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 | #ifndef DOWNCAST_H |
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18 | #include <downcast.h> |
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19 | #endif |
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20 | |
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21 | extern class DNA_Table { |
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22 | char char_to_enum_table[256]; |
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23 | public: |
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24 | DNA_Base char_to_enum(char i) { |
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25 | return (DNA_Base)char_to_enum_table[(unsigned char)i]; |
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26 | } |
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27 | DNA_Table(); |
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28 | } dna_table; |
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29 | |
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30 | const size_t ST_MAX_SEQ_PART = 256; /* should be greater than the editor width (otherwise extrem performance penalties) |
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31 | * (Please note: this value has as well a small influence on the calculated results) |
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32 | */ |
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33 | |
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34 | const int ST_BUCKET_SIZE = 16; // at minimum ST_BUCKET_SIZE characters are calculated per call |
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35 | const int LD_BUCKET_SIZE = 4; // log dualis of ST_BUCKET_SIZE |
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36 | |
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37 | class ST_ML; |
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38 | |
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39 | class MostLikelySeq : public AP_sequence { // derived from a Noncopyable |
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40 | /*! contains existing sequence or ancestor sequence |
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41 | * as max. likelihood vectors |
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42 | */ |
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43 | public: |
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44 | static ST_base_vector *tmp_out; // len = alignment length (@@@ could be member of ST_ML ? ) |
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45 | |
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46 | private: |
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47 | ST_ML *st_ml; // link to a global ST object (@@@ could be static) |
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48 | ST_base_vector *sequence; // A part of the sequence |
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49 | bool up_to_date; |
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50 | public: |
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51 | // @@@ move the 2 following members into one new class and put one pointer here |
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52 | ST_ML_Color *color_out; |
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53 | int *color_out_valid_till; // color_out is valid up to |
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54 | |
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55 | private: |
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56 | AP_FLOAT count_weighted_bases() const OVERRIDE; |
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57 | |
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58 | void set(const char *sequence) OVERRIDE; |
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59 | void unset() OVERRIDE; |
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60 | |
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61 | public: |
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62 | |
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63 | MostLikelySeq(const AliView *aliview, ST_ML *st_ml_); |
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64 | ~MostLikelySeq() OVERRIDE; |
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65 | |
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66 | bool is_up_to_date() const { return up_to_date; } |
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67 | |
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68 | AP_sequence *dup() const OVERRIDE; |
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69 | AP_FLOAT combine(const AP_sequence* lefts, const AP_sequence *rights, char *mutation_per_site = 0) OVERRIDE; |
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70 | void partial_match(const AP_sequence* part, long *overlap, long *penalty) const OVERRIDE; |
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71 | uint32_t checksum() const OVERRIDE; |
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72 | |
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73 | bool equals(const MostLikelySeq */*other*/) const { arb_assert(0); return false; } // unused |
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74 | bool equals(const AP_sequence *other) const OVERRIDE { return equals(DOWNCAST(const MostLikelySeq*, other)); } |
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75 | |
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76 | GB_ERROR bind_to_species(GBDATA *gb_species); |
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77 | void unbind_from_species(bool remove_callbacks); |
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78 | GBDATA *get_bound_species_data() const { return AP_sequence::get_bound_species_data(); } |
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79 | |
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80 | void sequence_change(); // sequence has changed in db |
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81 | void set_sequence(); // start at st_ml->base |
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82 | |
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83 | void calculate_ancestor(const MostLikelySeq *lefts, double leftl, const MostLikelySeq *rights, double rightl); |
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84 | void forget_sequence() { up_to_date = false; } |
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85 | |
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86 | void calc_out(const MostLikelySeq *sequence_of_brother, double dist); |
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87 | void print(); |
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88 | }; |
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89 | |
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90 | |
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91 | #else |
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92 | #error MostLikelySeq.hxx included twice |
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93 | #endif // MOSTLIKELYSEQ_HXX |
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94 | |
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