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<a href="cafe_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_TREE_H__</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#define __CAFE_TREE_H__</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<<a class="code" href="family_8h.html">family.h</a>></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include<<a class="code" href="gmatrix_8h.html">gmatrix.h</a>></span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include <<a class="code" href="chooseln__cache_8h.html">chooseln_cache.h</a>></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"><a class="line" href="structCafeFamilyItem.html"> 8</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</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"><a class="line" href="structCafeFamilyItem.html#a54820da0a69b82325b4f0674190acbb3"> 10</a></span>  <span class="keywordtype">char</span>* <a class="code" href="structCafeFamilyItem.html#a54820da0a69b82325b4f0674190acbb3">id</a>;</div><div class="line"><a name="l00011"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#aee6335126c3badcb9c769842f8fc9de3"> 11</a></span>  <span class="keywordtype">int</span>* <a class="code" href="structCafeFamilyItem.html#aee6335126c3badcb9c769842f8fc9de3">count</a>;</div><div class="line"><a name="l00012"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#a5cd05a08a1d10c93ccee1c81422a7e3e"> 12</a></span>  <span class="keywordtype">char</span>* <a class="code" href="structCafeFamilyItem.html#a5cd05a08a1d10c93ccee1c81422a7e3e">desc</a>;</div><div class="line"><a name="l00013"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#a392c3dd4b13f840d08b691026b1a2c80"> 13</a></span>  <span class="keywordtype">int</span> <a class="code" href="structCafeFamilyItem.html#a392c3dd4b13f840d08b691026b1a2c80">maxlh</a>;</div><div class="line"><a name="l00014"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#a2622c49f6ade1c226b01015d1c502be6"> 14</a></span>  <span class="keywordtype">int</span> <a class="code" href="structCafeFamilyItem.html#a2622c49f6ade1c226b01015d1c502be6">ref</a>;</div><div class="line"><a name="l00015"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#aceb0544cc984588d0a569865f71ce0f3"> 15</a></span>  <span class="keywordtype">double</span>* <a class="code" href="structCafeFamilyItem.html#aceb0544cc984588d0a569865f71ce0f3">lambda</a>;</div><div class="line"><a name="l00016"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#a44e45d1dec5d5927b6811af6512366c7"> 16</a></span>  <span class="keywordtype">double</span>* <a class="code" href="structCafeFamilyItem.html#a44e45d1dec5d5927b6811af6512366c7">mu</a>;</div><div class="line"><a name="l00017"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#a308e63724aea49bb9e5126fb972766d5"> 17</a></span>  <span class="keywordtype">double</span>* <a class="code" href="structCafeFamilyItem.html#a308e63724aea49bb9e5126fb972766d5">z_membership</a>;</div><div class="line"><a name="l00018"></a><span class="lineno"><a class="line" href="structCafeFamilyItem.html#a48e400ddb19b19bed1b92f3e8fa17cf5"> 18</a></span>  <span class="keywordtype">int</span> <a class="code" href="structCafeFamilyItem.html#a48e400ddb19b19bed1b92f3e8fa17cf5">holder</a>;</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> }<a class="code" href="structCafeFamilyItem.html">CafeFamilyItem</a>;</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"><a class="line" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93"> 21</a></span> <span class="keyword">typedef</span> <a class="code" href="structCafeFamilyItem.html">CafeFamilyItem</a>* <a class="code" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a>;</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> </div><div class="line"><a name="l00024"></a><span class="lineno"><a class="line" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4"> 24</a></span> <span class="keyword">typedef</span> <span class="keyword">enum</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> {</div><div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4af665c1b9f44643486f81aa6d78ac8957"> 26</a></span>  <a class="code" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4af665c1b9f44643486f81aa6d78ac8957">CAFE_REPORT_TEXT</a> = 0,</div><div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a1ad4b84850cdafe9597dd8000dc7f248"> 27</a></span>  <a class="code" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a1ad4b84850cdafe9597dd8000dc7f248">CAFE_REPORT_HTML</a>,</div><div class="line"><a name="l00028"></a><span class="lineno"><a class="line" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a8c91521fc74032cd1d6013092f96a3dd"> 28</a></span>  <a class="code" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a8c91521fc74032cd1d6013092f96a3dd">CAFE_REPORT_PDF</a>,</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> }<a class="code" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4">enumCafeReport</a>;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">/****************************************************************************</span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment"> * Cafe Tree</span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">****************************************************************************/</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="cafe_8h.html#af1e282522a8c75ed3ea3a186ccbba962">cafe_get_posterior</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="cafe_8h.html#af9ae3976765e29062e2d678af52322da">cafe_set_prior_rfsize_empirical</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">extern</span> <a class="code" href="structCafeTree.html">pCafeTree</a> <a class="code" href="cafe_8h.html#ab108f5d959d962bcfea2cbaab0a9fd10">cafe_tree_new</a>(<span class="keywordtype">char</span>* sztree, <span class="keywordtype">int</span> familysizes[], <span class="keywordtype">int</span> rootfamilysizes[], <span class="keywordtype">double</span> lambda, <span class="keywordtype">double</span> mu);</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">extern</span> <a class="code" href="structtagTreeNode.html">pTreeNode</a> <a class="code" href="cafe_8h.html#abf94be4e512caec06b7bbe6391c054a5">cafe_tree_new_empty_node</a>(<a class="code" href="structtagTree.html">pTree</a> pcafe);</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a4a9ceeeaec1f37178a4ad6519f815ad6">cafe_tree_set_parameters</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <span class="keywordtype">int</span> familysizes[], <span class="keywordtype">int</span> rootfamilysizes[], <span class="keywordtype">double</span> lambda);</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">extern</span> <a class="code" href="structCafeTree.html">pCafeTree</a> <a class="code" href="cafe_8h.html#aaacc74335f3e18b9aae2dce03ca3ba95">cafe_tree_copy</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> psrc);</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">extern</span> <a class="code" href="structCafeTree.html">pCafeTree</a> <a class="code" href="cafe_8h.html#a59a369f120ab05629245fb707dabe441">cafe_tree_split</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <span