Changeset 2739


Ignore:
Timestamp:
Jun 8, 2012, 12:22:47 AM (9 years ago)
Author:
Peter
Message:

refs #703 using a non-recursive Makefile. Old Makefile.am are kept but
rather than being source for sub-Makefiles they are included into
topdir Makefile.am. This implies Make rules must be modified to work
from topdir. A temporary code snippet will remove old Makefiles and
Makefile.ins at configure time. This code will be removed in a week or
so and is mainly there for autobuilds and prepare for future
sub-Makefiles (that will have a all: rule in sub-directories.

Location:
trunk
Files:
35 edited

Legend:

Unmodified
Added
Removed
  • trunk/Makefile.am

    r2604 r2739  
    2828ACLOCAL_AMFLAGS = -I m4
    2929
    30 SUBDIRS = build_support m4 yat test doc
     30CLEANFILES =
     31DOXYGEN_INPUT =
     32EXTRA_DIST =
     33MOSTLYCLEANFILES =
    3134
    32 .PHONY: doc doxygen_mk maintainer-check news-check svn-check svn-clean release
    33 doc: doxygen_mk
    34   @(cd doc; $(MAKE) $(AM_MAKEFLAGS) $@)
     35FORCE:
    3536
    36 doxygen_mk:; @(cd yat; $(MAKE) $(AM_MAKEFLAGS) $@)
     37include build_support/Makefile.am
     38## yat/Makefile.am contains DOXYGEN definitions, so needs to be
     39## included before doc/Makefile
     40include yat/Makefile.am
     41include doc/Makefile.am
     42include m4/Makefile.am
     43include test/Makefile.am
    3744
    38 lazycheck recheck: all
    39   @(cd test && $(MAKE) $(AM_MAKEFLAGS) $@)
     45OLDFILES =
     46OLDFILES += $(srcdir)/build_support/Makefile.in
     47OLDFILES += build_support/Makefile
     48OLDFILES += $(srcdir)/doc/Makefile.in
     49OLDFILES += doc/Makefile
     50OLDFILES += $(srcdir)/m4/Makefile.in
     51OLDFILES += m4/Makefile
     52OLDFILES += $(srcdir)/test/Makefile.in
     53OLDFILES += test/Makefile
     54OLDFILES += $(srcdir)/yat/Makefile.in
     55OLDFILES += yat/Makefile
     56OLDFILES += $(srcdir)/classifier/Makefile.in
     57OLDFILES += classifier/Makefile
     58OLDFILES += $(srcdir)/normalizer/Makefile.in
     59OLDFILES += normalizer/Makefile
     60OLDFILES += $(srcdir)/omic/Makefile.in
     61OLDFILES += omic/Makefile
     62OLDFILES += $(srcdir)/random/Makefile.in
     63OLDFILES += random/Makefile
     64OLDFILES += $(srcdir)/regression/Makefile.in
     65OLDFILES += regression/Makefile
     66OLDFILES += $(srcdir)/statistics/Makefile.in
     67OLDFILES += statistics/Makefile
     68OLDFILES += $(srcdir)/utility/Makefile.in
     69OLDFILES += utility/Makefile
    4070
     71# temporary target (for automatic builds)
     72all-local: Makefile
     73  rm -f $(OLDFILES)
     74
     75clean-local:
     76  rm -rf doc/$(DX_HTML_OUTPUT) test/yathello test/testSubDir
     77
     78.PHONY: doc maintainer-check news-check svn-check svn-clean release
    4179
    4280# like the normal install target, but does not update header files
     
    4684
    4785###############################################################
    48 ## 
     86##
    4987## Some targets useful for the maintainer
    5088##
     
    63101  esac
    64102
    65 maintainer-check-local: 
     103maintainer-check-local:
    66104  mkdir _inst
    67105  @mcl_install=`cd _inst && pwd` \
     
    69107  && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install \
    70108  && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install install \
    71   && cd test && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install installcheck
     109  && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install installcheck
    72110
    73111# check that yat.pc is correctly generated with different combinations
     
    78116yat-pc-check:
    79117  $(SHELL) $(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) \
    80   && cd build_support \
    81   && rm -f yat.pc && make \
    82   && $(GREP) '^prefix=/usr/local' yat.pc \
    83   && $(GREP) '^exec_prefix=$${prefix}' yat.pc \
    84   && $(GREP) '^libdir=$${exec_prefix}/lib' yat.pc \
    85   && $(GREP) '^includedir=$${prefix}/include' yat.pc \
    86   && rm -f yat.pc && make prefix=foo \
    87   && $(GREP) '^prefix=foo' yat.pc \
    88   && $(GREP) '^exec_prefix=$${prefix}' yat.pc \
    89   && $(GREP) '^libdir=$${exec_prefix}/lib' yat.pc \
    90   && $(GREP) '^includedir=$${prefix}/include' yat.pc \
    91   && rm -f yat.pc && make prefix=foo exec_prefix=bar \
    92   && $(GREP) '^prefix=foo' yat.pc \
    93   && $(GREP) '^exec_prefix=bar' yat.pc \
    94   && $(GREP) '^libdir=$${exec_prefix}/lib' yat.pc \
    95   && $(GREP) '^includedir=$${prefix}/include' yat.pc \
    96   && rm -f yat.pc && make prefix=foo exec_prefix=bar libdir=baz includedir=quz\
    97   && $(GREP) '^prefix=foo' yat.pc \
    98   && $(GREP) '^exec_prefix=bar' yat.pc \
    99   && $(GREP) '^libdir=baz' yat.pc \
    100   && $(GREP) '^includedir=quz' yat.pc \
     118  && rm -f build_support/yat.pc && make \
     119  && $(GREP) '^prefix=/usr/local' build_support/yat.pc \
     120  && $(GREP) '^exec_prefix=$${prefix}' build_support/yat.pc \
     121  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
     122  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
     123  && rm -f build_support/yat.pc && make prefix=foo \
     124  && $(GREP) '^prefix=foo' build_support/yat.pc \
     125  && $(GREP) '^exec_prefix=$${prefix}' build_support/yat.pc \
     126  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
     127  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
     128  && rm -f build_support/yat.pc && make prefix=foo exec_prefix=bar \
     129  && $(GREP) '^prefix=foo' build_support/yat.pc \
     130  && $(GREP) '^exec_prefix=bar' build_support/yat.pc \
     131  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
     132  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
     133  && rm -f build_support/yat.pc \
     134  && make prefix=foo exec_prefix=bar libdir=baz includedir=quz \
     135  && $(GREP) '^prefix=foo' build_support/yat.pc \
     136  && $(GREP) '^exec_prefix=bar' build_support/yat.pc \
     137  && $(GREP) '^libdir=baz' build_support/yat.pc \
     138  && $(GREP) '^includedir=quz' build_support/yat.pc \
    101139  && cd .. \
    102140  && $(SHELL) $(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) exec_prefix=/t \
    103141  && cd build_support \
    104   && rm -f yat.pc && make \
    105   && $(GREP) '^prefix=/usr/local' yat.pc \
    106   && $(GREP) '^exec_prefix=/t' yat.pc \
    107   && $(GREP) '^libdir=$${exec_prefix}/lib' yat.pc \
    108   && $(GREP) '^includedir=$${prefix}/include' yat.pc \
    109   && rm -f yat.pc && make prefix=foo \
    110   && $(GREP) '^prefix=foo' yat.pc \
    111   && $(GREP) '^exec_prefix=/t' yat.pc \
    112   && $(GREP) '^libdir=$${exec_prefix}/lib' yat.pc \
    113   && $(GREP) '^includedir=$${prefix}/include' yat.pc \
    114   && rm -f yat.pc && make prefix=foo exec_prefix=bar \
    115   && $(GREP) '^prefix=foo' yat.pc \
    116   && $(GREP) '^exec_prefix=bar' yat.pc \
    117   && $(GREP) '^libdir=$${exec_prefix}/lib' yat.pc \
    118   && $(GREP) '^includedir=$${prefix}/include' yat.pc \
    119   && rm -f yat.pc && make prefix=foo exec_prefix=bar libdir=baz includedir=quz\
    120   && $(GREP) '^prefix=foo' yat.pc \
    121   && $(GREP) '^exec_prefix=bar' yat.pc \
    122   && $(GREP) '^libdir=baz' yat.pc \
    123   && $(GREP) '^includedir=quz' yat.pc 
     142  && rm -f build_support/yat.pc && make \
     143  && $(GREP) '^prefix=/usr/local' build_support/yat.pc \
     144  && $(GREP) '^exec_prefix=/t' build_support/yat.pc \
     145  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
     146  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
     147  && rm -f build_support/yat.pc && make prefix=foo \
     148  && $(GREP) '^prefix=foo' build_support/yat.pc \
     149  && $(GREP) '^exec_prefix=/t' build_support/yat.pc \
     150  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
     151  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
     152  && rm -f build_support/yat.pc && make prefix=foo exec_prefix=bar \
     153  && $(GREP) '^prefix=foo' build_support/yat.pc \
     154  && $(GREP) '^exec_prefix=bar' build_support/yat.pc \
     155  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
     156  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
     157  && rm -f build_support/yat.pc \
     158  && make prefix=foo exec_prefix=bar libdir=baz includedir=quz \
     159  && $(GREP) '^prefix=foo' build_support/yat.pc \
     160  && $(GREP) '^exec_prefix=bar' build_support/yat.pc \
     161  && $(GREP) '^libdir=baz' build_support/yat.pc \
     162  && $(GREP) '^includedir=quz' build_support/yat.pc
    124163
    125164SVN = svn
  • trunk/build_support/Makefile.am

    r2605 r2739  
    2020# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2121
    22 noinst_SCRIPTS = tag_and_release.sh
    23 bin_SCRIPTS=for_installation/yat-config
     22noinst_SCRIPTS = build_support/tag_and_release.sh
     23bin_SCRIPTS = build_support/for_installation/yat-config
    2424
    2525pkgconfigexecdir = $(libdir)/pkgconfig
    26 pkgconfigexec_DATA= yat.pc
     26pkgconfigexec_DATA= build_support/yat.pc
    2727
    28 CLEANFILES = yat.pc yat-config for_installation/yat-config
     28CLEANFILES += build_support/yat.pc build_support/yat-config
     29CLEANFILES += build_support/for_installation/yat-config
    2930
    30 EXTRA_DIST =  yat-config.in yat.pc.in
     31EXTRA_DIST +=  build_support/yat-config.in build_support/yat.pc.in
    3132
    3233edit = $(SED) \
     
    6263  -e 's|@boost_version[@]|$(boost_version)|g'
    6364
    64 yat-config: Makefile $(srcdir)/yat-config.in
     65build_support/yat-config: Makefile $(srcdir)/build_support/yat-config.in
    6566  @rm -f $@ $@.tmp
    6667  @echo "#! $(SHELL)" > $@.tmp
     
    7273  @echo creating $@
    7374
    74 for_installation/yat-config: yat-config
     75build_support/for_installation/yat-config: build_support/yat-config
    7576  @rm -f $@ $@-t \
    76   && $(MKDIR_P) for_installation \
    77   && sed 's|installed=no|installed=yes|g' < yat-config > $@-t \
     77  && $(MKDIR_P) build_support/for_installation \
     78  && sed 's|installed=no|installed=yes|g' < build_support/yat-config > $@-t \
    7879  && mv $@-t $@ && echo creating $@
    7980
    80 yat.pc: $(srcdir)/yat.pc.in gen_yat_pc.sh Makefile
    81   @rm -f $@ $@-t \
     81build_support/yat.pc: $(srcdir)/build_support/yat.pc.in build_support/gen_yat_pc.sh Makefile
     82  rm -f $@ $@-t \
     83  && cd build_support \
    8284  && $(SHELL) gen_yat_pc.sh --prefix="$(prefix)" \
    8385  --exec-prefix="$(exec_prefix)" \
    8486  --libdir="$(libdir)" --includedir="$(includedir)" \
    85   --input="$(srcdir)/yat.pc.in" > $@-t && mv $@-t $@ && echo creating $@
     87  --input="../$(srcdir)/build_support/yat.pc.in" > yat.pc-t \
     88  && mv yat.pc-t yat.pc && echo creating $@
  • trunk/configure.ac

    r2729 r2739  
    4545
    4646# Set default htmldir to ${docdir}/html
    47 AS_IF([test $htmldir = '${docdir}'], [htmldir='${docdir}/html']) 
     47AS_IF([test $htmldir = '${docdir}'], [htmldir='${docdir}/html'])
    4848
    4949dnl FIXME remove when we assume autoconf 2.64
    50 m4_ifndef([AC_PACKAGE_URL], 
     50m4_ifndef([AC_PACKAGE_URL],
    5151          [AC_DEFINE([PACKAGE_URL], ["http://dev.thep.lu.se/yat"],
    5252                     [Define to home page for this package])
     
    5757
    5858AC_CONFIG_HEADERS([config.h])
    59 AM_INIT_AUTOMAKE([1.11 std-options color-tests parallel-tests silent-rules])
     59AM_INIT_AUTOMAKE([1.11 std-options color-tests parallel-tests silent-rules -Werror subdir-objects])
    6060
    6161# Set default programming language
     
    7070  fi
    7171done
    72 AC_SUBST(DISTCHECK_CONFIGURE_FLAGS) 
     72AC_SUBST(DISTCHECK_CONFIGURE_FLAGS)
    7373
    7474# Let user overide default CXXFLAGS
     
    108108    [@%:@include <limits>],
    109109    [return !std::numeric_limits<double>::has_quiet_NaN])],
    110   [quiet_nan=yes 
     110  [quiet_nan=yes
    111111   AC_MSG_RESULT($quiet_nan)],
    112   [quiet_nan=no 
     112  [quiet_nan=no
    113113   AC_MSG_RESULT($quiet_nan)],
    114114  # if we are cross-compiling fall back on compilation test
     
    133133  [has_infinity=yes
    134134   AC_MSG_RESULT($has_infinity)],
    135   [has_infinity=no 
     135  [has_infinity=no
    136136   AC_MSG_RESULT($has_infinity)],
    137137  # if we are cross-compiling fall back on compilation test
     
    149149AC_MSG_CHECKING([g++ deprecation attribute])
    150150AC_COMPILE_IFELSE(
    151    [AC_LANG_PROGRAM([[void f() __attribute__ ((deprecated));]],)], 
    152    [AC_DEFINE([YAT_HAVE_GCC_DEPRECATED], [1], 
    153               [Define if compiler supports deprecated attribute, as in g++ 4.0]) 
     151   [AC_LANG_PROGRAM([[void f() __attribute__ ((deprecated));]],)],
     152   [AC_DEFINE([YAT_HAVE_GCC_DEPRECATED], [1],
     153              [Define if compiler supports deprecated attribute, as in g++ 4.0])
    154154    AC_MSG_RESULT([yes])],
    155155   [AC_MSG_RESULT([no])] )
    156156
    157157AC_MSG_CHECKING([if std::multiset::iterator is mutable])
    158 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[@%:@include <set> 
     158AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[@%:@include <set>
    159159                                     @%:@include <vector>]],
    160160                                   [[std::set<std::vector<double> > s;
     
    163163                                     s.begin()->reserve(100);
    164164                                   ]])],
    165                   [AC_DEFINE([MULTISET_ITERATOR_IS_MUTABLE], [1], 
    166                              [Define if std::multiset::iterator is mutable]) 
     165                  [AC_DEFINE([MULTISET_ITERATOR_IS_MUTABLE], [1],
     166                             [Define if std::multiset::iterator is mutable])
    167167                   AC_MSG_RESULT([yes])
    168168                  ],
     
    224224AC_SYS_LARGEFILE
    225225if test "$enable_largefile" = "no"; then
    226   AC_DEFINE([YAT_LFS_DISABLED], 1, 
     226  AC_DEFINE([YAT_LFS_DISABLED], 1,
    227227            [defined to 1 if large file support is disabled])
    228228fi
     
