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2989 lines
196 KiB
Beef
2989 lines
196 KiB
Beef
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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">454.bf</strong>
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<img alt="@nlhepler" class="avatar" data-user="38372" height="24" src="https://avatars0.githubusercontent.com/u/38372?v=3&s=48" width="24" />
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<span class="author"><a href="/nlhepler" rel="contributor">nlhepler</a></span>
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<time datetime="2011-09-12T20:30:31Z" is="relative-time">Sep 12, 2011</time>
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<a href="/veg/hyphy/commit/50ae2ee049e8fd7dce5ba3f0627fd70ace1ea9ad" class="message" data-pjax="true" title="HYPHY_BASE_DIRECTORY --> HYPHY_LIB_DIRECTORY and mac2unix some obstinate template hbfs">HYPHY_BASE_DIRECTORY --> HYPHY_LIB_DIRECTORY and mac2unix some obstin…</a>
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<div class="participation">
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<p class="quickstat">
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<a href="#blob_contributors_box" rel="facebox">
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<strong>1</strong>
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contributor
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</a>
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</p>
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</div>
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<div id="blob_contributors_box" style="display:none">
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<h2 class="facebox-header">Users who have contributed to this file</h2>
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<ul class="facebox-user-list">
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<li class="facebox-user-list-item">
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<img alt="@nlhepler" data-user="38372" height="24" src="https://avatars0.githubusercontent.com/u/38372?v=3&s=48" width="24" />
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<a href="/nlhepler">nlhepler</a>
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</li>
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</ul>
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</div>
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</div>
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<div class="file">
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<div class="file-header">
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<div class="file-actions">
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<div class="btn-group">
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<a href="/veg/hyphy/raw/master/res/TemplateBatchFiles/454.bf" class="btn btn-sm " id="raw-url">Raw</a>
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<a href="/veg/hyphy/blame/master/res/TemplateBatchFiles/454.bf" class="btn btn-sm js-update-url-with-hash">Blame</a>
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<a href="/veg/hyphy/commits/master/res/TemplateBatchFiles/454.bf" class="btn btn-sm " rel="nofollow">History</a>
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</div>
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<a class="octicon-btn tooltipped tooltipped-nw"
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href="https://mac.github.com"
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aria-label="Open this file in GitHub for Mac">
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<span class="octicon octicon-device-desktop"></span>
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</a>
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<form accept-charset="UTF-8" action="/veg/hyphy/edit/master/res/TemplateBatchFiles/454.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="pNFn+uw4BOgUbKBVeHv/yb7jzSVPtjUhF58B/ivVKCKqA7fdem5ZBsgbljKljqZiUA8FHGnnTAmE0xBBllLaug==" /></div>
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<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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<span class="octicon octicon-pencil"></span>
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</button>
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</form>
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<form accept-charset="UTF-8" action="/veg/hyphy/delete/master/res/TemplateBatchFiles/454.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="om+teEogZx0Cl2uUz1T6yVjlxZs8uwPkeHpRrRKyYWsk/4HAZiEMF4vfslkqx/zNo9O19rv4QKs/iysK/gzcpA==" /></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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<span class="octicon octicon-trashcan"></span>
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</button>
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</form> </div>
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<div class="file-info">
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538 lines (451 sloc)
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<span class="file-info-divider"></span>
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14.93 kb
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</div>
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</div>
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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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<tr>
|
|
<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">ExecuteAFile ("Utility/GrabBag</span><span class="pl-en">.</span><span class="pl-c">bf");</span></td>
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</tr>
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<tr>
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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">ExecuteAFile ("Utility/DBTools</span><span class="pl-en">.</span><span class="pl-c">ibf");</span></td>
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</tr>
|
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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"></span></td>
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</tr>
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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"></span></td>
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</tr>
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<tr>
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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">alignOptions = {};</span></td>
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</tr>
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<tr>
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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"></span></td>
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</tr>
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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">SetDialogPrompt ("Sequence File:");</span></td>
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</tr>
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<tr>
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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">DataSet unal = ReadDataFile (PROMPT_FOR_FILE);</span></td>
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</tr>
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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">BASE_FILE_PATH = LAST_FILE_PATH;</span></td>
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</tr>
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<tr>
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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">DB_FILE_PATH = LAST_FILE_PATH </span><span class="pl-c1">+</span><span class="pl-c"> "</span><span class="pl-en">.</span><span class="pl-c">db";</span></td>
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</tr>
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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"></span></td>
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</tr>
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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">ANALYSIS_DB_ID = _openCacheDB (DB_FILE_PATH);</span></td>
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</tr>
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<tr>
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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"></span></td>
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</tr>
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<tr>
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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">haveTable = _TableExists (ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c"> "SETTINGS");</span></td>
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</tr>
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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="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (haveTable)</span></td>
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</tr>
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<tr>
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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">{</span></td>
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</tr>
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<tr>
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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"> existingSettings = _ExecuteSQL (ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c"> "SELECT * FROM SETTINGS");</span></td>
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</tr>
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<tr>
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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">}</span></td>
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</tr>
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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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</tr>
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<tr>
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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">if (Abs(existingSettings))</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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</tr>
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<tr>
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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"> existingSettings = existingSettings </span>[<span class="pl-c">0</span>]<span class="pl-c">;</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="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ExecuteCommands ("_Genetic_Code = " </span><span class="pl-c1">+</span><span class="pl-c"> existingSettings</span>[<span class="pl-c">"GENETIC_CODE"</span>]<span class="pl-c">);</span></td>
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</tr>
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<tr>
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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"> ExecuteCommands (existingSettings</span>[<span class="pl-c">"OPTIONS"</span>]<span class="pl-c"> ^ {{"_hyphyAssociativeArray"</span><span class="pl-en">,</span><span class="pl-c">"alignOptions"}});</span></td>
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</tr>
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<tr>
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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"> masterReferenceSequence = existingSettings</span>[<span class="pl-c">"REFERENCE"</span>]<span class="pl-c">;</span></td>
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</tr>
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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"> dbSequences = _ExecuteSQL (ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c"> "SELECT SEQUENCE_ID FROM SEQUENCES WHERE STAGE = 0");</span></td>
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</tr>
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<tr>
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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"> unalSequenceCount = Abs(dbSequences);</span></td>
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</tr>
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<tr>
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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"> toDoSequences = {unalSequenceCount</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="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"> for (k = 0; k </span><span class="pl-k"><</span><span class="pl-c"> unalSequenceCount; k=k</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="L30" class="blob-num js-line-number" data-line-number="30"></td>
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<td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
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</tr>
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<tr>
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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"> toDoSequences</span>[<span class="pl-c">k</span>]<span class="pl-c"> = (dbSequences</span>[<span class="pl-c">k</span>]<span class="pl-c">)</span>[<span class="pl-c">"SEQUENCE_ID"</span>]<span class="pl-c">;</span></td>
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</tr>
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<tr>
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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"> }</span></td>
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</tr>
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<tr>
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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"> dbSequences = 0;</span></td>
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</tr>
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<tr>
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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"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "</span>[<span class="pl-c">PHASE 1</span>]<span class="pl-c"> Reloaded "</span><span class="pl-en">,</span><span class="pl-c"> unalSequenceCount</span><span class="pl-en">,</span><span class="pl-c"> " unprocessed sequences\n");</span></td>