class="keywordtype">int</span> idx );</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a399b895da5463457ea8dcd62b31131dd">cafe_tree_free</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a4451115a25f07ac5f3e52d75e71d25d5">__cafe_tree_free_node</a>(<a class="code" href="structtagTree.html">pTree</a> ptree, <a class="code" href="structtagTreeNode.html">pTreeNode</a> ptnode, va_list ap);</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a311afa341f0108d84af1366cec16779c">cafe_tree_string_name</a>(<a class="code" href="structString.html">pString</a> pstr, <a class="code" href="structtagPhylogenyNode.html">pPhylogenyNode</a> ptnode);</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">extern</span> <a class="code" href="structString.html">pString</a> <a class="code" href="cafe_8h.html#a539b2a7307047507d08628f9232dbf8a">cafe_tree_string_with_lambda</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">extern</span> <a class="code" href="structString.html">pString</a> <a class="code" href="cafe_8h.html#ad446b2b7910dffecb400baa082f1c3ff">cafe_tree_string_with_id</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">extern</span> <a class="code" href="structString.html">pString</a> <a class="code" href="cafe_8h.html#a9a17222518181cb6ac05c07aaf5e24ca">cafe_tree_string</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">extern</span> <a class="code" href="structString.html">pString</a> <a class="code" href="cafe_8h.html#a2b97ef12468c64ad91fe9ee06a225e4b">cafe_tree_string_with_familysize_lambda</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">extern</span> <a class="code" href="structString.html">pString</a> <a class="code" href="cafe_8h.html#a75e35397e2535cef3466c37ab9c2cb8f">cafe_tree_string_with_familysize</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a9ef8856ece7dbaba92fde32c4107a72c">cafe_tree_string_print</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a6f3c8e11014de17b334ac29067126bd8">__cafe_tree_node_compute_likelihood</a>(<a class="code" href="structtagTree.html">pTree</a> ptree, <a class="code" href="structtagTreeNode.html">pTreeNode</a> ptnode, va_list ap1);</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#af9688d286dddb037fabf069aa7209b86">compute_internal_node_likelihood</a>(<a class="code" href="structtagTree.html">pTree</a> ptree, <a class="code" href="structtagTreeNode.html">pTreeNode</a> ptnode, <span class="keyword">struct</span> <a class="code" href="structchooseln__cache.html">chooseln_cache</a> *<a class="code" href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">cache</a>);</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a513624edfd78aba059fa55835275f11d">compute_leaf_node_likelihood</a>(<a class="code" href="structtagTree.html">pTree</a> ptree, <a class="code" href="structtagTreeNode.html">pTreeNode</a> ptnode);</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a64a3240a3e126af2fed45b08cde3d2c0">compute_likelihood</a>(<a class="code" href="structtagTree.html">pTree</a> ptree, <a class="code" href="structtagTreeNode.html">pTreeNode</a> ptnode, <span class="keyword">struct</span> <a class="code" href="structchooseln__cache.html">chooseln_cache</a>* <a class="code" href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">cache</a>);</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* <a class="code" href="cafe_8h.html#a0e6b1095efd5b1cbccf38139848de2f5">cafe_tree_likelihood</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a376f0defba082c9243fe89ccb93de0fa">cafe_tree_node_free_clustered_likelihoods</a> (<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>** <a class="code" href="cafe_8h.html#a15e83cea0140d989624ca021fc1316ee">cafe_tree_clustered_likelihood</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe); </div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#ad797e3a6bd04c8fcaab1209548b4f5ef">cafe_tree_viterbi</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#ae7993697889a09c5f071cf1fa7563da1">cafe_tree_clustered_viterbi</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a86b7d92c6d9843ce4010340025eecf42">cafe_tree_viterbi_posterior</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* <a class="code" href="cafe_8h.html#a2890c7c910b5839063244d54b5896dd3">cafe_tree_random_probabilities</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <span class="keywordtype">int</span> rootFamilysize, <span class="keywordtype">int</span> trials );</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* <a class="code" href="cafe_8h.html#a0b50a33f038ffa9a07ce30621f2cac77">cafe_tree_p_values</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <span class="keywordtype">double</span>* p, <a class="code" href="structArrayList.html">pArrayList</a> pconddist, <span class="keywordtype">int</span> cdlen);</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>** <a class="code" href="cafe_8h.html#a31b86ce1fc4f0db908fe9fa7fc7fb2f3">cafe_tree_p_values_of_two_trees</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe1, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe2, </div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordtype">double</span>** p,</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <a class="code" href="structArrayList.html">pArrayList</a> pconddist1, <a class="code" href="structArrayList.html">pArrayList</a> pconddist2,</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">int</span> cdlen );</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keyword">extern</span> <a class="code" href="structtagCafeParam.html">pCafeParam</a> <a class="code" href="cafe_8h.html#a0a54e602c59702bd6cc844332b6c2a7a">cafe_copy_parameters</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> psrc);</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a72db0fc19498016c5023420f510bad9c">cafe_free_copy_parameters</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <a class="code" href="structArrayList.html">pArrayList</a> <a class="code" href="cafe_8h.html#a45d46d04142f35bd3b8ad2b106719976">cafe_tree_conditional_distribution</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <span class="keywordtype">int</span> range_start, <span class="keywordtype">int</span> range_end, <span class="keywordtype">int</span> num_trials);</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="cafe_8h.html#a06ef016855f349979f4cef37ac196b1d">cafe_tree_mp_remark</a>(<a class="code" href="structString.html">pString</a> <a class="code" href="namespacemcl2rawcafe.html#af780bb55a0996190d3f4b1f0a89fa48d">str</a>, <a class="code" href="structtagTree.html">pTree</a> ptree, <a class="code" href="structtagMetapostConfig.html">pMetapostConfig</a> pmc, va_list ap);</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="cafe_8h.html#a583f3346ac4cd4ac0da2d295ab798631">cafe_tree_mp_annotation</a>(<a class="code" href="structString.html">pString</a> <a class="code" href="namespacemcl2rawcafe.html#af780bb55a0996190d3f4b1f0a89fa48d">str</a>, <a class="code" href="structtagTreeNode.html">pTreeNode</a> pnode, <a class="code" href="structtagMetapostConfig.html">pMetapostConfig</a> pmc, va_list ap);</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="keyword">extern</span> <a class="code" href="structtagMetapostConfig.html">pMetapostConfig</a> <a