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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
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<title>CAFE: /mnt/c/Users/befulton/Documents/GIT/CAFE/cafe/cafe.h File Reference</title>
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<div id="projectname">CAFE
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<li class="navelem"><a class="el" href="dir_815ec9b478b15e8b47eb45d0c766f1f4.html">cafe</a></li> </ul>
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<div class="header">
<div class="summary">
<a href="#nested-classes">Data Structures</a> |
<a href="#typedef-members">Typedefs</a> |
<a href="#enum-members">Enumerations</a> |
<a href="#func-members">Functions</a> </div>
<div class="headertitle">
<div class="title">cafe.h File Reference</div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><code>#include <<a class="el" href="family_8h_source.html">family.h</a>></code><br />
<code>#include <<a class="el" href="gmatrix_8h_source.html">gmatrix.h</a>></code><br />
<code>#include <<a class="el" href="chooseln__cache_8h_source.html">chooseln_cache.h</a>></code><br />
</div>
<p><a href="cafe_8h_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Data Structures</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structCafeFamilyItem.html">CafeFamilyItem</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="typedef-members"></a>
Typedefs</h2></td></tr>
<tr class="memitem:a7df7eea55178141f0d7cef33a0712b93"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structCafeFamilyItem.html">CafeFamilyItem</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a></td></tr>
<tr class="separator:a7df7eea55178141f0d7cef33a0712b93"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="enum-members"></a>
Enumerations</h2></td></tr>
<tr class="memitem:a941d27c486c2ae1ffb39a864a7ec5cc4"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4">enumCafeReport</a> { <a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4af665c1b9f44643486f81aa6d78ac8957">CAFE_REPORT_TEXT</a> = 0,
<a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a1ad4b84850cdafe9597dd8000dc7f248">CAFE_REPORT_HTML</a>,
<a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a8c91521fc74032cd1d6013092f96a3dd">CAFE_REPORT_PDF</a>
}</td></tr>
<tr class="separator:a941d27c486c2ae1ffb39a864a7ec5cc4"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:af1e282522a8c75ed3ea3a186ccbba962"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#af1e282522a8c75ed3ea3a186ccbba962">cafe_get_posterior</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:af1e282522a8c75ed3ea3a186ccbba962"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af9ae3976765e29062e2d678af52322da"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#af9ae3976765e29062e2d678af52322da">cafe_set_prior_rfsize_empirical</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="memdesc:af9ae3976765e29062e2d678af52322da"><td class="mdescLeft"> </td><td class="mdescRight">set empirical prior on rootsize based on the assumption that rootsize follows leaf size distribution <a href="#af9ae3976765e29062e2d678af52322da">More...</a><br /></td></tr>
<tr class="separator:af9ae3976765e29062e2d678af52322da"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab108f5d959d962bcfea2cbaab0a9fd10"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ab108f5d959d962bcfea2cbaab0a9fd10">cafe_tree_new</a> (char *sztree, int familysizes[], int rootfamilysizes[], double lambda, double mu)</td></tr>
<tr class="separator:ab108f5d959d962bcfea2cbaab0a9fd10"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abf94be4e512caec06b7bbe6391c054a5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#abf94be4e512caec06b7bbe6391c054a5">cafe_tree_new_empty_node</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> pcafe)</td></tr>
<tr class="separator:abf94be4e512caec06b7bbe6391c054a5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a9ceeeaec1f37178a4ad6519f815ad6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a4a9ceeeaec1f37178a4ad6519f815ad6">cafe_tree_set_parameters</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int familysizes[], int rootfamilysizes[], double lambda)</td></tr>
<tr class="separator:a4a9ceeeaec1f37178a4ad6519f815ad6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaacc74335f3e18b9aae2dce03ca3ba95"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#aaacc74335f3e18b9aae2dce03ca3ba95">cafe_tree_copy</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> psrc)</td></tr>
<tr class="separator:aaacc74335f3e18b9aae2dce03ca3ba95"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a59a369f120ab05629245fb707dabe441"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a59a369f120ab05629245fb707dabe441">cafe_tree_split</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int idx)</td></tr>
<tr class="separator:a59a369f120ab05629245fb707dabe441"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a399b895da5463457ea8dcd62b31131dd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a399b895da5463457ea8dcd62b31131dd">cafe_tree_free</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a399b895da5463457ea8dcd62b31131dd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4451115a25f07ac5f3e52d75e71d25d5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a4451115a25f07ac5f3e52d75e71d25d5">__cafe_tree_free_node</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> ptnode, va_list ap)</td></tr>
