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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title>CAFE: /mnt/c/Users/befulton/Documents/GIT/CAFE/cafe/cafe_tree.c 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="#func-members">Functions</a> </div>
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<div class="title">cafe_tree.c File Reference</div> </div>
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<div class="contents">
<div class="textblock"><code>#include "<a class="el" href="cafe_8h_source.html">cafe.h</a>"</code><br />
<code>#include <stdlib.h></code><br />
<code>#include <<a class="el" href="io_8h_source.html">io.h</a>></code><br />
<code>#include <math.h></code><br />
<code>#include <<a class="el" href="mathfunc_8h_source.html">mathfunc.h</a>></code><br />
<code>#include <<a class="el" href="chooseln__cache_8h_source.html">chooseln_cache.h</a>></code><br />
<code>#include "time.h"</code><br />
</div><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:a09e1e073ca86780e3b2c1513452f8fbf"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a09e1e073ca86780e3b2c1513452f8fbf">__phylogeny_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 ap1)</td></tr>
<tr class="separator:a09e1e073ca86780e3b2c1513452f8fbf"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a011da805ee2cfebac9290554242a8355"><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__tree_8c.html#a011da805ee2cfebac9290554242a8355">cafe_tree_new_empty_node</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree)</td></tr>
<tr class="separator:a011da805ee2cfebac9290554242a8355"><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__tree_8c.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:a9c72b08f1ace310ab2e21d70c3b5a6d3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a9c72b08f1ace310ab2e21d70c3b5a6d3">__cafe_tree_new</a> (<a class="el" href="tree_8h.html#a0c3ebd3525303a855841551b467247cd">tree_func_node_new</a> new_tree_node_func, int size)</td></tr>
<tr class="separator:a9c72b08f1ace310ab2e21d70c3b5a6d3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad08d95479c047e932edc6ec7bf7aef3a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#ad08d95479c047e932edc6ec7bf7aef3a">cafe_tree_parse_node</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:ad08d95479c047e932edc6ec7bf7aef3a"><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__tree_8c.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:a11a7847e76a2d35bee3c2e196c5c3005"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a11a7847e76a2d35bee3c2e196c5c3005">__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 ap1)</td></tr>
<tr class="separator:a11a7847e76a2d35bee3c2e196c5c3005"><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__tree_8c.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:a311afa341f0108d84af1366cec16779c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.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:af4fdb853fab02b6c7ebbc7595f6ce87d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#af4fdb853fab02b6c7ebbc7595f6ce87d">cafe_tree_string_familysize_lambda</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:af4fdb853fab02b6c7ebbc7595f6ce87d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1153877204eeb1a10be18ce0b1f8441d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a1153877204eeb1a10be18ce0b1f8441d">cafe_tree_string_familysize</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:a1153877204eeb1a10be18ce0b1f8441d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad3436926d8fb0a0119e3686c0e4709f1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#ad3436926d8fb0a0119e3686c0e4709f1">cafe_tree_string_lambda</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:ad3436926d8fb0a0119e3686c0e4709f1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3965d669f5f3e118547696bdf6d28def"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a3965d669f5f3e118547696bdf6d28def">cafe_tree_string_id</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#a47c8b5d175cf4f1946a873dd28b77516">pPhylogenyNode</a> pnode)</td></tr>
<tr class="separator:a3965d669f5f3e118547696bdf6d28def"><td class="memSeparator" colspan="2"> </td></tr>
<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__tree_8c.html#a2b97ef12468c64ad91fe9ee06a225e4b">cafe_tree_string_with_familysize_lambda</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a2b97ef12468c64ad91fe9ee06a225e4b"><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__tree_8c.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: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__tree_8c.html#a75e35397e2535cef3466c37ab9c2cb8f">cafe_tree_string_with_familysize</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a75e35397e2535cef3466c37ab9c2cb8f"><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__tree_8c.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__tree_8c.html#a9a17222518181cb6ac05c07aaf5e24ca">cafe_tree_string</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a9a17222518181cb6ac05c07aaf5e24ca"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9ef8856ece7dbaba92fde32c4107a72c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a9ef8856ece7dbaba92fde32c4107a72c">cafe_tree_string_print</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a9ef8856ece7dbaba92fde32c4107a72c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab994a6c910f779f783ab58d245c1c5d7"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#ab994a6c910f779f783ab58d245c1c5d7">cafe_tree_mp_remark</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> pmc, va_list ap1)</td></tr>
<tr class="separator:ab994a6c910f779f783ab58d245c1c5d7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa801f48d06f60d6a7f22695ea0f2fc1e"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#aa801f48d06f60d6a7f22695ea0f2fc1e">cafe_tree_mp_annotation</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> pnode, <a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> pmc, va_list ap1)</td></tr>
<tr class="separator:aa801f48d06f60d6a7f22695ea0f2fc1e"><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__tree_8c.html#a5095cbb3b4652801b2da11512d0aadb0">cafe_tree_get_default_mpconfig</a> (int id, double width, double height)</td></tr>
<tr class="separator:a5095cbb3b4652801b2da11512d0aadb0"><td class="memSeparator" colspan="2"> </td></tr>
<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__tree_8c.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>
