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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_family.c File Reference</title>
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<li class="navelem"><a class="el" href="dir_815ec9b478b15e8b47eb45d0c766f1f4.html">cafe</a></li> </ul>
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<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 <stdio.h></code><br />
<code>#include <<a class="el" href="mathfunc_8h_source.html">mathfunc.h</a>></code><br />
<code>#include <<a class="el" href="memalloc_8h_source.html">memalloc.h</a>></code><br />
<code>#include <<a class="el" href="utils_8h_source.html">utils.h</a>></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:ac0f33fd9c128da13747c622d086393d5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#ac0f33fd9c128da13747c622d086393d5">__cafe_famliy_check_the_pattern</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf)</td></tr>
<tr class="separator:ac0f33fd9c128da13747c622d086393d5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3fd75aa9642276bb88e81e75e32a69df"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#a3fd75aa9642276bb88e81e75e32a69df">cafe_family_read_cvquery</a> (char *file)</td></tr>
<tr class="separator:a3fd75aa9642276bb88e81e75e32a69df"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac195a0fc4ae61c03289db9cd8da09a63"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#ac195a0fc4ae61c03289db9cd8da09a63">cafe_family_split_cvfiles_byfamily</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:ac195a0fc4ae61c03289db9cd8da09a63"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3d85789c6ea2856d46189f9c9fa1d646"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#a3d85789c6ea2856d46189f9c9fa1d646">cafe_family_clean_cvfiles_byfamily</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:a3d85789c6ea2856d46189f9c9fa1d646"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afba87dc49ad3f7b86e5306b9c7ea5208"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#afba87dc49ad3f7b86e5306b9c7ea5208">cafe_family_split_cvfiles_byspecies</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:afba87dc49ad3f7b86e5306b9c7ea5208"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77b40a8fbd5a7221a2b3003ba8317b7f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#a77b40a8fbd5a7221a2b3003ba8317b7f">cafe_family_clean_cvfiles_byspecies</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:a77b40a8fbd5a7221a2b3003ba8317b7f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5676d8efaccbc638b19e6028ab859e34"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#a5676d8efaccbc638b19e6028ab859e34">cafe_family_read_query_family</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, char *file)</td></tr>
<tr class="separator:a5676d8efaccbc638b19e6028ab859e34"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9a579f7aa906dda3855e76e0c966bace"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#a9a579f7aa906dda3855e76e0c966bace">cafe_family_read_validate_species</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, char *file)</td></tr>
<tr class="separator:a9a579f7aa906dda3855e76e0c966bace"><td class="memSeparator" colspan="2"> </td></tr>
<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__family_8c.html#ac14285c2a2a32972442da6f3e6503e7a">cafe_family_init</a> (<a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> data)</td></tr>
<tr class="separator:ac14285c2a2a32972442da6f3e6503e7a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8040846f0c636e51a56193028a1ff59c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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>
<tr class="separator:a8040846f0c636e51a56193028a1ff59c"><td class="memSeparator" colspan="2"> </td></tr>
<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__family_8c.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__family_8c.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:a5d2f54e37c36caf8d59811800f4f559b"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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__family_8c.html#ab4b6f407abda4eaea384743c2b1f9a02">cafe_family_get_species_index</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf, char *speciesname)</td></tr>
<tr class="separator:ab4b6f407abda4eaea384743c2b1f9a02"><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__family_8c.html#a5c952ff06eb0153eb4021557da22005d">cafe_family_free</a> (<a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> pcf)</td></tr>
<tr class="separator:a5c952ff06eb0153eb4021557da22005d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad44ab3a046a4ffa4ea72ccbb024a83c1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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>
<tr class="separator:ad44ab3a046a4ffa4ea72ccbb024a83c1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acb02e7cc3e369942626ca994ff0c823d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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>
<tr class="separator:acb02e7cc3e369942626ca994ff0c823d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a671e8a36c74d72e2f7e9427ef48e0418"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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>
<tr class="separator:a671e8a36c74d72e2f7e9427ef48e0418"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1d18390e5a79329e67b3278e174c473d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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>
<tr class="separator:a1d18390e5a79329e67b3278e174c473d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3f6a9deb3b221594e1357c270c3e31f4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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>
<tr class="separator:a3f6a9deb3b221594e1357c270c3e31f4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae3f218b4542078f06e79492ffa8f42e7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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:aadf7360c79f3684e025281f746be2c6e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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__family_8c.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:a26c9f424ab9c48359becc47840ec6776"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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:a3c807482b5b5d8c827b53fcd6b55c29f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.html#a3c807482b5b5d8c827b53fcd6b55c29f">cafe_family_filter</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:a3c807482b5b5d8c827b53fcd6b55c29f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae881b40f3dab7d87a0db2d6bfb74653f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__family_8c.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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<h2 class="groupheader">Function Documentation</h2>
