Version up

* add a hidden option for using Vienna's default parameters.

Makefile.in

@@ -89,7 +89,11 @@ build_triplet = @build@
 host_triplet = @host@
 subdir = .
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/ac_cxx_have_stl.m4 \
+	$(top_srcdir)/m4/ac_cxx_namespaces.m4 \
+	$(top_srcdir)/m4/ax_boost_base.m4 \
+	$(top_srcdir)/m4/ax_boost_program_options.m4 \
+	$(top_srcdir)/m4/ax_boost_system.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for centroid_fold 0.0.13.
+# Generated by GNU Autoconf 2.69 for centroid_fold 0.0.14.
 #
 # Report bugs to <no-define>.
 #
@@ -579,8 +579,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='centroid_fold'
 PACKAGE_TARNAME='centroid_fold'
-PACKAGE_VERSION='0.0.13'
-PACKAGE_STRING='centroid_fold 0.0.13'
+PACKAGE_VERSION='0.0.14'
+PACKAGE_STRING='centroid_fold 0.0.14'
 PACKAGE_BUGREPORT='no-define'
 PACKAGE_URL=''
 
@@ -1298,7 +1298,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures centroid_fold 0.0.13 to adapt to many kinds of systems.
+\`configure' configures centroid_fold 0.0.14 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1368,7 +1368,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of centroid_fold 0.0.13:";;
+     short | recursive ) echo "Configuration of centroid_fold 0.0.14:";;
    esac
   cat <<\_ACEOF
 
@@ -1488,7 +1488,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-centroid_fold configure 0.0.13
+centroid_fold configure 0.0.14
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1949,7 +1949,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by centroid_fold $as_me 0.0.13, which was
+It was created by centroid_fold $as_me 0.0.14, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2812,7 +2812,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='centroid_fold'
- VERSION='0.0.13'
+ VERSION='0.0.14'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -4343,10 +4343,11 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the compiler implements namespaces" >&5
 $as_echo_n "checking whether the compiler implements namespaces... " >&6; }
-if ${ax_cv_cxx_namespaces+:} false; then :
+if ${ac_cv_cxx_namespaces+:} false; then :
   $as_echo_n "(cached) " >&6
 else
-  ac_ext=cpp
+
+ ac_ext=cpp
 ac_cpp='$CXXCPP $CPPFLAGS'
 ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
 ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
@@ -4355,12 +4356,18 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 namespace Outer { namespace Inner { int i = 0; }}
-                                   using namespace Outer::Inner; int foo(void) { return i;}
+int
+main ()
+{
+using namespace Outer::Inner; return i;
+  ;
+  return 0;
+}
 _ACEOF
 if ac_fn_cxx_try_compile "$LINENO"; then :
-  ax_cv_cxx_namespaces=yes
+  ac_cv_cxx_namespaces=yes
 else
-  ax_cv_cxx_namespaces=no
+  ac_cv_cxx_namespaces=no
 fi
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
  ac_ext=cpp
@@ -4371,17 +4378,17 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_cxx_namespaces" >&5
-$as_echo "$ax_cv_cxx_namespaces" >&6; }
-if test "$ax_cv_cxx_namespaces" = yes; then
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_namespaces" >&5
+$as_echo "$ac_cv_cxx_namespaces" >&6; }
+if test "$ac_cv_cxx_namespaces" = yes; then
 
 $as_echo "#define HAVE_NAMESPACES /**/" >>confdefs.h
 
 fi
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the compiler supports Standard Template Library" >&5
 $as_echo_n "checking whether the compiler supports Standard Template Library... " >&6; }
-if ${ax_cv_cxx_have_stl+:} false; then :
+if ${ac_cv_cxx_have_stl+:} false; then :
   $as_echo_n "(cached) " >&6
 else
 
@@ -4409,9 +4416,9 @@ list<int>::iterator iter = x.begin(); if (iter != x.end()) ++iter; return 0;
 }
 _ACEOF
 if ac_fn_cxx_try_compile "$LINENO"; then :
-  ax_cv_cxx_have_stl=yes
+  ac_cv_cxx_have_stl=yes
 else
-  ax_cv_cxx_have_stl=no
+  ac_cv_cxx_have_stl=no
 fi
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
  ac_ext=cpp
@@ -4422,9 +4429,9 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_cxx_have_stl" >&5
-$as_echo "$ax_cv_cxx_have_stl" >&6; }
-if test "$ax_cv_cxx_have_stl" = yes; then
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_have_stl" >&5
+$as_echo "$ac_cv_cxx_have_stl" >&6; }
+if test "$ac_cv_cxx_have_stl" = yes; then
 
