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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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<li class="navelem"><a class="el" href="dir_815ec9b478b15e8b47eb45d0c766f1f4.html">cafe</a></li> </ul>
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<a href="#nested-classes">Data Structures</a> |
<a href="#typedef-members">Typedefs</a> |
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<a href="#func-members">Functions</a> |
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<div class="title">cafe_shell.h File Reference</div> </div>
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<div class="textblock"><code>#include <<a class="el" href="utils_8h_source.html">utils.h</a>></code><br />
<code>#include <<a class="el" href="utils__string_8h_source.html">utils_string.h</a>></code><br />
<code>#include <<a class="el" href="family_8h_source.html">family.h</a>></code><br />
</div>
<p><a href="cafe__shell_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="structCafeShellCommand.html">CafeShellCommand</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structArgument.html">Argument</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structErrorMeasure.html">ErrorMeasure</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:a51ff5547bac4f92fa086dc7357394899"><td class="memItemLeft" align="right" valign="top">typedef int(* </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a51ff5547bac4f92fa086dc7357394899">cafe_command</a>) (int argc, char *argv[])</td></tr>
<tr class="separator:a51ff5547bac4f92fa086dc7357394899"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa7abe47d38cdee313d556384fc2f793f"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structCafeShellCommand.html">CafeShellCommand</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#aa7abe47d38cdee313d556384fc2f793f">pCafeShellCommand</a></td></tr>
<tr class="separator:aa7abe47d38cdee313d556384fc2f793f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac5a9bebec6d47b2a769221139a167876"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structArgument.html">Argument</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#ac5a9bebec6d47b2a769221139a167876">pArgument</a></td></tr>
<tr class="separator:ac5a9bebec6d47b2a769221139a167876"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7e86eeb5f7fc48869e805c9f1142959e"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structErrorMeasure.html">ErrorMeasure</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a7e86eeb5f7fc48869e805c9f1142959e">pErrorMeasure</a></td></tr>
<tr class="separator:a7e86eeb5f7fc48869e805c9f1142959e"><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:a938245e829e8fe18be69f63031bd3b7d"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a938245e829e8fe18be69f63031bd3b7d">enumCafeSehll</a> { <a class="el" href="cafe__shell_8h.html#a938245e829e8fe18be69f63031bd3b7da47d68f1580d224f79e73d03276db8bbc">CAFE_SHELL_EXIT</a> = 10000,
<a class="el" href="cafe__shell_8h.html#a938245e829e8fe18be69f63031bd3b7da1f99d7b11913e364c56c5c877dc3170a">CAFE_SHELL_NO_COMMAND</a>
}</td></tr>
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</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:a82e7144c7b62a989a5fd3d855a1500a8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a82e7144c7b62a989a5fd3d855a1500a8">cafe_shell_set_sizes</a> ()</td></tr>
<tr class="separator:a82e7144c7b62a989a5fd3d855a1500a8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3adf5f4770c6c89b152417ee4b03e360"><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__shell_8h.html#a3adf5f4770c6c89b152417ee4b03e360">cafe_shell_build_argument</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a3adf5f4770c6c89b152417ee4b03e360"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adbb978cbbd721d21fcecfd372604af76"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#adbb978cbbd721d21fcecfd372604af76">cafe_shell_prompt</a> (char *prompt, char *format,...)</td></tr>
<tr class="separator:adbb978cbbd721d21fcecfd372604af76"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6f6ca009bdfa80e59a3e2550412abfe4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a6f6ca009bdfa80e59a3e2550412abfe4">cafe_shell_init</a> (int quiet)</td></tr>
<tr class="memdesc:a6f6ca009bdfa80e59a3e2550412abfe4"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the global <a class="el" href="lambda__tests_8cpp.html#a52bf660ab9a3b7f0206fbd8d8311d24b">cafe_param</a> that holds the data acted upon by cafe. Called at program startup. <a href="#a6f6ca009bdfa80e59a3e2550412abfe4">More...</a><br /></td></tr>
<tr class="separator:a6f6ca009bdfa80e59a3e2550412abfe4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7cffc0eb3c396c12222d50a19817fe25"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a7cffc0eb3c396c12222d50a19817fe25">cafe_shell_score</a> ()</td></tr>
<tr class="separator:a7cffc0eb3c396c12222d50a19817fe25"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a18d0bfb6dae3e9520ffb9c5a534d1aa5"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a18d0bfb6dae3e9520ffb9c5a534d1aa5">cafe_cmd_tree</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a18d0bfb6dae3e9520ffb9c5a534d1aa5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab7b88336a604d317c2eea7ebcb1371e8"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#ab7b88336a604d317c2eea7ebcb1371e8">cafe_cmd_branchlength</a> (int argc, char *argv[])</td></tr>
