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Merged
eseiler merged 21 commits into from
Sep 29, 2023
Merged

[FEATURE] Clang support #3195

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909247c
[FIX] Remove __cpp_nontype_template_parameter_class
eseiler Sep 28, 2023
a8f17b4
[FIX] Unused variables
eseiler Sep 28, 2023
fcaeab2
[FIX] Ambiguous function call
eseiler Sep 28, 2023
1dc6c27
[FIX] explicit ctor/assign is implicitly deleted
eseiler Sep 28, 2023
5ba6a51
[FIX] Missing check for include
eseiler Sep 28, 2023
19b2ff6
[FIX] cvtsi64x is deprecated
eseiler Sep 28, 2023
92380a1
[FIX] Workaround clang __builtin_constant_p
eseiler Sep 28, 2023
fe386b2
[FIX] Constraint/template differs in redeclaration
eseiler Sep 28, 2023
a3304ab
[FIX] Mismatched tags (class/struct)
eseiler Sep 28, 2023
1baf50f
[FIX] Member might not be default initializable
eseiler Sep 28, 2023
5040fc5
[FIX] Workaround clang span alphabet_variant
eseiler Sep 28, 2023
9fa8e39
[FIX] Parentheses in requires
eseiler Sep 28, 2023
362ee37
[FIX] Comparison of repeat_view
eseiler Sep 28, 2023
87fec13
[FIX] Cyclic requires
eseiler Sep 28, 2023
24a3fa1
[FIX] Workaround cpp23+clang tuple weirdness
eseiler Sep 28, 2023
13c900d
[FIX] Braces around scalar initializer
eseiler Sep 28, 2023
923fc7d
[FIX] Operator precedence
eseiler Sep 28, 2023
ea9956b
[INFRA] CMake
eseiler Sep 28, 2023
dfba50b
[INFRA] CI
eseiler Sep 28, 2023
64dc64b
[FIX] Change constexpr test
eseiler Sep 28, 2023
62392a1
[FIX] take_until_view_test
eseiler Sep 28, 2023
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[FIX] Braces around scalar initializer 
Clang in CPP20 mode emits bogus warnings for seqan3::pod_tuple
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@eseiler
eseiler committed Sep 29, 2023
commit 13c900dcc625ccc66d55169c56f7aca676e86350
2 changes: 1 addition & 1 deletion include/seqan3/argument_parser/argument_parser.hpp
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Expand Up @@ -773,7 +773,7 @@ class argument_parser
{
if (argv_len <= i + 1)
throw too_few_arguments{"Option --export-help must be followed by a value."};
export_format = {argv[i + 1]};
export_format = argv[i + 1];
}

if (export_format == "html")
Expand Down
13 changes: 12 additions & 1 deletion include/seqan3/utility/tuple/split.hpp
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Expand Up @@ -37,15 +37,21 @@ template <size_t beg, template <typename...> typename tuple_t, size_t... Is, typ
requires tuple_like<tuple_t<ts...>> && tuple_like<tuple_t<>>
constexpr auto tuple_split(tuple_t<ts...> const & t, std::index_sequence<Is...> const & SEQAN3_DOXYGEN_ONLY(idx))
{
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wmissing-braces"
return tuple_t<std::tuple_element_t<beg + Is, tuple_t<ts...>>...>{std::get<beg + Is>(t)...};
#pragma GCC diagnostic pop
}

//!\copydoc seqan3::detail::tuple_split
template <size_t beg, template <typename...> typename tuple_t, size_t... Is, typename... ts>
requires tuple_like<tuple_t<ts...>> && tuple_like<tuple_t<>>
constexpr auto tuple_split(tuple_t<ts...> && t, std::index_sequence<Is...> const & SEQAN3_DOXYGEN_ONLY(idx))
{
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wmissing-braces"
return tuple_t<std::tuple_element_t<beg + Is, tuple_t<ts...>>...>{std::move(std::get<beg + Is>(t))...};
#pragma GCC diagnostic pop
}
} // namespace seqan3::detail

Expand Down Expand Up @@ -85,8 +91,11 @@ constexpr auto tuple_split(tuple_t<ts...> const & t)
{
static_assert(pivot_c <= sizeof...(ts));

