Port of datatypes UG. (#1829)

* Port of datatypes UG.

* Formatting fix

45 files changed, 5 insertions, 173 deletions

diff --git a/doxygen/CMakeLists.txt b/doxygen/CMakeLists.txt
index e75c899..1a3946f 100644
--- a/doxygen/CMakeLists.txt
+++ b/doxygen/CMakeLists.txt
@@ -11,7 +11,7 @@ if (DOXYGEN_FOUND)
   set (DOXYGEN_INCLUDE_ALIASES aliases)
   set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
   set (DOXYGEN_PROJECT_LOGO ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png)
-  set (DOXYGEN_PROJECT_BRIEF "C-API Reference")
+  set (DOXYGEN_PROJECT_BRIEF "API Reference")
   set (DOXYGEN_INPUT_DIRECTORY "${HDF5_SOURCE_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}")
   set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
   set (DOXYGEN_MACRO_EXPANSION YES)
diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in
index e391422..1837027 100644
--- a/doxygen/Doxyfile.in
+++ b/doxygen/Doxyfile.in
@@ -870,6 +870,9 @@ FILE_PATTERNS          = H5*public.h \
                          H5FDstdio.h \
                          H5FDwindows.h \
                          H5version.h \
+                         H5*.java \
+                         HDF*.java \
+                         *.F90 \
                          *.dox
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
diff --git a/doxygen/dox/DDLBNF110.dox b/doxygen/dox/DDLBNF110.dox
index f7e4267..6d6b67e 100644
--- a/doxygen/dox/DDLBNF110.dox
+++ b/doxygen/dox/DDLBNF110.dox
@@ -126,7 +126,7 @@ This section contains a brief explanation of the symbols used in the DDL.
 
 <reference> ::= H5T_REFERENCE { <ref_type> }
 
-<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG | H5T_STD_REF | UNDEFINED
+<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG
 
