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1828 lines
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Beef
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253 lines (199 sloc)
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<td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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<td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (Rows (modelMatrixList) == 0)</span></td>
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<td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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<td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
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<td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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<td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> modelMatrixList = </span></td>
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<td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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<td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
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<td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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<td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"Equal Input"</span><span class="pl-en">,</span><span class="pl-c"> "EIAA</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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<td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"Dayhoff"</span><span class="pl-en">,</span><span class="pl-c">"Dayhoff</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c">"0"}</span></td>
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<td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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<td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"Dayhoff</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c">"Dayhoff_F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c">"19"}</span></td>
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<td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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<td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"JTT"</span><span class="pl-en">,</span><span class="pl-c"> "Jones</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "0"}</span></td>
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<td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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<td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"JTT</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c"> "Jones_F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
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<td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"WAG"</span><span class="pl-en">,</span><span class="pl-c"> "WAG</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "0"}</span></td>
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<td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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<td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"WAG</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c"> "WAG_F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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<td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"rtREV"</span><span class="pl-en">,</span><span class="pl-c"> "rtREV</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "0"}</span></td>
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<td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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<td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"rtREV</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c"> "rtREV_F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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<td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"mtMAM"</span><span class="pl-en">,</span><span class="pl-c"> "mtMAM</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "0"}</span></td>
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<td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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<td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"mtMAM</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c"> "mtMAM_F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
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<td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"mtREV 24"</span><span class="pl-en">,</span><span class="pl-c"> "mtREV_24</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "0"}</span></td>
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<td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
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<td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"mtREV 24</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c"> "mtREV_24_F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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<td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"HIV within"</span><span class="pl-en">,</span><span class="pl-c"> "HIVwithin</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "0"}</span></td>
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<td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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<td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"HIV within</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c"> "HIVwithin</span><span class="pl-c1">+</span><span class="pl-c">F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
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<td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"HIV between"</span><span class="pl-en">,</span><span class="pl-c"> "HIVbetween</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "0"}</span></td>
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<td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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<td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"HIV between</span><span class="pl-c1">+</span><span class="pl-c">F"</span><span class="pl-en">,</span><span class="pl-c"> "HIVbetween</span><span class="pl-c1">+</span><span class="pl-c">F</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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<td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"REV</span><span class="pl-c1">-</span><span class="pl-c">1 step"</span><span class="pl-en">,</span><span class="pl-c"> "reducedREV</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