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</tr>
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<tr>
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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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</tr>
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<tr>
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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">else</span></td>
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</tr>
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<tr>
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<td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
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<td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
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</tr>
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<tr>
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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"> tableDefines = {};</span></td>
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</tr>
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<tr>
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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"> tableDefines </span>[<span class="pl-c">"SETTINGS"</span>]<span class="pl-c"> = {};</span></td>
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</tr>
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<tr>
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<td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
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<td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SETTINGS"</span>]<span class="pl-c">)</span>[<span class="pl-c">"RUN_DATE"</span>]<span class="pl-c"> = "DATE";</span></td>
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</tr>
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<tr>
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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"> (tableDefines </span>[<span class="pl-c">"SETTINGS"</span>]<span class="pl-c">)</span>[<span class="pl-c">"OPTIONS"</span>]<span class="pl-c"> = "TEXT";</span></td>
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</tr>
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<tr>
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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"> (tableDefines </span>[<span class="pl-c">"SETTINGS"</span>]<span class="pl-c">)</span>[<span class="pl-c">"REFERENCE"</span>]<span class="pl-c"> = "TEXT";</span></td>
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</tr>
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<tr>
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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"> (tableDefines </span>[<span class="pl-c">"SETTINGS"</span>]<span class="pl-c">)</span>[<span class="pl-c">"GENETIC_CODE"</span>]<span class="pl-c"> = "TEXT";</span></td>
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</tr>
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<tr>
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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"> (tableDefines </span>[<span class="pl-c">"SETTINGS"</span>]<span class="pl-c">)</span>[<span class="pl-c">"THRESHOLD"</span>]<span class="pl-c"> = "REAL";</span></td>
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</tr>
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<tr>
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<td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
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<td id="LC45" 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="L46" class="blob-num js-line-number" data-line-number="46"></td>
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<td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c"> = {};</span></td>
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</tr>
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<tr>
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<td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
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<td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"SEQUENCE_ID"</span>]<span class="pl-c"> = "TEXT UNIQUE";</span></td>
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</tr>
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<tr>
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<td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
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<td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"LENGTH"</span>]<span class="pl-c"> = "INTEGER";</span></td>
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</tr>
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<tr>
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<td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
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<td id="LC49" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"STAGE"</span>]<span class="pl-c"> = "INTEGER"; </span></td>
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</tr>
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<tr>
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<td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
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<td id="LC50" 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="L51" class="blob-num js-line-number" data-line-number="51"></td>
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<td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> 0 </span><span class="pl-c1">-</span><span class="pl-c"> initial import</span></td>
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</tr>
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<tr>
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<td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
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<td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> 1 </span><span class="pl-c1">-</span><span class="pl-c"> in frame without a fix </span></td>
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</tr>
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<tr>
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<td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
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<td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> 2 </span><span class="pl-c1">-</span><span class="pl-c"> one frame shift / fixed</span></td>
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</tr>
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<tr>
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<td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
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<td id="LC54" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> 3 </span><span class="pl-c1">-</span><span class="pl-c"> out</span><span class="pl-c1">-</span><span class="pl-c">of</span><span class="pl-c1">-</span><span class="pl-c">frame; not fixed / not aligned</span></td>
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</tr>
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<tr>
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<td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
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<td id="LC55" 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="L56" class="blob-num js-line-number" data-line-number="56"></td>
|
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<td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"RAW"</span>]<span class="pl-c"> = "TEXT";</span></td>
|
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</tr>
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<tr>
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<td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
|
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<td id="LC57" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"ALIGNED_AA"</span>]<span class="pl-c"> = "TEXT"; /* aligned aa</span><span class="pl-en">.</span><span class="pl-c"> sequence */</span></td>
|
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</tr>
|
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<tr>
|
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<td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
|
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<td id="LC58" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"ALIGNED"</span>]<span class="pl-c"> = "TEXT"; /* aligned nucleotide sequence */</span></td>
|
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</tr>
|
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<tr>
|
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<td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
|
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<td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"OFFSET"</span>]<span class="pl-c"> = "INTEGER"; /* start offset w</span><span class="pl-en">.</span><span class="pl-c">r</span><span class="pl-en">.</span><span class="pl-c">t the reference sequence */</span></td>
|
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</tr>
|
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<tr>
|
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<td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
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<td id="LC60" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"END_OFFSET"</span>]<span class="pl-c"> = "INTEGER"; /* end offset w</span><span class="pl-en">.</span><span class="pl-c">r</span><span class="pl-en">.</span><span class="pl-c">t the reference sequence */</span></td>
|
|
</tr>
|
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<tr>
|
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<td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
|
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<td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"SCORE"</span>]<span class="pl-c"> = "REAL";</span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
|
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<td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> (tableDefines </span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-c">)</span>[<span class="pl-c">"FRAME"</span>]<span class="pl-c"> = "INTEGER";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
|
|
<td id="LC63" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
|
|
<td id="LC64" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> _CreateTableIfNeeded (ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c"> "SETTINGS"</span><span class="pl-en">,</span><span class="pl-c"> tableDefines</span>[<span class="pl-c">"SETTINGS"</span>]<span class="pl-en">,</span><span class="pl-c"> 0);</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"> _CreateTableIfNeeded (ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c"> "SEQUENCES"</span><span class="pl-en">,</span><span class="pl-c"> tableDefines</span>[<span class="pl-c">"SEQUENCES"</span>]<span class="pl-en">,</span><span class="pl-c"> 1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
<td id="LC66" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
<td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> /* START ALIGNMENT SETTINGS */</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"> LoadFunctionLibrary ("SeqAlignShared</span><span class="pl-en">.</span><span class="pl-c">ibf");</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"> DataSetFilter filteredData = CreateFilter (unal</span><span class="pl-en">,</span><span class="pl-c">1);</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"> GetInformation (UnalignedSeqs</span><span class="pl-en">,</span><span class="pl-c">filteredData);</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"> /* preprocess sequences */</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
<td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
|
|
<td id="LC75" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> unalSequenceCount = Rows(UnalignedSeqs)*Columns(UnalignedSeqs);</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"> GetString (sequenceNames</span><span class="pl-en">,</span><span class="pl-c"> unal</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="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"></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"> longestSequence = 0;</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"> longestSequenceIDX = 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"> seqRecord = {};</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"></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"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "</span>[<span class="pl-c">PHASE 1</span>]<span class="pl-c"> Initial Processing of "</span><span class="pl-en">,</span><span class="pl-c"> unalSequenceCount</span><span class="pl-en">,</span><span class="pl-c"> " sequences\n");</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"></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"> for (seqCounter = 0; seqCounter </span><span class="pl-k"><</span><span class="pl-c"> unalSequenceCount; seqCounter = seqCounter</span><span class="pl-c1">+</span><span class="pl-c">1)</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"> {</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"> UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">^{{"</span>[<span class="pl-c">^a</span><span class="pl-c1">-</span><span class="pl-c">zA</span><span class="pl-c1">-</span><span class="pl-c">Z</span>]<span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">""}};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
|
|
<td id="LC88" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">^{{"^N</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">,</span><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"> UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">^{{"N</span><span class="pl-c1">+</span><span class="pl-c">$"</span><span class="pl-en">,</span><span class="pl-c">""}};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
|
|
