| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : NT_species_set.h // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Institute of Microbiology (Technical University Munich) // |
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| 7 | // http://www.arb-home.de/ // |
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| 8 | // // |
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| 9 | // =============================================================== // |
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| 10 | |
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| 11 | #ifndef NT_SPECIES_SET_H |
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| 12 | #define NT_SPECIES_SET_H |
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| 13 | |
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| 14 | #ifndef NT_TREE_CMP_H |
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| 15 | #include "NT_tree_cmp.h" |
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| 16 | #endif |
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| 17 | #ifndef ARBTOOLS_H |
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| 18 | #include <arbtools.h> |
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| 19 | #endif |
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| 20 | #ifndef AP_TREE_HXX |
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| 21 | #include <AP_Tree.hxx> |
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| 22 | #endif |
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| 23 | |
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| 24 | class AWT_species_set; |
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| 25 | class arb_progress; |
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| 26 | |
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| 27 | class AWT_species_set_root : virtual Noncopyable { |
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| 28 | long species_counter; |
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| 29 | long nspecies; |
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| 30 | long nsets; |
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| 31 | |
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| 32 | AWT_species_set **sets; |
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| 33 | int diff_bits[256]; |
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| 34 | |
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| 35 | arb_progress *progress; |
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| 36 | GBDATA *gb_main; |
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| 37 | GB_HASH *species_hash; |
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| 38 | |
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| 39 | public: |
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| 40 | AWT_species_set_root(GBDATA *gb_main, long nspecies_, arb_progress *progress_); |
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| 41 | ~AWT_species_set_root(); |
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| 42 | |
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| 43 | void add(const char *species_name); // max nspecies |
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| 44 | void add(AWT_species_set *set); // max 2 * nspecies !!! |
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| 45 | AWT_species_set *search_best_match(const AWT_species_set *set, long& best_cost); |
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| 46 | int search_and_remember_best_match_and_log_errors(const AWT_species_set *set, FILE *log_file); |
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| 47 | GB_ERROR copy_node_information(FILE *log, bool delete_old_nodes, bool nodes_with_marked_only); |
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| 48 | AWT_species_set *find_best_matches_info(AP_tree *tree_source, FILE *log, bool setinner_node); |
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| 49 | AWT_species_set *move_tree_2_ssr(AP_tree *node); |
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| 50 | |
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| 51 | void finish(GB_ERROR& error); |
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| 52 | |
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| 53 | long bitstring_bytes() const { return nspecies/8 + 1; } |
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| 54 | long bitstring_longs() const { return bitstring_bytes()/sizeof(long) + 1; } |
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| 55 | |
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| 56 | long get_species_index(const char *species_name) const { return GBS_read_hash(species_hash, species_name); } |
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| 57 | }; |
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| 58 | |
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| 59 | |
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| 60 | class AWT_species_set : virtual Noncopyable { |
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| 61 | void init(AP_tree *nodei, const AWT_species_set_root *ssr); |
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| 62 | public: |
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| 63 | // @@@ make member private |
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| 64 | unsigned char *bitstring; |
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| 65 | |
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| 66 | int unfound_species_count; |
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| 67 | double best_cost; |
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| 68 | AP_tree *best_node; |
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| 69 | AP_tree *node; |
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| 70 | |
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| 71 | // REAL PUBLIC: |
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| 72 | |
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| 73 | AWT_species_set(AP_tree *nodei, const AWT_species_set_root *ssr, const char *species_name); |
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| 74 | AWT_species_set(AP_tree *nodei, const AWT_species_set_root *ssr, const AWT_species_set *l, const AWT_species_set *r); // or of two subsets |
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| 75 | ~AWT_species_set(); |
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| 76 | |
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| 77 | bool is_leaf_set() const { return node && node->is_leaf; } // @@@ might be wrong for zombies |
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| 78 | }; |
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| 79 | |
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| 80 | #else |
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| 81 | #error NT_species_set.h included twice |
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| 82 | #endif // NT_SPECIES_SET_H |
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