    268268      typedef std::pointer_to_unary_function<double, double> F;
    269269      std::vector<double> vec;
    270       transform_iterator<F, std::vector<double>::iterator> 
     270      transform_iterator<F, std::vector<double>::iterator>
    271271        i(vec.begin(), std::ptr_fun(fabs));
    272272  ])],
     
    279279DX_HTML_OUTPUT=html
    280280AC_SUBST(DX_HTML_OUTPUT)
    281 # create dummie version of doxygen.mk
    282 AC_CONFIG_COMMANDS([doxygen.mk],
    283 [for f in $CONFIG_FILES; do
    284 # for each directory in yat that has a Makefile, create a doxygen.mk
    285 case $f in #(
    286   yat/*/Makefile) :
    287    outfile=`echo $f | sed 's,Makefile,doxygen.mk,'`;
    288    test -e $outfile || echo '# dummie' > $outfile;
    289    stampfile=`echo $f | sed 's,Makefile,dx-stamp,'`;
    290    # if doxygen.mk is a dummie version remove stamp-file to ensure make
    291    # rule is triggered to generate real doxygen.mk
    292    head -n 1 $outfile | $GREP -v '^# dummie' > /dev/null \
    293    || { rm -f $stampfile && need_sleep=1; }
    294 esac
    295 done
    296 # avoid time stamp ties between doxygen.mk and its dx-stamp
    297 test x$need_sleep = x1 && sleep 2
    298 ])
    299 
    300 
    301 AC_CONFIG_FILES([build_support/gen_yat_pc.sh],
     281
     282AC_CONFIG_FILES([build_support/gen_yat_pc.sh],
    302283                [chmod +x build_support/gen_yat_pc.sh])
    303 AC_CONFIG_FILES([build_support/tag_and_release.sh], 
     284AC_CONFIG_FILES([build_support/tag_and_release.sh],
    304285                [chmod +x-w build_support/tag_and_release.sh])
    305286AC_CONFIG_FILES([Makefile
    306      build_support/Makefile
    307      doc/Makefile
    308287     doc/doxygen.config
    309288     doc/first_page.doxygen
    310      m4/Makefile
    311      test/Makefile
    312289     test/common_defs.sh
    313      yat/Makefile
    314      yat/classifier/Makefile
    315      yat/normalizer/Makefile
    316      yat/omic/Makefile
    317      yat/random/Makefile
    318      yat/regression/Makefile
    319      yat/statistics/Makefile
    320      yat/utility/Makefile])
     290])
     291
     292# temporary code to clean up obsoleted recursive Make file structure
     293rm -f $srcdir/build_support/Makefile.in
     294rm -f build_support/Makefile
     295rm -f $srcdir/doc/Makefile.in
     296rm -f doc/Makefile
     297rm -f $srcdir/m4/Makefile.in
     298rm -f m4/Makefile
     299rm -f $srcdir/test/Makefile.in
     300rm -f test/Makefile
     301rm -f $srcdir/yat/Makefile.in
     302rm -f yat/Makefile
     303rm -f $srcdir/yat/*/Makefile.in
     304rm -f yat/*/Makefile
    321305
    322306AC_CONFIG_HEADERS([yat/utility/config_public.h])
    323307# for the test suite
    324308yat_abs_top_srcdir=`cd $srcdir && pwd`
    325 AC_DEFINE_UNQUOTED([YAT_ABS_TOP_SRCDIR], ["$yat_abs_top_srcdir"], 
     309AC_DEFINE_UNQUOTED([YAT_ABS_TOP_SRCDIR], ["$yat_abs_top_srcdir"],
    326310                   [Define to absolute path to top yat src dir])
    327311
     
    358342  GSL $gsl_version (or newer) not found. The GNU Scientific Library
    359343  (GSL) library cannot be found. Please make sure GSL is
    360   installed. Please refer to warnings above for more details]) 
     344  installed. Please refer to warnings above for more details])
    361345fi
    362346
     
    366350  all_reqs_ok="false"
    367351  AC_MSG_WARN([
    368   Boost ${boost_version} (or newer) not found. Please make sure Boost 
     352  Boost ${boost_version} (or newer) not found. Please make sure Boost
    369353  is installed.])
    370354fi
     
    379363fi
    380364
    381 # Reset flags 
     365# Reset flags
    382366APR_RESTORE_THE_ENVIRONMENT(CPPFLAGS, YAT_)
    383367APR_RESTORE_THE_ENVIRONMENT(CXXFLAGS, YAT_)
     
    452436Now type `make'. dnl
    453437])
    454 
  • trunk/doc/Makefile.am

    r2631 r2739  
    2424
    2525
    26 DOXYGEN_FILES = $(srcdir)/build_tool.doxygen \
    27 $(builddir)/first_page.doxygen \
    28 $(srcdir)/deprecated.doxygen \
    29 $(srcdir)/footer.html \
    30 $(srcdir)/namespaces.doxygen \
    31 $(srcdir)/concepts.doxygen \
    32 $(srcdir)/Statistics.doxygen
     26DOXYGEN_FILES = $(srcdir)/doc/build_tool.doxygen \
     27$(builddir)/doc/first_page.doxygen \
     28$(srcdir)/doc/deprecated.doxygen \
     29$(srcdir)/doc/footer.html \
     30$(srcdir)/doc/namespaces.doxygen \
     31$(srcdir)/doc/concepts.doxygen \
     32$(srcdir)/doc/Statistics.doxygen
    3333
    34 EXTRA_DIST = $(DOXYGEN_FILES)
     34EXTRA_DIST += $(DOXYGEN_FILES)
    3535
    36 @am__include@ @am__quote@./$(top_builddir)/yat/classifier/doxygen.mk@am__quote@
    37 @am__include@ @am__quote@./$(top_builddir)/yat/normalizer/doxygen.mk@am__quote@
    38 @am__include@ @am__quote@./$(top_builddir)/yat/omic/doxygen.mk@am__quote@
    39 @am__include@ @am__quote@./$(top_builddir)/yat/random/doxygen.mk@am__quote@
    40 @am__include@ @am__quote@./$(top_builddir)/yat/regression/doxygen.mk@am__quote@
    41 @am__include@ @am__quote@./$(top_builddir)/yat/statistics/doxygen.mk@am__quote@
    42 @am__include@ @am__quote@./$(top_builddir)/yat/utility/doxygen.mk@am__quote@
     36DOXYGEN_INPUT += $(DOXYGEN_FILES)
     37DOXYGEN_INPUT += $(nobase_include_HEADERS)
     38DOXYGEN_INPUT += $(nobase_nodist_include_HEADERS)
    4339
    44 DOXYGEN_INPUT=$(yat_classifier_doxygen_input) \
    45 $(yat_normalizer_doxygen_input) \
    46 $(yat_omic_doxygen_input) \
    47 $(yat_random_doxygen_input) \
    48 $(yat_regression_doxygen_input) \
    49 $(yat_statistics_doxygen_input) \
    50 $(yat_utility_doxygen_input) \
    51 $(DOXYGEN_FILES)
    52 
    53 DOXYGEN_DEPS = $(DOXYGEN_INPUT) doxygen.config \
    54 $(top_builddir)/yat/classifier/doxygen.mk \
    55 $(top_builddir)/yat/normalizer/doxygen.mk \
    56 $(top_builddir)/yat/omic/doxygen.mk \
    57 $(top_builddir)/yat/random/doxygen.mk \
    58 $(top_builddir)/yat/regression/doxygen.mk \
    59 $(top_builddir)/yat/statistics/doxygen.mk \
    60 $(top_builddir)/yat/utility/doxygen.mk
    61 
    62 doc: html
    63 
     40DOXYGEN_DEPS = $(DOXYGEN_INPUT) doc/doxygen.config
    6441
    6542# these are supported by automake and *-local will add target to *
    6643if DX_ENABLE_HTML
    67 html-local: $(DX_HTML_OUTPUT)/index.html
     44html-local: doc/$(DX_HTML_OUTPUT)/index.html
    6845endif
    6946
     
    7249dx_dev_null_0 = > /dev/null
    7350
    74 $(DX_HTML_OUTPUT)/index.html: $(DOXYGEN_DEPS)
     51doc/$(DX_HTML_OUTPUT)/index.html: $(DOXYGEN_DEPS)
    7552  $(AM_V_GEN)
    76   $(AM_V_at){ cat doxygen.config && echo "INPUT = $(DOXYGEN_INPUT)" && \
     53  $(AM_V_at){ cat doc/doxygen.config && echo "INPUT = $(DOXYGEN_INPUT)" && \
    7754  echo GENERATE_HTML = YES; } | $(DOXYGEN) - $(dx_dev_null);
    7855
    79 install-data-hook:
    80   @$(NORMAL_INSTALL)
    81   @$(MAKE) $(AM_MAKEFLAGS) install-html
     56install-data-hook: install-html
    8257
    8358installdirs-local:
     
    9570    test -z "$(DESTDIR)$(htmldir)" || \
    9671    { $(MKDIR_P) "$(DESTDIR)$(htmldir)"; \
    97       $(INSTALL_DATA) $(DX_HTML_OUTPUT)/* $(DESTDIR)$(htmldir); \
     72      $(INSTALL_DATA) doc/$(DX_HTML_OUTPUT)/* $(DESTDIR)$(htmldir); \
    9873    } \
    9974  fi
     
    10378  rm -rf $(DESTDIR)$(htmldir)
    10479
    105 mostlyclean-local:
    106   rm -f doxygen.error *~
    107 
    108 clean-local:
    109   rm -rf $(DX_HTML_OUTPUT)
    110 
    111 FORCE:
     80MOSTLYCLEANFILES += doc/doxygen.error
  • trunk/doc/doxygen.config.in