<tr class="separator:ab7b88336a604d317c2eea7ebcb1371e8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a412249d0e5fa5ca96da764607f38b6b3"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a412249d0e5fa5ca96da764607f38b6b3">cafe_cmd_family</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a412249d0e5fa5ca96da764607f38b6b3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a32ece228b3ba07db144f79452afdb125"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a32ece228b3ba07db144f79452afdb125">cafe_cmd_viterbi</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a32ece228b3ba07db144f79452afdb125"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3610b289bae55dc6033b293591ec9662"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a3610b289bae55dc6033b293591ec9662">cafe_cmd_print_param</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a3610b289bae55dc6033b293591ec9662"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a135a720eb39deef29c04097793ceb20e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a135a720eb39deef29c04097793ceb20e">cafe_cmd_load</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a135a720eb39deef29c04097793ceb20e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aae07af4b31abc31ec549e9e95b1a1cfc"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#aae07af4b31abc31ec549e9e95b1a1cfc">cafe_cmd_save</a> (int argc, char *argv[])</td></tr>
<tr class="separator:aae07af4b31abc31ec549e9e95b1a1cfc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a72ba1fc4c9e0e0d85b1a9db4712ba9e2"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a72ba1fc4c9e0e0d85b1a9db4712ba9e2">cafe_cmd_lambda_mu</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a72ba1fc4c9e0e0d85b1a9db4712ba9e2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a633fa681f5ff83b688c7666bf36892a4"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a633fa681f5ff83b688c7666bf36892a4">cafe_cmd_version</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a3041a622c7035c1e3bcf48bd5c9609ea"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a3041a622c7035c1e3bcf48bd5c9609ea">cafe_cmd_pvalue</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a58d8686f881b69565a59206239f5d3da"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a58d8686f881b69565a59206239f5d3da">cafe_cmd_score</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:gae4ff9c32d2375ec8487fd99d140d9134"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#gae4ff9c32d2375ec8487fd99d140d9134">cafe_cmd_log</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:gae4ff9c32d2375ec8487fd99d140d9134"><td class="mdescLeft"> </td><td class="mdescRight">Echoes parameters to the current output. <a href="group__Commands.html#gae4ff9c32d2375ec8487fd99d140d9134">More...</a><br /></td></tr>
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<tr class="memitem:a7486ee9a8e4fc6f64458540628e3026f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a7486ee9a8e4fc6f64458540628e3026f">cafe_cmd_retrieve</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:ga1f8d08708948fe6cc47a16d64cff2d4d"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#ga1f8d08708948fe6cc47a16d64cff2d4d">cafe_cmd_sim_extinct</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:ga1f8d08708948fe6cc47a16d64cff2d4d"><td class="mdescLeft"> </td><td class="mdescRight">Runs a Monte Carlo simulation against the data and reports the number of extinctions that occurred. <a href="group__Commands.html#ga1f8d08708948fe6cc47a16d64cff2d4d">More...</a><br /></td></tr>
<tr class="separator:ga1f8d08708948fe6cc47a16d64cff2d4d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ga92a5e46c97a72fdc0e6201f093fdfd6f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#ga92a5e46c97a72fdc0e6201f093fdfd6f">cafe_cmd_extinct</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:ga92a5e46c97a72fdc0e6201f093fdfd6f"><td class="mdescLeft"> </td><td class="mdescRight">Runs a simulation to determine how many families are likely to have gone extinct. <a href="group__Commands.html#ga92a5e46c97a72fdc0e6201f093fdfd6f">More...</a><br /></td></tr>
<tr class="separator:ga92a5e46c97a72fdc0e6201f093fdfd6f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1662205f714c446de8c6e470a9fb625a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a1662205f714c446de8c6e470a9fb625a">cafe_cmd_lh_test</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:gadce5da31072dab7c010d7e7e4d39320c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#gadce5da31072dab7c010d7e7e4d39320c">cafe_cmd_root_dist</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:gadce5da31072dab7c010d7e7e4d39320c"><td class="mdescLeft"> </td><td class="mdescRight">Specify root family size distribution for simulation. <a href="group__Commands.html#gadce5da31072dab7c010d7e7e4d39320c">More...</a><br /></td></tr>
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<tr class="memitem:a76c01528f87cf7e6476970494839e071"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a76c01528f87cf7e6476970494839e071">cafe_cmd_esterror</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:aadf1c94ef1f1c3b60b5423e130dc992e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#aadf1c94ef1f1c3b60b5423e130dc992e">cafe_cmd_error_model</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a5042da408e75bc07b76173def161b9fb"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a5042da408e75bc07b76173def161b9fb">cafe_cmd_no_error_model</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:abbe36aca1d1e9b22cc4ec3c2e56012ca"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#abbe36aca1d1e9b22cc4ec3c2e56012ca">cafe_cmd_simerror</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a938b50ea7ad7ec3b3753c876025d3337"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a938b50ea7ad7ec3b3753c876025d3337">cafe_cmd_reconstruction_accuracy</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a9303ebc40d4020bdf2d539dd76d59c7e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a9303ebc40d4020bdf2d539dd76d59c7e">cafe_cmd_crossvalidation_by_species</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a8c9eeffa3b9732dd1a46b30475e86ff5"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a8c9eeffa3b9732dd1a46b30475e86ff5">cafe_cmd_crossvalidation_by_family</a> (int argc, char *argv[])</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="var-members"></a>
