diff options
| -rw-r--r-- | MANIFEST | 4 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/CMakeLists.txt | 22 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 16 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/callbacks/package-info.java | 27 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/exceptions/package-info.java | 31 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/package-info.java | 174 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/structs/package-info.java | 17 |
7 files changed, 282 insertions, 9 deletions
@@ -3293,6 +3293,7 @@ ./java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java ./java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java ./java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java +./java/src/hdf/hdf5lib/callbacks/package-info.java ./java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java ./java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java @@ -3318,6 +3319,7 @@ ./java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java ./java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java ./java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java +./java/src/hdf/hdf5lib/exceptions/package-info.java ./java/src/hdf/hdf5lib/structs/H5_ih_info_t.java ./java/src/hdf/hdf5lib/structs/H5A_info_t.java @@ -3332,12 +3334,14 @@ ./java/src/hdf/hdf5lib/structs/H5O_info_t.java ./java/src/hdf/hdf5lib/structs/H5O_native_info_t.java ./java/src/hdf/hdf5lib/structs/H5O_token_t.java +./java/src/hdf/hdf5lib/structs/package-info.java ./java/src/hdf/hdf5lib/H5.java ./java/src/hdf/hdf5lib/HDF5Constants.java ./java/src/hdf/hdf5lib/HDF5GroupInfo.java ./java/src/hdf/hdf5lib/HDFArray.java ./java/src/hdf/hdf5lib/HDFNativeData.java +./java/src/hdf/hdf5lib/package-info.java ./java/examples/Makefile.am ./java/examples/CMakeLists.txt diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt index 5651031..a26e117 100644 --- a/java/src/hdf/hdf5lib/CMakeLists.txt +++ b/java/src/hdf/hdf5lib/CMakeLists.txt @@ -40,6 +40,11 @@ set (HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES callbacks/Callbacks.java ) +set (HDF5_JAVADOC_HDF_HDF5_CALLBACKS_SOURCES + ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES} + callbacks/package-info.java +) + set (HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES exceptions/HDF5Exception.java exceptions/HDF5IdException.java @@ -67,6 +72,11 @@ set (HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES exceptions/HDF5SymbolTableException.java ) +set (HDF5_JAVADOC_HDF_HDF5_EXCEPTIONS_SOURCES + ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES} + exceptions/package-info.java +) + set (HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES structs/H5_ih_info_t.java structs/H5A_info_t.java @@ -83,6 +93,11 @@ set (HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES structs/H5O_token_t.java ) +set (HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES + ${HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES} + structs/package-info.java +) + set (HDF5_JAVA_HDF_HDF5_SOURCES HDFArray.java HDF5Constants.java @@ -91,6 +106,11 @@ set (HDF5_JAVA_HDF_HDF5_SOURCES H5.java ) +set (HDF5_JAVADOC_HDF_HDF5_SOURCES + ${HDF5_JAVA_HDF_HDF5_SOURCES} + package-info.java +) + set (CMAKE_JNI_TARGET TRUE) file (WRITE ${PROJECT_BINARY_DIR}/Manifest.txt @@ -114,7 +134,7 @@ add_dependencies (${HDF5_JAVA_HDF5_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_TARGET}) set_target_properties (${HDF5_JAVA_HDF5_LIB_TARGET} PROPERTIES FOLDER libraries/java) create_javadoc(hdf5_java_doc - FILES ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVA_HDF_HDF5_SOURCES} + FILES ${HDF5_JAVADOC_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_SOURCES} OVERVIEW ${HDF5_JAVA_HDF5_SRC_DIR}/overview.html CLASSPATH ${CMAKE_JAVA_INCLUDE_PATH} WINDOWTITLE "HDF5 Java" diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index cfff680..3a485da 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -64,8 +64,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * 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> + * For details of the HDF5 library, see the HDF5 Documentation at: + * <a href="http://hdfgroup.org/HDF5/">http://hdfgroup.org/HDF5/</a> * <hr> * <p> * <b>Mapping of arguments for Java</b> @@ -162,8 +162,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * <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> layed 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 + * 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 @@ -187,8 +187,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * <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 + * 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> @@ -204,8 +204,8 @@ import hdf.hdf5lib.structs.H5O_token_t; * 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 + * 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 diff --git a/java/src/hdf/hdf5lib/callbacks/package-info.java b/java/src/hdf/hdf5lib/callbacks/package-info.java new file mode 100644 index 0000000..0833162 --- /dev/null +++ b/java/src/hdf/hdf5lib/callbacks/package-info.java @@ -0,0 +1,27 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/** 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 + * a callback which has been GC'd, you will likely crash the VM. If + * there is no method to deregister the callback (e.g. <code>atexit</code> + * in the C library), you must ensure that you always keep a live reference + * to the callback object.