AC_DEFUN([RNA_GET_FEATURE],[
  _features_active=0
  ## collect the subpackages/programs we gonna build
  AS_IF([test "x$with_svm" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [SVM])
    _features_active=1
  ])
  AS_IF([test "x$with_json" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [JSON])
    _features_active=1
  ])
  AS_IF([test "x$with_gsl" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [GSL])
    _features_active=1
  ])
  AS_IF([test "x$enable_boustrophedon" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [Boustrophedon])
    _features_active=1
  ])
  AS_IF([test "x$enable_openmp" != "xno"], [
    AC_RNA_APPEND_VAR_COMMA($1, [OpenMP])
    _features_active=1
  ])
  AS_IF([test "x$enable_lto" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [LTO])
    _features_active=1
  ])
  AS_IF([test "x$enable_floatpf" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [Float Precision(PF)])
    _features_active=1
  ])
  AS_IF([test "x$with_warn_deprecated" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [Deprecation Warnings])
    _features_active=1
  ])
  AS_IF([test "x$enable_c11" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [C11])
    _features_active=1
  ])
  AS_IF([test "x$enable_tty_colors" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [Color])
    _features_active=1
  ])
  AS_IF([test "x$enable_sse" = "xyes"], [
    AC_RNA_APPEND_VAR_COMMA($1, [SSE4.1])
    _features_active=1
  ])
  AS_IF([test "$_features_active" -eq "0"],[
    AC_RNA_APPEND_VAR_COMMA($1, [None])
  ])
])

#
# SVM support for Lfold -z
#

AC_DEFUN([RNA_ENABLE_SVM],[

  SVM_VERSION=3.22

  RNA_ADD_PACKAGE([svm],
                  [svm classifiers],
                  [yes],[],[],
                  [${srcdir}/src/libsvm-${SVM_VERSION}/svm.cpp ${srcdir}/src/libsvm-${SVM_VERSION}/svm.h])

  RNA_PACKAGE_IF_ENABLED([svm],[
    AC_SUBST([LIBSVM_DIR], [libsvm-${SVM_VERSION}])
    ## substitution for reference manual config
    AC_SUBST([REFDOC_PREDEF_SVM], [VRNA_WITH_SVM])
    AC_DEFINE([VRNA_WITH_SVM], [1], [Compute z-scores for RNALfold])
    CONFIG_SVM="#define VRNA_WITH_SVM"
  ])

  AC_SUBST(CONFIG_SVM)
  AM_CONDITIONAL(VRNA_AM_SWITCH_SVM, test "$with_svm" != "no")
])


#
# JSON serializer/deserializer
#

AC_DEFUN([RNA_ENABLE_JSON],[

  RNA_ADD_PACKAGE([json],
                  [json in/out support],
                  [yes],[],[],
                  [${srcdir}/src/json/json.c ${srcdir}/src/json/json.h])

  RNA_PACKAGE_IF_ENABLED([json],[
    ## substitution for reference manual config
    AC_SUBST([REFDOC_PREDEF_JSON], [VRNA_WITH_JSON_SUPPORT])
    AC_DEFINE([VRNA_WITH_JSON_SUPPORT], [1], [Add JSON support for input and output functions])
    CONFIG_JSON="#define VRNA_WITH_JSON_SUPPORT"
  ])

  AC_SUBST(CONFIG_JSON)
  AM_CONDITIONAL(VRNA_AM_SWITCH_JSON, test "$with_json" != "no")
])


#
# GSL support for RNApvmin
#

AC_DEFUN([RNA_ENABLE_GSL],[

  RNA_ADD_PACKAGE([gsl],
                  [GNU Scientific Library],
                  [yes])

