.reflect.Array.getLength(in); + int in[] = HDFNativeData.byteToInt(bin); + int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; for (int i = 0; i < nelems; i++) { @@ -581,8 +592,8 @@ public class HDFArray { private Integer[] ByteToInteger(int start, int len, byte[] bin) { - int in[] = HDFNativeData.byteToInt(start, len, bin); - int nelems = java.lang.reflect.Array.getLength(in); + int in[] = HDFNativeData.byteToInt(start, len, bin); + int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; for (int i = 0; i < nelems; i++) { @@ -593,7 +604,7 @@ public class HDFArray { private byte[] ShortToByte(Short in[]) { - int nelems = java.lang.reflect.Array.getLength(in); + int nelems = java.lang.reflect.Array.getLength(in); short[] out = new short[nelems]; for (int i = 0; i < nelems; i++) { @@ -604,8 +615,8 @@ public class HDFArray { private Short[] ByteToShort(byte[] bin) { - short in[] = HDFNativeData.byteToShort(bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + short in[] = HDFNativeData.byteToShort(bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Short[] out = new Short[nelems]; for (int i = 0; i < nelems; i++) { @@ -616,8 +627,8 @@ public class HDFArray { private Short[] ByteToShort(int start, int len, byte[] bin) { - short in[] = (short[]) HDFNativeData.byteToShort(start, len, bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + short in[] = (short[])HDFNativeData.byteToShort(start, len, bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Short[] out = new Short[nelems]; for (int i = 0; i < nelems; i++) { @@ -628,7 +639,7 @@ public class HDFArray { private byte[] ByteObjToByte(Byte in[]) { - int nelems = java.lang.reflect.Array.getLength((Object) in); + int nelems = java.lang.reflect.Array.getLength((Object)in); byte[] out = new byte[nelems]; for (int i = 0; i < nelems; i++) { @@ -639,7 +650,7 @@ public class HDFArray { private Byte[] ByteToByteObj(byte[] bin) { - int nelems = java.lang.reflect.Array.getLength((Object) bin); + int nelems = java.lang.reflect.Array.getLength((Object)bin); Byte[] out = new Byte[nelems]; for (int i = 0; i < nelems; i++) { @@ -660,7 +671,7 @@ public class HDFArray { private byte[] FloatObjToByte(Float in[]) { - int nelems = java.lang.reflect.Array.getLength((Object) in); + int nelems = java.lang.reflect.Array.getLength((Object)in); float[] out = new float[nelems]; for (int i = 0; i < nelems; i++) { @@ -671,8 +682,8 @@ public class HDFArray { private Float[] ByteToFloatObj(byte[] bin) { - float in[] = (float[]) HDFNativeData.byteToFloat(bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + float in[] = (float[])HDFNativeData.byteToFloat(bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Float[] out = new Float[nelems]; for (int i = 0; i < nelems; i++) { @@ -683,8 +694,8 @@ public class HDFArray { private Float[] ByteToFloatObj(int start, int len, byte[] bin) { - float in[] = (float[]) HDFNativeData.byteToFloat(start, len, bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + float in[] = (float[])HDFNativeData.byteToFloat(start, len, bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Float[] out = new Float[nelems]; for (int i = 0; i < nelems; i++) { @@ -695,7 +706,7 @@ public class HDFArray { private byte[] DoubleObjToByte(Double in[]) { - int nelems = java.lang.reflect.Array.getLength((Object) in); + int nelems = java.lang.reflect.Array.getLength((Object)in); double[] out = new double[nelems]; for (int i = 0; i < nelems; i++) { @@ -706,8 +717,8 @@ public class HDFArray { private Double[] ByteToDoubleObj(byte[] bin) { - double in[] = (double[]) HDFNativeData.byteToDouble(bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + double in[] = (double[])HDFNativeData.byteToDouble(bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Double[] out = new Double[nelems]; for (int i = 0; i < nelems; i++) { @@ -718,8 +729,8 @@ public class HDFArray { private Double[] ByteToDoubleObj(int start, int len, byte[] bin) { - double in[] = (double[]) HDFNativeData.byteToDouble(start, len, bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + double in[] = (double[])HDFNativeData.byteToDouble(start, len, bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Double[] out = new Double[nelems]; for (int i = 0; i < nelems; i++) { @@ -730,7 +741,7 @@ public class HDFArray { private byte[] LongObjToByte(Long in[]) { - int nelems = java.lang.reflect.Array.getLength((Object) in); + int nelems = java.lang.reflect.Array.getLength((Object)in); long[] out = new long[nelems]; for (int i = 0; i < nelems; i++) { @@ -741,8 +752,8 @@ public class HDFArray { private Long[] ByteToLongObj(byte[] bin) { - long in[] = (long[]) HDFNativeData.byteToLong(bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + long in[] = (long[])HDFNativeData.byteToLong(bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Long[] out = new Long[nelems]; for (int i = 0; i < nelems; i++) { @@ -753,8 +764,8 @@ public class HDFArray { private Long[] ByteToLongObj(int start, int len, byte[] bin) { - long in[] = (long[]) HDFNativeData.byteToLong(start, len, bin); - int nelems = java.lang.reflect.Array.getLength((Object) in); + long in[] = (long[])HDFNativeData.byteToLong(start, len, bin); + int nelems = java.lang.reflect.Array.getLength((Object)in); Long[] out = new Long[nelems]; for (int i = 0; i < nelems; i++) { @@ -770,18 +781,18 @@ public class HDFArray { * We use java.lang.reflection here. */ class ArrayDescriptor { - static String theType = ""; - static Class theClass = null; - static int[] dimlen = null; - static int[] dimstart = null; + static String theType = ""; + static Class theClass = null; + static int[] dimlen = null; + static int[] dimstart = null; static int[] currentindex = null; - static int[] bytetoindex = null; - static int totalSize = 0; - static int totalElements = 0; - static Object[] objs = null; - static char NT = ' '; /* must be B,S,I,L,F,D, else error */ - static int NTsize = 0; - static int dims = 0; + static int[] bytetoindex = null; + static int totalSize = 0; + static int totalElements = 0; + static Object[] objs = null; + static char NT = ' '; /* must be B,S,I,L,F,D, else error */ + static int NTsize = 0; + static int dims = 0; static String className; public ArrayDescriptor(Object anArray) throws HDF5JavaException @@ -790,7 +801,7 @@ class ArrayDescriptor { if (tc.isArray() == false) { /* exception: not an array */ HDF5JavaException ex = new HDF5JavaException("ArrayDescriptor: not an array?: "); - throw (ex); + throw(ex); } theClass = tc; @@ -799,10 +810,10 @@ class ArrayDescriptor { * parse the type descriptor to discover the shape of the array */ String ss = tc.toString(); - theType = ss; - int n = 6; - dims = 0; - char c = ' '; + theType = ss; + int n = 6; + dims = 0; + char c = ' '; while (n < ss.length()) { c = ss.charAt(n); n++; @@ -811,10 +822,10 @@ class ArrayDescriptor { } } - String css = ss.substring(ss.lastIndexOf('[') + 1); + String css = ss.substring(ss.lastIndexOf('[') + 1); Class compC = tc.getComponentType(); - String cs = compC.toString(); - NT = c; /* must be B,S,I,L,F,D, else error */ + String cs = compC.toString(); + NT = c; /* must be B,S,I,L,F,D, else error */ if (NT == 'B') { NTsize = 1; } @@ -828,68 +839,69 @@ class ArrayDescriptor { NTsize = 8; } else if (css.startsWith("Ljava.lang.Byte")) { - NT = 'L'; + NT = 'L'; className = "java.lang.Byte"; - NTsize = 1; + NTsize = 1; } else if (css.startsWith("Ljava.lang.Short")) { - NT = 'L'; + NT = 'L'; className = "java.lang.Short"; - NTsize = 2; + NTsize = 2; } else if (css.startsWith("Ljava.lang.Integer")) { - NT = 'L'; + NT = 'L'; className = "java.lang.Integer"; - NTsize = 4; + NTsize = 4; } else if (css.startsWith("Ljava.lang.Float")) { - NT = 'L'; + NT = 'L'; className = "java.lang.Float"; - NTsize = 4; + NTsize = 4; } else if (css.startsWith("Ljava.lang.Double")) { - NT = 'L'; + NT = 'L'; className = "java.lang.Double"; - NTsize = 8; + NTsize = 8; } else if (css.startsWith("Ljava.lang.Long")) { - NT = 'L'; + NT = 'L'; className = "java.lang.Long"; - NTsize = 8; + NTsize = 8; } else if (css.startsWith("Ljava.lang.String")) { - NT = 'L'; + NT = 'L'; className = "java.lang.String"; - NTsize = 1; - throw new HDF5JavaException(new String("ArrayDesciptor: Warning: String array not fully supported yet")); + NTsize = 1; + throw new HDF5JavaException( + new String("ArrayDesciptor: Warning: String array not fully supported yet")); } else { /* * exception: not a numeric type */ throw new HDF5JavaException( - new String("ArrayDesciptor: Error: array is not numeric (type is " + css + ") ?")); + new String("ArrayDesciptor: Error: array is not numeric (type is " + css + ") ?")); } /* fill in the table */ - dimlen = new int[dims + 1]; - dimstart = new int[dims + 1]; + dimlen = new int[dims + 1]; + dimstart = new int[dims + 1]; currentindex = new int[dims + 1]; - bytetoindex = new int[dims + 1]; - objs = new Object[dims + 1]; + bytetoindex = new int[dims + 1]; + objs = new Object[dims + 1]; - Object o = anArray; - objs[0] = o; - dimlen[0] = 1; - dimstart[0] = 0; + Object o = anArray; + objs[0] = o; + dimlen[0] = 1; + dimstart[0] = 0; currentindex[0] = 0; - int elements = 1; + int elements = 1; int i; for (i = 1; i <= dims; i++) { - dimlen[i] = java.lang.reflect.Array.getLength((Object) o); - o = java.lang.reflect.Array.get((Object) o, 0); - objs[i] = o; - dimstart[i] = 0; + dimlen[i] = java.lang.reflect.Array.getLength((Object)o); + o = java.lang.reflect.Array.get((Object)o, 0); + objs[i] = o; + dimstart[i] = 0; currentindex[i] = 0; elements *= dimlen[i]; } @@ -917,14 +929,15 @@ class ArrayDescriptor { System.out.println("Type: " + theType); System.out.println("Class: " + theClass); System.out.println("NT: " + NT + " NTsize: " + NTsize); - System.out.println("Array has " + dims + " dimensions (" + totalSize - + " bytes, " + totalElements + " elements)"); + System.out.println("Array has " + dims + " dimensions (" + totalSize + " bytes, " + totalElements + + " elements)"); int i; for (i = 0; i <= dims; i++) { - Class tc = objs[i].getClass(); + Class tc = objs[i].getClass(); String ss = tc.toString(); - System.out.println(i + ": start " + dimstart[i] + ": len " + dimlen[i] + " current " + currentindex[i] - + " bytetoindex " + bytetoindex[i] + " object " + objs[i] + " otype " + ss); + System.out.println(i + ": start " + dimstart[i] + ": len " + dimlen[i] + " current " + + currentindex[i] + " bytetoindex " + bytetoindex[i] + " object " + objs[i] + + " otype " + ss); } } } diff --git a/java/src/hdf/hdf5lib/HDFNativeData.java b/java/src/hdf/hdf5lib/HDFNativeData.java index 85378db..c497043 100644 --- a/java/src/hdf/hdf5lib/HDFNativeData.java +++ b/java/src/hdf/hdf5lib/HDFNativeData.java @@ -95,8 +95,7 @@ public class HDFNativeData { * The input array of bytes * @return an array of 'len' int */ - public synchronized static native int[] byteToInt(int start, int len, - byte[] data); + public synchronized static native int[] byteToInt(int start, int len, byte[] data); /** * Convert 4 bytes from an array of bytes into a single int @@ -107,9 +106,10 @@ public class HDFNativeData { * The input array of bytes * @return The integer value of the bytes. */ - public synchronized static int byteToInt(byte[] data, int start) { + public synchronized static int byteToInt(byte[] data, int start) + { int[] ival = new int[1]; - ival = byteToInt(start, 1, data); + ival = byteToInt(start, 1, data); return (ival[0]); } @@ -124,8 +124,7 @@ public class HDFNativeData { * The input array of bytes * @return an array of 'len' short */ - public synchronized static native short[] byteToShort(int start, int len, - byte[] data); + public synchronized static native short[] byteToShort(int start, int len, byte[] data); /** * Convert 2 bytes from an array of bytes into a single short @@ -136,9 +135,10 @@ public class HDFNativeData { * The input array of bytes * @return The short value of the bytes. */ - public synchronized static short byteToShort(byte[] data, int start) { + public synchronized static short byteToShort(byte[] data, int start) + { short[] sval = new short[1]; - sval = byteToShort(start, 1, data); + sval = byteToShort(start, 1, data); return (sval[0]); } @@ -164,9 +164,10 @@ public class HDFNativeData { * The input array of bytes * @return The float value of the bytes. */ - public synchronized static float byteToFloat(byte[] data, int start) { + public synchronized static float byteToFloat(byte[] data, int start) + { float[] fval = new float[1]; - fval = byteToFloat(start, 1, data); + fval = byteToFloat(start, 1, data); return (fval[0]); } @@ -181,8 +182,7 @@ public class HDFNativeData { * The input array of bytes * @return an array of 'len' long */ - public synchronized static native long[] byteToLong(int start, int len, - byte[] data); + public synchronized static native long[] byteToLong(int start, int len, byte[] data); /** * Convert 8 bytes from an array of bytes into a single long @@ -193,9 +193,10 @@ public class HDFNativeData { * The input array of bytes * @return The long value of the bytes. */ - public synchronized static long byteToLong(byte[] data, int start) { + public synchronized static long byteToLong(byte[] data, int start) + { long[] lval = new long[1]; - lval = byteToLong(start, 1, data); + lval = byteToLong(start, 1, data); return (lval[0]); } @@ -210,8 +211,7 @@ public class HDFNativeData { * The input array of bytes * @return an array of 'len' double */ - public synchronized static native double[] byteToDouble(int start, int len, - byte[] data); + public synchronized static native double[] byteToDouble(int start, int len, byte[] data); /** * Convert 8 bytes from an array of bytes into a single double @@ -222,9 +222,10 @@ public class HDFNativeData { * The input array of bytes * @return The double value of the bytes. */ - public synchronized static double byteToDouble(byte[] data, int start) { + public synchronized static double byteToDouble(byte[] data, int start) + { double[] dval = new double[1]; - dval = byteToDouble(start, 1, data); + dval = byteToDouble(start, 1, data); return (dval[0]); } @@ -239,8 +240,7 @@ public class HDFNativeData { * The input array of int * @return an array of bytes */ - public synchronized static native byte[] intToByte(int start, int len, - int[] data); + public synchronized static native byte[] intToByte(int start, int len, int[] data); /** * Convert a range from an array of short into an array of bytes. @@ -253,8 +253,7 @@ public class HDFNativeData { * The input array of short * @return an array of bytes */ - public synchronized static native byte[] shortToByte(int start, int len, - short[] data); + public synchronized static native byte[] shortToByte(int start, int len, short[] data); /** * Convert a range from an array of float into an array of bytes. @@ -267,8 +266,7 @@ public class HDFNativeData { * The input array of float * @return an array of bytes */ - public synchronized static native byte[] floatToByte(int start, int len, - float[] data); + public synchronized static native byte[] floatToByte(int start, int len, float[] data); /** * Convert a range from an array of long into an array of bytes. @@ -281,8 +279,7 @@ public class HDFNativeData { * The input array of long * @return an array of bytes */ - public synchronized static native byte[] longToByte(int start, int len, - long[] data); + public synchronized static native byte[] longToByte(int start, int len, long[] data); /** * Convert a range from an array of double into an array of bytes. @@ -295,8 +292,7 @@ public class HDFNativeData { * The input array of double * @return an array of bytes */ - public synchronized static native byte[] doubleToByte(int start, int len, - double[] data); + public synchronized static native byte[] doubleToByte(int start, int len, double[] data); /** * Convert a single byte into an array of one byte. @@ -318,9 +314,7 @@ public class HDFNativeData { * The input Byte * @return an array of bytes */ - public synchronized static byte[] byteToByte(Byte data) { - return byteToByte(data.byteValue()); - } + public synchronized static byte[] byteToByte(Byte data) { return byteToByte(data.byteValue()); } /** * Convert a single int into an array of 4 bytes. @@ -338,9 +332,7 @@ public class HDFNativeData { * The input Integer * @return an array of bytes */ - public synchronized static byte[] intToByte(Integer data) { - return intToByte(data.intValue()); - } + public synchronized static byte[] intToByte(Integer data) { return intToByte(data.intValue()); } /** * Convert a single short into an array of 2 bytes. @@ -358,9 +350,7 @@ public class HDFNativeData { * The input Short * @return an array of bytes */ - public synchronized static byte[] shortToByte(Short data) { - return shortToByte(data.shortValue()); - } + public synchronized static byte[] shortToByte(Short data) { return shortToByte(data.shortValue()); } /** * Convert a single float into an array of 4 bytes. @@ -378,9 +368,7 @@ public class HDFNativeData { * The input Float * @return an array of bytes */ - public synchronized static byte[] floatToByte(Float data) { - return floatToByte(data.floatValue()); - }; + public synchronized static byte[] floatToByte(Float data) { return floatToByte(data.floatValue()); }; /** * Convert a single long into an array of 8 bytes. @@ -398,9 +386,7 @@ public class HDFNativeData { * The input Long * @return an array of bytes */ - public synchronized static byte[] longToByte(Long data) { - return longToByte(data.longValue()); - } + public synchronized static byte[] longToByte(Long data) { return longToByte(data.longValue()); } /** * Convert a single double into an array of 8 bytes. @@ -418,9 +404,7 @@ public class HDFNativeData { * The input Double * @return an array of bytes */ - public synchronized static byte[] doubleToByte(Double data) { - return doubleToByte(data.doubleValue()); - } + public synchronized static byte[] doubleToByte(Double data) { return doubleToByte(data.doubleValue()); } /** * Create a Number object from an array of bytes. @@ -435,40 +419,39 @@ public class HDFNativeData { * @exception HDF5Exception * - Error unsupported type. */ - public synchronized static Object byteToNumber(byte[] barray, Object obj) - throws HDF5Exception + public synchronized static Object byteToNumber(byte[] barray, Object obj) throws HDF5Exception { Class theClass = obj.getClass(); - String type = theClass.getName(); - Object retobj = null; + String type = theClass.getName(); + Object retobj = null; if (type.equals("java.lang.Integer")) { int[] i = hdf.hdf5lib.HDFNativeData.byteToInt(0, 1, barray); - retobj = Integer.valueOf(i[0]); + retobj = Integer.valueOf(i[0]); } else if (type.equals("java.lang.Byte")) { retobj = Byte.valueOf(barray[0]); } else if (type.equals("java.lang.Short")) { short[] f = hdf.hdf5lib.HDFNativeData.byteToShort(0, 1, barray); - retobj = Short.valueOf(f[0]); + retobj = Short.valueOf(f[0]); } else if (type.equals("java.lang.Float")) { float[] f = hdf.hdf5lib.HDFNativeData.byteToFloat(0, 1, barray); - retobj = Float.valueOf(f[0]); + retobj = Float.valueOf(f[0]); } else if (type.equals("java.lang.Long")) { long[] f = hdf.hdf5lib.HDFNativeData.byteToLong(0, 1, barray); - retobj = Long.valueOf(f[0]); + retobj = Long.valueOf(f[0]); } else if (type.equals("java.lang.Double")) { double[] f = hdf.hdf5lib.HDFNativeData.byteToDouble(0, 1, barray); - retobj = Double.valueOf(f[0]); + retobj = Double.valueOf(f[0]); } else { /* exception: unsupported type */ HDF5Exception ex = new HDF5JavaException("byteToNumber: setfield bad type: " + obj + " " + type); - throw (ex); + throw(ex); } return (retobj); } diff --git a/java/src/hdf/hdf5lib/callbacks/Callbacks.java b/java/src/hdf/hdf5lib/callbacks/Callbacks.java index 11fa465..86d6193 100644 --- a/java/src/hdf/hdf5lib/callbacks/Callbacks.java +++ b/java/src/hdf/hdf5lib/callbacks/Callbacks.java @@ -12,7 +12,8 @@ package hdf.hdf5lib.callbacks; -/** All