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Beef
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<form accept-charset="UTF-8" action="/veg/hyphy/edit/master/res/TemplateBatchFiles/BS2007.bf" class="inline-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="VU8jp+WE5XbyhnkpEKNpaETUGCfMlU0fA4l9d5+qhQLPpVgzo2M/thn0tFY4q1xC17oLjtNBhj7iiDJlRPnbGQ==" /></div>
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<form accept-charset="UTF-8" action="/veg/hyphy/delete/master/res/TemplateBatchFiles/BS2007.bf" class="inline-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="j0l2dHshq4N5ytS28qjodhR4X15YnkH5EVY8gCPZprN5st1RKuoslNfK3bf17XN0jxem4Ajqr02N1ql+u7z0pw==" /></div>
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<div class="file-info">
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296 lines (239 sloc)
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<span class="file-info-divider"></span>
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9.281 kb
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<div class="blob-wrapper data type-brainfuck">
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<table class="highlight tab-size-8 js-file-line-container">
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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">/* 1</span><span class="pl-en">.</span><span class="pl-c"> include a file to define the genetic code</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"> Note the use of base directory and path forming variables to make this analysis </span></td>
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<tr>
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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"> independent of directory placement</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"></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">incFileName = HYPHY_LIB_DIRECTORY</span><span class="pl-c1">+</span><span class="pl-c">"TemplateBatchFiles"</span><span class="pl-c1">+</span><span class="pl-c">DIRECTORY_SEPARATOR</span><span class="pl-c1">+</span><span class="pl-c">"TemplateModels"</span><span class="pl-c1">+</span><span class="pl-c">DIRECTORY_SEPARATOR</span><span class="pl-c1">+</span><span class="pl-c">"chooseGeneticCode</span><span class="pl-en">.</span><span class="pl-c">def";</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">ExecuteCommands ("#include \""</span><span class="pl-c1">+</span><span class="pl-c">incFileName</span><span class="pl-c1">+</span><span class="pl-c">"\";");</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"></span></td>
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<tr>
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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">/* 2</span><span class="pl-en">.</span><span class="pl-c"> load a codon partition */</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"></span></td>
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<tr>
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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">SetDialogPrompt ("Please locate a coding alignment:");</span></td>
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<tr>
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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">DataSet ds = ReadDataFile (PROMPT_FOR_FILE);</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">DataSetFilter filteredData = CreateFilter (ds</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><span class="pl-en">,</span><span class="pl-c">GeneticCodeExclusions);</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">coding_path = LAST_FILE_PATH;</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"></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">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\nLoaded a "</span><span class="pl-en">,</span><span class="pl-c"> filteredData</span><span class="pl-en">.</span><span class="pl-c">species</span><span class="pl-en">,</span><span class="pl-c"> " sequence alignment with "</span><span class="pl-en">,</span><span class="pl-c"> filteredData</span><span class="pl-en">.</span><span class="pl-c">sites</span><span class="pl-en">,</span><span class="pl-c"> " codons from\n"</span><span class="pl-en">,</span><span class="pl-c">coding_path</span><span class="pl-en">,</span><span class="pl-c">"\n");</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"></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">/* 3</span><span class="pl-en">.</span><span class="pl-c"> include a file to prompt for a tree */</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"></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">incFileName = HYPHY_LIB_DIRECTORY</span><span class="pl-c1">+</span><span class="pl-c">"TemplateBatchFiles"</span><span class="pl-c1">+</span><span class="pl-c">DIRECTORY_SEPARATOR</span><span class="pl-c1">+</span><span class="pl-c">"queryTree</span><span class="pl-en">.</span><span class="pl-c">bf";</span></td>
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</tr>
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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">ExecuteCommands ("#include \""</span><span class="pl-c1">+</span><span class="pl-c">incFileName</span><span class="pl-c1">+</span><span class="pl-c">"\";");</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"></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">/* 4</span><span class="pl-en">.</span><span class="pl-c"> Compute nucleotide counts by position for the F3x4 estimator */</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="L25" class="blob-num js-line-number" data-line-number="25"></td>
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<td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-c">COUNT_GAPS_IN_FREQUENCIES = 0;</span></td>
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<td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
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<td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-c">HarvestFrequencies (baseFreqs</span><span class="pl-en">,</span><span class="pl-c">filteredData</span><span class="pl-en">,</span><span class="pl-c">3</span><span class="pl-en">,</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
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<td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
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<td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c">COUNT_GAPS_IN_FREQUENCIES = 1;</span></td>
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<td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
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<td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
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<td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
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<td id="LC29" 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"> "\nBase composition:\n\tA: "</span><span class="pl-en">,</span><span class="pl-c"> Format (baseFreqs</span>[<span class="pl-c">0</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">0</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">0</span>][<span class="pl-c">2</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c"></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"> "\n\tC: "</span><span class="pl-en">,</span><span class="pl-c"> Format (baseFreqs</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">1</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">1</span>][<span class="pl-c">2</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><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"> "\n\tG: "</span><span class="pl-en">,</span><span class="pl-c"> Format (baseFreqs</span>[<span class="pl-c">2</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">2</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">2</span>][<span class="pl-c">2</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c"> </span></td>
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<td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
