| 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 | |
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| 25 | #define INTEGRATED_ALIGNERS_TITLE "Integrated Aligners" |
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| 26 | |
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| 27 | typedef char* (*Aligner_get_consensus_func)(const char *species_name, PosRange range); |
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| 28 | typedef bool (*Aligner_get_selected_range)(PosRange& range); |
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| 29 | typedef GBDATA* (*Aligner_get_first_selected_species)(int *total_no_of_selected_species); |
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| 30 | typedef GBDATA* (*Aligner_get_next_selected_species)(void); |
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| 31 | |
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| 32 | struct AlignDataAccess { |
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| 33 | int do_refresh; // if do_refresh == TRUE then FastAligner_start() does a refresh |
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| 34 | void (*refresh_display)(); // via calling refresh_display() |
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| 35 | |
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| 36 | Aligner_get_consensus_func get_group_consensus; // changed behavior in [8165]: returns only given range |
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| 37 | Aligner_get_selected_range get_selected_range; |
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| 38 | Aligner_get_first_selected_species get_first_selected_species; |
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| 39 | Aligner_get_next_selected_species get_next_selected_species; |
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| 40 | |
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| 41 | char *helix_string; // currently only used for island hopping |
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| 42 | GBDATA *gb_main; // used by faligner |
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| 43 | }; |
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| 44 | |
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| 45 | // -------------------------------------------------------------------------------- |
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| 46 | |
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| 47 | AW_window *FastAligner_create_window(AW_root *awr, const AlignDataAccess *data_access); |
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| 48 | |
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| 49 | void FastAligner_create_variables(AW_root *root, AW_default db1); |
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| 50 | void FastAligner_set_align_current(AW_root *root, AW_default db1); |
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| 51 | void FastAligner_set_reference_species(AW_window *, AW_CL cl_AW_root); |
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| 52 | |
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| 53 | void FastAligner_start(AW_window *aw, AW_CL cl_AlignDataAccess); |
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| 54 | ARB_ERROR FastAligner_delete_temp_entries(GBDATA *gb_main, const char *alignment); |
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| 55 | |
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| 56 | // -------------------------------------------------------------------------------- |
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| 57 | |
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| 58 | #else |
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| 59 | #error fast_aligner.hxx included twice |
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| 60 | #endif // FAST_ALIGNER_HXX |
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