class="code" href="cafe_8h.html#a5095cbb3b4652801b2da11512d0aadb0">cafe_tree_get_default_mpconfig</a>(<span class="keywordtype">int</span> <span class="keywordtype">id</span>, <span class="keywordtype">double</span> width, <span class="keywordtype">double</span> height );</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="keyword">extern</span> <a class="code" href="structString.html">pString</a> <a class="code" href="cafe_8h.html#ab02dad48034bd27652cf2d011b71e98e">cafe_tree_metapost</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <span class="keywordtype">int</span> <span class="keywordtype">id</span>, <span class="keywordtype">char</span>* title, <span class="keywordtype">double</span> width, <span class="keywordtype">double</span> height);</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="cafe_8h.html#ab203b685b05382fbb18d1dd78f81fafb">cafe_tree_random_familysize</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe, <span class="keywordtype">int</span> rootFamilysize );</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="comment">/****************************************************************************</span></div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="comment"> * Cafe Family</span></div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="comment">****************************************************************************/</span></div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <a class="code" href="structCafeFamily.html">pCafeFamily</a> <a class="code" href="cafe_8h.html#ac14285c2a2a32972442da6f3e6503e7a">cafe_family_init</a>(<a class="code" href="structArrayList.html">pArrayList</a> data);</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a8040846f0c636e51a56193028a1ff59c">cafe_family_add_item</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <a class="code" href="structArrayList.html">pArrayList</a> data);</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="keyword">extern</span> <a class="code" href="structCafeFamily.html">pCafeFamily</a> <a class="code" href="cafe_8h.html#a5551576d8d41b117a0b48b346a96fece">cafe_family_new</a>(<span class="keywordtype">char</span>* file, <span class="keywordtype">int</span> bpatcheck);</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a2b38ef57e2463389db47965232c5ac98">cafe_family_item_free</a>(<a class="code" href="structCafeFamilyItem.html">pCafeFamilyItem</a> pitem );</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a5c952ff06eb0153eb4021557da22005d">cafe_family_free</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf);</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#ad44ab3a046a4ffa4ea72ccbb024a83c1">cafe_family_set_size</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">int</span> idx, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="cafe_8h.html#a5d2f54e37c36caf8d59811800f4f559b">cafe_family_set_species_index</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe );</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="cafe_8h.html#ab4b6f407abda4eaea384743c2b1f9a02">cafe_family_get_species_index</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">char</span>* speciesname); </div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a26c9f424ab9c48359becc47840ec6776">cafe_family_set_size_for_split</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">int</span> idx, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a671e8a36c74d72e2f7e9427ef48e0418">cafe_family_set_size_with_family</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">int</span> idx, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe );</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a1d18390e5a79329e67b3278e174c473d">cafe_family_set_truesize_with_family</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">int</span> idx, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe );</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a3f6a9deb3b221594e1357c270c3e31f4">cafe_family_set_size_by_species</a>(<span class="keywordtype">char</span>* speciesname, <span class="keywordtype">int</span> size, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="cafe_8h.html#aadf7360c79f3684e025281f746be2c6e">cafe_family_get_index</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">char</span>* szid);</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> <span class="keyword">extern</span> <a class="code" href="structCafeFamilyItem.html">pCafeFamilyItem</a> <a class="code" href="cafe_8h.html#ad87d747e20a51592e6ce2920b32632c3">cafe_family_get_family_item</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">char</span>* szid );</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#acb02e7cc3e369942626ca994ff0c823d">cafe_family_set_size_with_family_forced</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf, <span class="keywordtype">int</span> idx, <a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a3c807482b5b5d8c827b53fcd6b55c29f">cafe_family_filter</a>( <a class="code" href="structtagCafeParam.html">pCafeParam</a> param );</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="cafe_8h.html#ae881b40f3dab7d87a0db2d6bfb74653f">cafe_family_print_cluster_membership</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#ae3f218b4542078f06e79492ffa8f42e7">cafe_family_reset_maxlh</a>(<a class="code" href="structCafeFamily.html">pCafeFamily</a> pcf);</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a9a579f7aa906dda3855e76e0c966bace">cafe_family_read_validate_species</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">char</span>* file);</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="cafe_8h.html#ac195a0fc4ae61c03289db9cd8da09a63">cafe_family_split_cvfiles_byfamily</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a3d85789c6ea2856d46189f9c9fa1d646">cafe_family_clean_cvfiles_byfamily</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#afba87dc49ad3f7b86e5306b9c7ea5208">cafe_family_split_cvfiles_byspecies</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a77b40a8fbd5a7221a2b3003ba8317b7f">cafe_family_clean_cvfiles_byspecies</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param); </div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a5676d8efaccbc638b19e6028ab859e34">cafe_family_read_query_family</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">char</span>* file);</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> </div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> <span class="comment">/****************************************************************************</span></div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="comment"> * Cafe Main</span></div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="comment">****************************************************************************/</span></div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a41fd4a22d96314d20f0c9192c6f02339">cafe_log</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keyword">const</span> <span class="keywordtype">char</span>* msg, ... );</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#aeb4ab292a60df57301d00e11cfd01822">cafe_set_birthdeath_cache</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a41e16620ee39f8c3fcfcdfce15f8f874">cafe_set_birthdeath_cache_thread</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> tree, <span