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removing incorrect samples
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Mike Doud
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samples/HyPhy/454.bf
2988
samples/HyPhy/454.bf
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data-ga-click="Repository, click unstar button, action:blob#show; text:Unstar">
|
|
||||||
<span class="octicon octicon-star"></span>
|
|
||||||
Unstar
|
|
||||||
</button>
|
|
||||||
<a class="social-count js-social-count" href="/veg/hyphy/stargazers">
|
|
||||||
33
|
|
||||||
</a>
|
|
||||||
</form>
|
|
||||||
<form accept-charset="UTF-8" action="/veg/hyphy/star" class="js-toggler-form unstarred js-star-button" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="RDW9y+YIVPIAXzSr4O54H3wIXuG75vRosCRGFg/0zqc8orOJe2NDSTYZGTvV6VQ/fklKlkawn3ZfxetoUV2IFw==" /></div>
|
|
||||||
<button
|
|
||||||
class="btn btn-sm btn-with-count js-toggler-target"
|
|
||||||
aria-label="Star this repository" title="Star veg/hyphy"
|
|
||||||
data-ga-click="Repository, click star button, action:blob#show; text:Star">
|
|
||||||
<span class="octicon octicon-star"></span>
|
|
||||||
Star
|
|
||||||
</button>
|
|
||||||
<a class="social-count js-social-count" href="/veg/hyphy/stargazers">
|
|
||||||
33
|
|
||||||
</a>
|
|
||||||
</form> </div>
|
|
||||||
|
|
||||||
</li>
|
|
||||||
|
|
||||||
<li>
|
|
||||||
<a href="#fork-destination-box" class="btn btn-sm btn-with-count"
|
|
||||||
title="Fork your own copy of veg/hyphy to your account"
|
|
||||||
aria-label="Fork your own copy of veg/hyphy to your account"
|
|
||||||
rel="facebox"
|
|
||||||
data-ga-click="Repository, show fork modal, action:blob#show; text:Fork">
|
|
||||||
<span class="octicon octicon-repo-forked"></span>
|
|
||||||
Fork
|
|
||||||
</a>
|
|
||||||
<a href="/veg/hyphy/network" class="social-count">19</a>
|
|
||||||
|
|
||||||
<div id="fork-destination-box" style="display: none;">
|
|
||||||
<h2 class="facebox-header">Where should we fork this repository?</h2>
|
|
||||||
<include-fragment src=""
|
|
||||||
class="js-fork-select-fragment fork-select-fragment"
|
|
||||||
data-url="/veg/hyphy/fork?fragment=1">
|
|
||||||
<img alt="Loading" height="64" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-128-338974454bb5c32803e82f601beb051d373744b024fe8742a76009700fd7e033.gif" width="64" />
|
|
||||||
</include-fragment>
|
|
||||||
</div>
|
|
||||||
</li>
|
|
||||||
|
|
||||||
</ul>
|
|
||||||
|
|
||||||
<h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public">
|
|
||||||
<span class="mega-octicon octicon-repo"></span>
|
|
||||||
<span class="author"><a href="/veg" class="url fn" itemprop="url" rel="author"><span itemprop="title">veg</span></a></span><!--
|
|
||||||
--><span class="path-divider">/</span><!--
|
|
||||||
--><strong><a href="/veg/hyphy" class="js-current-repository" data-pjax="#js-repo-pjax-container">hyphy</a></strong>
|
|
||||||
|
|
||||||
<span class="page-context-loader">
|
|
||||||
<img alt="" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</span>
|
|
||||||
|
|
||||||
</h1>
|
|
||||||
</div><!-- /.container -->
|
|
||||||
</div><!-- /.repohead -->
|
|
||||||
|
|
||||||
<div class="container">
|
|
||||||
<div class="repository-with-sidebar repo-container new-discussion-timeline ">
|
|
||||||
|
|
||||||
<div class="repository-sidebar clearfix">
|
|
||||||
|
|
||||||
<nav class="sunken-menu repo-nav js-repo-nav js-sidenav-container-pjax js-octicon-loaders"
|
|
||||||
role="navigation"
|
|
||||||
data-pjax="#js-repo-pjax-container"
|
|
||||||
data-issue-count-url="/veg/hyphy/issues/counts">
|
|
||||||
<ul class="sunken-menu-group">
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Code">
