1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
|
#include <algorithm>
#include <set>
#include <tuple>
#include <vector>
//! [create]
#include <seqan3/alphabet/all.hpp> // for working with alphabets directly
using seqan3::operator""_dna4;
int main ()
{
// Two objects of seqan3::dna4 alphabet constructed with a char literal.
seqan3::dna4 ade = 'A'_dna4;
seqan3::dna4 gua = 'G'_dna4;
// Two additional objects assigned explicitly from char or rank.
seqan3::dna4 cyt, thy;
cyt.assign_char('C');
thy.assign_rank(3);
// Further code here...
//! [create]
assert(cyt == 'C'_dna4);
assert(thy == 'T'_dna4);
//! [rank]
// Get the rank type of the alphabet (here uint8_t).
using rank_type = seqan3::alphabet_rank_t<seqan3::dna4>;
// Retrieve the numerical representation (rank) of the objects.
rank_type rank_a = ade.to_rank(); // => 0
rank_type rank_g = gua.to_rank(); // => 2
//! [rank]
assert(rank_a == 0u);
assert(rank_g == 2u);
//! [char]
// Get the character type of the alphabet (here char).
using char_type = seqan3::alphabet_char_t<seqan3::dna4>;
// Retrieve the character representation.
char_type char_a = ade.to_char(); // => 'A'
char_type char_g = gua.to_char(); // => 'G'
//! [char]
assert(char_a == 'A');
assert(char_g == 'G');
//! [char_strict]
// Assign from character with value check.
seqan3::assign_char_strictly_to('C', cyt);
// seqan3::assign_char_strictly_to('X', thy); // would throw seqan3::invalid_char_assignment
//! [char_strict]
assert(cyt == 'C'_dna4);
//! [size]
// Get the alphabet size as class member of the alphabet.
uint8_t const size1 = seqan3::dna4::alphabet_size; // => 4
//! [size]
assert(size1 == 4u);
//! [compare]
// Equality and comparison of seqan::dna4 symbols.
bool eq = (cyt == 'C'_dna4); // true
bool neq = (thy != 'C'_dna4); // true
bool geq = (cyt >= 'C'_dna4); // true
bool gt = (thy > 'C'_dna4); // true
bool seq = (cyt <= 'C'_dna4); // true
bool st = (ade < 'C'_dna4); // true
// Sort a vector of symbols.
std::vector<seqan3::dna4> some_nucl{"GTA"_dna4};
std::sort(some_nucl.begin(), some_nucl.end()); // some_nucl: "AGT"
//! [compare]
assert(eq && neq && geq && gt && seq && st);
assert(some_nucl == "AGT"_dna4);
//! [gapped]
// Assign a gap symbol to a gapped RNA alphabet.
seqan3::gapped<seqan3::rna5> sym = seqan3::gap{}; // => -
using seqan3::operator""_rna5;
// Each seqan3::rna5 symbol is still valid.
sym = 'U'_rna5; // => U
// The alphabet size is six (AUGCN-).
uint8_t const size2 = seqan3::gapped<seqan3::rna5>::alphabet_size; // => 6
//! [gapped]
assert(size2 == 6u);
//! [containers]
using seqan3::operator""_dna5;
// Examples of different container types with SeqAn's alphabets.
std::vector<seqan3::dna5> dna_sequence{"GATTANAG"_dna5};
std::pair<seqan3::gapped<seqan3::dna4>, seqan3::gapped<seqan3::dna4>> alignment_column{seqan3::gap{}, thy};
std::set<seqan3::dna4> pyrimidines{'C'_dna4, 'T'_dna4};
//! [containers]
// Prevent -Wunused-variable warnings.
(void)rank_a;
(void)rank_g;
(void)char_a;
(void)char_g;
(void)size1;
(void)size2;
(void)dna_sequence;
(void)alignment_column;
(void)pyrimidines;
(void)eq;
(void)neq;
(void)geq;
(void)gt;
(void)seq;
(void)st;
//! [closing]
return 0;
}
//! [closing]
|
