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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#include <gtest/gtest.h>
#include <seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/rna5.hpp>
#include <seqan3/utility/range/to.hpp>
using seqan3::operator""_dna4;
using seqan3::operator""_rna5;
TEST(debug_stream_test, multiple_alignment_without_gaps)
{
std::string const expected{" 0 . : . : . : . : . :\n"
" GCGGGTCACTGAGGGCTGGGATGAGGACGGCCACCACTTCGAGGAGTCCC\n"
" | || | | | | ||| | |\n"
" CTACGGCAGAAGAAGACATCCGAAAAAGCTGACACCTCTCGCCTACAAGC\n"
" ||||||||||||||||||||| || |||||||||||||||||||||||||\n"
" CTACGGCAGAAGAAGACATCCCAAGAAGCTGACACCTCTCGCCTACAAGC\n"
"\n"
" 50 . : . : . : . : . :\n"
" TTCACTACGAGGGCAGGGCCGTGGACATCACCACGTCAGACAGGGACAAG\n"
" | || | | | | | | | | | | \n"
" AGTTCATACCTAATGTCGCGGAGAAGACCTTAGGGGCCAGCGGCAGATAC\n"
" |||| |||||||||||||||||||||||||||||||||||||||||||||\n"
" AGTTTATACCTAATGTCGCGGAGAAGACCTTAGGGGCCAGCGGCAGATAC\n"
"\n"
" 100 . : . : . : . :\n"
" AGCAAGTACGGCACCCTGTCCAGACTGGCGGTGGAAGCTG\n"
" | || | | | ||| \n"
" GAGGGCAAGATAACGCGCAATTCGGAGAGATTTAAAGAAC\n"
" ||||||||||| ||||||||||||||||||||||||||||\n"
" GAGGGCAAGATCACGCGCAATTCGGAGAGATTTAAAGAAC\n"};
std::tuple<std::vector<seqan3::gapped<seqan3::dna4>>,
std::vector<seqan3::gapped<seqan3::dna4>>,
std::vector<seqan3::gapped<seqan3::dna4>>> const alignment{
"GCGGGTCACTGAGGGCTGGGATGAGGACGGCCACCACTTCGAGGAGTCCCTTCACTACGAGGGCAGGGCCGTGGACATCACCACGTCAGACAGGGACAAGAGCAAGTA"
"CGGCACCCTGTCCAGACTGGCGGTGGAAGCTG"_dna4
| seqan3::ranges::to<std::vector<seqan3::gapped<seqan3::dna4>>>(),
"CTACGGCAGAAGAAGACATCCGAAAAAGCTGACACCTCTCGCCTACAAGCAGTTCATACCTAATGTCGCGGAGAAGACCTTAGGGGCCAGCGGCAGATACGAGGGCAA"
"GATAACGCGCAATTCGGAGAGATTTAAAGAAC"_dna4
| seqan3::ranges::to<std::vector<seqan3::gapped<seqan3::dna4>>>(),
"CTACGGCAGAAGAAGACATCCCAAGAAGCTGACACCTCTCGCCTACAAGCAGTTTATACCTAATGTCGCGGAGAAGACCTTAGGGGCCAGCGGCAGATACGAGGGCAA"
"GATCACGCGCAATTCGGAGAGATTTAAAGAAC"_dna4
| seqan3::ranges::to<std::vector<seqan3::gapped<seqan3::dna4>>>()};
std::ostringstream oss;
seqan3::debug_stream_type stream{oss};
stream << alignment;
EXPECT_EQ(expected, oss.str());
}
TEST(debug_stream_test, pairwise_alignment_with_gaps)
{
std::string const expected{" 0 . \n"
" CUUC-G\n"
" || |\n"
" CU-NGG\n"};
std::pair<std::vector<seqan3::gapped<seqan3::rna5>>, std::vector<seqan3::gapped<seqan3::rna5>>> const alignment{
{'C'_rna5, 'U'_rna5, 'U'_rna5, 'C'_rna5, seqan3::gap{}, 'G'_rna5},
{'C'_rna5, 'U'_rna5, seqan3::gap{}, 'N'_rna5, 'G'_rna5, 'G'_rna5}};
std::ostringstream oss;
seqan3::debug_stream_type stream{oss};
stream << alignment;
EXPECT_EQ(expected, oss.str());
}
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