    r2632 r2739  
    4040#---------------------------------------------------------------------------
    4141
    42 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
     42# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
    4343# by quotes) that should identify the project.
    4444
    4545PROJECT_NAME           = "@PACKAGE@"
    4646
    47 # The PROJECT_NUMBER tag can be used to enter a project or revision number. 
    48 # This could be handy for archiving the generated documentation or 
     47# The PROJECT_NUMBER tag can be used to enter a project or revision number.
     48# This could be handy for archiving the generated documentation or
    4949# if some version control system is used.
    5050
    5151PROJECT_NUMBER         = @PACKAGE_VERSION@
    5252
    53 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
    54 # base path where the generated documentation will be put. 
    55 # If a relative path is entered, it will be relative to the location 
     53# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
     54# base path where the generated documentation will be put.
     55# If a relative path is entered, it will be relative to the location
    5656# where doxygen was started. If left blank the current directory will be used.
    5757
    58 OUTPUT_DIRECTORY       = .
    59 
    60 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
    61 # documentation generated by doxygen is written. Doxygen will use this 
    62 # information to generate all constant output in the proper language. 
    63 # The default language is English, other supported languages are: 
    64 # Brazilian, Chinese, Croatian, Czech, Danish, Dutch, Finnish, French, 
    65 # German, Greek, Hungarian, Italian, Japanese, Korean, Norwegian, Polish, 
     58OUTPUT_DIRECTORY       = doc
     59
     60# The OUTPUT_LANGUAGE tag is used to specify the language in which all
     61# documentation generated by doxygen is written. Doxygen will use this
     62# information to generate all constant output in the proper language.
     63# The default language is English, other supported languages are:
     64# Brazilian, Chinese, Croatian, Czech, Danish, Dutch, Finnish, French,
     65# German, Greek, Hungarian, Italian, Japanese, Korean, Norwegian, Polish,
    6666# Portuguese, Romanian, Russian, Slovak, Slovene, Spanish and Swedish.
    6767
    6868OUTPUT_LANGUAGE        = English
    6969
    70 # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
    71 # documentation are documented, even if no documentation was available. 
    72 # Private class members and static file members will be hidden unless 
     70# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
     71# documentation are documented, even if no documentation was available.
     72# Private class members and static file members will be hidden unless
    7373# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
    7474
    7575EXTRACT_ALL            = NO
    7676
    77 # If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
     77# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
    7878# will be included in the documentation.
    7979
    8080EXTRACT_PRIVATE        = NO
    8181
    82 # If the EXTRACT_STATIC tag is set to YES all static members of a file 
     82# If the EXTRACT_STATIC tag is set to YES all static members of a file
    8383# will be included in the documentation.
    8484
    8585EXTRACT_STATIC         = NO
    8686
    87 # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
    88 # defined locally in source files will be included in the documentation. 
     87# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
     88# defined locally in source files will be included in the documentation.
    8989# If set to NO only classes defined in header files are included.
    9090
    9191EXTRACT_LOCAL_CLASSES  = YES
    9292
    93 # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
    94 # undocumented members of documented classes, files or namespaces. 
    95 # If set to NO (the default) these members will be included in the 
    96 # various overviews, but no documentation section is generated. 
     93# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
     94# undocumented members of documented classes, files or namespaces.
     95# If set to NO (the default) these members will be included in the
     96# various overviews, but no documentation section is generated.
    9797# This option has no effect if EXTRACT_ALL is enabled.
    9898
    9999HIDE_UNDOC_MEMBERS     = NO
    100100
    101 # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
    102 # undocumented classes that are normally visible in the class hierarchy. 
    103 # If set to NO (the default) these class will be included in the various 
     101# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
     102# undocumented classes that are normally visible in the class hierarchy.
     103# If set to NO (the default) these class will be included in the various
    104104# overviews. This option has no effect if EXTRACT_ALL is enabled.
    105105
    106106HIDE_UNDOC_CLASSES     = NO
    107107
    108 # If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
    109 # include brief member descriptions after the members that are listed in 
    110 # the file and class documentation (similar to JavaDoc). 
     108# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
     109# include brief member descriptions after the members that are listed in
     110# the file and class documentation (similar to JavaDoc).
    111111# Set to NO to disable this.
    112112
    113113BRIEF_MEMBER_DESC      = YES
    114114
    115 # If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
    116 # the brief description of a member or function before the detailed description. 
    117 # Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
     115# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
     116# the brief description of a member or function before the detailed description.
     117# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
    118118# brief descriptions will be completely suppressed.
    119119
    120120REPEAT_BRIEF           = YES
    121121
    122 # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
    123 # Doxygen will generate a detailed section even if there is only a brief 
     122# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
     123# Doxygen will generate a detailed section even if there is only a brief
    124124# description.
    125125
    126126ALWAYS_DETAILED_SEC    = NO
    127127
    128 # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited 
    129 # members of a class in the documentation of that class as if those members were 
    130 # ordinary class members. Constructors, destructors and assignment operators of 
     128# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited
     129# members of a class in the documentation of that class as if those members were
     130# ordinary class members. Constructors, destructors and assignment operators of
    131131# the base classes will not be shown.
    132132
    133133INLINE_INHERITED_MEMB  = YES
    134134
    135 # If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
    136 # path before files name in the file list and in the header files. If set 
     135# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
     136# path before files name in the file list and in the header files. If set
    137137# to NO the shortest path that makes the file name unique will be used.
    138138
    139139FULL_PATH_NAMES        = YES
    140140
    141 # If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
    142 # can be used to strip a user defined part of the path. Stripping is 
    143 # only done if one of the specified strings matches the left-hand part of 
     141# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
     142# can be used to strip a user defined part of the path. Stripping is
     143# only done if one of the specified strings matches the left-hand part of
    144144# the path. It is allowed to use relative paths in the argument list.
    145145
    146 STRIP_FROM_PATH        = @top_srcdir@
    147 
    148 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
    149 # the path mentioned in the documentation of a class, which tells 
    150 # the reader which header file to include in order to use a class. 
    151 # If left blank only the name of the header file containing the class 
    152 # definition is used. Otherwise one should specify the include paths that 
     146STRIP_FROM_PATH        = @srcdir@
     147
     148# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
     149# the path mentioned in the documentation of a class, which tells
     150# the reader which header file to include in order to use a class.
     151# If left blank only the name of the header file containing the class
     152# definition is used. Otherwise one should specify the include paths that
    153153# are normally passed to the compiler using the -I flag.
    154154
    155 STRIP_FROM_INC_PATH    = @top_srcdir@
    156 
    157 # The INTERNAL_DOCS tag determines if documentation 
    158 # that is typed after a \internal command is included. If the tag is set 
    159 # to NO (the default) then the documentation will be excluded. 
     155STRIP_FROM_INC_PATH    = @srcdir@
     156
     157# The INTERNAL_DOCS tag determines if documentation
     158# that is typed after a \internal command is included. If the tag is set
     159# to NO (the default) then the documentation will be excluded.
    160160# Set it to YES to include the internal documentation.
    161161
    162162INTERNAL_DOCS          = YES
    163163
    164 # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
    165 # doxygen to hide any special comment blocks from generated source code 
     164# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
     165# doxygen to hide any special comment blocks from generated source code
    166166# fragments. Normal C and C++ comments will always remain visible.
    167167
    168168STRIP_CODE_COMMENTS    = YES
    169169
    170 # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
    171 # file names in lower case letters. If set to YES upper case letters are also 
    172 # allowed. This is useful if you have classes or files whose names only differ 
    173 # in case and if your file system supports case sensitive file names. Windows 
     170# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
     171# file names in lower case letters. If set to YES upper case letters are also
     172# allowed. This is useful if you have classes or files whose names only differ
     173# in case and if your file system supports case sensitive file names. Windows
    174174# users are adviced to set this option to NO.
    175175
    176176CASE_SENSE_NAMES       = YES
    177177
    178 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
    179 # (but less readable) file names. This can be useful is your file systems 
     178# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
     179# (but less readable) file names. This can be useful is your file systems
    180180# doesn't support long names like on DOS, Mac, or CD-ROM.
    181181
    182182SHORT_NAMES            = NO
    183183
    184 # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
    185 # will show members with their full class and namespace scopes in the 
     184# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
     185# will show members with their full class and namespace scopes in the
    186186# documentation. If set to YES the scope will be hidden.
    187187
    188188HIDE_SCOPE_NAMES       = NO
    189189
    190 # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
    191 # will generate a verbatim copy of the header file for each class for 
     190# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
     191# will generate a verbatim copy of the header file for each class for
    192192# which an include is specified. Set to NO to disable this.
    193193
    194194VERBATIM_HEADERS       = YES
    195195
    196 # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
    197 # will put list of the files that are included by a file in the documentation 
     196# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
     197# will put list of the files that are included by a file in the documentation
    198198# of that file.
    199199
    200200SHOW_INCLUDE_FILES     = YES
    201201
    202 # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
    203 # will interpret the first line (until the first dot) of a JavaDoc-style 
    204 # comment as the brief description. If set to NO, the JavaDoc 
    205 # comments  will behave just like the Qt-style comments (thus requiring an 
     202# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
     203# will interpret the first line (until the first dot) of a JavaDoc-style
     204# comment as the brief description. If set to NO, the JavaDoc
     205# comments  will behave just like the Qt-style comments (thus requiring an
    206206# explict @brief command for a brief description.
    207207
    208208JAVADOC_AUTOBRIEF      = NO
    209209
    210 # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
    211 # member inherits the documentation from any documented member that it 
     210# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
     211# member inherits the documentation from any documented member that it
    212212# reimplements.
    213213
    214214INHERIT_DOCS           = YES
    215215
    216 # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
     216# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
    217217# is inserted in the documentation for inline members.
    218218
    219219INLINE_INFO            = YES
    220220
    221 # If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
    222 # will sort the (detailed) documentation of file and class members 
    223 # alphabetically by member name. If set to NO the members will appear in 
     221# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
     222# will sort the (detailed) documentation of file and class members
     223# alphabetically by member name. If set to NO the members will appear in
    224224# declaration order.
    225225
    226226SORT_MEMBER_DOCS       = YES
    227227
    228 # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
    229 # sorted by fully-qualified names, including namespaces. If set to 
    230 # NO (the default), the class list will be sorted only by class name, 
    231 # not including the namespace part. 
     228# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
     229# sorted by fully-qualified names, including namespaces. If set to
     230# NO (the default), the class list will be sorted only by class name,
     231# not including the namespace part.
    232232# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
    233 # Note: This option applies only to the class list, not to the 
     233# Note: This option applies only to the class list, not to the
    234234# alphabetical list.
    235235
    236236SORT_BY_SCOPE_NAME     = YES
    237237
    238 # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
    239 # tag is set to YES, then doxygen will reuse the documentation of the first 
    240 # member in the group (if any) for the other members of the group. By default 
     238# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
     239# tag is set to YES, then doxygen will reuse the documentation of the first
     240# member in the group (if any) for the other members of the group. By default
    241241# all members of a group must be documented explicitly.
    242242
    243243DISTRIBUTE_GROUP_DOC   = YES
    244244
    245 # The TAB_SIZE tag can be used to set the number of spaces in a tab. 
     245# The TAB_SIZE tag can be used to set the number of spaces in a tab.
    246246# Doxygen uses this value to replace tabs by spaces in code fragments.
    247247
    248248TAB_SIZE               = 2
    249249
    250 # The GENERATE_TODOLIST tag can be used to enable (YES) or 
    251 # disable (NO) the todo list. This list is created by putting \todo 
     250# The GENERATE_TODOLIST tag can be used to enable (YES) or
     251# disable (NO) the todo list. This list is created by putting \todo
    252252# commands in the documentation.
    253253
    254254GENERATE_TODOLIST      = NO
    255255
    256 # The GENERATE_TESTLIST tag can be used to enable (YES) or 
    257 # disable (NO) the test list. This list is created by putting \test 
     256# The GENERATE_TESTLIST tag can be used to enable (YES) or
     257# disable (NO) the test list. This list is created by putting \test
    258258# commands in the documentation.
    259259
    260260GENERATE_TESTLIST      = NO
    261261
    262 # The GENERATE_BUGLIST tag can be used to enable (YES) or 
    263 # disable (NO) the bug list. This list is created by putting \bug 
     262# The GENERATE_BUGLIST tag can be used to enable (YES) or
     263# disable (NO) the bug list. This list is created by putting \bug
    264264# commands in the documentation.
    265265
    266266GENERATE_BUGLIST       = NO
    267267
    268 # This tag can be used to specify a number of aliases that acts 
    269 # as commands in the documentation. An alias has the form "name=value". 
    270 # For example adding "sideeffect=\par Side Effects:\n" will allow you to 
    271 # put the command \sideeffect (or @sideeffect) in the documentation, which 
    272 # will result in a user defined paragraph with heading "Side Effects:". 
     268# This tag can be used to specify a number of aliases that acts
     269# as commands in the documentation. An alias has the form "name=value".
     270# For example adding "sideeffect=\par Side Effects:\n" will allow you to
     271# put the command \sideeffect (or @sideeffect) in the documentation, which
     272# will result in a user defined paragraph with heading "Side Effects:".
    273273# You can put \n's in the value part of an alias to insert newlines.
    274274
     
    281281ALIASES += "boost_url=http://www.boost.org/doc/libs/1_35_0/libs"
    282282
    283 # The ENABLED_SECTIONS tag can be used to enable conditional 
     283# The ENABLED_SECTIONS tag can be used to enable conditional
    284284# documentation sections, marked by \if sectionname ... \endif.
    285285
    286 ENABLED_SECTIONS       = 
    287 
    288 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
    289 # the initial value of a variable or define consist of for it to appear in 
    290 # the documentation. If the initializer consists of more lines than specified 
    291 # here it will be hidden. Use a value of 0 to hide initializers completely. 
    292 # The appearance of the initializer of individual variables and defines in the 
    293 # documentation can be controlled using \showinitializer or \hideinitializer 
     286ENABLED_SECTIONS       =
     287
     288# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
     289# the initial value of a variable or define consist of for it to appear in
     290# the documentation. If the initializer consists of more lines than specified
     291# here it will be hidden. Use a value of 0 to hide initializers completely.
     292# The appearance of the initializer of individual variables and defines in the
     293# documentation can be controlled using \showinitializer or \hideinitializer
    294294# command in the documentation regardless of this setting.
    295295
    296296MAX_INITIALIZER_LINES  = 30
    297297
    298 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources 
    299 # only. Doxygen will then generate output that is more tailored for C. 
    300 # For instance some of the names that are used will be different. The list 
     298# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
     299# only. Doxygen will then generate output that is more tailored for C.
     300# For instance some of the names that are used will be different. The list
    301301# of all members will be omitted, etc.
    302302
     
    307307#---------------------------------------------------------------------------
    308308
    309 # The QUIET tag can be used to turn on/off the messages that are generated 
     309# The QUIET tag can be used to turn on/off the messages that are generated
    310310# by doxygen. Possible values are YES and NO. If left blank NO is used.
    311311
    312312QUIET                  = NO
    313313
    314 # The WARNINGS tag can be used to turn on/off the warning messages that are 
    315 # generated by doxygen. Possible values are YES and NO. If left blank 
     314# The WARNINGS tag can be used to turn on/off the warning messages that are
     315# generated by doxygen. Possible values are YES and NO. If left blank
    316316# NO is used.
    317317
    318318WARNINGS               = YES
    319319
    320 # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
    321 # for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
     320# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
     321# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
    322322# automatically be disabled.
    323323
    324324WARN_IF_UNDOCUMENTED   = YES
    325325
    326 # The WARN_FORMAT tag determines the format of the warning messages that 
    327 # doxygen can produce. The string should contain the $file, $line, and $text 
    328 # tags, which will be replaced by the file and line number from which the 
     326# The WARN_FORMAT tag determines the format of the warning messages that
     327# doxygen can produce. The string should contain the $file, $line, and $text
     328# tags, which will be replaced by the file and line number from which the
    329329# warning originated and the warning text.
    330330
    331 WARN_FORMAT            = 
    332 
    333 # The WARN_LOGFILE tag can be used to specify a file to which warning 
    334 # and error messages should be written. If left blank the output is written 
     331WARN_FORMAT            =
     332
     333# The WARN_LOGFILE tag can be used to specify a file to which warning
     334# and error messages should be written. If left blank the output is written
    335335# to stderr.
    336336
    337 WARN_LOGFILE           = doxygen.error
     337WARN_LOGFILE           = doc/doxygen.error
    338338
    339339#---------------------------------------------------------------------------
     
    341341#---------------------------------------------------------------------------
    342342
    343 # The RECURSIVE tag can be used to turn specify whether or not subdirectories 
    344 # should be searched for input files as well. Possible values are YES and NO. 
     343# The RECURSIVE tag can be used to turn specify whether or not subdirectories
     344# should be searched for input files as well. Possible values are YES and NO.
    345345# If left blank NO is used.
    346346
    347347RECURSIVE              = YES
    348348
    349 # The EXCLUDE tag can be used to specify files and/or directories that should 
    350 # excluded from the INPUT source files. This way you can easily exclude a 
     349# The EXCLUDE tag can be used to specify files and/or directories that should
     350# excluded from the INPUT source files. This way you can easily exclude a
    351351# subdirectory from a directory tree whose root is specified with the INPUT tag.
    352352
    353 EXCLUDE                = 
    354 
    355 # If the value of the INPUT tag contains directories, you can use the 
    356 # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
     353EXCLUDE                =
     354
     355# If the value of the INPUT tag contains directories, you can use the
     356# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
    357357# certain files from those directories.
    358358
    359359EXCLUDE_PATTERNS       = .svn .deps .libs .svndigest
    360360
    361 # The EXAMPLE_PATH tag can be used to specify one or more files or 
    362 # directories that contain example code fragments that are included (see 
     361# The EXAMPLE_PATH tag can be used to specify one or more files or
     362# directories that contain example code fragments that are included (see
    363363# the \include command).
    364364
    365 EXAMPLE_PATH           = 
    366 
    367 # If the value of the EXAMPLE_PATH tag contains directories, you can use the 
    368 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
    369 # and *.h) to filter out the source-files in the directories. If left 
     365EXAMPLE_PATH           =
     366
     367# If the value of the EXAMPLE_PATH tag contains directories, you can use the
     368# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
     369# and *.h) to filter out the source-files in the directories. If left
    370370# blank all files are included.
    371371
    372 EXAMPLE_PATTERNS       = 
    373 
    374 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
    375 # searched for input files to be used with the \include or \dontinclude 
    376 # commands irrespective of the value of the RECURSIVE tag. 
     372EXAMPLE_PATTERNS       =
     373
     374# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
     375# searched for input files to be used with the \include or \dontinclude
     376# commands irrespective of the value of the RECURSIVE tag.
    377377# Possible values are YES and NO. If left blank NO is used.
    378378
    379379EXAMPLE_RECURSIVE      = NO
    380380
    381 # The IMAGE_PATH tag can be used to specify one or more files or 
    382 # directories that contain image that are included in the documentation (see 
     381# The IMAGE_PATH tag can be used to specify one or more files or
     382# directories that contain image that are included in the documentation (see
    383383# the \image command).
    384384
    385 IMAGE_PATH             = 
    386 
    387 # The INPUT_FILTER tag can be used to specify a program that doxygen should 
    388 # invoke to filter for each input file. Doxygen will invoke the filter program 
    389 # by executing (via popen()) the command <filter> <input-file>, where <filter> 
    390 # is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
    391 # input file. Doxygen will then use the output that the filter program writes 
     385IMAGE_PATH             =
     386
     387# The INPUT_FILTER tag can be used to specify a program that doxygen should
     388# invoke to filter for each input file. Doxygen will invoke the filter program
     389# by executing (via popen()) the command <filter> <input-file>, where <filter>
     390# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
     391# input file. Doxygen will then use the output that the filter program writes
    392392# to standard output.
    393393
    394 INPUT_FILTER           = 
    395 
    396 # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
    397 # INPUT_FILTER) will be used to filter the input files when producing source 
     394INPUT_FILTER           =
     395
     396# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
     397# INPUT_FILTER) will be used to filter the input files when producing source
    398398# files to browse.
    399399
     
    404404#---------------------------------------------------------------------------
    405405
    406 # If the SOURCE_BROWSER tag is set to YES then a list of source files will 
     406# If the SOURCE_BROWSER tag is set to YES then a list of source files will
    407407# be generated. Documented entities will be cross-referenced with these sources.
    408408
    409409SOURCE_BROWSER         = NO
    410410
    411 # Setting the INLINE_SOURCES tag to YES will include the body 
     411# Setting the INLINE_SOURCES tag to YES will include the body
    412412# of functions and classes directly in the documentation.
    413413
    414414INLINE_SOURCES         = NO
    415415
    416 # If the REFERENCED_BY_RELATION tag is set to YES (the default) 
    417 # then for each documented function all documented 
     416# If the REFERENCED_BY_RELATION tag is set to YES (the default)
     417# then for each documented function all documented
    418418# functions referencing it will be listed.
    419419
    420420REFERENCED_BY_RELATION = NO
    421421
    422 # If the REFERENCES_RELATION tag is set to YES (the default) 
    423 # then for each documented function all documented entities 
     422# If the REFERENCES_RELATION tag is set to YES (the default)
     423# then for each documented function all documented entities
    424424# called/used by that function will be listed.
    425425
     
    430430#---------------------------------------------------------------------------
    431431
    432 # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
    433 # of all compounds will be generated. Enable this if the project 
     432# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
     433# of all compounds will be generated. Enable this if the project
    434434# contains a lot of classes, structs, unions or interfaces.
    435435
    436436ALPHABETICAL_INDEX     = YES
    437437
    438 # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
    439 # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
     438# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
     439# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
    440440# in which this list will be split (can be a number in the range [1..20])
    441441
    442442COLS_IN_ALPHA_INDEX    = 5
    443443
    444 # In case all classes in a project start with a common prefix, all 
    445 # classes will be put under the same header in the alphabetical index. 
    446 # The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
     444# In case all classes in a project start with a common prefix, all
     445# classes will be put under the same header in the alphabetical index.
     446# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
    447447# should be ignored while generating the index headers.
    448448
    449 IGNORE_PREFIX          = 
     449IGNORE_PREFIX          =
    450450
    451451#---------------------------------------------------------------------------
     
