alg/nway_paths.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 "alg/flp.hh"
  22 #include "alg/conserved_path.h"
  23
  24 class NwayPaths
  25 {
  26   friend class ConnView;
  27   friend class SeqView;
  28   protected:
  29     int threshold;
  30     int win_size;
  31     int soft_thres;
  32
  33     double ent_thres;
  34     std::vector<char *> c_sequences; //used by entropy_path_search
  35
  36   public:
  37     NwayPaths();
  38     //! setup an nway comparison, initialize # of species, window size,
  39     //! threshold
  40     void setup(int w, int t);
  41     void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
  42     void set_soft_thres(int soft_thres);
  43
  44     void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  45     void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  46     void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  47     double path_entropy(std::vector<int> path);
  48
  49   // old recursive transitive nway ... has issues checking all links?
  50     void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
  51     void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, int depth);
  52
  53     void simple_refine();
  54     void save(std::string save_file_path);
  55     //! load a muway file, \throws mussa_load_error
  56     void load(std::string load_file_path);
  57     void add_path(int threshold, std::vector<int>& loaded_path);
  58     void add_path(ConservedPath loaded_path);
  59     //! how many sequences are in our comparison
  60     size_t sequence_count();
  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(std::list<std::vector<int> >&);
  67
  68     // these probably shouldn't be public, but lets start
  69     // simple
  70     std::list<ConservedPath> pathz;
  71     std::list<ExtendedConservedPath > refined_pathz;
  72 };
  73 #endif