ARB
pars_main.hxx
Go to the documentation of this file.
1 // =============================================================== //
2 // //
3 // File : pars_main.hxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #ifndef PARS_MAIN_HXX
12 #define PARS_MAIN_HXX
13 
14 #ifndef PARS_DTREE_HXX
15 #include "pars_dtree.hxx"
16 #endif
17 
18 #define MIN_SEQUENCE_LENGTH 20
19 
20 class WeightedFilter;
21 class AP_tree_nlen;
22 
23 struct KL_Settings;
24 
25 class ArbParsimony {
27 
28 public:
29  ArbParsimony() : tree(NULp) {}
30 
31  AWT_graphic_parsimony *get_tree() const { return tree; }
32 
33  DEFINE_READ_ACCESSORS(AP_tree_nlen*, get_root_node, get_tree()->get_root_node());
34 
35  void generate_tree(WeightedFilter *pars_weighted_filter);
36  void set_tree(AWT_graphic_parsimony *tree_);
37 
38  void optimize_tree(AP_tree_nlen *at, const KL_Settings& settings, arb_progress& progress);
39  void kernighan_optimize_tree(AP_tree_nlen *at, const KL_Settings& settings, const Mutations *pars_global_start, bool dumpPerf);
40 };
41 
42 void PARS_map_viewer(GBDATA *gb_species, AD_MAP_VIEWER_TYPE vtype);
43 
44 #else
45 #error pars_main.hxx included twice
46 #endif // PARS_MAIN_HXX
void set_tree(AWT_graphic_parsimony *tree_)
Definition: PARS_main.cxx:66
void PARS_map_viewer(GBDATA *gb_species, AD_MAP_VIEWER_TYPE vtype)
Definition: PARS_main.cxx:1980
AD_MAP_VIEWER_TYPE
static SearchSettings * settings[SEARCH_PATTERNS]
Definition: ED4_search.cxx:628
AWT_graphic_parsimony * get_tree() const
Definition: pars_main.hxx:31
void generate_tree(WeightedFilter *pars_weighted_filter)
Definition: PARS_dtree.cxx:295
long Mutations
Definition: AP_sequence.hxx:99
void optimize_tree(AP_tree_nlen *at, const KL_Settings &settings, arb_progress &progress)
Definition: PARS_dtree.cxx:190
void kernighan_optimize_tree(AP_tree_nlen *at, const KL_Settings &settings, const Mutations *pars_global_start, bool dumpPerf)
Definition: PARS_dtree.cxx:96
DEFINE_READ_ACCESSORS(AP_tree_nlen *, get_root_node, get_tree() ->get_root_node())
#define NULp
Definition: cxxforward.h:97