|
|
||||||
<a href="/veg/hyphy" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /veg/hyphy">
|
|
||||||
<span class="octicon octicon-code"></span> <span class="full-word">Code</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Issues">
|
|
||||||
<a href="/veg/hyphy/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /veg/hyphy/issues">
|
|
||||||
<span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span>
|
|
||||||
<span class="js-issue-replace-counter"></span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Pull requests">
|
|
||||||
<a href="/veg/hyphy/pulls" aria-label="Pull requests" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g p" data-selected-links="repo_pulls /veg/hyphy/pulls">
|
|
||||||
<span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull requests</span>
|
|
||||||
<span class="js-pull-replace-counter"></span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Wiki">
|
|
||||||
<a href="/veg/hyphy/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g w" data-selected-links="repo_wiki /veg/hyphy/wiki">
|
|
||||||
<span class="octicon octicon-book"></span> <span class="full-word">Wiki</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
</ul>
|
|
||||||
<div class="sunken-menu-separator"></div>
|
|
||||||
<ul class="sunken-menu-group">
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Pulse">
|
|
||||||
<a href="/veg/hyphy/pulse" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-selected-links="pulse /veg/hyphy/pulse">
|
|
||||||
<span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Graphs">
|
|
||||||
<a href="/veg/hyphy/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-selected-links="repo_graphs repo_contributors /veg/hyphy/graphs">
|
|
||||||
<span class="octicon octicon-graph"></span> <span class="full-word">Graphs</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
</ul>
|
|
||||||
|
|
||||||
|
|
||||||
</nav>
|
|
||||||
|
|
||||||
<div class="only-with-full-nav">
|
|
||||||
|
|
||||||
<div class="clone-url open"
|
|
||||||
data-protocol-type="http"
|
|
||||||
data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone">
|
|
||||||
<h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
|
|
||||||
<div class="input-group js-zeroclipboard-container">
|
|
||||||
<input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
||||||
value="https://github.com/veg/hyphy.git" readonly="readonly">
|
|
||||||
<span class="input-group-button">
|
|
||||||
<button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
<div class="clone-url "
|
|
||||||
data-protocol-type="ssh"
|
|
||||||
data-url="/users/set_protocol?protocol_selector=ssh&protocol_type=clone">
|
|
||||||
<h3><span class="text-emphasized">SSH</span> clone URL</h3>
|
|
||||||
<div class="input-group js-zeroclipboard-container">
|
|
||||||
<input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
||||||
value="git@github.com:veg/hyphy.git" readonly="readonly">
|
|
||||||
<span class="input-group-button">
|
|
||||||
<button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
<div class="clone-url "
|
|
||||||
data-protocol-type="subversion"
|
|
||||||
data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone">
|
|
||||||
<h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
|
|
||||||
<div class="input-group js-zeroclipboard-container">
|
|
||||||
<input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
||||||
value="https://github.com/veg/hyphy" readonly="readonly">
|
|
||||||
<span class="input-group-button">
|
|
||||||
<button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<p class="clone-options">You can clone with
|
|
||||||
<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>.
