mussa_class.hh

   1 //                        ----------------------------------------
   2 //                          ---------- mussa_class.hh -----------
   3 //                        ----------------------------------------
   4
   5 #include "mussa_gui_conn.hh"
   6
   7
   8 class Mussa
   9 {
  10   private:
  11     string para_file_path, ana_name;
  12     int seq_num, window, threshold;
  13     list<string> seq_files, annot_files;
  14     list<int> fasta_indices, sub_seq_starts, sub_seq_ends;
  15     bool win_override, thres_override;
  16     bool win_append, thres_append;
  17
  18     vector<Sequence> the_Seqs;
  19     vector<vector<FLPs> > all_comps;
  20     Nway_Paths the_paths;
  21
  22   public:
  23     Mussa();
  24     char parse_args(int argc, char **argv);
  25     void setup();
  26     void get_Seqs();
  27     void seqcomp();
  28     void nway();
  29     void save();
  30     void load();
  31     void FuckingPieceOfShit(int x_max, int y_max);
  32
  33     // deprecated - support bridge for python version of mussa
  34     void save_old();
  35     void load_old(char * load_file_path, int s_num);
  36
  37 };
  38