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#include <mutex>
#include <vector>
#include <seqan3/alignment/configuration/all.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
int main()
{
// Generate some sequences.
using seqan3::operator""_dna4;
using sequence_pair_t = std::pair<seqan3::dna4_vector, seqan3::dna4_vector>;
std::vector<sequence_pair_t> sequences{100, {"AGTGCTACG"_dna4, "ACGTGCGACTAG"_dna4}};
// Use edit distance with 4 threads.
auto const alignment_config = seqan3::align_cfg::method_global{} |
seqan3::align_cfg::edit_scheme |
seqan3::align_cfg::parallel{4};
// Compute the alignments in parallel and output them in order based on the input.
for (auto && result : seqan3::align_pairwise(sequences, alignment_config))
seqan3::debug_stream << result << '\n';
seqan3::debug_stream << '\n';
// prints:
// [id: 0 score: -4]
// [id: 1 score: -4]
// [id: 2 score: -4]
// [id: 3 score: -4]
// [id: 4 score: -4]
// [id: 5 score: -4]
// ...
// [id: 98 score: -4]
// [id: 99 score: -4]
// Compute the alignments in parallel and output them unordered using the callback (order is not deterministic).
std::mutex write_to_debug_stream{}; // Need mutex to synchronise the output.
auto const alignment_config_with_callback = alignment_config |
seqan3::align_cfg::on_result{[&] (auto && result)
{
std::lock_guard sync{write_to_debug_stream}; // critical section
seqan3::debug_stream << result << '\n';
}};
seqan3::align_pairwise(sequences, alignment_config_with_callback); // seqan3::align_pairwise is now declared void.
// might print:
// [id: 0 score: -4]
// [id: 1 score: -4]
// [id: 2 score: -4]
// [id: 6 score: -4]
// [id: 7 score: -4]
// [id: 3 score: -4]
// ...
// [id: 99 score: -4]
// [id: 92 score: -4]
}
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