<tr class="separator:a4451115a25f07ac5f3e52d75e71d25d5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a311afa341f0108d84af1366cec16779c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a311afa341f0108d84af1366cec16779c">cafe_tree_string_name</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#a47c8b5d175cf4f1946a873dd28b77516">pPhylogenyNode</a> ptnode)</td></tr>
<tr class="separator:a311afa341f0108d84af1366cec16779c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a539b2a7307047507d08628f9232dbf8a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a539b2a7307047507d08628f9232dbf8a">cafe_tree_string_with_lambda</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a539b2a7307047507d08628f9232dbf8a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad446b2b7910dffecb400baa082f1c3ff"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ad446b2b7910dffecb400baa082f1c3ff">cafe_tree_string_with_id</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:ad446b2b7910dffecb400baa082f1c3ff"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9a17222518181cb6ac05c07aaf5e24ca"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a9a17222518181cb6ac05c07aaf5e24ca">cafe_tree_string</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a2b97ef12468c64ad91fe9ee06a225e4b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a2b97ef12468c64ad91fe9ee06a225e4b">cafe_tree_string_with_familysize_lambda</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a75e35397e2535cef3466c37ab9c2cb8f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a75e35397e2535cef3466c37ab9c2cb8f">cafe_tree_string_with_familysize</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a9ef8856ece7dbaba92fde32c4107a72c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a9ef8856ece7dbaba92fde32c4107a72c">cafe_tree_string_print</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a6f3c8e11014de17b334ac29067126bd8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a6f3c8e11014de17b334ac29067126bd8">__cafe_tree_node_compute_likelihood</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> ptnode, va_list ap1)</td></tr>
<tr class="separator:a6f3c8e11014de17b334ac29067126bd8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af9688d286dddb037fabf069aa7209b86"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#af9688d286dddb037fabf069aa7209b86">compute_internal_node_likelihood</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> ptnode, struct <a class="el" href="structchooseln__cache.html">chooseln_cache</a> *<a class="el" href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">cache</a>)</td></tr>
<tr class="separator:af9688d286dddb037fabf069aa7209b86"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a513624edfd78aba059fa55835275f11d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a513624edfd78aba059fa55835275f11d">compute_leaf_node_likelihood</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> ptnode)</td></tr>
<tr class="separator:a513624edfd78aba059fa55835275f11d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a64a3240a3e126af2fed45b08cde3d2c0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a64a3240a3e126af2fed45b08cde3d2c0">compute_likelihood</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> ptnode, struct <a class="el" href="structchooseln__cache.html">chooseln_cache</a> *<a class="el" href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">cache</a>)</td></tr>
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<tr class="memitem:a0e6b1095efd5b1cbccf38139848de2f5"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a0e6b1095efd5b1cbccf38139848de2f5">cafe_tree_likelihood</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a0e6b1095efd5b1cbccf38139848de2f5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a376f0defba082c9243fe89ccb93de0fa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a376f0defba082c9243fe89ccb93de0fa">cafe_tree_node_free_clustered_likelihoods</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a15e83cea0140d989624ca021fc1316ee"><td class="memItemLeft" align="right" valign="top">double ** </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a15e83cea0140d989624ca021fc1316ee">cafe_tree_clustered_likelihood</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:ad797e3a6bd04c8fcaab1209548b4f5ef"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ad797e3a6bd04c8fcaab1209548b4f5ef">cafe_tree_viterbi</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:ad797e3a6bd04c8fcaab1209548b4f5ef"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae7993697889a09c5f071cf1fa7563da1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ae7993697889a09c5f071cf1fa7563da1">cafe_tree_clustered_viterbi</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a86b7d92c6d9843ce4010340025eecf42"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a86b7d92c6d9843ce4010340025eecf42">cafe_tree_viterbi_posterior</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, <a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:a86b7d92c6d9843ce4010340025eecf42"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2890c7c910b5839063244d54b5896dd3"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a2890c7c910b5839063244d54b5896dd3">cafe_tree_random_probabilities</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int rootFamilysize, int trials)</td></tr>