callback definitions must derive from this interface. Any +/** + * All callback definitions must derive from this interface. Any * derived interfaces must define a single public method named "callback". * You are responsible for deregistering your callback (if necessary) * in its {@link Object#finalize} method. If native code attempts to call @@ -26,5 +27,4 @@ package hdf.hdf5lib.callbacks; * handler. */ public interface Callbacks { - } diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java index d612db3..45bde9a 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5A_iterate_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java index 7fdb454..cb17896 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5D_append_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java index 305cf98..fb48c73 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5D_iterate_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java index 5bf0c8b..131b33f 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5E_walk_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java index d89fd2a..c657dbc 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java @@ -17,5 +17,4 @@ package hdf.hdf5lib.callbacks; * */ public interface H5L_iterate_opdata_t { - } diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java index fd643b4..f4a4412 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java @@ -17,5 +17,4 @@ package hdf.hdf5lib.callbacks; * */ public interface H5O_iterate_opdata_t { - } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java index 11e3a99..059addf 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5P_cls_close_func_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java index 78e5282..4b7cf11 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5P_cls_copy_func_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java index d919d97..917264d 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5P_cls_create_func_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java index 0035619..9c0d0eb 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java @@ -17,7 +17,8 @@ package hdf.hdf5lib.callbacks; * */ public interface H5P_iterate_t { -/** public ArrayList iterdata = new ArrayList(); - * Any derived interfaces must define the single public variable as above. - */ + /** + * public ArrayList iterdata = new ArrayList(); + * Any derived interfaces must define the single public variable as above. + */ } diff --git a/java/src/hdf/hdf5lib/callbacks/package-info.java b/java/src/hdf/hdf5lib/callbacks/package-info.java index 0833162..114045c 100644 --- a/java/src/hdf/hdf5lib/callbacks/package-info.java +++ b/java/src/hdf/hdf5lib/callbacks/package-info.java @@ -11,7 +11,8 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/** All callback definitions must derive from the Callbacks interface. Any +/** + * All callback definitions must derive from the Callbacks interface. Any * derived interfaces must define a single public method named "callback". * You are responsible for deregistering your callback (if necessary) * in its {@link Object#finalize} method. If native code attempts to call diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java b/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java index 86dad88..4cb7b1d 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java @@ -23,9 +23,7 @@ public class HDF5AttributeException extends HDF5LibraryException { * Constructs an <code>HDF5AttributeException</code> with no specified * detail message. */ - public HDF5AttributeException() { - super(); - } + public HDF5AttributeException() { super(); } /** * Constructs an <code>HDF5AttributeException</code> with the specified @@ -34,7 +32,5 @@ public class HDF5AttributeException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5AttributeException(String s) { - super(s); - } + public HDF5AttributeException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java b/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java index 97585d3..9f70456 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java @@ -23,9 +23,7 @@ public class HDF5BtreeException extends HDF5LibraryException { * Constructs an <code>HDF5BtreeException</code> with no specified detail * message. */ - public HDF5BtreeException() { - super(); - } + public HDF5BtreeException() { super(); } /** * Constructs an <code>HDF5BtreeException</code> with the specified detail @@ -34,7 +32,5 @@ public class HDF5BtreeException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5BtreeException(String s) { - super(s); - } + public HDF5BtreeException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java index b02d815..b4397b7 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java @@ -23,9 +23,7 @@ public class HDF5DataFiltersException extends HDF5LibraryException { * Constructs an <code>HDF5DataFiltersException</code> with no specified * detail message. */ - public HDF5DataFiltersException() { - super(); - } + public HDF5DataFiltersException() { super(); } /** * Constructs an <code>HDF5DataFiltersException</code> with the specified @@ -34,7 +32,5 @@ public class HDF5DataFiltersException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5DataFiltersException(String s) { - super(s); - } + public HDF5DataFiltersException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java index 416b06a..f6993a8 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java @@ -24,9 +24,7 @@ public class HDF5DataStorageException extends HDF5LibraryException { * Constructs an <code>HDF5DataStorageExceptionn</code> with no specified * detail message. */ - public HDF5DataStorageException() { - super(); - } + public HDF5DataStorageException() { super(); } /** * Constructs an <code>HDF5DataStorageException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5DataStorageException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5DataStorageException(String s) { - super(s); - } + public HDF5DataStorageException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java index 7bb22fa..8fd4ae9 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java @@ -23,9 +23,7 @@ public class HDF5DatasetInterfaceException extends HDF5LibraryException { * Constructs an <code>HDF5DatasetInterfaceException</code> with no * specified detail message. */ - public HDF5DatasetInterfaceException() { - super(); - } + public HDF5DatasetInterfaceException() { super(); } /** * Constructs an <code>HDF5DatasetInterfaceException</code> with the @@ -34,7 +32,5 @@ public class HDF5DatasetInterfaceException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5DatasetInterfaceException(String s) { - super(s); - } + public HDF5DatasetInterfaceException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java index 9a85ff0..d0d2a09 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java @@ -24,9 +24,7 @@ public class HDF5DataspaceInterfaceException extends HDF5LibraryException { * Constructs an <code>HDF5DataspaceInterfaceException</code> with no * specified detail message. */ - public HDF5DataspaceInterfaceException() { - super(); - } + public HDF5DataspaceInterfaceException() { super(); } /** * Constructs an <code>HDF5DataspaceInterfaceException</code> with the @@ -35,7 +33,5 @@ public class HDF5DataspaceInterfaceException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5DataspaceInterfaceException(String s) { - super(s); - } + public HDF5DataspaceInterfaceException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java index 45b0c55..2ab4ff9 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java @@ -24,9 +24,7 @@ public class HDF5DatatypeInterfaceException extends HDF5LibraryException { * Constructs an <code>HDF5DatatypeInterfaceException</code> with no * specified detail message. */ - public HDF5DatatypeInterfaceException() { - super(); - } + public HDF5DatatypeInterfaceException() { super(); } /** * Constructs an <code>HDF5DatatypeInterfaceException</code> with the @@ -35,7 +33,5 @@ public class HDF5DatatypeInterfaceException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5DatatypeInterfaceException(String s) { - super(s); - } + public HDF5DatatypeInterfaceException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java index 0c23af1..b098a12 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java @@ -40,9 +40,7 @@ public class HDF5Exception extends RuntimeException { * Constructs an <code>HDF5Exception</code> with no specified detail * message. */ - public HDF5Exception() { - super(); - } + public HDF5Exception() { super(); } /** * Constructs an <code>HDF5Exception</code> with the specified detail @@ -51,7 +49,8 @@ public class HDF5Exception extends RuntimeException { * @param message * the detail message. */ - public HDF5Exception(String message) { + public HDF5Exception(String message) + { super(); detailMessage = message; } @@ -63,7 +62,8 @@ public class HDF5Exception extends RuntimeException { * have a detail message. */ @Override - public String getMessage() { + public String getMessage() + { return detailMessage; } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java index 73bf069..c8df3d0 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java @@ -24,9 +24,7 @@ public class HDF5ExternalFileListException extends HDF5LibraryException { * Constructs an <code>HDF5ExternalFileListException</code> with no * specified detail message. */ - public HDF5ExternalFileListException() { - super(); - } + public HDF5ExternalFileListException() { super(); } /** * Constructs an <code>HDF5ExternalFileListException</code> with the @@ -35,7 +33,5 @@ public class HDF5ExternalFileListException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5ExternalFileListException(String s) { - super(s); - } + public HDF5ExternalFileListException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java index ac82258..afd6d69 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java @@ -24,9 +24,7 @@ public class