std'ing vectors, pairs, ...

src/cost.hh

@@ -6,7 +6,7 @@
  *  and in the @f$ (\oplus = min, \otimes = plus) @f$ tropical semi-ring
  *
  *
- *  @see matrix, automaton 
+ *  @see matrix, automaton
  */
 
 // @{
@@ -35,7 +35,7 @@ using namespace std;
  *  (C++ operators  @f$+@f$ and @f$\times@f$) can be used in both cases : either on costs, otherwise on more
  *  traditional floating point values...
  *
- *  @see matrix, automaton 
+ *  @see matrix, automaton
  */
 
 template<typename C> class cost {

src/macro.cc

@@ -19,10 +19,10 @@ int                    gv_subalignment_length = 0;
 int                    gv_subalignment_function_index = 0;
 char *                 gv_subalignment_functions_names[SUBALIGNMENT_FUNCTIONS_NUMBER] = {(char *)"min",(char *)"max",(char *)"avg", (char*)"med"};
 
-template<typename T> double min_vector(vector<T> & v) {return (double)(*(std::min_element(v.begin(),v.end())));}
-template<typename T> double max_vector(vector<T> & v) {return (double)(*(std::max_element(v.begin(),v.end())));}
-template<typename T> double avg_vector(vector<T> & v) {return (double)(std::accumulate(v.begin(), v.end(), 0.0)) / v.size();}
-template<typename T> double med_vector(vector<T> & v) {size_t n = v.size() / 2; nth_element(v.begin(), v.begin()+n, v.end()); return (double)v[n];}
+template<typename T> double min_vector(std::vector<T> & v) {return (double)(*(std::min_element(v.begin(),v.end())));}
+template<typename T> double max_vector(std::vector<T> & v) {return (double)(*(std::max_element(v.begin(),v.end())));}
+template<typename T> double avg_vector(std::vector<T> & v) {return (double)(std::accumulate(v.begin(), v.end(), 0.0)) / v.size();}
+template<typename T> double med_vector(std::vector<T> & v) {size_t n = v.size() / 2; nth_element(v.begin(), v.begin()+n, v.end()); return (double)v[n];}
 
 subalignment_function_int gv_subalignment_functions_int[SUBALIGNMENT_FUNCTIONS_NUMBER] = {
   (subalignment_function_int)  &min_vector<int>,
@@ -40,16 +40,16 @@ subalignment_function_double gv_subalignment_functions_double[SUBALIGNMENT_FUNCT
 
 int                    gv_align_alphabet_size = 2;
 int                    gv_seed_alphabet_size = 2;
-vector< double >       gv_bsel_weight;
-vector< int >          gv_signature;
+std::vector<double>    gv_bsel_weight;
+std::vector<int>       gv_signature;
 bool                   gv_signature_flag = false;
 bool                   gv_signature_shuffle_from_m_pattern_flag = false;
 double                 gv_bsel_minprob,gv_bsel_maxprob;
 int                    gv_minspan = 1, gv_maxspan = 16;
 double                 gv_minweight = -1e32, gv_maxweight = 1e32;
 bool                   gv_weight_interval_flag = false;
 bool                   gv_lossless_flag = false;
-vector<int>            gv_lossless_costs_vector;
+std::vector<int>       gv_lossless_costs_vector;
 int                    gv_lossless_cost_threshold = 0;
 char *                 gv_bsymbols_array = NULL;
 bool                   gv_bsymbols_flag  = false;

src/macro.h

@@ -72,11 +72,11 @@ extern int                    gv_subalignment_function_index;
 /// number of functions proposed in the "subalignment" computation
 #define SUBALIGNMENT_FUNCTIONS_NUMBER 4
 /// type of the int functions proposed in the "subalignment" computation
-typedef double (*subalignment_function_int)(vector<int> &);
+typedef double (*subalignment_function_int)(std::vector<int> &);
 /// vector of int functions proposed in the "subalignment" computation, see @ref gv_subalignment_functions_names for their names
 extern subalignment_function_int    gv_subalignment_functions_int[SUBALIGNMENT_FUNCTIONS_NUMBER];
 /// type of the double functions proposed in the "subalignment" computation
-typedef double (*subalignment_function_double)(vector<double> &);
+typedef double (*subalignment_function_double)(std::vector<double> &);
 /// vector of double functions proposed in the "subalignment" computation, see @ref gv_subalignment_functions_names for their names
 extern subalignment_function_double gv_subalignment_functions_double[SUBALIGNMENT_FUNCTIONS_NUMBER];
 /// names of the functions proposed in the "subalignment" computation, see @ref gv_subalignment_functions_int and @ref gv_subalignment_functions_double for their respective implementation
@@ -116,7 +116,7 @@ extern int gv_verbose;
 /// number of seed runs (0 when full enumeration of all possible seeds)
 extern int                    gv_nbruns;
 /// signature vector (number of seed letters per seed)
-extern vector<int>            gv_signature;
+extern std::vector<int>       gv_signature;
 /// signature flag that enable the signature selection @see gv_signature
 extern bool                   gv_signature_flag;
 /// signature shuffle flag that enable only shuffle from the -m pattern and is not compatible with signature @see gv_signature_flag
@@ -162,7 +162,7 @@ extern double                 gv_bsel_minprob;
 /// max seed letter selectivity for the seed alphabet
 extern double                 gv_bsel_maxprob;
 /// weight as @f$\frac{ \log(\mathrm{seed\ letter\ selectivity})}{log (max (\mathrm{seed\ letter\ selectivity}))}@f$  for each seed  letter
-extern vector<double>         gv_bsel_weight;
+extern std::vector<double>    gv_bsel_weight;
 /// computer the weight (gv_bsel_weight) according to background probabilities (gv_bsel)
 extern void computeWeight();
 // @}
@@ -174,7 +174,7 @@ extern void computeWeight();
 /// flag that activates lossless computation (default lossy computation)
 extern bool                   gv_lossless_flag;
 /// the lossless cost for A when lossless flag is activated @see gv_lossless_flag,gv_lossless_cost_threshold
-extern vector<int>            gv_lossless_costs_vector;
+extern std::vector<int>       gv_lossless_costs_vector;
 /// lossless cost for an alignment (must be at most equal to this value) @see gv_lossless_costs_vector
 extern int                    gv_lossless_cost_threshold;
 // @}