<td id="LC90" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </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"> seqRecord </span>[<span class="pl-c">"SEQUENCE_ID"</span>]<span class="pl-c"> = sequenceNames</span>[<span class="pl-c">seqCounter</span>]<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"> seqRecord </span>[<span class="pl-c">"LENGTH"</span>]<span class="pl-c"> = Abs (UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">);</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"> seqRecord </span>[<span class="pl-c">"STAGE"</span>]<span class="pl-c"> = 0;</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"> seqRecord </span>[<span class="pl-c">"RAW"</span>]<span class="pl-c"> = UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
|
|
<td id="LC95" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
|
|
<td id="LC96" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (doLongestSequence)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
|
|
<td id="LC97" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
|
|
<td id="LC98" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (doLongestSequence == 1 || seqCounter != unalSequenceCount</span><span class="pl-c1">-</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
|
|
<td id="LC99" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
|
|
<td id="LC100" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (Abs (UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">) </span><span class="pl-k">></span><span class="pl-c"> longestSequence)</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"> longestSequence = Abs (UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<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"> longestSequenceIDX = seqCounter;</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"> }</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"> </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"> _InsertRecord (ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c"> "SEQUENCES"</span><span class="pl-en">,</span><span class="pl-c"> seqRecord);</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"> SetParameter (STATUS_BAR_STATUS_STRING</span><span class="pl-en">,</span><span class="pl-c"> "Initial processing ("</span><span class="pl-c1">+</span><span class="pl-c">seqCounter</span><span class="pl-c1">+</span><span class="pl-c">"/"</span><span class="pl-c1">+</span><span class="pl-c">unalSequenceCount</span><span class="pl-c1">+</span><span class="pl-c">" done)"</span><span class="pl-en">,</span><span class="pl-c">0);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
|
|
<td id="LC110" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
|
|
<td id="LC111" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </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"> if (refSeq == 0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
|
|
<td id="LC113" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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"> masterReferenceSequence = UnalignedSeqs</span>[<span class="pl-c">0</span>]<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>
|
|
</tr>
|
|
<tr>
|
|
<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>
|
|
</tr>
|
|
<tr>
|
|
<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>
|
|
</tr>
|
|
<tr>
|
|
<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"> if (doLongestSequence)</span></td>
|
|
</tr>
|
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<tr>
|
|
<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>
|
|
</tr>
|
|
<tr>
|
|
<td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
|
|
<td id="LC120" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\nSelected sequence "</span><span class="pl-en">,</span><span class="pl-c"> sequenceNames</span>[<span class="pl-c">longestSequenceIDX</span>]<span class="pl-en">,</span><span class="pl-c"> " as reference</span><span class="pl-en">.</span><span class="pl-c">");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
|
|
<td id="LC121" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> masterReferenceSequence = UnalignedSeqs</span>[<span class="pl-c">longestSequenceIDX</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
|
|
<td id="LC122" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
|
|
<td id="LC123" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
|
|
<td id="LC124" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> 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>
|
|
</tr>
|
|
<tr>
|
|
<td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
|
|
<td id="LC125" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> 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>
|
|
</tr>
|
|
<tr>
|
|
<td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
|
|
<td id="LC126" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
|
|
<td id="LC127" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> doLongestSequence = (refSeq==1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
|
|
<td id="LC128" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aRecord = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
|
|
<td id="LC129" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aRecord</span>[<span class="pl-c">"RUN_DATE"</span>]<span class="pl-c"> = _ExecuteSQL(ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c">"SELECT DATE('NOW') AS CURRENT_DATE");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
|
|
<td id="LC130" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aRecord</span>[<span class="pl-c">"RUN_DATE"</span>]<span class="pl-c"> = ((aRecord</span>[<span class="pl-c">"RUN_DATE"</span>]<span class="pl-c">)</span>[<span class="pl-c">0</span>]<span class="pl-c">)</span>[<span class="pl-c">"CURRENT_DATE"</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
|
|
<td id="LC131" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aRecord</span>[<span class="pl-c">"OPTIONS"</span>]<span class="pl-c"> = "" </span><span class="pl-c1">+</span><span class="pl-c"> alignOptions;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
|
|
<td id="LC132" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aRecord</span>[<span class="pl-c">"REFERENCE"</span>]<span class="pl-c"> = masterReferenceSequence;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
|
|
<td id="LC133" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aRecord</span>[<span class="pl-c">"GENETIC_CODE"</span>]<span class="pl-c"> = "" </span><span class="pl-c1">+</span><span class="pl-c"> _Genetic_Code;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
|
|
<td id="LC134" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> _InsertRecord (ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c"> "SETTINGS"</span><span class="pl-en">,</span><span class="pl-c"> aRecord);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
|
|
<td id="LC135" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> toDoSequences = sequenceNames;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
|
|
<td id="LC136" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> UnalignedSequences = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
|
|
<td id="LC137" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
|
|
<td id="LC138" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
|
|
<td id="LC139" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
|
|
<td id="LC140" class="blob-code blob-code-inner js-file-line"><span class="pl-c">skipOutliers = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
|
|
<td id="LC141" class="blob-code blob-code-inner js-file-line"><span class="pl-c">doRC = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
|
|
<td id="LC142" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
|
|
<td id="LC143" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/* build codon translation table */</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
|
|
<td id="LC144" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
|
|
<td id="LC145" class="blob-code blob-code-inner js-file-line"><span class="pl-c">codonToAAMap = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
|
|
<td id="LC146" class="blob-code blob-code-inner js-file-line"><span class="pl-c">codeToAA = "FLIMVSPTAYXHQNKDECWRG";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
|
|
<td id="LC147" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
|
|
<td id="LC148" class="blob-code blob-code-inner js-file-line"><span class="pl-c">nucChars = "ACGT";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
|
|
<td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
|
|
<td id="LC150" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (p1=0; p1</span><span class="pl-k"><</span><span class="pl-c">64; p1=p1</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
|
|
<td id="LC151" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
|
|
<td id="LC152" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> codon = nucChars</span>[<span class="pl-c">p1$16</span>]<span class="pl-c1">+</span><span class="pl-c">nucChars</span>[<span class="pl-c">p1%16$4</span>]<span class="pl-c1">+</span><span class="pl-c">nucChars</span>[<span class="pl-c">p1%4</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
|
|
<td id="LC153" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ccode = _Genetic_Code</span>[<span class="pl-c">p1</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
|
|
<td id="LC154" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> codonToAAMap</span>[<span class="pl-c">codon</span>]<span class="pl-c"> = codeToAA</span>[<span class="pl-c">ccode</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
|
|
<td id="LC155" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
|
|
<td id="LC156" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
|
|
<td id="LC157" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/* determine reading frames */</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
|
|
<td id="LC158" class="blob-code blob-code-inner js-file-line"><span class="pl-c">ProteinSequences = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
|
|
<td id="LC159" class="blob-code blob-code-inner js-file-line"><span class="pl-c">AllTranslations = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
|
|
<td id="LC160" class="blob-code blob-code-inner js-file-line"><span class="pl-c">ReadingFrames = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
|
|
<td id="LC161" class="blob-code blob-code-inner js-file-line"><span class="pl-c">StopCodons = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
|
|
<td id="LC162" class="blob-code blob-code-inner js-file-line"><span class="pl-c">StopPositions = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
|
<td id="LC163" class="blob-code blob-code-inner js-file-line"><span class="pl-c">RC = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
|
|
<td id="LC164" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
|
|
<td id="LC165" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n</span>[<span class="pl-c">PHASE 2</span>]<span class="pl-c"> Detecting reading frames for each unprocessed sequence</span><span class="pl-en">...</span><span class="pl-c">\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
|
|
<td id="LC166" class="blob-code blob-code-inner js-file-line"><span class="pl-c">frameCounter = {3</span><span class="pl-en">,</span><span class="pl-c">2};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
|
|
<td id="LC167" class="blob-code blob-code-inner js-file-line"><span class="pl-c">stillHasStops = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
|
<td id="LC168" class="blob-code blob-code-inner js-file-line"><span class="pl-c">aRecord = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
|
<td id="LC169" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
|
|
<td id="LC170" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (seqCounter = 0; seqCounter </span><span class="pl-k"><</span><span class="pl-c"> unalSequenceCount; seqCounter = seqCounter</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
|
<td id="LC171" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
|
<td id="LC172" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> rawSeq = (_ExecuteSQL(ANALYSIS_DB_ID</span><span class="pl-en">,</span><span class="pl-c">"SELECT RAW FROM SEQUENCES WHERE SEQUENCE_ID = '" </span><span class="pl-c1">+</span><span class="pl-c"> toDoSequences</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> </span><span class="pl-c1">+</span><span class="pl-c"> "'"));</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
|
|
<td id="LC173" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aSeq = (rawSeq</span>[<span class="pl-c">0</span>]<span class="pl-c">)</span>[<span class="pl-c">"RAW"</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
|
|
<td id="LC174" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> seqLen = Abs(aSeq)</span><span class="pl-c1">-</span><span class="pl-c">2;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
|
|
<td id="LC175" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
|
|
<td id="LC176" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> minStops = 1e20;</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"> tString = "";</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"> rFrame = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
|
|
<td id="LC179" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> rrc = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
|
|
<td id="LC180" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> allTran = {3</span><span class="pl-en">,</span><span class="pl-c">2};</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"> stopPosn = {6</span><span class="pl-en">,</span><span class="pl-c">2};</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"> </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"> for (rc = 0; rc</span><span class="pl-k"><</span><span class="pl-c">=doRC; rc = rc</span><span class="pl-c1">+</span><span class="pl-c">1)</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"> {</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"> if (rc)</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"> aSeq = nucleotideReverseComplement (aSeq)</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"> }</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"> for (offset = 0; offset </span><span class="pl-k"><</span><span class="pl-c"> 3; offset = offset</span><span class="pl-c1">+</span><span class="pl-c">1)</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"> {</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"> translString = "";</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"> translString * (seqLen/3</span><span class="pl-c1">+</span><span class="pl-c">1);</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"> for (seqPos = offset; seqPos </span><span class="pl-k"><</span><span class="pl-c"> seqLen; seqPos = seqPos</span><span class="pl-c1">+</span><span class="pl-c">3)</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"> {</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"> codon = aSeq</span>[<span class="pl-c">seqPos</span>][<span class="pl-c">seqPos</span><span class="pl-c1">+</span><span class="pl-c">2</span>]<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"> prot = codonToAAMap</span>[<span class="pl-c">codon</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
