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| <title>core_binaryreconcile.go</title> | ||
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| <meta name="viewport" content="width=device-width, target-densitydpi=160dpi, initial-scale=1.0; maximum-scale=1.0; user-scalable=0;"> | ||
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| rmq.go | ||
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| core_binaryreconcile.go | ||
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| core_speciestree.go | ||
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| refine_weightgt.go | ||
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| util_contract.go | ||
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| <h1>core_binaryreconcile.go</h1> | ||
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| <div class="content"><div class='highlight'><pre><span class="hljs-keyword">package</span> tree</pre></div></div> | ||
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| <a class="pilcrow" href="#section-2">¶</a> | ||
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| <p>BinaryCost finds the duplication, loss, and deep coalescence cost | ||
| for input binary gene tree and species tree.</p> | ||
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| <div class="content"><div class='highlight'><pre><span class="hljs-keyword">func</span> BinaryCost(gt *Tree, st *SpeciesTree) (dup, loss, dc <span class="hljs-typename">int</span>, err error) { | ||
| lm, err := LcaMap(gt, st) | ||
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| <span class="hljs-keyword">if</span> err != <span class="hljs-constant">nil</span> { | ||
| <span class="hljs-keyword">return</span><span class="hljs-number"> 0</span>,<span class="hljs-number"> 0</span>,<span class="hljs-number"> 0</span>, err | ||
| } | ||
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| <span class="hljs-keyword">for</span> _, n := <span class="hljs-keyword">range</span> gt.Nodes { | ||
| <span class="hljs-keyword">if</span> !n.IsLeaf() { | ||
| m := lm.Map[n.Id] | ||
| l := lm.Map[n.Children<span class="hljs-number">[0</span>].Id] | ||
| r := lm.Map[n.Children<span class="hljs-number">[1</span>].Id] | ||
| loss += (l.Level + r.Level -<span class="hljs-number"> 2</span>*m.Level) | ||
| dc += (l.Level + r.Level -<span class="hljs-number"> 2</span>*m.Level) | ||
| <span class="hljs-keyword">if</span> m == l || m == r { | ||
| dup++ | ||
| } <span class="hljs-keyword">else</span> { | ||
| loss -=<span class="hljs-number"> 2</span> | ||
| } | ||
| } | ||
| } | ||
| dc -= <span class="hljs-built_in">len</span>(st.Nodes) -<span class="hljs-number"> 1</span> | ||
| <span class="hljs-keyword">return</span> | ||
| }</pre></div></div> | ||
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