|
|
||||||
<a href="https://help.github.com/articles/which-remote-url-should-i-use" class="help tooltipped tooltipped-n" aria-label="Get help on which URL is right for you.">
|
|
||||||
<span class="octicon octicon-question"></span>
|
|
||||||
</a>
|
|
||||||
</p>
|
|
||||||
|
|
||||||
<a href="https://mac.github.com" class="btn btn-sm sidebar-button" title="Save veg/hyphy to your computer and use it in GitHub Desktop." aria-label="Save veg/hyphy to your computer and use it in GitHub Desktop.">
|
|
||||||
<span class="octicon octicon-device-desktop"></span>
|
|
||||||
Clone in Desktop
|
|
||||||
</a>
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<a href="/veg/hyphy/archive/master.zip"
|
|
||||||
class="btn btn-sm sidebar-button"
|
|
||||||
aria-label="Download the contents of veg/hyphy as a zip file"
|
|
||||||
title="Download the contents of veg/hyphy as a zip file"
|
|
||||||
rel="nofollow">
|
|
||||||
<span class="octicon octicon-cloud-download"></span>
|
|
||||||
Download ZIP
|
|
||||||
</a>
|
|
||||||
</div>
|
|
||||||
</div><!-- /.repository-sidebar -->
|
|
||||||
|
|
||||||
<div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container>
|
|
||||||
|
|
||||||
|
|
||||||
<a href="/veg/hyphy/blob/66b2da6b42ae878820f9ac1e34be2fef8db8d145/res/TemplateBatchFiles/AnalyzeDiNucData.bf" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a>
|
|
||||||
|
|
||||||
<!-- blob contrib key: blob_contributors:v21:8bb6546cf3a31fd355f2ed73eeffdd28 -->
|
|
||||||
|
|
||||||
<div class="file-navigation js-zeroclipboard-container">
|
|
||||||
|
|
||||||
<div class="select-menu js-menu-container js-select-menu left">
|
|
||||||
<span class="btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w"
|
|
||||||
data-master-branch="master"
|
|
||||||
data-ref="master"
|
|
||||||
title="master"
|
|
||||||
role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true">
|
|
||||||
<span class="octicon octicon-git-branch"></span>
|
|
||||||
<i>branch:</i>
|
|
||||||
<span class="js-select-button css-truncate-target">master</span>
|
|
||||||
</span>
|
|
||||||
|
|
||||||
<div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true">
|
|
||||||
|
|
||||||
<div class="select-menu-modal">
|
|
||||||
<div class="select-menu-header">
|
|
||||||
<span class="select-menu-title">Switch branches/tags</span>
|
|
||||||
<span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
<div class="select-menu-filters">
|
|
||||||
<div class="select-menu-text-filter">
|
|
||||||
<input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags">
|
|
||||||
</div>
|
|
||||||
<div class="select-menu-tabs">
|
|
||||||
<ul>
|
|
||||||
<li class="select-menu-tab">
|
|
||||||
<a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab">Branches</a>
|
|
||||||
</li>
|
|
||||||
<li class="select-menu-tab">
|
|
||||||
<a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab">Tags</a>
|
|
||||||
</li>
|
|
||||||
</ul>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
<div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches">
|
|
||||||
|
|
||||||
<div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
|
|
||||||
|
|
||||||
|
|
||||||
<a class="select-menu-item js-navigation-item js-navigation-open "
|
|
||||||
href="/veg/hyphy/blob/art/res/TemplateBatchFiles/AnalyzeDiNucData.bf"
|
|
||||||
data-name="art"
|
|
||||||
data-skip-pjax="true"
|
|
||||||
rel="nofollow">
|
|
||||||
<span class="select-menu-item-icon octicon octicon-check"></span>
|
|
||||||
<span class="select-menu-item-text css-truncate-target" title="art">
|
|
||||||
art
|
|
||||||
</span>
|
|
||||||
</a>
|
|
||||||
<a class="select-menu-item js-navigation-item js-navigation-open "
|
|
||||||
href="/veg/hyphy/blob/bgm/res/TemplateBatchFiles/AnalyzeDiNucData.bf"
|
|
||||||
data-name="bgm"
|
|
||||||
data-skip-pjax="true"
|
|
||||||
rel="nofollow">
|
|
||||||
<span class="select-menu-item-icon octicon octicon-check"></span>
|
|
||||||
<span class="select-menu-item-text css-truncate-target" title="bgm">
|
|
||||||
bgm
|
|
||||||
</span>
|
|
||||||
</a>
|
|
||||||
<a class="select-menu-item js-navigation-item js-navigation-open "
|
|
||||||
href="/veg/hyphy/blob/gh-pages/res/TemplateBatchFiles/AnalyzeDiNucData.bf"
|
|
||||||
data-name="gh-pages"
|
|
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data-skip-pjax="true"
|
|
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rel="nofollow">
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|
||||||
<span class="select-menu-item-icon octicon octicon-check"></span>
|
|
||||||
<span class="select-menu-item-text css-truncate-target" title="gh-pages">
|
|
||||||
gh-pages
|
|
||||||
</span>
|
|
||||||
</a>
|
|
||||||
<a class="select-menu-item js-navigation-item js-navigation-open "
|
|
||||||
href="/veg/hyphy/blob/hyphyqt/res/TemplateBatchFiles/AnalyzeDiNucData.bf"
|
|
||||||
data-name="hyphyqt"
|
|
||||||
data-skip-pjax="true"