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<td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"REV"</span><span class="pl-en">,</span><span class="pl-c"> "mtREV</span><span class="pl-en">.</span><span class="pl-c">mdl"</span><span class="pl-en">,</span><span class="pl-c"> "19"}</span></td>
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<td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
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<td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> };</span></td>
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<td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
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<td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/*___________________________________________________________________________________________________________*/</span></td>
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<td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-c">function runAModel (modelID</span><span class="pl-en">,</span><span class="pl-c"> fileName</span><span class="pl-en">,</span><span class="pl-c"> xtraP</span><span class="pl-en">,</span><span class="pl-c"> midx)</span></td>
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<td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
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<td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
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<td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
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<td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("#include \"TemplateModels/"</span><span class="pl-c1">+</span><span class="pl-c">fileName</span><span class="pl-c1">+</span><span class="pl-c">"\";"); </span></td>
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<td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> Tree givenTree = treeString;</span></td>
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<td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> LikelihoodFunction lf = (filteredData</span><span class="pl-en">,</span><span class="pl-c">givenTree);</span></td>
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<td id="LC34" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
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<td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> GetString (lf_info</span><span class="pl-en">,</span><span class="pl-c"> lf</span><span class="pl-en">,</span><span class="pl-c"> </span><span class="pl-c1">-</span><span class="pl-c">1);</span></td>
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<td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
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<td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> locals = lf_info</span>[<span class="pl-c">"Local Independent"</span>]<span class="pl-c">;</span></td>
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<td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
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<td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
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<td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
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<td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (Columns (branchLengthStash))</span></td>
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<td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
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<td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
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<td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
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<td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> USE_LAST_RESULTS = 1;</span></td>
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<td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
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<td id="LC41" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (_iv = 0; _iv </span><span class="pl-k"><</span><span class="pl-c"> Columns (locals); _iv = _iv</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
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<td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
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<td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
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<td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
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<td id="LC43" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands (locals</span>[<span class="pl-c">_iv</span>]<span class="pl-c"> </span><span class="pl-c1">+</span><span class="pl-c"> "=1;\n");</span></td>
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<td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
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<td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
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<td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> currentBL = BranchLength (givenTree</span><span class="pl-en">,</span><span class="pl-c">0);</span></td>
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<td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
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<td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> currentBN = BranchName (givenTree</span><span class="pl-en">,</span><span class="pl-c1">-</span><span class="pl-c">1);</span></td>
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<td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
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<td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (_iv = 0; _iv </span><span class="pl-k"><</span><span class="pl-c"> Columns (currentBN); _iv = _iv</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
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<td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
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<td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
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<td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
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<td id="LC49" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">currentBN</span>[<span class="pl-c">_iv</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t="</span><span class="pl-c1">+</span><span class="pl-c">branchLengthStash</span>[<span class="pl-c">_iv</span>]<span class="pl-c">/currentBL</span><span class="pl-c1">+</span><span class="pl-c">";");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
<td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
|
|
