| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : AP_seq_simple_pro.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 AP_SEQ_SIMPLE_PRO_HXX |
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| 12 | #define AP_SEQ_SIMPLE_PRO_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 | enum aas { |
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| 22 | ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILEU, LEU, LYS, MET, PHE, PRO, |
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| 23 | SER, THR, TRP, TYR, VAL, STOP, DEL, ASX, GLX, UNK, QUEST |
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| 24 | }; |
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| 25 | |
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| 26 | typedef unsigned char ap_pro; // aas but only one character used |
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| 27 | |
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| 28 | class AP_sequence_simple_protein : public AP_sequence { // derived from a Noncopyable |
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| 29 | ap_pro *sequence; |
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| 30 | |
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| 31 | AP_FLOAT count_weighted_bases() const OVERRIDE; |
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| 32 | |
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| 33 | void set(const char *sequence) OVERRIDE; |
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| 34 | void unset() OVERRIDE; |
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| 35 | |
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| 36 | public: |
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| 37 | |
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| 38 | AP_sequence_simple_protein(const AliView *aliview); |
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| 39 | ~AP_sequence_simple_protein() OVERRIDE; |
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| 40 | |
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| 41 | AP_sequence *dup() const OVERRIDE; // used to get the real new element |
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| 42 | |
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| 43 | AP_FLOAT combine(const AP_sequence *lefts, const AP_sequence *rights, char *mutation_per_site = 0) OVERRIDE; |
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| 44 | void partial_match(const AP_sequence* part, long *overlap, long *penalty) const OVERRIDE; |
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| 45 | uint32_t checksum() const OVERRIDE; |
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| 46 | |
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| 47 | bool equals(const AP_sequence_simple_protein */*other*/) const { arb_assert(0); return false; } // unused |
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| 48 | bool equals(const AP_sequence *other) const OVERRIDE { return equals(DOWNCAST(const AP_sequence_simple_protein*, other)); } |
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| 49 | |
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| 50 | const ap_pro *get_sequence() const { return sequence; } |
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| 51 | ap_pro *get_sequence() { return sequence; } |
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| 52 | }; |
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| 53 | |
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| 54 | |
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| 55 | #else |
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| 56 | #error AP_seq_simple_pro.hxx included twice |
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| 57 | #endif // AP_SEQ_SIMPLE_PRO_HXX |
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