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 class Nway_Paths
  24 {
  25   friend class ConnView;
  26   friend class SeqView;
  27   private:
  28     int species_num;
  29     int threshold;
  30     int win_size;
  31     int soft_thres;
  32
  33     double ent_thres;
  34     std::vector<char *> c_sequences;
  35
  36     std::list<std::vector<int> > pathz;
  37     std::list<std::vector<int> > refined_pathz;
  38
  39   public:
  40     Nway_Paths();
  41     //! setup an nway comparison, initialize # of species, window size,
  42     //! threshold
  43     void setup(int sp_num, int w, int t);
  44     void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
  45     void set_soft_thres(int soft_thres);
  46
  47     void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  48     void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  49     void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  50     double path_entropy(std::vector<int> path);
  51
  52   // old recursive transitive nway ... has issues checking all links?
  53     void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
  54     void path_search(std::vector<std::vector<FLPs> > all_comparisons, std::vector<int> path, int depth);
  55
  56     void simple_refine();
  57     void save(std::string save_file_path);
  58     std::string load(std::string load_file_path);
  59     void add_path(std::vector<int> loaded_path);
  60     int seq_num();
  61
  62     void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
  63     void refine();
  64
  65     void save_old(std::string save_file_path);
  66     void print();
  67 };
  68 #endif