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<a href="cafe__commands_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef CAFE_COMMANDS_H_B2201016_8693_4379_9225_8FFEC3562AFE</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#define CAFE_COMMANDS_H_B2201016_8693_4379_9225_8FFEC3562AFE</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="preprocessor">#include <vector></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include <iosfwd></span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> </div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="keyword">extern</span> <span class="stringliteral">"C"</span> {</div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include "<a class="code" href="family_8h.html">family.h</a>"</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> }</div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#a1d7bfdc8357f1dd1aab426ce78fb69e3">cafe_cmd_source</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, std::vector<std::string> tokens);</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#ac1ff1844757ace68bee073533a83a55a">cafe_cmd_list</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, std::vector<std::string> tokens);</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#a8b2fc001384e0d3c6b9be92650296efe">cafe_cmd_echo</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, std::vector<std::string> tokens);</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#a12e6bbaf64d232b049afc8320e618e12">cafe_cmd_date</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, std::vector<std::string> tokens);</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#a92f695a37bd42b626b1bd43c2daa2d7e">cafe_cmd_exit</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, std::vector<std::string> tokens);</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#a83bf15faf005ce18f8207893de62b2ce">cafe_cmd_gainloss</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, std::vector<std::string> tokens);</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#ac1ed4ef75f3a0677cea6a5f35fc0f83e">cafe_cmd_generate_random_family</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, std::vector<std::string> tokens);</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="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#aa8a41a2eb004f7f58059a2f76c1ae979">cafe_shell_dispatch_command</a>(<span class="keywordtype">char</span>* cmd);</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keywordtype">void</span> <a class="code" href="cafe__commands_8h.html#a2bfa532bad5b33246c667e1f7e8ddec5">list_commands</a>(std::ostream& ost);</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> std::vector<std::string> <a class="code" href="cafe__commands_8h.html#a84b7b60c6cfa36b6cadbc0cdc8845f7f">tokenize</a>(std::string s);</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="comment">// these functions should be moved to another file</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keywordtype">void</span> <a class="code" href="cafe__commands_8h.html#aa815aa35cb1ab8394c7107036deae1eb">clear_tree_viterbis</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> psum);</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#a1eef17676a8e71d3ece9e5d1b20bc7e8">get_num_trials</a>(std::vector<std::string> <a class="code" href="namespacemcl2rawcafe.html#afc88f4b3ae65b5f0a56d99a7b60d1b9a">args</a>);</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keywordtype">int</span> <a class="code" href="cafe__commands_8h.html#abc0614f4587f81c8eefb4c88270c031d">write_family_gainloss</a>(std::ostream& ofst, std::string family_id, <a class="code" href="structCafeTree.html">pCafeTree</a> tree1, <a class="code" href="structCafeTree.html">pCafeTree</a> tree2);</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="keywordtype">void</span> <a class="code" href="cafe__commands_8h.html#a42a737dbfebe0cedb89344f3c397923e">set_node_familysize</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> tree, <span class="keywordtype">int</span>** node_family_sizes, <span class="keywordtype">int</span> i);</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <a class="code" href="structArrayList.html">pArrayList</a> <a class="code" href="cafe__commands_8h.html#aeb6a15146efd70cce81611392a56e3e6">get_clusters</a>(<span class="keywordtype">int</span> parameterized_k_value, <span class="keywordtype">int</span> num_families, <span class="keywordtype">double</span>* k_weights);</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> </div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div><div class="ttc" id="cafe__commands_8h_html_ac1ed4ef75f3a0677cea6a5f35fc0f83e"><div class="ttname"><a href="cafe__commands_8h.html#ac1ed4ef75f3a0677cea6a5f35fc0f83e">cafe_cmd_generate_random_family</a></div><div class="ttdeci">int cafe_cmd_generate_random_family(pCafeParam param, std::vector< std::string > tokens)</div></div>
<div class="ttc" id="cafe__commands_8h_html_aa8a41a2eb004f7f58059a2f76c1ae979"><div class="ttname"><a href="cafe__commands_8h.html#aa8a41a2eb004f7f58059a2f76c1ae979">cafe_shell_dispatch_command</a></div><div class="ttdeci">int cafe_shell_dispatch_command(char *cmd)</div><div class="ttdef"><b>Definition:</b> cafe_commands.cpp:258</div></div>
