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removing incorrect samples
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Mike Doud
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samples/HyPhy/454.bf
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samples/HyPhy/454.bf
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<a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a>, <a href="#" class="js-clone-selector" data-protocol="ssh">SSH</a>, or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>.
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Clone in Desktop
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<tr>
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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">SetDialogPrompt ("Please specify a di</span><span class="pl-c1">-</span><span class="pl-c">nucleotide (e</span><span class="pl-en">.</span><span class="pl-c">g</span><span class="pl-en">.</span><span class="pl-c"> stem RNA) file:");</span></td>
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<td id="L2" class="blob-num js-line-number" data-line-number="2"></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">DataSet ds = ReadDataFile (PROMPT_FOR_FILE);</span></td>
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</tr>
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<tr>
|
||||
<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">DataSetFilter filteredData = CreateFilter (ds</span><span class="pl-en">,</span><span class="pl-c">2);</span></td>
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||||
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|
||||
<td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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||||
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||||
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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">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c">"\n______________READ THE FOLLOWING DATA______________\n"</span><span class="pl-en">,</span><span class="pl-c">ds);</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="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">SelectTemplateModel(filteredData);</span></td>
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||||
<td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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||||
<td id="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">_DO_TREE_REBALANCE_ = 1;</span></td>
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||||
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<td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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||||
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|
||||
<td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
|
||||
<td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-c">#include "queryTree</span><span class="pl-en">.</span><span class="pl-c">bf";</span></td>
|
||||
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|
||||
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|
||||
<td id="L13" class="blob-num js-line-number" data-line-number="13"></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">LikelihoodFunction lf = (filteredData</span><span class="pl-en">,</span><span class="pl-c">givenTree);</span></td>
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||||
</tr>
|
||||
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|
||||
<td id="L15" class="blob-num js-line-number" data-line-number="15"></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">timer = Time(0);</span></td>
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||||
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|
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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">USE_ADAPTIVE_VARIABLE_STEP = 0;</span></td>
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</tr>
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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">Optimize (res</span><span class="pl-en">,</span><span class="pl-c">lf);</span></td>
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</tr>
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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"></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">timer = Time(0)</span><span class="pl-c1">-</span><span class="pl-c">timer;</span></td>
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||||
</tr>
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<tr>
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<td id="L23" class="blob-num js-line-number" data-line-number="23"></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">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n______________RESULTS______________\nTime taken = "</span><span class="pl-en">,</span><span class="pl-c"> timer</span><span class="pl-en">,</span><span class="pl-c"> " seconds\nAIC Score = "</span><span class="pl-en">,</span><span class="pl-c"> </span></td>
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</tr>
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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"> 2(res</span>[<span class="pl-c">1</span>][<span class="pl-c">1</span>]<span class="pl-c1">-</span><span class="pl-c">res</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-c">)</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">lf);</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="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-c">#include "categoryEcho</span><span class="pl-en">.</span><span class="pl-c">bf";</span></td>
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<p class="loader-error">Cannot retrieve contributors at this time</p>
|
||||
</div>
|
||||
</include-fragment>
|
||||
<div class="file">
|
||||
<div class="file-header">
|
||||
<div class="file-actions">
|
||||
|
||||
<div class="btn-group">
|
||||
<a href="/veg/hyphy/raw/master/res/TemplateBatchFiles/AnalyzeNucProtData.bf" class="btn btn-sm " id="raw-url">Raw</a>
|
||||
<a href="/veg/hyphy/blame/master/res/TemplateBatchFiles/AnalyzeNucProtData.bf" class="btn btn-sm js-update-url-with-hash">Blame</a>
|
||||
<a href="/veg/hyphy/commits/master/res/TemplateBatchFiles/AnalyzeNucProtData.bf" class="btn btn-sm " rel="nofollow">History</a>
|
||||
</div>
|
||||
|
||||
<a class="octicon-btn tooltipped tooltipped-nw"
|
||||
href="https://mac.github.com"
|
||||
aria-label="Open this file in GitHub for Mac">
|
||||
<span class="octicon octicon-device-desktop"></span>
|
||||
</a>
|
||||
|
||||
<form accept-charset="UTF-8" action="/veg/hyphy/edit/master/res/TemplateBatchFiles/AnalyzeNucProtData.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="VF9/H6fUyPDrDwLKChfQZKdKObml/IO0dA8J7ZERpqJz/XcP3maZINrfFzaJlqEBOK7fb85wB18vCptILNs5+Q==" /></div>
|
||||
<button class="octicon-btn tooltipped tooltipped-n" type="submit" aria-label="Fork this project and edit the file" data-hotkey="e" data-disable-with>
|
||||
<span class="octicon octicon-pencil"></span>
|
||||
</button>
|
||||
</form>
|
||||
<form accept-charset="UTF-8" action="/veg/hyphy/delete/master/res/TemplateBatchFiles/AnalyzeNucProtData.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="GeO06MGspN1nhXP+naro11XyxNJLLbaclU5ipXWP2z0Wa2QoSBIC42O6A0kj20wEDugQDOwEhWqqKsBkTPNTiQ==" /></div>
|
||||
<button class="octicon-btn octicon-btn-danger tooltipped tooltipped-n" type="submit" aria-label="Fork this project and delete this file" data-disable-with>
|
||||
<span class="octicon octicon-trashcan"></span>
|
||||
</button>
|
||||
</form> </div>
|
||||
|
||||
<div class="file-info">
|
||||
29 lines (18 sloc)
|
||||
<span class="file-info-divider"></span>
|
||||
0.868 kb
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="blob-wrapper data type-brainfuck">
|
||||
<table class="highlight tab-size-8 js-file-line-container">
|
||||
<tr>
|
||||
<td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
|
||||
<td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-c">_Genetic_Code = 0;</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
|
||||
<td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
|
||||
<td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-c">ExecuteAFile("simpleBootstrap</span><span class="pl-en">.</span><span class="pl-c">bf");</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
|
||||
<td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
|
||||