class="keywordtype">int</span> k_value, <span class="keywordtype">int</span>* family_sizes, <span class="keywordtype">int</span>* rootfamily_sizes);</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* <a class="code" href="cafe_8h.html#a6276b68a56c6403d815d512080dc46a4">cafe_best_lambda_by_fminsearch</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">int</span> lambda_len, <span class="keywordtype">int</span> k);</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* <a class="code" href="cafe_8h.html#ac44e4ab06944b45e4a1cfd923c8eb9cb">cafe_best_lambda_mu_by_fminsearch</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">int</span> lambda_len, <span class="keywordtype">int</span> mu_len, <span class="keywordtype">int</span> k );</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* <a class="code" href="cafe_8h.html#a60fc1de991d240a8cb40ab7a98a06a91">cafe_best_lambda_mu_eqbg_by_fminsearch</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">int</span> lambda_len, <span class="keywordtype">int</span> mu_len );</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* <a class="code" href="cafe_8h.html#abc6a1f95000e9407117ed11904be6864">cafe_each_best_lambda_by_fminsearch</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">int</span> lambda_len );</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#ad5b326684624583b7c4274b9dd36b048">cafe_report</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">int</span> method);</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="keyword">extern</span> <a class="code" href="structArrayList.html">pArrayList</a> <a class="code" href="cafe_8h.html#a28b01083e12d908b4a3d54a7d1d02726">cafe_conditional_distribution</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#a4a269c2694070c23c8dd643d7bf219e1">cafe_lambda_set_default</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">double</span>* lambda);</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> </div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#af2ed23d5716b6075fa222a6b6cf326a8">cafe_free_birthdeath_cache</a>(<a class="code" href="structCafeTree.html">pCafeTree</a> pcafe);</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="keyword">extern</span> <a class="code" href="structArrayList.html">pArrayList</a> <a class="code" href="cafe_8h.html#a50a8afe408546920e6a0920cec164ed2">cafe_viterbi</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <a class="code" href="structArrayList.html">pArrayList</a> pCD);</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#adf53bc2a22b3f10d28b5bf5c226b371d">cafe_branch_cutting</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="cafe_8h.html#abc9d347c972a12d7a86277efdd4c6b9d">cafe_likelihood_ratio_test</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="keyword">extern</span> <a class="code" href="structGMatrix.html">pGMatrix</a> <a class="code" href="cafe_8h.html#a40e1fa38255505c9a57ad590afed6ddb">cafe_lambda_distribution</a>(<a class="code" href="structtagCafeParam.html">pCafeParam</a> param, <span class="keywordtype">int</span> numrange, <span class="keywordtype">double</span>** range );</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="cafe_8h.html#a1f28d19d9122353dbfba5f4091368a8e">cafe_report_retrieve_data</a>(<span class="keywordtype">char</span>* file, <a class="code" href="structtagCafeParam.html">pCafeParam</a> param);</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="preprocessor">#endif</span></div><div class="ttc" id="structCafeFamilyItem_html_a48e400ddb19b19bed1b92f3e8fa17cf5"><div class="ttname"><a href="structCafeFamilyItem.html#a48e400ddb19b19bed1b92f3e8fa17cf5">CafeFamilyItem::holder</a></div><div class="ttdeci">int holder</div><div class="ttdef"><b>Definition:</b> cafe.h:18</div></div>
<div class="ttc" id="structCafeFamilyItem_html_a308e63724aea49bb9e5126fb972766d5"><div class="ttname"><a href="structCafeFamilyItem.html#a308e63724aea49bb9e5126fb972766d5">CafeFamilyItem::z_membership</a></div><div class="ttdeci">double * z_membership</div><div class="ttdef"><b>Definition:</b> cafe.h:17</div></div>
<div class="ttc" id="structCafeFamilyItem_html_a54820da0a69b82325b4f0674190acbb3"><div class="ttname"><a href="structCafeFamilyItem.html#a54820da0a69b82325b4f0674190acbb3">CafeFamilyItem::id</a></div><div class="ttdeci">char * id</div><div class="ttdef"><b>Definition:</b> cafe.h:10</div></div>
<div class="ttc" id="cafe_8h_html_a2890c7c910b5839063244d54b5896dd3"><div class="ttname"><a href="cafe_8h.html#a2890c7c910b5839063244d54b5896dd3">cafe_tree_random_probabilities</a></div><div class="ttdeci">double * cafe_tree_random_probabilities(pCafeTree pcafe, int rootFamilysize, int trials)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1333</div></div>
<div class="ttc" id="cafe_8h_html_a5095cbb3b4652801b2da11512d0aadb0"><div class="ttname"><a href="cafe_8h.html#a5095cbb3b4652801b2da11512d0aadb0">cafe_tree_get_default_mpconfig</a></div><div class="ttdeci">pMetapostConfig cafe_tree_get_default_mpconfig(int id, double width, double height)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:307</div></div>
<div class="ttc" id="cafe_8h_html_a8040846f0c636e51a56193028a1ff59c"><div class="ttname"><a href="cafe_8h.html#a8040846f0c636e51a56193028a1ff59c">cafe_family_add_item</a></div><div class="ttdeci">void cafe_family_add_item(pCafeFamily pcf, pArrayList data)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:450</div></div>
<div class="ttc" id="cafe_8h_html_abf94be4e512caec06b7bbe6391c054a5"><div class="ttname"><a href="cafe_8h.html#abf94be4e512caec06b7bbe6391c054a5">cafe_tree_new_empty_node</a></div><div class="ttdeci">pTreeNode cafe_tree_new_empty_node(pTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:11</div></div>
<div class="ttc" id="cafe_8h_html_a399b895da5463457ea8dcd62b31131dd"><div class="ttname"><a href="cafe_8h.html#a399b895da5463457ea8dcd62b31131dd">cafe_tree_free</a></div><div class="ttdeci">void cafe_tree_free(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:149</div></div>
<div class="ttc" id="cafe_8h_html_a50a8afe408546920e6a0920cec164ed2"><div class="ttname"><a href="cafe_8h.html#a50a8afe408546920e6a0920cec164ed2">cafe_viterbi</a></div><div class="ttdeci">pArrayList cafe_viterbi(pCafeParam param, pArrayList pCD)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:1297</div></div>
<div class="ttc" id="cafe_8h_html_abc9d347c972a12d7a86277efdd4c6b9d"><div class="ttname"><a href="cafe_8h.html#abc9d347c972a12d7a86277efdd4c6b9d">cafe_likelihood_ratio_test</a></div><div class="ttdeci">void cafe_likelihood_ratio_test(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:1610</div></div>
<div class="ttc" id="cafe_8h_html_a1d18390e5a79329e67b3278e174c473d"><div class="ttname"><a href="cafe_8h.html#a1d18390e5a79329e67b3278e174c473d">cafe_family_set_truesize_with_family</a></div><div class="ttdeci">void cafe_family_set_truesize_with_family(pCafeFamily pcf, int idx, pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:698</div></div>
