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Emily Boudreaux
2025-07-24 11:10:45 -04:00
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@@ -5,7 +5,7 @@
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<title>GridFire: src/network/lib/io/network_file.cpp Source File</title>
<title>GridFire: src/lib/io/network_file.cpp Source File</title>
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@@ -146,7 +146,7 @@ $(function(){initNavTree('network__file_8cpp_source.html',''); initResizable(tru
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"><a class="line" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#afc8ed91e8c98205c505e3d9f0cff1993"> 42</a></span> <a class="code hl_function" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#afc8ed91e8c98205c505e3d9f0cff1993">SimpleReactionListFileParser::SimpleReactionListFileParser</a>() {}</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="foldopen" id="foldopen00044" data-start="{" data-end="}">
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"><a class="line" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#a4df01e3a93e1291d2cde0458545325f8"> 44</a></span> <a class="code hl_struct" href="structgridfire_1_1io_1_1_parsed_network_data.html">ParsedNetworkData</a> <a class="code hl_function" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#a4df01e3a93e1291d2cde0458545325f8">SimpleReactionListFileParser::parse</a>(<span class="keyword">const</span> std::string&amp; filename)<span class="keyword"> const </span>{</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"><a class="line" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#a4df01e3a93e1291d2cde0458545325f8"> 44</a></span> <a class="code hl_typedef" href="namespacegridfire_1_1io.html#abcbdcbd13cfa8c9fbe1b48e8ee2cc352">ParsedNetworkData</a> <a class="code hl_function" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#a4df01e3a93e1291d2cde0458545325f8">SimpleReactionListFileParser::parse</a>(<span class="keyword">const</span> std::string&amp; filename)<span class="keyword"> const </span>{</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#acef7eafe3cbea159259f69c88d309b66">m_logger</a>, <span class="stringliteral">&quot;Parsing simple reaction list file: {}&quot;</span>, filename);</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> std::ifstream file(filename);</div>
@@ -156,44 +156,41 @@ $(function(){initNavTree('network__file_8cpp_source.html',''); initResizable(tru
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">&quot;Could not open file: &quot;</span> + filename);</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> }</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> </div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <a class="code hl_struct" href="structgridfire_1_1io_1_1_parsed_network_data.html">ParsedNetworkData</a> parsed;</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <a class="code hl_typedef" href="namespacegridfire_1_1io.html#abcbdcbd13cfa8c9fbe1b48e8ee2cc352">ParsedNetworkData</a> parsed;</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> std::string line;</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="keywordtype">int</span> line_number = 0;</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <span class="keywordflow">while</span> (std::getline(file, line)) {</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> line_number++;</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> LOG_TRACE_L3(<a class="code hl_variable" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#acef7eafe3cbea159259f69c88d309b66">m_logger</a>, <span class="stringliteral">&quot;Parsing reaction list file {}, line {}: {}&quot;</span>, filename, line_number, line);</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> </div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> comment_pos = line.find(<span class="charliteral">&#39;#&#39;</span>);</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keywordflow">if</span> (comment_pos != std::string::npos) {</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> line = line.substr(0, comment_pos);</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> }</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="keywordflow">while</span> (std::getline(file, line)) {</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> LOG_TRACE_L3(<a class="code hl_variable" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#acef7eafe3cbea159259f69c88d309b66">m_logger</a>, <span class="stringliteral">&quot;Parsing reaction list file {}, line: {}&quot;</span>, filename, line);</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> comment_pos = line.find(<span class="charliteral">&#39;#&#39;</span>);</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <span class="keywordflow">if</span> (comment_pos != std::string::npos) {</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> line = line.substr(0, comment_pos);</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> }</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> </div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> trim(line);</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> trim(line);</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> <span class="keywordflow">if</span> (line.empty()) {</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <span class="keywordflow">continue</span>; <span class="comment">// Skip empty lines</span></div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> }</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> parsed.