|
|
<td id="LC197" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (Abs(prot))</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
|
|
<td id="LC198" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
|
|
<td id="LC199" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> translString * prot;</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"> else</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"> {</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"> translString * "?";</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"> }</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"> translString * 0;</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"> translString = translString^{{"X$"</span><span class="pl-en">,</span><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"> stopPos = translString||"X";</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"> if (stopPos</span>[<span class="pl-c">0</span>]<span class="pl-k">></span><span class="pl-c">=0)</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"> {</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"> stopCount = Rows(stopPos)$2;</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"> stopPosn</span>[<span class="pl-c">3*rc</span><span class="pl-c1">+</span><span class="pl-c">offset</span>][<span class="pl-c">0</span>]<span class="pl-c"> = stopPos</span>[<span class="pl-c">0</span>]<span class="pl-c">;</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"> stopPosn</span>[<span class="pl-c">3*rc</span><span class="pl-c1">+</span><span class="pl-c">offset</span>][<span class="pl-c">1</span>]<span class="pl-c"> = stopPos</span>[<span class="pl-c">stopCount*2</span><span class="pl-c1">-</span><span class="pl-c">1</span>]<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"> }</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"> else</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
|
|
<td id="LC216" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
|
|
<td id="LC217" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> stopCount = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
|
|
<td id="LC218" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
|
|
<td id="LC219" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (stopCount</span><span class="pl-k"><</span><span class="pl-c">minStops)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
|
|
<td id="LC220" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
|
|
<td id="LC221" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> minStops = stopCount;</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"> rFrame = offset;</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"> rrc = rc;</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"> tString = translString;</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"> allTran</span>[<span class="pl-c">offset</span>][<span class="pl-c">rc</span>]<span class="pl-c"> = translString;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
|
|
<td id="LC227" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
|
|
<td id="LC228" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
|
|
<td id="LC229" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </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"> ReadingFrames </span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = rFrame;</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"> ProteinSequences </span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = tString;</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"> frameCounter </span>[<span class="pl-c">rFrame</span>][<span class="pl-c">rrc</span>]<span class="pl-c"> = frameCounter</span>[<span class="pl-c">rFrame</span>][<span class="pl-c">rrc</span>]<span class="pl-c1">+</span><span class="pl-c">1;</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"> StopPositions </span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = stopPosn;</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"> AllTranslations </span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = allTran;</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"> RC </span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = rrc;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
|
|
<td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
|
|
<td id="LC237" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> SetParameter (STATUS_BAR_STATUS_STRING</span><span class="pl-en">,</span><span class="pl-c"> "Reading frame analysis ("</span><span class="pl-c1">+</span><span class="pl-c">seqCounter</span><span class="pl-c1">+</span><span class="pl-c">"/"</span><span class="pl-c1">+</span><span class="pl-c">unalSequenceCount</span><span class="pl-c1">+</span><span class="pl-c">" done)"</span><span class="pl-en">,</span><span class="pl-c">0);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
|
|
<td id="LC238" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
|
|
<td id="LC239" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
|
|
<td id="LC240" class="blob-code blob-code-inner js-file-line"><span class="pl-c">_closeCacheDB (ANALYSIS_DB_ID);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
|
|
<td id="LC241" class="blob-code blob-code-inner js-file-line"><span class="pl-c">return 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
|
|
<td id="LC242" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
|
|
<td id="LC243" class="blob-code blob-code-inner js-file-line"><span class="pl-c">s1 = ProteinSequences</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
|
|
<td id="LC244" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\nFound:\n\t"</span><span class="pl-en">,</span><span class="pl-c"> frameCounter</span>[<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c"> " sequences in reading frame 1\n\t"</span><span class="pl-en">,</span><span class="pl-c">frameCounter</span>[<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c"> " sequences in reading frame 2\n\t"</span><span class="pl-en">,</span><span class="pl-c">frameCounter</span>[<span class="pl-c">2</span>]<span class="pl-en">,</span><span class="pl-c"> " sequences in reading frame 3\n\nThere were "</span><span class="pl-en">,</span><span class="pl-c"> Abs(stillHasStops)</span><span class="pl-en">,</span><span class="pl-c"> " sequences with apparent frameshift/sequencing errors\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
|
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<td id="LC245" 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="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>
|
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</tr>
|
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<tr>
|
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<td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
|
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<td id="LC247" class="blob-code blob-code-inner js-file-line"><span class="pl-c">skipSeqs = {};</span></td>
|
|
</tr>
|
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<tr>
|
|
<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"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
|
|
<td id="LC249" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (k=0; k</span><span class="pl-k"><</span><span class="pl-c">Abs(stillHasStops); k=k</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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"> seqCounter = stillHasStops</span>[<span class="pl-c">k</span>]<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"> seqName = sequenceNames</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
|
|
<td id="LC253" 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">"Sequence "</span><span class="pl-en">,</span><span class="pl-c"> seqCounter</span><span class="pl-c1">+</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c"> " ("</span><span class="pl-en">,</span><span class="pl-c"> seqName</span><span class="pl-en">,</span><span class="pl-c"> ") seems to have");</span></td>
|
|
</tr>
|
|
<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"> stopPosn = StopPositions</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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"> </span></td>
|
|
</tr>
|
|
<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"> fStart = </span><span class="pl-c1">-</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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"> fEnd = </span><span class="pl-c1">-</span><span class="pl-c">1;</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"> fMin = 1e10;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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"> frame1 = 0;</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"> frame2 = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
|
|
<td id="LC261" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
|
|
<td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> checkFramePosition (stopPosn</span>[<span class="pl-c">0</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">stopPosn</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">0</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
|
|
<td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> checkFramePosition (stopPosn</span>[<span class="pl-c">1</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">stopPosn</span>[<span class="pl-c">0</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">0);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
|
|
<td id="LC264" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> checkFramePosition (stopPosn</span>[<span class="pl-c">0</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">stopPosn</span>[<span class="pl-c">2</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">0</span><span class="pl-en">,</span><span class="pl-c">2);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
|
|
<td id="LC265" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> checkFramePosition (stopPosn</span>[<span class="pl-c">2</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">stopPosn</span>[<span class="pl-c">0</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">2</span><span class="pl-en">,</span><span class="pl-c">0);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
|
|
<td id="LC266" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> checkFramePosition (stopPosn</span>[<span class="pl-c">2</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">stopPosn</span>[<span class="pl-c">1</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">2</span><span class="pl-en">,</span><span class="pl-c">1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
|
|
<td id="LC267" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> checkFramePosition (stopPosn</span>[<span class="pl-c">1</span>][<span class="pl-c">1</span>]<span class="pl-en">,</span><span class="pl-c">stopPosn</span>[<span class="pl-c">2</span>][<span class="pl-c">0</span>]<span class="pl-en">,</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">2);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
|
|
<td id="LC268" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
|
|
<td id="LC269" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (fStart</span><span class="pl-k">></span><span class="pl-c">=0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
|
|
<td id="LC270" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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"> allTran = AllTranslations</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
|
|
<td id="LC272" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> useq = UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
|
|
<td id="LC273" 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"> " a shift from frame "</span><span class="pl-en">,</span><span class="pl-c"> frame2</span><span class="pl-c1">+</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c"> " to frame "</span><span class="pl-en">,</span><span class="pl-c"> frame1</span><span class="pl-c1">+</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c"> " between a</span><span class="pl-en">.</span><span class="pl-c">a</span><span class="pl-en">.</span><span class="pl-c"> positions "</span><span class="pl-en">,</span><span class="pl-c"> fStart</span><span class="pl-en">,</span><span class="pl-c"> " and "</span><span class="pl-en">,</span><span class="pl-c"> fEnd</span><span class="pl-en">,</span><span class="pl-c"> "</span><span class="pl-en">.</span><span class="pl-c">");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="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"> fStart2 = Max(fStart</span><span class="pl-c1">-</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">0);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
|
|
<td id="LC275" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fEnd2 = Min(fEnd</span><span class="pl-c1">+</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c">Min(Abs(allTran</span>[<span class="pl-c">frame1</span>]<span class="pl-c">)</span><span class="pl-en">,</span><span class="pl-c">Abs(allTran</span>[<span class="pl-c">frame2</span>]<span class="pl-c">))</span><span class="pl-c1">-</span><span class="pl-c">1);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
|
|
<td id="LC276" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> tempString = allTran</span>[<span class="pl-c">frame2</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
|
|
