ARB
AP_codon_table.hxx
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1 // =============================================================== //
2 // //
3 // File : AP_codon_table.hxx //
4 // Purpose : codon definitions for DNA -> AA translation //
5 // //
6 // Coded by Ralf Westram (coder@reallysoft.de) //
7 // Institute of Microbiology (Technical University Munich) //
8 // http://www.arb-home.de/ //
9 // //
10 // =============================================================== //
11 
12 #ifndef AP_CODON_TABLE_HXX
13 #define AP_CODON_TABLE_HXX
14 
15 #ifndef ARB_ASSERT_H
16 #include <arb_assert.h>
17 #endif
18 #ifndef STATIC_ASSERT_H
19 #include <static_assert.h>
20 #endif
21 #ifndef _STDINT_H
22 #include <stdint.h>
23 #endif
24 
25 #define pn_assert(cond) arb_assert(cond)
26 
27 // @@@ fix all historical prefixes to 'PN_' or remove them
28 // @@@ fix filenames
29 
30 // --------------------------------------------------------------------------------
31 
33  const char *name;
34  const char *aa; // amino-codes
35  const char *startStop; // may contain 'M', '*' and '-'
36  int embl_feature_transl_table; // number of transl_table-entry in EMBL/GENEBANK features list
37 };
38 
39 #define AWT_CODON_TABLES 25 // number of different translation tables (aka genetic codes and codon tables)
40 #define AWT_MAX_CODONS 64 // maximum of possible codon ( = 4^3)
41 
42 const int AWAR_PROTEIN_TYPE_bacterial_code_index = 8; // contains the index of the bacterial code table
43 
44 // --------------------------------------------------------------------------------
45 // initialize this module
46 
47 void AP_initialize_codon_tables(); // call early
48 
49 // --------------------------------------------------------------------------------
50 
51 #define ALL_TABLES_MASK ((1<<AWT_CODON_TABLES)-1)
52 
54  TTIT_ARB, // arb internal table numbering [0 .. AWT_CODON_TABLES-1]. consecutive.
55  TTIT_EMBL // embl numbering (AWT_Codon_Code_Definition::embl_feature_transl_table)
56 };
57 
58 int TTIT_embl2arb(int embl_code_nr);
59 int TTIT_arb2embl(int arb_code_nr);
60 
61 // --------------------------------------------------------------------------------
62 
63 class TransTables {
64  uint32_t allowed; // one bit for each arb-translation-table
65 
66  static uint32_t bitmask(int nr) { pn_assert(nr >= 0 && nr<AWT_CODON_TABLES); return 1<<nr; }
67 
68 public:
70 
71  bool is_allowed(int nr) const { return (allowed & bitmask(nr)) != 0; }
72  bool any() const { return allowed; }
73  bool none() const { return !allowed; }
74  bool all() const { return allowed == ALL_TABLES_MASK; }
75 
76  void allow(int nr) { allowed |= bitmask(nr); }
77  void forbid(int nr) { allowed &= ~bitmask(nr); }
78  void forbid(const TransTables& other) { allowed &= ~other.allowed; }
79 
80  void allowAll() {
81  STATIC_ASSERT((sizeof(allowed)*8) > AWT_CODON_TABLES); // one bit wasted
82  allowed = ALL_TABLES_MASK;
83  }
84  void forbidAll() { allowed = 0; }
85  void forbidAllBut(int nr) { allowed &= bitmask(nr); }
86 
87  int explicit_table() const {
88  // return explicit table number (or -1 if not exactly one table is allowed)
89  if (any()) {
90  uint32_t tabs = allowed;
91  for (int t = 0; t<AWT_CODON_TABLES; ++t) {
92  if (tabs&1) return (tabs == 1) ? t : -1;
93  tabs >>= 1;
94  }
95  pn_assert(0);
96  }
97  return -1;
98  }
99 
100  bool is_subset_of(const TransTables& other) const { return (allowed&other.allowed) == allowed; }
101 
103  const int MAX_LEN = AWT_CODON_TABLES*3-1+1;
104  static char buffer[MAX_LEN];
105  char *out = buffer;
106 
107  for (int a = 0; a<AWT_CODON_TABLES; ++a) {
108  if (is_allowed(a)) {
109  int shownNum =
110  type == TTIT_ARB
111  ? a
112  : TTIT_arb2embl(a);
113 
114  out += sprintf(out, ",%i", shownNum);
115  }
116  }
117  pn_assert((out-buffer)<MAX_LEN);
118  out[0] = 0;
119  return buffer+1;
120  }
121 
122 };
123 
124 // --------------------------------------------------------------------------------
125 
126 bool AWT_is_codon(char protein, const char *const dna, const TransTables& allowed, TransTables& allowed_left, const char **fail_reason_ptr = NULp);
127 const char *AP_get_codons(char protein, int code_nr);
128 
129 const char *getAminoAcidAbbr(char aa);
130 const char* AWT_get_codon_code_name(int code);
131 
132 #ifdef DEBUG
133 void AWT_dump_codons(TranslationTableIndexType type, bool skipX);
134 void test_AWT_get_codons();
135 #endif
136 
137 // --------------------------------------------------------------------------------
138 
139 #else
140 #error AP_codon_table.hxx included twice
141 #endif // AP_CODON_TABLE_HXX
int TTIT_embl2arb(int embl_code_nr)
GB_TYPES type
void AP_initialize_codon_tables()
#define ALL_TABLES_MASK
bool AWT_is_codon(char protein, const char *const dna, const TransTables &allowed, TransTables &allowed_left, const char **fail_reason_ptr=NULp)
const char * to_string(TranslationTableIndexType type) const
void forbidAllBut(int nr)
int TTIT_arb2embl(int arb_code_nr)
const char * AWT_get_codon_code_name(int code)
char buffer[MESSAGE_BUFFERSIZE]
Definition: seq_search.cxx:34
const char * getAminoAcidAbbr(char aa)
void forbid(const TransTables &other)
bool none() const
bool all() const
bool any() const
void allow(int nr)
#define pn_assert(cond)
const int AWAR_PROTEIN_TYPE_bacterial_code_index
int explicit_table() const
#define AWT_CODON_TABLES
void forbid(int nr)
#define NULp
Definition: cxxforward.h:97
const char * AP_get_codons(char protein, int code_nr)
bool is_allowed(int nr) const
#define STATIC_ASSERT(const_expression)
Definition: static_assert.h:36
bool is_subset_of(const TransTables &other) const
TranslationTableIndexType