* bug fix

satoken · Sep 14, 2012 · 524759b · 524759b
1 parent f7850d1
commit 524759b
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Showing 2 changed files with 13 additions and 23 deletions.
diff --git a/src/alifold.cpp b/src/alifold.cpp
@@ -52,13 +52,12 @@ fold(const ALN& aln, const std::vector<Fasta>& fa, BP& bp) const
   char** seqs = alloc_aln(aln, fa);
 
   // scaling parameters to avoid overflow
-  char* res = new char[L+1];
+  std::string res(L+1, ' ');
 #ifdef HAVE_VIENNA20
-  double min_en = Vienna::alifold((const char**)seqs, res);
+  double min_en = Vienna::alifold((const char**)seqs, &res[0]);
 #else
-  double min_en = Vienna::alifold(seqs, res);
+  double min_en = Vienna::alifold(seqs, &res[0]);
 #endif
-  delete[] res;
   double kT = (Vienna::temperature+273.15)*1.98717/1000.; /* in Kcal */
   Vienna::pf_scale = exp(-(1.07*min_en)/kT/L);
   Vienna::free_alifold_arrays();
@@ -95,25 +94,22 @@ fold(const ALN& aln, const std::vector<Fasta>& fa, const std::string& str, BP& b
   char** seqs = alloc_aln(aln, fa);
 
   // scaling parameters to avoid overflow
-  char* res = new char[L+1];
-  strcpy(res, p.c_str());
+  std::string res(p);
 #ifdef HAVE_VIENNA20
-  double min_en = Vienna::alifold((const char**)seqs, res);
+  double min_en = Vienna::alifold((const char**)seqs, &res[0]);
 #else
-  double min_en = Vienna::alifold(seqs, res);
+  double min_en = Vienna::alifold(seqs, &res[0]);
 #endif
   double kT = (Vienna::temperature+273.15)*1.98717/1000.; /* in Kcal */
   Vienna::pf_scale = exp(-(1.07*min_en)/kT/L);
   Vienna::free_alifold_arrays();
 
-  strcpy(res, p.c_str());
   pair_info* pi;
 #ifdef HAVE_VIENNA20
-  Vienna::alipf_fold((const char**)seqs, res, &pi);
+  Vienna::alipf_fold((const char**)seqs, &p[0], &pi);
 #else
-  Vienna::alipf_fold(seqs, res, &pi);
+  Vienna::alipf_fold(seqs, &p[0], &pi);
 #endif
-  delete[] res;
 
   bp.resize(L);
   for (uint k=0; pi[k].i!=0; ++k)

diff --git a/src/fold.cpp b/src/fold.cpp
@@ -81,9 +81,8 @@ calculate(const std::string& seq, BP& bp)
   // scaling parameters to avoid overflow
   if (1 /*L>1600*/)
   {
-    char *res = new char[L+1];
-    float min_en = Vienna::fold(const_cast<char*>(seq.c_str()), res);
-    delete[] res;
+    std::string res(L+1, ' ');
+    float min_en = Vienna::fold(const_cast<char*>(seq.c_str()), &res[0]);
     float sfact = 1.07;
     float kT = (Vienna::temperature+273.15)*1.98717/1000.; /* in Kcal */
     Vienna::pf_scale = exp(-(sfact*min_en)/kT/seq.size());
@@ -130,10 +129,8 @@ calculate(const std::string& seq, const std::string& str, BP& bp)
   // scaling parameters to avoid overflow
   if (1 /*L>1600*/)
   {
-    char* res = new char[L+1];
-    strcpy(res, p.c_str());
-    float min_en = Vienna::fold(const_cast<char*>(seq.c_str()), res);
-    delete[] res;
+    std::string res(p);
+    float min_en = Vienna::fold(const_cast<char*>(seq.c_str()), &res[0]);
     float sfact = 1.07;
     float kT = (Vienna::temperature+273.15)*1.98717/1000.; /* in Kcal */
     Vienna::pf_scale = exp(-(sfact*min_en)/kT/seq.size());
@@ -143,10 +140,7 @@ calculate(const std::string& seq, const std::string& str, BP& bp)
 #ifndef HAVE_VIENNA20
   Vienna::init_pf_fold(L);
 #endif
-  char* res = new char[L+1];
-  strcpy(res, p.c_str());
-  Vienna::pf_fold(const_cast<char*>(seq.c_str()), res);
-  delete[] res;
+  Vienna::pf_fold(const_cast<char*>(seq.c_str()), &p[0]);
 
 #ifdef HAVE_VIENNA20
   FLT_OR_DBL* pr = Vienna::export_bppm();