 <compound_type> ::= H5T_COMPOUND {
                         <member_type_def>+
diff --git a/doxygen/examples/H5R_examples.c b/doxygen/examples/H5R_examples.c
deleted file mode 100644
index b40b992..0000000
--- a/doxygen/examples/H5R_examples.c
+++ /dev/null
@@ -1,171 +0,0 @@
-/* -*- c-file-style: "stroustrup" -*- */
-
-#include "hdf5.h"
-
-#include <assert.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-int
-main(void)
-{
-    int ret_val = EXIT_SUCCESS;
-
-    //! <!-- [create] -->
-    {
-        __label__ fail_file, fail_fspace, fail_dset, fail_sel, fail_aspace, fail_attr, fail_awrite;
-        hid_t     file, fspace, dset, aspace, attr;
-        H5R_ref_t ref;
-
-        if ((file = H5Fcreate("reference.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-        // create a region reference which selects all elements of the dataset at "/data"
-        if ((fspace = H5Screate_simple(2, (hsize_t[]){10, 20}, NULL)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_fspace;
-        }
-        if ((dset = H5Dcreate(file, "data", H5T_STD_I32LE, fspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) ==
-            H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_dset;
-        }
-        if (H5Sselect_all(fspace) < 0 || H5Rcreate_region(file, "data", fspace, H5P_DEFAULT, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_sel;
-        }
-        // store the region reference in a scalar attribute of the root group called "region"
-        if ((aspace = H5Screate(H5S_SCALAR)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_aspace;
-        }
-        if ((attr = H5Acreate(file, "region", H5T_STD_REF, aspace, H5P_DEFAULT, H5P_DEFAULT)) ==
-            H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_attr;
-        }
-        if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_awrite;
-        }
-
-fail_awrite:
-        H5Aclose(attr);
-fail_attr:
-        H5Sclose(aspace);
-fail_aspace:
-        H5Rdestroy(&ref);
-fail_sel:
-        H5Dclose(dset);
-fail_dset:
-        H5Sclose(fspace);
-fail_fspace:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [create] -->
-
-    //! <!-- [read] -->
-    {
-        __label__ fail_file, fail_attr, fail_aread;
-        hid_t     file, attr;
-        H5R_ref_t ref;
-
-        if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-
-        // read the dataset region reference from the attribute
-        if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_attr;
-        }
-        if (H5Aread(attr, H5T_STD_REF, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_aread;
-        }
-        assert(H5Rget_type(&ref) == H5R_DATASET_REGION2);
-
-        // get an HDF5 path name for the dataset of the region reference
-        {
-            char buf[255];
-            if (H5Rget_obj_name(&ref, H5P_DEFAULT, buf, 255) < 0) {
-                ret_val = EXIT_FAILURE;
-            }
-            printf("Object name: \"%s\"\n", buf);
-        }
-
-        H5Rdestroy(&ref);
-fail_aread:
-        H5Aclose(attr);
-fail_attr:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [read] -->
-
-    //! <!-- [update] -->
-    {
-        __label__ fail_file, fail_attr, fail_ref;
-        hid_t     file, attr;
-        H5R_ref_t ref;
-
-        if ((file = H5Fopen("reference.h5", H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-
-        // H5T_STD_REF is a generic reference type
-        // we can "update" the attribute value to refer to the attribute itself
-        if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_attr;
-        }
-        if (H5Rcreate_attr(file, "data", "region", H5P_DEFAULT, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_ref;
-        }
-
-        assert(H5Rget_type(&ref) == H5R_ATTR);
-
-        if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-        }