#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wmissing-braces"
return tuple_t{detail::tuple_split<0>(t, std::make_index_sequence<pivot_c>{}),
detail::tuple_split<pivot_c>(t, std::make_index_sequence<sizeof...(ts) - pivot_c>{})};
#pragma GCC diagnostic pop
}

//!\copydoc seqan3::tuple_split
Expand All @@ -95,9 +104,11 @@ template <size_t pivot_c, template <typename...> typename tuple_t, typename... t
constexpr auto tuple_split(tuple_t<ts...> && t)
{
static_assert(pivot_c <= sizeof...(ts));

#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wmissing-braces"
return tuple_t{detail::tuple_split<0>(std::move(t), std::make_index_sequence<pivot_c>{}),
detail::tuple_split<pivot_c>(std::move(t), std::make_index_sequence<sizeof...(ts) - pivot_c>{})};
#pragma GCC diagnostic pop
}

/*!\brief Splits a tuple like data structure at the first position of the given type.
Expand Down
2 changes: 1 addition & 1 deletion test/unit/argument_parser/detail/format_help_test.cpp
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Expand Up @@ -48,7 +48,7 @@ std::string const basic_version_str = "VERSION\n"

std::string license_text()
{
std::ifstream license_file{std::string{{SEQAN3_TEST_LICENSE_DIR}} + "/LICENSE.md"};
std::ifstream license_file{std::string{SEQAN3_TEST_LICENSE_DIR} + "/LICENSE.md"};
EXPECT_TRUE(license_file) << "Could not open file '" SEQAN3_TEST_LICENSE_DIR "/LICENSE.md'";
std::stringstream buffer;
buffer << license_file.rdbuf();
Expand Down
100 changes: 50 additions & 50 deletions test/unit/io/sequence_file/sequence_file_format_fastq_test.cpp
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Expand Up @@ -109,69 +109,69 @@ struct read : public sequence_file_data

TEST_F(read, newline_before_eof)
{
input = {"@ID1\n"
"ACGTTTTTTTTTTTTTTT\n"
"+\n"
"!##$%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
"+\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTTTA\n"
"+\n"
"!!!!!!!"};
input = "@ID1\n"
"ACGTTTTTTTTTTTTTTT\n"
"+\n"
"!##$%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
"+\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTTTA\n"
"+\n"
"!!!!!!!";
do_read_test(input);
}

TEST_F(read, whitespace_in_seq_qual)
{
input = {"@ID1\n"
"ACGTTTTTTTT\nTTTTTTT\n"
"+\n"
"!##$\n%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTT\r\nTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTT\n"
"+\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBD\nEBDEB\nDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTT\nTA\n"
"+\n"
"!!!!!\n!!\n"};
input = "@ID1\n"
"ACGTTTTTTTT\nTTTTTTT\n"
"+\n"
"!##$\n%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTT\r\nTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTT\n"
"+\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBD\nEBDEB\nDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTT\nTA\n"
"+\n"
"!!!!!\n!!\n";
do_read_test(input);
}

TEST_F(read, double_id_style)
{
input = {"@ID1\n"
"ACGTTTTTTTTTTTTTTT\n"
"+ID1\n"
"!##$%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
"+ID2\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTTTA\n"
"+ID3 lala\n"
"!!!!!!!\n"};
input = "@ID1\n"
"ACGTTTTTTTTTTTTTTT\n"
"+ID1\n"
"!##$%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
"+ID2\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTTTA\n"
"+ID3 lala\n"
"!!!!!!!\n";
do_read_test(input);
}

TEST_F(read, mixed_issues)
{
input = {"@ID1\n"
"ACGTTTTTTTT\nTTTTTTT\n"
"+\n"
"!##$\n%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTT\r\nTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTT\n"
"+\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBD\nEBDEB\nDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTT\nTA\n"
"+ID3 lala\n"
"!!!!!\n!!"};
input = "@ID1\n"
"ACGTTTTTTTT\nTTTTTTT\n"
"+\n"
"!##$\n%&'()*+,-./++-\n"
"@ID2\n"
"ACGTTTTTTTTTT\r\nTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTT\n"
"+\n"
"!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBD\nEBDEB\nDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
"@ID3 lala\n"
"ACGTT\nTA\n"
"+ID3 lala\n"
"!!!!!\n!!";
do_read_test(input);
}

