[svn-r29399] HDFFV-9717: add overview section to javadocs

MANIFEST

@@ -2493,6 +2493,7 @@
 
 ./java/src/hdf/CMakeLists.txt
 ./java/src/hdf/hdf5lib/CMakeLists.txt
+./java/src/hdf/hdf5lib/overview.html
 
 ./java/src/hdf/hdf5lib/callbacks/Callbacks.java
 ./java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java

config/cmake/HDF518_Examples.cmake.in

@@ -37,9 +37,13 @@ if(NOT DEFINED CTEST_SOURCE_NAME)
 endif()
 if(NOT DEFINED STATIC_LIBRARIES)
     set(STATICLIBRARIES "YES")
+else(NOT DEFINED STATIC_LIBRARIES)
+    set(STATICLIBRARIES "NO")
 endif()
 if(NOT DEFINED FORTRAN_LIBRARIES)
     set(FORTRANLIBRARIES "NO")
+else(NOT DEFINED FORTRAN_LIBRARIES)
+    set(FORTRANLIBRARIES "YES")
 endif()
 
 #TAR_SOURCE - name of tarfile

config/cmake/UseJava.cmake

@@ -184,7 +184,7 @@
 #                       This is used by install_jni_symlink().
 #    JAR_FILE           The location of the jar file so that you can include
 #                       it.
-#    CLASS_DIR          The directory where the class files can be found. For
+#    CLASSDIR           The directory where the class files can be found. For
 #                       example to use them with javah.
 #
 # ::
@@ -444,7 +444,7 @@ function(add_jar _TARGET_NAME)
 
     if (_add_jar_MANIFEST)
         set(_MANIFEST_OPTION m)
-        set(_MANIFEST_VALUE ${_add_jar_MANIFEST})
+        get_filename_component (_MANIFEST_VALUE "${_add_jar_MANIFEST}" ABSOLUTE)
     endif ()
 
     if (LIBRARY_OUTPUT_PATH)
@@ -865,6 +865,7 @@ endfunction ()
 function(create_javadoc _target)
     set(_javadoc_packages)
     set(_javadoc_files)
+    set(_javadoc_overview)
     set(_javadoc_sourcepath)
     set(_javadoc_classpath)
     set(_javadoc_installpath "${CMAKE_INSTALL_PREFIX}/share/javadoc")
@@ -884,6 +885,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -907,6 +910,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -929,6 +934,8 @@ function(create_javadoc _target)
                 set(_state "packages")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -951,6 +958,8 @@ function(create_javadoc _target)
                 set(_state "packages")
             elseif (${arg} STREQUAL "FILES")
                 set(_state "files")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -975,6 +984,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "INSTALLPATH")
                 set(_state "installpath")
             elseif (${arg} STREQUAL "DOCTITLE")
@@ -997,6 +1008,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "DOCTITLE")
                 set(_state "doctitle")
             elseif (${arg} STREQUAL "WINDOWTITLE")
@@ -1017,6 +1030,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "INSTALLPATH")
                 set(_state "installpath")
             elseif (${arg} STREQUAL "CLASSPATH")
@@ -1039,6 +1054,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -1061,6 +1078,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -1085,6 +1104,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -1109,6 +1130,8 @@ function(create_javadoc _target)
                 set(_state "files")
             elseif (${arg} STREQUAL "SOURCEPATH")
                 set(_state "sourcepath")
+            elseif (${arg} STREQUAL "OVERVIEW")
+                set(_state "overview")
             elseif (${arg} STREQUAL "CLASSPATH")
                 set(_state "classpath")
             elseif (${arg} STREQUAL "INSTALLPATH")
@@ -1126,6 +1149,30 @@ function(create_javadoc _target)
             else ()
                 set(_javadoc_version ${arg})
             endif ()
+        elseif (${_state} STREQUAL "overview")
+            if (${arg} STREQUAL "PACKAGES")
+                set(_state "packages")
+            elseif (${arg} STREQUAL "FILES")
+                set(_state "files")
+            elseif (${arg} STREQUAL "SOURCEPATH")
+                set(_state "sourcepath")
+            elseif (${arg} STREQUAL "CLASSPATH")
+                set(_state "classpath")
+            elseif (${arg} STREQUAL "INSTALLPATH")
+                set(_state "installpath")
+            elseif (${arg} STREQUAL "DOCTITLE")
+                set(_state "doctitle")
+            elseif (${arg} STREQUAL "WINDOWTITLE")
+                set(_state "windowtitle")
+            elseif (${arg} STREQUAL "AUTHOR")
+                set(_state "author")
+            elseif (${arg} STREQUAL "USE")
+                set(_state "use")
+            elseif (${arg} STREQUAL "VERSION")
+                set(_state "version")
+            else ()
+                list(APPEND _javadoc_overview ${arg})
+            endif ()
         endif ()
     endforeach ()
 
