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<div class="title">DNAYaml.hpp</div> </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef DNAYAML_HPP</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#define DNAYAML_HPP</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> </div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">/* BIG FAT WARNING!!!</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * The type-structure of this file is expected to remain consistent for 'atdna'</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * Any changes to the types or namespacing must be reflected in 'atdna/main.cpp'</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> */</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> </div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include <yaml.h></span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#include <utf8proc.h></span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include "DNA.hpp"</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "FileReader.hpp"</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> </div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="keyword">namespace </span><a class="code" href="namespaceathena.html">athena</a></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> {</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="keyword">namespace </span>io</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> {</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> std::string base64_encode(<span class="keyword">const</span> atUint8* bytes_to_encode, <span class="keywordtype">size_t</span> in_len);</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> std::unique_ptr<atUint8[]> base64_decode(<span class="keyword">const</span> std::string& encoded_string);</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keywordtype">void</span> HandleYAMLParserError(yaml_parser_t* parser);</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keywordtype">void</span> HandleYAMLEmitterError(yaml_emitter_t* emitter);</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="structathena_1_1io_1_1_y_a_m_l_std_string_reader_state.html"> 27</a></span> <span class="keyword">struct </span><a class="code" href="structathena_1_1io_1_1_y_a_m_l_std_string_reader_state.html">YAMLStdStringReaderState</a></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> {</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  std::string::const_iterator begin;</div><div class="line"><a name="l00030"></a><span clas
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<div class="ttc" id="structathena_1_1io_1_1_string_yaml_html_ad092367c1272a03b0fa0ec6369f637dc"><div class="ttname"><a href="structathena_1_1io_1_1_string_yaml.html#ad092367c1272a03b0fa0ec6369f637dc">athena::io::StringYaml::read</a></div><div class="ttdeci">void read(IStreamReader &reader)</div><div class="ttdoc">Common virtual read function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01254">DNAYaml.hpp:1254</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_y_a_m_l_node_html"><div class="ttname"><a href="structathena_1_1io_1_1_y_a_m_l_node.html">athena::io::YAMLNode</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l00041">DNAYaml.hpp:41</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_yaml_html_aa96163345ee4653222227c276e5b6328"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_yaml.html#aa96163345ee4653222227c276e5b6328">athena::io::WStringYaml::read</a></div><div class="ttdeci">void read(IStreamReader &reader)</div><div class="ttdoc">Common virtual read function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01274">DNAYaml.hpp:1274</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_reader_html_ac1e2c0114677d05fd2a79cc5f7fb35a7"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_reader.html#ac1e2c0114677d05fd2a79cc5f7fb35a7">athena::io::IStreamReader::readWStringAsString</a></div><div class="ttdeci">std::string readWStringAsString(atInt32 fixedLen=-1)</div><div class="ttdoc">Reads a wide-char string (using endianness from setEndian), converts to UTF8 and advances the positio...</div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_reader_8hpp_source.html#l00881">IStreamReader.hpp:881</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_reader_html_aebbd3a9f64e552d76a2392e2ae3fe9f8"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_reader.html#aebbd3a9f64e552d76a2392e2ae3fe9f8">athena::io::IStreamReader::readWString</a></div><div class="ttdeci">std::wstring readWString(atInt32 fixedLen=-1)</div><div class="ttdoc">Reads a wstring and advances the position in the file. </div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_reader_8hpp_source.html#l01035">IStreamReader.hpp:1035</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_writer_html_a5fdba54e5835aecb20aa18373729c440"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_writer.html#a5fdba54e5835aecb20aa18373729c440">athena::io::IStreamWriter::writeWString</a></div><div class="ttdeci">void writeWString(const std::wstring &str, atInt32 fixedLen=-1)</div><div class="ttdoc">Writes an wstring to the buffer and advances the buffer. </div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_writer_8hpp_source.html#l00897">IStreamWriter.hpp:897</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_d_n_a_html"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a.html">athena::io::DNA</a></div><div class="ttdoc">Base DNA class used against &#39;atdna&#39;. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00045">DNA.hpp:45</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_writer_html_a643d08a3c8fd0d8774c44188663f8de4"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_writer.html#a643d08a3c8fd0d8774c44188663f8de4">athena::io::IStreamWriter::writeUBytes</a></div><div class="ttdeci">virtual void writeUBytes(const atUint8 *data, atUint64 len)=0</div><div class="ttdoc">Writes the given buffer with the specified length, buffers can be bigger than the length however it&#39;s...</div></div>