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<td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> "\n\tT: "</span><span class="pl-en">,</span><span class="pl-c"> Format (baseFreqs</span>[<span class="pl-c">3</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">3</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">Format (baseFreqs</span>[<span class="pl-c">3</span>][<span class="pl-c">2</span>]<span class="pl-en">,</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c">5)</span><span class="pl-en">,</span><span class="pl-c"> "\n");</span></td>
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<td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
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<td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
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<td id="L34" class="blob-num js-line-number" data-line-number="34"></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="L35" class="blob-num js-line-number" data-line-number="35"></td>
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<td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></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">/* 6</span><span class="pl-en">.</span><span class="pl-c"> define the GY94 rate matrix; for now each branch will have it's own</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"> dS and dN</span><span class="pl-en">,</span><span class="pl-c"> we will constrain them later */</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"></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">global kappa_inv = 1;</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="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">ModelMatrixDimension = 64;</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">for (h = 0; h</span><span class="pl-k"><</span><span class="pl-c">64; h=h</span><span class="pl-c1">+</span><span class="pl-c">1) </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">{</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"> if (_Genetic_Code</span>[<span class="pl-c">h</span>]<span class="pl-c">==10) /* stop codon */</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
<td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
<td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ModelMatrixDimension = ModelMatrixDimension</span><span class="pl-c1">-</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
<td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
<td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
<td id="LC49" class="blob-code blob-code-inner js-file-line"><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">GY_Matrix = {ModelMatrixDimension</span><span class="pl-en">,</span><span class="pl-c">ModelMatrixDimension};</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">hshift = 0;</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">for (h=0; h</span><span class="pl-k"><</span><span class="pl-c">64; h=h</span><span class="pl-c1">+</span><span class="pl-c">1)</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">{</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"> if (_Genetic_Code</span>[<span class="pl-c">h</span>]<span class="pl-c">==10) </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"> {</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"> hshift = hshift</span><span class="pl-c1">+</span><span class="pl-c">1;</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"> }</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"> else</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"> {</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"> vshift = hshift;</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"> for (v = h</span><span class="pl-c1">+</span><span class="pl-c">1; v</span><span class="pl-k"><</span><span class="pl-c">64; v=v</span><span class="pl-c1">+</span><span class="pl-c">1)</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"> {</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"> diff = v</span><span class="pl-c1">-</span><span class="pl-c">h;</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"> if (_Genetic_Code</span>[<span class="pl-c">v</span>]<span class="pl-c">==10) </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"> {</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"> vshift = vshift</span><span class="pl-c1">+</span><span class="pl-c">1;</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"> }</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"> else</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"> if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0)) /* one step */</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"> {</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"> if (h$4==v$4)</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"> {</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"> transition = v%4;</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"> transition2= h%4;</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"> if(diff%16==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"> transition = v$16;</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"> transition2= h$16;</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"> }</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"> else</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"> transition = v%16$4;</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"> transition2= h%16$4;</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"> }</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"> if (_Genetic_Code</span>[<span class="pl-c">0</span>][<span class="pl-c">h</span>]<span class="pl-c">==_Genetic_Code</span>[<span class="pl-c">0</span>][<span class="pl-c">v</span>]<span class="pl-c">) /* synonymous */</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 (Abs(transition</span><span class="pl-c1">-</span><span class="pl-c">transition2)%2) /* transversion */</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"> GY_Matrix</span>[<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>][<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>]<span class="pl-c"> := kappa_inv*synRate;</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"> GY_Matrix</span>[<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>][<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>]<span class="pl-c"> := kappa_inv*synRate;</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"> }</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"> else</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"> {</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"> GY_Matrix</span>[<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>][<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>]<span class="pl-c"> := synRate;</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"> GY_Matrix</span>[<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>][<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>]<span class="pl-c"> := synRate; </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"> }</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"> else</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"> {</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"> if (Abs(transition</span><span class="pl-c1">-</span><span class="pl-c">transition2)%2) /* transversion */</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"> {</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"> GY_Matrix</span>[<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>][<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>]<span class="pl-c"> := kappa_inv*nonSynRate;</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"> GY_Matrix</span>[<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>][<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>]<span class="pl-c"> := kappa_inv*nonSynRate;</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"> }</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"> else</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"> {</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"> GY_Matrix</span>[<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>][<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>]<span class="pl-c"> := nonSynRate;</span></td>
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</tr>
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<tr>
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<td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