<div class="ttc" id="cafe_8h_html_ad87d747e20a51592e6ce2920b32632c3"><div class="ttname"><a href="cafe_8h.html#ad87d747e20a51592e6ce2920b32632c3">cafe_family_get_family_item</a></div><div class="ttdeci">pCafeFamilyItem cafe_family_get_family_item(pCafeFamily pcf, char *szid)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:784</div></div>
<div class="ttc" id="structCafeFamilyItem_html_a392c3dd4b13f840d08b691026b1a2c80"><div class="ttname"><a href="structCafeFamilyItem.html#a392c3dd4b13f840d08b691026b1a2c80">CafeFamilyItem::maxlh</a></div><div class="ttdeci">int maxlh</div><div class="ttdef"><b>Definition:</b> cafe.h:13</div></div>
<div class="ttc" id="cafe_8h_html_a64a3240a3e126af2fed45b08cde3d2c0"><div class="ttname"><a href="cafe_8h.html#a64a3240a3e126af2fed45b08cde3d2c0">compute_likelihood</a></div><div class="ttdeci">void compute_likelihood(pTree ptree, pTreeNode ptnode, struct chooseln_cache *cache)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:767</div></div>
<div class="ttc" id="cafe_8h_html_a941d27c486c2ae1ffb39a864a7ec5cc4a8c91521fc74032cd1d6013092f96a3dd"><div class="ttname"><a href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a8c91521fc74032cd1d6013092f96a3dd">CAFE_REPORT_PDF</a></div><div class="ttdef"><b>Definition:</b> cafe.h:28</div></div>
<div class="ttc" id="cafe_8h_html_a311afa341f0108d84af1366cec16779c"><div class="ttname"><a href="cafe_8h.html#a311afa341f0108d84af1366cec16779c">cafe_tree_string_name</a></div><div class="ttdeci">void cafe_tree_string_name(pString pstr, pPhylogenyNode ptnode)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:176</div></div>
<div class="ttc" id="cafe_8h_html_a2b38ef57e2463389db47965232c5ac98"><div class="ttname"><a href="cafe_8h.html#a2b38ef57e2463389db47965232c5ac98">cafe_family_item_free</a></div><div class="ttdeci">void cafe_family_item_free(pCafeFamilyItem pitem)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:523</div></div>
<div class="ttc" id="structGMatrix_html"><div class="ttname"><a href="structGMatrix.html">GMatrix</a></div><div class="ttdef"><b>Definition:</b> gmatrix.h:4</div></div>
<div class="ttc" id="cafe_8h_html_adf53bc2a22b3f10d28b5bf5c226b371d"><div class="ttname"><a href="cafe_8h.html#adf53bc2a22b3f10d28b5bf5c226b371d">cafe_branch_cutting</a></div><div class="ttdeci">void cafe_branch_cutting(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:1438</div></div>
<div class="ttc" id="cafe_8h_html_a941d27c486c2ae1ffb39a864a7ec5cc4a1ad4b84850cdafe9597dd8000dc7f248"><div class="ttname"><a href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a1ad4b84850cdafe9597dd8000dc7f248">CAFE_REPORT_HTML</a></div><div class="ttdef"><b>Definition:</b> cafe.h:27</div></div>
<div class="ttc" id="structString_html"><div class="ttname"><a href="structString.html">String</a></div><div class="ttdef"><b>Definition:</b> utils_string.h:12</div></div>
<div class="ttc" id="cafe_8h_html_a59a369f120ab05629245fb707dabe441"><div class="ttname"><a href="cafe_8h.html#a59a369f120ab05629245fb707dabe441">cafe_tree_split</a></div><div class="ttdeci">pCafeTree cafe_tree_split(pCafeTree pcafe, int idx)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1277</div></div>
<div class="ttc" id="cafe_8h_html_a5676d8efaccbc638b19e6028ab859e34"><div class="ttname"><a href="cafe_8h.html#a5676d8efaccbc638b19e6028ab859e34">cafe_family_read_query_family</a></div><div class="ttdeci">void cafe_family_read_query_family(pCafeParam param, char *file)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:314</div></div>
<div class="ttc" id="structCafeFamilyItem_html_a44e45d1dec5d5927b6811af6512366c7"><div class="ttname"><a href="structCafeFamilyItem.html#a44e45d1dec5d5927b6811af6512366c7">CafeFamilyItem::mu</a></div><div class="ttdeci">double * mu</div><div class="ttdef"><b>Definition:</b> cafe.h:16</div></div>
<div class="ttc" id="cafe_8h_html_a40e1fa38255505c9a57ad590afed6ddb"><div class="ttname"><a href="cafe_8h.html#a40e1fa38255505c9a57ad590afed6ddb">cafe_lambda_distribution</a></div><div class="ttdeci">pGMatrix cafe_lambda_distribution(pCafeParam param, int numrange, double **range)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:121</div></div>
<div class="ttc" id="cafe_8h_html_a4451115a25f07ac5f3e52d75e71d25d5"><div class="ttname"><a href="cafe_8h.html#a4451115a25f07ac5f3e52d75e71d25d5">__cafe_tree_free_node</a></div><div class="ttdeci">void __cafe_tree_free_node(pTree ptree, pTreeNode ptnode, va_list ap)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:135</div></div>
<div class="ttc" id="structCafeFamilyItem_html_aceb0544cc984588d0a569865f71ce0f3"><div class="ttname"><a href="structCafeFamilyItem.html#aceb0544cc984588d0a569865f71ce0f3">CafeFamilyItem::lambda</a></div><div class="ttdeci">double * lambda</div><div class="ttdef"><b>Definition:</b> cafe.h:15</div></div>
<div class="ttc" id="cafe_8h_html_a4a9ceeeaec1f37178a4ad6519f815ad6"><div class="ttname"><a href="cafe_8h.html#a4a9ceeeaec1f37178a4ad6519f815ad6">cafe_tree_set_parameters</a></div><div class="ttdeci">void cafe_tree_set_parameters(pCafeTree pcafe, int familysizes[], int rootfamilysizes[], double lambda)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:24</div></div>
<div class="ttc" id="cafe_8h_html_ac44e4ab06944b45e4a1cfd923c8eb9cb"><div class="ttname"><a href="cafe_8h.html#ac44e4ab06944b45e4a1cfd923c8eb9cb">cafe_best_lambda_mu_by_fminsearch</a></div><div class="ttdeci">double * cafe_best_lambda_mu_by_fminsearch(pCafeParam param, int lambda_len, int mu_len, int k)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:851</div></div>
<div class="ttc" id="cafe_8h_html_a75e35397e2535cef3466c37ab9c2cb8f"><div class="ttname"><a href="cafe_8h.html#a75e35397e2535cef3466c37ab9c2cb8f">cafe_tree_string_with_familysize</a></div><div class="ttdeci">pString cafe_tree_string_with_familysize(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:230</div></div>
<div class="ttc" id="cafe_8h_html_a513624edfd78aba059fa55835275f11d"><div class="ttname"><a href="cafe_8h.html#a513624edfd78aba059fa55835275f11d">compute_leaf_node_likelihood</a></div><div class="ttdeci">void compute_leaf_node_likelihood(pTree ptree, pTreeNode ptnode)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:722</div></div>
<div class="ttc" id="cafe_8h_html_acb02e7cc3e369942626ca994ff0c823d"><div class="ttname"><a href="cafe_8h.html#acb02e7cc3e369942626ca994ff0c823d">cafe_family_set_size_with_family_forced</a></div><div class="ttdeci">void cafe_family_set_size_with_family_forced(pCafeFamily pcf, int idx, pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:650</div></div>
<div class="ttc" id="cafe_8h_html_a0e6b1095efd5b1cbccf38139848de2f5"><div class="ttname"><a href="cafe_8h.html#a0e6b1095efd5b1cbccf38139848de2f5">cafe_tree_likelihood</a></div><div class="ttdeci">double * cafe_tree_likelihood(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1151</div></div>
<div class="ttc" id="structCafeFamilyItem_html_a5cd05a08a1d10c93ccee1c81422a7e3e"><div class="ttname"><a href="structCafeFamilyItem.html#a5cd05a08a1d10c93ccee1c81422a7e3e">CafeFamilyItem::desc</a></div><div class="ttdeci">char * desc</div><div class="ttdef"><b>Definition:</b> cafe.h:12</div></div>
