mussa_nway.hh

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