mussa_nway.hh

   1 #ifndef _MUSSA_NWAY_H_
   2 #define _MUSSA_NWAY_H_
   3 //  This file is part of the Mussa source distribution.
   4 //  http://mussa.caltech.edu/
   5 //  Contact author: Tristan  De Buysscher, tristan@caltech.edu
   6
   7 // This program and all associated source code files are Copyright (C) 2005
   8 // the California Institute of Technology, Pasadena, CA, 91125 USA.  It is
   9 // under the GNU Public License; please see the included LICENSE.txt
  10 // file for more information, or contact Tristan directly.
  11
  12
  13 //                        ----------------------------------------
  14 //                         ----------  mussa_nway.hh  -----------
  15 //                        ----------------------------------------
  16
  17 #include <list>
  18 #include <string>
  19 #include <vector>
  20
  21 #include "flp.hh"
  22
  23
  24 class Nway_Paths
  25 {
  26   friend class ConnView;
  27   friend class SeqView;
  28   private:
  29     int species_num;
  30     int threshold;
  31     int win_size;
  32     int soft_thres;
  33
  34     double ent_thres;
  35     std::vector<char *> c_sequences;
  36
  37     std::list<std::vector<int> > pathz;
  38     std::list<std::vector<int> > refined_pathz;
  39
  40
  41
  42   public:
  43     Nway_Paths();
  44     void setup(int sp_num, int w, int t);
  45     void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
  46     void set_soft_thres(int soft_thres);
  47
  48     void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  49     void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  50     void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  51     double path_entropy(std::vector<int> path);
  52
  53   // old recursive transitive nway ... has issues checking all links?
  54     void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
  55     void path_search(std::vector<std::vector<FLPs> > all_comparisons, std::vector<int> path, int depth);
  56
  57     void simple_refine();
  58     void save(std::string save_file_path);
  59     std::string load(std::string load_file_path);
  60     void add_path(std::vector<int> loaded_path);
  61     int seq_num();
  62
  63     void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
  64     void refine();
  65
  66     void save_old(std::string save_file_path);
  67     void print();
  68 };
  69 #endif