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
|
//![start]
#include <vector>
#include <seqan3/alignment/configuration/align_config_edit.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
int main()
{
using seqan3::operator""_dna4;
//![start]
// Configure the alignment kernel.
auto config = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
{
//![example1]
std::pair p{"ACGTAGC"_dna4, "AGTACGACG"_dna4};
auto result = seqan3::align_pairwise(p, config);
//![example1]
}
{
//![example2]
std::vector vec{"ACCA"_dna4, "ATTA"_dna4};
auto result = seqan3::align_pairwise(std::tie(vec[0], vec[1]), config);
//![example2]
}
//![example3]
std::vector vec{std::pair{"AGTGCTACG"_dna4, "ACGTGCGACTAG"_dna4},
std::pair{"AGTAGACTACG"_dna4, "ACGTACGACACG"_dna4},
std::pair{"AGTTACGAC"_dna4, "AGTAGCGATCG"_dna4}};
// Compute the alignment of a single pair.
auto edit_config = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
for (auto const & res : seqan3::align_pairwise(std::tie(vec[0].first, vec[0].second), edit_config))
seqan3::debug_stream << "The score: " << res.score() << "\n";
// Compute the alignment over a range of pairs.
for (auto const & res : seqan3::align_pairwise(vec, edit_config))
seqan3::debug_stream << "The score: " << res.score() << "\n";
//![example3]
//![end]
}
//![end]
|