<tr class="separator:ab02dad48034bd27652cf2d011b71e98e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa376e9c07861e59aadc553cdea478af4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#aa376e9c07861e59aadc553cdea478af4">__cafe_tree_node_compute_viterbi</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:aa376e9c07861e59aadc553cdea478af4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6cdbb6a7ace9d78d83e20b5e3f67d5b8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a6cdbb6a7ace9d78d83e20b5e3f67d5b8">__cafe_tree_node_backtrack_viterbi</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:a6cdbb6a7ace9d78d83e20b5e3f67d5b8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1409701cd90b6c7402937996dea72ec2"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a1409701cd90b6c7402937996dea72ec2">__cafe_tree_node_compute_clustered_viterbi</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:a1409701cd90b6c7402937996dea72ec2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad797e3a6bd04c8fcaab1209548b4f5ef"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.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__tree_8c.html#ae7993697889a09c5f071cf1fa7563da1">cafe_tree_clustered_viterbi</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:ae7993697889a09c5f071cf1fa7563da1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a86b7d92c6d9843ce4010340025eecf42"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.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:af9688d286dddb037fabf069aa7209b86"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.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__tree_8c.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__tree_8c.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>
<tr class="separator:a64a3240a3e126af2fed45b08cde3d2c0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6f3c8e11014de17b334ac29067126bd8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.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:a7f31442e243c02662d2884b19dcaee91"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a7f31442e243c02662d2884b19dcaee91">__cafe_tree_node_compute_likelihood_using_cache</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:a7f31442e243c02662d2884b19dcaee91"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6d1958e0896f5c8733c72fe6e021d731"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a6d1958e0896f5c8733c72fe6e021d731">__cafe_tree_node_compute_clustered_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 unused)</td></tr>
<tr class="separator:a6d1958e0896f5c8733c72fe6e021d731"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab84cb146105aa92a38ba06b13c6cb6b2"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#ab84cb146105aa92a38ba06b13c6cb6b2">__cafe_tree_node_compute_clustered_likelihood_using_cache</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 unused)</td></tr>
<tr class="separator:ab84cb146105aa92a38ba06b13c6cb6b2"><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__tree_8c.html#a376f0defba082c9243fe89ccb93de0fa">cafe_tree_node_free_clustered_likelihoods</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:a376f0defba082c9243fe89ccb93de0fa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a15e83cea0140d989624ca021fc1316ee"><td class="memItemLeft" align="right" valign="top">double ** </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a15e83cea0140d989624ca021fc1316ee">cafe_tree_clustered_likelihood</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a15e83cea0140d989624ca021fc1316ee"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0e6b1095efd5b1cbccf38139848de2f5"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a0e6b1095efd5b1cbccf38139848de2f5">cafe_tree_likelihood</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
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<tr class="memitem:af19c1320c9ff90f2c75d361119924e39"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#af19c1320c9ff90f2c75d361119924e39">__cafe_tree_set_birthdeath</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:af19c1320c9ff90f2c75d361119924e39"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a41fd9c8764418b4ce51f6b66a2471553"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a41fd9c8764418b4ce51f6b66a2471553">cafe_tree_set_birthdeath</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:a41fd9c8764418b4ce51f6b66a2471553"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a00cfedbd547c6db177c1f88bfd8210be"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a00cfedbd547c6db177c1f88bfd8210be">cafe_tree_node_copy</a> (<a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> psrc, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> pdest)</td></tr>
<tr class="separator:a00cfedbd547c6db177c1f88bfd8210be"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a086c9dd816e70d698e66352b41d12ce1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a086c9dd816e70d698e66352b41d12ce1">__cafe_tree_copy_new_fill</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> psrc, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pdest)</td></tr>
<tr class="separator:a086c9dd816e70d698e66352b41d12ce1"><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__tree_8c.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__tree_8c.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:a6e2eaa5ca1388ff49e73f9739f24c7dd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a6e2eaa5ca1388ff49e73f9739f24c7dd">__cafe_tree_node_random_familysize</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> pnode, va_list ap1)</td></tr>
<tr class="separator:a6e2eaa5ca1388ff49e73f9739f24c7dd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab203b685b05382fbb18d1dd78f81fafb"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#ab203b685b05382fbb18d1dd78f81fafb">cafe_tree_random_familysize</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int rootFamilysize)</td></tr>
<tr class="separator:ab203b685b05382fbb18d1dd78f81fafb"><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__tree_8c.html#a2890c7c910b5839063244d54b5896dd3">cafe_tree_random_probabilities</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, int rootFamilysize, int trials)</td></tr>
<tr class="separator:a2890c7c910b5839063244d54b5896dd3"><td class="memSeparator" colspan="2"> </td></tr>
<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__tree_8c.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>
