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<a href="aa27_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="comment">// -----------------------------------------------------------------------------------------------------</span></div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="comment">// Copyright (c) 2022 deCODE Genetics</span></div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="comment">// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin</span></div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="comment">// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik</span></div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="comment">// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License</span></div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="comment">// shipped with this file and also available at: https://github.com/biocpp/biocpp-core/blob/main/LICENSE.md</span></div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span><span class="comment">// -----------------------------------------------------------------------------------------------------</span></div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span> </div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#pragma once</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span> </div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include <<a class="codeRef" target="_blank" href="https://en.cppreference.com/w/cpp/header/vector.html">vector</a>></span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include <<a class="code" href="aminoacid__base_8hpp.html">bio/alphabet/aminoacid/aminoacid_base.hpp</a>></span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include <<a class="code" href="alphabet_2aminoacid_2concept_8hpp.html">bio/alphabet/aminoacid/concept.hpp</a>></span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#include <bio/alphabet/detail/to_lower.hpp></span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> </div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacebio_1_1alphabet.html">bio::alphabet</a></div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span>{</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html"> 44</a></span><span class="keyword">class </span><a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> : <span class="keyword">public</span> <a class="code hl_class" href="classbio_1_1alphabet_1_1aminoacid__base.html">aminoacid_base</a><aa27, 27></div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span>{</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span><span class="keyword">private</span>:</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">using </span><a class="code hl_class" href="classbio_1_1alphabet_1_1aminoacid__base.html">base_t</a> = <a class="code hl_class" href="classbio_1_1alphabet_1_1aminoacid__base.html">aminoacid_base<aa27, 27></a>;</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> </div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">friend</span> <a class="code hl_class" href="classbio_1_1alphabet_1_1aminoacid__base.html">base_t</a>;</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <span class="keyword">friend</span> <a class="code hl_class" href="classbio_1_1alphabet_1_1base.html">base_t::base_t</a>;</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span><span class="keyword">public</span>:</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#ab6b7912c578a863d8a84d61bc3808cbc"> 60</a></span> <span class="keyword">constexpr</span> <a class="code hl_function" href="classbio_1_1alphabet_1_1aa27.html#ab6b7912c578a863d8a84d61bc3808cbc">aa27</a>() noexcept = default; </div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#a6b706d4d369799dce0ecc5740eab9087"> 61</a></span> constexpr <a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a>(<a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> const &) noexcept = default; </div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#a725c3ac7fc8a35563c525c0563d4daed"> 62</a></span> constexpr <a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a>(<a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> &&) noexcept = default; </div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#a4adfd51c56a47d1373018d42fd96af60"> 63</a></span> constexpr <a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> & operator=(<a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> const &) noexcept = default; </div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#abfcd90dd8d5c9b74925d774187b2fcdd"> 64</a></span> constexpr <a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> & operator=(<a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> &&) noexcept = default; </div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#aecf564402e50a1057e311ba4fd140767"> 65</a></span> ~<a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a>() noexcept = default; </div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> using <a class="code hl_class" href="classbio_1_1alphabet_1_1aminoacid__base.html">base_t</a>::<a class="code hl_class" href="classbio_1_1alphabet_1_1aminoacid__base.html">base_t</a>;</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span>protected:</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#a80d91dbdd86bb9afe5a4d613ad7119c4"> 72</a></span> static constexpr <a class="code hl_namespaceRef" target="_blank" href="https://en.cppreference.com/w/namespacestd.html">std</a>::array<<a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/types/conditional.html">char_type</a>, <a class="code hl_variable" href="classbio_1_1alphabet_1_1base.html#a834f007f409b2761dc774fc45e457b11">alphabet_size</a>> <a