deploy: 07dead5

newick_generator.html

@@ -217,9 +217,9 @@ <h3><a class="anchor" id="autotoc_md57"></a>
 <div class="ttc" id="astructquetzal_1_1format_1_1newick_1_1TreeAlign_html"><div class="ttname"><a href="structquetzal_1_1format_1_1newick_1_1TreeAlign.html">quetzal::format::newick::TreeAlign</a></div><div class="ttdoc">Set a root node branch length to zero. Remove all nested comments.</div><div class="ttdef"><b>Definition:</b> from_network.hpp:180</div></div>
 </div><!-- fragment --><p>Since there are no comments stored in the labels of the generated random tree, the output of the different flavors are here quite similar:</p>
 <p><b>Output</b></p>
-<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;(((,),(,)),):0.0;</div>
-<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;(((,),(,)),);</div>
-<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;(((,),(,)),);</div>
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;((,((,),)),):0.0;</div>
+<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;((,((,),)),);</div>
+<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;((,((,),)),);</div>
 </div><!-- fragment --><hr  />
 <h3><a class="anchor" id="autotoc_md59"></a>
 Custom properties</h3>
@@ -280,7 +280,7 @@ <h3><a class="anchor" id="autotoc_md59"></a>
 <div class="ttc" id="astructedge__info_html"><div class="ttname"><a href="structedge__info.html">edge_info</a></div><div class="ttdef"><b>Definition:</b> newick_parser_2.cpp:12</div></div>
 <div class="ttc" id="astructvertex__info_html"><div class="ttname"><a href="structvertex__info.html">vertex_info</a></div><div class="ttdef"><b>Definition:</b> coalescence_binary_tree_2.cpp:5</div></div>
 </div><!-- fragment --><p><b>Output</b></p>
-<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;((((T:0,F:0)N:0,O:3)M:4,N:5)H:1,X:9)M:0.0;</div>
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;(M:5,((L:6,P:9)O:0,(S:0,P:3)N:9)E:7)Q:0.0;</div>
 </div><!-- fragment --><hr  />
 <h2><a class="anchor" id="autotoc_md61"></a>
 From a Quetzal k-ary tree</h2>
@@ -320,9 +320,9 @@ <h3><a class="anchor" id="autotoc_md63"></a>
 <div class="ttc" id="anamespacequetzal_1_1coalescence_html_a0db3e22d1bbb2f5554754792baa77efb"><div class="ttname"><a href="namespacequetzal_1_1coalescence.html#a0db3e22d1bbb2f5554754792baa77efb">quetzal::coalescence::get_random_k_ary_tree</a></div><div class="ttdeci">std::pair&lt; quetzal::coalescence::k_ary_tree&lt; Vertex, Edge &gt;, typename quetzal::coalescence::k_ary_tree&lt; Vertex, Edge &gt;::vertex_descriptor &gt; get_random_k_ary_tree(int n_leaves, Generator &amp;rng)</div><div class="ttdoc">Generate a random k-ary tree.</div><div class="ttdef"><b>Definition:</b> k_ary_tree.hpp:761</div></div>
 </div><!-- fragment --><p>Since there are no comments stored in the labels of the generated random tree, the output of the different flavors are here quite similar:</p>
 <p><b>Output</b></p>
-<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;((,(,)),(,)):0.0;</div>
-<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;((,(,)),(,));</div>
-<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;((,(,)),(,));</div>
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;(,(,(,(,)))):0.0;</div>
+<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;(,(,(,(,))));</div>
+<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;(,(,(,(,))));</div>
 </div><!-- fragment --><hr  />
 <h3><a class="anchor" id="autotoc_md65"></a>
 Custom properties</h3>
@@ -385,7 +385,7 @@ <h3><a class="anchor" id="autotoc_md65"></a>
 <div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;2</div>
 <div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;2</div>
 <div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;2</div>
-<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;((G:2,(D:3,O:5)B:7)J:2,(V:4,N:9)Z:9)P;</div>
+<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;(E:2,(B:8,(O:6,(A:4,A:9)B:9)S:9)Q:2)R;</div>
 </div><!-- fragment --><hr  />
 <h2><a class="anchor" id="autotoc_md67"></a>
 Interfacing legacy code</h2>