    453453#---------------------------------------------------------------------------
    454454
    455 # If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
     455# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
    456456# generate HTML output.
    457457
    458458GENERATE_HTML          = NO
    459459
    460 # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
    461 # If a relative path is entered the value of OUTPUT_DIRECTORY will be 
     460# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
     461# If a relative path is entered the value of OUTPUT_DIRECTORY will be
    462462# put in front of it. If left blank `html' will be used as the default path.
    463463
    464464HTML_OUTPUT            = @DX_HTML_OUTPUT@
    465465
    466 # The HTML_HEADER tag can be used to specify a personal HTML header for 
    467 # each generated HTML page. If it is left blank doxygen will generate a 
     466# The HTML_HEADER tag can be used to specify a personal HTML header for
     467# each generated HTML page. If it is left blank doxygen will generate a
    468468# standard header.
    469469
    470 HTML_HEADER            = 
    471 
    472 # The HTML_FOOTER tag can be used to specify a personal HTML footer for 
    473 # each generated HTML page. If it is left blank doxygen will generate a 
     470HTML_HEADER            =
     471
     472# The HTML_FOOTER tag can be used to specify a personal HTML footer for
     473# each generated HTML page. If it is left blank doxygen will generate a
    474474# standard footer.
    475475
    476 HTML_FOOTER            = @srcdir@/footer.html
    477 
    478 # The HTML_STYLESHEET tag can be used to specify a user defined cascading 
    479 # style sheet that is used by each HTML page. It can be used to 
    480 # fine-tune the look of the HTML output. If the tag is left blank doxygen 
     476HTML_FOOTER            = @srcdir@/doc/footer.html
     477
     478# The HTML_STYLESHEET tag can be used to specify a user defined cascading
     479# style sheet that is used by each HTML page. It can be used to
     480# fine-tune the look of the HTML output. If the tag is left blank doxygen
    481481# will generate a default style sheet
    482482
    483 HTML_STYLESHEET        = 
    484 
    485 # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
    486 # files or namespaces will be aligned in HTML using tables. If set to 
     483HTML_STYLESHEET        =
     484
     485# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
     486# files or namespaces will be aligned in HTML using tables. If set to
    487487# NO a bullet list will be used.
    488488
    489489HTML_ALIGN_MEMBERS     = YES
    490490
    491 # If the GENERATE_HTMLHELP tag is set to YES, additional index files 
    492 # will be generated that can be used as input for tools like the 
    493 # Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
     491# If the GENERATE_HTMLHELP tag is set to YES, additional index files
     492# will be generated that can be used as input for tools like the
     493# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
    494494# of the generated HTML documentation.
    495495
    496496GENERATE_HTMLHELP      = NO
    497497
    498 # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
    499 # controls if a separate .chi index file is generated (YES) or that 
     498# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
     499# controls if a separate .chi index file is generated (YES) or that
    500500# it should be included in the master .chm file (NO).
    501501
    502502GENERATE_CHI           = NO
    503503
    504 # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
    505 # controls whether a binary table of contents is generated (YES) or a 
     504# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
     505# controls whether a binary table of contents is generated (YES) or a
    506506# normal table of contents (NO) in the .chm file.
    507507
    508508BINARY_TOC             = NO
    509509
    510 # The TOC_EXPAND flag can be set to YES to add extra items for group members 
     510# The TOC_EXPAND flag can be set to YES to add extra items for group members
    511511# to the contents of the Html help documentation and to the tree view.
    512512
    513513TOC_EXPAND             = NO
    514514
    515 # The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
    516 # top of each HTML page. The value NO (the default) enables the index and 
     515# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
     516# top of each HTML page. The value NO (the default) enables the index and
    517517# the value YES disables it.
    518518
    519519DISABLE_INDEX          = NO
    520520
    521 # This tag can be used to set the number of enum values (range [1..20]) 
     521# This tag can be used to set the number of enum values (range [1..20])
    522522# that doxygen will group on one line in the generated HTML documentation.
    523523
     
    525525
    526526# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
    527 # generated containing a tree-like index structure (just like the one that 
    528 # is generated for HTML Help). For this to work a browser that supports 
    529 # JavaScript and frames is required (for instance Mozilla, Netscape 4.0+, 
    530 # or Internet explorer 4.0+). Note that for large projects the tree generation 
    531 # can take a very long time. In such cases it is better to disable this feature. 
     527# generated containing a tree-like index structure (just like the one that
     528# is generated for HTML Help). For this to work a browser that supports
     529# JavaScript and frames is required (for instance Mozilla, Netscape 4.0+,
     530# or Internet explorer 4.0+). Note that for large projects the tree generation
     531# can take a very long time. In such cases it is better to disable this feature.
    532532# Windows users are probably better off using the HTML help feature.
    533533
    534534GENERATE_TREEVIEW      = NO
    535535
    536 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
    537 # used to set the initial width (in pixels) of the frame in which the tree 
     536# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
     537# used to set the initial width (in pixels) of the frame in which the tree
    538538# is shown.
    539539
     
    544544#---------------------------------------------------------------------------
    545545
    546 # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
     546# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
    547547# generate Latex output.
    548548
    549549GENERATE_LATEX         = NO
    550550
    551 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
    552 # If a relative path is entered the value of OUTPUT_DIRECTORY will be 
     551# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
     552# If a relative path is entered the value of OUTPUT_DIRECTORY will be
    553553# put in front of it. If left blank `latex' will be used as the default path.
    554554
    555 LATEX_OUTPUT           = 
    556 
    557 # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
    558 # LaTeX documents. This may be useful for small projects and may help to 
     555LATEX_OUTPUT           =
     556
     557# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
     558# LaTeX documents. This may be useful for small projects and may help to
    559559# save some trees in general.
    560560
    561561COMPACT_LATEX          = NO
    562562
    563 # The PAPER_TYPE tag can be used to set the paper type that is used 
    564 # by the printer. Possible values are: a4, a4wide, letter, legal and 
     563# The PAPER_TYPE tag can be used to set the paper type that is used
     564# by the printer. Possible values are: a4, a4wide, letter, legal and
    565565# executive. If left blank a4wide will be used.
    566566
    567567PAPER_TYPE             = a4wide
    568568
    569 # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
     569# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
    570570# packages that should be included in the LaTeX output.
    571571
    572 EXTRA_PACKAGES         = 
    573 
    574 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
    575 # the generated latex document. The header should contain everything until 
    576 # the first chapter. If it is left blank doxygen will generate a 
     572EXTRA_PACKAGES         =
     573
     574# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
     575# the generated latex document. The header should contain everything until
     576# the first chapter. If it is left blank doxygen will generate a
    577577# standard header. Notice: only use this tag if you know what you are doing!
    578578
    579 LATEX_HEADER           = 
    580 
    581 # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
    582 # is prepared for conversion to pdf (using ps2pdf). The pdf file will 
    583 # contain links (just like the HTML output) instead of page references 
     579LATEX_HEADER           =
     580
     581# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
     582# is prepared for conversion to pdf (using ps2pdf). The pdf file will
     583# contain links (just like the HTML output) instead of page references
    584584# This makes the output suitable for online browsing using a pdf viewer.
    585585
    586586PDF_HYPERLINKS         = YES
    587587
    588 # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
    589 # plain latex in the generated Makefile. Set this option to YES to get a 
     588# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
     589# plain latex in the generated Makefile. Set this option to YES to get a
    590590# higher quality PDF documentation.
    591591
    592592USE_PDFLATEX           = YES
    593593
    594 # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
    595 # command to the generated LaTeX files. This will instruct LaTeX to keep 
    596 # running if errors occur, instead of asking the user for help. 
     594# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
     595# command to the generated LaTeX files. This will instruct LaTeX to keep
     596# running if errors occur, instead of asking the user for help.
    597597# This option is also used when generating formulas in HTML.
    598598
     
    603603#---------------------------------------------------------------------------
    604604
    605 # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
    606 # The RTF output is optimised for Word 97 and may not look very pretty with 
     605# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
     606# The RTF output is optimised for Word 97 and may not look very pretty with
    607607# other RTF readers or editors.
    608608
    609609GENERATE_RTF           = NO
    610610
    611 # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
    612 # If a relative path is entered the value of OUTPUT_DIRECTORY will be 
     611# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
     612# If a relative path is entered the value of OUTPUT_DIRECTORY will be
    613613# put in front of it. If left blank `rtf' will be used as the default path.
    614614
    615 RTF_OUTPUT             = 
    616 
    617 # If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
    618 # RTF documents. This may be useful for small projects and may help to 
     615RTF_OUTPUT             =
     616
     617# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
     618# RTF documents. This may be useful for small projects and may help to
    619619# save some trees in general.
    620620
    621621COMPACT_RTF            = NO
    622622
    623 # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
    624 # will contain hyperlink fields. The RTF file will 
    625 # contain links (just like the HTML output) instead of page references. 
    626 # This makes the output suitable for online browsing using WORD or other 
    627 # programs which support those fields. 
     623# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
     624# will contain hyperlink fields. The RTF file will
     625# contain links (just like the HTML output) instead of page references.
     626# This makes the output suitable for online browsing using WORD or other
     627# programs which support those fields.
    628628# Note: wordpad (write) and others do not support links.
    629629
    630630RTF_HYPERLINKS         = NO
    631631
    632 # Load stylesheet definitions from file. Syntax is similar to doxygen's 
    633 # config file, i.e. a series of assigments. You only have to provide 
     632# Load stylesheet definitions from file. Syntax is similar to doxygen's
     633# config file, i.e. a series of assigments. You only have to provide
    634634# replacements, missing definitions are set to their default value.
    635635
    636 RTF_STYLESHEET_FILE    = 
    637 
    638 # Set optional variables used in the generation of an rtf document. 
     636RTF_STYLESHEET_FILE    =
     637
     638# Set optional variables used in the generation of an rtf document.
    639639# Syntax is similar to doxygen's config file.
    640640
    641 RTF_EXTENSIONS_FILE    = 
     641RTF_EXTENSIONS_FILE    =
    642642
    643643#---------------------------------------------------------------------------
     
    645645#---------------------------------------------------------------------------
    646646
    647 # If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
     647# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
    648648# generate man pages
    649649
    650650GENERATE_MAN           = NO
    651651
    652 # The MAN_OUTPUT tag is used to specify where the man pages will be put. 
    653 # If a relative path is entered the value of OUTPUT_DIRECTORY will be 
     652# The MAN_OUTPUT tag is used to specify where the man pages will be put.
     653# If a relative path is entered the value of OUTPUT_DIRECTORY will be
    654654# put in front of it. If left blank `man' will be used as the default path.
    655655
    656 MAN_OUTPUT             = 
    657 
    658 # The MAN_EXTENSION tag determines the extension that is added to 
     656MAN_OUTPUT             =
     657
     658# The MAN_EXTENSION tag determines the extension that is added to
    659659# the generated man pages (default is the subroutine's section .3)
    660660
    661 MAN_EXTENSION          = 
    662 
    663 # If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
    664 # then it will generate one additional man file for each entity 
    665 # documented in the real man page(s). These additional files 
    666 # only source the real man page, but without them the man command 
     661MAN_EXTENSION          =
     662
     663# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
     664# then it will generate one additional man file for each entity
     665# documented in the real man page(s). These additional files
     666# only source the real man page, but without them the man command
    667667# would be unable to find the correct page. The default is NO.
    668668
     
    673673#---------------------------------------------------------------------------
    674674
    675 # If the GENERATE_XML tag is set to YES Doxygen will 
    676 # generate an XML file that captures the structure of 
    677 # the code including all documentation. Note that this 
    678 # feature is still experimental and incomplete at the 
     675# If the GENERATE_XML tag is set to YES Doxygen will
     676# generate an XML file that captures the structure of
     677# the code including all documentation. Note that this
     678# feature is still experimental and incomplete at the
    679679# moment.
    680680
     
    685685#---------------------------------------------------------------------------
    686686
    687 # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
    688 # generate an AutoGen Definitions (see autogen.sf.net) file 
    689 # that captures the structure of the code including all 
    690 # documentation. Note that this feature is still experimental 
     687# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
     688# generate an AutoGen Definitions (see autogen.sf.net) file
     689# that captures the structure of the code including all
     690# documentation. Note that this feature is still experimental
    691691# and incomplete at the moment.
    692692
     
    694694
    695695#---------------------------------------------------------------------------
    696 # Configuration options related to the preprocessor   
    697 #---------------------------------------------------------------------------
    698 
    699 # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
    700 # evaluate all C-preprocessor directives found in the sources and include 
     696# Configuration options related to the preprocessor
     697#---------------------------------------------------------------------------
     698
     699# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
     700# evaluate all C-preprocessor directives found in the sources and include
    701701# files.
    702702
    703703ENABLE_PREPROCESSING   = YES
    704704
    705 # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
    706 # names in the source code. If set to NO (the default) only conditional 
    707 # compilation will be performed. Macro expansion can be done in a controlled 
     705# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
     706# names in the source code. If set to NO (the default) only conditional
     707# compilation will be performed. Macro expansion can be done in a controlled
    708708# way by setting EXPAND_ONLY_PREDEF to YES.
    709709
    710710MACRO_EXPANSION        = YES
    711711
    712 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
    713 # then the macro expansion is limited to the macros specified with the 
     712# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
     713# then the macro expansion is limited to the macros specified with the
    714714# PREDEFINED and EXPAND_AS_PREDEFINED tags.
    715715
    716716EXPAND_ONLY_PREDEF     = YES
    717717
    718 # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
     718# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
    719719# in the INCLUDE_PATH (see below) will be search if a #include is found.
    720720
    721721SEARCH_INCLUDES        = YES
    722722
    723 # The INCLUDE_PATH tag can be used to specify one or more directories that 
    724 # contain include files that are not input files but should be processed by 
     723# The INCLUDE_PATH tag can be used to specify one or more directories that
     724# contain include files that are not input files but should be processed by
    725725# the preprocessor.
    726726
    727 INCLUDE_PATH           = 
    728 
    729 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
    730 # patterns (like *.h and *.hpp) to filter out the header-files in the 
    731 # directories. If left blank, the patterns specified with FILE_PATTERNS will 
     727INCLUDE_PATH           =
     728
     729# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
     730# patterns (like *.h and *.hpp) to filter out the header-files in the
     731# directories. If left blank, the patterns specified with FILE_PATTERNS will
    732732# be used.
    733733
    734 INCLUDE_FILE_PATTERNS  = 
    735 
    736 # The PREDEFINED tag can be used to specify one or more macro names that 
    737 # are defined before the preprocessor is started (similar to the -D option of 
    738 # gcc). The argument of the tag is a list of macros of the form: name 
    739 # or name=definition (no spaces). If the definition and the = are 
     734INCLUDE_FILE_PATTERNS  =
     735
     736# The PREDEFINED tag can be used to specify one or more macro names that
     737# are defined before the preprocessor is started (similar to the -D option of
     738# gcc). The argument of the tag is a list of macros of the form: name
     739# or name=definition (no spaces). If the definition and the = are
    740740# omitted =1 is assumed.
    741741
    742742PREDEFINED             = YAT_DEPRECATE=
    743743
    744 # If the MACRO_EXPANSION and EXPAND_PREDEF_ONLY tags are set to YES then 
    745 # this tag can be used to specify a list of macro names that should be expanded. 
    746 # The macro definition that is found in the sources will be used. 
     744# If the MACRO_EXPANSION and EXPAND_PREDEF_ONLY tags are set to YES then
     745# this tag can be used to specify a list of macro names that should be expanded.
     746# The macro definition that is found in the sources will be used.
    747747# Use the PREDEFINED tag if you want to use a different macro definition.
    748748
    749 EXPAND_AS_DEFINED      = 
    750 
    751 # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
    752 # doxygen's preprocessor will remove all function-like macros that are alone 
    753 # on a line and do not end with a semicolon. Such function macros are typically 
     749EXPAND_AS_DEFINED      =
     750
     751# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
     752# doxygen's preprocessor will remove all function-like macros that are alone
     753# on a line and do not end with a semicolon. Such function macros are typically
    754754# used for boiler-plate code, and will confuse the parser if not removed.
    755755
     