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<tr class="memitem:a0b50a33f038ffa9a07ce30621f2cac77"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a0b50a33f038ffa9a07ce30621f2cac77">cafe_tree_p_values</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, double *p, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pconddist, int cdlen)</td></tr>
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<tr class="memitem:a31b86ce1fc4f0db908fe9fa7fc7fb2f3"><td class="memItemLeft" align="right" valign="top">double ** </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a31b86ce1fc4f0db908fe9fa7fc7fb2f3">cafe_tree_p_values_of_two_trees</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe1, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe2, double **p, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pconddist1, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pconddist2, int cdlen)</td></tr>
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<tr class="memitem:a0a54e602c59702bd6cc844332b6c2a7a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a0a54e602c59702bd6cc844332b6c2a7a">cafe_copy_parameters</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> psrc)</td></tr>
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<tr class="memitem:a72db0fc19498016c5023420f510bad9c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a72db0fc19498016c5023420f510bad9c">cafe_free_copy_parameters</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a45d46d04142f35bd3b8ad2b106719976"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a45d46d04142f35bd3b8ad2b106719976">cafe_tree_conditional_distribution</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int range_start, int range_end, int num_trials)</td></tr>
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<tr class="memitem:a06ef016855f349979f4cef37ac196b1d"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a06ef016855f349979f4cef37ac196b1d">cafe_tree_mp_remark</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> str, <a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> pmc, va_list ap)</td></tr>
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<tr class="memitem:a583f3346ac4cd4ac0da2d295ab798631"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a583f3346ac4cd4ac0da2d295ab798631">cafe_tree_mp_annotation</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> str, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> pnode, <a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> pmc, va_list ap)</td></tr>
<tr class="separator:a583f3346ac4cd4ac0da2d295ab798631"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5095cbb3b4652801b2da11512d0aadb0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a5095cbb3b4652801b2da11512d0aadb0">cafe_tree_get_default_mpconfig</a> (int id, double width, double height)</td></tr>
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<tr class="memitem:ab02dad48034bd27652cf2d011b71e98e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ab02dad48034bd27652cf2d011b71e98e">cafe_tree_metapost</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int id, char *title, double width, double height)</td></tr>
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<tr class="memitem:ab203b685b05382fbb18d1dd78f81fafb"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ab203b685b05382fbb18d1dd78f81fafb">cafe_tree_random_familysize</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int rootFamilysize)</td></tr>
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<tr class="memitem:ac14285c2a2a32972442da6f3e6503e7a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ac14285c2a2a32972442da6f3e6503e7a">cafe_family_init</a> (<a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> data)</td></tr>
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<tr class="memitem:a8040846f0c636e51a56193028a1ff59c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a8040846f0c636e51a56193028a1ff59c">cafe_family_add_item</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> data)</td></tr>
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<tr class="memitem:a5551576d8d41b117a0b48b346a96fece"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a5551576d8d41b117a0b48b346a96fece">cafe_family_new</a> (char *file, int bpatcheck)</td></tr>
<tr class="separator:a5551576d8d41b117a0b48b346a96fece"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2b38ef57e2463389db47965232c5ac98"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a2b38ef57e2463389db47965232c5ac98">cafe_family_item_free</a> (<a class="el" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a> pitem)</td></tr>
<tr class="separator:a2b38ef57e2463389db47965232c5ac98"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5c952ff06eb0153eb4021557da22005d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a5c952ff06eb0153eb4021557da22005d">cafe_family_free</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf)</td></tr>