<td id="LC277" 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\tRegion "</span><span class="pl-en">,</span><span class="pl-c"> fStart2</span><span class="pl-en">,</span><span class="pl-c"> "</span><span class="pl-c1">-</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c"> fEnd2</span><span class="pl-en">,</span><span class="pl-c"> " in frame "</span><span class="pl-en">,</span><span class="pl-c"> frame2</span><span class="pl-c1">+</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c"> ":\n\t"</span><span class="pl-en">,</span><span class="pl-c"> tempString</span>[<span class="pl-c">fStart2</span>][<span class="pl-c">fEnd2</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
|
|
<td id="LC278" 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\t"</span><span class="pl-en">,</span><span class="pl-c"> useq</span>[<span class="pl-c">3*fStart2</span><span class="pl-c1">+</span><span class="pl-c">frame2</span>][<span class="pl-c">3*fEnd2</span><span class="pl-c1">+</span><span class="pl-c">frame2</span><span class="pl-c1">-</span><span class="pl-c">1</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
|
|
<td id="LC279" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> tempString = allTran</span>[<span class="pl-c">frame1</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
|
|
<td id="LC280" 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\tRegion "</span><span class="pl-en">,</span><span class="pl-c"> fStart2</span><span class="pl-en">,</span><span class="pl-c"> "</span><span class="pl-c1">-</span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c"> fEnd2</span><span class="pl-en">,</span><span class="pl-c"> " in frame "</span><span class="pl-en">,</span><span class="pl-c"> frame1</span><span class="pl-c1">+</span><span class="pl-c">1</span><span class="pl-en">,</span><span class="pl-c"> ":\n\t"</span><span class="pl-en">,</span><span class="pl-c"> tempString</span>[<span class="pl-c">fStart2</span>][<span class="pl-c">fEnd2</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<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"> fprintf (stdout</span><span class="pl-en">,</span><span class="pl-c"> "\n\t"</span><span class="pl-en">,</span><span class="pl-c"> useq</span>[<span class="pl-c">3*fStart2</span><span class="pl-c1">+</span><span class="pl-c">frame1</span>][<span class="pl-c">3*fEnd2</span><span class="pl-c1">+</span><span class="pl-c">frame1</span><span class="pl-c1">-</span><span class="pl-c">1</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
|
|
<td id="LC282" 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\t\tAttempting to resolve by alignment to reference</span><span class="pl-en">.</span><span class="pl-c"> ");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
|
|
<td id="LC283" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </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"> f1s = allTran</span>[<span class="pl-c">frame1</span>]<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"> f2s = allTran</span>[<span class="pl-c">frame2</span>]<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"> f1l = Abs(f1s);</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"> bestScore = </span><span class="pl-c1">-</span><span class="pl-c">1e10;</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"> bestSplice = </span><span class="pl-c1">-</span><span class="pl-c">1;</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"> for (k2=fStart; k2</span><span class="pl-k"><</span><span class="pl-c">fEnd; k2=k2</span><span class="pl-c1">+</span><span class="pl-c">1)</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"> {</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"> s2 = f2s</span>[<span class="pl-c">0</span>][<span class="pl-c">k2</span>]<span class="pl-c1">+</span><span class="pl-c">f1s</span>[<span class="pl-c">k2</span><span class="pl-c1">+</span><span class="pl-c">1</span>][<span class="pl-c">Abs(f1s)</span>]<span class="pl-c">;</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"> inStr = {{s1</span><span class="pl-en">,</span><span class="pl-c">s2}};</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"> AlignSequences(aligned</span><span class="pl-en">,</span><span class="pl-c"> inStr</span><span class="pl-en">,</span><span class="pl-c"> alignOptions);</span></td>
|
|
</tr>
|
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<tr>
|
|
<td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
|
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<td id="LC296" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned = aligned</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
|
|
<td id="LC297" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned = aligned</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L298" class="blob-num js-line-number" data-line-number="298"></td>
|
|
<td id="LC298" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (aligned </span><span class="pl-k">></span><span class="pl-c"> bestScore)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
|
|
<td id="LC299" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
|
|
<td id="LC300" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bestScore = aligned;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
|
|
<td id="LC301" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bestSplice = k2;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
|
|
<td id="LC302" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> bestString = s2;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
|
|
<td id="LC303" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
|
|
<td id="LC304" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
|
|
<td id="LC305" 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"> "Best splice site appears to be at a</span><span class="pl-en">.</span><span class="pl-c">a</span><span class="pl-en">.</span><span class="pl-c"> position "</span><span class="pl-en">,</span><span class="pl-c"> bestSplice</span><span class="pl-en">,</span><span class="pl-c"> "\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
|
|
<td id="LC306" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> /* update best spliced string */</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
|
|
<td id="LC307" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
|
|
<td id="LC308" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ProteinSequences</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = bestString;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L309" class="blob-num js-line-number" data-line-number="309"></td>
|
|
<td id="LC309" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> ReadingFrames</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
|
|
<td id="LC310" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
|
|
<td id="LC311" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = useq</span>[<span class="pl-c">frame2</span>][<span class="pl-c">frame2</span><span class="pl-c1">+</span><span class="pl-c">3*bestSplice</span><span class="pl-c1">+</span><span class="pl-c">2</span>]<span class="pl-c"> </span><span class="pl-c1">+</span><span class="pl-c"> useq</span>[<span class="pl-c">frame1</span><span class="pl-c1">+</span><span class="pl-c">3*bestSplice</span><span class="pl-c1">+</span><span class="pl-c">3</span>][<span class="pl-c">Abs(useq)</span><span class="pl-c1">-</span><span class="pl-c">1</span>]<span class="pl-c"> </span><span class="pl-c1">+</span><span class="pl-c"> "</span><span class="pl-c1">---</span><span class="pl-c">";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
|
|
<td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
|
|
<td id="LC313" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> else</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
|
|
<td id="LC314" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
|
|
<td id="LC315" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
|
|
<td id="LC316" 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"> " multiple frameshifts\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
|
|
<td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> skipSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
|
|
<td id="LC318" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> } </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
|
|
<td id="LC319" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
|
|
<td id="LC320" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L321" class="blob-num js-line-number" data-line-number="321"></td>
|
|
<td id="LC321" class="blob-code blob-code-inner js-file-line"><span class="pl-c">SeqAlignments = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
|
|
<td id="LC322" class="blob-code blob-code-inner js-file-line"><span class="pl-c">startingPosition = {unalSequenceCount</span><span class="pl-en">,</span><span class="pl-c">2};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
|
|
<td id="LC323" class="blob-code blob-code-inner js-file-line"><span class="pl-c">refLength = Abs(ProteinSequences</span>[<span class="pl-c">0</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L324" class="blob-num js-line-number" data-line-number="324"></td>
|
|
<td id="LC324" class="blob-code blob-code-inner js-file-line"><span class="pl-c">refInsertions = {refLength</span><span class="pl-en">,</span><span class="pl-c">1};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
|
|
<td id="LC325" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
|
|
<td id="LC326" 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">"\nPerforming pairwise alignment with reference sequences\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
|
|
<td id="LC327" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
|
|
<td id="LC328" class="blob-code blob-code-inner js-file-line"><span class="pl-c">alignmentScores = {};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
|
|
<td id="LC329" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
|
|
<td id="LC330" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (seqCounter = 1; seqCounter </span><span class="pl-k"><</span><span class="pl-c"> unalSequenceCount; seqCounter = seqCounter</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
|
|
<td id="LC331" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
|
|
<td id="LC332" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (skipSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> == 0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
|
|
<td id="LC333" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
|
|
<td id="LC334" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> s2 = ProteinSequences</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
|
|
<td id="LC335" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> inStr = {{s1</span><span class="pl-en">,</span><span class="pl-c">s2}};</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
|
|
<td id="LC336" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> AlignSequences(aligned</span><span class="pl-en">,</span><span class="pl-c"> inStr</span><span class="pl-en">,</span><span class="pl-c"> alignOptions);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
|
|
<td id="LC337" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned = aligned</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
|
|
<td id="LC338" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> SeqAlignments</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = aligned;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
|
|
<td id="LC339" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> alignmentScores</span>[<span class="pl-c">Abs(alignmentScores)</span>]<span class="pl-c"> = aligned</span>[<span class="pl-c">0</span>]<span class="pl-c">/Abs(aligned</span>[<span class="pl-c">1</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
|
|
<td id="LC340" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned = aligned</span>[<span class="pl-c">1</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
|
|
<td id="LC341" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> myStartingPosition = aligned$"</span>[<span class="pl-c">^</span><span class="pl-c1">-</span>]<span class="pl-c">";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
|
|
<td id="LC342" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> myEndingPosition = Abs (aligned)</span><span class="pl-c1">-</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
|
|
<td id="LC343" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> while (aligned</span>[<span class="pl-c">myEndingPosition</span>]<span class="pl-c">=="</span><span class="pl-c1">-</span><span class="pl-c">")</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
|
|
<td id="LC344" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
|
|
<td id="LC345" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> myEndingPosition = myEndingPosition </span><span class="pl-c1">-</span><span class="pl-c"> 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L346" class="blob-num js-line-number" data-line-number="346"></td>
|
|
<td id="LC346" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L347" class="blob-num js-line-number" data-line-number="347"></td>
|
|
<td id="LC347" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> myStartingPosition = myStartingPosition</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L348" class="blob-num js-line-number" data-line-number="348"></td>
|
|
<td id="LC348" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> startingPosition</span>[<span class="pl-c">seqCounter</span>][<span class="pl-c">0</span>]<span class="pl-c"> = myStartingPosition;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L349" class="blob-num js-line-number" data-line-number="349"></td>
|
|
<td id="LC349" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> startingPosition</span>[<span class="pl-c">seqCounter</span>][<span class="pl-c">1</span>]<span class="pl-c"> = myEndingPosition;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L350" class="blob-num js-line-number" data-line-number="350"></td>
|
|
<td id="LC350" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned = aligned</span>[<span class="pl-c">myStartingPosition</span>][<span class="pl-c">myEndingPosition</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L351" class="blob-num js-line-number" data-line-number="351"></td>
|
|
<td id="LC351" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> refInsert = aligned||"</span><span class="pl-c1">-+</span><span class="pl-c">";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L352" class="blob-num js-line-number" data-line-number="352"></td>