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<td id="LC113" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> GY_Matrix</span>[<span class="pl-c">v</span><span class="pl-c1">-</span><span class="pl-c">vshift</span>][<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>]<span class="pl-c"> := nonSynRate; </span></td>
|
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</tr>
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<tr>
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<td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
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<td id="LC114" 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="L115" class="blob-num js-line-number" data-line-number="115"></td>
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<td id="LC115" 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="L116" class="blob-num js-line-number" data-line-number="116"></td>
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<td id="LC116" 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="L117" class="blob-num js-line-number" data-line-number="117"></td>
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<td id="LC117" 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="L118" class="blob-num js-line-number" data-line-number="118"></td>
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<td id="LC118" 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="L119" class="blob-num js-line-number" data-line-number="119"></td>
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<td id="LC119" 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="L120" class="blob-num js-line-number" data-line-number="120"></td>
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<td id="LC120" 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="L121" class="blob-num js-line-number" data-line-number="121"></td>
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<td id="LC121" 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="L122" class="blob-num js-line-number" data-line-number="122"></td>
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<td id="LC122" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/*8</span><span class="pl-en">.</span><span class="pl-c"> build codon frequencies (use the F3x4 estimator) */</span></td>
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</tr>
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<tr>
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<td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
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<td id="LC123" 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="L124" class="blob-num js-line-number" data-line-number="124"></td>
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<td id="LC124" class="blob-code blob-code-inner js-file-line"><span class="pl-c">PIStop = 1</span><span class="pl-en">.</span><span class="pl-c">0;</span></td>
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</tr>
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<tr>
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<td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
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<td id="LC125" class="blob-code blob-code-inner js-file-line"><span class="pl-c">codonFreqs = {ModelMatrixDimension</span><span class="pl-en">,</span><span class="pl-c">1};</span></td>
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</tr>
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<tr>
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<td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
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<td id="LC126" class="blob-code blob-code-inner js-file-line"><span class="pl-c">hshift = 0;</span></td>
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</tr>
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<tr>
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<td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
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<td id="LC127" 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="L128" class="blob-num js-line-number" data-line-number="128"></td>
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<td id="LC128" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (h=0; h</span><span class="pl-k"><</span><span class="pl-c">64; h=h</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
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</tr>
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<tr>
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<td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
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<td id="LC129" 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="L130" class="blob-num js-line-number" data-line-number="130"></td>
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<td id="LC130" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> first = h$16;</span></td>
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</tr>
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<tr>
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<td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
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<td id="LC131" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> second = h%16$4;</span></td>
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</tr>
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<tr>
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<td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
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<td id="LC132" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> third = h%4;</span></td>
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</tr>
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<tr>
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<td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
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<td id="LC133" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (_Genetic_Code</span>[<span class="pl-c">h</span>]<span class="pl-c">==10) </span></td>
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</tr>
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<tr>
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<td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
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<td id="LC134" 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="L135" class="blob-num js-line-number" data-line-number="135"></td>
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<td id="LC135" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> hshift = hshift</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
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</tr>
|
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<tr>
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<td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
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<td id="LC136" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> PIStop = PIStop</span><span class="pl-c1">-</span><span class="pl-c">baseFreqs</span>[<span class="pl-c">first</span>][<span class="pl-c">0</span>]<span class="pl-c">*baseFreqs</span>[<span class="pl-c">second</span>][<span class="pl-c">1</span>]<span class="pl-c">*baseFreqs</span>[<span class="pl-c">third</span>][<span class="pl-c">2</span>]<span class="pl-c">;</span></td>
|
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</tr>
|
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<tr>
|
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<td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
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<td id="LC137" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> continue; </span></td>
|
|
</tr>
|
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<tr>
|
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<td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
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<td id="LC138" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
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<tr>
|