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<tr class="memitem:ad44ab3a046a4ffa4ea72ccbb024a83c1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ad44ab3a046a4ffa4ea72ccbb024a83c1">cafe_family_set_size</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, int idx, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a5d2f54e37c36caf8d59811800f4f559b"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a5d2f54e37c36caf8d59811800f4f559b">cafe_family_set_species_index</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="memdesc:a5d2f54e37c36caf8d59811800f4f559b"><td class="mdescLeft"> </td><td class="mdescRight">Synchronize a family and tree together. <a href="#a5d2f54e37c36caf8d59811800f4f559b">More...</a><br /></td></tr>
<tr class="separator:a5d2f54e37c36caf8d59811800f4f559b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab4b6f407abda4eaea384743c2b1f9a02"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ab4b6f407abda4eaea384743c2b1f9a02">cafe_family_get_species_index</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, char *speciesname)</td></tr>
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<tr class="memitem:a26c9f424ab9c48359becc47840ec6776"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a26c9f424ab9c48359becc47840ec6776">cafe_family_set_size_for_split</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, int idx, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a671e8a36c74d72e2f7e9427ef48e0418"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a671e8a36c74d72e2f7e9427ef48e0418">cafe_family_set_size_with_family</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, int idx, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a1d18390e5a79329e67b3278e174c473d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a1d18390e5a79329e67b3278e174c473d">cafe_family_set_truesize_with_family</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, int idx, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a3f6a9deb3b221594e1357c270c3e31f4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a3f6a9deb3b221594e1357c270c3e31f4">cafe_family_set_size_by_species</a> (char *speciesname, int size, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:aadf7360c79f3684e025281f746be2c6e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#aadf7360c79f3684e025281f746be2c6e">cafe_family_get_index</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, char *szid)</td></tr>
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<tr class="memitem:ad87d747e20a51592e6ce2920b32632c3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ad87d747e20a51592e6ce2920b32632c3">cafe_family_get_family_item</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, char *szid)</td></tr>
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<tr class="memitem:acb02e7cc3e369942626ca994ff0c823d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#acb02e7cc3e369942626ca994ff0c823d">cafe_family_set_size_with_family_forced</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, int idx, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a3c807482b5b5d8c827b53fcd6b55c29f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a3c807482b5b5d8c827b53fcd6b55c29f">cafe_family_filter</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:ae881b40f3dab7d87a0db2d6bfb74653f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ae881b40f3dab7d87a0db2d6bfb74653f">cafe_family_print_cluster_membership</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:ae3f218b4542078f06e79492ffa8f42e7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ae3f218b4542078f06e79492ffa8f42e7">cafe_family_reset_maxlh</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf)</td></tr>
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<tr class="memitem:a9a579f7aa906dda3855e76e0c966bace"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a9a579f7aa906dda3855e76e0c966bace">cafe_family_read_validate_species</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, char *file)</td></tr>
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<tr class="memitem:ac195a0fc4ae61c03289db9cd8da09a63"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ac195a0fc4ae61c03289db9cd8da09a63">cafe_family_split_cvfiles_byfamily</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a3d85789c6ea2856d46189f9c9fa1d646"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a3d85789c6ea2856d46189f9c9fa1d646">cafe_family_clean_cvfiles_byfamily</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:afba87dc49ad3f7b86e5306b9c7ea5208"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#afba87dc49ad3f7b86e5306b9c7ea5208">cafe_family_split_cvfiles_byspecies</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a77b40a8fbd5a7221a2b3003ba8317b7f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a77b40a8fbd5a7221a2b3003ba8317b7f">cafe_family_clean_cvfiles_byspecies</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a5676d8efaccbc638b19e6028ab859e34"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a5676d8efaccbc638b19e6028ab859e34">cafe_family_read_query_family</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, char *file)</td></tr>
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<tr class="memitem:a41fd4a22d96314d20f0c9192c6f02339"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a41fd4a22d96314d20f0c9192c6f02339">cafe_log</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, const char *msg,...)</td></tr>
