* several modifications for Vienna RNA package 2.0.x.

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.61)
-AC_INIT(centroid_fold, 0.0.9, no-define)
+AC_INIT(centroid_fold, 0.0.10, no-define)
 AM_INIT_AUTOMAKE([-Wall foreign])
 AM_CONFIG_HEADER(config.h)
 AC_CONFIG_SRCDIR([src/centroid_fold.cpp])
@@ -72,7 +72,10 @@ AC_ARG_WITH([vienna-rna], AS_HELP_STRING([--with-vienna-rna], [support Vienna RN
      LDFLAGS="-L${with_vienna_rna}/lib $LDFLAGS"
   fi
 )
-AC_CHECK_LIB(RNA, init_pf_fold)
+AC_CHECK_LIB(RNA, pf_fold)
+
+AC_CHECK_FUNC(energy_of_structure,
+	      [AC_DEFINE([HAVE_VIENNA20], [], [have the Vienna RNA package version 1.8 or above])])
 
 # Checks for header files.
 AC_CHECK_HEADER([ViennaRNA/ribo.h],

src/Makefile.am

@@ -30,4 +30,4 @@ libcentroid_a_SOURCES = \
         probconsRNA/probcons.h \
 	contralign/contralign.h \
         diana.cpp diana.h ps_plot.cpp ps_plot.h naview.c \
-	engine/new_param.h engine/new_param.c
+	engine/boltzmann_param.h engine/boltzmann_param.c

src/aln.cpp

@@ -282,7 +282,12 @@ energy_of_struct(const std::string& paren) const
     }
     s.erase(std::remove(s.begin(), s.end(), '-'), s.end());
     p.erase(std::remove(p.begin(), p.end(), '-'), p.end());
+#ifdef HAVE_VIENNA20
+    e += Vienna::energy_of_structure(s.c_str(), p.c_str(), -1);
+#else
+    Vienna::eos_debug=-1;
     e += Vienna::energy_of_struct(s.c_str(), p.c_str());
+#endif
   }
   return e/num_aln();
 }

src/engine/alifold.cpp

@@ -49,7 +49,7 @@ extern "C" {
 };
 
 extern "C" {
-#include "engine/new_param.h"
+#include "engine/boltzmann_param.h"
 };
 
 AliFoldModel::
@@ -76,7 +76,7 @@ AliFoldModel(bool canonical_only, uint max_bp_dist,
     xsubi[2] += (unsigned short) ((unsigned)seed >> 12);
   }
 
-  copy_new_parameters();
+  copy_boltzmann_parameters();
   if (param) Vienna::read_parameter_file(param);
 }
 
@@ -126,7 +126,11 @@ calculate_posterior(const Aln& aln)
     strcpy(str2, str_.c_str());
   }
   // scaling parameters to avoid overflow
+#ifdef HAVE_VIENNA20
+  double min_en = Vienna::alifold((const char**)seqs, str2);
+#else
   double min_en = Vienna::alifold(seqs, str2);
+#endif
   double kT = (Vienna::temperature+273.15)*1.98717/1000.; /* in Kcal */
   Vienna::pf_scale = exp(-(1.07*min_en)/kT/aln.size());
   Vienna::free_alifold_arrays();
@@ -137,7 +141,11 @@ calculate_posterior(const Aln& aln)
   Vienna::pair_info* pi;
 #endif
   if (!str_.empty()) strcpy(str2, str_.c_str());
+#ifdef HAVE_VIENNA20
+  Vienna::alipf_fold((const char**)seqs, str2, &pi);
+#else
   Vienna::alipf_fold(seqs, str2, &pi);
+#endif
   for (uint k=0; pi[k].i!=0; ++k)
     bp_.update(pi[k].i-1, pi[k].j-1, pi[k].p);
   free(pi);
@@ -162,7 +170,11 @@ prepare_stochastic_traceback(const Aln& aln)
     strcpy(str2, str_.c_str());
   }
   // scaling parameters to avoid overflow
+#ifdef HAVE_VIENNA20
+  double min_en = Vienna::alifold((const char**)seqs, str2);
+#else
   double min_en = Vienna::alifold(seqs, str2);
+#endif
   double kT = (Vienna::temperature+273.15)*1.98717/1000.; /* in Kcal */
   Vienna::pf_scale = exp(-(1.07*min_en)/kT/aln.size());
   Vienna::free_alifold_arrays();
@@ -173,7 +185,11 @@ prepare_stochastic_traceback(const Aln& aln)
   Vienna::pair_info* pi;
 #endif
   if (!str_.empty()) strcpy(str2, str_.c_str());
+#ifdef HAVE_VIENNA20
+  Vienna::alipf_fold((const char**)seqs, str2, &pi);
+#else
   Vienna::alipf_fold(seqs, str2, &pi);
+#endif
 
   if (str2) delete[] str2;
   free_aln(seqs);

src/engine/new_param.c → src/engine/boltzmann_param.c

@@ -4,6 +4,10 @@
   http://www.cs.ubc.ca/labs/beta/Projects/RNA-Params/data/parameters_BLstar_Vienna.txt
  */
 