|
|
||||||
rel="nofollow">
|
|
||||||
<span class="select-menu-item-icon octicon octicon-check"></span>
|
|
||||||
<span class="select-menu-item-text css-truncate-target" title="hyphyqt">
|
|
||||||
hyphyqt
|
|
||||||
</span>
|
|
||||||
</a>
|
|
||||||
<a class="select-menu-item js-navigation-item js-navigation-open selected"
|
|
||||||
href="/veg/hyphy/blob/master/res/TemplateBatchFiles/AnalyzeDiNucData.bf"
|
|
||||||
data-name="master"
|
|
||||||
data-skip-pjax="true"
|
|
||||||
rel="nofollow">
|
|
||||||
<span class="select-menu-item-icon octicon octicon-check"></span>
|
|
||||||
<span class="select-menu-item-text css-truncate-target" title="master">
|
|
||||||
master
|
|
||||||
</span>
|
|
||||||
</a>
|
|
||||||
<a class="select-menu-item js-navigation-item js-navigation-open "
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data-name="v2.2.2"
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rel="nofollow"
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class="js-navigation-open select-menu-item-text css-truncate-target"
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title="v2.2.2">v2.2.2</a>
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rel="nofollow"
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class="js-navigation-open select-menu-item-text css-truncate-target"
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rel="nofollow"
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class="js-navigation-open select-menu-item-text css-truncate-target"
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title="2.2.3">2.2.3</a>
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class="js-navigation-open select-menu-item-text css-truncate-target"
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data-name="2.1.2"
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||||||
data-skip-pjax="true"
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||||||
rel="nofollow"
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||||||
class="js-navigation-open select-menu-item-text css-truncate-target"
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||||||
title="2.1.2">2.1.2</a>
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||||||
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||||||
<a href="/veg/hyphy/tree/2.1.1/res/TemplateBatchFiles/AnalyzeDiNucData.bf"
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data-name="2.1.1"
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||||||
data-skip-pjax="true"
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||||||
rel="nofollow"
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||||||
class="js-navigation-open select-menu-item-text css-truncate-target"
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||||||
title="2.1.1">2.1.1</a>
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||||||
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||||||
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|
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</a>
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<button aria-label="Copy file path to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
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|
||||||
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|
||||||
|
|
||||||
<div class="breadcrumb js-zeroclipboard-target">
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|
||||||
<span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/veg/hyphy" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">hyphy</span></a></span></span><span class="separator">/</span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/veg/hyphy/tree/master/res" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">res</span></a></span><span class="separator">/</span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/veg/hyphy/tree/master/res/TemplateBatchFiles" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">TemplateBatchFiles</span></a></span><span class="separator">/</span><strong class="final-path">AnalyzeDiNucData.bf</strong>
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||||||
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||||||
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|
||||||
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|
||||||
<include-fragment class="commit commit-loader file-history-tease" src="/veg/hyphy/contributors/master/res/TemplateBatchFiles/AnalyzeDiNucData.bf">
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||||||
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Fetching contributors…
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|
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||||||
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|
||||||
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|
||||||