 $as_echo "#define HAVE_STL /**/" >>confdefs.h
 
@@ -5066,10 +5073,6 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
             if test "x$succeeded" != "xyes"; then
-        CPPFLAGS="$CPPFLAGS_SAVED"
-        LDFLAGS="$LDFLAGS_SAVED"
-        BOOST_CPPFLAGS=
-        BOOST_LDFLAGS=
         _version=0
         if test "$ac_boost_path" != ""; then
             if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
@@ -5082,11 +5085,6 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
                     VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
                     BOOST_CPPFLAGS="-I$ac_boost_path/include/boost-$VERSION_UNDERSCORE"
                 done
-                                if test -z "$BOOST_CPPFLAGS"; then
-                    if test -d "$ac_boost_path/boost" && test -r "$ac_boost_path/boost"; then
-                        BOOST_CPPFLAGS="-I$ac_boost_path"
-                    fi
-                fi
             fi
         else
             if test "$cross_compiling" != yes; then
@@ -5663,12 +5661,12 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 				cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
-#include <boost/program_options/errors.hpp>
+#include <boost/program_options.hpp>
 
 int
 main ()
 {
-boost::program_options::error err("Error message");
+boost::program_options::options_description generic("Generic options");
                                    return 0;
   ;
   return 0;
@@ -7105,7 +7103,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by centroid_fold $as_me 0.0.13, which was
+This file was extended by centroid_fold $as_me 0.0.14, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -7171,7 +7169,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-centroid_fold config.status 0.0.13
+centroid_fold config.status 0.0.14
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.61)
-AC_INIT(centroid_fold, 0.0.13, no-define)
+AC_INIT(centroid_fold, 0.0.14, no-define)
 AM_INIT_AUTOMAKE([-Wall foreign])
 AM_CONFIG_HEADER(config.h)
 AC_CONFIG_SRCDIR([src/centroid_fold.cpp])

src/Makefile.in

@@ -93,7 +93,11 @@ bin_PROGRAMS = centroid_fold$(EXEEXT) centroid_alifold$(EXEEXT) \
 	centroid_homfold$(EXEEXT)
 subdir = src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/ac_cxx_have_stl.m4 \
+	$(top_srcdir)/m4/ac_cxx_namespaces.m4 \
+	$(top_srcdir)/m4/ax_boost_base.m4 \
+	$(top_srcdir)/m4/ax_boost_program_options.m4 \
+	$(top_srcdir)/m4/ax_boost_system.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)

src/contrafold/Makefile.in

@@ -90,7 +90,11 @@ build_triplet = @build@
 host_triplet = @host@
 subdir = src/contrafold
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/ac_cxx_have_stl.m4 \
+	$(top_srcdir)/m4/ac_cxx_namespaces.m4 \
+	$(top_srcdir)/m4/ax_boost_base.m4 \
+	$(top_srcdir)/m4/ax_boost_program_options.m4 \
+	$(top_srcdir)/m4/ax_boost_system.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)

src/contralign/Makefile.in

@@ -90,7 +90,11 @@ build_triplet = @build@
 host_triplet = @host@
 subdir = src/contralign
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/ac_cxx_have_stl.m4 \
+	$(top_srcdir)/m4/ac_cxx_namespaces.m4 \
+	$(top_srcdir)/m4/ax_boost_base.m4 \
+	$(top_srcdir)/m4/ax_boost_program_options.m4 \
+	$(top_srcdir)/m4/ax_boost_system.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)

src/engine/alifold.cpp

@@ -76,8 +76,13 @@ AliFoldModel(bool canonical_only, uint max_bp_dist,
     xsubi[2] += (unsigned short) ((unsigned)seed >> 12);
   }
 
-  copy_boltzmann_parameters();
-  if (param) Vienna::read_parameter_file(param);
+  if (param)
+  {
+    if (strcmp(param, "default")!=0)
+      Vienna::read_parameter_file(param);
+  }
+  else
+    copy_boltzmann_parameters();
 }
 
 void

src/engine/mccaskillhom.cpp

@@ -31,6 +31,10 @@ extern "C" {
 };
 #endif
 
+extern "C" {
+#include "engine/boltzmann_param.h"
+};
+
 McCaskillHomModel::
 McCaskillHomModel(const std::string& engine_a, bool canonical_only, uint max_bp_dist,
                const char* param /*=NULL*/, uint seed /*=0*/, bool run_as_mea /*=false*/)
@@ -56,7 +60,14 @@ McCaskillHomModel(const std::string& engine_a, bool canonical_only, uint max_bp_
     xsubi[2] += (unsigned short) ((unsigned)seed >> 12);
   }
 
-  if (param && std::string(param) != "") Vienna::read_parameter_file(param);
+  if (param)
+  {
+    if (strcmp(param, "default")!=0)
+      Vienna::read_parameter_file(param);
+  }
+  else
+    copy_boltzmann_parameters();
+
   param_ = param;
 
   engine_a_ = engine_a;

src/probconsRNA/Makefile.in

@@ -90,7 +90,11 @@ build_triplet = @build@
 host_triplet = @host@
 subdir = src/probconsRNA
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/ac_cxx_have_stl.m4 \
+	$(top_srcdir)/m4/ac_cxx_namespaces.m4 \
+	$(top_srcdir)/m4/ax_boost_base.m4 \
+	$(top_srcdir)/m4/ax_boost_program_options.m4 \
+	$(top_srcdir)/m4/ax_boost_system.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)