<a class="code hl_variable" href="structgridfire_1_1io_1_1_parsed_network_data.html#a5145c672877638e6113abf1f719b246d">reactionPENames</a>.push_back(line);</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> }</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#acef7eafe3cbea159259f69c88d309b66">m_logger</a>, <span class="stringliteral">&quot;Parsed {} reactions from file: {}&quot;</span>, parsed.<a class="code hl_variable" href="structgridfire_1_1io_1_1_parsed_network_data.html#a5145c672877638e6113abf1f719b246d">reactionPENames</a>.size(), filename);</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <span class="keywordflow">return</span> parsed;</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> }</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="keywordflow">if</span> (line.empty()) {</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="keywordflow">continue</span>; <span class="comment">// Skip empty lines</span></div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> }</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> parsed.push_back(line);</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> }</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#acef7eafe3cbea159259f69c88d309b66">m_logger</a>, <span class="stringliteral">&quot;Parsed {} reactions from file: {}&quot;</span>, parsed.size(), filename);</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <span class="keywordflow">return</span> parsed;</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> }</div>
</div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span>}</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span>}</div>
<div class="ttc" id="aclassgridfire_1_1io_1_1_simple_reaction_list_file_parser_html_a4df01e3a93e1291d2cde0458545325f8"><div class="ttname"><a href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#a4df01e3a93e1291d2cde0458545325f8">gridfire::io::SimpleReactionListFileParser::parse</a></div><div class="ttdeci">ParsedNetworkData parse(const std::string &amp;filename) const override</div><div class="ttdoc">Parses a simple reaction list file.</div><div class="ttdef"><b>Definition</b> <a href="#l00044">network_file.cpp:44</a></div></div>
<div class="ttc" id="aclassgridfire_1_1io_1_1_simple_reaction_list_file_parser_html_acef7eafe3cbea159259f69c88d309b66"><div class="ttname"><a href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#acef7eafe3cbea159259f69c88d309b66">gridfire::io::SimpleReactionListFileParser::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00123">network_file.h:123</a></div></div>
<div class="ttc" id="aclassgridfire_1_1io_1_1_simple_reaction_list_file_parser_html_acef7eafe3cbea159259f69c88d309b66"><div class="ttname"><a href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#acef7eafe3cbea159259f69c88d309b66">gridfire::io::SimpleReactionListFileParser::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00107">network_file.h:107</a></div></div>
<div class="ttc" id="aclassgridfire_1_1io_1_1_simple_reaction_list_file_parser_html_afc8ed91e8c98205c505e3d9f0cff1993"><div class="ttname"><a href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#afc8ed91e8c98205c505e3d9f0cff1993">gridfire::io::SimpleReactionListFileParser::SimpleReactionListFileParser</a></div><div class="ttdeci">SimpleReactionListFileParser()</div><div class="ttdoc">Constructs a SimpleReactionListFileParser.</div><div class="ttdef"><b>Definition</b> <a href="#l00042">network_file.cpp:42</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1io_html"><div class="ttname"><a href="namespacegridfire_1_1io.html">gridfire::io</a></div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00011">network_file.h:11</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1io_html_abcbdcbd13cfa8c9fbe1b48e8ee2cc352"><div class="ttname"><a href="namespacegridfire_1_1io.html#abcbdcbd13cfa8c9fbe1b48e8ee2cc352">gridfire::io::ParsedNetworkData</a></div><div class="ttdeci">std::vector&lt; std::string &gt; ParsedNetworkData</div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00012">network_file.h:12</a></div></div>
<div class="ttc" id="anetwork__file_8h_html"><div class="ttname"><a href="network__file_8h.html">network_file.h</a></div></div>
<div class="ttc" id="astructgridfire_1_1io_1_1_parsed_network_data_html"><div class="ttname"><a href="structgridfire_1_1io_1_1_parsed_network_data.html">gridfire::io::ParsedNetworkData</a></div><div class="ttdoc">Holds the data parsed from a network file.</div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00020">network_file.h:20</a></div></div>
<div class="ttc" id="astructgridfire_1_1io_1_1_parsed_network_data_html_a5145c672877638e6113abf1f719b246d"><div class="ttname"><a href="structgridfire_1_1io_1_1_parsed_network_data.html#a5145c672877638e6113abf1f719b246d">gridfire::io::ParsedNetworkData::reactionPENames</a></div><div class="ttdeci">std::vector&lt; std::string &gt; reactionPENames</div><div class="ttdoc">A vector of reaction names in their PEN-style format.</div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00027">network_file.h:27</a></div></div>
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