<tr class="separator:a45d46d04142f35bd3b8ad2b106719976"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4a9ad319cf10a53ac37115183946951"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#ac4a9ad319cf10a53ac37115183946951">cafe_tree_p_values</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, double *pvalues, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pconddist, int cdlen)</td></tr>
<tr class="separator:ac4a9ad319cf10a53ac37115183946951"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8251dabcb52172da3776385b9fef0158"><td class="memItemLeft" align="right" valign="top">double ** </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__tree_8c.html#a8251dabcb52172da3776385b9fef0158">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 **pvalues, <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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<h2 class="groupheader">Function Documentation</h2>
<a id="a086c9dd816e70d698e66352b41d12ce1"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a086c9dd816e70d698e66352b41d12ce1">§ </a></span>__cafe_tree_copy_new_fill()</h2>
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<td class="memname">void __cafe_tree_copy_new_fill </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>psrc</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pdest</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a11a7847e76a2d35bee3c2e196c5c3005">§ </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 class="paramkey"></td>
<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>ap1</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a9c72b08f1ace310ab2e21d70c3b5a6d3">§ </a></span>__cafe_tree_new()</h2>
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<td class="memname"><a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> __cafe_tree_new </td>
<td>(</td>
<td class="paramtype"><a class="el" href="tree_8h.html#a0c3ebd3525303a855841551b467247cd">tree_func_node_new</a> </td>
<td class="paramname"><em>new_tree_node_func</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>size</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a6cdbb6a7ace9d78d83e20b5e3f67d5b8">§ </a></span>__cafe_tree_node_backtrack_viterbi()</h2>
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<td class="memname">void __cafe_tree_node_backtrack_viterbi </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 class="paramkey"></td>
<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>ap1</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a6d1958e0896f5c8733c72fe6e021d731">§ </a></span>__cafe_tree_node_compute_clustered_likelihood()</h2>
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<td class="memname">void __cafe_tree_node_compute_clustered_likelihood </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 class="paramkey"></td>
<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>unused</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab84cb146105aa92a38ba06b13c6cb6b2">§ </a></span>__cafe_tree_node_compute_clustered_likelihood_using_cache()</h2>
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<td class="memname">void __cafe_tree_node_compute_clustered_likelihood_using_cache </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 class="paramkey"></td>
<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>unused</em> </td>
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<td>)</td>
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<a id="a1409701cd90b6c7402937996dea72ec2"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a1409701cd90b6c7402937996dea72ec2">§ </a></span>__cafe_tree_node_compute_clustered_viterbi()</h2>
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<td class="memname">void __cafe_tree_node_compute_clustered_viterbi </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 class="paramkey"></td>
<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>
<td>)</td>
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<a id="a6f3c8e11014de17b334ac29067126bd8"></a>
<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>
<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 class="paramkey"></td>
<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>
<td>)</td>
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<a id="a7f31442e243c02662d2884b19dcaee91"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a7f31442e243c02662d2884b19dcaee91">§ </a></span>__cafe_tree_node_compute_likelihood_using_cache()</h2>
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<td class="memname">void __cafe_tree_node_compute_likelihood_using_cache </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 class="paramkey"></td>
<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>
<td>)</td>
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<a id="aa376e9c07861e59aadc553cdea478af4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa376e9c07861e59aadc553cdea478af4">§ </a></span>__cafe_tree_node_compute_viterbi()</h2>
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<td class="memname">void __cafe_tree_node_compute_viterbi </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 class="paramkey"></td>
<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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<h2 class="memtitle"><span class="permalink"><a href="#a6e2eaa5ca1388ff49e73f9739f24c7dd">§ </a></span>__cafe_tree_node_random_familysize()</h2>
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<td class="memname">void __cafe_tree_node_random_familysize </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 class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> </td>
<td class="paramname"><em>pnode</em>, </td>
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<td></td>
<td class="paramtype">va_list </td>
<td class="paramname"><em>ap1</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#af19c1320c9ff90f2c75d361119924e39">§ </a></span>__cafe_tree_set_birthdeath()</h2>
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<td class="memname">void __cafe_tree_set_birthdeath </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 class="paramkey"></td>
<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>ap1</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a09e1e073ca86780e3b2c1513452f8fbf">§ </a></span>__phylogeny_free_node()</h2>
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<td class="memname">void __phylogeny_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>ap1</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a15e83cea0140d989624ca021fc1316ee">§ </a></span>cafe_tree_clustered_likelihood()</h2>
