Add javadoc to packages - HDFFV-11285 (#1197)

6 files changed, 278 insertions, 9 deletions

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;