HDF5FileInterfaceException extends HDF5LibraryException { * Constructs an <code>HDF5FileInterfaceException</code> with no specified * detail message. */ - public HDF5FileInterfaceException() { - super(); - } + public HDF5FileInterfaceException() { super(); } /** * Constructs an <code>HDF5FileInterfaceException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5FileInterfaceException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5FileInterfaceException(String s) { - super(s); - } + public HDF5FileInterfaceException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java index c4fcf30..58e2980 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java @@ -24,9 +24,7 @@ public class HDF5FunctionArgumentException extends HDF5LibraryException { * Constructs an <code>HDF5FunctionArgumentException</code> with no * specified detail message. */ - public HDF5FunctionArgumentException() { - super(); - } + public HDF5FunctionArgumentException() { super(); } /** * Constructs an <code>HDF5FunctionArgumentException</code> with the @@ -35,7 +33,5 @@ public class HDF5FunctionArgumentException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5FunctionArgumentException(String s) { - super(s); - } + public HDF5FunctionArgumentException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java index ee34b59..db46aae 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java @@ -24,9 +24,7 @@ public class HDF5FunctionEntryExitException extends HDF5LibraryException { * Constructs an <code>HDF5FunctionEntryExitException</code> with no * specified detail message. */ - public HDF5FunctionEntryExitException() { - super(); - } + public HDF5FunctionEntryExitException() { super(); } /** * Constructs an <code>HDF5FunctionEntryExitException</code> with the @@ -35,7 +33,5 @@ public class HDF5FunctionEntryExitException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5FunctionEntryExitException(String s) { - super(s); - } + public HDF5FunctionEntryExitException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java b/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java index 1bb3251..7f1691d 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java @@ -24,9 +24,7 @@ public class HDF5HeapException extends HDF5LibraryException { * Constructs an <code>HDF5HeapException</code> with no specified detail * message. */ - public HDF5HeapException() { - super(); - } + public HDF5HeapException() { super(); } /** * Constructs an <code>HDF5HeapException</code> with the specified detail @@ -35,7 +33,5 @@ public class HDF5HeapException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5HeapException(String s) { - super(s); - } + public HDF5HeapException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5IdException.java b/java/src/hdf/hdf5lib/exceptions/HDF5IdException.java index 04ee0bc..5ce1f01 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5IdException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5IdException.java @@ -24,9 +24,7 @@ public class HDF5IdException extends HDF5LibraryException { * Constructs an <code>HDF5IdException</code> with no specified detail * message. */ - public HDF5IdException() { - super(); - } + public HDF5IdException() { super(); } /** * Constructs an <code>HDF5IdException</code> with the specified detail @@ -35,8 +33,5 @@ public class HDF5IdException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5IdException(String s) { - super(s); - } - + public HDF5IdException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java b/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java index 810c126..4489486 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java @@ -24,9 +24,7 @@ public class HDF5InternalErrorException extends HDF5LibraryException { * Constructs an <code>HDF5InternalErrorException</code> with no specified * detail message. */ - public HDF5InternalErrorException() { - super(); - } + public HDF5InternalErrorException() { super(); } /** * Constructs an <code>HDF5InternalErrorException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5InternalErrorException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5InternalErrorException(String s) { - super(s); - } + public HDF5InternalErrorException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java b/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java index 35720da..ae1cf85 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java @@ -26,9 +26,7 @@ public class HDF5JavaException extends HDF5Exception { * Constructs an <code>HDF5JavaException</code> with no specified detail * message. */ - public HDF5JavaException() { - super(); - } + public HDF5JavaException() { super(); } /** * Constructs an <code>HDF5JavaException</code> with the specified detail @@ -37,7 +35,5 @@ public class HDF5JavaException extends HDF5Exception { * @param s * the detail message. */ - public HDF5JavaException(String s) { - super(s); - } + public HDF5JavaException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java index 9f94882..2a4c8c7 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java @@ -39,7 +39,8 @@ public class HDF5LibraryException extends HDF5Exception { * Constructs an <code>HDF5LibraryException</code> with no specified detail * message. */ - public HDF5LibraryException() { + public HDF5LibraryException() + { super(); // this code forces the loading of the HDF-5 library @@ -52,7 +53,7 @@ public class HDF5LibraryException extends HDF5Exception { this.majorErrorNumber = _getMajorErrorNumber(); this.minorErrorNumber = _getMinorErrorNumber(); - detailMessage = getMinorError(minorErrorNumber); + detailMessage = getMinorError(minorErrorNumber); } /** @@ -62,7 +63,8 @@ public class HDF5LibraryException extends HDF5Exception { * @param s * the detail message. */ - public HDF5LibraryException(String s) { + public HDF5LibraryException(String s) + { super(s); // this code forces the loading of the HDF-5 library // to assure that the native methods are available @@ -81,10 +83,7 @@ public class HDF5LibraryException extends HDF5Exception { * * @return the major error number */ - public long getMajorErrorNumber() - { - return majorErrorNumber; - } + public long getMajorErrorNumber() { return majorErrorNumber; } private native long _getMajorErrorNumber(); /** @@ -93,10 +92,7 @@ public class HDF5LibraryException extends HDF5Exception { * * @return the minor error number */ - public long getMinorErrorNumber() - { - return minorErrorNumber; - } + public long getMinorErrorNumber() { return minorErrorNumber; } private native long _getMinorErrorNumber(); /** @@ -109,7 +105,8 @@ public class HDF5LibraryException extends HDF5Exception { * * @return the string of the minor error */ - public String getMinorError(long err_code) { + public String getMinorError(long err_code) + { if (err_code == 0) { return "special zero no error"; } @@ -356,9 +353,10 @@ public class HDF5LibraryException extends HDF5Exception { * stack, and and the Java stack trace to the standard error stream. */ @Override - public void printStackTrace() { + public void printStackTrace() + { System.err.println(this); - printStackTrace0(null); // the HDF-5 Library error stack + printStackTrace0(null); // the HDF-5 Library error stack super.printStackTrace(); // the Java stack trace } @@ -369,21 +367,21 @@ public class HDF5LibraryException extends HDF5Exception { * @param f * the file print stream. */ - public void printStackTrace(java.io.File f) { + public void printStackTrace(java.io.File f) + { if ((f == null) || !f.exists() || f.isDirectory() || !f.canWrite()) { printStackTrace(); } else { try { java.io.FileOutputStream o = new java.io.FileOutputStream(f); - java.io.PrintWriter p = new java.io.PrintWriter(o); + java.io.PrintWriter p = new java.io.PrintWriter(o); p.println(this); p.close(); } catch (Exception ex) { System.err.println(this); - } - ; + }; // the HDF-5 Library error stack printStackTrace0(f.getPath()); super.printStackTrace(); // the Java stack trace @@ -395,5 +393,4 @@ public class HDF5LibraryException extends HDF5Exception { * and error stack. */ private native void printStackTrace0(String s); - } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java b/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java index d61f4e9..fef5721 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java @@ -24,9 +24,7 @@ public class HDF5LowLevelIOException extends HDF5LibraryException { * Constructs an <code>HDF5LowLevelIOException</code> with no specified * detail message. */ - public HDF5LowLevelIOException() { - super(); - } + public HDF5LowLevelIOException() { super(); } /** * Constructs an <code>HDF5LowLevelIOException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5LowLevelIOException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5LowLevelIOException(String s) { - super(s); - } + public HDF5LowLevelIOException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java b/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java index 3b64b15..4f00006 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java @@ -24,9 +24,7 @@ public class HDF5MetaDataCacheException extends HDF5LibraryException { * Constructs an <code>HDF5MetaDataCacheException</code> with no specified * detail message. */ - public HDF5MetaDataCacheException() { - super(); - } + public HDF5MetaDataCacheException() { super(); } /** * Constructs an <code>HDF5MetaDataCacheException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5MetaDataCacheException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5MetaDataCacheException(String s) { - super(s); - } + public HDF5MetaDataCacheException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java index b9f40f8..9675354 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java @@ -24,9 +24,7 @@ public class HDF5ObjectHeaderException extends HDF5LibraryException { * Constructs an <code>HDF5ObjectHeaderException</code> with no specified * detail message. */ - public HDF5ObjectHeaderException() { - super(); - } + public