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<tr class="memitem:aeb4ab292a60df57301d00e11cfd01822"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#aeb4ab292a60df57301d00e11cfd01822">cafe_set_birthdeath_cache</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a41e16620ee39f8c3fcfcdfce15f8f874"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a41e16620ee39f8c3fcfcdfce15f8f874">cafe_set_birthdeath_cache_thread</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> tree, int k_value, int *family_sizes, int *rootfamily_sizes)</td></tr>
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<tr class="memitem:a6276b68a56c6403d815d512080dc46a4"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a6276b68a56c6403d815d512080dc46a4">cafe_best_lambda_by_fminsearch</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int k)</td></tr>
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<tr class="memitem:ac44e4ab06944b45e4a1cfd923c8eb9cb"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ac44e4ab06944b45e4a1cfd923c8eb9cb">cafe_best_lambda_mu_by_fminsearch</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int mu_len, int k)</td></tr>
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<tr class="memitem:a60fc1de991d240a8cb40ab7a98a06a91"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a60fc1de991d240a8cb40ab7a98a06a91">cafe_best_lambda_mu_eqbg_by_fminsearch</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int mu_len)</td></tr>
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<tr class="memitem:abc6a1f95000e9407117ed11904be6864"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#abc6a1f95000e9407117ed11904be6864">cafe_each_best_lambda_by_fminsearch</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len)</td></tr>
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<tr class="memitem:ad5b326684624583b7c4274b9dd36b048"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#ad5b326684624583b7c4274b9dd36b048">cafe_report</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int method)</td></tr>
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<tr class="memitem:a28b01083e12d908b4a3d54a7d1d02726"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a28b01083e12d908b4a3d54a7d1d02726">cafe_conditional_distribution</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a4a269c2694070c23c8dd643d7bf219e1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a4a269c2694070c23c8dd643d7bf219e1">cafe_lambda_set_default</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, double *lambda)</td></tr>
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<tr class="memitem:af2ed23d5716b6075fa222a6b6cf326a8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#af2ed23d5716b6075fa222a6b6cf326a8">cafe_free_birthdeath_cache</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:a50a8afe408546920e6a0920cec164ed2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a50a8afe408546920e6a0920cec164ed2">cafe_viterbi</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pCD)</td></tr>
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<tr class="memitem:adf53bc2a22b3f10d28b5bf5c226b371d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#adf53bc2a22b3f10d28b5bf5c226b371d">cafe_branch_cutting</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:abc9d347c972a12d7a86277efdd4c6b9d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#abc9d347c972a12d7a86277efdd4c6b9d">cafe_likelihood_ratio_test</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a40e1fa38255505c9a57ad590afed6ddb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="gmatrix_8h.html#aba3fd0ac2746bc814d237f210086a0ff">pGMatrix</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a40e1fa38255505c9a57ad590afed6ddb">cafe_lambda_distribution</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int numrange, double **range)</td></tr>
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<tr class="memitem:a1f28d19d9122353dbfba5f4091368a8e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe_8h.html#a1f28d19d9122353dbfba5f4091368a8e">cafe_report_retrieve_data</a> (char *file, <a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<h2 class="groupheader">Typedef Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a7df7eea55178141f0d7cef33a0712b93">§ </a></span>pCafeFamilyItem</h2>
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<td class="memname">typedef <a class="el" href="structCafeFamilyItem.html">CafeFamilyItem</a>* <a class="el" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a></td>
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<h2 class="groupheader">Enumeration Type Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a941d27c486c2ae1ffb39a864a7ec5cc4">§ </a></span>enumCafeReport</h2>
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<td class="memname">enum <a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4">enumCafeReport</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a941d27c486c2ae1ffb39a864a7ec5cc4af665c1b9f44643486f81aa6d78ac8957"></a>CAFE_REPORT_TEXT </td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a941d27c486c2ae1ffb39a864a7ec5cc4a1ad4b84850cdafe9597dd8000dc7f248"></a>CAFE_REPORT_HTML </td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a941d27c486c2ae1ffb39a864a7ec5cc4a8c91521fc74032cd1d6013092f96a3dd"></a>CAFE_REPORT_PDF </td><td class="fielddoc"></td></tr>