<td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
|
|
<td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
|
|
<td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> else</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
|
|
<td id="LC54" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
|
|
<td id="LC55" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (_iv = 0; _iv </span><span class="pl-k"><</span><span class="pl-c"> Columns (locals); _iv = _iv</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
|
|
<td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
|
|
<td id="LC57" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands (locals</span>[<span class="pl-c">_iv</span>]<span class="pl-c"> </span><span class="pl-c1">+</span><span class="pl-c"> "=0</span><span class="pl-en">.</span><span class="pl-c">1;\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
|
|
<td id="LC58" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
|
|
<td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> USE_LAST_RESULTS = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
|
<td id="LC60" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
|
|
<td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
|
|
<td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> Optimize (res</span><span class="pl-en">,</span><span class="pl-c">lf);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
|
|
<td id="LC63" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
|
|
<td id="LC64" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "| "</span><span class="pl-en">,</span><span class="pl-c"> modelID);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
<td id="LC65" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (k=0; k</span><span class="pl-k"><</span><span class="pl-c">maxModelWidth</span><span class="pl-c1">-</span><span class="pl-c">Abs(modelID)</span><span class="pl-c1">-</span><span class="pl-c">1; k=k</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
<td id="LC66" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
<td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> " ");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
|
|
<td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
|
|
<td id="LC69" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
|
|
<td id="LC70" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> params = res</span>[<span class="pl-c">1</span>][<span class="pl-c">1</span>]<span class="pl-c1">+</span><span class="pl-c">xtraP;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
|
|
<td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> AIC = 2(</span><span class="pl-c1">-</span><span class="pl-c">res</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-c1">+</span><span class="pl-c">params);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
|
|
<td id="LC72" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
|
|
<td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (filteredData</span><span class="pl-en">.</span><span class="pl-c">sites</span><span class="pl-c1">-</span><span class="pl-c">params</span><span class="pl-k">></span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
<td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
|
|
<td id="LC75" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> cAIC = 2(</span><span class="pl-c1">-</span><span class="pl-c">res</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-c1">+</span><span class="pl-c">params*(filteredData</span><span class="pl-en">.</span><span class="pl-c">sites/(filteredData</span><span class="pl-en">.</span><span class="pl-c">sites</span><span class="pl-c1">-</span><span class="pl-c">params</span><span class="pl-c1">-</span><span class="pl-c">1)));</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
|
|
<td id="LC76" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
|
|
<td id="LC77" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> else</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
|
|
<td id="LC78" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
|
|
<td id="LC79" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> cAIC = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
|
|
<td id="LC80" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
|
|
<td id="LC81" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
|
|
<td id="LC82" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> branchLengths = BranchLength (givenTree</span><span class="pl-en">,</span><span class="pl-c1">-</span><span class="pl-c">1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
|
|
<td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> TL = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
|
|
<td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (k=Rows(branchLengths)*Columns(branchLengths)</span><span class="pl-c1">-</span><span class="pl-c">1; k</span><span class="pl-k">></span><span class="pl-c">=0; k=k</span><span class="pl-c1">-</span><span class="pl-c">1) </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
|
|
<td id="LC85" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
|
|
<td id="LC86" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> TL = TL </span><span class="pl-c1">+</span><span class="pl-c"> branchLengths</span>[<span class="pl-c">k</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
|
|
<td id="LC87" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
|
|
<td id="LC88" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
|
|
<td id="LC89" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "| "</span><span class="pl-en">,</span><span class="pl-c"> Format (res</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">14</span><span class="pl-en">,</span><span class="pl-c">3)</span><span class="pl-en">,</span><span class="pl-c"> " | "</span><span class="pl-en">,</span><span class="pl-c"> Format (params</span><span class="pl-en">,</span><span class="pl-c">5</span><span class="pl-en">,</span><span class="pl-c">0)</span><span class="pl-en">,</span><span class="pl-c"> " | "</span><span class="pl-en">,</span><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
|
|
<td id="LC90" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> Format (AIC</span><span class="pl-en">,</span><span class="pl-c"> 9</span><span class="pl-en">,</span><span class="pl-c">3)</span><span class="pl-en">,</span><span class="pl-c"> " | "</span><span class="pl-en">,</span><span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
|
|
<td id="LC91" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
|
|
<td id="LC92" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (cAIC </span><span class="pl-k">></span><span class="pl-c"> 0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
|
|
<td id="LC93" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
|
|