|
|
<td id="LC352" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (refInsert</span>[<span class="pl-c">0</span>]<span class="pl-k">></span><span class="pl-c">0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L353" class="blob-num js-line-number" data-line-number="353"></td>
|
|
<td id="LC353" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L354" class="blob-num js-line-number" data-line-number="354"></td>
|
|
<td id="LC354" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> insCount = Rows (refInsert)/2;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L355" class="blob-num js-line-number" data-line-number="355"></td>
|
|
<td id="LC355" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> offset = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L356" class="blob-num js-line-number" data-line-number="356"></td>
|
|
<td id="LC356" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (insN = 0; insN </span><span class="pl-k"><</span><span class="pl-c"> insCount; insN = insN</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L357" class="blob-num js-line-number" data-line-number="357"></td>
|
|
<td id="LC357" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L358" class="blob-num js-line-number" data-line-number="358"></td>
|
|
<td id="LC358" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> insPos = refInsert</span>[<span class="pl-c">insN*2</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L359" class="blob-num js-line-number" data-line-number="359"></td>
|
|
<td id="LC359" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> insLength = refInsert</span>[<span class="pl-c">insN*2</span><span class="pl-c1">+</span><span class="pl-c">1</span>]<span class="pl-c1">-</span><span class="pl-c">insPos</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L360" class="blob-num js-line-number" data-line-number="360"></td>
|
|
<td id="LC360" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> insPos = insPos</span><span class="pl-c1">-</span><span class="pl-c">offset;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L361" class="blob-num js-line-number" data-line-number="361"></td>
|
|
<td id="LC361" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (refInsertions</span>[<span class="pl-c">insPos</span>]<span class="pl-k"><</span><span class="pl-c">insLength)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L362" class="blob-num js-line-number" data-line-number="362"></td>
|
|
<td id="LC362" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L363" class="blob-num js-line-number" data-line-number="363"></td>
|
|
<td id="LC363" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> refInsertions</span>[<span class="pl-c">insPos</span>]<span class="pl-c">=insLength;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L364" class="blob-num js-line-number" data-line-number="364"></td>
|
|
<td id="LC364" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L365" class="blob-num js-line-number" data-line-number="365"></td>
|
|
<td id="LC365" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> offset = offset </span><span class="pl-c1">+</span><span class="pl-c"> insLength;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L366" class="blob-num js-line-number" data-line-number="366"></td>
|
|
<td id="LC366" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L367" class="blob-num js-line-number" data-line-number="367"></td>
|
|
<td id="LC367" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L368" class="blob-num js-line-number" data-line-number="368"></td>
|
|
<td id="LC368" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L369" class="blob-num js-line-number" data-line-number="369"></td>
|
|
<td id="LC369" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L370" class="blob-num js-line-number" data-line-number="370"></td>
|
|
<td id="LC370" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L371" class="blob-num js-line-number" data-line-number="371"></td>
|
|
<td id="LC371" class="blob-code blob-code-inner js-file-line"><span class="pl-c">alignmentScoresM = avlToMatrix ("alignmentScores");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L372" class="blob-num js-line-number" data-line-number="372"></td>
|
|
<td id="LC372" class="blob-code blob-code-inner js-file-line"><span class="pl-c">ExecuteAFile ("Utility/DescriptiveStatistics</span><span class="pl-en">.</span><span class="pl-c">bf");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L373" class="blob-num js-line-number" data-line-number="373"></td>
|
|
<td id="LC373" class="blob-code blob-code-inner js-file-line"><span class="pl-c">distInfo = GatherDescriptiveStats (alignmentScoresM);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L374" class="blob-num js-line-number" data-line-number="374"></td>
|
|
<td id="LC374" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/*lowerCuttoff = 0</span><span class="pl-en">.</span><span class="pl-c">25;*/</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L375" class="blob-num js-line-number" data-line-number="375"></td>
|
|
<td id="LC375" class="blob-code blob-code-inner js-file-line"><span class="pl-c">distInfo</span>[<span class="pl-c">"Mean"</span>]<span class="pl-c"> </span><span class="pl-c1">-</span><span class="pl-c"> 2*distInfo</span>[<span class="pl-c">"Std</span><span class="pl-en">.</span><span class="pl-c">Dev"</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L376" class="blob-num js-line-number" data-line-number="376"></td>
|
|
<td id="LC376" class="blob-code blob-code-inner js-file-line"><span class="pl-c">/* produce a fully gapped reference sequence */</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L377" class="blob-num js-line-number" data-line-number="377"></td>
|
|
<td id="LC377" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L378" class="blob-num js-line-number" data-line-number="378"></td>
|
|
<td id="LC378" 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">"\nMerging pairwise alignments into a MSA\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L379" class="blob-num js-line-number" data-line-number="379"></td>
|
|
<td id="LC379" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L380" class="blob-num js-line-number" data-line-number="380"></td>
|
|
<td id="LC380" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeq = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L381" class="blob-num js-line-number" data-line-number="381"></td>
|
|
<td id="LC381" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeq * refLength;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L382" class="blob-num js-line-number" data-line-number="382"></td>
|
|
<td id="LC382" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeq * (s1</span>[<span class="pl-c">0</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L383" class="blob-num js-line-number" data-line-number="383"></td>
|
|
<td id="LC383" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L384" class="blob-num js-line-number" data-line-number="384"></td>
|
|
<td id="LC384" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L385" class="blob-num js-line-number" data-line-number="385"></td>
|
|
<td id="LC385" class="blob-code blob-code-inner js-file-line"><span class="pl-c">s1N = UnalignedSeqs</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L386" class="blob-num js-line-number" data-line-number="386"></td>
|
|
<td id="LC386" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L387" class="blob-num js-line-number" data-line-number="387"></td>
|
|
<td id="LC387" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeqN = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L388" class="blob-num js-line-number" data-line-number="388"></td>
|
|
<td id="LC388" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeqN * (3*refLength);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L389" class="blob-num js-line-number" data-line-number="389"></td>
|
|
<td id="LC389" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeqN * (s1N</span>[<span class="pl-c">0</span>][<span class="pl-c">2</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L390" class="blob-num js-line-number" data-line-number="390"></td>
|
|
<td id="LC390" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L391" class="blob-num js-line-number" data-line-number="391"></td>
|
|
<td id="LC391" class="blob-code blob-code-inner js-file-line"><span class="pl-c">frameShift = ReadingFrames</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L392" class="blob-num js-line-number" data-line-number="392"></td>
|
|
<td id="LC392" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L393" class="blob-num js-line-number" data-line-number="393"></td>
|
|
<td id="LC393" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (seqCounter=1;seqCounter</span><span class="pl-k"><</span><span class="pl-c">refLength;seqCounter=seqCounter</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L394" class="blob-num js-line-number" data-line-number="394"></td>
|
|
<td id="LC394" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L395" class="blob-num js-line-number" data-line-number="395"></td>
|
|
<td id="LC395" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gapCount = refInsertions</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L396" class="blob-num js-line-number" data-line-number="396"></td>
|
|
<td id="LC396" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (k=0; k</span><span class="pl-k"><</span><span class="pl-c">gapCount;k=k</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L397" class="blob-num js-line-number" data-line-number="397"></td>
|
|
<td id="LC397" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L398" class="blob-num js-line-number" data-line-number="398"></td>
|
|
<td id="LC398" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fullRefSeq*("</span><span class="pl-c1">-</span><span class="pl-c">");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L399" class="blob-num js-line-number" data-line-number="399"></td>
|
|
<td id="LC399" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fullRefSeqN*("</span><span class="pl-c1">---</span><span class="pl-c">");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L400" class="blob-num js-line-number" data-line-number="400"></td>
|
|
<td id="LC400" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> } </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L401" class="blob-num js-line-number" data-line-number="401"></td>
|
|
<td id="LC401" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fullRefSeq * (s1</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L402" class="blob-num js-line-number" data-line-number="402"></td>
|
|
<td id="LC402" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fullRefSeqN * (s1N</span>[<span class="pl-c">frameShift</span><span class="pl-c1">+</span><span class="pl-c">seqCounter*3</span>][<span class="pl-c">frameShift</span><span class="pl-c1">+</span><span class="pl-c">seqCounter*3</span><span class="pl-c1">+</span><span class="pl-c">2</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L403" class="blob-num js-line-number" data-line-number="403"></td>
|
|
<td id="LC403" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L404" class="blob-num js-line-number" data-line-number="404"></td>
|
|
<td id="LC404" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L405" class="blob-num js-line-number" data-line-number="405"></td>
|
|
<td id="LC405" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeq * 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L406" class="blob-num js-line-number" data-line-number="406"></td>
|
|
<td id="LC406" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fullRefSeqN * 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L407" class="blob-num js-line-number" data-line-number="407"></td>
|
|
<td id="LC407" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L408" class="blob-num js-line-number" data-line-number="408"></td>
|
|
<td id="LC408" class="blob-code blob-code-inner js-file-line"><span class="pl-c">return 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L409" class="blob-num js-line-number" data-line-number="409"></td>
|
|
<td id="LC409" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L410" class="blob-num js-line-number" data-line-number="410"></td>
|
|
<td id="LC410" class="blob-code blob-code-inner js-file-line"><span class="pl-c">refLength = Abs(fullRefSeq);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L411" class="blob-num js-line-number" data-line-number="411"></td>
|
|
<td id="LC411" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L412" class="blob-num js-line-number" data-line-number="412"></td>
|
|
<td id="LC412" class="blob-code blob-code-inner js-file-line"><span class="pl-c">SetDialogPrompt ("Save alignment to:");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L413" class="blob-num js-line-number" data-line-number="413"></td>
|
|
<td id="LC413" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L414" class="blob-num js-line-number" data-line-number="414"></td>
|
|
<td id="LC414" class="blob-code blob-code-inner js-file-line"><span class="pl-c">seqName=sequenceNames</span>[<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L415" class="blob-num js-line-number" data-line-number="415"></td>
|
|
<td id="LC415" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fprintf (PROMPT_FOR_FILE</span><span class="pl-en">,</span><span class="pl-c">CLEAR_FILE</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-k">></span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">seqName</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">fullRefSeq);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L416" class="blob-num js-line-number" data-line-number="416"></td>
|
|
<td id="LC416" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fName = LAST_FILE_PATH;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L417" class="blob-num js-line-number" data-line-number="417"></td>
|
|
<td id="LC417" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fNameC = fName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">nuc";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L418" class="blob-num js-line-number" data-line-number="418"></td>
|
|