<p> + * A callback should generally never throw an exception, since it doesn't + * necessarily have an encompassing Java environment to catch it. Any + * exceptions thrown will be passed to the default callback exception + * handler. + */ +package hdf.hdf5lib.callbacks; diff --git a/java/src/hdf/hdf5lib/exceptions/package-info.java b/java/src/hdf/hdf5lib/exceptions/package-info.java new file mode 100644 index 0000000..8640ccb --- /dev/null +++ b/java/src/hdf/hdf5lib/exceptions/package-info.java @@ -0,0 +1,31 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/** + * <p> + * The package exceptions contains error classes for the Java HDF5 Interface. + * <p> + * There are two sub-classes of exceptions defined: + * <ol> + * <li> + * HDF5LibraryException -- errors raised the HDF5 library code + * <li> + * HDF5JavaException -- errors raised the HDF5 Java wrapper code + * </ol> + * <p> + * The HDF5LibraryException is the base class for the classes that represent specific error conditions. + * In particular, HDF5LibraryException has a sub-class for each major + * error code returned by the HDF5 library. + * + */ +package hdf.hdf5lib.exceptions;
\ No newline at end of file diff --git a/java/src/hdf/hdf5lib/package-info.java b/java/src/hdf/hdf5lib/package-info.java new file mode 100644 index 0000000..838a266 --- /dev/null +++ b/java/src/hdf/hdf5lib/package-info.java @@ -0,0 +1,174 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * 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 + * 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> + * <hr> + * <p> + * <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. + * + * <table border=1> + * <caption><b>HDF-5 C types to Java types</b> </caption> + * <tr> + * <td><b>HDF-5</b></td> + * <td><b>Java</b></td> + * </tr> + * <tr> + * <td>H5T_NATIVE_INT</td> + * <td>int, Integer</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_SHORT</td> + * <td>short, Short</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_FLOAT</td> + * <td>float, Float</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_DOUBLE</td> + * <td>double, Double</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_CHAR</td> + * <td>byte, Byte</td> + * </tr> + * <tr> + * <td>H5T_C_S1</td> + * <td>java.lang.String</td> + * </tr> + * <tr> + * <td>void * <BR> + * (i.e., pointer to `Any')</td> + * <td>Special -- see HDFArray</td> + * </tr> + * </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. + * <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. + * <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. + * <p> + * For instance, a function that returns two integers is declared: + * + * <pre> + * h_err_t HDF5dummy( int *a1, int *a2) + * </pre> + * + * For the Java interface, this would be declared: + * + * <pre> + * public synchronized static native void HDF5dummy(int args[]); + * </pre> + * + * where <i>a1</i> is <i>args[0]</i> and <i>a2</i> is <i>args[1]</i>, and would be invoked: + * + * <pre> + * H5.HDF5dummy(a); + * </pre> + * + * <p> + * 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, + * + * <pre> + * 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). + * <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> layed 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: + * + * <pre> + * 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[][]. + * <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 + * <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: + * + * <pre> + * long data_type = HDF5CDataTypes.JH5T_NATIVE_INT; + * </pre> + * + * The Java application uses both types of constants the same way, the only difference is that the + * <b><i>HDF5CDataTypes</i></b> may have different values on different platforms. + * <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 + * 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. + * <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. + * <hr> + * + * <b>See also: <a href="http://hdfgroup.org/HDF5/"> http://hdfgroup.org/HDF5"</a></b> + **/ +package hdf.hdf5lib;
\ No newline at end of file diff --git a/java/src/hdf/hdf5lib/structs/package-info.java b/java/src/hdf/hdf5lib/structs/package-info.java new file mode 100644 index 0000000..8a9d97d --- /dev/null +++ b/java/src/hdf/hdf5lib/structs/package-info.java @@ -0,0 +1,17 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/** 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; |