    757757
    758758#---------------------------------------------------------------------------
    759 # Configuration::addtions related to external references   
     759# Configuration::addtions related to external references
    760760#---------------------------------------------------------------------------
    761761
    762762# The TAGFILES tag can be used to specify one or more tagfiles.
    763763
    764 TAGFILES               = 
    765 
    766 # When a file name is specified after GENERATE_TAGFILE, doxygen will create 
     764TAGFILES               =
     765
     766# When a file name is specified after GENERATE_TAGFILE, doxygen will create
    767767# a tag file that is based on the input files it reads.
    768768
    769 GENERATE_TAGFILE       = 
    770 
    771 # If the ALLEXTERNALS tag is set to YES all external classes will be listed 
    772 # in the class index. If set to NO only the inherited external classes 
     769GENERATE_TAGFILE       =
     770
     771# If the ALLEXTERNALS tag is set to YES all external classes will be listed
     772# in the class index. If set to NO only the inherited external classes
    773773# will be listed.
    774774
    775775ALLEXTERNALS           = NO
    776776
    777 # The PERL_PATH should be the absolute path and name of the perl script 
     777# The PERL_PATH should be the absolute path and name of the perl script
    778778# interpreter (i.e. the result of `which perl').
    779779
     
    781781
    782782#---------------------------------------------------------------------------
    783 # Configuration options related to the dot tool   
    784 #---------------------------------------------------------------------------
    785 
    786 # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
    787 # generate a inheritance diagram (in Html, RTF and LaTeX) for classes with base or 
    788 # super classes. Setting the tag to NO turns the diagrams off. Note that this 
    789 # option is superceded by the HAVE_DOT option below. This is only a fallback. It is 
     783# Configuration options related to the dot tool
     784#---------------------------------------------------------------------------
     785
     786# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
     787# generate a inheritance diagram (in Html, RTF and LaTeX) for classes with base or
     788# super classes. Setting the tag to NO turns the diagrams off. Note that this
     789# option is superceded by the HAVE_DOT option below. This is only a fallback. It is
    790790# recommended to install and use dot, since it yield more powerful graphs.
    791791
    792792CLASS_DIAGRAMS         = YES
    793793
    794 # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
    795 # available from the path. This tool is part of Graphviz, a graph visualization 
    796 # toolkit from AT&T and Lucent Bell Labs. The other options in this section 
     794# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
     795# available from the path. This tool is part of Graphviz, a graph visualization
     796# toolkit from AT&T and Lucent Bell Labs. The other options in this section
    797797# have no effect if this option is set to NO (the default)
    798798
    799799HAVE_DOT               = NO
    800800
    801 # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
    802 # will generate a graph for each documented class showing the direct and 
    803 # indirect inheritance relations. Setting this tag to YES will force the 
     801# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
     802# will generate a graph for each documented class showing the direct and
     803# indirect inheritance relations. Setting this tag to YES will force the
    804804# the CLASS_DIAGRAMS tag to NO.
    805805
    806806CLASS_GRAPH            = YES
    807807
    808 # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
    809 # will generate a graph for each documented class showing the direct and 
    810 # indirect implementation dependencies (inheritance, containment, and 
     808# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
     809# will generate a graph for each documented class showing the direct and
     810# indirect implementation dependencies (inheritance, containment, and
    811811# class references variables) of the class with other documented classes.
    812812
    813813COLLABORATION_GRAPH    = YES
    814814
    815 # If set to YES, the inheritance and collaboration graphs will show the 
     815# If set to YES, the inheritance and collaboration graphs will show the
    816816# relations between templates and their instances.
    817817
    818818TEMPLATE_RELATIONS     = YES
    819819
    820 # If set to YES, the inheritance and collaboration graphs will hide 
    821 # inheritance and usage relations if the target is undocumented 
     820# If set to YES, the inheritance and collaboration graphs will hide
     821# inheritance and usage relations if the target is undocumented
    822822# or is not a class.
    823823
    824824HIDE_UNDOC_RELATIONS   = YES
    825825
    826 # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
    827 # tags are set to YES then doxygen will generate a graph for each documented 
    828 # file showing the direct and indirect include dependencies of the file with 
     826# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
     827# tags are set to YES then doxygen will generate a graph for each documented
     828# file showing the direct and indirect include dependencies of the file with
    829829# other documented files.
    830830
    831831INCLUDE_GRAPH          = YES
    832832
    833 # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
    834 # HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
    835 # documented header file showing the documented files that directly or 
     833# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
     834# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
     835# documented header file showing the documented files that directly or
    836836# indirectly include this file.
    837837
    838838INCLUDED_BY_GRAPH      = YES
    839839
    840 # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
     840# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
    841841# will graphical hierarchy of all classes instead of a textual one.
    842842
    843843GRAPHICAL_HIERARCHY    = YES
    844844
    845 # The tag DOT_PATH can be used to specify the path where the dot tool can be 
     845# The tag DOT_PATH can be used to specify the path where the dot tool can be
    846846# found. If left blank, it is assumed the dot tool can be found on the path.
    847847
    848 DOT_PATH               = 
    849 
    850 # The DOTFILE_DIRS tag can be used to specify one or more directories that 
    851 # contain dot files that are included in the documentation (see the 
     848DOT_PATH               =
     849
     850# The DOTFILE_DIRS tag can be used to specify one or more directories that
     851# contain dot files that are included in the documentation (see the
    852852# \dotfile command).
    853853
    854 DOTFILE_DIRS           = 
    855 
    856 # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
    857 # generate a legend page explaining the meaning of the various boxes and 
     854DOTFILE_DIRS           =
     855
     856# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
     857# generate a legend page explaining the meaning of the various boxes and
    858858# arrows in the dot generated graphs.
    859859
    860860GENERATE_LEGEND        = YES
    861861
    862 # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
    863 # remove the intermedate dot files that are used to generate 
     862# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
     863# remove the intermedate dot files that are used to generate
    864864# the various graphs.
    865865
     
    867867
    868868#---------------------------------------------------------------------------
    869 # Configuration::addtions related to the search engine   
    870 #---------------------------------------------------------------------------
    871 
    872 # The SEARCHENGINE tag specifies whether or not a search engine should be 
     869# Configuration::addtions related to the search engine
     870#---------------------------------------------------------------------------
     871
     872# The SEARCHENGINE tag specifies whether or not a search engine should be
    873873# used. If set to NO the values of all tags below this one will be ignored.
    874874
    875875SEARCHENGINE           = NO
    876876
    877 # The CGI_NAME tag should be the name of the CGI script that 
    878 # starts the search engine (doxysearch) with the correct parameters. 
     877# The CGI_NAME tag should be the name of the CGI script that
     878# starts the search engine (doxysearch) with the correct parameters.
    879879# A script with this name will be generated by doxygen.
    880880
    881 #CGI_NAME               = 
    882 
    883 # The CGI_URL tag should be the absolute URL to the directory where the 
    884 # cgi binaries are located. See the documentation of your http daemon for 
     881#CGI_NAME               =
     882
     883# The CGI_URL tag should be the absolute URL to the directory where the
     884# cgi binaries are located. See the documentation of your http daemon for
    885885# details.
    886886
    887 #CGI_URL                = 
    888 
    889 # The DOC_URL tag should be the absolute URL to the directory where the 
    890 # documentation is located. If left blank the absolute path to the 
     887#CGI_URL                =
     888
     889# The DOC_URL tag should be the absolute URL to the directory where the
     890# documentation is located. If left blank the absolute path to the
    891891# documentation, with file:// prepended to it, will be used.
    892892
    893 #DOC_URL                = 
    894 
    895 # The DOC_ABSPATH tag should be the absolute path to the directory where the 
    896 # documentation is located. If left blank the directory on the local machine 
     893#DOC_URL                =
     894
     895# The DOC_ABSPATH tag should be the absolute path to the directory where the
     896# documentation is located. If left blank the directory on the local machine
    897897# will be used.
    898898
    899 #DOC_ABSPATH            = 
    900 
    901 # The BIN_ABSPATH tag must point to the directory where the doxysearch binary 
     899#DOC_ABSPATH            =
     900
     901# The BIN_ABSPATH tag must point to the directory where the doxysearch binary
    902902# is installed.
    903903
    904 #BIN_ABSPATH            = 
    905 
    906 # The EXT_DOC_PATHS tag can be used to specify one or more paths to 
    907 # documentation generated for other projects. This allows doxysearch to search 
     904#BIN_ABSPATH            =
     905
     906# The EXT_DOC_PATHS tag can be used to specify one or more paths to
     907# documentation generated for other projects. This allows doxysearch to search
    908908# the documentation for these projects as well.
    909909
    910 #EXT_DOC_PATHS          = 
     910#EXT_DOC_PATHS          =
  • trunk/m4/Makefile.am

    r2608 r2739  
    2222aclocaldir = $(datadir)/aclocal
    2323## macros to install - we only install our own macros (not 3rd party)
    24 aclocal_DATA = yat.m4
    25 aclocal_DATA += yat_add_flag.m4
    26 aclocal_DATA += yat_am_macros.m4
    27 aclocal_DATA += yat_cblas.m4
    28 aclocal_DATA += yat_common.m4
    29 aclocal_DATA += yat_gsl.m4
    30 aclocal_DATA += yat_lt_link_ifelse.m4
    31 aclocal_DATA += yat_msg_error.m4
    32 aclocal_DATA += yat_svn_release.m4
     24aclocal_DATA = m4/yat.m4
     25aclocal_DATA += m4/yat_add_flag.m4
     26aclocal_DATA += m4/yat_am_macros.m4
     27aclocal_DATA += m4/yat_cblas.m4
     28aclocal_DATA += m4/yat_common.m4
     29aclocal_DATA += m4/yat_gsl.m4
     30aclocal_DATA += m4/yat_lt_link_ifelse.m4
     31aclocal_DATA += m4/yat_msg_error.m4
     32aclocal_DATA += m4/yat_svn_release.m4
    3333
    3434## make sure all our macros are included in dist
    35 EXTRA_DIST = $(aclocal_DATA)
     35EXTRA_DIST += $(aclocal_DATA)
    3636## include macro that we only use in tests and not in configure.ac
    37 EXTRA_DIST += ax_ac_append_to_file.m4
     37EXTRA_DIST += m4/ax_ac_append_to_file.m4
  • trunk/test/Makefile.am

    r2680 r2739  
    2727AM_DEFAULT_SOURCE_EXT = .cc
    2828
    29 noinst_HEADERS = Suite.h
    30 
    31 check_LTLIBRARIES = libyattest.la
    32 
    33 check_SCRIPTS = common_defs.sh
    34 
    35 .PHONY: FORCE
    36 
    37 clean-local:; rm -rf yathello testSubDir
    38 
    39 FORCE:
    40 
    41 EXTRA_PROGRAMS = alignment.test averager.test \
    42   codon.test commandline.test \
    43   concept.test \
    44   consensus_inputranker.test data_lookup_1d.test  \
    45   data_weight.test data_weight_proxy.test distance.test \
    46   dna.test ensemble.test feature_selection.test fileutil.test \
    47   fisher.test genomic_position.test getline_iterator.test \
    48   gff.test help.test histogram.test \
    49   igp.test index.test inputranker.test interpolation.test \
    50   iterator.test kendall.test kernel_lookup.test kernel_pca.test kernel.test \
    51   knn.test kolmogorov_smirnov.test large_file.test matrix_lookup.test \
    52   matrix_lookup_weighted.test matrix.test \
    53   matrix_weighted.test merge.test nbc.test \
    54   ncc.test nni.test normalization.test pca.test \
    55   range.test regression.test rnd.test roc.test \
    56   score.test  segment.test smart_ptr.test   \
    57   smoother.test spearman.test \
    58   split.test statistics.test stream_redirect.test \
    59   subset_generator.test svd.test svm.test \
    60   svm_multi_class.test target.test \
    61   ttest.test tukey.test \
    62   utility.test vector.test version.test view.test
     29noinst_HEADERS = test/Suite.h
     30
     31check_LTLIBRARIES = test/libyattest.la
     32
     33check_SCRIPTS = test/common_defs.sh
     34
     35EXTRA_PROGRAMS = test/alignment.test test/averager.test \
     36  test/codon.test test/commandline.test \
     37  test/concept.test \
     38  test/consensus_inputranker.test test/data_lookup_1d.test  \
     39  test/data_weight.test test/data_weight_proxy.test test/distance.test \
     40  test/dna.test test/ensemble.test test/feature_selection.test \
     41  test/fileutil.test \
     42  test/fisher.test test/genomic_position.test test/getline_iterator.test \
     43  test/gff.test test/help.test test/histogram.test \
     44  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
     45  test/iterator.test test/kendall.test test/kernel_lookup.test \
     46  test/kernel_pca.test test/kernel.test \
     47  test/knn.test test/kolmogorov_smirnov.test test/large_file.test \
     48  test/matrix_lookup.test \
     49  test/matrix_lookup_weighted.test test/matrix.test \
     50  test/matrix_weighted.test test/merge.test test/nbc.test \
     51  test/ncc.test test/nni.test test/normalization.test test/pca.test \
     52  test/range.test test/regression.test test/rnd.test test/roc.test \
     53  test/score.test test/segment.test test/smart_ptr.test   \
     54  test/smoother.test test/spearman.test \
     55  test/split.test test/statistics.test test/stream_redirect.test \
     56  test/subset_generator.test test/svd.test test/svm.test \
     57  test/svm_multi_class.test test/target.test \
     58  test/ttest.test test/tukey.test \
     59  test/utility.test test/vector.test test/version.test test/view.test
    6360
    6461TESTS = $(EXTRA_PROGRAMS)
    65 CLEANFILES = $(EXTRA_PROGRAMS)
     62CLEANFILES += $(EXTRA_PROGRAMS)
    6663
    6764# tests not passing through yet
     