<p class="loader-loading"><img alt="" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-EAF2F5-0bdc57d34b85c4a4de9d0d1db10cd70e8a95f33ff4f46c5a8c48b4bf4e5a9abe.gif" width="16" /></p>
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||||||
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||||||
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||||||
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||||||
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||||||
<div class="file-actions">
|
|
||||||
|
|
||||||
<div class="btn-group">
|
|
||||||
<a href="/veg/hyphy/raw/master/res/TemplateBatchFiles/AnalyzeDiNucData.bf" class="btn btn-sm " id="raw-url">Raw</a>
|
|
||||||
<a href="/veg/hyphy/blame/master/res/TemplateBatchFiles/AnalyzeDiNucData.bf" class="btn btn-sm js-update-url-with-hash">Blame</a>
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|
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<a href="/veg/hyphy/commits/master/res/TemplateBatchFiles/AnalyzeDiNucData.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">
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|
||||||
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|
||||||
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|
||||||
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|
||||||
<form accept-charset="UTF-8" action="/veg/hyphy/edit/master/res/TemplateBatchFiles/AnalyzeDiNucData.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="XLDmKBLAZSbb4wG6DAH/JapHYPuC3akKl4JwhLXPqs3QZv1M+rhd/rn0NAmp46wxqAIrfx6SZ9c9587xEzd+dA==" /></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>
|
|
||||||
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|
|
||||||
</button>
|
|
||||||
</form>
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||||||
<form accept-charset="UTF-8" action="/veg/hyphy/delete/master/res/TemplateBatchFiles/AnalyzeDiNucData.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="8jsW8AVF7y8g2mB63A5z2CvHp28dcI4nhkLdU0fDY/xN/VUSz9BaIfC7NsGUWsSy0blxuEdLdkd0+GfkdAEF+A==" /></div>
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|
||||||
<button class="octicon-btn octicon-btn-danger tooltipped tooltipped-n" type="submit" aria-label="Fork this project and delete this file" data-disable-with>
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|
||||||
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||||||
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||||||
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||||||
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||||||
<div class="file-info">
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||||||
29 lines (15 sloc)
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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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||||||
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<td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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<td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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<td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-c">DataSet ds = ReadDataFile (PROMPT_FOR_FILE);</span></td>
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||||||
</tr>
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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">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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<td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></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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||||||
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<tr>
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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"></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">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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<td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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<td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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<td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-c">#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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||||||
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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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<td id="L17" class="blob-num js-line-number" data-line-number="17"></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="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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<td id="L21" class="blob-num js-line-number" data-line-number="21"></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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||||||
