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Cigar operation #2388

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Mar 15, 2021
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Cigar operation #2388

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c70d501
[MISC] deprecate seqan3::cigar_op and add changelog
marehr Mar 11, 2021
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marehr Mar 12, 2021
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7 changes: 6 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -88,8 +88,13 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.

#### Alphabet

* Removed seqan3::char_is_valid_for requirement from seqan3::writable_alphabet and seqan3::writable_constexpr_alphabet
* Removed seqan3::char_is_valid_for requirement from seqan3::writable_alphabet and
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seqan3::detail::writable_constexpr_alphabet
([\#2337](https://github.com/seqan/seqan3/pull/2337)).
* Removed seqan3::cigar_op, please use seqan3::cigar::operation instead
([\#2388](https://github.com/seqan/seqan3/pull/2388)).
* The literal 'M'_cigar_op was renamed to 'M'_cigar_operation
([\#2388](https://github.com/seqan/seqan3/pull/2388)).

#### Argument Parser

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6 changes: 6 additions & 0 deletions include/seqan3/alphabet/cigar/cigar.hpp
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Expand Up @@ -232,6 +232,12 @@ inline cigar::operation operator""_cigar_operation(char const c) noexcept
{
return cigar::operation{}.assign_char(c);
}

//!\deprecated Please use seqan3::""_cigar_operation instead.
SEQAN3_DEPRECATED_310 inline cigar::operation operator""_cigar_op(char const c) noexcept
{
return cigar::operation{}.assign_char(c);
}
//!\}

} // namespace seqan3
26 changes: 26 additions & 0 deletions include/seqan3/alphabet/cigar/cigar_op.hpp
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@@ -0,0 +1,26 @@
// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------

/*!\file
* \brief [DEPRECATED] Introduces the seqan3::cigar_op alphabet.
* \author Joshua Kim <joshua.kim AT fu-berlin.de>
* \deprecated This header will be removed in 3.1.0; Please \#include <seqan3/alphabet/cigar/cigar.hpp>
* instead.
*/

#pragma once

#include <seqan3/alphabet/cigar/cigar.hpp>

namespace seqan3
{
//!\deprecated Please use seqan3::cigar::operation instead.
using cigar_op SEQAN3_DEPRECATED_310 = seqan3::cigar::operation;
} // namespace seqan3

SEQAN3_DEPRECATED_HEADER(
"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/alphabet/cigar/cigar.hpp> instead.")