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<td class="memname">double** cafe_tree_clustered_likelihood </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ae7993697889a09c5f071cf1fa7563da1">§ </a></span>cafe_tree_clustered_viterbi()</h2>
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<td class="memname">void cafe_tree_clustered_viterbi </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a45d46d04142f35bd3b8ad2b106719976">§ </a></span>cafe_tree_conditional_distribution()</h2>
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<td class="memname"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> cafe_tree_conditional_distribution </td>
<td>(</td>
<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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<td class="paramtype">int </td>
<td class="paramname"><em>range_start</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>range_end</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>num_trials</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#aaacc74335f3e18b9aae2dce03ca3ba95">§ </a></span>cafe_tree_copy()</h2>
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<td class="memname"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> cafe_tree_copy </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>psrc</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a399b895da5463457ea8dcd62b31131dd">§ </a></span>cafe_tree_free()</h2>
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<td class="memname">void cafe_tree_free </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><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a5095cbb3b4652801b2da11512d0aadb0">§ </a></span>cafe_tree_get_default_mpconfig()</h2>
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<td class="memname"><a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> cafe_tree_get_default_mpconfig </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>id</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"><em>width</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"><em>height</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a0e6b1095efd5b1cbccf38139848de2f5">§ </a></span>cafe_tree_likelihood()</h2>
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<td class="memname">double* cafe_tree_likelihood </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab02dad48034bd27652cf2d011b71e98e">§ </a></span>cafe_tree_metapost()</h2>
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<td class="memname"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> cafe_tree_metapost </td>
<td>(</td>
<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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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>id</em>, </td>
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<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>title</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>width</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>height</em> </td>
</tr>
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<td></td>
<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#aa801f48d06f60d6a7f22695ea0f2fc1e">§ </a></span>cafe_tree_mp_annotation()</h2>
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<td class="memname">double cafe_tree_mp_annotation </td>
<td>(</td>
<td class="paramtype"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td>
<td class="paramname"><em>pstr</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> </td>
<td class="paramname"><em>pnode</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> </td>
<td class="paramname"><em>pmc</em>, </td>
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<td></td>
<td class="paramtype">va_list </td>
<td class="paramname"><em>ap1</em> </td>
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<td></td>
<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab994a6c910f779f783ab58d245c1c5d7">§ </a></span>cafe_tree_mp_remark()</h2>
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<td class="memname">double cafe_tree_mp_remark </td>
<td>(</td>
<td class="paramtype"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td>
<td class="paramname"><em>pstr</em>, </td>
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<td class="paramkey"></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 class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> </td>
<td class="paramname"><em>pmc</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>
</tr>
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<td></td>
<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab108f5d959d962bcfea2cbaab0a9fd10">§ </a></span>cafe_tree_new()</h2>
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<td class="memname"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> cafe_tree_new </td>
<td>(</td>
<td class="paramtype">char * </td>
<td class="paramname"><em>sztree</em>, </td>
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<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>familysizes</em>[], </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>rootfamilysizes</em>[], </td>
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<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>lambda</em>, </td>
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<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>mu</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a011da805ee2cfebac9290554242a8355">§ </a></span>cafe_tree_new_empty_node()</h2>
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<td class="memname"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> cafe_tree_new_empty_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><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a00cfedbd547c6db177c1f88bfd8210be">§ </a></span>cafe_tree_node_copy()</h2>
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<td class="memname">void cafe_tree_node_copy </td>
<td>(</td>
<td class="paramtype"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> </td>
<td class="paramname"><em>psrc</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>pdest</em> </td>
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<td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a376f0defba082c9243fe89ccb93de0fa">§ </a></span>cafe_tree_node_free_clustered_likelihoods()</h2>
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