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</div>
<h2 class="groupheader">Function Documentation</h2>
<a id="a4451115a25f07ac5f3e52d75e71d25d5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a4451115a25f07ac5f3e52d75e71d25d5">§ </a></span>__cafe_tree_free_node()</h2>
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<td class="memname">void __cafe_tree_free_node </td>
<td>(</td>
<td class="paramtype"><a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> </td>
<td class="paramname"><em>ptree</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> </td>
<td class="paramname"><em>ptnode</em>, </td>
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<td></td>
<td class="paramtype">va_list </td>
<td class="paramname"><em>ap</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a6f3c8e11014de17b334ac29067126bd8">§ </a></span>__cafe_tree_node_compute_likelihood()</h2>
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<td class="memname">void __cafe_tree_node_compute_likelihood </td>
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<td class="paramtype"><a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> </td>
<td class="paramname"><em>ptree</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> </td>
<td class="paramname"><em>ptnode</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">va_list </td>
<td class="paramname"><em>ap1</em> </td>
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<td>)</td>
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<a id="a6276b68a56c6403d815d512080dc46a4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6276b68a56c6403d815d512080dc46a4">§ </a></span>cafe_best_lambda_by_fminsearch()</h2>
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<td class="memname">double* cafe_best_lambda_by_fminsearch </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>k</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ac44e4ab06944b45e4a1cfd923c8eb9cb">§ </a></span>cafe_best_lambda_mu_by_fminsearch()</h2>
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<td class="memname">double* cafe_best_lambda_mu_by_fminsearch </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>mu_len</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>k</em> </td>
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<td></td>
<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a60fc1de991d240a8cb40ab7a98a06a91">§ </a></span>cafe_best_lambda_mu_eqbg_by_fminsearch()</h2>
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<td class="memname">double* cafe_best_lambda_mu_eqbg_by_fminsearch </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>mu_len</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#adf53bc2a22b3f10d28b5bf5c226b371d">§ </a></span>cafe_branch_cutting()</h2>
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<td class="memname">void cafe_branch_cutting </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a28b01083e12d908b4a3d54a7d1d02726">§ </a></span>cafe_conditional_distribution()</h2>
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<td class="memname"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> cafe_conditional_distribution </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<a id="a0a54e602c59702bd6cc844332b6c2a7a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a0a54e602c59702bd6cc844332b6c2a7a">§ </a></span>cafe_copy_parameters()</h2>
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<td class="memname"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> cafe_copy_parameters </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>psrc</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#abc6a1f95000e9407117ed11904be6864">§ </a></span>cafe_each_best_lambda_by_fminsearch()</h2>
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<td class="memname">double* cafe_each_best_lambda_by_fminsearch </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a8040846f0c636e51a56193028a1ff59c">§ </a></span>cafe_family_add_item()</h2>
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<td class="memname">void cafe_family_add_item </td>
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<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> </td>
<td class="paramname"><em>data</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a3d85789c6ea2856d46189f9c9fa1d646">§ </a></span>cafe_family_clean_cvfiles_byfamily()</h2>
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<td class="memname">void cafe_family_clean_cvfiles_byfamily </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a77b40a8fbd5a7221a2b3003ba8317b7f">§ </a></span>cafe_family_clean_cvfiles_byspecies()</h2>
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<td class="memname">void cafe_family_clean_cvfiles_byspecies </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a3c807482b5b5d8c827b53fcd6b55c29f">§ </a></span>cafe_family_filter()</h2>
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<td class="memname">void cafe_family_filter </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a5c952ff06eb0153eb4021557da22005d">§ </a></span>cafe_family_free()</h2>