<div class="ttc" id="cafe_8h_html_a41fd4a22d96314d20f0c9192c6f02339"><div class="ttname"><a href="cafe_8h.html#a41fd4a22d96314d20f0c9192c6f02339">cafe_log</a></div><div class="ttdeci">void cafe_log(pCafeParam param, const char *msg,...)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:39</div></div>
<div class="ttc" id="cafe_8h_html_a2b97ef12468c64ad91fe9ee06a225e4b"><div class="ttname"><a href="cafe_8h.html#a2b97ef12468c64ad91fe9ee06a225e4b">cafe_tree_string_with_familysize_lambda</a></div><div class="ttdeci">pString cafe_tree_string_with_familysize_lambda(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:220</div></div>
<div class="ttc" id="cafe_8h_html_a0b50a33f038ffa9a07ce30621f2cac77"><div class="ttname"><a href="cafe_8h.html#a0b50a33f038ffa9a07ce30621f2cac77">cafe_tree_p_values</a></div><div class="ttdeci">double * cafe_tree_p_values(pCafeTree pcafe, double *p, pArrayList pconddist, int cdlen)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1386</div></div>
<div class="ttc" id="cafe_8h_html_ad446b2b7910dffecb400baa082f1c3ff"><div class="ttname"><a href="cafe_8h.html#ad446b2b7910dffecb400baa082f1c3ff">cafe_tree_string_with_id</a></div><div class="ttdeci">pString cafe_tree_string_with_id(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:235</div></div>
<div class="ttc" id="cafe_8h_html_af2ed23d5716b6075fa222a6b6cf326a8"><div class="ttname"><a href="cafe_8h.html#af2ed23d5716b6075fa222a6b6cf326a8">cafe_free_birthdeath_cache</a></div><div class="ttdeci">void cafe_free_birthdeath_cache(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:59</div></div>
<div class="ttc" id="cafe_8h_html_af9ae3976765e29062e2d678af52322da"><div class="ttname"><a href="cafe_8h.html#af9ae3976765e29062e2d678af52322da">cafe_set_prior_rfsize_empirical</a></div><div class="ttdeci">double cafe_set_prior_rfsize_empirical(pCafeParam param)</div><div class="ttdoc">set empirical prior on rootsize based on the assumption that rootsize follows leaf size distribution ...</div><div class="ttdef"><b>Definition:</b> cafe_main.c:491</div></div>
<div class="ttc" id="gmatrix_8h_html"><div class="ttname"><a href="gmatrix_8h.html">gmatrix.h</a></div></div>
<div class="ttc" id="cafe_8h_html_a60fc1de991d240a8cb40ab7a98a06a91"><div class="ttname"><a href="cafe_8h.html#a60fc1de991d240a8cb40ab7a98a06a91">cafe_best_lambda_mu_eqbg_by_fminsearch</a></div><div class="ttdeci">double * cafe_best_lambda_mu_eqbg_by_fminsearch(pCafeParam param, int lambda_len, int mu_len)</div></div>
<div class="ttc" id="cafe_8h_html_af9688d286dddb037fabf069aa7209b86"><div class="ttname"><a href="cafe_8h.html#af9688d286dddb037fabf069aa7209b86">compute_internal_node_likelihood</a></div><div class="ttdeci">void compute_internal_node_likelihood(pTree ptree, pTreeNode ptnode, struct chooseln_cache *cache)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:668</div></div>
<div class="ttc" id="cafe_8h_html_ad44ab3a046a4ffa4ea72ccbb024a83c1"><div class="ttname"><a href="cafe_8h.html#ad44ab3a046a4ffa4ea72ccbb024a83c1">cafe_family_set_size</a></div><div class="ttdeci">void cafe_family_set_size(pCafeFamily pcf, int idx, pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:626</div></div>
<div class="ttc" id="cafe_8h_html_ae3f218b4542078f06e79492ffa8f42e7"><div class="ttname"><a href="cafe_8h.html#ae3f218b4542078f06e79492ffa8f42e7">cafe_family_reset_maxlh</a></div><div class="ttdeci">void cafe_family_reset_maxlh(pCafeFamily pcf)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:761</div></div>
<div class="ttc" id="cafe_8h_html_a15e83cea0140d989624ca021fc1316ee"><div class="ttname"><a href="cafe_8h.html#a15e83cea0140d989624ca021fc1316ee">cafe_tree_clustered_likelihood</a></div><div class="ttdeci">double ** cafe_tree_clustered_likelihood(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1114</div></div>
<div class="ttc" id="cafe_8h_html_a45d46d04142f35bd3b8ad2b106719976"><div class="ttname"><a href="cafe_8h.html#a45d46d04142f35bd3b8ad2b106719976">cafe_tree_conditional_distribution</a></div><div class="ttdeci">pArrayList cafe_tree_conditional_distribution(pCafeTree pcafe, int range_start, int range_end, int num_trials)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1375</div></div>
<div class="ttc" id="namespacemcl2rawcafe_html_af780bb55a0996190d3f4b1f0a89fa48d"><div class="ttname"><a href="namespacemcl2rawcafe.html#af780bb55a0996190d3f4b1f0a89fa48d">mcl2rawcafe.str</a></div><div class="ttdeci">str</div><div class="ttdef"><b>Definition:</b> mcl2rawcafe.py:44</div></div>
<div class="ttc" id="cafe_8h_html_af1e282522a8c75ed3ea3a186ccbba962"><div class="ttname"><a href="cafe_8h.html#af1e282522a8c75ed3ea3a186ccbba962">cafe_get_posterior</a></div><div class="ttdeci">double cafe_get_posterior(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:174</div></div>
<div class="ttc" id="chooseln__cache_8h_html"><div class="ttname"><a href="chooseln__cache_8h.html">chooseln_cache.h</a></div></div>
<div class="ttc" id="cafe_8h_html_afba87dc49ad3f7b86e5306b9c7ea5208"><div class="ttname"><a href="cafe_8h.html#afba87dc49ad3f7b86e5306b9c7ea5208">cafe_family_split_cvfiles_byspecies</a></div><div class="ttdeci">void cafe_family_split_cvfiles_byspecies(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:218</div></div>
<div class="ttc" id="cafe_8h_html_a86b7d92c6d9843ce4010340025eecf42"><div class="ttname"><a href="cafe_8h.html#a86b7d92c6d9843ce4010340025eecf42">cafe_tree_viterbi_posterior</a></div><div class="ttdeci">void cafe_tree_viterbi_posterior(pCafeTree pcafe, pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:634</div></div>
<div class="ttc" id="cafe_8h_html_a941d27c486c2ae1ffb39a864a7ec5cc4"><div class="ttname"><a href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4">enumCafeReport</a></div><div class="ttdeci">enumCafeReport</div><div class="ttdef"><b>Definition:</b> cafe.h:24</div></div>
<div class="ttc" id="cafe_8h_html_a9ef8856ece7dbaba92fde32c4107a72c"><div class="ttname"><a href="cafe_8h.html#a9ef8856ece7dbaba92fde32c4107a72c">cafe_tree_string_print</a></div><div class="ttdeci">void cafe_tree_string_print(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:246</div></div>
<div class="ttc" id="structtagMetapostConfig_html"><div class="ttname"><a href="structtagMetapostConfig.html">tagMetapostConfig</a></div><div class="ttdef"><b>Definition:</b> tree.h:147</div></div>
<div class="ttc" id="cafe_8h_html_ad797e3a6bd04c8fcaab1209548b4f5ef"><div class="ttname"><a href="cafe_8h.html#ad797e3a6bd04c8fcaab1209548b4f5ef">cafe_tree_viterbi</a></div><div class="ttdeci">void cafe_tree_viterbi(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:584</div></div>
<div class="ttc" id="cafe_8h_html_aaacc74335f3e18b9aae2dce03ca3ba95"><div class="ttname"><a href="cafe_8h.html#aaacc74335f3e18b9aae2dce03ca3ba95">cafe_tree_copy</a></div><div class="ttdeci">pCafeTree cafe_tree_copy(pCafeTree psrc)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1266</div></div>
<div class="ttc" id="cafe_8h_html_a941d27c486c2ae1ffb39a864a7ec5cc4af665c1b9f44643486f81aa6d78ac8957"><div class="ttname"><a href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4af665c1b9f44643486f81aa6d78ac8957">CAFE_REPORT_TEXT</a></div><div class="ttdef"><b>Definition:</b> cafe.h:26</div></div>