    6966
    7067DISTRIBUTED_TESTS = \
    71 doxygen_test.sh \
    72 help_test.sh \
    73 static_test.sh \
    74 yat_config_test.sh \
    75 yat_config_cblas_test.sh \
    76 yat_cpp_add_flag_test.sh \
    77 yat_cxx_add_flag_test.sh \
    78 yat_ld_add_flag_test.sh \
    79 yat_have_svn_wc_test.sh \
    80 yat_lt_link_ifelse_test.sh \
    81 yat_msg_error_test.sh \
    82 yat_msg_error_test2.sh \
    83 yat_m4_test.sh \
    84 yat_m4_test2.sh \
    85 yat_prog_move_if_change_test.sh \
    86 yat_revision_header_test.sh \
    87 yat_svn_release_year_test.sh \
    88 yat_svn_revision_test.sh
     68test/doxygen_test.sh \
     69test/help_test.sh \
     70test/static_test.sh \
     71test/yat_config_test.sh \
     72test/yat_config_cblas_test.sh \
     73test/yat_cpp_add_flag_test.sh \
     74test/yat_cxx_add_flag_test.sh \
     75test/yat_ld_add_flag_test.sh \
     76test/yat_have_svn_wc_test.sh \
     77test/yat_lt_link_ifelse_test.sh \
     78test/yat_msg_error_test.sh \
     79test/yat_msg_error_test2.sh \
     80test/yat_m4_test.sh \
     81test/yat_m4_test2.sh \
     82test/yat_prog_move_if_change_test.sh \
     83test/yat_revision_header_test.sh \
     84test/yat_svn_release_year_test.sh \
     85test/yat_svn_revision_test.sh
    8986
    9087TESTS += $(DISTRIBUTED_TESTS)
    91 EXTRA_DIST = $(DISTRIBUTED_TESTS)
     88EXTRA_DIST += $(DISTRIBUTED_TESTS)
    9289
    9390TEST_EXTENSIONS = .sh .test
    9491
    95 LDADD = $(top_builddir)/yat/libyat.la libyattest.la $(YAT_LIBS)
    96 
    97 large_file_test_LDADD = libyattest.la
    98 
    99 libyattest_la_SOURCES = Suite.cc
     92LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)
     93
     94test_large_file_test_LDADD = test/libyattest.la
     95
     96test_libyattest_la_SOURCES = test/Suite.cc
    10097
    10198lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=
    10299
    103100# dependencies for lazycheck
    104 help_test.log: help.test common_defs.sh
    105 static_test.log: $(top_srcdir)/m4/yat.m4 common_defs.sh
    106 yat_config_test.log: $(top_builddir)/build_support/yat-config \
    107   $(top_builddir)/build_support/for_installation/yat-config common_defs.sh
    108 yat_config_cblas_test.log: $(top_builddir)/build_support/yat-config \
    109   common_defs.sh
    110 yat_cpp_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
    111   $(top_srcdir)/m4/ax_append_flag.m4 \
    112   $(top_srcdir)/m4/ax_check_preproc_flag.m4 \
    113   common_defs.sh
    114 yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
     101test/help_test.log: test/help.test test/common_defs.sh
     102test/static_test.log: $(srcdir)/m4/yat.m4 test/common_defs.sh
     103test/yat_config_test.log: build_support/yat-config \
     104  build_support/for_installation/yat-config test/common_defs.sh
     105test/yat_config_cblas_test.log: build_support/yat-config test/common_defs.sh
     106test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
     107  $(srcdir)/m4/ax_append_flag.m4 \
     108  $(srcdir)/m4/ax_check_preproc_flag.m4 \
     109  test/common_defs.sh
     110test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
    115111  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
    116112  $(top_srcdir)/m4/ax_append_flag.m4 \
    117113  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
    118   common_defs.sh
    119 yat_have_svn_wc_test.log: $(top_srcdir)/m4/yat_am_macros.m4 common_defs.sh
    120 yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
     114  test/common_defs.sh
     115test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 test/common_defs.sh
     116test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
    121117  $(top_srcdir)/m4/ax_append_flag.m4 \
    122118  $(top_srcdir)/m4/ax_append_link_flags.m4 \
    123119  $(top_srcdir)/m4/ax_check_link_flag.m4 \
    124   common_defs.sh
    125 yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
    126   $(top_srcdir)/m4/yat.m4 common_defs.sh \
     120  test/common_defs.sh
     121test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
     122  $(top_srcdir)/m4/yat.m4 test/common_defs.sh \
    127123  $(top_builddir)/build_support/yat-config
    128 yat_m4_test.log:$(top_srcdir)/m4/yat.m4 common_defs.sh \
     124test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 test/common_defs.sh \
    129125  $(top_builddir)/build_support/yat-config
    130 yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 common_defs.sh
    131 yat_msg_error_test.log:$(top_srcdir)/m4/yat_msg_error.m4 common_defs.sh
    132 yat_msg_error_test2.log:$(top_srcdir)/m4/yat_msg_error.m4 common_defs.sh
    133 yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
     126test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 test/common_defs.sh
     127test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 test/common_defs.sh
     128test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 test/common_defs.sh
     129test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
    134130  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
    135131  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
    136132  $(top_srcdir)/m4/ax_file_escapes.m4 \
    137   common_defs.sh
    138 yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 common_defs.sh \
     133  test/common_defs.sh
     134test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
     135  test/common_defs.sh \
    139136  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
    140137  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
    141138  $(top_srcdir)/m4/ax_file_escapes.m4
    142 yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
    143   common_defs.sh \
     139test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
     140  test/common_defs.sh \
    144141  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
    145142  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
    146143  $(top_srcdir)/m4/ax_file_escapes.m4
    147 yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 common_defs.sh \
     144test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
     145  test/common_defs.sh \
    148146  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
    149147  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
     
    155153## words, we always run the test but let the logic for 'make doc' take
    156154## care of whether doxygen will run or not.
    157 doxygen_test.log: FORCE
     155test/doxygen_test.log: FORCE
    158156
    159157
    160158# yat-hello is an example of a tiny package that uses yat
    161 noinst_DATA = $(srcdir)/yat-hello-1.0.tar.gz
     159noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz
    162160
    163161# Directory yat-hello contains what a developer would check out
    164162# from a VCS, i.e., no files generated by autotools.
    165163yat_hello_sources  =
    166 yat_hello_sources += $(srcdir)/yat-hello/configure.ac
    167 yat_hello_sources += $(srcdir)/yat-hello/Makefile.am
    168 yat_hello_sources += $(srcdir)/yat-hello/hello.cc
     164yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
     165yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
     166yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc
    169167
    170168EXTRA_DIST += $(yat_hello_sources)
     
    184182yat_hello_deps += $(top_srcdir)/m4/version.m4
    185183
    186 EXTRA_DIST += $(srcdir)/yat-hello-1.0.tar.gz
    187 
    188 $(srcdir)/yat-hello-1.0.tar.gz: $(yat_hello_deps)
    189   cd $(srcdir)/yat-hello \
     184EXTRA_DIST += $(srcdir)/test/yat-hello-1.0.tar.gz
     185
     186$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
     187  cd $(srcdir)/test/yat-hello \
    190188  && $(MKDIR_P) m4 \
    191189  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
     
    195193  && $(MAKE) $(AM_MAKEFLAGS) distclean \
    196194  && mv yat-hello-1.0.tar.gz .. \
    197   && rm -rf $(yat_hello_tmp_files) 
     195  && rm -rf $(yat_hello_tmp_files)
    198196
    199197installcheck-local: yat-hello-check
    200198
    201 yat-hello-check: $(srcdir)/yat-hello-1.0.tar.gz
    202   GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/yat-hello-1.0.tar.gz | $(am__untar) \
     199yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
     200  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
    203201  && cd yat-hello-1.0 \
    204202  && ./configure --with-yat=$(bindir) \
     
    211209## test data
    212210EXTRA_DIST += \
    213 data/isoform.peaks \
    214 data/knni_matrix.data \
    215 data/knni_result.data \
    216 data/knni_weight.data \
    217 data/nm_alpha_linear_matlab.txt \
    218 data/nm_data_centralized.txt \
    219 data/nm_kernel.txt \
    220 data/nm_kernel2.txt \
    221 data/nm_kernel_gaussian.txt \
    222 data/nm_target_bin.txt \
    223 data/normalization_test.data \
    224 data/rank_data.txt \
    225 data/rank_target.txt \
    226 data/regression_gauss.data \
    227 data/small.gff2 \
    228 data/small.gff3 \
    229 data/sorlie_centroid_classes.txt \
    230 data/sorlie_centroid_data.txt \
    231 data/sorlie_centroid_predictions.txt \
    232 data/sorlie_centroids.txt \
    233 data/vector1.data \
    234 data/vector2.data \
    235 data/vector3.data \
    236 data/vector4.data \
    237 data/vector5.data \
    238 data/vector6.data \
    239 data/vector7.data \
    240 data/wenni_result.data \
    241 data/wenni_weight.data
     211test/data/isoform.peaks \
     212test/data/knni_matrix.data \
     213test/data/knni_result.data \
     214test/data/knni_weight.data \
     215test/data/nm_alpha_linear_matlab.txt \
     216test/data/nm_data_centralized.txt \
     217test/data/nm_kernel.txt \
     218test/data/nm_kernel2.txt \
     219test/data/nm_kernel_gaussian.txt \
     220test/data/nm_target_bin.txt \
     221test/data/normalization_test.data \
     222test/data/rank_data.txt \
     223test/data/rank_target.txt \
     224test/data/regression_gauss.data \
     225test/data/small.gff2 \
     226test/data/small.gff3 \
     227test/data/sorlie_centroid_classes.txt \
     228test/data/sorlie_centroid_data.txt  \
     229test/data/sorlie_centroid_predictions.txt \
     230test/data/sorlie_centroids.txt \
     231test/data/vector1.data  \
     232test/data/vector2.data \
     233test/data/vector3.data \
     234test/data/vector4.data \
     235test/data/vector5.data \
     236test/data/vector6.data  \
     237test/data/vector7.data \
     238test/data/wenni_result.data \
     239test/data/wenni_weight.data
  • trunk/test/commandline.cc

    r2705 r2739  
    5757
    5858int main(int argc, char* argv[])
    59 { 
     59{
    6060  yat::test::Suite suite(argc, argv);
    6161
     
    6363
    6464  // Peter, creation of this directory should perhaps be in a more central place
    65   FileUtil dir("testSubDir");
     65  FileUtil dir("test/testSubDir");
    6666  if (!dir.exists())
    6767    if (mkdir(dir.path().c_str(), 0755)) {
     
    6969      return 1;
    7070    }
    71   FileUtil subdir("testSubDir/commandline_test.dir");
     71  FileUtil subdir("test/testSubDir/commandline_test.dir");
    7272  if (!subdir.exists()) {
    7373    if (mkdir(subdir.path().c_str(), 0755)) {
     
    9494  }
    9595  catch (std::runtime_error& e) {
    96     suite.err() << "Error: unexpected exception thrown\n" << e.what() 
     96    suite.err() << "Error: unexpected exception thrown\n" << e.what()
    9797                << std::endl;
    9898    suite.add(false);
     
    112112  OptionArg<std::string> dir(cmd, "d,dir", "output directory");
    113113  OptionHelp help(cmd);
    114   OptionArg<std::string> target(cmd, "T,target", "treat DEST as a normal file", 
     114  OptionArg<std::string> target(cmd, "T,target", "treat DEST as a normal file",
    115115                                true);
    116116  target.print_arg("=TARGET");
     
    151151  OptionSwitch cmd_memory(cmd, "m", "transpose in a memory cheap manner");
    152152  OptionArg<size_t> cmd_n(cmd, "n", "number of rows to print in each iteration");
    153   OptionSwitch cmd_numeric(cmd, "numeric", 
     153  OptionSwitch cmd_numeric(cmd, "numeric",
    154154                                         "input is a numeric matrix");
    155155  OptionFile outdata(cmd, "o,out", "output file",true, false,"w");
     
    165165    if (msg.size()<15) {
    166166      suite.add(false);
    167       suite.err() << "Error: short exception message\n" 
    168                   << "  exception message is: `" << msg 
    169                   << "' that is " << msg.size() << " characters long.\n" 
     167      suite.err() << "Error: short exception message\n"
     168                  << "  exception message is: `" << msg
     169                  << "' that is " << msg.size() << " characters long.\n"
    170170                  << "  expected at least 15 characters\n";
    171171    }
     
    449449      strafree(av, ac);
    450450      ok=false;
    451       suite.err() << "error: expected parse to throw\n"; 
     451      suite.err() << "error: expected parse to throw\n";
    452452    }
    453453    catch (std::runtime_error& e) {
     
    572572  suite.err() << "Testing OptionArg required ...";
    573573  {
    574     OptionArg<std::string> required(cmd, "required", "required", true); 
     574    OptionArg<std::string> required(cmd, "required", "required", true);
    575575    int ac = 1;
    576576    const char* cav[] = { "test_prog" };
     
    604604  {
    605605    int ac = 7;
    606     const char* cav[] = { "test_prog", "--clones", "commandline_test.cc", 
    607                           "--data", "commandline_test.cc", "-o", 
     606    const char* cav[] = { "test_prog", "--clones", "commandline_test.cc",
     607                          "--data", "commandline_test.cc", "-o",
    608608                          "commandline_test.cc"};
    609609    char** av = stradup(cav, ac);
     
    626626  }
    627627
    628   FileUtil subdir("testSubDir/commandline_test.dir/write-protected");
     628  FileUtil subdir("test/testSubDir/commandline_test.dir/write-protected");
    629629  if (!subdir.exists()) {
    630630    if (mkdir(subdir.path().c_str(), 0555)) {
     
    639639    }
    640640
    641   FileUtil file("testSubDir/commandline_test.dir/write-protected/out.txt");
     641  FileUtil file("test/testSubDir/commandline_test.dir/write-protected/out.txt");
    642642  if (file.exists()) {
    643643    suite.err() << "FileUtil::exists returns true unexpectedly\n";
     
    657657  {
    658658    int ac = 3;
    659     const char* cav[] = { "test_prog", "--out", 
    660                     "testSubDir/commandline_test.dir/write-protected/out.txt"};
     659    const char* cav[] = { "test_prog", "--out",
     660                "test/testSubDir/commandline_test.dir/write-protected/out.txt"};
    661661    char** av = stradup(cav, ac);
    662662    try {
     
    693693  OptionFile file(cmd, "file", "", true, false, perm);
    694694
    695   suite.err() << "Testing OptionFile '" << perm << "' ... "; 
     695  suite.err() << "Testing OptionFile '" << perm << "' ... ";
    696696  int ac = 3;
    697697  const char* cav[] = { "test_prog", "--file", "sjhgaw/jmegb/tmp.tmpx"};
     
    714714bool test_file4(yat::test::Suite& suite)
    715715{
    716   FileUtil file("testSubDir/commandline_test.dir/test_file4.txt");
     716  FileUtil file("test/testSubDir/commandline_test.dir/test_file4.txt");
    717717  if (!file.exists()) {
    718718    std::ofstream os(file.path().c_str());
    719   } 
     719  }
    720720  chmod(file.path().c_str(), 0);
    721721
     
    735735  OptionFile file(cmd, "file", "", true, false, perm);
    736736
    737   suite.err() << "Testing OptionFile '" << perm << "' ... "; 
     737  suite.err() << "Testing OptionFile '" << perm << "' ... ";
    738738  if (yat::test::run_as_root()) {
    739739    suite.err() << "skipped because user is root\n";
     
    742742  try {
    743743    int ac = 3;
    744     const char* cav[] = { "test_prog", "--file", 
    745                           "testSubDir/commandline_test.dir/test_file4.txt"};
     744    const char* cav[] = { "test_prog", "--file",
     745                         "test/testSubDir/commandline_test.dir/test_file4.txt"};
    746746    char** av = stradup(cav, ac);
    747747    cmd.parse(ac,av);
  • trunk/test/common_defs.sh.in

    r2692 r2739  
    104104# some defs we need in tests
    105105test_dir=`echo $me.dir | sed -e 's,.*[\\/],,'`
    106 test_dir="testSubDir/$test_dir"
     106test_dir="test/testSubDir/$test_dir"
    107107abs_top_builddir=@abs_top_builddir@
    108108abs_top_srcdir=@abs_top_srcdir@
  • trunk/test/doxygen_test.sh

    r2526 r2739  
    2323
    2424required=doxygen
    25 . ./common_defs.sh || exit 99
     25. test/common_defs.sh || exit 99
    2626
    2727printf "doxygen "
    2828$DOXYGEN --version
    29 (cd $abs_top_builddir/doc && make doc < /dev/null) || exit_fail
     29(cd $abs_top_builddir && make doc < /dev/null) || exit_fail
    3030
    3131cat $abs_top_builddir/doc/doxygen.error || test_fail
  • trunk/test/help_test.sh

    r2520 r2739  
    2424set -e
    2525
    26 . ./common_defs.sh || exit 99
     26. test/common_defs.sh || exit 99
    2727
    2828run ../../help.test 0 --nonsense --help
  • trunk/test/static_test.sh

    r2698 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030cat >> configure.ac <<EOF
  • trunk/test/yat_config_cblas_test.sh

    r2526 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030export YAT_CBLAS_LIB=BOGUSBOGUS
  • trunk/test/yat_config_test.sh

    r2622 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030prog=${abs_top_builddir}/build_support/for_installation/yat-config
  • trunk/test/yat_cpp_add_flag_test.sh

    r2527 r2739  
    2727set -e
    2828
    29 . ./common_defs.sh || exit 99
     29. test/common_defs.sh || exit 99
    3030
    3131cat >> configure.ac <<EOF
     