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<div class="ttc" id="structathena_1_1io_1_1_y_a_m_l_std_string_reader_state_html"><div class="ttname"><a href="structathena_1_1io_1_1_y_a_m_l_std_string_reader_state.html">athena::io::YAMLStdStringReaderState</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l00027">DNAYaml.hpp:27</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_as_string_html"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string.html">athena::io::WStringAsString</a></div><div class="ttdoc">Concrete converting-wstring type used by DNA::WStringAsString. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00033">DNA.hpp:33</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_reader_html"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_reader.html">athena::io::IStreamReader</a></div><div class="ttdoc">The IStreamReader class defines a basic API for reading from streams, Implementors are provided with ...</div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_reader_8hpp_source.html#l00018">IStreamReader.hpp:18</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_buffer_yaml_html"><div class="ttname"><a href="structathena_1_1io_1_1_buffer_yaml.html">athena::io::BufferYaml</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01120">DNAYaml.hpp:1120</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_y_a_m_l_doc_writer_html"><div class="ttname"><a href="classathena_1_1io_1_1_y_a_m_l_doc_writer.html">athena::io::YAMLDocWriter</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l00821">DNAYaml.hpp:821</a></div></div>
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<div class="ttc" id="namespaceathena_html"><div class="ttname"><a href="namespaceathena.html">athena</a></div><div class="ttdef"><b>Definition:</b> <a href="_a_l_t_t_p_enums_8hpp_source.html#l00006">ALTTPEnums.hpp:6</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_buffer_html"><div class="ttname"><a href="structathena_1_1io_1_1_buffer.html">athena::io::Buffer</a></div><div class="ttdoc">Concrete buffer type used by DNA::Buffer. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00024">DNA.hpp:24</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_d_n_a_yaml_html"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a_yaml.html">athena::io::DNAYaml</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01132">DNAYaml.hpp:1132</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_as_string_yaml_html_ad32eb49e0fed10e0d3faa5cf21e9bf2f"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string_yaml.html#ad32eb49e0fed10e0d3faa5cf21e9bf2f">athena::io::WStringAsStringYaml::write</a></div><div class="ttdeci">void write(IStreamWriter &writer) const </div><div class="ttdoc">Common virtual write function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01302">DNAYaml.hpp:1302</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_string_yaml_html_a47e6fd1288cfb89646ebc99d9b8bbd60"><div class="ttname"><a href="structathena_1_1io_1_1_string_yaml.html#a47e6fd1288cfb89646ebc99d9b8bbd60">athena::io::StringYaml::write</a></div><div class="ttdeci">void write(IStreamWriter &writer) const </div><div class="ttdoc">Common virtual write function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01256">DNAYaml.hpp:1256</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_writer_html_a17261b2ee9c1d716589120b18cd9339b"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_writer.html#a17261b2ee9c1d716589120b18cd9339b">athena::io::IStreamWriter::writeStringAsWString</a></div><div class="ttdeci">void writeStringAsWString(const std::string &str, atInt32 fixedLen=-1)</div><div class="ttdoc">Converts a UTF8 string to a wide-char string in the buffer and advances the buffer. It also swaps the bytes depending on the platform and Stream settings. </div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_writer_8hpp_source.html#l00686">IStreamWriter.hpp:686</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_as_string_yaml_html_a42cf54aa556c7434bdc8ef7b122a6a38"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string_yaml.html#a42cf54aa556c7434bdc8ef7b122a6a38">athena::io::WStringAsStringYaml::binarySize</a></div><div class="ttdeci">size_t binarySize(size_t __isz) const </div><div class="ttdoc">Common virtual binary size computation for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01304">DNAYaml.hpp:1304</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_html"><div class="ttname"><a href="structathena_1_1io_1_1_w_string.html">athena::io::WString</a></div><div class="ttdoc">Concrete wstring type used by DNA::WString. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00030">DNA.hpp:30</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_as_string_yaml_html_a727430b87d311bb488ef8c17d36aacfa"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string_yaml.html#a727430b87d311bb488ef8c17d36aacfa">athena::io::WStringAsStringYaml::read</a></div><div class="ttdeci">void read(IStreamReader &reader)</div><div class="ttdoc">Common virtual read function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01300">DNAYaml.hpp:1300</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_reader_html_a525eeaf5c6571b4067a35ab951a66703"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_reader.html#a525eeaf5c6571b4067a35ab951a66703">athena::io::IStreamReader::readString</a></div><div class="ttdeci">std::string readString(atInt32 fixedLen=-1)</div><div class="ttdoc">Reads a string and advances the position in the file. </div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_reader_8hpp_source.html#l01003">IStreamReader.hpp:1003</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_reader_html_ab02b8fd04541d1c87c6bafab84842463"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_reader.html#ab02b8fd04541d1c87c6bafab84842463">athena::io::IStreamReader::position</a></div><div class="ttdeci">virtual atUint64 position() const =0</div><div class="ttdoc">Returns the current position in the stream. </div></div>