HDF5ObjectHeaderException() { super(); } /** * Constructs an <code>HDF5ObjectHeaderException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5ObjectHeaderException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5ObjectHeaderException(String s) { - super(s); - } + public HDF5ObjectHeaderException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java index d2a20e0..66f0bd1 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java @@ -24,9 +24,7 @@ public class HDF5PropertyListInterfaceException extends HDF5LibraryException { * Constructs an <code>HDF5PropertyListInterfaceException</code> with no * specified detail message. */ - public HDF5PropertyListInterfaceException() { - super(); - } + public HDF5PropertyListInterfaceException() { super(); } /** * Constructs an <code>HDF5PropertyListInterfaceException</code> with the @@ -35,7 +33,5 @@ public class HDF5PropertyListInterfaceException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5PropertyListInterfaceException(String s) { - super(s); - } + public HDF5PropertyListInterfaceException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java index 0701244..4feaba7 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java @@ -24,9 +24,7 @@ public class HDF5ReferenceException extends HDF5LibraryException { * Constructs an <code>HDF5ReferenceException</code> with no specified * detail message. */ - public HDF5ReferenceException() { - super(); - } + public HDF5ReferenceException() { super(); } /** * Constructs an <code>HDF5ReferenceException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5ReferenceException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5ReferenceException(String s) { - super(s); - } + public HDF5ReferenceException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java index ad052b5..1a007e7 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java @@ -24,9 +24,7 @@ public class HDF5ResourceUnavailableException extends HDF5LibraryException { * Constructs an <code>HDF5ResourceUnavailableException</code> with no * specified detail message. */ - public HDF5ResourceUnavailableException() { - super(); - } + public HDF5ResourceUnavailableException() { super(); } /** * Constructs an <code>HDF5FunctionArgumentException</code> with the @@ -35,7 +33,5 @@ public class HDF5ResourceUnavailableException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5ResourceUnavailableException(String s) { - super(s); - } + public HDF5ResourceUnavailableException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java b/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java index ba9150f..4fb8c2e 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java @@ -24,9 +24,7 @@ public class HDF5SymbolTableException extends HDF5LibraryException { * Constructs an <code>HDF5SymbolTableException</code> with no specified * detail message. */ - public HDF5SymbolTableException() { - super(); - } + public HDF5SymbolTableException() { super(); } /** * Constructs an <code>HDF5SymbolTableException</code> with the specified @@ -35,7 +33,5 @@ public class HDF5SymbolTableException extends HDF5LibraryException { * @param s * the detail message. */ - public HDF5SymbolTableException(String s) { - super(s); - } + public HDF5SymbolTableException(String s) { super(s); } } diff --git a/java/src/hdf/hdf5lib/package-info.java b/java/src/hdf/hdf5lib/package-info.java index 2863f5a..c04b862 100644 --- a/java/src/hdf/hdf5lib/package-info.java +++ b/java/src/hdf/hdf5lib/package-info.java @@ -11,11 +11,11 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - /** * This package 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 + * 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: @@ -25,7 +25,8 @@ * <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 + * In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in + the HDF * Reference Manual. * * <table border=1> @@ -66,16 +67,21 @@ * </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, + * 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 + * 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 + * 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: @@ -97,11 +103,13 @@ * </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 + * 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> @@ -109,39 +117,53 @@ * </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 + * 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). * <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 + * 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 + * <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: * * <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 + * 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 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". + * 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 + * <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> @@ -153,22 +175,31 @@ * <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 available from the - * JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural + * The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is + available 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 + * <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 + * 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> * * <b>See also: <a href="http://hdfgroup.org/HDF5/"> http://hdfgroup.org/HDF5"</a></b> - **/ + * + */ package hdf.hdf5lib; diff --git a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java index cf84532..a224124 100644 --- a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java +++ b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java @@ -18,7 +18,7 @@ import java.io.Serializable; * Information struct for H5Pget_mdc_config/H5Pset_mdc_config * */ -public class H5AC_cache_config_t implements Serializable{ +public class H5AC_cache_config_t implements Serializable { private static final long serialVersionUID = -6748085696476149972L; // general configuration fields /** @@ -27,7 +27,7 @@ public class H5AC_cache_config_t implements Serializable{ * H5AC_cache_config_t passed to the cache must have a known * version number, or an error will be flagged. */ - public int version; + public int version; /** * rpt_fcn_enabled: Boolean field used to enable and disable the default * reporting function. This function is invoked every time the @@ -35,80 +35,80 @@ public class H5AC_cache_config_t implements Serializable{ * * This is a debugging function, and should normally be turned off. */ - public boolean rpt_fcn_enabled; + public boolean rpt_fcn_enabled; /** * open_trace_file: Boolean field indicating whether the trace_file_name * field should be used to open a trace file for the cache. * * *** DEPRECATED *** Use H5Fstart/stop logging functions instead */ - public boolean open_trace_file; + public boolean open_trace_file; /** * close_trace_file: Boolean field indicating whether the current trace * file (if any) should be closed. * * *** DEPRECATED *** Use H5Fstart/stop logging functions instead */ - public boolean close_trace_file; + public boolean close_trace_file; /** * trace_file_name: Full path of the trace file to be opened if the * open_trace_file field is TRUE. * * *** DEPRECATED *** Use H5Fstart/stop logging functions instead */ - public String trace_file_name; + public String trace_file_name; /** * evictions_enabled: Boolean field used to either report the current * evictions enabled status of the cache, or to set the cache's * evictions enabled status. */ - public boolean evictions_enabled; + public boolean evictions_enabled; /** * set_initial_size: Boolean flag indicating whether the size of the * initial size of the cache is to be set to the value given in * the initial_size field. If set_initial_size is FALSE, the * initial_size field is ignored. */ - public boolean set_initial_size; + public boolean set_initial_size; /** * initial_size: If enabled, this field contain the size the cache is * to be set to upon receipt of this structure. Needless to say, * initial_size must lie in the closed interval [min_size, max_size]. */ - public long initial_size; + public long initial_size; /** * min_clean_fraction: double in the range 0 to 1 indicating the fraction * of the cache that is to be kept clean. This field is only used * in parallel mode. Typical values are 0.1 to 0.5. */ - public double min_clean_fraction; + public double min_clean_fraction; /** * max_size: Maximum size to which the cache can be adjusted. The * supplied value must fall in the closed interval * [MIN_MAX_CACHE_SIZE, MAX_MAX_CACHE_SIZE]. Also, max_size must * be greater than or equal to min_size. */ - public long max_size; + public long max_size; /** * min_size: Minimum size to which the cache can be adjusted. The * supplied value must fall in the closed interval * [H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE]. Also, min_size * must be less than or equal to max_size. */ - public long min_size; + public long min_size; /** * epoch_length: Number of accesses on the cache over which to collect * hit rate stats before running the automatic cache resize code, * if it is enabled. */ - public long epoch_length; + public long epoch_length; // size increase control fields /** * incr_mode: Instance of the H5C_cache_incr_mode enumerated type whose * value indicates how we determine whether the cache size should be * increased. At present there are two possible values. */ - public int incr_mode; + public int incr_mode; /** * lower_hr_threshold: Lower hit rate threshold. If the increment mode * (incr_mode) is H5C_incr__threshold and the hit rate drops below the @@ -117,105 +117,106 @@ public class H5AC_cache_config_t implements Serializable{ * max_size, and that the increment may be further restricted by the * max_increment field if it is enabled. */ - public double lower_hr_threshold; + public double lower_hr_threshold; /** * increment: Double containing the