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<td class="memname">void cafe_family_free </td>
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<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ad87d747e20a51592e6ce2920b32632c3">§ </a></span>cafe_family_get_family_item()</h2>
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<td class="memname"><a class="el" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a> cafe_family_get_family_item </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>szid</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#aadf7360c79f3684e025281f746be2c6e">§ </a></span>cafe_family_get_index()</h2>
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<td class="memname">int cafe_family_get_index </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>szid</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab4b6f407abda4eaea384743c2b1f9a02">§ </a></span>cafe_family_get_species_index()</h2>
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<td class="memname">int cafe_family_get_species_index </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>speciesname</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ac14285c2a2a32972442da6f3e6503e7a">§ </a></span>cafe_family_init()</h2>
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<td class="memname"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> cafe_family_init </td>
<td>(</td>
<td class="paramtype"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> </td>
<td class="paramname"><em>data</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a2b38ef57e2463389db47965232c5ac98">§ </a></span>cafe_family_item_free()</h2>
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<td class="memname">void cafe_family_item_free </td>
<td>(</td>
<td class="paramtype"><a class="el" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a> </td>
<td class="paramname"><em>pitem</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a5551576d8d41b117a0b48b346a96fece">§ </a></span>cafe_family_new()</h2>
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<td class="memname"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> cafe_family_new </td>
<td>(</td>
<td class="paramtype">char * </td>
<td class="paramname"><em>file</em>, </td>
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<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>bpatcheck</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ae881b40f3dab7d87a0db2d6bfb74653f">§ </a></span>cafe_family_print_cluster_membership()</h2>
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<td class="memname">int cafe_family_print_cluster_membership </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a5676d8efaccbc638b19e6028ab859e34">§ </a></span>cafe_family_read_query_family()</h2>
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<td class="memname">void cafe_family_read_query_family </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>file</em> </td>
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<td></td>
<td>)</td>
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<p>end read count </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a9a579f7aa906dda3855e76e0c966bace">§ </a></span>cafe_family_read_validate_species()</h2>
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<td class="memname">void cafe_family_read_validate_species </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>file</em> </td>
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<td></td>
<td>)</td>
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<p>end read count </p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae3f218b4542078f06e79492ffa8f42e7">§ </a></span>cafe_family_reset_maxlh()</h2>
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<td class="memname">void cafe_family_reset_maxlh </td>
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<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#ad44ab3a046a4ffa4ea72ccbb024a83c1">§ </a></span>cafe_family_set_size()</h2>
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<td class="memname">void cafe_family_set_size </td>
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<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em>, </td>
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<td class="paramtype">int </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a3f6a9deb3b221594e1357c270c3e31f4">§ </a></span>cafe_family_set_size_by_species()</h2>
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<td class="memname">void cafe_family_set_size_by_species </td>
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<td class="paramtype">char * </td>
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<td class="paramtype">int </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a26c9f424ab9c48359becc47840ec6776">§ </a></span>cafe_family_set_size_for_split()</h2>
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<td class="memname">void cafe_family_set_size_for_split </td>
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<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em>, </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a671e8a36c74d72e2f7e9427ef48e0418">§ </a></span>cafe_family_set_size_with_family()</h2>
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