| 1 | // ==================================================================== // |
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| 2 | // // |
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| 3 | // File : merge.hxx // |
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| 4 | // Purpose : Local header for usage inside directory MERGE // |
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| 5 | // // |
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| 6 | // // |
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| 7 | // Copyright Department of Microbiology (Technical University Munich) // |
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| 8 | // // |
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| 9 | // Visit our web site at: http://www.arb-home.de/ // |
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| 10 | // // |
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| 11 | // ==================================================================== // |
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| 12 | |
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| 13 | #ifndef MERGE_HXX |
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| 14 | #define MERGE_HXX |
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| 15 | |
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| 16 | #ifndef ARB_ASSERT_H |
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| 17 | #include <arb_assert.h> |
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| 18 | #endif |
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| 19 | #define mg_assert(bed) arb_assert(bed) |
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| 20 | |
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| 21 | #define AWAR_MERGE_DB "tmp/merge1/db" |
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| 22 | #define AWAR_MAIN_DB "tmp/merge2/db" |
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| 23 | |
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| 24 | AW_window *MG_merge_alignment_cb(AW_root *awr); |
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| 25 | AW_window *MG_merge_names_cb(AW_root *awr); |
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| 26 | AW_window *MG_merge_species_cb(AW_root *awr); |
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| 27 | AW_window *MG_select_preserves_cb(AW_root *awr); |
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| 28 | AW_window *MG_merge_extendeds_cb(AW_root *awr); |
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| 29 | AW_window *MG_merge_trees_cb(AW_root *awr); |
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| 30 | AW_window *MG_merge_configs_cb(AW_root *awr); |
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| 31 | AW_window *create_mg_check_fields(AW_root *aw_root); |
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| 32 | |
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| 33 | void MG_create_config_awar(AW_root *aw_root, AW_default aw_def); |
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| 34 | void MG_create_trees_awar(AW_root *aw_root, AW_default aw_def); |
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| 35 | void MG_create_extendeds_awars(AW_root *aw_root, AW_default aw_def); |
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| 36 | void MG_create_alignment_awars(AW_root *aw_root,AW_default aw_def); |
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| 37 | void MG_create_species_awars(AW_root *aw_root, AW_default aw_def); |
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| 38 | void MG_create_rename_awars(AW_root *aw_root, AW_default aw_def); |
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| 39 | |
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| 40 | |
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| 41 | void MG_create_db_dependent_rename_awars(AW_root *aw_root, GBDATA *gb_merge, GBDATA *gb_dest); |
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| 42 | |
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| 43 | void MG_set_renamed(bool renamed, AW_root *aw_root, const char *reason); |
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| 44 | GB_ERROR MG_expect_renamed(); |
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| 45 | |
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| 46 | int MG_check_alignment(AW_window *aww, int fast = 0); |
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| 47 | |
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| 48 | // export of gene-species: |
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| 49 | |
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| 50 | void MG_create_gene_species_awars(AW_root *aw_root, AW_default aw_def); |
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| 51 | AW_window *MG_gene_species_create_field_transfer_def_window(AW_root *aw_root); |
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| 52 | GB_ERROR MG_export_fields(AW_root *aw_root, GBDATA *gb_source, GBDATA *gb_dest, GB_HASH *error_suppressor, GB_HASH *source_organism_hash); // export defined fields |
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| 53 | |
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| 54 | #define AWAR_REMAP_SPECIES_LIST "merge/remap_species_list" |
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| 55 | #define AWAR_REMAP_ENABLE "merge/remap_enable" |
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| 56 | |
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| 57 | #define AWAR_MERGE_GENE_SPECIES_BASE "merge/gene_species/" |
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| 58 | |
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| 59 | const char *MG_left_AWAR_SPECIES_NAME(); |
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| 60 | const char *MG_right_AWAR_SPECIES_NAME(); |
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| 61 | |
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| 62 | class MG_remap { |
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| 63 | int in_length; |
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| 64 | int out_length; |
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| 65 | int *remap_tab; |
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| 66 | int *soft_remap_tab; |
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| 67 | int compiled; |
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| 68 | public: |
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| 69 | MG_remap(); |
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| 70 | ~MG_remap(); |
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| 71 | GB_ERROR set(const char *in_reference, const char *out_reference); // returns only warnings |
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| 72 | GB_ERROR compile(); // after last set |
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| 73 | char *remap(const char *sequence); // returns 0 on error, else copy of sequence |
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| 74 | }; |
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| 75 | |
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| 76 | class AW_root; |
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| 77 | |
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| 78 | class MG_remaps { |
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| 79 | public: |
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| 80 | int n_remaps; |
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| 81 | char **alignment_names; |
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| 82 | MG_remap **remaps; |
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| 83 | MG_remaps(GBDATA *gb_left,GBDATA *gb_right,AW_root *awr); |
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| 84 | ~MG_remaps(); |
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| 85 | }; |
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| 86 | |
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| 87 | #ifndef MG_MERGE_HXX |
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| 88 | #include "mg_merge.hxx" |
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| 89 | #endif |
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| 90 | |
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| 91 | #else |
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| 92 | #error merge.hxx included twice |
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| 93 | #endif // MERGE_HXX |
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