<td id="LC94" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> Format (cAIC</span><span class="pl-en">,</span><span class="pl-c">11</span><span class="pl-en">,</span><span class="pl-c">3)</span><span class="pl-en">,</span><span class="pl-c"> " | ");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
|
|
<td id="LC95" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
|
|
<td id="LC96" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> else</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
|
|
<td id="LC97" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
|
|
<td id="LC98" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> " N/A | ");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
|
|
<td id="LC99" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
|
|
<td id="LC100" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
|
|
<td id="LC101" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> Format (TL</span><span class="pl-en">,</span><span class="pl-c">11</span><span class="pl-en">,</span><span class="pl-c">3)</span><span class="pl-en">,</span><span class="pl-c"> " |\n"</span><span class="pl-en">,</span><span class="pl-c"> sepString);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
|
|
<td id="LC102" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
|
|
<td id="LC103" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> resultMatrix</span>[<span class="pl-c">midx</span>][<span class="pl-c">0</span>]<span class="pl-c"> = res</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
|
|
<td id="LC104" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> resultMatrix</span>[<span class="pl-c">midx</span>][<span class="pl-c">1</span>]<span class="pl-c"> = params;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
|
|
<td id="LC105" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> resultMatrix</span>[<span class="pl-c">midx</span>][<span class="pl-c">2</span>]<span class="pl-c"> = AIC;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
|
|
<td id="LC106" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> resultMatrix</span>[<span class="pl-c">midx</span>][<span class="pl-c">3</span>]<span class="pl-c"> = cAIC;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
|
|
<td id="LC107" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> resultMatrix</span>[<span class="pl-c">midx</span>][<span class="pl-c">4</span>]<span class="pl-c"> = TL;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
|
|
<td id="LC108" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
|
|
<td id="LC109" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (AIC </span><span class="pl-k"><</span><span class="pl-c"> bestAIC)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
|
|
<td id="LC110" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
|
|
<td id="LC111" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bestAIC = AIC;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
|
|
<td id="LC112" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bestAICidx = midx;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
|
|
<td id="LC113" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> branchLengthStash = BranchLength (givenTree</span><span class="pl-en">,</span><span class="pl-c1">-</span><span class="pl-c">1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
|
|
<td id="LC114" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
|
|
<td id="LC115" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
|
|
<td id="LC116" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (cAIC </span><span class="pl-k">></span><span class="pl-c"> 0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
|
|
<td id="LC117" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
|
|
<td id="LC118" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (bestCAIC </span><span class="pl-k">></span><span class="pl-c"> cAIC)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
|
|
<td id="LC119" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
|
|
<td id="LC120" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bestCAIC = cAIC;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
|
|
<td id="LC121" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bestCAICidx = midx;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
|
|
<td id="LC122" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
|
|
<td id="LC123" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
|
|
<td id="LC124" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
|
|
<td id="LC125" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
|
|
<td id="LC126" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> return 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
|
|
<td id="LC127" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
|
|
<td id="LC128" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
|
|
<td id="LC129" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
|
|
<td id="LC130" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/*___________________________________________________________________________________________________________*/</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
|
|
<td id="LC131" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
|
|
<td id="LC132" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
|
|
<td id="LC133" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
|
|
<td id="LC134" class="blob-code blob-code-inner js-file-line"><span class="pl-c">maxModelWidth = 7;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
|
|
<td id="LC135" class="blob-code blob-code-inner js-file-line"><span class="pl-c">skipCodeSelectionStep = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
|
|
<td id="LC136" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
|
|
<td id="LC137" class="blob-code blob-code-inner js-file-line"><span class="pl-c">ChoiceList (doREV</span><span class="pl-en">,</span><span class="pl-c"> "Include REV?"</span><span class="pl-en">,</span><span class="pl-c"> 1</span><span class="pl-en">,</span><span class="pl-c"> SKIP_NONE</span><span class="pl-en">,</span><span class="pl-c"> "Yes"</span><span class="pl-en">,</span><span class="pl-c"> "Include REV and reduced REV models</span><span class="pl-en">.</span><span class="pl-c"> CAUTION: these models take a long time to fit</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
|
|
<td id="LC138" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> "No"</span><span class="pl-en">,</span><span class="pl-c"> "Only use empirical models");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
|
|
<td id="LC139" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
|
|
<td id="LC140" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (doREV </span><span class="pl-k"><</span><span class="pl-c"> 0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
|
|
<td id="LC141" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
|
|