Variables</h2></td></tr>
<tr class="memitem:a2a7dd10e437aaa34998d08c16965d4ab"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structCafeShellCommand.html">CafeShellCommand</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8h.html#a2a7dd10e437aaa34998d08c16965d4ab">cafe_cmd</a> []</td></tr>
<tr class="memdesc:a2a7dd10e437aaa34998d08c16965d4ab"><td class="mdescLeft"> </td><td class="mdescRight">Holds the list of commands that are available in Cafe. <a href="#a2a7dd10e437aaa34998d08c16965d4ab">More...</a><br /></td></tr>
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<h2 class="groupheader">Typedef Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a51ff5547bac4f92fa086dc7357394899">§ </a></span>cafe_command</h2>
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<td class="memname">typedef int(* cafe_command) (int argc, char *argv[])</td>
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<td class="memname">typedef <a class="el" href="structArgument.html">Argument</a>* <a class="el" href="cafe__shell_8h.html#ac5a9bebec6d47b2a769221139a167876">pArgument</a></td>
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<h2 class="memtitle"><span class="permalink"><a href="#aa7abe47d38cdee313d556384fc2f793f">§ </a></span>pCafeShellCommand</h2>
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<td class="memname">typedef <a class="el" href="structCafeShellCommand.html">CafeShellCommand</a>* <a class="el" href="cafe__shell_8h.html#aa7abe47d38cdee313d556384fc2f793f">pCafeShellCommand</a></td>
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<td class="memname">typedef <a class="el" href="structErrorMeasure.html">ErrorMeasure</a>* <a class="el" href="cafe__shell_8h.html#a7e86eeb5f7fc48869e805c9f1142959e">pErrorMeasure</a></td>
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<h2 class="groupheader">Enumeration Type Documentation</h2>
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<td class="memname">enum <a class="el" href="cafe__shell_8h.html#a938245e829e8fe18be69f63031bd3b7d">enumCafeSehll</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a938245e829e8fe18be69f63031bd3b7da47d68f1580d224f79e73d03276db8bbc"></a>CAFE_SHELL_EXIT </td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a938245e829e8fe18be69f63031bd3b7da1f99d7b11913e364c56c5c877dc3170a"></a>CAFE_SHELL_NO_COMMAND </td><td class="fielddoc"></td></tr>
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<h2 class="groupheader">Function Documentation</h2>
<a id="ab7b88336a604d317c2eea7ebcb1371e8"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ab7b88336a604d317c2eea7ebcb1371e8">§ </a></span>cafe_cmd_branchlength()</h2>
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<td class="memname">int cafe_cmd_branchlength </td>
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<td class="paramtype">int </td>
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<td class="paramtype">char * </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a8c9eeffa3b9732dd1a46b30475e86ff5">§ </a></span>cafe_cmd_crossvalidation_by_family()</h2>
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<td class="memname">int cafe_cmd_crossvalidation_by_family </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a9303ebc40d4020bdf2d539dd76d59c7e">§ </a></span>cafe_cmd_crossvalidation_by_species()</h2>
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<td class="memname">int cafe_cmd_crossvalidation_by_species </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#aadf1c94ef1f1c3b60b5423e130dc992e">§ </a></span>cafe_cmd_error_model()</h2>
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<td class="memname">int cafe_cmd_error_model </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a76c01528f87cf7e6476970494839e071">§ </a></span>cafe_cmd_esterror()</h2>
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<td class="memname">int cafe_cmd_esterror </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<td class="memname">int cafe_cmd_family </td>
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<td class="paramtype">int </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a72ba1fc4c9e0e0d85b1a9db4712ba9e2">§ </a></span>cafe_cmd_lambda_mu()</h2>
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<td class="memname">int cafe_cmd_lambda_mu </td>
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<td class="paramtype">int </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a1662205f714c446de8c6e470a9fb625a">§ </a></span>cafe_cmd_lh_test()</h2>
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<td class="memname">int cafe_cmd_lh_test </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a135a720eb39deef29c04097793ceb20e">§ </a></span>cafe_cmd_load()</h2>
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<td class="memname">int cafe_cmd_load </td>
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<td class="paramtype">int </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<p>!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a5042da408e75bc07b76173def161b9fb">§ </a></span>cafe_cmd_no_error_model()</h2>