@@ -1145,6 +1192,19 @@ function(create_javadoc _target)
         set(_javadoc_options ${_javadoc_options} -sourcepath ${_sourcepath})
     endif ()
 
+    if (_javadoc_overview)
+        set(_start TRUE)
+        foreach(_path ${_javadoc_overview})
+            if (_start)
+                set(_overview ${_path})
+                set(_start FALSE)
+            else ()
+                set(_overview ${_overview}:${_path})
+            endif ()
+        endforeach()
+        set(_javadoc_options ${_javadoc_options} -overview ${_overview})
+    endif ()
+
     if (_javadoc_classpath)
         set(_start TRUE)
         foreach(_path ${_javadoc_classpath})
@@ -1212,7 +1272,7 @@ function (create_javah)
 
     set (_output_files)
     if (WIN32 AND NOT CYGWIN AND CMAKE_HOST_SYSTEM_NAME MATCHES "Windows")
-      set(_classpath_sep ";")
+      set(_classpath_sep "$<SEMICOLON>")
     else ()
       set(_classpath_sep ":")
     endif()
@@ -1242,7 +1302,7 @@ function (create_javah)
         endif()
       endforeach()
       string (REPLACE ";" "${_classpath_sep}" _classpath "${_classpath}")
-      list (APPEND _javah_options -classpath ${_classpath})
+      list (APPEND _javah_options -classpath "${_classpath}")
     endif()
 
     if (_create_javah_OUTPUT_DIR)

java/src/hdf/hdf5lib/CMakeLists.txt

@@ -114,6 +114,7 @@ set_target_properties (${HDF5_JAVA_HDF5_LIB_TARGET} PROPERTIES FOLDER libraries/
 
 create_javadoc(hdf5_java_doc
     FILES ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SRCS} ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SRCS} ${HDF5_JAVA_HDF_HDF5_STRUCTS_SRCS} ${HDF5_JAVA_HDF_HDF5_SRCS}
+    OVERVIEW ${HDF5_JAVA_HDF5_SRC_DIR}/overview.html
     CLASSPATH ${CMAKE_JAVA_INCLUDE_PATH}
     WINDOWTITLE "HDF5 Java"
     DOCTITLE "<h1>HDF5 Java Wrapper</h1>"