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<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"> codonFreqs</span>[<span class="pl-c">h</span><span class="pl-c1">-</span><span class="pl-c">hshift</span>]<span class="pl-c">=baseFreqs</span>[<span class="pl-c">first</span>][<span class="pl-c">0</span>]<span class="pl-c">*baseFreqs</span>[<span class="pl-c">second</span>][<span class="pl-c">1</span>]<span class="pl-c">*baseFreqs</span>[<span class="pl-c">third</span>][<span class="pl-c">2</span>]<span class="pl-c">;</span></td>
|
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</tr>
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<tr>
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<td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
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<td id="LC140" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
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<tr>
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<td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
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<td id="LC141" 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="L142" class="blob-num js-line-number" data-line-number="142"></td>
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<td id="LC142" class="blob-code blob-code-inner js-file-line"><span class="pl-c">codonFreqs = codonFreqs*(1</span><span class="pl-en">.</span><span class="pl-c">0/PIStop);</span></td>
|
|
</tr>
|
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<tr>
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<td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
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<td id="LC143" 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="L144" class="blob-num js-line-number" data-line-number="144"></td>
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<td id="LC144" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/*9</span><span class="pl-en">.</span><span class="pl-c"> define the codon model */</span></td>
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</tr>
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<tr>
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<td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
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<td id="LC145" 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="L146" class="blob-num js-line-number" data-line-number="146"></td>
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<td id="LC146" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Model GY_Model = (GY_Matrix</span><span class="pl-en">,</span><span class="pl-c">codonFreqs</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
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</tr>
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<tr>
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<td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
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<td id="LC147" 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="L148" class="blob-num js-line-number" data-line-number="148"></td>
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<td id="LC148" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/*10</span><span class="pl-en">.</span><span class="pl-c"> Define the tree and pick the foreground branch</span><span class="pl-en">,</span><span class="pl-c"> displaying a tree window to facilitate selection; </span></td>
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</tr>
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<tr>
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<td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
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<td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-c">the latter step is executed for 2 of 3 model choices */</span></td>
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</tr>
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<tr>
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<td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
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<td id="LC150" 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="L151" class="blob-num js-line-number" data-line-number="151"></td>
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<td id="LC151" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Tree givenTree1 = treeString;</span></td>
|
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</tr>
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<tr>
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<td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
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<td id="LC152" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Tree givenTree2 = treeString;</span></td>
|
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</tr>
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<tr>
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<td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
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<td id="LC153" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Tree givenTree3 = treeString;</span></td>
|
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</tr>
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<tr>
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<td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
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<td id="LC154" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Tree givenTree4 = treeString;</span></td>
|
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</tr>
|
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<tr>
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<td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
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<td id="LC155" 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="L156" class="blob-num js-line-number" data-line-number="156"></td>
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<td id="LC156" class="blob-code blob-code-inner js-file-line"><span class="pl-c">USE_LAST_RESULTS = 0;</span></td>
|
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</tr>
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<tr>
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<td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
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<td id="LC157" class="blob-code blob-code-inner js-file-line"><span class="pl-c">OPTIMIZATION_METHOD = 4;</span></td>
|
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</tr>
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<tr>
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<td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
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<td id="LC158" 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="L159" class="blob-num js-line-number" data-line-number="159"></td>
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<td id="LC159" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/* Approximate kappa and branch lengths using an HKY85 fit */</span></td>
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</tr>
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<tr>
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<td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
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<td id="LC160" 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="L161" class="blob-num js-line-number" data-line-number="161"></td>
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<td id="LC161" class="blob-code blob-code-inner js-file-line"><span class="pl-c">HKY85_Matrix = {{*</span><span class="pl-en">,</span><span class="pl-c">t*kappa_inv</span><span class="pl-en">,</span><span class="pl-c">t</span><span class="pl-en">,</span><span class="pl-c">t*kappa_inv}</span></td>
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</tr>
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<tr>
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<td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
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<td id="LC162" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {t*kappa_inv</span><span class="pl-en">,</span><span class="pl-c">*</span><span class="pl-en">,</span><span class="pl-c">kappa_inv*t</span><span class="pl-en">,</span><span class="pl-c">t}</span></td>
