mussa_nway.hh

   1 //                        ----------------------------------------
   2 //                         ----------  mussa_nway.hh  -----------
   3 //                        ----------------------------------------
   4
   5 #include "flp.hh"
   6
   7
   8 class Nway_Paths
   9 {
  10   friend class ConnView;
  11   friend class SeqView;
  12   private:
  13     int species_num;
  14     int threshold;
  15     int win_size;
  16     int soft_thres;
  17
  18     double ent_thres;
  19     vector<char *> c_sequences;
  20
  21     list<vector<int> > pathz;
  22     list<vector<int> > refined_pathz;
  23
  24
  25
  26   public:
  27     Nway_Paths();
  28     void setup(int sp_num, int w, int t);
  29     void setup_ent(double new_entropy_thres, vector<string> some_Seqs);
  30     void set_soft_thres(int soft_thres);
  31
  32     void radiate_path_search(vector<vector<FLPs> > all_comparisons);
  33     void trans_path_search(vector<vector<FLPs> > all_comparisons);
  34     void entropy_path_search(vector<vector<FLPs> > all_comparisons);
  35     double path_entropy(vector<int> path);
  36
  37   // old recursive transitive nway ... has issues checking all links?
  38     void find_paths_r(vector<vector<FLPs> > all_comparisons);
  39     void path_search(vector<vector<FLPs> > all_comparisons, vector<int> path, int depth);
  40
  41     void simple_refine();
  42     void save(string save_file_path);
  43     string load(string load_file_path);
  44     void add_path(vector<int> loaded_path);
  45     int seq_num();
  46
  47     void find_paths(vector<vector<FLPs> > all_comparisons);
  48     void refine();
  49
  50     void save_old(string save_file_path);
  51     void print();
  52 };