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<div class="ttc" id="unionalignas_html"><div class="ttname"><a href="unionalignas.html">alignas</a></div><div class="ttdef"><b>Definition:</b> <a href="_types_8hpp_source.html#l00035">Types.hpp:35</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_reader_html_a4ba4e1ac641161d5c738c9375b5d2012"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_reader.html#a4ba4e1ac641161d5c738c9375b5d2012">athena::io::IStreamReader::seek</a></div><div class="ttdeci">virtual void seek(atInt64 pos, SeekOrigin origin=SeekOrigin::Current)=0</div><div class="ttdoc">Sets the buffers position relative to the specified position. It seeks relative to the current posit...</div></div>
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<div class="ttc" id="structathena_1_1io_1_1_buffer_yaml_html_ab7409a9073477082fe400cb010e6b745"><div class="ttname"><a href="structathena_1_1io_1_1_buffer_yaml.html#ab7409a9073477082fe400cb010e6b745">athena::io::BufferYaml::read</a></div><div class="ttdeci">void read(IStreamReader &reader)</div><div class="ttdoc">Common virtual read function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01231">DNAYaml.hpp:1231</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_writer_html"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_writer.html">athena::io::IStreamWriter</a></div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_writer_8hpp_source.html#l00012">IStreamWriter.hpp:12</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_buffer_yaml_html_a397e9d5931a71d4cf28181c0c8183c05"><div class="ttname"><a href="structathena_1_1io_1_1_buffer_yaml.html#a397e9d5931a71d4cf28181c0c8183c05">athena::io::BufferYaml::binarySize</a></div><div class="ttdeci">size_t binarySize(size_t __isz) const </div><div class="ttdoc">Common virtual binary size computation for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01240">DNAYaml.hpp:1240</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_yaml_html_a8c7cf90a1886810379bd7ea671fde7f9"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_yaml.html#a8c7cf90a1886810379bd7ea671fde7f9">athena::io::WStringYaml::binarySize</a></div><div class="ttdeci">size_t binarySize(size_t __isz) const </div><div class="ttdoc">Common virtual binary size computation for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01284">DNAYaml.hpp:1284</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_yaml_html_af201e200f6272e6bd8d639ced6e0f5c4"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_yaml.html#af201e200f6272e6bd8d639ced6e0f5c4">athena::io::WStringYaml::write</a></div><div class="ttdeci">void write(IStreamWriter &writer) const </div><div class="ttdoc">Common virtual write function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01279">DNAYaml.hpp:1279</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_as_string_yaml_html"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string_yaml.html">athena::io::WStringAsStringYaml</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01129">DNAYaml.hpp:1129</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_writer_html_a23b7b46e18bfa2cac97141a90b46ca97"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_writer.html#a23b7b46e18bfa2cac97141a90b46ca97">athena::io::IStreamWriter::writeString</a></div><div class="ttdeci">void writeString(const std::string &str, atInt32 fixedLen=-1)</div><div class="ttdoc">Writes an string to the buffer and advances the buffer. </div><div class="ttdef"><b>Definition:</b> <a href="_i_stream_writer_8hpp_source.html#l00858">IStreamWriter.hpp:858</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_string_html"><div class="ttname"><a href="structathena_1_1io_1_1_string.html">athena::io::String</a></div><div class="ttdoc">Concrete string type used by DNA::String. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00027">DNA.hpp:27</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_i_stream_reader_html_ad90233be645b52f421b1560d63cd07bd"><div class="ttname"><a href="classathena_1_1io_1_1_i_stream_reader.html#ad90233be645b52f421b1560d63cd07bd">athena::io::IStreamReader::readUBytesToBuf</a></div><div class="ttdeci">virtual atUint64 readUBytesToBuf(void *buf, atUint64 len)=0</div><div class="ttdoc">Attempts to read a fixed length of data into a pre-allocated buffer, this function is client defined ...</div></div>
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<div class="ttc" id="structathena_1_1io_1_1_string_yaml_html_a38b3446cea33f93e04bd0346b128a6a4"><div class="ttname"><a href="structathena_1_1io_1_1_string_yaml.html#a38b3446cea33f93e04bd0346b128a6a4">athena::io::StringYaml::binarySize</a></div><div class="ttdeci">size_t binarySize(size_t __isz) const </div><div class="ttdoc">Common virtual binary size computation for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01258">DNAYaml.hpp:1258</a></div></div>
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<div class="ttc" id="classathena_1_1io_1_1_y_a_m_l_doc_reader_html"><div class="ttname"><a href="classathena_1_1io_1_1_y_a_m_l_doc_reader.html">athena::io::YAMLDocReader</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l00496">DNAYaml.hpp:496</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_string_yaml_html"><div class="ttname"><a href="structathena_1_1io_1_1_string_yaml.html">athena::io::StringYaml</a></div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01123">DNAYaml.hpp:1123</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_buffer_yaml_html_a5340ceaeac46ac8bf8dd076637855ae5"><div class="ttname"><a href="structathena_1_1io_1_1_buffer_yaml.html#a5340ceaeac46ac8bf8dd076637855ae5">athena::io::BufferYaml::write</a></div><div class="ttdeci">void write(IStreamWriter &writer) const </div><div class="ttdoc">Common virtual write function for all DNA types. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_yaml_8hpp_source.html#l01236">DNAYaml.hpp:1236</a></div></div>
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<li class="navelem"><a class="el" href="dir_d44c64559bbebec7f509842c48db8b23.html">include</a></li><li class="navelem"><a class="el" href="dir_9b3fbfcb7fc609b7105d1ff63111043b.html">athena</a></li><li class="navelem"><b>DNAYaml.hpp</b></li>
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