|
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</tr>
|
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<tr>
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<td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
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<td id="LC163" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {t</span><span class="pl-en">,</span><span class="pl-c">t*kappa_inv</span><span class="pl-en">,</span><span class="pl-c">*</span><span class="pl-en">,</span><span class="pl-c">kappa_inv*t}</span></td>
|
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</tr>
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<tr>
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<td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
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<td id="LC164" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {t*kappa_inv</span><span class="pl-en">,</span><span class="pl-c">t</span><span class="pl-en">,</span><span class="pl-c">kappa_inv*t</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="L165" class="blob-num js-line-number" data-line-number="165"></td>
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<td id="LC165" 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="L166" class="blob-num js-line-number" data-line-number="166"></td>
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<td id="LC166" class="blob-code blob-code-inner js-file-line"><span class="pl-c">HarvestFrequencies (nucFreqs</span><span class="pl-en">,</span><span class="pl-c">ds</span><span class="pl-en">,</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
|
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</tr>
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<tr>
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<td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
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<td id="LC167" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Model HKY85_Model = (HKY85_Matrix</span><span class="pl-en">,</span><span class="pl-c">nucFreqs</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
|
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</tr>
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<tr>
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<td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
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<td id="LC168" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
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<tr>
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<td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
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<td id="LC169" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Tree nucTree = treeString;</span></td>
|
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</tr>
|
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<tr>
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<td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
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<td id="LC170" class="blob-code blob-code-inner js-file-line"><span class="pl-c">DataSetFilter nucData = CreateFilter (ds</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
|
|
</tr>
|
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<tr>
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<td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
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<td id="LC171" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
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<tr>
|
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<td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
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<td id="LC172" 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"> "Obtaining nucleotide branch lengths and kappa to be used as starting values</span><span class="pl-en">...</span><span class="pl-c">\n");</span></td>
|
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</tr>
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<tr>
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<td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
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<td id="LC173" class="blob-code blob-code-inner js-file-line"><span class="pl-c">LikelihoodFunction nuc_lf = (nucData</span><span class="pl-en">,</span><span class="pl-c">nucTree);</span></td>
|
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</tr>
|
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<tr>
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<td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
|
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<td id="LC174" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Optimize (nuc_mle</span><span class="pl-en">,</span><span class="pl-c">nuc_lf);</span></td>
|
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</tr>
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<tr>
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<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">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n"</span><span class="pl-en">,</span><span class="pl-c"> Format (nucTree</span><span class="pl-en">,</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">1)</span><span class="pl-en">,</span><span class="pl-c"> "\nkappa="</span><span class="pl-en">,</span><span class="pl-c"> Format (1/kappa_inv</span><span class="pl-en">,</span><span class="pl-c">8</span><span class="pl-en">,</span><span class="pl-c">3)</span><span class="pl-en">,</span><span class="pl-c"> "\n");</span></td>
|
|
</tr>
|
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<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"></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">USE_LAST_RESULTS = 1;</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"></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">mxTreeSpec = {5</span><span class="pl-en">,</span><span class="pl-c">1};</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">mxTreeSpec </span>[<span class="pl-c">0</span>]<span class="pl-c"> = "nucTree";</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">mxTreeSpec </span>[<span class="pl-c">1</span>]<span class="pl-c"> = "8240";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
|
|
<td id="LC182" class="blob-code blob-code-inner js-file-line"><span class="pl-c">mxTreeSpec </span>[<span class="pl-c">2</span>]<span class="pl-c"> = "10</span><span class="pl-en">,</span><span class="pl-c">40</span><span class="pl-en">,</span><span class="pl-c1">-</span><span class="pl-c">10</span><span class="pl-en">,</span><span class="pl-c1">-</span><span class="pl-c">175</span><span class="pl-en">,</span><span class="pl-c">1";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
|
|
<td id="LC183" class="blob-code blob-code-inner js-file-line"><span class="pl-c">mxTreeSpec </span>[<span class="pl-c">3</span>]<span class="pl-c"> = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
|
|
<td id="LC184" class="blob-code blob-code-inner js-file-line"><span class="pl-c">mxTreeSpec </span>[<span class="pl-c">4</span>]<span class="pl-c"> = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
|
|
<td id="LC185" class="blob-code blob-code-inner js-file-line"><span class="pl-c">OpenWindow (TREEWINDOW</span><span class="pl-en">,</span><span class="pl-c"> mxTreeSpec</span><span class="pl-en">,</span><span class="pl-c">"(SCREEN_WIDTH</span><span class="pl-c1">-</span><span class="pl-c">50)/2;(SCREEN_HEIGHT</span><span class="pl-c1">-</span><span class="pl-c">50)/2;30</span><span class="pl-c1">+</span><span class="pl-c">(SCREEN_WIDTH</span><span class="pl-c1">-</span><span class="pl-c">30)/2;45"); </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
|
|
<td id="LC186" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
|
|
<td id="LC187" class="blob-code blob-code-inner js-file-line"><span class="pl-c">leafNodes = TipCount (givenTree); </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
|
|
<td id="LC188" class="blob-code blob-code-inner js-file-line"><span class="pl-c">internalNodes = BranchCount(givenTree);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