multiplier used to derive the new * cache size from the old if a cache size increment is triggered. * The increment must be greater than 1.0, and should not exceed 2.0. */ - public double increment; + public double increment; /** * apply_max_increment: Boolean flag indicating whether the max_increment * field should be used to limit the maximum cache size increment. */ - public boolean apply_max_increment; + public boolean apply_max_increment; /** * max_increment: If enabled by the apply_max_increment field described * above, this field contains the maximum number of bytes by which the * cache size can be increased in a single re-size. */ - public long max_increment; + public long max_increment; /** * flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated * type whose value indicates whether and by which algorithm we should * make flash increases in the size of the cache to accommodate insertion * of large entries and large increases in the size of a single entry. */ - public int flash_incr_mode; + public int flash_incr_mode; /** * flash_multiple: Double containing the multiple described above in the * H5C_flash_incr__add_space section of the discussion of the * flash_incr_mode section. This field is ignored unless flash_incr_mode * is H5C_flash_incr__add_space. */ - public double flash_multiple; + public double flash_multiple; /** * flash_threshold: Double containing the factor by which current max cache * size is multiplied to obtain the size threshold for the add_space flash * increment algorithm. The field is ignored unless flash_incr_mode is * H5C_flash_incr__add_space. */ - public double flash_threshold; + public double flash_threshold; // size decrease control fields /** * decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose * value indicates how we determine whether the cache size should be * decreased. At present there are four possibilities. */ - public int decr_mode; + public int decr_mode; /** * upper_hr_threshold: Upper hit rate threshold. The use of this field * varies according to the current decr_mode. */ - public double upper_hr_threshold; + public double upper_hr_threshold; /** * decrement: This field is only used when the decr_mode is * H5C_decr__threshold. */ - public double decrement; + public double decrement; /** * apply_max_decrement: Boolean flag used to determine whether decrements * in cache size are to be limited by the max_decrement field. */ - public boolean apply_max_decrement; + public boolean apply_max_decrement; /** * max_decrement: Maximum number of bytes by which the cache size can be * decreased in a single re-size. Note that decrements may also be * restricted by the min_size of the cache, and (in age out modes) by * the empty_reserve field. */ - public long max_decrement; + public long max_decrement; /** * epochs_before_eviction: Integer field used in H5C_decr__age_out and * H5C_decr__age_out_with_threshold decrement modes. */ - public int epochs_before_eviction; + public int epochs_before_eviction; /** * apply_empty_reserve: Boolean field controlling whether the empty_reserve * field is to be used in computing the new cache size when the * decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold. */ - public boolean apply_empty_reserve; + public boolean apply_empty_reserve; /** * empty_reserve: To avoid a constant racheting down of cache size by small * amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold * modes, this field allows one to require that any cache size * reductions leave the specified fraction of unused space in the cache. */ - public double empty_reserve; + public double empty_reserve; // parallel configuration fields /** * dirty_bytes_threshold: Threshold of dirty byte creation used to * synchronize updates between caches. */ - public long dirty_bytes_threshold; + public long dirty_bytes_threshold; /** * metadata_write_strategy: Integer field containing a code indicating the * desired metadata write strategy. */ - public int metadata_write_strategy; + public int metadata_write_strategy; - /** H5AC_cache_config_t is a public structure intended for use in public APIs. + /** + * H5AC_cache_config_t is a public structure intended for use in public APIs. * At least in its initial incarnation, it is basically a copy of struct * H5C_auto_size_ctl_t, minus the report_fcn field, and plus the * dirty_bytes_threshold field. @@ -283,46 +284,47 @@ public class H5AC_cache_config_t implements Serializable{ * synchronize updates between caches. * @param metadata_write_strategy: Integer field containing a code indicating the * desired metadata write strategy. - */ - public H5AC_cache_config_t (int version, boolean rpt_fcn_enabled, boolean open_trace_file, - boolean close_trace_file, String trace_file_name, boolean evictions_enabled, - boolean set_initial_size, long initial_size, double min_clean_fraction, long max_size, - long min_size, long epoch_length, int incr_mode, double lower_hr_threshold, - double increment, boolean apply_max_increment, long max_increment, int flash_incr_mode, - double flash_multiple, double flash_threshold, int decr_mode, double upper_hr_threshold, - double decrement, boolean apply_max_decrement, long max_decrement, - int epochs_before_eviction, boolean apply_empty_reserve, double empty_reserve, - long dirty_bytes_threshold, int metadata_write_strategy) + */ + public H5AC_cache_config_t(int version, boolean rpt_fcn_enabled, boolean open_trace_file, + boolean close_trace_file, String trace_file_name, boolean evictions_enabled, + boolean set_initial_size, long initial_size, double min_clean_fraction, + long max_size, long min_size, long epoch_length, int incr_mode, + double lower_hr_threshold, double increment, boolean apply_max_increment, + long max_increment, int flash_incr_mode, double flash_multiple, + double flash_threshold, int decr_mode, double upper_hr_threshold, + double decrement, boolean apply_max_decrement, long max_decrement, + int epochs_before_eviction, boolean apply_empty_reserve, double empty_reserve, + long dirty_bytes_threshold, int metadata_write_strategy) { - this.version = version; - this.rpt_fcn_enabled = rpt_fcn_enabled; - this.open_trace_file = open_trace_file; - this.close_trace_file = close_trace_file; - this.trace_file_name = trace_file_name; - this.evictions_enabled = evictions_enabled; - this.set_initial_size = set_initial_size; - this.initial_size = initial_size; - this.min_clean_fraction = min_clean_fraction; - this.max_size = max_size; - this.min_size = min_size; - this.epoch_length = epoch_length; - this.incr_mode = incr_mode; - this.lower_hr_threshold = lower_hr_threshold; - this.increment = increment; - this.apply_max_increment = apply_max_increment; - this.max_increment = flash_incr_mode; - this.flash_incr_mode = flash_incr_mode; - this.flash_multiple = flash_multiple; - this.flash_threshold = flash_threshold; - this.decr_mode = decr_mode; - this.upper_hr_threshold = upper_hr_threshold; - this.decrement = decrement; - this.apply_max_decrement = apply_max_decrement; - this.max_decrement = max_decrement; - this.epochs_before_eviction = epochs_before_eviction; - this.apply_empty_reserve = apply_empty_reserve; - this.empty_reserve = empty_reserve; - this.dirty_bytes_threshold = dirty_bytes_threshold; + this.version = version; + this.rpt_fcn_enabled = rpt_fcn_enabled; + this.open_trace_file = open_trace_file; + this.close_trace_file = close_trace_file; + this.trace_file_name = trace_file_name; + this.evictions_enabled = evictions_enabled; + this.set_initial_size = set_initial_size; + this.initial_size = initial_size; + this.min_clean_fraction = min_clean_fraction; + this.max_size = max_size; + this.min_size = min_size; + this.epoch_length = epoch_length; + this.incr_mode = incr_mode; + this.lower_hr_threshold = lower_hr_threshold; + this.increment = increment; + this.apply_max_increment = apply_max_increment; + this.max_increment = flash_incr_mode; + this.flash_incr_mode = flash_incr_mode; + this.flash_multiple = flash_multiple; + this.flash_threshold = flash_threshold; + this.decr_mode = decr_mode; + this.upper_hr_threshold = upper_hr_threshold; + this.decrement = decrement; + this.apply_max_decrement = apply_max_decrement; + this.max_decrement = max_decrement; + this.epochs_before_eviction = epochs_before_eviction; + this.apply_empty_reserve = apply_empty_reserve; + this.empty_reserve = empty_reserve; + this.dirty_bytes_threshold = dirty_bytes_threshold; this.metadata_write_strategy = metadata_write_strategy; } } diff --git a/java/src/hdf/hdf5lib/structs/H5A_info_t.java b/java/src/hdf/hdf5lib/structs/H5A_info_t.java index f2c10f0..364e480 100644 --- a/java/src/hdf/hdf5lib/structs/H5A_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5A_info_t.java @@ -18,7 +18,7 @@ import java.io.Serializable; * Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name) * */ -public class H5A_info_t implements Serializable{ +public class H5A_info_t implements Serializable { private static final long serialVersionUID = 2791443594041667613L; /** Indicate if creation order is valid */ public boolean corder_valid; @@ -29,10 +29,11 @@ public class H5A_info_t implements Serializable{ /** Size of raw data */ public long data_size; - H5A_info_t(boolean corder_valid, long corder, int cset, long data_size) { + H5A_info_t(boolean corder_valid, long corder, int cset, long data_size) + { this.corder_valid = corder_valid; - this.corder = corder; - this.cset = cset; - this.data_size = data_size; + this.corder = corder; + this.cset = cset; + this.data_size = data_size; } } diff --git a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java index 5981fc7..1be836f 100644 --- a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java +++ b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java @@ -18,16 +18,16 @@ import java.io.Serializable; * Information struct for Attribute (For H5Ewalk) * */ -public class H5E_error2_t implements Serializable{ +public