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||||||
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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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|
||||||
<span class="octicon octicon-gear"></span>
|
|
||||||
</a>
|
|
||||||
</li>
|
|
||||||
|
|
||||||
<li class="header-nav-item">
|
|
||||||
<form accept-charset="UTF-8" action="/logout" class="logout-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="BoRqBv5lBGb8dIB2lJFJ+2khX57NsA9SMpwq10d+LIt0dtSqkpj+wxbiR69VkR1pqifSVw6/bH4MuQ9YfawL+w==" /></div>
|
|
||||||
<button class="header-nav-link sign-out-button tooltipped tooltipped-s" aria-label="Sign out" data-ga-click="Header, sign out, icon:logout">
|
|
||||||
<span class="octicon octicon-sign-out"></span>
|
|
||||||
</button>
|
|
||||||
</form> </li>
|
|
||||||
|
|
||||||
</ul>
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<div id="start-of-content" class="accessibility-aid"></div>
|
|
||||||
<div class="site" itemscope itemtype="http://schema.org/WebPage">
|
|
||||||
<div id="js-flash-container">
|
|
||||||
|
|
||||||
</div>
|
|
||||||
<div class="pagehead repohead instapaper_ignore readability-menu">
|
|
||||||
<div class="container">
|
|
||||||
|
|
||||||
<ul class="pagehead-actions">
|
|
||||||
|
|
||||||
<li>
|
|
||||||
<form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="L3E1Ti6uxKGXAsj7+Im6+rzdniZhZ6kMQhtYHjkMQ8ZPBg2oQowBAg4Rakqd6qxQvHo3cOYu7JnsblNb6hURmA==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="2304875" />
|
|
||||||
|
|
||||||
<div class="select-menu js-menu-container js-select-menu">
|
|
||||||
<a href="/veg/hyphy/subscription"
|
|
||||||
class="btn btn-sm btn-with-count select-menu-button js-menu-target" role="button" tabindex="0" aria-haspopup="true"
|
|
||||||
data-ga-click="Repository, click Watch settings, action:blob#show">
|
|
||||||
<span class="js-select-button">
|
|
||||||
<span class="octicon octicon-eye"></span>
|
|
||||||
Watch
|
|
||||||
</span>
|
|
||||||
</a>
|
|
||||||
<a class="social-count js-social-count" href="/veg/hyphy/watchers">
|
|
||||||
16
|
|
||||||
</a>
|
|
||||||
|
|
||||||
<div class="select-menu-modal-holder">
|
|
||||||
<div class="select-menu-modal subscription-menu-modal js-menu-content" aria-hidden="true">
|
|
||||||
<div class="select-menu-header">
|
|
||||||
<span class="select-menu-title">Notifications</span>
|
|
||||||
<span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
<div class="select-menu-list js-navigation-container" role="menu">
|
|
||||||
|
|
||||||
<div class="select-menu-item js-navigation-item selected" role="menuitem" tabindex="0">
|
|
||||||
<span class="select-menu-item-icon octicon octicon-check"></span>
|
|
||||||
<div class="select-menu-item-text">
|
|
||||||
<input checked="checked" id="do_included" name="do" type="radio" value="included" />
|
|
||||||
<span class="select-menu-item-heading">Not watching</span>
|
|
||||||
<span class="description">Be notified when participating or @mentioned.</span>
|
|
||||||
<span class="js-select-button-text hidden-select-button-text">
|
|
||||||
<span class="octicon octicon-eye"></span>
|
|
||||||
Watch
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
<div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0">
|
|
||||||
<span class="select-menu-item-icon octicon octicon octicon-check"></span>
|
|
||||||
<div class="select-menu-item-text">
|
|
||||||
<input id="do_subscribed" name="do" type="radio" value="subscribed" />
|
|
||||||
<span class="select-menu-item-heading">Watching</span>
|
|
||||||
<span class="description">Be notified of all conversations.</span>
|
|
||||||
<span class="js-select-button-text hidden-select-button-text">
|
|
||||||
<span class="octicon octicon-eye"></span>
|
|
||||||
Unwatch
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
<div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0">
|
|
||||||
<span class="select-menu-item-icon octicon octicon-check"></span>
|
|
||||||
<div class="select-menu-item-text">
|
|
||||||
<input id="do_ignore" name="do" type="radio" value="ignore" />
|
|
||||||
<span class="select-menu-item-heading">Ignoring</span>
|
|
||||||
<span class="description">Never be notified.</span>
|
|
||||||
<span class="js-select-button-text hidden-select-button-text">
|
|
||||||
<span class="octicon octicon-mute"></span>
|
|
||||||
Stop ignoring
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
</div>
|
|
||||||
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
</form>
|
|
||||||
</li>
|
|
||||||
|
|
||||||
<li>
|
|
||||||
|
|
||||||
<div class="js-toggler-container js-social-container starring-container ">
|
|
||||||
|
|
||||||
<form accept-charset="UTF-8" action="/veg/hyphy/unstar" class="js-toggler-form starred js-unstar-button" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="D7ur7Wk6HuFwB1F7XFiuZhvzg26sNXggmOngeoCZz7RCt0GUyDC5ANCOuJWqUL1ehGMDX7Ccy0eObKZbdL+bDA==" /></div>