|
|
<td id="LC189" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
|
|
<td id="LC190" class="blob-code blob-code-inner js-file-line"><span class="pl-c">choiceMatrix = {internalNodes</span><span class="pl-c1">+</span><span class="pl-c">leafNodes</span><span class="pl-en">,</span><span class="pl-c">2};</span></td>
|
|
</tr>
|
|
<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">for (bc=0; bc</span><span class="pl-k"><</span><span class="pl-c">internalNodes; bc=bc</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
|
|
<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>
|
|
<td id="LC193" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> choiceMatrix</span>[<span class="pl-c">bc</span>][<span class="pl-c">0</span>]<span class="pl-c"> = BranchName(givenTree</span><span class="pl-en">,</span><span class="pl-c">bc);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
|
|
<td id="LC194" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> choiceMatrix</span>[<span class="pl-c">bc</span>][<span class="pl-c">1</span>]<span class="pl-c"> = "Internal Branch Rooting " </span><span class="pl-c1">+</span><span class="pl-c"> givenTree</span>[<span class="pl-c">bc</span>]<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">}</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">for (bc=0; bc</span><span class="pl-k"><</span><span class="pl-c">leafNodes; bc=bc</span><span class="pl-c1">+</span><span class="pl-c">1)</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">{</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"> choiceMatrix</span>[<span class="pl-c">bc</span><span class="pl-c1">+</span><span class="pl-c">internalNodes</span>][<span class="pl-c">0</span>]<span class="pl-c"> = TipName(givenTree</span><span class="pl-en">,</span><span class="pl-c">bc);</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"> choiceMatrix</span>[<span class="pl-c">bc</span><span class="pl-c1">+</span><span class="pl-c">internalNodes</span>][<span class="pl-c">1</span>]<span class="pl-c"> = "Leaf node " </span><span class="pl-c1">+</span><span class="pl-c"> choiceMatrix</span>[<span class="pl-c">bc</span><span class="pl-c1">+</span><span class="pl-c">internalNodes</span>][<span class="pl-c">0</span>]<span class="pl-c">;</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">}</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">ChoiceList (stOption</span><span class="pl-en">,</span><span class="pl-c">"Choose the foreground branch"</span><span class="pl-en">,</span><span class="pl-c">0</span><span class="pl-en">,</span><span class="pl-c">NO_SKIP</span><span class="pl-en">,</span><span class="pl-c">choiceMatrix);</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">if (stOption</span>[<span class="pl-c">0</span>]<span class="pl-c"> </span><span class="pl-k"><</span><span class="pl-c"> 0)</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"> return </span><span class="pl-c1">-</span><span class="pl-c">1;</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"></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">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n\n"</span><span class="pl-en">,</span><span class="pl-c"> Columns (stOption)</span><span class="pl-en">,</span><span class="pl-c">" foreground branch(es) set to: "</span><span class="pl-en">,</span><span class="pl-c"> "\n");</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">for (bc = 0; bc </span><span class="pl-k"><</span><span class="pl-c"> Columns (stOption); bc = bc </span><span class="pl-c1">+</span><span class="pl-c"> 1)</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"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> choiceMatrix</span>[<span class="pl-c">stOption</span>[<span class="pl-c">bc</span>]][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c"> "\n");</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">}</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">OpenWindow (CLOSEWINDOW</span><span class="pl-en">,</span><span class="pl-c"> "Tree nucTree");</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"> </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">/* 15</span><span class="pl-en">.</span><span class="pl-c"> Constrain dS and dN in the tree to based upon different models */</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"></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">global omega_1 = 0</span><span class="pl-en">.</span><span class="pl-c">25;</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">global omega_2 = 0</span><span class="pl-en">.</span><span class="pl-c">5;</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">global omega_3 = 1</span><span class="pl-en">.</span><span class="pl-c">5;</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">omega_1 :</span><span class="pl-k"><</span><span class="pl-c"> 1;</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">omega_2 :</span><span class="pl-k"><</span><span class="pl-c"> 1;</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">omega_3 :</span><span class="pl-k">></span><span class="pl-c"> 1;</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">ClearConstraints (givenTree1);</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">ClearConstraints (givenTree2);</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">ClearConstraints (givenTree3);</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">ClearConstraints (givenTree4);</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">/* 16</span><span class="pl-en">.</span><span class="pl-c"> define and optimize the likelihood function */</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">bNames = BranchName (givenTree</span><span class="pl-en">,</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">nucBL = BranchLength (nucTree</span><span class="pl-en">,</span><span class="pl-c1">-</span><span class="pl-c">1);</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"></span></td>
|
|
</tr>
|
|
<tr>
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<td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
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<td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (bc=0; bc</span><span class="pl-k"><</span><span class="pl-c">Columns(bNames)</span><span class="pl-c1">-</span><span class="pl-c">1; bc=bc</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
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</tr>
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<tr>
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<td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
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<td id="LC237" 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="L238" class="blob-num js-line-number" data-line-number="238"></td>
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<td id="LC238" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree1</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
|
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</tr>
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<tr>
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<td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
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<td id="LC239" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree1</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
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</tr>
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<tr>
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<td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
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<td id="LC240" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree2</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
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</tr>
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<tr>
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<td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
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<td id="LC241" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree2</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
|
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</tr>
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<tr>