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<td class="memname">int cafe_cmd_no_error_model </td>
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<td class="paramtype">int </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a3610b289bae55dc6033b293591ec9662">§ </a></span>cafe_cmd_print_param()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a3041a622c7035c1e3bcf48bd5c9609ea">§ </a></span>cafe_cmd_pvalue()</h2>
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<td class="memname">int cafe_cmd_pvalue </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a938b50ea7ad7ec3b3753c876025d3337">§ </a></span>cafe_cmd_reconstruction_accuracy()</h2>
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<td class="memname">int cafe_cmd_reconstruction_accuracy </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a7486ee9a8e4fc6f64458540628e3026f">§ </a></span>cafe_cmd_retrieve()</h2>
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<td class="memname">int cafe_cmd_retrieve </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
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<h2 class="memtitle"><span class="permalink"><a href="#aae07af4b31abc31ec549e9e95b1a1cfc">§ </a></span>cafe_cmd_save()</h2>
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<td class="memname">int cafe_cmd_save </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a58d8686f881b69565a59206239f5d3da">§ </a></span>cafe_cmd_score()</h2>
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<td class="memname">int cafe_cmd_score </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#abbe36aca1d1e9b22cc4ec3c2e56012ca">§ </a></span>cafe_cmd_simerror()</h2>
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<td class="memname">int cafe_cmd_simerror </td>
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<td class="paramname"><em>argc</em>, </td>
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<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a18d0bfb6dae3e9520ffb9c5a534d1aa5">§ </a></span>cafe_cmd_tree()</h2>
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<td class="memname">int cafe_cmd_tree </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a633fa681f5ff83b688c7666bf36892a4">§ </a></span>cafe_cmd_version()</h2>
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<td class="memname">int cafe_cmd_version </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a32ece228b3ba07db144f79452afdb125">§ </a></span>cafe_cmd_viterbi()</h2>
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<td class="memname">int cafe_cmd_viterbi </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>argc</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a3adf5f4770c6c89b152417ee4b03e360">§ </a></span>cafe_shell_build_argument()</h2>
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<td class="memname"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> cafe_shell_build_argument </td>
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<td class="paramname"><em>argc</em>, </td>
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<td class="paramname"><em>argv</em>[] </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a6f6ca009bdfa80e59a3e2550412abfe4">§ </a></span>cafe_shell_init()</h2>
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<td class="memname">void cafe_shell_init </td>
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<td class="paramname"><em>quiet</em></td><td>)</td>
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<p>Initializes the global <a class="el" href="lambda__tests_8cpp.html#a52bf660ab9a3b7f0206fbd8d8311d24b">cafe_param</a> that holds the data acted upon by cafe. Called at program startup. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#adbb978cbbd721d21fcecfd372604af76">§ </a></span>cafe_shell_prompt()</h2>
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<td class="memname">void cafe_shell_prompt </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>prompt</em>, </td>
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<td class="paramtype">char * </td>
<td class="paramname"><em>format</em>, </td>
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<td class="paramtype"> </td>
<td class="paramname"><em>...</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a7cffc0eb3c396c12222d50a19817fe25">§ </a></span>cafe_shell_score()</h2>
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<td class="memname">double cafe_shell_score </td>
<td>(</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a82e7144c7b62a989a5fd3d855a1500a8">§ </a></span>cafe_shell_set_sizes()</h2>
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<td class="memname">void cafe_shell_set_sizes </td>
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<h2 class="groupheader">Variable Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a2a7dd10e437aaa34998d08c16965d4ab">§ </a></span>cafe_cmd</h2>
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<td class="memname"><a class="el" href="structCafeShellCommand.html">CafeShellCommand</a> cafe_cmd[]</td>
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<p>Holds the list of commands that are available in Cafe. </p>
<p>Each element consists of a command and the function that is called to handle that command. Terminated by a NULL, NULL pair Functions include <a class="el" href="lambda_8h.html#a8ecc5bfbbd1d0ac61689fa3fce598ff2">cafe_cmd_lambda</a>, <a class="el" href="cafe__shell_8c.html#a412249d0e5fa5ca96da764607f38b6b3">cafe_cmd_family</a>, <a class="el" href="cafe__shell_8c.html#a18d0bfb6dae3e9520ffb9c5a534d1aa5">cafe_cmd_tree</a>, etc. </p>
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