<td id="LC142" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> return 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
|
|
<td id="LC143" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
|
|
<td id="LC144" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
|
|
<td id="LC145" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (doREV == 0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
|
|
<td id="LC146" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
|
|
<td id="LC147" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> #include "TemplateModels/chooseGeneticCode</span><span class="pl-en">.</span><span class="pl-c">def";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
|
|
<td id="LC148" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> skipCodeSelectionStep = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
|
|
<td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
|
|
<td id="LC150" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
|
|
<td id="LC151" class="blob-code blob-code-inner js-file-line"><span class="pl-c">modelCount = Rows (modelMatrixList) </span><span class="pl-c1">-</span><span class="pl-c"> 2*doREV;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
|
|
<td id="LC152" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
|
|
<td id="LC153" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (k=0; k</span><span class="pl-k"><</span><span class="pl-c">modelCount; k=k</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
|
|
<td id="LC154" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
|
|
<td id="LC155" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> maxModelWidth = Max(maxModelWidth</span><span class="pl-en">,</span><span class="pl-c">Abs (modelMatrixList</span>[<span class="pl-c">k</span>][<span class="pl-c">0</span>]<span class="pl-c">)</span><span class="pl-c1">+</span><span class="pl-c">2);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
|
|
<td id="LC156" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
|
|
<td id="LC157" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
|
|
<td id="LC158" class="blob-code blob-code-inner js-file-line"><span class="pl-c">sepString = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
|
|
<td id="LC159" class="blob-code blob-code-inner js-file-line"><span class="pl-c">capString = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
|
|
<td id="LC160" class="blob-code blob-code-inner js-file-line"><span class="pl-c">sepString * 256;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
|
|
<td id="LC161" class="blob-code blob-code-inner js-file-line"><span class="pl-c">sepString * "</span><span class="pl-c1">+</span><span class="pl-c">";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
|
|
<td id="LC162" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
|
<td id="LC163" class="blob-code blob-code-inner js-file-line"><span class="pl-c">capString * 256;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
|
|
<td id="LC164" class="blob-code blob-code-inner js-file-line"><span class="pl-c">capString * "| Model";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
|
|
<td id="LC165" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
|
|
<td id="LC166" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (k=0; k</span><span class="pl-k"><</span><span class="pl-c">maxModelWidth; k=k</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
|
|
<td id="LC167" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
|
<td id="LC168" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> sepString * "</span><span class="pl-c1">-</span><span class="pl-c">";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
|
<td id="LC169" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
|
|
<td id="LC170" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
|
<td id="LC171" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (k=0; k</span><span class="pl-k"><</span><span class="pl-c">maxModelWidth</span><span class="pl-c1">-</span><span class="pl-c">6; k=k</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
|
<td id="LC172" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
|
|
<td id="LC173" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> capString * " ";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
|
|
<td id="LC174" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
|
|
<td id="LC175" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
|
|
<td id="LC176" class="blob-code blob-code-inner js-file-line"><span class="pl-c">capString * "| Log Likelihood | #prms | AIC Score | c</span><span class="pl-c1">-</span><span class="pl-c">AIC Score | Tree Length |\n";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
|
|
<td id="LC177" class="blob-code blob-code-inner js-file-line"><span class="pl-c">sepString * "</span><span class="pl-c1">+----------------+-------+-----------+-------------+-------------+</span><span class="pl-c">\n";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
|
|
<td id="LC178" class="blob-code blob-code-inner js-file-line"><span class="pl-c">sepString * 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
|
|
<td id="LC179" class="blob-code blob-code-inner js-file-line"><span class="pl-c">capString * 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
|
|
<td id="LC180" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
|
|
<td id="LC181" class="blob-code blob-code-inner js-file-line"><span class="pl-c">branchLengthStash = 0;</span></td>
|
|
</tr>
|
|
<tr>
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<td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
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<td id="LC182" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
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</tr>
|
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<tr>
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<td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
|
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<td id="LC183" class="blob-code blob-code-inner js-file-line"><span class="pl-c">SKIP_MODEL_PARAMETER_LIST = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
|
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<td id="LC184" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
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</tr>
|
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<tr>
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<td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
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<td id="LC185" class="blob-code blob-code-inner js-file-line"><span class="pl-c">#include "TemplateModels/modelParameters2</span><span class="pl-en">.</span><span class="pl-c">mdl";</span></td>
|
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</tr>
|
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<tr>
|