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<td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
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<td id="LC242" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree3</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
|
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</tr>
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<tr>
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<td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
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<td id="LC243" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree3</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</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"> ExecuteCommands ("givenTree4</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
|
|
</tr>
|
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<tr>
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<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"> ExecuteCommands ("givenTree4</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
|
|
</tr>
|
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<tr>
|
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<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">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
|
|
<td id="LC247" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
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<tr>
|
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<td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
|
|
<td id="LC248" class="blob-code blob-code-inner js-file-line"><span class="pl-c">codBL = BranchLength (givenTree1</span><span class="pl-en">,</span><span class="pl-c1">-</span><span class="pl-c">1);</span></td>
|
|
</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></td>
|
|
</tr>
|
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<tr>
|
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<td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
|
|
<td id="LC250" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (bc=0; bc</span><span class="pl-k"><</span><span class="pl-c">Columns(bNames)</span><span class="pl-c1">-</span><span class="pl-c">1; bc=bc</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
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<tr>
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<td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
|
|
<td id="LC251" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
|
|
<td id="LC252" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (nucBL</span>[<span class="pl-c">bc</span>]<span class="pl-k">></span><span class="pl-c">0)</span></td>
|
|
</tr>
|
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<tr>
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<td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
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<td id="LC253" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
|
|
<td id="LC254" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> scalingFactor = nucBL</span>[<span class="pl-c">bc</span>]<span class="pl-c">/codBL</span>[<span class="pl-c">bc</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
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<tr>
|
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<td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
|
|
<td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree1</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate=nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</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">scalingFactor</span><span class="pl-c1">+</span><span class="pl-c">";");</span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
|
|
<td id="LC256" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree1</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate=nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</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">scalingFactor</span><span class="pl-c1">+</span><span class="pl-c">";");</span></td>
|
|
</tr>
|
|
<tr>
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|
<td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
|
|
<td id="LC257" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree2</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate=nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</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">scalingFactor</span><span class="pl-c1">+</span><span class="pl-c">";");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
|
|
<td id="LC258" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree2</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate=nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</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">scalingFactor</span><span class="pl-c1">+</span><span class="pl-c">";");</span></td>
|
|
</tr>
|
|
<tr>
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|
<td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
|
|
<td id="LC259" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree3</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate=nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</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">scalingFactor</span><span class="pl-c1">+</span><span class="pl-c">";");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
|
|
<td id="LC260" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree3</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate=nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</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">scalingFactor</span><span class="pl-c1">+</span><span class="pl-c">";");</span></td>
|
|
</tr>
|
|
<tr>
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|
<td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
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<td id="LC261" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree4</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
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|
<td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree4</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate =nucTree</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bNames</span>[<span class="pl-c">bc</span>]<span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">t;");</span></td>
|
|
</tr>
|
|
<tr>
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|
<td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
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<td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
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|
<tr>
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|
<td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
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<td id="LC264" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
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|
<tr>
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|
<td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
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<td id="LC265" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
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<tr>
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<td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
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<td id="LC266" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (bc = 0; bc </span><span class="pl-k"><</span><span class="pl-c"> Columns (stOption); bc = bc </span><span class="pl-c1">+</span><span class="pl-c"> 1)</span></td>
|
|
</tr>
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|
<tr>
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|
<td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
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<td id="LC267" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
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<tr>
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|
<td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
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<td id="LC268" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bName = choiceMatrix</span>[<span class="pl-c">stOption</span>[<span class="pl-c">bc</span>]][<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