-
-        H5Rdestroy(&ref);
-fail_ref:
-        H5Aclose(attr);
-fail_attr:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [update] -->
-
-    //! <!-- [delete] -->
-    {
-        __label__ fail_file, fail_ref;
-        hid_t     file;
-        H5R_ref_t ref;
-
-        // create an HDF5 object reference to the root group
-        if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-        if (H5Rcreate_object(file, ".", H5P_DEFAULT, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_ref;
-        }
-
-        // H5Rdestroy() releases all resources associated with an HDF5 reference
-        H5Rdestroy(&ref);
-fail_ref:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [delete] -->
-
-    return ret_val;
-}
diff --git a/doxygen/img/Dtypes_fig1.gif b/doxygen/img/Dtypes_fig1.gif
new file mode 100644
index 0000000..484f54f
--- /dev/null
+++ b/doxygen/img/Dtypes_fig1.gif
diff --git a/doxygen/img/Dtypes_fig10.gif b/doxygen/img/Dtypes_fig10.gif
new file mode 100644
index 0000000..60c8ba9
--- /dev/null
+++ b/doxygen/img/Dtypes_fig10.gif
diff --git a/doxygen/img/Dtypes_fig11.gif b/doxygen/img/Dtypes_fig11.gif
new file mode 100644
index 0000000..b5eda71
--- /dev/null
+++ b/doxygen/img/Dtypes_fig11.gif
diff --git a/doxygen/img/Dtypes_fig12.gif b/doxygen/img/Dtypes_fig12.gif
new file mode 100644
index 0000000..ee911b7
--- /dev/null
+++ b/doxygen/img/Dtypes_fig12.gif
diff --git a/doxygen/img/Dtypes_fig13a.gif b/doxygen/img/Dtypes_fig13a.gif
new file mode 100644
index 0000000..2f47b71
--- /dev/null
+++ b/doxygen/img/Dtypes_fig13a.gif
diff --git a/doxygen/img/Dtypes_fig13b.gif b/doxygen/img/Dtypes_fig13b.gif
new file mode 100644
index 0000000..fe3b5fb
--- /dev/null
+++ b/doxygen/img/Dtypes_fig13b.gif
diff --git a/doxygen/img/Dtypes_fig13c.gif b/doxygen/img/Dtypes_fig13c.gif
new file mode 100644
index 0000000..afd2834
--- /dev/null
+++ b/doxygen/img/Dtypes_fig13c.gif
diff --git a/doxygen/img/Dtypes_fig13d.gif b/doxygen/img/Dtypes_fig13d.gif
new file mode 100644
index 0000000..48805d8
--- /dev/null
+++ b/doxygen/img/Dtypes_fig13d.gif
diff --git a/doxygen/img/Dtypes_fig14.gif b/doxygen/img/Dtypes_fig14.gif
new file mode 100644
index 0000000..8f4d787
--- /dev/null
+++ b/doxygen/img/Dtypes_fig14.gif
diff --git a/doxygen/img/Dtypes_fig15.gif b/doxygen/img/Dtypes_fig15.gif
new file mode 100644
index 0000000..82a34d0
--- /dev/null
+++ b/doxygen/img/Dtypes_fig15.gif
diff --git a/doxygen/img/Dtypes_fig16.gif b/doxygen/img/Dtypes_fig16.gif
new file mode 100644
index 0000000..e83d379
--- /dev/null
+++ b/doxygen/img/Dtypes_fig16.gif
diff --git a/doxygen/img/Dtypes_fig16a.gif b/doxygen/img/Dtypes_fig16a.gif
new file mode 100644
index 0000000..7e68cc0
--- /dev/null
+++ b/doxygen/img/Dtypes_fig16a.gif
diff --git a/doxygen/img/Dtypes_fig16b.gif b/doxygen/img/Dtypes_fig16b.gif
new file mode 100644
index 0000000..b7919be
--- /dev/null
+++ b/doxygen/img/Dtypes_fig16b.gif
diff --git a/doxygen/img/Dtypes_fig16c.gif b/doxygen/img/Dtypes_fig16c.gif
new file mode 100644
index 0000000..cca285a
--- /dev/null
+++ b/doxygen/img/Dtypes_fig16c.gif
diff --git a/doxygen/img/Dtypes_fig16d.gif b/doxygen/img/Dtypes_fig16d.gif
new file mode 100644
index 0000000..8ca0fd7
--- /dev/null
+++ b/doxygen/img/Dtypes_fig16d.gif
diff --git a/doxygen/img/Dtypes_fig17a.gif b/doxygen/img/Dtypes_fig17a.gif
new file mode 100644
index 0000000..cdfaa29
--- /dev/null
+++ b/doxygen/img/Dtypes_fig17a.gif
diff --git a/doxygen/img/Dtypes_fig17b.gif b/doxygen/img/Dtypes_fig17b.gif
new file mode 100644
index 0000000..4a3ba33
--- /dev/null
+++ b/doxygen/img/Dtypes_fig17b.gif
diff --git a/doxygen/img/Dtypes_fig18.gif b/doxygen/img/Dtypes_fig18.gif
new file mode 100644
index 0000000..73c33e0
--- /dev/null
+++ b/doxygen/img/Dtypes_fig18.gif