class="code hl_variable" href="classbio_1_1alphabet_1_1aa27.html#a80d91dbdd86bb9afe5a4d613ad7119c4">rank_to_char</a>{<span class="charliteral">'A'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'C'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'E'</span>, <span class="charliteral">'F'</span>, <span class="charliteral">'G'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'I'</span>,</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <span class="charliteral">'J'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'L'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'O'</span>, <span class="charliteral">'P'</span>, <span class="charliteral">'Q'</span>, <span class="charliteral">'R'</span>,</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <span class="charliteral">'S'</span>, <span class="charliteral">'T'</span>, <span class="charliteral">'U'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'X'</span>, <span class="charliteral">'Y'</span>, <span class="charliteral">'Z'</span>, <span class="charliteral">'*'</span>};</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#ac8af7766d3bc6d093331cb29eaae99c8"> 77</a></span> <span class="keyword">static</span> <span class="keyword">constexpr</span> <a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/container/array.html">std::array<rank_type, 256></a> <a class="code hl_variable" href="classbio_1_1alphabet_1_1aa27.html#ac8af7766d3bc6d093331cb29eaae99c8">char_to_rank</a> = []() <span class="keyword">constexpr</span></div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> {</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> <a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/container/array.html">std::array<rank_type, 256></a> ret{};</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> <span class="comment">// initialize with UNKNOWN</span></div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> ret.<a class="code hl_functionRef" target="_blank" href="https://en.cppreference.com/w/cpp/container/array/fill.html">fill</a>(23); <span class="comment">// value of 'X'</span></div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <span class="comment">// reverse mapping for characters and their lowercase</span></div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> <span class="keywordflow">for</span> (<a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/types/conditional.html">rank_type</a> rnk = 0u; rnk < <a class="code hl_variable" href="classbio_1_1alphabet_1_1base.html#a834f007f409b2761dc774fc45e457b11">alphabet_size</a>; ++rnk)</div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> {</div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> ret[<span class="keyword">static_cast<</span><a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/types/conditional.html">rank_type</a><span class="keyword">></span>(<a class="code hl_variable" href="classbio_1_1alphabet_1_1aa27.html#a80d91dbdd86bb9afe5a4d613ad7119c4">rank_to_char</a>[rnk])] = rnk;</div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> ret[<span class="keyword">static_cast<</span><a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/types/conditional.html">rank_type</a><span class="keyword">></span>(detail::to_lower(<a class="code hl_variable" href="classbio_1_1alphabet_1_1aa27.html#a80d91dbdd86bb9afe5a4d613ad7119c4">rank_to_char</a>[rnk]))] = rnk;</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> }</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="keywordflow">return</span> ret;</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> }();</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span>};</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span>} <span class="comment">// namespace bio::alphabet</span></div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span><span class="comment">// ------------------------------------------------------------------</span></div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span><span class="comment">// literals</span></div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span><span class="comment">// ------------------------------------------------------------------</span></div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacebio_1_1alphabet.html">bio::alphabet</a></div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span>{</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span><span class="keyword">inline</span> <span class="keyword">namespace </span>literals</div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span>{</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#af53f45723a3ee86f96959059182ee599"> 115</a></span><span class="keyword">consteval</span> <a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a> <span class="keyword">operator</span><span class="stringliteral">""</span>_aa27(<span class="keywordtype">char</span> <span class="keyword">const</span> c)</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span>{</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="keywordflow">if</span> (!char_is_valid_for<aa27>(c))</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="keywordflow">throw</span> <a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/error/invalid_argument.html">std::invalid_argument</a>{<span class="stringliteral">"Illegal character in character literal."</span>};</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> </div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> <span class="keywordflow">return</span> <a class="code hl_class" href="classbio_1_1alphabet_1_1aa27.html">aa27</a>{}.