fine-tune

Doxyfile

@@ -226,7 +226,7 @@ SEPARATE_MEMBER_PAGES  = NO
 # uses this value to replace tabs by spaces in code fragments.
 # Minimum value: 1, maximum value: 16, default value: 4.
 
-TAB_SIZE               = 4
+TAB_SIZE               = 2
 
 # This tag can be used to specify a number of aliases that act as commands in
 # the documentation. An alias has the form:
@@ -413,6 +413,7 @@ TYPEDEF_HIDES_STRUCT   = NO
 # Minimum value: 0, maximum value: 9, default value: 0.
 
 LOOKUP_CACHE_SIZE      = 0
+SYMBOL_CACHE_SIZE      = 0
 
 #---------------------------------------------------------------------------
 # Build related configuration options
@@ -432,19 +433,19 @@ EXTRACT_ALL            = YES
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = NO
+EXTRACT_PRIVATE        = YES
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PACKAGE        = NO
+EXTRACT_PACKAGE        = YES
 
 # If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
 # included in the documentation.
 # The default value is: NO.
 
-EXTRACT_STATIC         = NO
+EXTRACT_STATIC         = YES
 
 # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
 # locally in source files will be included in the documentation. If set to NO,
@@ -659,6 +660,12 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
+# If the sources in your project are distributed over multiple directories 
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES       = YES
+
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
 # will remove the Files entry from the Quick Index and from the Folder Tree View
 # (if specified).
@@ -781,7 +788,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src
+INPUT                  = inst/include src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -826,7 +833,6 @@ FILE_PATTERNS          = *.c \
                          *.hpp \
                          *.h++ \
                          *.cs \
-                         *.d \
                          *.php \
                          *.php4 \
                          *.php5 \
@@ -849,6 +855,26 @@ FILE_PATTERNS          = *.c \
                          *.qsf \
                          *.as \
                          *.js
+                         *.C \
+                         *.CC \
+                         *.C++ \
+                         *.II \
+                         *.I++ \
+                         *.H \
+                         *.HH \
+                         *.H++ \
+                         *.CS \
+                         *.PHP \
+                         *.PHP3 \
+                         *.M \
+                         *.MM \
+                         *.PY \
+                         *.F90 \
+                         *.F \
+                         *.VHD \
+                         *.VHDL \
+                         *.r \
+                         *.R
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -991,7 +1017,7 @@ SOURCE_BROWSER         = YES
 # classes and enums directly into the documentation.
 # The default value is: NO.
 
-INLINE_SOURCES         = NO
+INLINE_SOURCES         = YES
 
 # Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
 # special comment blocks from generated source code fragments. Normal C, C++ and
@@ -1004,13 +1030,13 @@ STRIP_CODE_COMMENTS    = YES
 # function all documented functions referencing it will be listed.
 # The default value is: NO.
 
-REFERENCED_BY_RELATION = NO
+REFERENCED_BY_RELATION = YES
 
 # If the REFERENCES_RELATION tag is set to YES then for each documented function
 # all documented entities called/used by that function will be listed.
 # The default value is: NO.
 
-REFERENCES_RELATION    = NO
+REFERENCES_RELATION    = YES
 
 # If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
 # to YES then the hyperlinks from functions in REFERENCES_RELATION and
@@ -1231,7 +1257,13 @@ HTML_COLORSTYLE_GAMMA  = 80
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_TIMESTAMP         = NO
+HTML_TIMESTAMP         = YES
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
+# files or namespaces will be aligned in HTML using tables. If set to 
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS     = YES
 
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
@@ -1468,7 +1500,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
@@ -2173,7 +2205,7 @@ PERL_PATH              = /usr/bin/perl
 # powerful graphs.
 # The default value is: YES.
 
-CLASS_DIAGRAMS         = NO
+CLASS_DIAGRAMS         = YES
 
 # You can define message sequence charts within doxygen comments using the \msc
 # command. Doxygen will then run the mscgen tool (see:
@@ -2224,7 +2256,7 @@ DOT_NUM_THREADS        = 0
 # The default value is: Helvetica.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_FONTNAME           = Helvetica
+DOT_FONTNAME           = FreeSans
 
 # The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
 # dot graphs.
@@ -2440,7 +2472,7 @@ DOT_GRAPH_MAX_NODES    = 50
 # Minimum value: 0, maximum value: 1000, default value: 0.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-MAX_DOT_GRAPH_DEPTH    = 0
+MAX_DOT_GRAPH_DEPTH    = 998
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
 # background. This is disabled by default, because dot on Windows does not seem
@@ -2452,7 +2484,7 @@ MAX_DOT_GRAPH_DEPTH    = 0
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_TRANSPARENT        = NO
+DOT_TRANSPARENT        = YES
 
 # Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
 # files in one run (i.e. multiple -o and -T options on the command line). This
@@ -2461,7 +2493,7 @@ DOT_TRANSPARENT        = NO
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_MULTI_TARGETS      = NO
+DOT_MULTI_TARGETS      = YES
 
 # If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
 # explaining the meaning of the various boxes and arrows in the dot generated