|
|
||||||
<button
|
|
||||||
class="btn btn-sm btn-with-count js-toggler-target"
|
|
||||||
aria-label="Unstar this repository" title="Unstar veg/hyphy"
|
|
||||||
data-ga-click="Repository, click unstar button, action:blob#show; text:Unstar">
|
|
||||||
<span class="octicon octicon-star"></span>
|
|
||||||
Unstar
|
|
||||||
</button>
|
|
||||||
<a class="social-count js-social-count" href="/veg/hyphy/stargazers">
|
|
||||||
33
|
|
||||||
</a>
|
|
||||||
</form>
|
|
||||||
<form accept-charset="UTF-8" action="/veg/hyphy/star" class="js-toggler-form unstarred js-star-button" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="hiBhB1z3Bi8cHeqC8/5aCulC/0rUFWHVjBK4BMoMXHiLwjuBbNW5VXKyyZ55krGg0Y/3qNOQyTq0HlwPzt9Eng==" /></div>
|
|
||||||
<button
|
|
||||||
class="btn btn-sm btn-with-count js-toggler-target"
|
|
||||||
aria-label="Star this repository" title="Star veg/hyphy"
|
|
||||||
data-ga-click="Repository, click star button, action:blob#show; text:Star">
|
|
||||||
<span class="octicon octicon-star"></span>
|
|
||||||
Star
|
|
||||||
</button>
|
|
||||||
<a class="social-count js-social-count" href="/veg/hyphy/stargazers">
|
|
||||||
33
|
|
||||||
</a>
|
|
||||||
</form> </div>
|
|
||||||
|
|
||||||
</li>
|
|
||||||
|
|
||||||
<li>
|
|
||||||
<a href="#fork-destination-box" class="btn btn-sm btn-with-count"
|
|
||||||
title="Fork your own copy of veg/hyphy to your account"
|
|
||||||
aria-label="Fork your own copy of veg/hyphy to your account"
|
|
||||||
rel="facebox"
|
|
||||||
data-ga-click="Repository, show fork modal, action:blob#show; text:Fork">
|
|
||||||
<span class="octicon octicon-repo-forked"></span>
|
|
||||||
Fork
|
|
||||||
</a>
|
|
||||||
<a href="/veg/hyphy/network" class="social-count">19</a>
|
|
||||||
|
|
||||||
<div id="fork-destination-box" style="display: none;">
|
|
||||||
<h2 class="facebox-header">Where should we fork this repository?</h2>
|
|
||||||
<include-fragment src=""
|
|
||||||
class="js-fork-select-fragment fork-select-fragment"
|
|
||||||
data-url="/veg/hyphy/fork?fragment=1">
|
|
||||||
<img alt="Loading" height="64" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-128-338974454bb5c32803e82f601beb051d373744b024fe8742a76009700fd7e033.gif" width="64" />
|
|
||||||
</include-fragment>
|
|
||||||
</div>
|
|
||||||
</li>
|
|
||||||
|
|
||||||
</ul>
|
|
||||||
|
|
||||||
<h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public">
|
|
||||||
<span class="mega-octicon octicon-repo"></span>
|
|
||||||
<span class="author"><a href="/veg" class="url fn" itemprop="url" rel="author"><span itemprop="title">veg</span></a></span><!--
|
|
||||||
--><span class="path-divider">/</span><!--
|
|
||||||
--><strong><a href="/veg/hyphy" class="js-current-repository" data-pjax="#js-repo-pjax-container">hyphy</a></strong>
|
|
||||||
|
|
||||||
<span class="page-context-loader">
|
|
||||||
<img alt="" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</span>
|
|
||||||
|
|
||||||
</h1>
|
|
||||||
</div><!-- /.container -->
|
|
||||||
</div><!-- /.repohead -->
|
|
||||||
|
|
||||||
<div class="container">
|
|
||||||
<div class="repository-with-sidebar repo-container new-discussion-timeline ">
|
|
||||||
|
|
||||||
<div class="repository-sidebar clearfix">
|
|
||||||
|
|
||||||
<nav class="sunken-menu repo-nav js-repo-nav js-sidenav-container-pjax js-octicon-loaders"
|
|
||||||
role="navigation"
|
|
||||||
data-pjax="#js-repo-pjax-container"
|
|
||||||
data-issue-count-url="/veg/hyphy/issues/counts">
|
|
||||||
<ul class="sunken-menu-group">
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Code">
|
|
||||||
<a href="/veg/hyphy" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /veg/hyphy">
|
|
||||||
<span class="octicon octicon-code"></span> <span class="full-word">Code</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Issues">
|
|
||||||
<a href="/veg/hyphy/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /veg/hyphy/issues">
|
|
||||||
<span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span>
|
|
||||||
<span class="js-issue-replace-counter"></span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Pull requests">
|
|
||||||
<a href="/veg/hyphy/pulls" aria-label="Pull requests" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g p" data-selected-links="repo_pulls /veg/hyphy/pulls">
|
|
||||||
<span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull requests</span>
|
|
||||||
<span class="js-pull-replace-counter"></span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Wiki">
|
|
||||||
<a href="/veg/hyphy/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g w" data-selected-links="repo_wiki /veg/hyphy/wiki">
|
|
||||||
<span class="octicon octicon-book"></span> <span class="full-word">Wiki</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
</ul>
|
|
||||||