<a class="code hl_function" href="classbio_1_1alphabet_1_1base.html#a9dfef1259c4c0112e490255343de0d2f">assign_char</a>(c);</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span>}</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> </div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span><span class="keyword">template</span> <meta::detail::literal_buffer_<span class="keywordtype">string</span> str></div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"><a class="line" href="classbio_1_1alphabet_1_1aa27.html#a0155dc839dc88fbcdc0d2ca759d9e797"> 133</a></span><span class="keyword">constexpr</span> <a class="code hl_classRef" target="_blank" href="https://en.cppreference.com/w/cpp/container/vector.html">std::vector<aa27></a> <span class="keyword">operator</span><span class="stringliteral">""</span>_aa27()</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span>{</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> <span class="keywordflow">return</span> detail::string_literal<str, aa27>();</div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span>}</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span>} <span class="comment">// namespace literals</span></div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span>} <span class="comment">// namespace bio::alphabet</span></div>
<div class="ttc" id="aalphabet_2aminoacid_2concept_8hpp_html"><div class="ttname"><a href="alphabet_2aminoacid_2concept_8hpp.html">concept.hpp</a></div><div class="ttdoc">Provides bio::alphabet::aminoacid.</div></div>
<div class="ttc" id="aaminoacid__base_8hpp_html"><div class="ttname"><a href="aminoacid__base_8hpp.html">aminoacid_base.hpp</a></div><div class="ttdoc">Provides bio::alphabet::aminoacid_base.</div></div>
<div class="ttc" id="aarray_html"><div class="ttname"><a href="https://en.cppreference.com/w/cpp/container/array.html">std::array</a></div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1aa27_html"><div class="ttname"><a href="classbio_1_1alphabet_1_1aa27.html">bio::alphabet::aa27</a></div><div class="ttdoc">The twenty-seven letter amino acid alphabet..</div><div class="ttdef"><b>Definition:</b> aa27.hpp:45</div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1aa27_html_a80d91dbdd86bb9afe5a4d613ad7119c4"><div class="ttname"><a href="classbio_1_1alphabet_1_1aa27.html#a80d91dbdd86bb9afe5a4d613ad7119c4">bio::alphabet::aa27::rank_to_char</a></div><div class="ttdeci">static constexpr std::array< char_type, alphabet_size > rank_to_char</div><div class="ttdoc">Value to char conversion table.</div><div class="ttdef"><b>Definition:</b> aa27.hpp:72</div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1aa27_html_ab6b7912c578a863d8a84d61bc3808cbc"><div class="ttname"><a href="classbio_1_1alphabet_1_1aa27.html#ab6b7912c578a863d8a84d61bc3808cbc">bio::alphabet::aa27::aa27</a></div><div class="ttdeci">constexpr aa27() noexcept=default</div><div class="ttdoc">Defaulted.</div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1aa27_html_ac8af7766d3bc6d093331cb29eaae99c8"><div class="ttname"><a href="classbio_1_1alphabet_1_1aa27.html#ac8af7766d3bc6d093331cb29eaae99c8">bio::alphabet::aa27::char_to_rank</a></div><div class="ttdeci">static constexpr std::array< rank_type, 256 > char_to_rank</div><div class="ttdoc">Char to value conversion table.</div><div class="ttdef"><b>Definition:</b> aa27.hpp:77</div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1aminoacid__base_html"><div class="ttname"><a href="classbio_1_1alphabet_1_1aminoacid__base.html">bio::alphabet::aminoacid_base</a></div><div class="ttdoc">A CRTP-base that refines bio::alphabet::base and is used by the amino acids.</div><div class="ttdef"><b>Definition:</b> aminoacid_base.hpp:31</div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1base_html"><div class="ttname"><a href="classbio_1_1alphabet_1_1base.html">bio::alphabet::base< aa27, size, char ></a></div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1base_html_a834f007f409b2761dc774fc45e457b11"><div class="ttname"><a href="classbio_1_1alphabet_1_1base.html#a834f007f409b2761dc774fc45e457b11">bio::alphabet::base::alphabet_size</a></div><div class="ttdeci">static constexpr size_t alphabet_size</div><div class="ttdoc">The size of the alphabet, i.e. the number of different values it can take.</div><div class="ttdef"><b>Definition:</b> base.hpp:177</div></div>
<div class="ttc" id="aclassbio_1_1alphabet_1_1base_html_a9dfef1259c4c0112e490255343de0d2f"><div class="ttname"><a href="classbio_1_1alphabet_1_1base.html#a9dfef1259c4c0112e490255343de0d2f">bio::alphabet::base::assign_char</a></div><div class="ttdeci">constexpr derived_type & assign_char(char_type const c) noexcept</div><div class="ttdoc">Assign from a character, implicitly converts invalid characters.</div><div class="ttdef"><b>Definition:</b> base.hpp:145</div></div>
<div class="ttc" id="aconditional_html"><div class="ttname"><a href="https://en.cppreference.com/w/cpp/types/conditional.html">std::conditional_t</a></div></div>
<div class="ttc" id="afill_html"><div class="ttname"><a href="https://en.cppreference.com/w/cpp/container/array/fill.html">std::array::fill</a></div><div class="ttdeci">T fill(T... args)</div></div>
<div class="ttc" id="ainvalid_argument_html"><div class="ttname"><a href="https://en.cppreference.com/w/cpp/error/invalid_argument.html">std::invalid_argument</a></div></div>
<div class="ttc" id="anamespacebio_1_1alphabet_html"><div class="ttname"><a href="namespacebio_1_1alphabet.html">bio::alphabet</a></div><div class="ttdoc">The alphabet module's namespace.</div><div class="ttdef"><b>Definition:</b> aa10li.hpp:23</div></div>
<div class="ttc" id="anamespacestd_html"><div class="ttname"><a href="https://en.cppreference.com/w/namespacestd.html">std</a></div></div>
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