    4747grep 'YAT_CPPFLAGS__' Makefile || exit_fail
    4848grep 'YAT_CPPFLAGS__.*HAVE_SOMETHING' Makefile || exit_fail
    49 grep 'YAT_CPPFLAGS__.*SOMETHING.*SOMETHING' Makefile && exit_fail 
     49grep 'YAT_CPPFLAGS__.*SOMETHING.*SOMETHING' Makefile && exit_fail
    5050grep 'YAT_CPPFLAGS__.*usr/' Makefile && exit_fail "found usr/"
    5151
  • trunk/test/yat_cxx_add_flag_test.sh

    r2528 r2739  
    2727set -e
    2828
    29 . ./common_defs.sh || exit 99
     29. test/common_defs.sh || exit 99
    3030
    3131cat >> configure.ac <<EOF
  • trunk/test/yat_have_svn_wc_test.sh

    r2543 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030cat >> configure.ac <<EOF
  • trunk/test/yat_ld_add_flag_test.sh

    r2527 r2739  
    2727set -e
    2828
    29 . ./common_defs.sh || exit 99
     29. test/common_defs.sh || exit 99
    3030
    3131cat >> configure.ac <<EOF
  • trunk/test/yat_lt_link_ifelse_test.sh

    r2622 r2739  
    2727set -e
    2828
    29 . ./common_defs.sh || exit 99
     29. ./test/common_defs.sh || exit 99
    3030
    3131cat >> configure.ac <<EOF
     
    4747
    4848YAT_FIND_YAT
    49 m4_define([PROG], 
     49m4_define([PROG],
    5050          [AC_LANG_PROGRAM([@%:@include <string>
    5151                            namespace theplu{
     
    5454                              std::string version(void);
    5555                            }}}
    56                            ], 
     56                           ],
    5757                           [using namespace theplu::yat::utility;
    5858                            std::string s=version();
  • trunk/test/yat_m4_test.sh

    r2694 r2739  
    2727set -e
    2828
    29 . ./common_defs.sh || exit 99
     29. test/common_defs.sh || exit 99
    3030
    3131cat >> configure.ac <<EOF
  • trunk/test/yat_m4_test2.sh

    r2608 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030cat >> configure.ac <<EOF
     
    3333AC_PROG_CXX
    3434YAT_FIND_YAT(,[AC_MSG_ERROR([yat_find_yat failed - see warning above])])
    35 YAT_CHECK_VERSION([1.60.2], 
     35YAT_CHECK_VERSION([1.60.2],
    3636                  [AC_MSG_ERROR([yat_check_version failed - see warning above])])
    3737YAT_CHECK_HEADER(,[AC_MSG_ERROR([yat_check_header failed - see warning above])])
  • trunk/test/yat_msg_error_test.sh

    r2673 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. ./test/common_defs.sh || exit 99
    2929
    3030specific_msg='some specific message a51965'
  • trunk/test/yat_msg_error_test2.sh

    r2673 r2739  
    2727set -e
    2828
    29 . ./common_defs.sh || exit 99
     29. test/common_defs.sh || exit 99
    3030
    3131cat >> configure.ac <<EOF
  • trunk/test/yat_prog_move_if_change_test.sh

    r2728 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030cat >> configure.ac <<EOF
  • trunk/test/yat_revision_header_test.sh

    r2552 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030cat >> configure.ac <<EOF
  • trunk/test/yat_svn_release_year_test.sh

    r2680 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030cat >> configure.ac <<EOF
  • trunk/test/yat_svn_revision_test.sh

    r2543 r2739  
    2626set -e
    2727
    28 . ./common_defs.sh || exit 99
     28. test/common_defs.sh || exit 99
    2929
    3030cat >> configure.ac <<EOF
  • trunk/yat/Makefile.am

    r2341 r2739  
    2323# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2424
    25 SUBDIRS = classifier normalizer omic random regression statistics utility
     25lib_LTLIBRARIES = yat/libyat.la
    2626
    27 lib_LTLIBRARIES = libyat.la
    28 
    29 libyat_la_SOURCES =
     27yat_libyat_la_SOURCES =
    3028
    3129# Dummy C++ source to cause C++ linking.
    32 nodist_EXTRA_libyat_la_SOURCES = dummy.cc
     30nodist_EXTRA_yat_libyat_la_SOURCES = dummy.cc
    3331
    34 libyat_la_LDFLAGS = -version-info $(YAT_LT_VERSION) $(AM_LDFLAGS)
     32yat_libyat_la_LDFLAGS = -version-info $(YAT_LT_VERSION) $(AM_LDFLAGS)
    3533
    36 libyat_la_LIBADD = \
    37   classifier/libclassifier.la \
    38   normalizer/libnormalizer.la \
    39   omic/libomic.la \
    40   random/librandom.la \
    41   regression/libregression.la \
    42   statistics/libstatistics.la \
    43   utility/libutility.la \
    44   $(YAT_PRIMARY_LIBS) $(LIBM) 
     34yat_libyat_la_LIBADD = \
     35  yat/classifier/libclassifier.la \
     36  yat/normalizer/libnormalizer.la \
     37  yat/omic/libomic.la \
     38  yat/random/librandom.la \
     39  yat/regression/libregression.la \
     40  yat/statistics/libstatistics.la \
     41  yat/utility/libutility.la \
     42  $(YAT_PRIMARY_LIBS) $(LIBM)
    4543
    46 .PHONY: doxygen_mk
     44noinst_LTLIBRARIES =
     45nobase_include_HEADERS =
    4746
    48 html-local:doxygen_mk
    49 dvi-local:doxygen_mk
    50 ps-local:doxygen_mk
    51 pdf-local:doxygen_mk
    52 
    53 doxygen_mk:
    54   @for subdir in $(SUBDIRS); do \
    55     (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) doxygen.mk) \
    56   done;
     47include yat/classifier/Makefile.am
     48include yat/normalizer/Makefile.am
     49include yat/omic/Makefile.am
     50include yat/random/Makefile.am
     51include yat/regression/Makefile.am
     52include yat/statistics/Makefile.am
     53include yat/utility/Makefile.am
  • trunk/yat/classifier/Makefile.am

    r2384 r2739  
    2121# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2222
    23 noinst_LTLIBRARIES = libclassifier.la
    24 libclassifier_la_SOURCES = \
    25   BootstrapSampler.cc \
    26   ConsensusInputRanker.cc \
    27   CrossValidationSampler.cc \
    28   DataLookup1D.cc \
    29   DataLookupWeighted1D.cc \
    30   FeatureSelector.cc \
    31   FeatureSelectorIR.cc \
    32   FeatureSelectorRandom.cc \
    33   GaussianKernelFunction.cc \
    34   InputRanker.cc \
    35   Kernel.cc \
    36   Kernel_MEV.cc \
    37   Kernel_SEV.cc \
    38   KernelLookup.cc \
    39   KNN_Uniform.cc \
    40   KNN_ReciprocalDistance.cc \
    41   KNN_ReciprocalRank.cc \
    42   MatrixLookup.cc \
    43   MatrixLookupWeighted.cc \
    44   NBC.cc \
    45   PolynomialKernelFunction.cc \
    46   Sampler.cc \
    47   SupervisedClassifier.cc \
    48   SVindex.cc \
    49   SVM.cc \
    50   SvmMultiClass.cc \
    51   Target.cc \
    52   utility.cc
     23noinst_LTLIBRARIES += yat/classifier/libclassifier.la
     24yat_classifier_libclassifier_la_SOURCES = \
     25  yat/classifier/BootstrapSampler.cc \
     26  yat/classifier/ConsensusInputRanker.cc \
     27  yat/classifier/CrossValidationSampler.cc \
     28  yat/classifier/DataLookup1D.cc \
     29  yat/classifier/DataLookupWeighted1D.cc \
     30  yat/classifier/FeatureSelector.cc \
     31  yat/classifier/FeatureSelectorIR.cc \
     32  yat/classifier/FeatureSelectorRandom.cc \
     33  yat/classifier/GaussianKernelFunction.cc \
     34  yat/classifier/InputRanker.cc \
     35  yat/classifier/Kernel.cc \
     36  yat/classifier/Kernel_MEV.cc \
     37  yat/classifier/Kernel_SEV.cc \
     38  yat/classifier/KernelLookup.cc \
     39  yat/classifier/KNN_Uniform.cc \
     40  yat/classifier/KNN_ReciprocalDistance.cc \
     41  yat/classifier/KNN_ReciprocalRank.cc \
     42  yat/classifier/MatrixLookup.cc \
     43  yat/classifier/MatrixLookupWeighted.cc \
     44  yat/classifier/NBC.cc \
     45  yat/classifier/PolynomialKernelFunction.cc \
     46  yat/classifier/Sampler.cc \
     47  yat/classifier/SupervisedClassifier.cc \
     48  yat/classifier/SVindex.cc \
     49  yat/classifier/SVM.cc \
     50  yat/classifier/SvmMultiClass.cc \
     51  yat/classifier/Target.cc \
     52  yat/classifier/utility.cc
    5353
    54 include_classifierdir = $(includedir)/yat/classifier
    55 
    56 include_classifier_HEADERS = \
    57   BootstrapSampler.h \
    58   ConsensusInputRanker.h \
    59   CrossValidationSampler.h \
    60   DataLookup1D.h \
    61   DataLookupWeighted1D.h \
    62   EnsembleBuilder.h \
    63   FeatureSelector.h \
    64   FeatureSelectorIR.h \
    65   FeatureSelectorRandom.h \
    66   GaussianKernelFunction.h \
    67   IGP.h \
    68   IRRank.h \
    69   IRRetrieve.h \
    70   InputRanker.h \
    71   Kernel.h \
    72   KernelFunction.h \
    73   KernelLookup.h \
    74   Kernel_MEV.h \
    75   Kernel_SEV.h \
    76   KNN.h \
    77   KNN_ReciprocalDistance.h \
    78   KNN_ReciprocalRank.h \
    79   KNN_Uniform.h \
    80   MatrixLookup.h \
    81   MatrixLookupWeighted.h \
    82   NBC.h \
    83   NCC.h \
    84   PolynomialKernelFunction.h \
    85   SVM.h \
    86   SvmMultiClass.h \
    87   SVindex.h \
    88   Sampler.h \
    89   SubsetGenerator.h \
    90   SupervisedClassifier.h \
    91   Target.h \
    92   utility.h
    93 
    94 DISTCLEANFILES = doxygen.mk
    95 
    96 all-local: doxygen.mk
    97 
    98 DOXYGEN_INPUT=$(include_classifier_HEADERS)
    99 
    100 include $(top_srcdir)/am/doxygen.am
     54nobase_include_HEADERS += \
     55  yat/classifier/BootstrapSampler.h \
     56  yat/classifier/ConsensusInputRanker.h \
     57  yat/classifier/CrossValidationSampler.h \
     58  yat/classifier/DataLookup1D.h \
     59  yat/classifier/DataLookupWeighted1D.h \
     60  yat/classifier/EnsembleBuilder.h \
     61  yat/classifier/FeatureSelector.h \
     62  yat/classifier/FeatureSelectorIR.h \
     63  yat/classifier/FeatureSelectorRandom.h \
     64  yat/classifier/GaussianKernelFunction.h \
     65  yat/classifier/IGP.h \
     66  yat/classifier/IRRank.h \
     67  yat/classifier/IRRetrieve.h \
     68  yat/classifier/InputRanker.h \
     69  yat/classifier/Kernel.h \
     70  yat/classifier/KernelFunction.h \
     71  yat/classifier/KernelLookup.h \
     72  yat/classifier/Kernel_MEV.h \
     73  yat/classifier/Kernel_SEV.h \
     74  yat/classifier/KNN.h \
     75  yat/classifier/KNN_ReciprocalDistance.h \
     76  yat/classifier/KNN_ReciprocalRank.h \
     77  yat/classifier/KNN_Uniform.h \
     78  yat/classifier/MatrixLookup.h \
     79  yat/classifier/MatrixLookupWeighted.h \
     80  yat/classifier/NBC.h \
     81  yat/classifier/NCC.h \
     82  yat/classifier/PolynomialKernelFunction.h \
     83  yat/classifier/SVM.h \
     84  yat/classifier/SvmMultiClass.h \
     85  yat/classifier/SVindex.h \
     86  yat/classifier/Sampler.h \
     87  yat/classifier/SubsetGenerator.h \
     88  yat/classifier/SupervisedClassifier.h \
     89  yat/classifier/Target.h \
     90  yat/classifier/utility.h
  • trunk/yat/normalizer/Makefile.am

    r2224 r2739  
    2121# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2222
    23 noinst_LTLIBRARIES = libnormalizer.la
    24 libnormalizer_la_SOURCES = qQuantileNormalizer.cc QuantileNormalizer.cc
     23noinst_LTLIBRARIES += yat/normalizer/libnormalizer.la
     24yat_normalizer_libnormalizer_la_SOURCES = \
     25  yat/normalizer/qQuantileNormalizer.cc \
     26  yat/normalizer/QuantileNormalizer.cc
    2527
    26 include_normalizerdir = $(includedir)/yat/normalizer
    27 
    28 include_normalizer_HEADERS = Centralizer.h ColumnNormalizer.h \
    29   Gauss.h qQuantileNormalizer.h QuantileNormalizer.h RowNormalizer.h  \
    30   Spearman.h utility.h Zscore.h
    31 
    32 DISTCLEANFILES = doxygen.mk
    33 
    34 all-local: doxygen.mk
    35 
    36 DOXYGEN_INPUT=$(include_normalizer_HEADERS)
    37 
    38 include $(top_srcdir)/am/doxygen.am
     28nobase_include_HEADERS += \
     29  yat/normalizer/Centralizer.h \
     30  yat/normalizer/ColumnNormalizer.h \
     31  yat/normalizer/Gauss.h \
     32  yat/normalizer/qQuantileNormalizer.h \
     33  yat/normalizer/QuantileNormalizer.h \
     34  yat/normalizer/RowNormalizer.h  \
     35  yat/normalizer/Spearman.h \
     36  yat/normalizer/utility.h \
     37  yat/normalizer/Zscore.h
  • trunk/yat/omic/Makefile.am

    r2482 r2739  
    2020# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2121
    22 noinst_LTLIBRARIES = libomic.la
    23 libomic_la_SOURCES =
    24 libomic_la_SOURCES += Codon.cc
    25 libomic_la_SOURCES += DNA.cc
    26 libomic_la_SOURCES += GenomicPosition.cc
    27 libomic_la_SOURCES += GFF.cc
    28 libomic_la_SOURCES += GFF2.cc
    29 libomic_la_SOURCES += GFF3.cc
     22noinst_LTLIBRARIES += yat/omic/libomic.la
     23yat_omic_libomic_la_SOURCES =
     24yat_omic_libomic_la_SOURCES += yat/omic/Codon.cc
     25yat_omic_libomic_la_SOURCES += yat/omic/DNA.cc
     26yat_omic_libomic_la_SOURCES += yat/omic/GenomicPosition.cc
     27yat_omic_libomic_la_SOURCES += yat/omic/GFF.cc
     28yat_omic_libomic_la_SOURCES += yat/omic/GFF2.cc
     29yat_omic_libomic_la_SOURCES += yat/omic/GFF3.cc
    3030
    31 include_omicdir = $(includedir)/yat/omic
    32 
    33 include_omic_HEADERS =
    34 include_omic_HEADERS += Codon.h
    35 include_omic_HEADERS += DNA.h
    36 include_omic_HEADERS += GenomicPosition.h
    37 include_omic_HEADERS += GFF.h
    38 include_omic_HEADERS += GFF2.h
    39 include_omic_HEADERS += GFF3.h
    40 
    41 DISTCLEANFILES = doxygen.mk
    42 
    43 all-local: doxygen.mk
    44 
    45 DOXYGEN_INPUT=$(include_omic_HEADERS)
    46 
    47 include $(top_srcdir)/am/doxygen.am
     31nobase_include_HEADERS += yat/omic/Codon.h
     32nobase_include_HEADERS += yat/omic/DNA.h
     33nobase_include_HEADERS += yat/omic/GenomicPosition.h
     34nobase_include_HEADERS += yat/omic/GFF.h
     35nobase_include_HEADERS += yat/omic/GFF2.h
     36nobase_include_HEADERS += yat/omic/GFF3.h
  • trunk/yat/random/Makefile.am

