| 1 | // =========================================================== // |
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| 2 | // // |
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| 3 | // File : fast_aligner.hxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in 1998 // |
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| 7 | // Institute of Microbiology (Technical University Munich) // |
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| 8 | // http://www.arb-home.de/ // |
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| 9 | // // |
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| 10 | // =========================================================== // |
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| 11 | |
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| 12 | #ifndef FAST_ALIGNER_HXX |
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| 13 | #define FAST_ALIGNER_HXX |
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| 14 | |
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| 15 | #ifndef AW_BASE_HXX |
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| 16 | #include <aw_base.hxx> |
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| 17 | #endif |
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| 18 | #ifndef ARB_ERROR_H |
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| 19 | #include <arb_error.h> |
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| 20 | #endif |
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| 21 | #ifndef POS_RANGE_H |
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| 22 | #include <pos_range.h> |
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| 23 | #endif |
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| 24 | #ifndef _GLIBCXX_STRING |
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| 25 | #include <string> |
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| 26 | #endif |
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| 27 | |
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| 28 | #define INTEGRATED_ALIGNERS_TITLE "Integrated Aligners" |
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| 29 | |
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| 30 | typedef char* (*Aligner_get_consensus_func)(const char *species_name, PosRange range); |
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| 31 | typedef bool (*Aligner_get_selected_range)(PosRange& range); |
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| 32 | typedef GBDATA* (*Aligner_get_first_selected_species)(int *total_no_of_selected_species); |
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| 33 | typedef GBDATA* (*Aligner_get_next_selected_species)(void); |
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| 34 | typedef char* (*Aligner_get_helix_string)(GBDATA *gb_main, const char *alignment_name); // returns heap-copy! |
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| 35 | |
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| 36 | struct AlignDataAccess { |
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| 37 | GBDATA *gb_main; |
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| 38 | |
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| 39 | std::string alignment_name; |
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| 40 | |
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| 41 | bool do_refresh; // if do_refresh == true then FastAligner_start() does a refresh |
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| 42 | void (*refresh_display)(); // via calling refresh_display() |
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| 43 | |
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| 44 | Aligner_get_consensus_func get_group_consensus; // changed behavior in [8165]: returns only given range |
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| 45 | Aligner_get_selected_range get_selected_range; |
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| 46 | Aligner_get_first_selected_species get_first_selected_species; |
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| 47 | Aligner_get_next_selected_species get_next_selected_species; |
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| 48 | Aligner_get_helix_string get_helix_string; |
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| 49 | |
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| 50 | char *getHelixString() const { return get_helix_string(gb_main, alignment_name.c_str()); } |
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| 51 | |
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| 52 | AlignDataAccess(GBDATA *gb_main_, |
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| 53 | const char *alignment_name_, |
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| 54 | bool do_refresh_, |
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| 55 | void (*refresh_display_)(), |
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| 56 | Aligner_get_consensus_func get_group_consensus_, |
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| 57 | Aligner_get_selected_range get_selected_range_, |
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| 58 | Aligner_get_first_selected_species get_first_selected_species_, |
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| 59 | Aligner_get_next_selected_species get_next_selected_species_, |
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| 60 | Aligner_get_helix_string get_helix_string_) |
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| 61 | : gb_main(gb_main_), |
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| 62 | alignment_name(alignment_name_), |
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| 63 | do_refresh(do_refresh_), |
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| 64 | refresh_display(refresh_display_), |
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| 65 | get_group_consensus(get_group_consensus_), |
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| 66 | get_selected_range(get_selected_range_), |
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| 67 | get_first_selected_species(get_first_selected_species_), |
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| 68 | get_next_selected_species(get_next_selected_species_), |
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| 69 | get_helix_string(get_helix_string_) |
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| 70 | {} |
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| 71 | |
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| 72 | AlignDataAccess(const AlignDataAccess& other) |
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| 73 | : gb_main(other.gb_main), |
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| 74 | alignment_name(other.alignment_name), |
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| 75 | do_refresh(other.do_refresh), |
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| 76 | refresh_display(other.refresh_display), |
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| 77 | get_group_consensus(other.get_group_consensus), |
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| 78 | get_selected_range(other.get_selected_range), |
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| 79 | get_first_selected_species(other.get_first_selected_species), |
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| 80 | get_next_selected_species(other.get_next_selected_species), |
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| 81 | get_helix_string(other.get_helix_string) |
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| 82 | {} |
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| 83 | |
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| 84 | DECLARE_ASSIGNMENT_OPERATOR(AlignDataAccess); |
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| 85 | }; |
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| 86 | |
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| 87 | // -------------------------------------------------------------------------------- |
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| 88 | |
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| 89 | AW_window *FastAligner_create_window(AW_root *awr, const AlignDataAccess *data_access); |
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| 90 | |
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| 91 | void FastAligner_create_variables(AW_root *root, AW_default db1); |
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| 92 | void FastAligner_set_align_current(AW_root *root, AW_default db1); |
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| 93 | void FastAligner_set_reference_species(AW_root *root); |
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| 94 | |
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| 95 | void FastAligner_start(AW_window *aw, const AlignDataAccess *data_access); |
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| 96 | ARB_ERROR FastAligner_delete_temp_entries(GBDATA *gb_main, const char *alignment); |
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| 97 | |
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| 98 | // -------------------------------------------------------------------------------- |
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| 99 | |
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| 100 | #else |
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| 101 | #error fast_aligner.hxx included twice |
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| 102 | #endif // FAST_ALIGNER_HXX |
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