<td id="LC418" class="blob-code blob-code-inner js-file-line"><span class="pl-c">fprintf (fNameC</span><span class="pl-en">,</span><span class="pl-c">CLEAR_FILE</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-k">></span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">seqName</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">fullRefSeqN);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L419" class="blob-num js-line-number" data-line-number="419"></td>
|
|
<td id="LC419" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L420" class="blob-num js-line-number" data-line-number="420"></td>
|
|
<td id="LC420" class="blob-code blob-code-inner js-file-line"><span class="pl-c">alCounter = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L421" class="blob-num js-line-number" data-line-number="421"></td>
|
|
<td id="LC421" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L422" class="blob-num js-line-number" data-line-number="422"></td>
|
|
<td id="LC422" class="blob-code blob-code-inner js-file-line"><span class="pl-c">for (seqCounter = 1; seqCounter </span><span class="pl-k"><</span><span class="pl-c"> unalSequenceCount; seqCounter = seqCounter</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L423" class="blob-num js-line-number" data-line-number="423"></td>
|
|
<td id="LC423" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L424" class="blob-num js-line-number" data-line-number="424"></td>
|
|
<td id="LC424" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (skipSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> == 0)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L425" class="blob-num js-line-number" data-line-number="425"></td>
|
|
<td id="LC425" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L426" class="blob-num js-line-number" data-line-number="426"></td>
|
|
<td id="LC426" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (skipOutliers == 0 && alignmentScoresM</span>[<span class="pl-c">alCounter</span>]<span class="pl-c"> </span><span class="pl-k"><</span><span class="pl-c"> lowerCuttoff)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L427" class="blob-num js-line-number" data-line-number="427"></td>
|
|
<td id="LC427" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L428" class="blob-num js-line-number" data-line-number="428"></td>
|
|
<td id="LC428" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> seqName=sequenceNames</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L429" class="blob-num js-line-number" data-line-number="429"></td>
|
|
<td id="LC429" 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"> "Sequence "</span><span class="pl-en">,</span><span class="pl-c"> seqName </span><span class="pl-en">,</span><span class="pl-c">" was skipped because of a poor alignment score</span><span class="pl-en">.</span><span class="pl-c">\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L430" class="blob-num js-line-number" data-line-number="430"></td>
|
|
<td id="LC430" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> skipSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c"> = 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L431" class="blob-num js-line-number" data-line-number="431"></td>
|
|
<td id="LC431" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> alCounter = alCounter </span><span class="pl-c1">+</span><span class="pl-c"> 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L432" class="blob-num js-line-number" data-line-number="432"></td>
|
|
<td id="LC432" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> continue;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L433" class="blob-num js-line-number" data-line-number="433"></td>
|
|
<td id="LC433" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L434" class="blob-num js-line-number" data-line-number="434"></td>
|
|
<td id="LC434" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> alCounter = alCounter </span><span class="pl-c1">+</span><span class="pl-c"> 1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L435" class="blob-num js-line-number" data-line-number="435"></td>
|
|
<td id="LC435" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> seqName=sequenceNames</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L436" class="blob-num js-line-number" data-line-number="436"></td>
|
|
<td id="LC436" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned = SeqAlignments</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L437" class="blob-num js-line-number" data-line-number="437"></td>
|
|
<td id="LC437" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L438" class="blob-num js-line-number" data-line-number="438"></td>
|
|
<td id="LC438" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned1 = aligned</span>[<span class="pl-c">1</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L439" class="blob-num js-line-number" data-line-number="439"></td>
|
|
<td id="LC439" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> aligned2 = aligned</span>[<span class="pl-c">2</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L440" class="blob-num js-line-number" data-line-number="440"></td>
|
|
<td id="LC440" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L441" class="blob-num js-line-number" data-line-number="441"></td>
|
|
<td id="LC441" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> s2 = startingPosition</span>[<span class="pl-c">seqCounter</span>][<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L442" class="blob-num js-line-number" data-line-number="442"></td>
|
|
<td id="LC442" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> e2 = startingPosition</span>[<span class="pl-c">seqCounter</span>][<span class="pl-c">1</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L443" class="blob-num js-line-number" data-line-number="443"></td>
|
|
<td id="LC443" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L444" class="blob-num js-line-number" data-line-number="444"></td>
|
|
<td id="LC444" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeq = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L445" class="blob-num js-line-number" data-line-number="445"></td>
|
|
<td id="LC445" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeq * Abs(aligned2);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L446" class="blob-num js-line-number" data-line-number="446"></td>
|
|
<td id="LC446" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L447" class="blob-num js-line-number" data-line-number="447"></td>
|
|
<td id="LC447" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L448" class="blob-num js-line-number" data-line-number="448"></td>
|
|
<td id="LC448" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> k=0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L449" class="blob-num js-line-number" data-line-number="449"></td>
|
|
<td id="LC449" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L450" class="blob-num js-line-number" data-line-number="450"></td>
|
|
<td id="LC450" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> while (k</span><span class="pl-k"><</span><span class="pl-c">refLength)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L451" class="blob-num js-line-number" data-line-number="451"></td>
|
|
<td id="LC451" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L452" class="blob-num js-line-number" data-line-number="452"></td>
|
|
<td id="LC452" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> while (fullRefSeq</span>[<span class="pl-c">k</span>]<span class="pl-c">!=aligned1</span>[<span class="pl-c">s2</span>]<span class="pl-c">)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L453" class="blob-num js-line-number" data-line-number="453"></td>
|
|
<td id="LC453" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L454" class="blob-num js-line-number" data-line-number="454"></td>
|
|
<td id="LC454" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeq*("</span><span class="pl-c1">-</span><span class="pl-c">");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L455" class="blob-num js-line-number" data-line-number="455"></td>
|
|
<td id="LC455" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> k=k</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L456" class="blob-num js-line-number" data-line-number="456"></td>
|
|
<td id="LC456" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L457" class="blob-num js-line-number" data-line-number="457"></td>
|
|
<td id="LC457" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeq*(aligned2</span>[<span class="pl-c">s2</span>]<span class="pl-c">);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L458" class="blob-num js-line-number" data-line-number="458"></td>
|
|
<td id="LC458" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> s2=s2</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L459" class="blob-num js-line-number" data-line-number="459"></td>
|
|
<td id="LC459" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> k=k</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L460" class="blob-num js-line-number" data-line-number="460"></td>
|
|
<td id="LC460" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L461" class="blob-num js-line-number" data-line-number="461"></td>
|
|
<td id="LC461" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L462" class="blob-num js-line-number" data-line-number="462"></td>
|
|
<td id="LC462" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeq * 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L463" class="blob-num js-line-number" data-line-number="463"></td>
|
|
<td id="LC463" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L464" class="blob-num js-line-number" data-line-number="464"></td>
|
|
<td id="LC464" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeqN = "";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L465" class="blob-num js-line-number" data-line-number="465"></td>
|
|
<td id="LC465" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeqN * (3*Abs(aligned2));</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L466" class="blob-num js-line-number" data-line-number="466"></td>
|
|
<td id="LC466" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L467" class="blob-num js-line-number" data-line-number="467"></td>
|
|
<td id="LC467" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> frameShift = ReadingFrames</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L468" class="blob-num js-line-number" data-line-number="468"></td>
|
|
<td id="LC468" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L469" class="blob-num js-line-number" data-line-number="469"></td>
|
|
<td id="LC469" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> s1N = UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L470" class="blob-num js-line-number" data-line-number="470"></td>
|
|
<td id="LC470" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> s2N = ProteinSequences</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L471" class="blob-num js-line-number" data-line-number="471"></td>
|
|
<td id="LC471" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> s2 = startingPosition</span>[<span class="pl-c">seqCounter</span>][<span class="pl-c">0</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L472" class="blob-num js-line-number" data-line-number="472"></td>
|
|
<td id="LC472" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> k = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L473" class="blob-num js-line-number" data-line-number="473"></td>
|
|
<td id="LC473" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> e2 = Abs(gappedSeq);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L474" class="blob-num js-line-number" data-line-number="474"></td>
|
|
<td id="LC474" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> k = 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L475" class="blob-num js-line-number" data-line-number="475"></td>
|
|
<td id="LC475" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> while (k</span><span class="pl-k"><</span><span class="pl-c">e2)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L476" class="blob-num js-line-number" data-line-number="476"></td>
|
|
<td id="LC476" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L477" class="blob-num js-line-number" data-line-number="477"></td>
|
|
<td id="LC477" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> while ((s2N</span>[<span class="pl-c">s2</span>]<span class="pl-c">!=gappedSeq</span>[<span class="pl-c">k</span>]<span class="pl-c">)&&(k</span><span class="pl-k"><</span><span class="pl-c">e2))</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L478" class="blob-num js-line-number" data-line-number="478"></td>
|
|
<td id="LC478" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L479" class="blob-num js-line-number" data-line-number="479"></td>
|
|
<td id="LC479" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeqN * ("</span><span class="pl-c1">---</span><span class="pl-c">");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L480" class="blob-num js-line-number" data-line-number="480"></td>
|
|
<td id="LC480" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> k=k</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L481" class="blob-num js-line-number" data-line-number="481"></td>
|
|
<td id="LC481" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L482" class="blob-num js-line-number" data-line-number="482"></td>
|
|
<td id="LC482" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (k</span><span class="pl-k"><</span><span class="pl-c">e2)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L483" class="blob-num js-line-number" data-line-number="483"></td>
|
|
<td id="LC483" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L484" class="blob-num js-line-number" data-line-number="484"></td>
|
|
<td id="LC484" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeqN * s1N</span>[<span class="pl-c">frameShift</span><span class="pl-c1">+</span><span class="pl-c">s2*3</span>][<span class="pl-c">frameShift</span><span class="pl-c1">+</span><span class="pl-c">s2*3</span><span class="pl-c1">+</span><span class="pl-c">2</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L485" class="blob-num js-line-number" data-line-number="485"></td>
|
|
<td id="LC485" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> s2 = s2</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L486" class="blob-num js-line-number" data-line-number="486"></td>
|
|
<td id="LC486" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> k=k</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L487" class="blob-num js-line-number" data-line-number="487"></td>