    r2384 r2739  
    2222# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2323
    24 noinst_LTLIBRARIES = librandom.la
    25 librandom_la_SOURCES = \
    26   random.cc
     24noinst_LTLIBRARIES += yat/random/librandom.la
     25yat_random_librandom_la_SOURCES = yat/random/random.cc
    2726
    28 include_randomdir = $(includedir)/yat/random
    29 
    30 include_random_HEADERS = \
    31   random.h
    32 
    33 DISTCLEANFILES = doxygen.mk
    34 
    35 all-local: doxygen.mk
    36 
    37 DOXYGEN_INPUT=$(include_random_HEADERS)
    38 
    39 include $(top_srcdir)/am/doxygen.am
     27nobase_include_HEADERS += yat/random/random.h
  • trunk/yat/regression/Makefile.am

    r2526 r2739  
    2222# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2323
    24 noinst_LTLIBRARIES = libregression.la
    25 libregression_la_SOURCES = AkimaInterpolation.cc                      \
    26   AkimaPeriodicInterpolation.cc CSplineInterpolation.cc               \
    27   CSplinePeriodicInterpolation.cc GSLInterpolation.cc KernelBox.cc    \
    28   KernelTriCube.cc Linear.cc LinearInterpolation.cc LinearWeighted.cc \
    29   Local.cc MultiDimensional.cc MultiDimensionalWeighted.cc Naive.cc   \
    30   NaiveWeighted.cc OneDimensional.cc OneDimensionalWeighted.cc        \
    31   Polynomial.cc PolynomialInterpolation.cc PolynomialWeighted.cc \
    32   TukeyBiweight.cc
     24noinst_LTLIBRARIES += yat/regression/libregression.la
     25yat_regression_libregression_la_SOURCES = \
     26  yat/regression/AkimaInterpolation.cc  \
     27  yat/regression/AkimaPeriodicInterpolation.cc \
     28  yat/regression/CSplineInterpolation.cc                \
     29  yat/regression/CSplinePeriodicInterpolation.cc \
     30  yat/regression/GSLInterpolation.cc yat/regression/KernelBox.cc    \
     31  yat/regression/KernelTriCube.cc yat/regression/Linear.cc \
     32  yat/regression/LinearInterpolation.cc yat/regression/LinearWeighted.cc  \
     33  yat/regression/Local.cc yat/regression/MultiDimensional.cc \
     34  yat/regression/MultiDimensionalWeighted.cc yat/regression/Naive.cc    \
     35  yat/regression/NaiveWeighted.cc yat/regression/OneDimensional.cc \
     36  yat/regression/OneDimensionalWeighted.cc        \
     37  yat/regression/Polynomial.cc yat/regression/PolynomialInterpolation.cc \
     38  yat/regression/PolynomialWeighted.cc \
     39  yat/regression/TukeyBiweight.cc
    3340
    34 include_regressiondir = $(includedir)/yat/regression
    35 
    36 include_regression_HEADERS = AkimaInterpolation.h                     \
    37   AkimaPeriodicInterpolation.h CSplineInterpolation.h                 \
    38   CSplinePeriodicInterpolation.h GSLInterpolation.h Kernel.h          \
    39   KernelBox.h KernelTriCube.h Linear.h LinearInterpolation.h          \
    40   LinearWeighted.h Local.h MultiDimensional.h                         \
    41   MultiDimensionalWeighted.h Naive.h NaiveWeighted.h OneDimensional.h \
    42   OneDimensionalWeighted.h Polynomial.h PolynomialInterpolation.h   \
    43   PolynomialWeighted.h TukeyBiweight.h
    44 
    45 DISTCLEANFILES = doxygen.mk
    46 
    47 all-local: doxygen.mk
    48 
    49 DOXYGEN_INPUT=$(include_regression_HEADERS)
    50 
    51 include $(top_srcdir)/am/doxygen.am
     41nobase_include_HEADERS += \
     42  yat/regression/AkimaInterpolation.h \
     43  yat/regression/AkimaPeriodicInterpolation.h \
     44  yat/regression/CSplineInterpolation.h                 \
     45  yat/regression/CSplinePeriodicInterpolation.h \
     46  yat/regression/GSLInterpolation.h \
     47  yat/regression/Kernel.h         \
     48  yat/regression/KernelBox.h \
     49  yat/regression/KernelTriCube.h \
     50  yat/regression/Linear.h \
     51  yat/regression/LinearInterpolation.h          \
     52  yat/regression/LinearWeighted.h \
     53  yat/regression/Local.h \
     54  yat/regression/MultiDimensional.h                         \
     55  yat/regression/MultiDimensionalWeighted.h \
     56  yat/regression/Naive.h \
     57  yat/regression/NaiveWeighted.h \
     58  yat/regression/OneDimensional.h \
     59  yat/regression/OneDimensionalWeighted.h \
     60  yat/regression/Polynomial.h \
     61  yat/regression/PolynomialInterpolation.h    \
     62  yat/regression/PolynomialWeighted.h \
     63  yat/regression/TukeyBiweight.h
  • trunk/yat/statistics/Makefile.am

    r2649 r2739  
    2222# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2323
    24 noinst_LTLIBRARIES = libstatistics.la
    25 libstatistics_la_SOURCES = AUC.cc Averager.cc AveragerPair.cc \
    26   AveragerWeighted.cc AveragerPairWeighted.cc \
    27   Fisher.cc FoldChange.cc Histogram.cc \
    28   Kendall.cc KolmogorovSmirnov.cc Pearson.cc \
    29   PearsonCorrelation.cc Percentiler.cc ROC.cc \
    30   SAMScore.cc Score.cc Smoother.cc SNRScore.cc Spearman.cc tScore.cc tTest.cc \
    31   utility.cc VectorFunction.cc WilcoxonFoldChange.cc
     24noinst_LTLIBRARIES += yat/statistics/libstatistics.la
     25yat_statistics_libstatistics_la_SOURCES = \
     26  yat/statistics/AUC.cc yat/statistics/Averager.cc \
     27  yat/statistics/AveragerPair.cc \
     28  yat/statistics/AveragerWeighted.cc \
     29  yat/statistics/AveragerPairWeighted.cc \
     30  yat/statistics/Fisher.cc yat/statistics/FoldChange.cc \
     31  yat/statistics/Histogram.cc \
     32  yat/statistics/Kendall.cc yat/statistics/KolmogorovSmirnov.cc \
     33  yat/statistics/Pearson.cc \
     34  yat/statistics/PearsonCorrelation.cc yat/statistics/Percentiler.cc \
     35  yat/statistics/ROC.cc \
     36  yat/statistics/SAMScore.cc yat/statistics/Score.cc \
     37  yat/statistics/Smoother.cc yat/statistics/SNRScore.cc \
     38  yat/statistics/Spearman.cc yat/statistics/tScore.cc \
     39  yat/statistics/tTest.cc \
     40  yat/statistics/utility.cc yat/statistics/VectorFunction.cc \
     41  yat/statistics/WilcoxonFoldChange.cc
    3242
    33 include_statisticsdir = $(includedir)/yat/statistics
    34 
    35 include_statistics_HEADERS = AUC.h Average.h Averager.h AveragerPair.h \
    36   AveragerWeighted.h AveragerPairWeighted.h \
    37   averager_traits.h EuclideanDistance.h Fisher.h \
    38   FoldChange.h Histogram.h \
    39   Kendall.h KolmogorovSmirnov.h \
    40   Pearson.h PearsonCorrelation.h \
    41   PearsonDistance.h Percentiler.h ROC.h \
    42   SAMScore.h Score.h Smoother.h SNRScore.h \
    43   Spearman.h TukeyBiweightEstimator.h \
    44   tScore.h tTest.h \
    45   utility.h VectorFunction.h WilcoxonFoldChange.h
    46 DISTCLEANFILES = doxygen.mk
    47 
    48 all-local: doxygen.mk
    49 
    50 DOXYGEN_INPUT=$(include_statistics_HEADERS)
    51 
    52 include $(top_srcdir)/am/doxygen.am
     43nobase_include_HEADERS += \
     44  yat/statistics/AUC.h \
     45  yat/statistics/Average.h yat/statistics/Averager.h \
     46  yat/statistics/AveragerPair.h \
     47  yat/statistics/AveragerWeighted.h yat/statistics/AveragerPairWeighted.h \
     48  yat/statistics/averager_traits.h yat/statistics/EuclideanDistance.h \
     49  yat/statistics/Fisher.h \
     50  yat/statistics/FoldChange.h yat/statistics/Histogram.h \
     51  yat/statistics/Kendall.h yat/statistics/KolmogorovSmirnov.h \
     52  yat/statistics/Pearson.h yat/statistics/PearsonCorrelation.h \
     53  yat/statistics/PearsonDistance.h yat/statistics/Percentiler.h \
     54  yat/statistics/ROC.h \
     55  yat/statistics/SAMScore.h yat/statistics/Score.h yat/statistics/Smoother.h \
     56  yat/statistics/SNRScore.h \
     57  yat/statistics/Spearman.h yat/statistics/TukeyBiweightEstimator.h \
     58  yat/statistics/tScore.h yat/statistics/tTest.h \
     59  yat/statistics/utility.h yat/statistics/VectorFunction.h \
     60  yat/statistics/WilcoxonFoldChange.h
  • trunk/yat/utility/Makefile.am

    r2451 r2739  
    2121# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2222
    23 noinst_LTLIBRARIES = libutility.la
    24 libutility_la_SOURCES = \
    25   Alignment.cc ColumnStream.cc CommandLine.cc DataWeight.cc \
    26   Exception.cc FileUtil.cc GetlineIterator.cc Index.cc KernelPCA.cc kNNI.cc \
    27   Matrix.cc MatrixWeighted.cc NNI.cc Option.cc \
    28   OptionFile.cc OptionInFile.cc OptionOutFile.cc \
    29   OptionHelp.cc OptionSwitch.cc \
    30   PCA.cc sort_index.cc split.cc \
    31   stl_utility.cc SVD.cc TypeInfo.cc utility.cc Vector.cc \
    32   VectorBase.cc VectorConstView.cc VectorMutable.cc VectorView.cc \
    33   version.cc WeNNI.cc
     23noinst_LTLIBRARIES += yat/utility/libutility.la
     24yat_utility_libutility_la_SOURCES = \
     25  yat/utility/Alignment.cc \
     26  yat/utility/ColumnStream.cc \
     27  yat/utility/CommandLine.cc \
     28  yat/utility/DataWeight.cc \
     29  yat/utility/Exception.cc \
     30  yat/utility/FileUtil.cc \
     31  yat/utility/GetlineIterator.cc \
     32  yat/utility/Index.cc \
     33  yat/utility/KernelPCA.cc \
     34  yat/utility/kNNI.cc \
     35  yat/utility/Matrix.cc \
     36  yat/utility/MatrixWeighted.cc \
     37  yat/utility/NNI.cc \
     38  yat/utility/Option.cc \
     39  yat/utility/OptionFile.cc \
     40  yat/utility/OptionInFile.cc \
     41  yat/utility/OptionOutFile.cc \
     42  yat/utility/OptionHelp.cc \
     43  yat/utility/OptionSwitch.cc \
     44  yat/utility/PCA.cc \
     45  yat/utility/sort_index.cc \
     46  yat/utility/split.cc \
     47  yat/utility/stl_utility.cc \
     48  yat/utility/SVD.cc \
     49  yat/utility/TypeInfo.cc \
     50  yat/utility/utility.cc \
     51  yat/utility/Vector.cc \
     52  yat/utility/VectorBase.cc \
     53  yat/utility/VectorConstView.cc \
     54  yat/utility/VectorMutable.cc \
     55  yat/utility/VectorView.cc \
     56  yat/utility/version.cc \
     57  yat/utility/WeNNI.cc
    3458
    35 include_utilitydir = $(includedir)/yat/utility
     59nobase_include_HEADERS += \
     60  yat/utility/Alignment.h \
     61  yat/utility/ColumnStream.h \
     62  yat/utility/CommandLine.h \
     63  yat/utility/concept_check.h \
     64  yat/utility/Container2DIterator.h \
     65  yat/utility/DataIterator.h \
     66  yat/utility/DataWeight.h \
     67  yat/utility/DataWeightProxy.h \
     68  yat/utility/deprecate.h \
     69  yat/utility/Exception.h \
     70  yat/utility/FileUtil.h \
     71  yat/utility/GetlineIterator.h \
     72  yat/utility/Index.h \
     73  yat/utility/iterator_traits.h \
     74  yat/utility/KernelPCA.h \
     75  yat/utility/kNNI.h \
     76  yat/utility/Matrix.h \
     77  yat/utility/MatrixWeighted.h \
     78  yat/utility/merge.h \
     79  yat/utility/NNI.h \
     80  yat/utility/Option.h \
     81  yat/utility/OptionArg.h \
     82  yat/utility/OptionFile.h \
     83  yat/utility/OptionInFile.h \
     84  yat/utility/OptionOutFile.h \
     85  yat/utility/OptionHelp.h \
     86  yat/utility/OptionSwitch.h \
     87  yat/utility/PCA.h \
     88  yat/utility/Segment.h \
     89  yat/utility/SegmentMap.h \
     90  yat/utility/SegmentSet.h \
     91  yat/utility/SegmentTree.h \
     92  yat/utility/SmartPtr.h \
     93  yat/utility/sort_index.h \
     94  yat/utility/split.h \
     95  yat/utility/StreamRedirect.h \
     96  yat/utility/Range.h \
     97  yat/utility/stl_utility.h \
     98  yat/utility/StrideIterator.h \
     99  yat/utility/SVD.h \
     100  yat/utility/TypeInfo.h \
     101  yat/utility/utility.h \
     102  yat/utility/Vector.h \
     103  yat/utility/VectorBase.h \
     104  yat/utility/VectorConstView.h \
     105  yat/utility/VectorMutable.h \
     106  yat/utility/VectorView.h \
     107  yat/utility/version.h \
     108  yat/utility/WeightedIterator.h \
     109  yat/utility/WeightIterator.h \
     110  yat/utility/WeNNI.h \
     111  yat/utility/yat_assert.h
    36112
    37 include_utility_HEADERS = \
    38   Alignment.h ColumnStream.h CommandLine.h concept_check.h \
    39   Container2DIterator.h DataIterator.h DataWeight.h DataWeightProxy.h \
    40   deprecate.h Exception.h FileUtil.h GetlineIterator.h Index.h \
    41   iterator_traits.h \
    42   KernelPCA.h kNNI.h Matrix.h MatrixWeighted.h merge.h NNI.h \
    43   Option.h OptionArg.h OptionFile.h OptionInFile.h OptionOutFile.h \
    44   OptionHelp.h OptionSwitch.h \
    45   PCA.h \
    46   Segment.h SegmentMap.h SegmentSet.h SegmentTree.h \
    47   SmartPtr.h sort_index.h split.h StreamRedirect.h \
    48   Range.h stl_utility.h StrideIterator.h \
    49   SVD.h TypeInfo.h utility.h Vector.h \
    50   VectorBase.h VectorConstView.h VectorMutable.h VectorView.h \
    51   version.h WeightedIterator.h WeightIterator.h WeNNI.h yat_assert.h
    52 
    53 extra_headersdir = $(include_utilitydir)
    54 extra_headers_DATA = config_public.h
    55 
    56 DISTCLEANFILES = doxygen.mk
    57 
    58 all-local: doxygen.mk
    59 
    60 DOXYGEN_INPUT=$(include_utility_HEADERS) $(extra_headers_DATA)
    61 
    62 include $(top_srcdir)/am/doxygen.am
     113nobase_nodist_include_HEADERS = yat/utility/config_public.h
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