| 1 | // ================================================================ // |
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| 2 | // // |
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| 3 | // File : MostLikelySeq.hxx // |
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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 MOSTLIKELYSEQ_HXX |
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| 12 | #define MOSTLIKELYSEQ_HXX |
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| 13 | |
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| 14 | #ifndef AP_SEQUENCE_HXX |
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| 15 | #include <AP_sequence.hxx> |
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| 16 | #endif |
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| 17 | |
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| 18 | extern class DNA_Table { |
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| 19 | char char_to_enum_table[256]; |
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| 20 | public: |
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| 21 | DNA_Base char_to_enum(char i) { |
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| 22 | return (DNA_Base)char_to_enum_table[(unsigned char)i]; |
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| 23 | } |
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| 24 | DNA_Table(); |
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| 25 | } dna_table; |
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| 26 | |
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| 27 | const size_t ST_MAX_SEQ_PART = 256; /* should be greater than the editor width (otherwise extrem performance penalties) |
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| 28 | * (Please note: this value has as well a small influence on the calculated results) |
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| 29 | */ |
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| 30 | |
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| 31 | const int ST_BUCKET_SIZE = 16; // at minimum ST_BUCKET_SIZE characters are calculated per call |
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| 32 | const int LD_BUCKET_SIZE = 4; // log dualis of ST_BUCKET_SIZE |
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| 33 | |
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| 34 | class ST_ML; |
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| 35 | |
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| 36 | class MostLikelySeq : public AP_sequence { // derived from a Noncopyable |
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| 37 | /*! contains existing sequence or ancestor sequence |
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| 38 | * as max. likelihood vectors |
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| 39 | */ |
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| 40 | public: |
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| 41 | static ST_base_vector *tmp_out; // len = alignment length (@@@ could be member of ST_ML ? ) |
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| 42 | |
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| 43 | private: |
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| 44 | ST_ML *st_ml; // link to a global ST object (@@@ could be static) |
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| 45 | ST_base_vector *sequence; // A part of the sequence |
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| 46 | bool up_to_date; |
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| 47 | public: |
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| 48 | // @@@ move the 2 following members into one new class and put one pointer here |
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| 49 | ST_ML_Color *color_out; |
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| 50 | int *color_out_valid_till; // color_out is valid up to |
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| 51 | |
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| 52 | private: |
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| 53 | AP_FLOAT count_weighted_bases() const OVERRIDE; |
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| 54 | |
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| 55 | void set(const char *sequence) OVERRIDE; |
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| 56 | void unset() OVERRIDE; |
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| 57 | |
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| 58 | public: |
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| 59 | |
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| 60 | MostLikelySeq(const AliView *aliview, ST_ML *st_ml_); |
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| 61 | ~MostLikelySeq() OVERRIDE; |
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| 62 | |
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| 63 | bool is_up_to_date() const { return up_to_date; } |
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| 64 | |
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| 65 | AP_sequence *dup() const OVERRIDE; |
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| 66 | AP_FLOAT combine(const AP_sequence* lefts, const AP_sequence *rights, char *mutation_per_site = 0) OVERRIDE; |
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| 67 | void partial_match(const AP_sequence* part, long *overlap, long *penalty) const OVERRIDE; |
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| 68 | |
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| 69 | GB_ERROR bind_to_species(GBDATA *gb_species); |
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| 70 | void unbind_from_species(bool remove_callbacks); |
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| 71 | GBDATA *get_bound_species_data() const { return AP_sequence::get_bound_species_data(); } |
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| 72 | |
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| 73 | void sequence_change(); // sequence has changed in db |
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| 74 | void set_sequence(); // start at st_ml->base |
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| 75 | |
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| 76 | void calculate_ancestor(const MostLikelySeq *lefts, double leftl, const MostLikelySeq *rights, double rightl); |
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| 77 | void forget_sequence() { up_to_date = false; } |
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| 78 | |
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| 79 | void calc_out(const MostLikelySeq *sequence_of_brother, double dist); |
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| 80 | void print(); |
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| 81 | }; |
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| 82 | |
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| 83 | |
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| 84 | #else |
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| 85 | #error MostLikelySeq.hxx included twice |
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| 86 | #endif // MOSTLIKELYSEQ_HXX |
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