ARB
AP_seq_protein.hxx
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1 // =============================================================== //
2 // //
3 // File : AP_seq_protein.hxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #ifndef AP_SEQ_PROTEIN_HXX
12 #define AP_SEQ_PROTEIN_HXX
13 
14 #ifndef AP_SEQUENCE_HXX
15 #include <AP_sequence.hxx>
16 #endif
17 #ifndef DOWNCAST_H
18 #include <downcast.h>
19 #endif
20 
23 
24  APP_A = (1 << 0), // Ala
25  APP_C = (1 << 1), // Cys
26  APP_D = (1 << 2), // Asp
27  APP_E = (1 << 3), // Glu
28  APP_F = (1 << 4), // Phe
29  APP_G = (1 << 5), // Gly
30  APP_H = (1 << 6), // His
31  APP_I = (1 << 7), // Ile
32  APP_K = (1 << 8), // Lys
33  APP_L = (1 << 9), // Leu
34  APP_M = (1 << 10), // Met
35  APP_N = (1 << 11), // Asn
36  APP_P = (1 << 12), // Pro
37  APP_Q = (1 << 13), // Gln
38  APP_R = (1 << 14), // Arg
39  APP_S = (1 << 15), // Ser
40  APP_T = (1 << 16), // Thr
41  APP_V = (1 << 17), // Val
42  APP_W = (1 << 18), // Trp
43  APP_Y = (1 << 19), // Tyr
44  APP_STAR = (1 << 20), // *
45  APP_GAP = (1 << 21), // known gap ('-')
46 
47  // -------------------- above are bit values, below combinations of them
48 
49  APP_X = (APP_GAP-1), // Xaa (any real codon)
50  APP_DOT = APP_X | APP_GAP, // maybe a codon, maybe a gap
51 
52  APP_B = APP_D | APP_N, // Asx ( = Asp | Asn )
53  APP_Z = APP_E | APP_Q, // Glx ( = Glu | Gln )
54  APP_J = APP_I | APP_L, // Xle ( = Ile | Leu )
55 
56  APP_MAX = (APP_GAP<<1)-1,
57 };
58 
59 class AP_sequence_protein FINAL_TYPE : public AP_combinableSeq { // derived from a Noncopyable
60  AP_PROTEINS *seq_prot;
61  AP_PROTEINS *mut1; // combination of sequences reachable with up to 1 nucleotide mutation per codon
62  AP_PROTEINS *mut2; // combination of sequences reachable with up to 2 nucleotide mutations per codons
63  // Note: ANY protein or a gap is reachable with up to 3 mutations per codon
64 
66  void set(const char *isequence) OVERRIDE;
67  void unset() OVERRIDE;
68 
69  const AP_PROTEINS *get_mut1() const { lazy_load_sequence(); ap_assert(mut1); return mut1; }
70  const AP_PROTEINS *get_mut2() const { lazy_load_sequence(); ap_assert(mut2); return mut2; }
71 
72 public:
73  AP_sequence_protein(const AliView *aliview);
74  ~AP_sequence_protein() OVERRIDE;
75 
76  const AP_PROTEINS *get_sequence() const { lazy_load_sequence(); ap_assert(seq_prot); return seq_prot; }
77 
78  AP_combinableSeq *dup() const OVERRIDE; // used to get the real new element
79  Mutations combine_seq(const AP_combinableSeq *lefts, const AP_combinableSeq *rights, char *mutation_per_site = NULp) OVERRIDE;
80  Mutations mutations_if_combined_with(const AP_combinableSeq *other) OVERRIDE;
81  void partial_match(const AP_combinableSeq *part, long *overlap, long *penalty) const OVERRIDE;
82  uint32_t checksum() const OVERRIDE;
83  int cmp_combined(const AP_combinableSeq *other) const OVERRIDE;
84 };
85 
86 
87 
88 #else
89 #error AP_seq_protein.hxx included twice
90 #endif // AP_SEQ_PROTEIN_HXX
virtual AP_FLOAT count_weighted_bases() const =0
AP_PROTEINS
double AP_FLOAT
Definition: AP_matrix.hxx:27
virtual AP_combinableSeq * dup() const =0
virtual void unset()=0
long Mutations
Definition: AP_sequence.hxx:99
#define ap_assert(cond)
xml element
#define OVERRIDE
Definition: cxxforward.h:93
#define NULp
Definition: cxxforward.h:97
void lazy_load_sequence() const
Definition: AP_sequence.hxx:67
virtual void set(const char *sequence)=0