class H5E_error2_t implements Serializable { private static final long serialVersionUID = 279144359041667613L; /** class ID */ - public long cls_id; + public long cls_id; /** major error ID */ - public long maj_num; + public long maj_num; /** minor error number */ - public long min_num; + public long min_num; /** line in file where error occurs */ - public int line; + public int line; /** function in which error occurred */ public String func_name; /** file in which error occurred */ @@ -35,13 +35,15 @@ public class H5E_error2_t implements Serializable{ /** optional supplied description */ public String desc; - H5E_error2_t(long cls_id, long maj_num, long min_num, int line, String func_name, String file_name, String desc) { - this.cls_id = cls_id; - this.maj_num = maj_num; - this.min_num = min_num; - this.line = line; + H5E_error2_t(long cls_id, long maj_num, long min_num, int line, String func_name, String file_name, + String desc) + { + this.cls_id = cls_id; + this.maj_num = maj_num; + this.min_num = min_num; + this.line = line; this.func_name = func_name; this.file_name = file_name; - this.desc = desc; + this.desc = desc; } } diff --git a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java index 95a9254..181d681 100644 --- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java +++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java @@ -26,17 +26,17 @@ public class H5FD_hdfs_fapl_t implements Serializable { private static final long serialVersionUID = 2072473407027648309L; /** Version number of the H5FD_hdfs_fapl_t structure. */ - private int version; + private int version; /** Name of "Name Node" to access as the HDFS server. */ private String namenode_name; /** Port number to use to connect with Name Node. */ - private int namenode_port; + private int namenode_port; /** Username to use when accessing file. */ private String user_name; /** Path to the location of the Kerberos authentication cache. */ private String kerberos_ticket_cache; /** Size (in bytes) of the file read stream buffer. */ - private int stream_buffer_size; + private int stream_buffer_size; /** * Create a fapl_t structure with the specified components. @@ -51,23 +51,20 @@ public class H5FD_hdfs_fapl_t implements Serializable { * @param stream_buffer_size * Size (in bytes) of the file read stream buffer. */ - public H5FD_hdfs_fapl_t( - String namenode_name, - int namenode_port, - String user_name, - String kerberos_ticket_cache, - int stream_buffer_size) + public H5FD_hdfs_fapl_t(String namenode_name, int namenode_port, String user_name, + String kerberos_ticket_cache, int stream_buffer_size) { - this.version = 1; - this.namenode_name = namenode_name; - this.namenode_port = namenode_port; - this.user_name = user_name; - this.kerberos_ticket_cache = kerberos_ticket_cache; - this.stream_buffer_size = stream_buffer_size; + this.version = 1; + this.namenode_name = namenode_name; + this.namenode_port = namenode_port; + this.user_name = user_name; + this.kerberos_ticket_cache = kerberos_ticket_cache; + this.stream_buffer_size = stream_buffer_size; } @Override - public boolean equals(Object o) { + public boolean equals(Object o) + { if (o == null) return false; if (!(o instanceof H5FD_hdfs_fapl_t)) @@ -90,7 +87,8 @@ public class H5FD_hdfs_fapl_t implements Serializable { } @Override - public int hashCode() { + public int hashCode() + { /* this is a _very bad_ hash algorithm for purposes of hashing! */ /* implemented to satisfy the "contract" regarding equality */ int k = (int)this.version; @@ -103,15 +101,11 @@ public class H5FD_hdfs_fapl_t implements Serializable { } @Override - public String toString() { - return "H5FD_hdfs_fapl_t (Version: " + this.version + ") {" + - "\n namenode_name: '" + this.namenode_name + - "'\n namenode_port: " + this.namenode_port + - "\n user_name: '" + this.user_name + - "'\n kerberos_ticket_cache: '" + this.kerberos_ticket_cache + - "'\n stream_buffer_size: " + this.stream_buffer_size + - "\n}\n"; + public String toString() + { + return "H5FD_hdfs_fapl_t (Version: " + this.version + ") {" + + "\n namenode_name: '" + this.namenode_name + "'\n namenode_port: " + this.namenode_port + + "\n user_name: '" + this.user_name + "'\n kerberos_ticket_cache: '" + + this.kerberos_ticket_cache + "'\n stream_buffer_size: " + this.stream_buffer_size + "\n}\n"; } } - - diff --git a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java index ad02979..67c2463 100644 --- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java +++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java @@ -46,7 +46,7 @@ public class H5FD_ros3_fapl_t implements Serializable { private static final long serialVersionUID = 8985533001471224030L; /** Version number of the H5FD_ros3_fapl_t structure */ - private int version; + private int version; /** Flag TRUE or FALSE whether or not requests are to be authenticated with the AWS4 algorithm. */ private boolean authenticate; /** region "aws region" for authenticating request */ @@ -59,11 +59,12 @@ public class H5FD_ros3_fapl_t implements Serializable { /** * Create a "default" fapl_t structure, for anonymous access. */ - public H5FD_ros3_fapl_t () { + public H5FD_ros3_fapl_t() + { /* H5FD_ros3_fapl_t("", "", ""); */ /* defer */ - this.version = 1; + this.version = 1; this.aws_region = ""; - this.secret_id = ""; + this.secret_id = ""; this.secret_key = ""; } @@ -76,16 +77,18 @@ public class H5FD_ros3_fapl_t implements Serializable { * @param id "secret id" or "access id" for authenticating request * @param key "secret key" or "access key" for authenticating request */ - public H5FD_ros3_fapl_t (String region, String id, String key) { - this.version = 1; /* must equal H5FD_CURR_ROS3_FAPL_T_VERSION */ - /* as found in H5FDros3.h */ + public H5FD_ros3_fapl_t(String region, String id, String key) + { + this.version = 1; /* must equal H5FD_CURR_ROS3_FAPL_T_VERSION */ + /* as found in H5FDros3.h */ this.aws_region = region; this.secret_id = id; this.secret_key = key; } @Override - public boolean equals(Object o) { + public boolean equals(Object o) + { if (o == null) return false; if (!(o instanceof H5FD_ros3_fapl_t)) @@ -104,7 +107,8 @@ public class H5FD_ros3_fapl_t implements Serializable { } @Override - public int hashCode() { + public int hashCode() + { /* this is a _very bad_ hash algorithm for purposes of hashing! */ /* implemented to satisfy the "contract" regarding equality */ int k = (int)this.version; @@ -115,13 +119,10 @@ public class H5FD_ros3_fapl_t implements Serializable { } @Override - public String toString() { - return "H5FD_ros3_fapl_t (Version:" + this.version + ") {" + - "\n aws_region : " + this.aws_region + - "\n secret_id : " + this.secret_id + - "\n secret_key : " + this.secret_key + - "\n}\n"; + public String toString() + { + return "H5FD_ros3_fapl_t (Version:" + this.version + ") {" + + "\n aws_region : " + this.aws_region + "\n secret_id : " + this.secret_id + + "\n secret_key : " + this.secret_key + "\n}\n"; } } - - diff --git a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java index 78e6d6c..1961b16 100644 --- a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java +++ b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java @@ -18,26 +18,26 @@ import java.io.Serializable; * Information struct for object (for H5Fget_info) * */ -public class H5F_info2_t implements Serializable{ +public class H5F_info2_t implements Serializable { private static final long serialVersionUID = 4691681162544054518L; /** Superblock version number */ - public int super_version; + public int super_version; /** Superblock size */ - public long super_size; + public long super_size; /** Superblock extension size */ - public long super_ext_size; + public long super_ext_size; /** Version number of file free space management */ - public int free_version; + public int free_version; /** Free space manager metadata size */ - public long free_meta_size; + public long free_meta_size; /** Amount of free space in the file */ - public long free_tot_space; + public long free_tot_space; /** Version number of shared object header info */ - public int sohm_version; + public int sohm_version; /** Shared object header message header size */ - public long sohm_hdr_size; + public long sohm_hdr_size; /** Shared object header message index and heap size */ - public H5_ih_info_t sohm_msgs_info; + public H5_ih_info_t sohm_msgs_info; /** * Constructor for current "global" information about file @@ -51,18 +51,18 @@ public class H5F_info2_t implements Serializable{ * @param sohm_hdr_size: Shared object header message header size * @param sohm_msgs_info: Shared object header message index and heap size */ - public H5F_info2_t (int super_version, long super_size, long super_ext_size, - int free_version, long free_meta_size, long free_tot_space, - int sohm_version, long sohm_hdr_size, H5_ih_info_t sohm_msgs_info) + public H5F_info2_t(int super_version, long super_size, long super_ext_size, int free_version, + long free_meta_size, long free_tot_space, int sohm_version, long sohm_hdr_size, + H5_ih_info_t sohm_msgs_info) { - this.super_version = super_version; - this.super_size = super_size; + this.super_version = super_version; + this.super_size = super_size; this.super_ext_size = super_ext_size; - this.free_version = free_version; + this.free_version = free_version; this.free_meta_size = free_meta_size; this.free_tot_space = free_tot_space; - this.sohm_version = sohm_version; - this.sohm_hdr_size = sohm_hdr_size; + this.sohm_version = sohm_version; + this.sohm_hdr_size = sohm_hdr_size; this.sohm_msgs_info = sohm_msgs_info; } } diff --git a/java/src/hdf/hdf5lib/structs/H5G_info_t.java b/java/src/hdf/hdf5lib/structs/H5G_info_t.java index e79f859..10ae76a 100644 --- a/java/src/hdf/hdf5lib/structs/H5G_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5G_info_t.java @@ -18,7 +18,7 @@ import java.io.Serializable; * Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) * */ -public class H5G_info_t implements Serializable{ +public class H5G_info_t implements Serializable { private static final long serialVersionUID = -3746463015312132912L; /** Type of storage for links in group */ public int storage_type; diff --git a/java/src/hdf/hdf5lib/structs/H5L_info_t.java b/java/src/hdf/hdf5lib/structs/H5L_info_t.java index a3011c0..38b64d6 100644 --- a/java/src/hdf/hdf5lib/structs/H5L_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5L_info_t.java @@ -23,39 +23,37 @@ import hdf.hdf5lib.HDF5Constants; public class H5L_info_t implements Serializable { private static final long serialVersionUID = -4754320605310155033L; /** Type of link */ - public int type; + public int type; /** Indicate if creation order is valid */ - public boolean corder_valid; + public boolean corder_valid; /** Creation order */ - public long corder; + public long corder; /** Character set of link name */ - public int cset; + public int cset; /** Character set of link name */ public H5O_token_t token; /** Size of a soft link or user-defined link value */ - public long val_size; + public long val_size; /** Constructor for using object token portion of C union */ - H5L_info_t (int type, boolean corder_valid, long corder, - int cset, H5O_token_t token) + H5L_info_t(int type, boolean corder_valid, long corder, int cset, H5O_token_t token) { - this.type = type; + this.type = type; this.corder_valid = corder_valid; - this.corder = corder; - this.cset = cset; - this.token = token; - this.val_size = -1; + this.corder = corder; + this.cset = cset; + this.token = token; + this.val_size = -1; } /** Constructor for using val_size portion of C union */ - H5L_info_t (int type, boolean corder_valid, long corder, - int cset, long val_size) + H5L_info_t(int type, boolean corder_valid, long corder, int cset, long val_size) { - this.type = type; + this.type = type; this.corder_valid = corder_valid; - this.corder = corder; - this.cset = cset; - this.token = HDF5Constants.H5O_TOKEN_UNDEF; - this.val_size = val_size; + this.corder = corder; + this.cset = cset; + this.token = HDF5Constants.H5O_TOKEN_UNDEF; + this.val_size = val_size; } } diff --git a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java index 2475dd9..16a0eae 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java @@ -41,31 +41,31 @@ public class H5O_hdr_info_t implements Serializable { /** Flags to indicate message type is shared in header */ public long mesg_shared; - H5O_hdr_info_t (int version, int nmesgs, int nchunks, int flags, - long space_total, long space_meta, long space_mesg, long space_free, - long mesg_present, long mesg_shared) + H5O_hdr_info_t(int version, int nmesgs, int nchunks, int flags, long space_total, long space_meta, + long space_mesg, long space_free, long mesg_present, long mesg_shared) { - this.version = version; - this.nmesgs = nmesgs; - this.nchunks = nchunks; - this.flags = flags; - this.space_total = space_total; - this.space_meta = space_meta; - this.space_mesg = space_mesg; - this.space_free = space_free; + this.version = version; + this.nmesgs = nmesgs; + this.nchunks = nchunks; + this.flags = flags; + this.space_total = space_total; + this.space_meta = space_meta; + this.space_mesg = space_mesg; + this.space_free = space_free; this.mesg_present = mesg_present; - this.mesg_shared = mesg_shared; + this.mesg_shared = mesg_shared; } @Override - public boolean equals(Object o) { + public boolean equals(Object o) + { if (this == o) return true; if (!(o instanceof H5O_hdr_info_t)) return false; - H5O_hdr_info_t info = (H5O_hdr_info_t) o; + H5O_hdr_info_t info = (H5O_hdr_info_t)o; if (this.version != info.version) return false; diff --git a/java/src/hdf/hdf5lib/structs/H5O_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_info_t.java index d2208d2..011a88e 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_info_t.java @@ -21,25 +21,26 @@ import java.io.Serializable; public class H5O_info_t implements Serializable { private static final long serialVersionUID = 4691681163544054518L; /** File number that object is located in */ - public long fileno; + public long fileno; /** Object token in file */ public H5O_token_t token; /** Basic object type (group, dataset, etc.) */ - public int type; + public int type; /** Reference count of object */ - public int rc; + public int rc; /** Access time */ - public long atime; + public long atime; /** Modification time */ - public long mtime; + public long mtime; /** Change time */ - public long ctime; + public long ctime; /** Birth time */ - public long btime; + public long btime; /** Number of attributes attached to object */ - public long num_attrs; + public long num_attrs; - /** Constructor for data model information struct for objects + /** + * Constructor for data model information struct for objects * * @param fileno: File number that object is located in * @param token: Object token in file @@ -51,17 +52,17 @@ public class H5O_info_t implements Serializable { * @param btime: Birth time * @param num_attrs: Number of attributes attached to object */ - public H5O_info_t (long fileno, H5O_token_t token, int type, - int rc, long atime, long mtime, long ctime, long btime, long num_attrs) + public H5O_info_t(long fileno, H5O_token_t token, int type, int rc, long atime, long mtime, long ctime, + long btime, long num_attrs) { - this.fileno = fileno; - this.token = token; - this.type = type; - this.rc = rc; - this.atime = atime; - this.mtime = mtime; - this.ctime = ctime; - this.btime = btime; + this.fileno = fileno; + this.token = token; + this.type = type; + this.rc = rc; + this.atime = atime; + this.mtime = mtime; + this.ctime = ctime; + this.btime = btime; this.num_attrs = num_attrs; } } diff --git a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java index 70e5231..ec01b40 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java @@ -15,7 +15,8 @@ package hdf.hdf5lib.structs; import java.io.Serializable; /** - * Information struct for native HDF5 object info, such as object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx). + * Information struct for native HDF5 object info, such as object header metadata (for + * H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx). * */ public class H5O_native_info_t implements Serializable { @@ -29,26 +30,26 @@ public class H5O_native_info_t implements Serializable { /** v2 B-tree and heap for attributes */ public H5_ih_info_t attr_info; - H5O_native_info_t (H5O_hdr_info_t oheader_info, H5_ih_info_t obj_info, H5_ih_info_t attr_info) + H5O_native_info_t(H5O_hdr_info_t oheader_info, H5_ih_info_t obj_info, H5_ih_info_t attr_info) { - this.hdr_info = oheader_info; - this.obj_info = obj_info; + this.hdr_info = oheader_info; + this.obj_info = obj_info; this.attr_info = attr_info; } @Override - public boolean equals(Object o) { + public boolean equals(Object o) + { if (this == o) return true; if (!(o instanceof H5O_native_info_t)) return false; - H5O_native_info_t info = (H5O_native_info_t) o; + H5O_native_info_t info = (H5O_native_info_t)o; - if (!this.hdr_info.equals(info.hdr_info) - || !this.obj_info.equals(info.obj_info) - || !this.attr_info.equals(info.attr_info)) + if (!this.hdr_info.equals(info.hdr_info) || !this.obj_info.equals(info.obj_info) || + !this.attr_info.equals(info.attr_info)) return false; return true; diff --git a/java/src/hdf/hdf5lib/structs/H5O_token_t.java b/java/src/hdf/hdf5lib/structs/H5O_token_t.java index f0bb978..8f2b7e2 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_token_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_token_t.java @@ -30,28 +30,25 @@ public class H5O_token_t implements Serializable { */ public byte[] data; - H5O_token_t (byte[] data) { - this.data = data; - } + H5O_token_t(byte[] data) { this.data = data; } /** * Check if token data is undefined * * @return true if token data is undefined */ - public boolean isUndefined() { - return this.equals(HDF5Constants.H5O_TOKEN_UNDEF); - } + public boolean isUndefined() { return this.equals(HDF5Constants.H5O_TOKEN_UNDEF); } @Override - public boolean equals(Object o) { + public boolean equals(Object o) + { if (this == o) return true; if (!(o instanceof H5O_token_t)) return false; - H5O_token_t token = (H5O_token_t) o; + H5O_token_t token = (H5O_token_t)o; return Arrays.equals(this.data, token.data); } diff --git a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java index 0c6111b..3213695 100644 --- a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java @@ -21,25 +21,26 @@ import java.io.Serializable; public class H5_ih_info_t implements Serializable { private static final long serialVersionUID = -142238015615462707L; /** btree and/or list size of index */ - public long index_size; + public long index_size; /** btree and/or list size of hp */ - public long heap_size; + public long heap_size; - H5_ih_info_t (long index_size, long heap_size) + H5_ih_info_t(long index_size, long heap_size) { this.index_size = index_size; - this.heap_size = heap_size; + this.heap_size = heap_size; } @Override - public boolean equals(Object o) { + public boolean equals(Object o) + { if (this == o) return true; if (!(o instanceof H5_ih_info_t)) return false; - H5_ih_info_t info = (H5_ih_info_t) o; + H5_ih_info_t info = (H5_ih_info_t)o; if (this.index_size != info.index_size) return false; diff --git a/java/src/hdf/hdf5lib/structs/package-info.java b/java/src/hdf/hdf5lib/structs/package-info.java index 8a9d97d..a3ec6cd 100644 --- a/java/src/hdf/hdf5lib/structs/package-info.java +++ b/java/src/hdf/hdf5lib/structs/package-info.java @@ -11,7 +11,8 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/** All structure definitions define java equivalents of the C structures needed +/** + * All structure definitions define java equivalents of the C structures needed * by the C API calls. See the C API for information about the structures. */ package hdf.hdf5lib.structs; |