  # check prerequisties for gsl support
  RNA_PACKAGE_IF_ENABLED([gsl],[
    AC_CHECK_LIB([gslcblas],[cblas_dgemm])
    AC_CHECK_LIB([gsl],[gsl_blas_dgemm])

    if test "$ac_cv_lib_gsl_gsl_blas_dgemm" != yes; then
      AC_MSG_WARN("Can't find libgsl. Falling back to default implementation.")
      enabled_but_failed_gsl="(libgsl not found)"
      with_gsl="no"
    fi
  ])
  RNA_PACKAGE_IF_ENABLED([gsl],[
    AC_DEFINE([VRNA_WITH_GSL], [1], [Use GNU Scientific Library])
    GSL_LIBS="-lgsl -lgslcblas"
    CONFIG_GSL="#define VRNA_WITH_GSL"
  ])

  AC_SUBST([GSL_LIBS])
  AC_SUBST([CONFIG_GSL])
  AM_CONDITIONAL(VRNA_AM_SWITCH_GSL, test "x$with_gsl" = "xyes")
])


#
# Boustrophedon scheme for stochastic backtracking
#

AC_DEFUN([RNA_ENABLE_BOUSTROPHEDON],[

  RNA_ADD_FEATURE([boustrophedon],
                  [Boustrophedon scheme for stochastic backtracking],
                  [yes])

  ## Add preprocessor define statement for Boustrophedon scheme in stochastic backtracking in part_func.c
  RNA_FEATURE_IF_ENABLED([boustrophedon],[
    AC_DEFINE([VRNA_WITH_BOUSTROPHEDON], [1], [Use Boustrophedon scheme for stochastic backtracking])
    CONFIG_BOUSTROPHEDON="#define VRNA_WITH_BOUSTROPHEDON"
  ])

  AC_SUBST(CONFIG_BOUSTROPHEDON)
])


#
# OpenMP support
#

AC_DEFUN([RNA_ENABLE_OPENMP],[

  RNA_ADD_FEATURE([openmp],
                  [OpenMP support],
                  [yes])

  RNA_FEATURE_IF_ENABLED([openmp],[
    AC_LANG_PUSH([C])
    AX_OPENMP([],[enable_openmp="no"])
    AC_LANG_POP([C])

    AS_IF([ test "x$enable_openmp" != "xno" ],[
      OMP_CFLAGS="$OPENMP_CFLAGS"

      AC_LANG_PUSH([C++])
      AX_OPENMP([],[enable_openmp="no"])
      AC_LANG_POP([C++])

      if test "x$enable_openmp" != "xno"
      then
        RNA_CFLAGS="${RNA_CFLAGS} ${OMP_CFLAGS}"
        RNA_CXXFLAGS="${RNA_CXXFLAGS} ${OPENMP_CXXFLAGS}"
        LIBGOMPFLAG="$OPENMP_CXXFLAGS"
        CONFIG_OPENMP="#define VRNA_WITH_OPENMP"
      fi
    ])
  ])

  AC_SUBST(CONFIG_OPENMP)
  AC_SUBST(LIBGOMPFLAG)
  AC_SUBST(OPENMP_CFLAGS)
  AC_SUBST(OPENMP_CXXFLAGS)
])


#
# C11 feature support
#

AC_DEFUN([RNA_ENABLE_C11],[

  RNA_ADD_FEATURE([c11],
                  [C11 feature support (unnamed unions of unnamed structs)],
                  [yes])

  RNA_FEATURE_IF_ENABLED([c11],[
    AC_MSG_CHECKING([whether the C compiler allows unnamed unions of unnamed structs])
    # save current global flags
    AC_LANG_PUSH([C])
    AC_RUN_IFELSE([AC_LANG_SOURCE([[#include <stdlib.h>
                                    struct bla {
                                      union {
                                        struct { int a; char  b;};
                                        struct { long c; double d;};
                                      };
                                    };
                                    int main (void) { return 0;} ]])],
                                    [enable_c11=yes],
                                    [enable_c11=no],
                                    [enable_c11=no])

    AC_LANG_POP([C])
    AC_MSG_RESULT([$enable_c11])