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
 #include <stdio.h>
 #include <string.h>
 #include <assert.h>
@@ -5971,12 +5975,20 @@ static void copy_MLparams(const int values[])
   ML_BASE37 = values[0];
   ML_closing37 = values[1];
   ML_intern37 = values[2];
+#ifdef HAVE_VIENNA20
+  TerminalAU37 = values[3];
+#else
   TerminalAU = values[3];
+#endif
 }
 
 static void copy_ninio(const int values[])
 {
+#ifdef HAVE_VIENNA20
+  ninio37 = values[0];
+#else
   F_ninio37[2] = values[0];
+#endif
   MAX_NINIO = values[1];
 }
 
@@ -5986,12 +5998,16 @@ static void copy_Tetra_loop(const struct tetra_loops tl[])
   while (tl[i].s!=NULL && i<200) {
     strcpy(&Tetraloops[7*i], tl[i].s);
     strcat(Tetraloops, " ");
+#ifdef HAVE_VIENNA20
+    Tetraloop37[i] = tl[i].e;
+#else
     TETRA_ENERGY37[i] = tl[i].e;
+#endif
     i++;
   }
 }
 
-void copy_new_parameters()
+void copy_boltzmann_parameters()
 {
   copy_stacks(stack37, stack37a);
   copy_mismatch(mismatchH37, mismatchH37a);

src/engine/boltzmann_param.h

@@ -0,0 +1,6 @@
+#ifndef __INC_BOLTZMANN_PARAM_H__
+#define __INC_BOLTZMANN_PARAM_H__
+
+void copy_boltzmann_parameters();
+
+#endif

src/engine/mccaskill.cpp

@@ -52,7 +52,7 @@ extern "C" {
 #endif
 
 extern "C" {
-#include "engine/new_param.h"
+#include "engine/boltzmann_param.h"
 };
 
 McCaskillModel::
@@ -80,7 +80,7 @@ McCaskillModel(bool canonical_only, uint max_bp_dist,
     xsubi[2] += (unsigned short) ((unsigned)seed >> 12);
   }
 
-  copy_new_parameters();
+  copy_boltzmann_parameters();
   if (param) Vienna::read_parameter_file(param);
 }
 
@@ -99,7 +99,9 @@ calculate_posterior(const std::string& seq)
 {
   bp_.resize(seq.size());
   Vienna::pf_scale = -1;
+#ifndef HAVE_VIENNA20
   Vienna::init_pf_fold(seq.size());
+#endif
   if (str_.empty()) {
     Vienna::pf_fold(const_cast<char*>(seq.c_str()), NULL);
   } else {
@@ -127,7 +129,9 @@ prepare_stochastic_traceback(const std::string& seq)
   bk_st_back_=Vienna::st_back;
   Vienna::st_back=1;
   Vienna::pf_scale = -1;
+#ifndef HAVE_VIENNA20
   Vienna::init_pf_fold(seq.size());
+#endif
   if (str_.empty()) {
     Vienna::pf_fold(const_cast<char*>(seq.c_str()), NULL);
   } else {

src/engine/mccaskillhom.cpp

@@ -132,7 +132,9 @@ calculate_posterior(const TH& th)
 
   bp_.resize(seq.size());
   Vienna::pf_scale = -1;
+#ifndef HAVE_VIENNA20
   Vienna::init_pf_fold(seq.size());
+#endif
   if (str_.empty()) {
     Vienna::pf_fold(const_cast<char*>(seq.c_str()), NULL);
   } else {

src/folding_engine.cpp

@@ -58,8 +58,12 @@ const std::string& get_seq(const std::string& t) { return t; }
 static
 float calc_energy(const std::string& t, const std::string& s)
 {
+#ifdef HAVE_VIENNA20
+  return Vienna::energy_of_structure(t.c_str(), s.c_str(), -1);
+#else
   Vienna::eos_debug = -1;
   return Vienna::energy_of_struct(t.c_str(), s.c_str());
+#endif
 }
 #endif
 
@@ -82,8 +86,12 @@ float calc_energy(const Aln& aln, const std::string& s)
 static
 float calc_energy(const TH& t, const std::string& s)
 {
+#ifdef HAVE_VIENNA20
+  return Vienna::energy_of_structure(t.first.c_str(), s.c_str(), -1);
+#else
   Vienna::eos_debug = -1;
   return Vienna::energy_of_struct(t.first.c_str(), s.c_str());
+#endif
 }
 #endif
 

src/util.h

@@ -102,7 +102,9 @@ pf_fold(CONTRALIGN::SparseMatrix<T>*& bp, const std::string& seq, const std::str
   //if (param) Vienna::read_parameter_file (param);
   if (bp!=NULL) delete bp;
   Vienna::pf_scale = -1;
+#ifndef HAVE_VIENNA20
   Vienna::init_pf_fold(seq.size());
+#endif
   if (str.empty()) {
     Vienna::pf_fold(const_cast<char*>(seq.c_str()), NULL);
   } else {