<div class="ttc" id="cafe_8h_html_ad5b326684624583b7c4274b9dd36b048"><div class="ttname"><a href="cafe_8h.html#ad5b326684624583b7c4274b9dd36b048">cafe_report</a></div><div class="ttdeci">void cafe_report(pCafeParam param, int method)</div><div class="ttdef"><b>Definition:</b> cafe_report.c:306</div></div>
<div class="ttc" id="cafe_8h_html_a5551576d8d41b117a0b48b346a96fece"><div class="ttname"><a href="cafe_8h.html#a5551576d8d41b117a0b48b346a96fece">cafe_family_new</a></div><div class="ttdeci">pCafeFamily cafe_family_new(char *file, int bpatcheck)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:485</div></div>
<div class="ttc" id="structCafeFamilyItem_html"><div class="ttname"><a href="structCafeFamilyItem.html">CafeFamilyItem</a></div><div class="ttdef"><b>Definition:</b> cafe.h:8</div></div>
<div class="ttc" id="cafe_8h_html_a72db0fc19498016c5023420f510bad9c"><div class="ttname"><a href="cafe_8h.html#a72db0fc19498016c5023420f510bad9c">cafe_free_copy_parameters</a></div><div class="ttdeci">void cafe_free_copy_parameters(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:1666</div></div>
<div class="ttc" id="structchooseln__cache_html"><div class="ttname"><a href="structchooseln__cache.html">chooseln_cache</a></div><div class="ttdoc">A cache of values of chooseln. </div><div class="ttdef"><b>Definition:</b> chooseln_cache.h:14</div></div>
<div class="ttc" id="cafe_8h_html_aadf7360c79f3684e025281f746be2c6e"><div class="ttname"><a href="cafe_8h.html#aadf7360c79f3684e025281f746be2c6e">cafe_family_get_index</a></div><div class="ttdeci">int cafe_family_get_index(pCafeFamily pcf, char *szid)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:772</div></div>
<div class="ttc" id="cafe_8h_html_a0a54e602c59702bd6cc844332b6c2a7a"><div class="ttname"><a href="cafe_8h.html#a0a54e602c59702bd6cc844332b6c2a7a">cafe_copy_parameters</a></div><div class="ttdeci">pCafeParam cafe_copy_parameters(pCafeParam psrc)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:1648</div></div>
<div class="ttc" id="cafe_8h_html_ab02dad48034bd27652cf2d011b71e98e"><div class="ttname"><a href="cafe_8h.html#ab02dad48034bd27652cf2d011b71e98e">cafe_tree_metapost</a></div><div class="ttdeci">pString cafe_tree_metapost(pCafeTree pcafe, int id, char *title, double width, double height)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:321</div></div>
<div class="ttc" id="cafe_8h_html_a583f3346ac4cd4ac0da2d295ab798631"><div class="ttname"><a href="cafe_8h.html#a583f3346ac4cd4ac0da2d295ab798631">cafe_tree_mp_annotation</a></div><div class="ttdeci">double cafe_tree_mp_annotation(pString str, pTreeNode pnode, pMetapostConfig pmc, va_list ap)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:266</div></div>
<div class="ttc" id="cafe_8h_html_ae881b40f3dab7d87a0db2d6bfb74653f"><div class="ttname"><a href="cafe_8h.html#ae881b40f3dab7d87a0db2d6bfb74653f">cafe_family_print_cluster_membership</a></div><div class="ttdeci">int cafe_family_print_cluster_membership(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:1105</div></div>
<div class="ttc" id="cafe_8h_html_a376f0defba082c9243fe89ccb93de0fa"><div class="ttname"><a href="cafe_8h.html#a376f0defba082c9243fe89ccb93de0fa">cafe_tree_node_free_clustered_likelihoods</a></div><div class="ttdeci">void cafe_tree_node_free_clustered_likelihoods(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1093</div></div>
<div class="ttc" id="cafe_8h_html_ab108f5d959d962bcfea2cbaab0a9fd10"><div class="ttname"><a href="cafe_8h.html#ab108f5d959d962bcfea2cbaab0a9fd10">cafe_tree_new</a></div><div class="ttdeci">pCafeTree cafe_tree_new(char *sztree, int familysizes[], int rootfamilysizes[], double lambda, double mu)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:81</div></div>
<div class="ttc" id="cafe_8h_html_a26c9f424ab9c48359becc47840ec6776"><div class="ttname"><a href="cafe_8h.html#a26c9f424ab9c48359becc47840ec6776">cafe_family_set_size_for_split</a></div><div class="ttdeci">void cafe_family_set_size_for_split(pCafeFamily pcf, int idx, pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:791</div></div>
<div class="ttc" id="cafe_8h_html_a77b40a8fbd5a7221a2b3003ba8317b7f"><div class="ttname"><a href="cafe_8h.html#a77b40a8fbd5a7221a2b3003ba8317b7f">cafe_family_clean_cvfiles_byspecies</a></div><div class="ttdeci">void cafe_family_clean_cvfiles_byspecies(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:271</div></div>
<div class="ttc" id="cafe_8h_html_a4a269c2694070c23c8dd643d7bf219e1"><div class="ttname"><a href="cafe_8h.html#a4a269c2694070c23c8dd643d7bf219e1">cafe_lambda_set_default</a></div><div class="ttdeci">void cafe_lambda_set_default(pCafeParam param, double *lambda)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:106</div></div>
<div class="ttc" id="cafe_8h_html_ab203b685b05382fbb18d1dd78f81fafb"><div class="ttname"><a href="cafe_8h.html#ab203b685b05382fbb18d1dd78f81fafb">cafe_tree_random_familysize</a></div><div class="ttdeci">int cafe_tree_random_familysize(pCafeTree pcafe, int rootFamilysize)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1324</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="cafe_8h_html_a3c807482b5b5d8c827b53fcd6b55c29f"><div class="ttname"><a href="cafe_8h.html#a3c807482b5b5d8c827b53fcd6b55c29f">cafe_family_filter</a></div><div class="ttdeci">void cafe_family_filter(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:964</div></div>
<div class="ttc" id="cafe_8h_html_a31b86ce1fc4f0db908fe9fa7fc7fb2f3"><div class="ttname"><a href="cafe_8h.html#a31b86ce1fc4f0db908fe9fa7fc7fb2f3">cafe_tree_p_values_of_two_trees</a></div><div class="ttdeci">double ** cafe_tree_p_values_of_two_trees(pCafeTree pcafe1, pCafeTree pcafe2, double **p, pArrayList pconddist1, pArrayList pconddist2, int cdlen)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:1400</div></div>
<div class="ttc" id="birthdeath_8c_html_a018ffb515cded9e77be4179f12b3aca6"><div class="ttname"><a href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">cache</a></div><div class="ttdeci">struct chooseln_cache cache</div><div class="ttdef"><b>Definition:</b> birthdeath.c:18</div></div>
<div class="ttc" id="cafe_8h_html_a28b01083e12d908b4a3d54a7d1d02726"><div class="ttname"><a href="cafe_8h.html#a28b01083e12d908b4a3d54a7d1d02726">cafe_conditional_distribution</a></div><div class="ttdeci">pArrayList cafe_conditional_distribution(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:1151</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_8h_html_a539b2a7307047507d08628f9232dbf8a"><div class="ttname"><a href="cafe_8h.html#a539b2a7307047507d08628f9232dbf8a">cafe_tree_string_with_lambda</a></div><div class="ttdeci">pString cafe_tree_string_with_lambda(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:225</div></div>
<div class="ttc" id="structCafeFamilyItem_html_aee6335126c3badcb9c769842f8fc9de3"><div class="ttname"><a href="structCafeFamilyItem.html#aee6335126c3badcb9c769842f8fc9de3">CafeFamilyItem::count</a></div><div class="ttdeci">int * count</div><div class="ttdef"><b>Definition:</b> cafe.h:11</div></div>
<div class="ttc" id="cafe_8h_html_a5d2f54e37c36caf8d59811800f4f559b"><div class="ttname"><a href="cafe_8h.html#a5d2f54e37c36caf8d59811800f4f559b">cafe_family_set_species_index</a></div><div class="ttdeci">int cafe_family_set_species_index(pCafeFamily pcf, pCafeTree pcafe)</div><div class="ttdoc">Synchronize a family and tree together. </div><div class="ttdef"><b>Definition:</b> cafe_family.c:546</div></div>
