Mercurial > repos > jankanis > blast2html
changeset 1:ffe82516a83c
add trimmed down html example
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed.html Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1615 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"><head> + +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1"> +<meta name="jig" content="ncbitoggler ncbiautocomplete ncbilocalnav ncbigrid ncbipopper"> +<meta name="ncbitoggler" content="animation:'none'"> +<meta name="ncbipopper" content="animation:'none',closeEvent: 'click',openEvent: 'click',destPosition: 'top right',triggerPosition: 'bottom right'"> + +<meta name="ncbi_app" content="blast"> +<meta name="ncbi_pdid" content="blastresults"> +<meta name="ncbi_stat" content="false"> +<meta name="ncbi_sessionid" content="8A8E11EE2CABF371_0000SID"> +<meta name="ncbi_phid" content="5AAB74D7368F2C81000000000000C9C8"> +<script type="text/javascript"> var ncbi_startTime = new Date(); </script> +<title>NCBI Blast:Nucleotide Sequence (16 letters)</title> +<script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jig.js"></script><link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/jig.themenull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery.ncbitogglernull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbitogglernull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbiautocompletenull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery.ncbiautocompletenull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery.ncbibasicmenunull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbibasicmenunull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbimenunull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery.ncbimenunull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery.ncbilocalnavnull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbilocalnavnull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery.buttonnull"></script><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery.ncbibuttonnull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbibuttonnull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbipoppernull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery.ncbipoppernull"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_002.ncbigridnull"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery.ncbigridnull"><link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/jig.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_002.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_005.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_004.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_004.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_007.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_003.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_007.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_003.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_008.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_008.js"></script><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_005.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_009.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_006.css"><script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/jquery_006.js"></script><link type="text/css" rel="stylesheet" href="Blast%20output%20page%20example%20trimmed_files/jquery_002.css"> +<script type="text/javascript"> jQuery.getScript("/core/alerts/alerts.js", function() { + galert(['div#header', 'body > *:nth-child(1)']) + });</script> +<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/main.css" media="screen"> +<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/blastRes.css" media="screen"> +<!--[if IE]> +<link rel="stylesheet" type="text/css" href="css/descriptionsIE.css" media="screen" /> +<![endif]--> +<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/print.css" media="print"> +<!--[if lte IE 6]> +<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" /> +<![endif]--> +<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/blastReq.css" media="screen"> +<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/results.css" media="screen"> +<link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/dynFormatRes.css" media="screen"> + +<style media="print" type="text/css">.print-log { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }.print-log li { list-style-image: url('/stat?jsevent=print&ncbi_app=blast&ncbi_pdid=blastresults&ncbi_phid=5AAB74D7368F2C81000000000000C9C8'); }</style><style type="text/css">.print-log { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; }</style><style type="text/css" charset="utf-8">/* See license.txt for terms of usage */ +/** reset styling **/ +.firebugResetStyles { + z-index: 2147483646 !important; + top: 0 !important; + left: 0 !important; + display: block !important; + border: 0 none !important; + margin: 0 !important; + padding: 0 !important; + outline: 0 !important; + min-width: 0 !important; + max-width: none !important; + min-height: 0 !important; + max-height: none !important; + position: fixed !important; + transform: rotate(0deg) !important; + transform-origin: 50% 50% !important; + border-radius: 0 !important; + box-shadow: none !important; + background: transparent none !important; + pointer-events: none !important; + white-space: normal !important; +} + +.firebugBlockBackgroundColor { + background-color: