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/conserved_path.hpp"
  23 #include "alg/flp.hpp"
  24 #include "alg/mussa_callback.hpp"
  25
  26 class NwayPaths
  27 {
  28   friend class ConnView;
  29   friend class SeqView;
  30   protected:
  31     int threshold;
  32     size_t win_size;
  33     int soft_thres;
  34
  35     double ent_thres;
  36     std::vector<char *> c_sequences; //used by entropy_path_search
  37     analysis_callback progress_cb;
  38
  39   public:
  40     NwayPaths();
  41     //! setup an nway comparison, initialize # of species, window size,
  42     //! threshold
  43     void setup(int w, int t);
  44     void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
  45     void set_soft_threshold(int soft_thres);
  46     //! return minimum threshold for this analysis
  47     int get_threshold() const;
  48     //! return window size used for this analysis
  49     int get_window() const;
  50     //! set analysis progress callback
  51     void set_progress_callback(analysis_callback cb);
  52     //! get analysis progress callback
  53     analysis_callback get_progress_callback() const;
  54
  55     void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  56     void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  57     void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
  58     double path_entropy(std::vector<int> path);
  59
  60   // old recursive transitive nway ... has issues checking all links?
  61     void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
  62     void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, size_t depth);
  63
  64     void simple_refine();
  65     void save(boost::filesystem::path save_file_path);
  66     //! load a muway file, \throws mussa_load_error
  67     void load(boost::filesystem::path load_file_path);
  68     void add_path(int threshold, std::vector<int>& loaded_path);
  69     void add_path(ConservedPath loaded_path);
  70     //! how many sequences are in our comparison
  71     size_t sequence_count();
  72
  73     void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
  74     void refine();
  75
  76     void save_old(boost::filesystem::path save_file_path);
  77     void print(std::list<std::vector<int> >&);
  78
  79     // The following iterator functions are mostly for the python interface
  80     // they'll have problems when being called from within a const object
  81     std::list<ConservedPath>::iterator pbegin() { return pathz.begin() ; }
  82     std::list<ConservedPath>::iterator pend() { return pathz.end() ; }
  83     size_t path_size() const { return refined_pathz.size(); }
  84     std::list<ConservedPath>::iterator rpbegin() { return refined_pathz.begin() ; }
  85     std::list<ConservedPath>::iterator rpend() { return refined_pathz.end() ; }
  86     size_t refined_path_size() const { return refined_pathz.size(); }
  87
  88     // these probably shouldn't be public, but lets start
  89     // simple
  90     std::list<ConservedPath> pathz;
  91     std::list<ConservedPath > refined_pathz;
  92 };
  93 #endif