    AS_IF([ test "x$enable_c11" != "xno" ],[
      AC_MSG_CHECKING([whether the C++ compiler allows unnamed unions of unnamed structs])
      AC_LANG_PUSH([C++])
      AC_RUN_IFELSE([AC_LANG_SOURCE([[extern "C" {
                                        #include <stdlib.h>
                                        struct bla {
                                          union {
                                            struct { int a; char  b;};
                                            struct { long c; double d;};
                                          };
                                        };
                                      };
                                      int main (void) { return 0;} ]])],
                                      [enable_c11=yes],
                                      [enable_c11=no],
                                      [enable_c11=no])

      AC_LANG_POP([C++])
      AC_MSG_RESULT([$enable_c11])
    ])
  ])

  AS_IF([ test "x$enable_c11" != "xyes" ],[
    DISABLE_C11_FEATURES=-DVRNA_DISABLE_C11_FEATURES
    CONFIG_DISABLE_C11_FEATURES="#define VRNA_DISABLE_C11_FEATURES"
    AX_APPEND_FLAG(["${DISABLE_C11_FEATURES}"], [RNA_CPPFLAGS])
  ])

  AC_SUBST(DISABLE_C11_FEATURES)
  AC_SUBST(CONFIG_DISABLE_C11_FEATURES)
])

#
#
#

AC_DEFUN([RNA_ENABLE_FLOATPF],[

  RNA_ADD_FEATURE([floatpf],
                  [Floating point precision in partition function computations],
                  [no])

  # Handle floating point precision flag
  RNA_FEATURE_IF_ENABLED([floatpf],[

    AC_DEFINE([USE_FLOAT_PF], [1], [Use floating point precision in partition function computations])
    CONFIG_FLOAT_PF="#define USE_FLOAT_PF"
    ## substitution for reference manual config
    AC_SUBST([REFDOC_PREDEF_FLOAT_PF], [USE_FLOAT_PF])
    AC_SUBST([FLOAT_PF_FLAG], [-DUSE_FLOAT_PF])
    AX_APPEND_FLAG([-DUSE_FLOAT_PF], [RNA_CPPFLAGS])
  ])

  AC_SUBST(CONFIG_FLOAT_PF)
])


#
# Warn about usage of deprecated symbols
#

AC_DEFUN([RNA_ENABLE_DEPRECATION_WARNINGS],[

  RNA_ADD_FEATURE([warn_deprecated],
                  [Warn upon usage of deprecated symbols],
                  [no])

  ## Add preprocessor define statement for deprecation warnings
  RNA_FEATURE_IF_ENABLED([warn_deprecated],[
    AC_DEFINE([VRNA_WARN_DEPRECATED], [1], [Warn upon usage of deprecated symbols])
    DEPRECATION_WARNING=-DVRNA_WARN_DEPRECATED
    AX_APPEND_FLAG([VRNA_WARN_DEPRECATED], [RNA_CPPFLAGS])
  ])
  AC_SUBST(DEPRECATION_WARNING)
])


#
# Colored TTY output
#

AC_DEFUN([RNA_ENABLE_COLORED_TTY],[

  RNA_ADD_FEATURE([tty_colors],
                  [Colored TTY output],
                  [yes])

  ## Add preprocessor define statement for Boustrophedon scheme in stochastic backtracking in part_func.c
  RNA_FEATURE_IF_DISABLED([tty_colors],[
    AC_DEFINE([VRNA_WITHOUT_TTY_COLORS], [1], [Do not use colors for TTY output])
    CONFIG_TTY_COLORS="#define VRNA_WITHOUT_TTY_COLORS"
  ])

  AC_SUBST(CONFIG_TTY_COLORS)
])


#
# Statically linked executables
#

AC_DEFUN([RNA_ENABLE_STATIC_BIN],[

  RNA_ADD_FEATURE([static_executables],
                  [Produce statically linked executable binaries],
                  [no])

  ## Check whether necessary static libraries are present
  RNA_FEATURE_IF_ENABLED([static_executables],[
    SAVED_LDFLAGS=$LDFLAGS
    LDFLAGS="$LDFLAGS -static"

    AC_MSG_NOTICE([Checking possiblity to build statically linked executables using C compiler])
    AC_LANG_PUSH([C])

    AC_RUN_IFELSE([AC_LANG_SOURCE([[ #include <math.h>
                                      int main (void) { return (int)log(1.);} ]])],
                                      [],
                                      [ AC_MSG_ERROR([[
############################################
Failed to statically link C program

Please make sure that static variants for
all libraries that are about to be linked
into the executables are present!

