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<div class="title">DNA.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 DNA_HPP</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#define DNA_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 "Global.hpp"</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include "IStreamReader.hpp"</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#include "IStreamWriter.hpp"</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include <memory></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> <span class="comment">/* forward-declaration dance for recursively-derived types */</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> </div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="keyword">template</span> <<span class="keywordtype">size_t</span> sizeVar, Endian VE></div><div class="line"><a name="l00024"></a><span class="lineno"><a class="line" href="structathena_1_1io_1_1_buffer.html"> 24</a></span> <span class="keyword">struct </span><a class="code" href="structathena_1_1io_1_1_buffer.html">Buffer</a>;</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="keyword">template</span> <atInt32 sizeVar, Endian VE></div><div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="structathena_1_1io_1_1_string.html"> 27</a></span> <span class="keyword">struct </span><a class="code" href="structathena_1_1io_1_1_string.html">String</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> <span class="keyword">template</span> <atInt32 sizeVar, Endian VE></div><div class="line"><a name="l00030"></a><span class="lineno"><a
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<div class="ttc" id="structathena_1_1io_1_1_w_string_html_a36e7cdd9a2fc0ee25d7f16b68852fa22"><div class="ttname"><a href="structathena_1_1io_1_1_w_string.html#a36e7cdd9a2fc0ee25d7f16b68852fa22">athena::io::WString::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_8hpp_source.html#l00201">DNA.hpp:201</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_html_adba389a039c69a3c6af86381bf2d97ad"><div class="ttname"><a href="structathena_1_1io_1_1_w_string.html#adba389a039c69a3c6af86381bf2d97ad">athena::io::WString::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_8hpp_source.html#l00206">DNA.hpp:206</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_d_n_a_1_1_delete_html"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a_1_1_delete.html">athena::io::DNA::Delete</a></div><div class="ttdoc">Meta Template preventing atdna from emitting read/write implementations. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00131">DNA.hpp:131</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="structathena_1_1io_1_1_d_n_a_html_a09693973df2cbdf1304dab0de1627661"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a.html#a09693973df2cbdf1304dab0de1627661">athena::io::DNA::write</a></div><div class="ttdeci">virtual void write(IStreamWriter &) const =0</div><div class="ttdoc">Common virtual write function for all DNA types. </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_string_html_ac37e667786002f38643b6aaedc1b0b7e"><div class="ttname"><a href="structathena_1_1io_1_1_string.html#ac37e667786002f38643b6aaedc1b0b7e">athena::io::String::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_8hpp_source.html#l00181">DNA.hpp:181</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_as_string_html_a7df789f2637078777affc17462be30b7"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string.html#a7df789f2637078777affc17462be30b7">athena::io::WStringAsString::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_8hpp_source.html#l00221">DNA.hpp:221</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="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_buffer_html_a6f04023324a82e215b0412fcf2512b91"><div class="ttname"><a href="structathena_1_1io_1_1_buffer.html#a6f04023324a82e215b0412fcf2512b91">athena::io::Buffer::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_8hpp_source.html#l00155">DNA.hpp:155</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_d_n_a_html_a1ffe91a70b3120b7307644ecb2a49d66"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a.html#a1ffe91a70b3120b7307644ecb2a49d66">athena::io::DNA::read</a></div><div class="ttdeci">virtual void read(IStreamReader &)=0</div><div class="ttdoc">Common virtual read function for all DNA types. </div></div>
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<div class="ttc" id="structathena_1_1io_1_1_buffer_html_a9c2f462edb3e08337b94ad7ab5c2f2c6"><div class="ttname"><a href="structathena_1_1io_1_1_buffer.html#a9c2f462edb3e08337b94ad7ab5c2f2c6">athena::io::Buffer::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_8hpp_source.html#l00164">DNA.hpp:164</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_html_aa1400b5412542c0323adb91a40651df6"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string.html#aa1400b5412542c0323adb91a40651df6">athena::io::WStringAsString::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_8hpp_source.html#l00223">DNA.hpp:223</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_as_string_html_a0769b8ed22bad841116817058a1f082b"><div class="ttname"><a href="structathena_1_1io_1_1_w_string_as_string.html#a0769b8ed22bad841116817058a1f082b">athena::io::WStringAsString::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_8hpp_source.html#l00225">DNA.hpp:225</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_string_html_a444b2b154084e3e7e12d4b300670a3e9"><div class="ttname"><a href="structathena_1_1io_1_1_string.html#a444b2b154084e3e7e12d4b300670a3e9">athena::io::String::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_8hpp_source.html#l00177">DNA.hpp:177</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_buffer_html_a1d71dc4060e9ce600fb7eaf62c3b7318"><div class="ttname"><a href="structathena_1_1io_1_1_buffer.html#a1d71dc4060e9ce600fb7eaf62c3b7318">athena::io::Buffer::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_8hpp_source.html#l00160">DNA.hpp:160</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="structathena_1_1io_1_1_d_n_a_1_1_align_html"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a_1_1_align.html">athena::io::DNA::Align</a></div><div class="ttdoc">Meta Template signaling atdna to insert an aligning stream seek where it&#39;s used. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00126">DNA.hpp:126</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_d_n_a_1_1_seek_html"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a_1_1_seek.html">athena::io::DNA::Seek</a></div><div class="ttdoc">Meta Template signaling atdna to insert a stream seek where it&#39;s used. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00119">DNA.hpp:119</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_d_n_a_html_ae3064c2a8e289c5020037c5593e2b008"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a.html#ae3064c2a8e289c5020037c5593e2b008">athena::io::DNA< VE >::Value</a></div><div class="ttdeci">T Value</div><div class="ttdoc">Template type signaling atdna to capture the value where it&#39;s used. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00070">DNA.hpp:70</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_string_html_a73409b4025e3dac314d9cef000286f05"><div class="ttname"><a href="structathena_1_1io_1_1_string.html#a73409b4025e3dac314d9cef000286f05">athena::io::String::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_8hpp_source.html#l00179">DNA.hpp:179</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="structathena_1_1io_1_1_d_n_a_html_a5852dadd55deeca4f56f0cffb131f477"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a.html#a5852dadd55deeca4f56f0cffb131f477">athena::io::DNA< VE >::Vector</a></div><div class="ttdeci">std::vector< T > Vector</div><div class="ttdoc">Template type wrapping std::vector and signaling atdna to manipulate it where it&#39;s used...</div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00079">DNA.hpp:79</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_d_n_a_html_aba07c0082c48d919ade16f09a37a19be"><div class="ttname"><a href="structathena_1_1io_1_1_d_n_a.html#aba07c0082c48d919ade16f09a37a19be">athena::io::DNA::__EnumerateSize</a></div><div class="ttdeci">static size_t __EnumerateSize(size_t __isz, const T &v)</div><div class="ttdoc">Internal DNA helper for accumulating binarySize. </div><div class="ttdef"><b>Definition:</b> <a href="_d_n_a_8hpp_source.html#l00140">DNA.hpp:140</a></div></div>
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<div class="ttc" id="structathena_1_1io_1_1_w_string_html_ab77da684bb6b3632608bc10471305333"><div class="ttname"><a href="structathena_1_1io_1_1_w_string.html#ab77da684bb6b3632608bc10471305333">athena::io::WString::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_8hpp_source.html#l00196">DNA.hpp:196</a></div></div>
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