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<tr>
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<td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
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|
<td id="LC269" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree1</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate:=omega_1*givenTree1</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
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<td id="LC270" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree2</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate:=omega_2*givenTree2</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate");</span></td>
|
|
</tr>
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<tr>
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<td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
|
|
<td id="LC271" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree3</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate:=givenTree3</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate");</span></td>
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</tr>
|
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<tr>
|
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<td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
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<td id="LC272" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("givenTree4</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nonSynRate:=omega_3*givenTree4</span><span class="pl-en">.</span><span class="pl-c">"</span><span class="pl-c1">+</span><span class="pl-c">bName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">synRate");</span></td>
|
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</tr>
|
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<tr>
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<td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
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<td id="LC273" 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>
|
|
<td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
|
|
<td id="LC274" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
|
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<td id="LC275" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
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<tr>
|
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<td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
|
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<td id="LC276" class="blob-code blob-code-inner js-file-line"><span class="pl-c">OPTIMIZATION_PRECISION = 0</span><span class="pl-en">.</span><span class="pl-c">001;</span></td>
|
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</tr>
|
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<tr>
|
|
<td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
|
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<td id="LC277" 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>
|
|
<td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
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<td id="LC278" class="blob-code blob-code-inner js-file-line"><span class="pl-c">global P_1 = 1/4;</span></td>
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</tr>
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<tr>
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<td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
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<td id="LC279" class="blob-code blob-code-inner js-file-line"><span class="pl-c">global P_2 = 1/3;</span></td>
|
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</tr>
|
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<tr>
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<td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
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<td id="LC280" class="blob-code blob-code-inner js-file-line"><span class="pl-c">global P_3 = 1/2;</span></td>
|
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</tr>
|
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<tr>
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|
<td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
|
|
<td id="LC281" class="blob-code blob-code-inner js-file-line"><span class="pl-c">P_1 :</span><span class="pl-k"><</span><span class="pl-c"> 1;</span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
|
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<td id="LC282" class="blob-code blob-code-inner js-file-line"><span class="pl-c">P_2 :</span><span class="pl-k"><</span><span class="pl-c"> 1;</span></td>
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</tr>
|
|
<tr>
|
|
<td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
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|
<td id="LC283" class="blob-code blob-code-inner js-file-line"><span class="pl-c">P_3 :</span><span class="pl-k"><</span><span class="pl-c"> 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
|
|
<td id="LC284" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
|
|
<td id="LC285" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
|
|
<td id="LC286" 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"> "\nFitting the model with selection</span><span class="pl-en">...</span><span class="pl-c">\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
|
|
<td id="LC287" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
|
|
<td id="LC288" 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"> givenTree1</span><span class="pl-en">,</span><span class="pl-c"> filteredData</span><span class="pl-en">,</span><span class="pl-c"> givenTree2</span><span class="pl-en">,</span><span class="pl-c">filteredData</span><span class="pl-en">,</span><span class="pl-c"> givenTree3</span><span class="pl-en">,</span><span class="pl-c">filteredData</span><span class="pl-en">,</span><span class="pl-c"> givenTree4</span><span class="pl-en">,</span><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
|
|
<td id="LC289" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> "Log(P_1*SITE_LIKELIHOOD</span>[<span class="pl-c">0</span>]<span class="pl-c1">+</span><span class="pl-c">(1</span><span class="pl-c1">-</span><span class="pl-c">P_1)*P_2*SITE_LIKELIHOOD</span>[<span class="pl-c">1</span>]<span class="pl-c1">+</span><span class="pl-c">(1</span><span class="pl-c1">-</span><span class="pl-c">P_1)(1</span><span class="pl-c1">-</span><span class="pl-c">P_2)*P_3*SITE_LIKELIHOOD</span>[<span class="pl-c">2</span>]<span class="pl-c1">+</span><span class="pl-c">(1</span><span class="pl-c1">-</span><span class="pl-c">P_1)(1</span><span class="pl-c1">-</span><span class="pl-c">P_2)(1</span><span class="pl-c1">-</span><span class="pl-c">P_3)*SITE_LIKELIHOOD</span>[<span class="pl-c">3</span>]<span class="pl-c">)");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
|
|
<td id="LC290" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
|
|
<td id="LC291" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
|
|
<td id="LC292" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Optimize (mles</span><span class="pl-en">,</span><span class="pl-c">lf);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
|
|
<td id="LC293" 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"> lf);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
|
|
<td id="LC294" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
|
|
<td id="LC295" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
</table>
|
|
|
|
</div>
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</div>
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<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a>
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<form accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div>
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<input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus>
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<button type="submit" class="btn">Go</button>
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<textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea>
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