| 1 | // =========================================================== // |
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| 2 | // // |
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| 3 | // File : awt_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 AWT_SEQ_SIMPLE_PRO_HXX |
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| 12 | #define AWT_SEQ_SIMPLE_PRO_HXX |
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| 13 | |
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| 14 | |
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| 15 | typedef enum { |
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| 16 | ala, arg, asn, asp, cys, gln, glu, gly, his, ileu, leu, lys, met, phe, pro, |
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| 17 | ser, thr, trp, tyr, val, stop, del, asx, glx, unk, quest |
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| 18 | } aas; |
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| 19 | |
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| 20 | typedef unsigned char ap_pro; // aas but only one character used |
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| 21 | |
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| 22 | class AP_sequence_simple_protein : public AP_sequence { |
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| 23 | |
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| 24 | public: |
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| 25 | ap_pro *sequence; |
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| 26 | //static char *table; |
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| 27 | AP_sequence_simple_protein(AP_tree_root *rooti); |
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| 28 | ~AP_sequence_simple_protein(void); |
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| 29 | AP_sequence *dup(void); // used to get the real new element |
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| 30 | void set(const char *sequence); |
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| 31 | double combine( const AP_sequence *lefts, const AP_sequence *rights); |
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| 32 | void partial_match(const AP_sequence* part, long *overlap, long *penalty) const; |
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| 33 | }; |
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| 34 | |
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| 35 | #else |
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| 36 | #error awt_seq_simple_pro.hxx included twice |
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| 37 | #endif // AWT_SEQ_SIMPLE_PRO_HXX |
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