Expand All @@ -188,8 +188,8 @@ TEST_F(read, only_qual)
//TODO fail_no_2nd_id
TEST_F(read, fail_no_seq_after_id)
{
std::stringstream istream{input = {"@ID1\n"
"ACGTTTTTTTTTTTTTTT"}};
std::stringstream istream{input = "@ID1\n"
"ACGTTTTTTTTTTTTTTT"};

seqan3::sequence_file_input fin{istream, seqan3::format_fastq{}};
EXPECT_THROW(fin.begin(), seqan3::unexpected_end_of_input);
Expand Down
114 changes: 57 additions & 57 deletions test/unit/io/structure_file/format_vienna_test.cpp
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Expand Up @@ -140,68 +140,68 @@ TEST_F(read, standard)

TEST_F(read, newline_before_eof)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))... (-3.71)"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))... (-3.71)";
do_read_test(input);
}

TEST_F(read, whitespace_in_seq)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCU CAGUUGGGAGAGCGCCAGACU GAAGAUUUGGAGGUC CUGUGUUCGAUCCACA GAAUU CGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"> example 2\n"
"UUGGAGUAC ACAACCUGUACAC UCUUUC \n"
"..(((((..(((...)))..)))))... (-3.71)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCU CAGUUGGGAGAGCGCCAGACU GAAGAUUUGGAGGUC CUGUGUUCGAUCCACA GAAUU CGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"> example 2\n"
"UUGGAGUAC ACAACCUGUACAC UCUUUC \n"
"..(((((..(((...)))..)))))... (-3.71)\n";
do_read_test(input);
}

TEST_F(read, no_energies)
{
check_energy = false;
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))).\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))...\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))).\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))...\n";
do_read_test(input);
}

TEST_F(read, no_ids)
{
check_id = false;
input = {"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))... (-3.71)\n"};
input = "GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))... (-3.71)\n";
do_read_test(input);
}

TEST_F(read, spaces_and_carriage_return)
{
check_id = false;
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\r\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\r\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.5)\r\n"
">example 2\r\n"
"UUGGAGUA CACAACCUGUACA CUCU UUC \r\n"
"..(((((..(((...)))..)))))... ( -3.71 )\r\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\r\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\r\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.5)\r\n"
">example 2\r\n"
"UUGGAGUA CACAACCUGUACA CUCU UUC \r\n"
"..(((((..(((...)))..)))))... ( -3.71 )\r\n";
do_read_test(input);
}

TEST_F(read, options_truncate_ids)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))... (-3.71)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"
"..(((((..(((...)))..)))))... (-3.71)\n";

options.truncate_ids = true;
expected_id = {"S.cerevisiae_tRNA-PHE", "example"};
Expand Down Expand Up @@ -280,78 +280,78 @@ TEST_F(read_fail, wrong_id)

TEST_F(read_fail, missing_seq)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}

TEST_F(read_fail, missing_structure)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"> example 2\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}

TEST_F(read_fail, missing_structure_and_id)
{
input = {"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n"};
input = "GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"UUGGAGUACACAACCUGUACACUCUUUC\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}

TEST_F(read_fail, structure_too_long)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))).. (-17.50)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))).. (-17.50)\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}

TEST_F(read_fail, structure_too_short)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))) (-17.50)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))) (-17.50)\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}

TEST_F(read_fail, structure_too_long_structured_seq)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))).. (-17.50)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))).. (-17.50)\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}, seqan3::fields<seqan3::field::structured_seq>{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}

TEST_F(read_fail, structure_too_short_structured_seq)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))) (-17.50)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))) (-17.50)\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}, seqan3::fields<seqan3::field::structured_seq>{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}

TEST_F(read_fail, wrong_char)
{
input = {"> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUICUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n"};
input = "> S.cerevisiae_tRNA-PHE M10740/1-73\n"
"GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUICUGUGUUCGAUCCACAGAAUUCGCA\n"
"(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))). (-17.50)\n";
std::stringstream istream{input};
seqan3::structure_file_input fin{istream, seqan3::format_vienna{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
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