Checked compiler flag setup:
 LDFLAGS = $LDFLAGS 
 LIBS    = $LIBS
 CLFAGS  = $CFLAGS
############################################]]) ],
                                      [enable_static_executables=no])

    AC_LANG_POP([C])
    AC_MSG_NOTICE([Building statically linked C executables seems to work fine])
    LDFLAGS=$SAVED_LDFLAGS
  ])

  RNA_FEATURE_IF_ENABLED([static_executables],[
    SAVED_LDFLAGS=$LDFLAGS
    LDFLAGS="$LDFLAGS -static -lstdc++"

    AC_MSG_NOTICE([Checking possiblity to build statically linked executables using C++ compiler])
    AC_LANG_PUSH([C++])

    AC_RUN_IFELSE([AC_LANG_SOURCE([[ int main (void) { return 0;} ]])],
                                      [],
                                      [ AC_MSG_ERROR([[
############################################
Failed to statically link C++ program

Please make sure that static variants for
all libraries that are about to be linked
into the executables are present!
############################################]]) ],
                                      [enable_static_executables=no])

    AC_LANG_POP([C++])
    AC_MSG_NOTICE([Building statically linked C++ executables seems to work fine])

    LDFLAGS=$SAVED_LDFLAGS
  ])

  AM_CONDITIONAL(VRNA_AM_SWITCH_STATIC_EXECUTABLES, test "x$enable_static_executables" = "xyes")
])


#
# SSE implementations
#

AC_DEFUN([RNA_ENABLE_SSE],[

  RNA_ADD_FEATURE([sse],
                  [Speed-up MFE computations using SSE 4.1 implementations],
                  [no])

  ## Add preprocessor define statement for Boustrophedon scheme in stochastic backtracking in part_func.c
  RNA_FEATURE_IF_ENABLED([sse],[
    if test "x$SIND_CFLAGS" = x; then
      case $ax_cv_c_compiler_vendor in
        gnu)
          AC_LANG_PUSH([C])
          AX_CHECK_COMPILE_FLAG([-msse4.1], [ac_sse41_supported=yes],[ac_sse41_supported=no],[],[])
          AC_LANG_POP([C])
          ;;
        intel)
          ;;
        *)
          ;;
      esac
    fi

    if test $ac_sse41_supported = no; then
      enable_sse=no;
    fi
  ])

  RNA_FEATURE_IF_ENABLED([sse],[
    AC_MSG_CHECKING([compiler support for SSE4.1 min function])
    ac_save_CFLAGS="$CFLAGS"
    CFLAGS="$ac_save_CFLAGS -msse4.1"
    AC_LANG(C)
    AC_COMPILE_IFELSE(
    [
      AC_LANG_PROGRAM([[
                        #include <smmintrin.h>
                        #include <limits.h>
                      ]],
                        [[__m128i a = _mm_set1_epi32(INT_MAX);
                          __m128i b = _mm_set1_epi32(INT_MIN);
                          b = _mm_min_epi32(a, b);
                      ]])
    ],
    [
      AC_MSG_RESULT([yes])
      SIMD_CFLAGS="${SIMD_CFLAGS} -msse4.1"
      AC_DEFINE([VRNA_WITH_SSE_IMPLEMENTATION], [1], [use SSE implementations])
      CONFIG_SSE_IMPLEMENTATION="#define VRNA_WITH_SSE_IMPLEMENTATION"
    ],
    [
      enable_sse=no
      AC_MSG_RESULT([no; using default implementation])
    ])
    CFLAGS="$ac_save_CFLAGS"
  ])

  AC_SUBST(SIMD_CFLAGS)
  AC_SUBST(CONFIG_SSE_IMPLEMENTATION)
])