3 // This file is part of the Mussa source distribution.
4 // http://mussa.caltech.edu/
5 // Contact author: Tristan De Buysscher, tristan@caltech.edu
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.
13 // ----------------------------------------
14 // ---------- mussa_nway.hh -----------
15 // ----------------------------------------
25 friend class ConnView;
34 std::vector<char *> c_sequences;
36 std::list<std::vector<int> > pathz;
37 std::list<std::vector<int> > refined_pathz;
41 void setup(int sp_num, int w, int t);
42 void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
43 void set_soft_thres(int soft_thres);
45 void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
46 void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
47 void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
48 double path_entropy(std::vector<int> path);
50 // old recursive transitive nway ... has issues checking all links?
51 void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
52 void path_search(std::vector<std::vector<FLPs> > all_comparisons, std::vector<int> path, int depth);
55 void save(std::string save_file_path);
56 std::string load(std::string load_file_path);
57 void add_path(std::vector<int> loaded_path);
60 void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
63 void save_old(std::string save_file_path);