<div class="sunken-menu-separator"></div>
|
|
||||||
<ul class="sunken-menu-group">
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Pulse">
|
|
||||||
<a href="/veg/hyphy/pulse" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-selected-links="pulse /veg/hyphy/pulse">
|
|
||||||
<span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
|
|
||||||
<li class="tooltipped tooltipped-w" aria-label="Graphs">
|
|
||||||
<a href="/veg/hyphy/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-selected-links="repo_graphs repo_contributors /veg/hyphy/graphs">
|
|
||||||
<span class="octicon octicon-graph"></span> <span class="full-word">Graphs</span>
|
|
||||||
<img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
||||||
</a> </li>
|
|
||||||
</ul>
|
|
||||||
|
|
||||||
|
|
||||||
</nav>
|
|
||||||
|
|
||||||
<div class="only-with-full-nav">
|
|
||||||
|
|
||||||
<div class="clone-url open"
|
|
||||||
data-protocol-type="http"
|
|
||||||
data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone">
|
|
||||||
<h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
|
|
||||||
<div class="input-group js-zeroclipboard-container">
|
|
||||||
<input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
||||||
value="https://github.com/veg/hyphy.git" readonly="readonly">
|
|
||||||
<span class="input-group-button">
|
|
||||||
<button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
<div class="clone-url "
|
|
||||||
data-protocol-type="ssh"
|
|
||||||
data-url="/users/set_protocol?protocol_selector=ssh&protocol_type=clone">
|
|
||||||
<h3><span class="text-emphasized">SSH</span> clone URL</h3>
|
|
||||||
<div class="input-group js-zeroclipboard-container">
|
|
||||||
<input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
||||||
value="git@github.com:veg/hyphy.git" readonly="readonly">
|
|
||||||
<span class="input-group-button">
|
|
||||||
<button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
<div class="clone-url "
|
|
||||||
data-protocol-type="subversion"
|
|
||||||
data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone">
|
|
||||||
<h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
|
|
||||||
<div class="input-group js-zeroclipboard-container">
|
|
||||||
<input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
||||||
value="https://github.com/veg/hyphy" readonly="readonly">
|
|
||||||
<span class="input-group-button">
|
|
||||||
<button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
||||||
</span>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<p class="clone-options">You can clone with
|
|
||||||
<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>.
|
|
||||||
<a href="https://help.github.com/articles/which-remote-url-should-i-use" class="help tooltipped tooltipped-n" aria-label="Get help on which URL is right for you.">
|
|
||||||
<span class="octicon octicon-question"></span>
|
|
||||||
</a>
|
|
||||||
</p>
|
|
||||||
|
|
||||||
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<td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-c">_Genetic_Code = 0;</span></td>
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|
||||||
<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">
|
|
||||||
<ul class="site-footer-links right">
|
|
||||||
<li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
|
|
||||||
<li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
|
|
||||||
<li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
|
|
||||||
<li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li>
|
|
||||||
<li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
|
|
||||||
<li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li>
|
|
||||||
|
|
||||||
</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>
|
|
||||||
<li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li>
|
|
||||||
<li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li>
|
|
||||||
<li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li>
|
|
||||||
<li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li>
|
|
||||||
</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">
|
|
||||||
<span class="mega-octicon octicon-screen-normal"></span>
|
|
||||||
</a>
|
|
||||||
<a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w"
|
|
||||||
aria-label="Switch themes">
|
|
||||||
<span class="octicon octicon-color-mode"></span>
|
|
||||||
</a>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<div id="ajax-error-message" class="flash flash-error">
|
|
||||||
<span class="octicon octicon-alert"></span>
|
|
||||||
<a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a>
|
|
||||||
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>
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<div class="js-socket-channel" data-channel="test:mbdoud"></div>
|
|
||||||
|
|
||||||
</body>
|
|
||||||
</html>
|
|
||||||
|
|
||||||
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user