java/src/hdf/overview.html

@@ -0,0 +1,96 @@
+<body>
+
+<h1>Java HDF5 Interface (JHI5)</h1>
+
+<h2><u>What it is</u></h2>
+The <b>Java HD5 Interface (JHI5)</b> is a Java package
+(<a href="../../hdf-java-html/javadocs/hdf/hdf5lib/package-summary.html">hdf.hdf5lib</a>)
+that ``wraps around'' the HDF5 library.
+<p />There are a large number of functions in the HDF5
+library (version 1.10). Some of the functions are not supported in JHI5. Most
+of the unsupported functions have C function pointers, which is not currently
+implemented in JHI5.
+
+<center><table BORDER=1 COLS=1 WIDTH="71%" BGCOLOR="#dbeaf5" >
+<tr>
+<td>
+<center>Note: The JHI5 does not support HDF4 or earlier.</center>
+</td>
+</tr>
+</table></center>
+
+<p>The JHI5 may be used by any Java application that needs to access HDF5
+files. It is extremely important to emphasize that <i>this package is not
+a pure Java implementation of the HDF5 library.</i> The JHI5 calls the
+same HDF5 library that is used by C or FORTRAN programs. (Note that this
+product cannot be used in most network browsers because it accesses the
+local disk using native code.)
+<p>The Java HDF5 Interface consists of Java classes and a dynamically
+linked native library. The Java classes declare native methods, and the
+library contains C functions which implement the native methods. The C
+functions call the standard HDF5 library, which is linked as part of the
+same library on most platforms.
+<p>The central part of the JHI5 is the Java class <i>
+<a href="../../hdf-java-html/javadocs/hdf/hdf5lib/H5.html">hdf.hdf5lib.H5</a></i>.
+The <i>H5 </i>class calls the standard (<i>i.e.</i>, `native' code) HDF5
+library, with native methods for most of the HDF5 functions.
+
+<h3>
+<u>How to use it</u></h3>
+The JHI5 is used by Java classes to call the HDF5 library, in order to
+create HDF5 files, and read and write data in existing HDF5 files.
+<p>For example, the HDF5 library has the function <b>H5Fopen</b> to open
+an HDF5 file. The Java interface is the class <i>
+<a href="../../hdf-java-html/javadocs/hdf/hdf5lib/H5.html">hdf.hdf5lib.H5</a></i>,
+which has a method:
+<pre><b>static native int H5Fopen(String filename, int flags, int access );</b></pre>
+The native method is implemented in C using the
+<a href="http://java.sun.com/javase/6/docs/technotes/guides/jni/index.html">Java
+Native Method Interface </a>(JNI). This is written something like the following:
+<pre><b>JNIEXPORT jint
+JNICALL Java_hdf_hdf5lib_H5_H5Fopen
+(
+&nbsp;JNIEnv *env,
+&nbsp;jclass class,
+&nbsp;jstring hdfFile,
+&nbsp;jint flags,
+&nbsp;jint access)
+&nbsp;{
+
+&nbsp;/* ...convert Java String to (char *) */
+
+&nbsp;/* call the HDF library */
+&nbsp;retVal = H5Fopen((char *)file, (unsigned)flags, (hid_t)access );
+
+&nbsp;/* ... */
+}</b></pre>
+This C function calls the HDF5 library and returns the result appropriately.
+<p>There is one native method for each HDF entry point (several hundred
+in all), which are compiled with the HDF library into a dynamically loaded
+library (<i>libhdf5_java</i>). Note that this library must be built for each
+platform.
+<p>To call the HDF `<b><i>H5Fopen</i></b>' function, a Java program would
+import the package '<i><b>hdf.hdf5lib.*</b>'</i>, and invoke the method
+on the class '<b><i>H5</i></b>'. The Java program would look something
+like this:
+<pre><b>import hdf.hdf5lib.*;
+
+{
+&nbsp;/* ... */
+
+&nbsp;try {
+&nbsp;file = H5.Hopen("myFile.hdf", flags, access );
+&nbsp;} catch (HDF5Exception ex) {
+&nbsp;//...
+&nbsp;}
+
+&nbsp;/* ... */
+}</b></pre>
+The <i><b>H5</b> </i>class automatically loads the native method implementations
+and the HDF5 library.
+
+<h3>
+<a NAME="DOWNLOAD"></a>To Obtain</h3>
+The JHI5 is included with the <a href="http://www.hdfgroup.org/HDF5/index.html">HDF5</a> library.
+
+</body>