diff --git a/doxygen/img/Dtypes_fig19.gif b/doxygen/img/Dtypes_fig19.gif
new file mode 100644
index 0000000..38ea6d4
--- /dev/null
+++ b/doxygen/img/Dtypes_fig19.gif
diff --git a/doxygen/img/Dtypes_fig2.gif b/doxygen/img/Dtypes_fig2.gif
new file mode 100644
index 0000000..52285a6
--- /dev/null
+++ b/doxygen/img/Dtypes_fig2.gif
diff --git a/doxygen/img/Dtypes_fig20a.gif b/doxygen/img/Dtypes_fig20a.gif
new file mode 100644
index 0000000..8406e77
--- /dev/null
+++ b/doxygen/img/Dtypes_fig20a.gif
diff --git a/doxygen/img/Dtypes_fig20b.gif b/doxygen/img/Dtypes_fig20b.gif
new file mode 100644
index 0000000..3f2331d
--- /dev/null
+++ b/doxygen/img/Dtypes_fig20b.gif
diff --git a/doxygen/img/Dtypes_fig20c.gif b/doxygen/img/Dtypes_fig20c.gif
new file mode 100644
index 0000000..5b60165
--- /dev/null
+++ b/doxygen/img/Dtypes_fig20c.gif
diff --git a/doxygen/img/Dtypes_fig20d.gif b/doxygen/img/Dtypes_fig20d.gif
new file mode 100644
index 0000000..fdcb59a
--- /dev/null
+++ b/doxygen/img/Dtypes_fig20d.gif
diff --git a/doxygen/img/Dtypes_fig21.gif b/doxygen/img/Dtypes_fig21.gif
new file mode 100644
index 0000000..6d30528
--- /dev/null
+++ b/doxygen/img/Dtypes_fig21.gif
diff --git a/doxygen/img/Dtypes_fig22.gif b/doxygen/img/Dtypes_fig22.gif
new file mode 100644
index 0000000..5e2ca99
--- /dev/null
+++ b/doxygen/img/Dtypes_fig22.gif
diff --git a/doxygen/img/Dtypes_fig23.gif b/doxygen/img/Dtypes_fig23.gif
new file mode 100644
index 0000000..f0c9882
--- /dev/null
+++ b/doxygen/img/Dtypes_fig23.gif
diff --git a/doxygen/img/Dtypes_fig24.gif b/doxygen/img/Dtypes_fig24.gif
new file mode 100644
index 0000000..a1c28f4
--- /dev/null
+++ b/doxygen/img/Dtypes_fig24.gif
diff --git a/doxygen/img/Dtypes_fig25a.gif b/doxygen/img/Dtypes_fig25a.gif
new file mode 100644
index 0000000..16d3bcc
--- /dev/null
+++ b/doxygen/img/Dtypes_fig25a.gif
diff --git a/doxygen/img/Dtypes_fig25c.gif b/doxygen/img/Dtypes_fig25c.gif
new file mode 100644
index 0000000..a625b74
--- /dev/null
+++ b/doxygen/img/Dtypes_fig25c.gif
diff --git a/doxygen/img/Dtypes_fig26.gif b/doxygen/img/Dtypes_fig26.gif
new file mode 100644
index 0000000..24b34fb
--- /dev/null
+++ b/doxygen/img/Dtypes_fig26.gif
diff --git a/doxygen/img/Dtypes_fig27.gif b/doxygen/img/Dtypes_fig27.gif
new file mode 100644
index 0000000..71f182a
--- /dev/null
+++ b/doxygen/img/Dtypes_fig27.gif
diff --git a/doxygen/img/Dtypes_fig28.gif b/doxygen/img/Dtypes_fig28.gif
new file mode 100644
index 0000000..56d8d1b
--- /dev/null
+++ b/doxygen/img/Dtypes_fig28.gif
diff --git a/doxygen/img/Dtypes_fig3.gif b/doxygen/img/Dtypes_fig3.gif
new file mode 100644
index 0000000..993d12e
--- /dev/null
+++ b/doxygen/img/Dtypes_fig3.gif
diff --git a/doxygen/img/Dtypes_fig4.gif b/doxygen/img/Dtypes_fig4.gif
new file mode 100644
index 0000000..67aedef
--- /dev/null
+++ b/doxygen/img/Dtypes_fig4.gif
diff --git a/doxygen/img/Dtypes_fig5.gif b/doxygen/img/Dtypes_fig5.gif
new file mode 100644
index 0000000..075417d
--- /dev/null
+++ b/doxygen/img/Dtypes_fig5.gif
diff --git a/doxygen/img/Dtypes_fig6.gif b/doxygen/img/Dtypes_fig6.gif
new file mode 100644
index 0000000..516ab95
--- /dev/null
+++ b/doxygen/img/Dtypes_fig6.gif
diff --git a/doxygen/img/Dtypes_fig7.gif b/doxygen/img/Dtypes_fig7.gif
new file mode 100644
index 0000000..c18e9dc
--- /dev/null
+++ b/doxygen/img/Dtypes_fig7.gif
diff --git a/doxygen/img/Dtypes_fig8.gif b/doxygen/img/Dtypes_fig8.gif
new file mode 100644
index 0000000..d75d998
--- /dev/null
+++ b/doxygen/img/Dtypes_fig8.gif
diff --git a/doxygen/img/Dtypes_fig9.gif b/doxygen/img/Dtypes_fig9.gif
new file mode 100644
index 0000000..873f0ab
--- /dev/null
+++ b/doxygen/img/Dtypes_fig9.gif
diff --git a/doxygen/img/dtypes_fig25b.gif b/doxygen/img/dtypes_fig25b.gif
new file mode 100644
index 0000000..9dbc225
--- /dev/null
+++ b/doxygen/img/dtypes_fig25b.gif