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<td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
|
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<td id="LC186" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (modelType == 1)</span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
|
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<td id="LC187" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
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<td id="LC188" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> #include "TemplateModels/defineGamma</span><span class="pl-en">.</span><span class="pl-c">mdl";</span></td>
|
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</tr>
|
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<tr>
|
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<td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
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<td id="LC189" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
|
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<td id="LC190" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
|
|
<td id="LC191" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (modelType == 2)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
|
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<td id="LC192" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
|
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<td id="LC193" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> #include "TemplateModels/defineHM</span><span class="pl-en">.</span><span class="pl-c">mdl";</span></td>
|
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</tr>
|
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<tr>
|
|
<td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
|
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<td id="LC194" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
|
|
<td id="LC195" class="blob-code blob-code-inner js-file-line"><span class="pl-c">SKIP_MODEL_PARAMETER_LIST = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
|
|
<td id="LC196" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
|
|
<td id="LC197" class="blob-code blob-code-inner js-file-line"><span class="pl-c">SetDialogPrompt ("Please load an amino</span><span class="pl-c1">-</span><span class="pl-c">acid data file:");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
|
|
<td id="LC198" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
|
|
<td id="LC199" class="blob-code blob-code-inner js-file-line"><span class="pl-c">DataSet ds = ReadDataFile (PROMPT_FOR_FILE);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
|
|
<td id="LC200" class="blob-code blob-code-inner js-file-line"><span class="pl-c">DataSetFilter filteredData = CreateFilter (ds</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
|
|
<td id="LC201" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
|
|
<td id="LC202" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c">"\nRunning aminoacid model comparisons on "</span><span class="pl-en">,</span><span class="pl-c"> LAST_FILE_PATH</span><span class="pl-en">,</span><span class="pl-c"> "\n\nThe alignment has "</span><span class="pl-en">,</span><span class="pl-c">ds</span><span class="pl-en">.</span><span class="pl-c">species</span><span class="pl-en">,</span><span class="pl-c"> " sequences and "</span><span class="pl-en">,</span><span class="pl-c"> ds</span><span class="pl-en">.</span><span class="pl-c">sites</span><span class="pl-en">,</span><span class="pl-c"> " sites\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
|
|
<td id="LC203" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
|
|
<td id="LC204" class="blob-code blob-code-inner js-file-line"><span class="pl-c">_DO_TREE_REBALANCE_ = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
|
|
<td id="LC205" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
|
|
<td id="LC206" class="blob-code blob-code-inner js-file-line"><span class="pl-c">#include "queryTree</span><span class="pl-en">.</span><span class="pl-c">bf";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
|
|
<td id="LC207" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
|
|
<td id="LC208" class="blob-code blob-code-inner js-file-line"><span class="pl-c">resultMatrix = {modelCount</span><span class="pl-en">,</span><span class="pl-c"> 5};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
|
|
<td id="LC209" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
|
|
<td id="LC210" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n"</span><span class="pl-en">,</span><span class="pl-c">sepString</span><span class="pl-en">,</span><span class="pl-c">capString</span><span class="pl-en">,</span><span class="pl-c">sepString);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
|
|
<td id="LC211" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
|
|
<td id="LC212" class="blob-code blob-code-inner js-file-line"><span class="pl-c">bestAIC = 1e100;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
|
|
<td id="LC213" class="blob-code blob-code-inner js-file-line"><span class="pl-c">bestCAIC = 1e100;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
|
|
<td id="LC214" class="blob-code blob-code-inner js-file-line"><span class="pl-c">bestAICidx = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
|
|
<td id="LC215" class="blob-code blob-code-inner js-file-line"><span class="pl-c">bestCAICidx = </span><span class="pl-c1">-</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
|
|
<td id="LC216" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
|
|
<td id="LC217" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (mid=0; mid</span><span class="pl-k"><</span><span class="pl-c">modelCount; mid=mid</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
|
|
<td id="LC218" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
|
|
<td id="LC219" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> runAModel (modelMatrixList</span>[<span class="pl-c">mid</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c"> modelMatrixList</span>[<span class="pl-c">mid</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c"> 0</span><span class="pl-c1">+</span><span class="pl-c">modelMatrixList</span>[<span class="pl-c">mid</span>][<span class="pl-c">2</span>]<span class="pl-en">,</span><span class="pl-c"> mid);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
|
|
<td id="LC220" class="blob-code blob-code-inner js-file-line"><span class="pl-c">} </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
|
|
<td id="LC221" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
|
|
<td id="LC222" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n\nBest AIC model:\n\t"</span><span class="pl-en">,</span><span class="pl-c"> modelMatrixList</span>[<span class="pl-c">bestAICidx</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c"> " with the score of "</span><span class="pl-en">,</span><span class="pl-c"> bestAIC);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