<a id="ac0f33fd9c128da13747c622d086393d5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac0f33fd9c128da13747c622d086393d5">§ </a></span>__cafe_famliy_check_the_pattern()</h2>
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<td class="memname">void __cafe_famliy_check_the_pattern </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="#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>
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<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>
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<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>
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<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></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>szid</em> </td>
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<td></td>
<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="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>szid</em> </td>
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<td></td>
<td>)</td>
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<a id="ab4b6f407abda4eaea384743c2b1f9a02"></a>
<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="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>speciesname</em> </td>
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<td></td>
<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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<a id="a2b38ef57e2463389db47965232c5ac98"></a>
<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>
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<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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<a id="a5551576d8d41b117a0b48b346a96fece"></a>
<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>
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<td class="paramtype">char * </td>
<td class="paramname"><em>file</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>bpatcheck</em> </td>
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<td>)</td>
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<a id="ae881b40f3dab7d87a0db2d6bfb74653f"></a>
<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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<a id="a3fd75aa9642276bb88e81e75e32a69df"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a3fd75aa9642276bb88e81e75e32a69df">§ </a></span>cafe_family_read_cvquery()</h2>
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<td class="memname">void cafe_family_read_cvquery </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>file</em></td><td>)</td>
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<a id="a5676d8efaccbc638b19e6028ab859e34"></a>
<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></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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<a id="a9a579f7aa906dda3855e76e0c966bace"></a>
<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>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>end read count </p>
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<a id="ae3f218b4542078f06e79492ffa8f42e7"></a>
<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>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#abe532152fa131d80a9ce7e4106821197">pCafeFamily</a> </td>
<td class="paramname"><em>pcf</em></td><td>)</td>
<td></td>
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<a id="ad44ab3a046a4ffa4ea72ccbb024a83c1"></a>
<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>
<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="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>idx</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>pcafe</em> </td>
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<td></td>
<td>)</td>
<td></td><td></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>
<td>(</td>
<td class="paramtype">char * </td>
<td class="paramname"><em>speciesname</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>size</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>pcafe</em> </td>
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<td></td>
<td>)</td>
<td></td><td></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>
<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="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>idx</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
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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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<td class="memname">void cafe_family_set_size_with_family </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="#acb02e7cc3e369942626ca994ff0c823d">§ </a></span>cafe_family_set_size_with_family_forced()</h2>
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<td class="memname">void cafe_family_set_size_with_family_forced </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>
<td class="paramname"><em>idx</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="#a5d2f54e37c36caf8d59811800f4f559b">§ </a></span>cafe_family_set_species_index()</h2>
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<td class="memname">int cafe_family_set_species_index </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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<p>Synchronize a family and tree together. </p>
<p>Sets the value of index in pcf to the node index in the tree of the leaf with the matching species ID. </p><dl class="section return"><dt>Returns</dt><dd>0 on success, or -1 if there is a species in the tree with no matching species in the family </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a1d18390e5a79329e67b3278e174c473d">§ </a></span>cafe_family_set_truesize_with_family()</h2>
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<td class="memname">void cafe_family_set_truesize_with_family </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>
<td class="paramname"><em>idx</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="#ac195a0fc4ae61c03289db9cd8da09a63">§ </a></span>cafe_family_split_cvfiles_byfamily()</h2>
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<td class="memname">int cafe_family_split_cvfiles_byfamily </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#afba87dc49ad3f7b86e5306b9c7ea5208">§ </a></span>cafe_family_split_cvfiles_byspecies()</h2>
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<td class="memname">void cafe_family_split_cvfiles_byspecies </td>
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<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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