<td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-c">SetDialogPrompt ("Please specify a nucleotide or amino</span><span class="pl-c1">-</span><span class="pl-c">acid data file:");</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
|
||||
<td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
|
||||
<td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-c">DataSet ds = ReadDataFile (PROMPT_FOR_FILE);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
|
||||
<td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-c">DataSetFilter filteredData = CreateFilter (ds</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
|
||||
<td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
|
||||
<td id="LC10" 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______________READ THE FOLLOWING DATA______________\n"</span><span class="pl-en">,</span><span class="pl-c">ds);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
|
||||
<td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
|
||||
<td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-c">SelectTemplateModel(filteredData);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
|
||||
<td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-c">_DO_TREE_REBALANCE_ = 1;</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
|
||||
<td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
|
||||
<td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-c">ExecuteAFile ("queryTree</span><span class="pl-en">.</span><span class="pl-c">bf");</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
|
||||
<td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
|
||||
<td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-c">LikelihoodFunction lf = (filteredData</span><span class="pl-en">,</span><span class="pl-c">givenTree);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
|
||||
<td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-c">timer = Time(0);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
|
||||
<td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-c">Optimize (res</span><span class="pl-en">,</span><span class="pl-c">lf);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
|
||||
<td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-c">timer = Time(0)</span><span class="pl-c1">-</span><span class="pl-c">timer;</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
|
||||
<td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
|
||||
<td id="LC22" 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______________RESULTS______________\nTime taken = "</span><span class="pl-en">,</span><span class="pl-c"> timer</span><span class="pl-en">,</span><span class="pl-c"> " seconds\nAIC Score = "</span><span class="pl-en">,</span><span class="pl-c"> </span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
|
||||
<td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> 2(res</span>[<span class="pl-c">1</span>][<span class="pl-c">1</span>]<span class="pl-c1">-</span><span class="pl-c">res</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-c">)</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">lf);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
|
||||
<td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
|
||||
<td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-c">ExecuteAFile ("categoryEcho</span><span class="pl-en">.</span><span class="pl-c">bf");</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
|
||||
<td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-c">GetString (lfInfo</span><span class="pl-en">,</span><span class="pl-c"> lf</span><span class="pl-en">,</span><span class="pl-c"> </span><span class="pl-c1">-</span><span class="pl-c">1);</span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
|
||||
<td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
|
||||
<td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-c">return {"Log(L)": res</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c"> "DF": res</span>[<span class="pl-c">1</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c"> "Tree": Format (givenTree</span><span class="pl-en">,</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">1)}</span></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
</div>
|
||||
|
||||
</div>
|
||||
|
||||
<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a>
|
||||
<div id="jump-to-line" style="display:none">
|
||||
<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>
|
||||
<input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus>
|
||||
<button type="submit" class="btn">Go</button>
|
||||
</form></div>
|
||||
|
||||
</div>
|
||||
|
||||
</div><!-- /.repo-container -->
|
||||
<div class="modal-backdrop"></div>
|
||||
</div><!-- /.container -->
|
||||
</div><!-- /.site -->
|
||||
|
||||
|
||||
</div><!-- /.wrapper -->
|
||||
|
||||
<div class="container">
|
||||
<div class="site-footer" role="contentinfo">
|
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<ul class="site-footer-links right">
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<li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
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<li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
|
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<li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li>
|
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|
||||
</ul>
|
||||
|
||||
<a href="https://github.com" aria-label="Homepage">
|
||||
<span class="mega-octicon octicon-mark-github" title="GitHub"></span>
|
||||
</a>
|
||||
<ul class="site-footer-links">
|
||||
<li>© 2015 <span title="0.09534s from github-fe142-cp1-prd.iad.github.net">GitHub</span>, Inc.</li>
|
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<li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li>
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<li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li>
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<li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li>
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<li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li>
|
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</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
<div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay">
|
||||
<div class="fullscreen-container js-suggester-container">
|
||||
<div class="textarea-wrap">
|
||||
<textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea>
|
||||
<div class="suggester-container">
|
||||
<div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="fullscreen-sidebar">
|
||||
<a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode">
|
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<span class="mega-octicon octicon-screen-normal"></span>
|
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</a>
|
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<a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w"
|
||||
aria-label="Switch themes">
|
||||
<span class="octicon octicon-color-mode"></span>
|
||||
</a>
|
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</div>
|
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</div>
|
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|
||||
|
||||
|
||||
|
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|
||||
|
||||
<div id="ajax-error-message" class="flash flash-error">
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<span class="octicon octicon-alert"></span>
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<a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a>
|
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Something went wrong with that request. Please try again.
|
||||
</div>
|
||||
|
||||
|
||||
<script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-2c8ae50712a47d2b83d740cb875d55cdbbb3fdbccf303951cc6b7e63731e0c38.js"></script>
|
||||
<script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-4a9486eb826000c3f9d69ae1adb4372c626ce3a2a602dc3d007aedd874f64c35.js"></script>
|
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|
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|
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|
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<div class="js-socket-channel" data-channel="test:mbdoud"></div>
|
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|
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</body>
|
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</html>
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|
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