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 // ----------------------------------------
19 #include <boost/filesystem/path.hpp>
25 #include "alg/conserved_path.hpp"
26 #include "alg/flp.hpp"
27 #include "alg/sequence.hpp"
29 class NwayPaths : public QObject
34 //! emit to indicate how much progress we've made
35 void progress(const QString& description, int cur, int max);
38 typedef std::list<ConservedPath> ConservedPaths;
41 NwayPaths(const NwayPaths&);
43 //! setup an nway comparison, initialize # of species, window size,
45 void setup(int w, int t);
46 void setup_ent(double new_entropy_thres, std::vector<Sequence> some_Seqs);
47 //! clear out our path
49 //! get the "soft" threshold (between the hard threshold and window size)
50 int get_soft_threshold() const;
51 //! set the score that a match must exceed inorder to be recorded as a path
52 void set_soft_threshold(int soft_thres);
53 //! return minimum threshold for this analysis
54 int get_threshold() const;
55 //! return window size used for this analysis
56 int get_window() const;
58 void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
59 void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
60 void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
61 double path_entropy(std::vector<int> path);
63 // old recursive transitive nway ... has issues checking all links?
64 void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
65 void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, size_t depth);
68 void save(boost::filesystem::path save_file_path);
69 //! load a muway file, \throws mussa_load_error
70 void load(boost::filesystem::path load_file_path);
71 void add_path(int threshold, std::vector<int>& loaded_path);
72 void add_path(ConservedPath loaded_path);
73 //! how many sequences are in our comparison
74 size_t sequence_count();
76 void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
79 void save_old(boost::filesystem::path save_file_path);
80 void print(std::list<std::vector<int> >&);
82 // The following iterator functions are mostly for the python interface
83 // they'll have problems when being called from within a const object
84 ConservedPaths::iterator pbegin() { return pathz.begin() ; }
85 ConservedPaths::iterator pend() { return pathz.end() ; }
86 size_t path_size() const { return refined_pathz.size(); }
87 ConservedPaths::iterator rpbegin() { return refined_pathz.begin() ; }
88 ConservedPaths::iterator rpend() { return refined_pathz.end() ; }
89 size_t refined_path_size() const { return refined_pathz.size(); }
91 // these probably shouldn't be public, but lets start
94 ConservedPaths refined_pathz;
102 std::vector<char *> c_sequences; //used by entropy_path_search