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 // ----------------------------------------
16 #include <boost/filesystem/path.hpp>
22 #include "alg/flp.hpp"
23 #include "alg/conserved_path.hpp"
27 friend class ConnView;
35 std::vector<char *> c_sequences; //used by entropy_path_search
39 //! setup an nway comparison, initialize # of species, window size,
41 void setup(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);
44 //! return minimum threshold for this analysis
45 int get_threshold() const;
46 //! return window size used for this analysis
47 int get_window() const;
49 void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
50 void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
51 void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
52 double path_entropy(std::vector<int> path);
54 // old recursive transitive nway ... has issues checking all links?
55 void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
56 void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, size_t depth);
59 void save(boost::filesystem::path save_file_path);
60 //! load a muway file, \throws mussa_load_error
61 void load(boost::filesystem::path load_file_path);
62 void add_path(int threshold, std::vector<int>& loaded_path);
63 void add_path(ConservedPath loaded_path);
64 //! how many sequences are in our comparison
65 size_t sequence_count();
67 void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
70 void save_old(boost::filesystem::path save_file_path);
71 void print(std::list<std::vector<int> >&);
73 // The following iterator functions are mostly for the python interface
74 // they'll have problems when being called from within a const object
75 std::list<ConservedPath>::iterator pbegin() { return pathz.begin() ; }
76 std::list<ConservedPath>::iterator pend() { return pathz.end() ; }
77 size_t path_size() const { return refined_pathz.size(); }
78 std::list<ExtendedConservedPath>::iterator rpbegin() { return refined_pathz.begin() ; }
79 std::list<ExtendedConservedPath>::iterator rpend() { return refined_pathz.end() ; }
80 size_t refined_path_size() const { return refined_pathz.size(); }
82 // these probably shouldn't be public, but lets start
84 std::list<ConservedPath> pathz;
85 std::list<ExtendedConservedPath > refined_pathz;