<div class="ttc" id="cafe_8h_html_abc6a1f95000e9407117ed11904be6864"><div class="ttname"><a href="cafe_8h.html#abc6a1f95000e9407117ed11904be6864">cafe_each_best_lambda_by_fminsearch</a></div><div class="ttdeci">double * cafe_each_best_lambda_by_fminsearch(pCafeParam param, int lambda_len)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:1016</div></div>
<div class="ttc" id="structtagTree_html"><div class="ttname"><a href="structtagTree.html">tagTree</a></div><div class="ttdef"><b>Definition:</b> tree.h:11</div></div>
<div class="ttc" id="cafe_8h_html_ac195a0fc4ae61c03289db9cd8da09a63"><div class="ttname"><a href="cafe_8h.html#ac195a0fc4ae61c03289db9cd8da09a63">cafe_family_split_cvfiles_byfamily</a></div><div class="ttdeci">int cafe_family_split_cvfiles_byfamily(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:98</div></div>
<div class="ttc" id="structtagTreeNode_html"><div class="ttname"><a href="structtagTreeNode.html">tagTreeNode</a></div><div class="ttdef"><b>Definition:</b> tree.h:26</div></div>
<div class="ttc" id="structCafeFamilyItem_html_a2622c49f6ade1c226b01015d1c502be6"><div class="ttname"><a href="structCafeFamilyItem.html#a2622c49f6ade1c226b01015d1c502be6">CafeFamilyItem::ref</a></div><div class="ttdeci">int ref</div><div class="ttdef"><b>Definition:</b> cafe.h:14</div></div>
<div class="ttc" id="cafe_8h_html_a3f6a9deb3b221594e1357c270c3e31f4"><div class="ttname"><a href="cafe_8h.html#a3f6a9deb3b221594e1357c270c3e31f4">cafe_family_set_size_by_species</a></div><div class="ttdeci">void cafe_family_set_size_by_species(char *speciesname, int size, pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:744</div></div>
<div class="ttc" id="cafe_8h_html_ac14285c2a2a32972442da6f3e6503e7a"><div class="ttname"><a href="cafe_8h.html#ac14285c2a2a32972442da6f3e6503e7a">cafe_family_init</a></div><div class="ttdeci">pCafeFamily cafe_family_init(pArrayList data)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:429</div></div>
<div class="ttc" id="cafe_8h_html_a6276b68a56c6403d815d512080dc46a4"><div class="ttname"><a href="cafe_8h.html#a6276b68a56c6403d815d512080dc46a4">cafe_best_lambda_by_fminsearch</a></div><div class="ttdeci">double * cafe_best_lambda_by_fminsearch(pCafeParam param, int lambda_len, int k)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:722</div></div>
<div class="ttc" id="cafe_8h_html_aeb4ab292a60df57301d00e11cfd01822"><div class="ttname"><a href="cafe_8h.html#aeb4ab292a60df57301d00e11cfd01822">cafe_set_birthdeath_cache</a></div><div class="ttdeci">void cafe_set_birthdeath_cache(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:975</div></div>
<div class="ttc" id="cafe_8h_html_a671e8a36c74d72e2f7e9427ef48e0418"><div class="ttname"><a href="cafe_8h.html#a671e8a36c74d72e2f7e9427ef48e0418">cafe_family_set_size_with_family</a></div><div class="ttdeci">void cafe_family_set_size_with_family(pCafeFamily pcf, int idx, pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:670</div></div>
<div class="ttc" id="structCafeFamily_html"><div class="ttname"><a href="structCafeFamily.html">CafeFamily</a></div><div class="ttdef"><b>Definition:</b> family.h:72</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="cafe_8h_html_a9a579f7aa906dda3855e76e0c966bace"><div class="ttname"><a href="cafe_8h.html#a9a579f7aa906dda3855e76e0c966bace">cafe_family_read_validate_species</a></div><div class="ttdeci">void cafe_family_read_validate_species(pCafeParam param, char *file)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:374</div></div>
<div class="ttc" id="cafe_8h_html_a3d85789c6ea2856d46189f9c9fa1d646"><div class="ttname"><a href="cafe_8h.html#a3d85789c6ea2856d46189f9c9fa1d646">cafe_family_clean_cvfiles_byfamily</a></div><div class="ttdeci">void cafe_family_clean_cvfiles_byfamily(pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:169</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_8h_html_a7df7eea55178141f0d7cef33a0712b93"><div class="ttname"><a href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a></div><div class="ttdeci">CafeFamilyItem * pCafeFamilyItem</div><div class="ttdef"><b>Definition:</b> cafe.h:21</div></div>
<div class="ttc" id="cafe_8h_html_ab4b6f407abda4eaea384743c2b1f9a02"><div class="ttname"><a href="cafe_8h.html#ab4b6f407abda4eaea384743c2b1f9a02">cafe_family_get_species_index</a></div><div class="ttdeci">int cafe_family_get_species_index(pCafeFamily pcf, char *speciesname)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:595</div></div>
<div class="ttc" id="cafe_8h_html_ae7993697889a09c5f071cf1fa7563da1"><div class="ttname"><a href="cafe_8h.html#ae7993697889a09c5f071cf1fa7563da1">cafe_tree_clustered_viterbi</a></div><div class="ttdeci">void cafe_tree_clustered_viterbi(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:609</div></div>
<div class="ttc" id="structtagPhylogenyNode_html"><div class="ttname"><a href="structtagPhylogenyNode.html">tagPhylogenyNode</a></div><div class="ttdef"><b>Definition:</b> tree.h:66</div></div>
<div class="ttc" id="cafe_8h_html_a06ef016855f349979f4cef37ac196b1d"><div class="ttname"><a href="cafe_8h.html#a06ef016855f349979f4cef37ac196b1d">cafe_tree_mp_remark</a></div><div class="ttdeci">double cafe_tree_mp_remark(pString str, pTree ptree, pMetapostConfig pmc, va_list ap)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:254</div></div>
<div class="ttc" id="cafe_8h_html_a6f3c8e11014de17b334ac29067126bd8"><div class="ttname"><a href="cafe_8h.html#a6f3c8e11014de17b334ac29067126bd8">__cafe_tree_node_compute_likelihood</a></div><div class="ttdeci">void __cafe_tree_node_compute_likelihood(pTree ptree, pTreeNode ptnode, va_list ap1)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:779</div></div>
<div class="ttc" id="cafe_8h_html_a9a17222518181cb6ac05c07aaf5e24ca"><div class="ttname"><a href="cafe_8h.html#a9a17222518181cb6ac05c07aaf5e24ca">cafe_tree_string</a></div><div class="ttdeci">pString cafe_tree_string(pCafeTree pcafe)</div><div class="ttdef"><b>Definition:</b> cafe_tree.c:241</div></div>
<div class="ttc" id="cafe_8h_html_a5c952ff06eb0153eb4021557da22005d"><div class="ttname"><a href="cafe_8h.html#a5c952ff06eb0153eb4021557da22005d">cafe_family_free</a></div><div class="ttdeci">void cafe_family_free(pCafeFamily pcf)</div><div class="ttdef"><b>Definition:</b> cafe_family.c:610</div></div>
<div class="ttc" id="cafe_8h_html_a1f28d19d9122353dbfba5f4091368a8e"><div class="ttname"><a href="cafe_8h.html#a1f28d19d9122353dbfba5f4091368a8e">cafe_report_retrieve_data</a></div><div class="ttdeci">int cafe_report_retrieve_data(char *file, pCafeParam param)</div><div class="ttdef"><b>Definition:</b> cafe_report.c:404</div></div>
<div class="ttc" id="cafe_8h_html_a41e16620ee39f8c3fcfcdfce15f8f874"><div class="ttname"><a href="cafe_8h.html#a41e16620ee39f8c3fcfcdfce15f8f874">cafe_set_birthdeath_cache_thread</a></div><div class="ttdeci">void cafe_set_birthdeath_cache_thread(pCafeTree tree, int k_value, int *family_sizes, int *rootfamily_sizes)</div><div class="ttdef"><b>Definition:</b> cafe_main.c:965</div></div>
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