<div class="ttc" id="cafe__commands_8h_html_aeb6a15146efd70cce81611392a56e3e6"><div class="ttname"><a href="cafe__commands_8h.html#aeb6a15146efd70cce81611392a56e3e6">get_clusters</a></div><div class="ttdeci">pArrayList get_clusters(int parameterized_k_value, int num_families, double *k_weights)</div><div class="ttdef"><b>Definition:</b> cafe_commands.cpp:384</div></div>
<div class="ttc" id="cafe__commands_8h_html_abc0614f4587f81c8eefb4c88270c031d"><div class="ttname"><a href="cafe__commands_8h.html#abc0614f4587f81c8eefb4c88270c031d">write_family_gainloss</a></div><div class="ttdeci">int write_family_gainloss(std::ostream &ofst, std::string family_id, pCafeTree tree1, pCafeTree tree2)</div></div>
<div class="ttc" id="cafe__commands_8h_html_a1eef17676a8e71d3ece9e5d1b20bc7e8"><div class="ttname"><a href="cafe__commands_8h.html#a1eef17676a8e71d3ece9e5d1b20bc7e8">get_num_trials</a></div><div class="ttdeci">int get_num_trials(std::vector< std::string > args)</div></div>
<div class="ttc" id="cafe__commands_8h_html_a12e6bbaf64d232b049afc8320e618e12"><div class="ttname"><a href="cafe__commands_8h.html#a12e6bbaf64d232b049afc8320e618e12">cafe_cmd_date</a></div><div class="ttdeci">int cafe_cmd_date(pCafeParam param, std::vector< std::string > tokens)</div></div>
<div class="ttc" id="cafe__commands_8h_html_aa815aa35cb1ab8394c7107036deae1eb"><div class="ttname"><a href="cafe__commands_8h.html#aa815aa35cb1ab8394c7107036deae1eb">clear_tree_viterbis</a></div><div class="ttdeci">void clear_tree_viterbis(pCafeTree psum)</div><div class="ttdef"><b>Definition:</b> cafe_commands.cpp:167</div></div>
<div class="ttc" id="cafe__commands_8h_html_a8b2fc001384e0d3c6b9be92650296efe"><div class="ttname"><a href="cafe__commands_8h.html#a8b2fc001384e0d3c6b9be92650296efe">cafe_cmd_echo</a></div><div class="ttdeci">int cafe_cmd_echo(pCafeParam param, std::vector< std::string > tokens)</div></div>
<div class="ttc" id="cafe__commands_8h_html_a84b7b60c6cfa36b6cadbc0cdc8845f7f"><div class="ttname"><a href="cafe__commands_8h.html#a84b7b60c6cfa36b6cadbc0cdc8845f7f">tokenize</a></div><div class="ttdeci">std::vector< std::string > tokenize(std::string s)</div></div>
<div class="ttc" id="cafe__commands_8h_html_a1d7bfdc8357f1dd1aab426ce78fb69e3"><div class="ttname"><a href="cafe__commands_8h.html#a1d7bfdc8357f1dd1aab426ce78fb69e3">cafe_cmd_source</a></div><div class="ttdeci">int cafe_cmd_source(pCafeParam param, std::vector< std::string > tokens)</div></div>
<div class="ttc" id="namespacemcl2rawcafe_html_afc88f4b3ae65b5f0a56d99a7b60d1b9a"><div class="ttname"><a href="namespacemcl2rawcafe.html#afc88f4b3ae65b5f0a56d99a7b60d1b9a">mcl2rawcafe.args</a></div><div class="ttdeci">args</div><div class="ttdef"><b>Definition:</b> mcl2rawcafe.py:48</div></div>
<div class="ttc" id="structtagCafeParam_html"><div class="ttname"><a href="structtagCafeParam.html">tagCafeParam</a></div><div class="ttdoc">Singleton structure that holds all of the global data that Cafe acts on. </div><div class="ttdef"><b>Definition:</b> family.h:95</div></div>
<div class="ttc" id="structArrayList_html"><div class="ttname"><a href="structArrayList.html">ArrayList</a></div><div class="ttdef"><b>Definition:</b> utils.h:11</div></div>
<div class="ttc" id="cafe__commands_8h_html_a83bf15faf005ce18f8207893de62b2ce"><div class="ttname"><a href="cafe__commands_8h.html#a83bf15faf005ce18f8207893de62b2ce">cafe_cmd_gainloss</a></div><div class="ttdeci">int cafe_cmd_gainloss(pCafeParam param, std::vector< std::string > tokens)</div></div>
<div class="ttc" id="cafe__commands_8h_html_a42a737dbfebe0cedb89344f3c397923e"><div class="ttname"><a href="cafe__commands_8h.html#a42a737dbfebe0cedb89344f3c397923e">set_node_familysize</a></div><div class="ttdeci">void set_node_familysize(pCafeTree tree, int **node_family_sizes, int i)</div><div class="ttdef"><b>Definition:</b> cafe_commands.cpp:172</div></div>
<div class="ttc" id="cafe__commands_8h_html_ac1ff1844757ace68bee073533a83a55a"><div class="ttname"><a href="cafe__commands_8h.html#ac1ff1844757ace68bee073533a83a55a">cafe_cmd_list</a></div><div class="ttdeci">int cafe_cmd_list(pCafeParam param, std::vector< std::string > tokens)</div></div>
<div class="ttc" id="cafe__commands_8h_html_a92f695a37bd42b626b1bd43c2daa2d7e"><div class="ttname"><a href="cafe__commands_8h.html#a92f695a37bd42b626b1bd43c2daa2d7e">cafe_cmd_exit</a></div><div class="ttdeci">int cafe_cmd_exit(pCafeParam param, std::vector< std::string > tokens)</div></div>
<div class="ttc" id="family_8h_html"><div class="ttname"><a href="family_8h.html">family.h</a></div></div>
<div class="ttc" id="structCafeTree_html"><div class="ttname"><a href="structCafeTree.html">CafeTree</a></div><div class="ttdef"><b>Definition:</b> family.h:8</div></div>
<div class="ttc" id="cafe__commands_8h_html_a2bfa532bad5b33246c667e1f7e8ddec5"><div class="ttname"><a href="cafe__commands_8h.html#a2bfa532bad5b33246c667e1f7e8ddec5">list_commands</a></div><div class="ttdeci">void list_commands(std::ostream &ost)</div><div class="ttdef"><b>Definition:</b> cafe_commands.cpp:134</div></div>
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