alg/nway_paths.hpp

   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 #include <boost/filesystem/path.hpp>
  17
  18 #include <list>
  19 #include <string>
  20 #include <vector>
  21
  22 #include "alg/flp.hpp"
  23 #include "alg/conserved_path.hpp"
  24
  25 class NwayPaths
  26 {
  27   friend class ConnView;
  28   friend class SeqView;
  29   protected:
  30     int threshold;
  31     size_t win_size;
  32     int soft_thres;
  33
  34     double ent_thres;
  35     std::vector<char *> c_sequences; //used by entropy_path_search
  36
  37   public:
  38     NwayPaths();
  39     //! setup an nway comparison, initialize # of species, window size,
  40     //! threshold
  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;
  48
  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);
  53
  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);
  57
  58     void simple_refine();
  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();
  66
  67     void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
  68     void refine();
  69
  70     void save_old(boost::filesystem::path save_file_path);
  71     void print(std::list<std::vector<int> >&);
  72
  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<ConservedPath>::iterator rpbegin() { return refined_pathz.begin() ; }
  79     std::list<ConservedPath>::iterator rpend() { return refined_pathz.end() ; }
  80     size_t refined_path_size() const { return refined_pathz.size(); }
  81
  82     // these probably shouldn't be public, but lets start
  83     // simple
  84     std::list<ConservedPath> pathz;
  85     std::list<ConservedPath > refined_pathz;
  86 };
  87 #endif