|
|
<td id="LC487" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L488" class="blob-num js-line-number" data-line-number="488"></td>
|
|
<td id="LC488" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L489" class="blob-num js-line-number" data-line-number="489"></td>
|
|
<td id="LC489" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> gappedSeqN * 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L490" class="blob-num js-line-number" data-line-number="490"></td>
|
|
<td id="LC490" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L491" class="blob-num js-line-number" data-line-number="491"></td>
|
|
<td id="LC491" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (refSeq2 && seqCounter == unalSequenceCount</span><span class="pl-c1">-</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L492" class="blob-num js-line-number" data-line-number="492"></td>
|
|
<td id="LC492" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L493" class="blob-num js-line-number" data-line-number="493"></td>
|
|
<td id="LC493" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fscanf (fName</span><span class="pl-en">,</span><span class="pl-c"> "Raw"</span><span class="pl-en">,</span><span class="pl-c"> soFar);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L494" class="blob-num js-line-number" data-line-number="494"></td>
|
|
<td id="LC494" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (fName</span><span class="pl-en">,</span><span class="pl-c"> CLEAR_FILE</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-k">></span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">seqName</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">gappedSeq</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">soFar);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L495" class="blob-num js-line-number" data-line-number="495"></td>
|
|
<td id="LC495" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fscanf (fNameC</span><span class="pl-en">,</span><span class="pl-c"> "Raw"</span><span class="pl-en">,</span><span class="pl-c"> soFar);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L496" class="blob-num js-line-number" data-line-number="496"></td>
|
|
<td id="LC496" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (fNameC</span><span class="pl-en">,</span><span class="pl-c">CLEAR_FILE</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-k">></span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">seqName</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">gappedSeqN</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">soFar); </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L497" class="blob-num js-line-number" data-line-number="497"></td>
|
|
<td id="LC497" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L498" class="blob-num js-line-number" data-line-number="498"></td>
|
|
<td id="LC498" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L499" class="blob-num js-line-number" data-line-number="499"></td>
|
|
<td id="LC499" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> else</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L500" class="blob-num js-line-number" data-line-number="500"></td>
|
|
<td id="LC500" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L501" class="blob-num js-line-number" data-line-number="501"></td>
|
|
<td id="LC501" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (fName</span><span class="pl-en">,</span><span class="pl-c">"\n</span><span class="pl-k">></span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">seqName</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">gappedSeq);</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L502" class="blob-num js-line-number" data-line-number="502"></td>
|
|
<td id="LC502" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (fNameC</span><span class="pl-en">,</span><span class="pl-c">"\n</span><span class="pl-k">></span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">seqName</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">gappedSeqN); </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L503" class="blob-num js-line-number" data-line-number="503"></td>
|
|
<td id="LC503" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L504" class="blob-num js-line-number" data-line-number="504"></td>
|
|
<td id="LC504" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L505" class="blob-num js-line-number" data-line-number="505"></td>
|
|
<td id="LC505" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L506" class="blob-num js-line-number" data-line-number="506"></td>
|
|
<td id="LC506" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L507" class="blob-num js-line-number" data-line-number="507"></td>
|
|
<td id="LC507" class="blob-code blob-code-inner js-file-line"><span class="pl-c">if (Abs(skipSeqs))</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L508" class="blob-num js-line-number" data-line-number="508"></td>
|
|
<td id="LC508" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L509" class="blob-num js-line-number" data-line-number="509"></td>
|
|
<td id="LC509" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fName = fName</span><span class="pl-c1">+</span><span class="pl-c">"</span><span class="pl-en">.</span><span class="pl-c">bad";</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L510" class="blob-num js-line-number" data-line-number="510"></td>
|
|
<td id="LC510" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> for (seqCounter = 1; seqCounter </span><span class="pl-k"><</span><span class="pl-c"> unalSequenceCount; seqCounter = seqCounter</span><span class="pl-c1">+</span><span class="pl-c">1)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L511" class="blob-num js-line-number" data-line-number="511"></td>
|
|
<td id="LC511" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L512" class="blob-num js-line-number" data-line-number="512"></td>
|
|
<td id="LC512" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (skipSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L513" class="blob-num js-line-number" data-line-number="513"></td>
|
|
<td id="LC513" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L514" class="blob-num js-line-number" data-line-number="514"></td>
|
|
<td id="LC514" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> seqName=sequenceNames</span>[<span class="pl-c">seqCounter</span>]<span class="pl-c">;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L515" class="blob-num js-line-number" data-line-number="515"></td>
|
|
<td id="LC515" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fprintf (fName</span><span class="pl-en">,</span><span class="pl-c">"</span><span class="pl-k">></span><span class="pl-c">"</span><span class="pl-en">,</span><span class="pl-c">seqName</span><span class="pl-en">,</span><span class="pl-c">"\n"</span><span class="pl-en">,</span><span class="pl-c">UnalignedSeqs</span>[<span class="pl-c">seqCounter</span>]<span class="pl-en">,</span><span class="pl-c">"\n");</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L516" class="blob-num js-line-number" data-line-number="516"></td>
|
|
<td id="LC516" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L517" class="blob-num js-line-number" data-line-number="517"></td>
|
|
<td id="LC517" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L518" class="blob-num js-line-number" data-line-number="518"></td>
|
|
<td id="LC518" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L519" class="blob-num js-line-number" data-line-number="519"></td>
|
|
<td id="LC519" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L520" class="blob-num js-line-number" data-line-number="520"></td>
|
|
<td id="LC520" class="blob-code blob-code-inner js-file-line"><span class="pl-c">function checkFramePosition (pos1</span><span class="pl-en">,</span><span class="pl-c"> pos2</span><span class="pl-en">,</span><span class="pl-c"> fr1</span><span class="pl-en">,</span><span class="pl-c"> fr2)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L521" class="blob-num js-line-number" data-line-number="521"></td>
|
|
<td id="LC521" class="blob-code blob-code-inner js-file-line"><span class="pl-c">{</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L522" class="blob-num js-line-number" data-line-number="522"></td>
|
|
<td id="LC522" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fSpan = pos2</span><span class="pl-c1">-</span><span class="pl-c">pos1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L523" class="blob-num js-line-number" data-line-number="523"></td>
|
|
<td id="LC523" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L524" class="blob-num js-line-number" data-line-number="524"></td>
|
|
<td id="LC524" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (fSpan</span><span class="pl-k">></span><span class="pl-c">1) /* first followed by second*/</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L525" class="blob-num js-line-number" data-line-number="525"></td>
|
|
<td id="LC525" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L526" class="blob-num js-line-number" data-line-number="526"></td>
|
|
<td id="LC526" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> if (fSpan </span><span class="pl-k"><</span><span class="pl-c"> fMin)</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L527" class="blob-num js-line-number" data-line-number="527"></td>
|
|
<td id="LC527" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> {</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L528" class="blob-num js-line-number" data-line-number="528"></td>
|
|
<td id="LC528" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fMin = fSpan;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L529" class="blob-num js-line-number" data-line-number="529"></td>
|
|
<td id="LC529" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> frame1 = fr1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L530" class="blob-num js-line-number" data-line-number="530"></td>
|
|
<td id="LC530" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> frame2 = fr2;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L531" class="blob-num js-line-number" data-line-number="531"></td>
|
|
<td id="LC531" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fStart = pos1</span><span class="pl-c1">+</span><span class="pl-c">1;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L532" class="blob-num js-line-number" data-line-number="532"></td>
|
|
<td id="LC532" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> fEnd = pos2;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L533" class="blob-num js-line-number" data-line-number="533"></td>
|
|
<td id="LC533" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> }</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L534" class="blob-num js-line-number" data-line-number="534"></td>
|
|
<td id="LC534" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> } </span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L535" class="blob-num js-line-number" data-line-number="535"></td>
|
|
<td id="LC535" class="blob-code blob-code-inner js-file-line"><span class="pl-c"> return 0;</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L536" class="blob-num js-line-number" data-line-number="536"></td>
|
|
<td id="LC536" class="blob-code blob-code-inner js-file-line"><span class="pl-c">}</span></td>
|
|
</tr>
|
|
<tr>
|
|
<td id="L537" class="blob-num js-line-number" data-line-number="537"></td>
|
|
<td id="LC537" class="blob-code blob-code-inner js-file-line"><span class="pl-c"></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 -->
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|
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|
</div><!-- /.wrapper -->
|
|
|
|
<div class="container">
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<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://developer.github.com" data-ga-click="Footer, go to api, text:api">API</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>
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<a href="https://github.com" aria-label="Homepage">
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<span class="mega-octicon octicon-mark-github" title="GitHub"></span>
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</a>
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<ul class="site-footer-links">
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<li>© 2015 <span title="0.07666s from github-fe117-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/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li>
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</ul>
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</div>
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</div>
|
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|
|
|
|
<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>
|
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</div>
|
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</div>
|
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</div>
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<div class="fullscreen-sidebar">
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<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"
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aria-label="Switch themes">
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<span class="octicon octicon-color-mode"></span>
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</a>
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</div>
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</div>
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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.
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</div>
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<script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-2c8ae50712a47d2b83d740cb875d55cdbbb3fdbccf303951cc6b7e63731e0c38.js"></script>
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<script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-4a9486eb826000c3f9d69ae1adb4372c626ce3a2a602dc3d007aedd874f64c35.js"></script>
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<div class="js-socket-channel" data-channel="test:mbdoud"></div>
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</body>
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</html>
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