| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : adGene.h // |
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| 4 | // Purpose : Specific defines for ARB genome // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in July 2002 // |
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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 ADGENE_H |
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| 13 | #define ADGENE_H |
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| 14 | |
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| 15 | #ifndef _GLIBCXX_CSTDLIB |
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| 16 | #include <cstdlib> |
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| 17 | #endif |
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| 18 | |
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| 19 | #define GENOM_ALIGNMENT "ali_genom" |
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| 20 | #define GENOM_DB_TYPE "genom_db" // main flag (true = genom db, false/missing=normal db) |
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| 21 | |
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| 22 | #define ARB_HIDDEN "ARB_display_hidden" |
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| 23 | |
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| 24 | /* GEN_position is interpreted as |
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| 25 | * |
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| 26 | * join( complement[0](start_pos[0]..stop_pos[0]), |
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| 27 | * complement[1](start_pos[1]..stop_pos[1]), |
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| 28 | * complement[2](start_pos[2], stop_pos[2]), |
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| 29 | * ... ) |
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| 30 | * |
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| 31 | * start_pos is always lower than stop_pos |
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| 32 | * joined genes on complementary strand are normally ordered backwards |
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| 33 | * (i.e. part with highest positions comes first) |
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| 34 | */ |
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| 35 | |
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| 36 | struct GEN_position { |
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| 37 | int parts; |
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| 38 | bool joinable; // true = join(...), false = order(...) aka not joinable or unknown |
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| 39 | size_t *start_pos; |
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| 40 | size_t *stop_pos; |
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| 41 | unsigned char *complement; // ASCII 0 = normal or ASCII 1 = complementary |
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| 42 | |
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| 43 | // [optional elements] |
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| 44 | |
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| 45 | // start_uncertain/stop_uncertain contain one char per part (or NULL which means "all positions are certain") |
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| 46 | // meaning of characters: |
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| 47 | // '<' = position MIGHT be lower |
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| 48 | // '=' = position is certain |
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| 49 | // '>' = position MIGHT be higher |
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| 50 | // '+' = position is directly BEHIND (but before next base position, i.e. specifies a location between to base positions) |
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| 51 | // '-' = position is BEFORE |
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| 52 | |
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| 53 | unsigned char *start_uncertain; |
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| 54 | unsigned char *stop_uncertain; |
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| 55 | }; |
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| 56 | |
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| 57 | #else |
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| 58 | #error adGene.h included twice |
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| 59 | #endif // ADGENE_H |
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