|
|
<td id="LC223" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
|
|
<td id="LC224" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (bestCAICidx</span><span class="pl-k">></span><span class="pl-c">=0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
|
|
<td id="LC225" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
|
|
<td id="LC226" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n\nBest c</span><span class="pl-c1">-</span><span class="pl-c">AIC model:\n\t"</span><span class="pl-en">,</span><span class="pl-c"> modelMatrixList</span>[<span class="pl-c">bestCAICidx</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c"> " with the score of "</span><span class="pl-en">,</span><span class="pl-c"> bestCAIC);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
|
|
<td id="LC227" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
|
|
<td id="LC228" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
|
|
<td id="LC229" class="blob-code blob-code-inner js-file-line"><span class="pl-c">labelMatrix = {{"Log</span><span class="pl-c1">-</span><span class="pl-c">likelihood"</span><span class="pl-en">,</span><span class="pl-c">"Parameters"</span><span class="pl-en">,</span><span class="pl-c">"AIC"</span><span class="pl-en">,</span><span class="pl-c">"c</span><span class="pl-c1">-</span><span class="pl-c">AIC"</span><span class="pl-en">,</span><span class="pl-c">"Total tree length"</span><span class="pl-en">,</span><span class="pl-c">""}};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
|
|
<td id="LC230" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
|
|
<td id="LC231" class="blob-code blob-code-inner js-file-line"><span class="pl-c">aaString = "Model";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
|
|
<td id="LC232" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
|
|
<td id="LC233" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (fC = 0; fC </span><span class="pl-k"><</span><span class="pl-c"> modelCount; fC = fC</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
|
|
<td id="LC234" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
|
|
<td id="LC235" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aaString = aaString </span><span class="pl-c1">+</span><span class="pl-c"> ";" </span><span class="pl-c1">+</span><span class="pl-c"> modelMatrixList</span>[<span class="pl-c">fC</span>][<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
|
|
<td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
|
|
<td id="LC237" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
|
|
<td id="LC238" class="blob-code blob-code-inner js-file-line"><span class="pl-c">USE_LAST_RESULTS = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
|
|
<td id="LC239" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
|
|
<td id="LC240" class="blob-code blob-code-inner js-file-line"><span class="pl-c">labelMatrix</span>[<span class="pl-c">5</span>]<span class="pl-c"> = aaString;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
|
|
<td id="LC241" class="blob-code blob-code-inner js-file-line"><span class="pl-c">skipCodeSelectionStep = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
|
|
<td id="LC242" class="blob-code blob-code-inner js-file-line"><span class="pl-c">OpenWindow (CHARTWINDOW</span><span class="pl-en">,</span><span class="pl-c">{{"Model Fits"}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
|
|
<td id="LC243" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"labelMatrix"}</span><span class="pl-en">,</span><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
|
|
<td id="LC244" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"resultMatrix"}</span><span class="pl-en">,</span><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
|
|
<td id="LC245" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"Bar Chart"}</span><span class="pl-en">,</span><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
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<td id="LC246" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"Index"}</span><span class="pl-en">,</span><span class="pl-c"></span></td>
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</tr>
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<tr>
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<td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
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<td id="LC247" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"c</span><span class="pl-c1">-</span><span class="pl-c">AIC"}</span><span class="pl-en">,</span><span class="pl-c"></span></td>
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</tr>
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<tr>
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<td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
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<td id="LC248" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"Model Index"}</span><span class="pl-en">,</span><span class="pl-c"></span></td>
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</tr>
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<tr>
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<td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
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<td id="LC249" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {""}</span><span class="pl-en">,</span><span class="pl-c"></span></td>
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</tr>
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<tr>
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<td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
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<td id="LC250" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {"AIC"}</span></td>
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</tr>
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<tr>
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<td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
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<td id="LC251" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span><span class="pl-en">,</span><span class="pl-c"></span></td>
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</tr>
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<tr>
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<td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
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<td id="LC252" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> "SCREEN_WIDTH</span><span class="pl-c1">-</span><span class="pl-c">60;SCREEN_HEIGHT</span><span class="pl-c1">-</span><span class="pl-c">60;30;30");</span></td>
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