transparent !important; +} + +.firebugResetStyles:before, .firebugResetStyles:after { + content: "" !important; +} +/**actual styling to be modified by firebug theme**/ +.firebugCanvas { + display: none !important; +} + +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ +.firebugLayoutBox { + width: auto !important; + position: static !important; +} + +.firebugLayoutBoxOffset { + opacity: 0.8 !important; + position: fixed !important; +} + +.firebugLayoutLine { + opacity: 0.4 !important; + background-color: #000000 !important; +} + +.firebugLayoutLineLeft, .firebugLayoutLineRight { + width: 1px !important; + height: 100% !important; +} + +.firebugLayoutLineTop, .firebugLayoutLineBottom { + width: 100% !important; + height: 1px !important; +} + +.firebugLayoutLineTop { + margin-top: -1px !important; + border-top: 1px solid #999999 !important; +} + +.firebugLayoutLineRight { + border-right: 1px solid #999999 !important; +} + +.firebugLayoutLineBottom { + border-bottom: 1px solid #999999 !important; +} + +.firebugLayoutLineLeft { + margin-left: -1px !important; + border-left: 1px solid #999999 !important; +} + +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ +.firebugLayoutBoxParent { + border-top: 0 none !important; + border-right: 1px dashed #E00 !important; + border-bottom: 1px dashed #E00 !important; + border-left: 0 none !important; + position: fixed !important; + width: auto !important; +} + +.firebugRuler{ + position: absolute !important; +} + +.firebugRulerH { + top: -15px !important; + left: 0 !important; + width: 100% !important; + height: 14px !important; + background: 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repeat-x !important; + border-top: 1px solid #BBBBBB !important; + border-right: 1px dashed #BBBBBB !important; + border-bottom: 1px solid #000000 !important; +} + +.firebugRulerV { + top: 0 !important; + left: -15px !important; + width: 14px !important; + height: 100% !important; + background: 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repeat-y !important; + border-left: 1px solid #BBBBBB !important; + border-right: 1px solid #000000 !important; + border-bottom: 1px dashed #BBBBBB !important; +} + +.overflowRulerX > .firebugRulerV { + left: 0 !important; +} + +.overflowRulerY > .firebugRulerH { + top: 0 !important; +} + +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ +.fbProxyElement { + position: fixed !important; + pointer-events: auto !important; +} +</style></head> + +<body id="type-a" class="noToggleCheck "> +<div id="wrap"> + + + <div id="content-wrap"> + + + + + + <!-- CDD info for old design --> + + + + + + + + + <div id="content"> + + <!--<ul id="msg" class="msg"><li class="info"><p class=""></p><p class=""></p><p class=""></p></li></ul>--> + + + + + + + + + <!-- Reformat and downlaod for new design --> + <!-- aria --> + <!-- aria --> + <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" name="overview0"> + + + +<div id="page"> + +<div id="summary" class=""> +<div id="ht"></div> +<h1>Nucleotide Sequence (16 letters) <span id="hdTitle" class="shownInl"></span></h1> +<div> +<div id="multipleSeqs" class="hidden"> +<label for="queryList">Results for:</label> +<select id="queryList" name="queryList"> +<option value="0" selected="selected" class="">lcl|59987 None(16bp)</option> +</select> +<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="queryInfo" title="Multiple quries help" id="queryHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> +<span class="ui-icon ui-icon-triangle-1-e"></span></a> +</div><!--/#multipleSeqs"--> + +<div class="ui-helper-reset" aria-live="assertive"> +<p aria-hidden="true" id="queryInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> +Your BLAST job specified more than one input sequence. +This box lets you choose which input sequence to show BLAST results for. +</p> +</div><!-- ARIA --> +</div> +<div id="summarylists"> +<dl> +<dt>RID</dt> +<dd> +<a title="BLAST search request ID" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014">PHWP1JNZ014</a> (Expires on 05-07 22:33 pm) +</dd> +</dl> +<div id="querysummary"> +<dl> +<dt>Query ID</dt> +<dd class="hidden"> +<a title="Find query in Entrez" href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=nucleotide&term=59987&dopt=GenBank" target="lnkPHWP1JNZ014">lcl|59987</a> +</dd> +<dd class="">lcl|59987</dd> +<dt>Description</dt> +<dd>None</dd> +<dt>Molecule type</dt> +<dd>nucleic acid</dd> +<dt>Query Length</dt> +<dd>16</dd> +</dl> +</div><!--/#querysummary--> + +<div id="dbsummary"> +<dl> +<dt> </dt><dd> </dd> +<dt>Database Name</dt> +<dd>pdb</dd> +<dt>Description</dt> +<dd>PDB nucleotide database <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="See multiple databases detailed information" class="jtg resArrowLinkB hidden jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="dbDetails" id="showDetails"><span class="ui-ncbitoggler-master-text">See details</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd> <!-- -- Database or subject info ----> +<dt class="xgl">Program</dt> +<dd class="xgl">BLASTN 2.2.29+ <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="How to cite BLAST in publications" class="resArrowLinkB hidden shown jig-ncbitoggler ui-ncbitoggler jtg ui-widget" data-ncbitoggler-toggles="refInfo" id="showRefs"><span class="ui-ncbitoggler-master-text">Citation</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></dd> +</dl> +</div><!--/#dbsummary--> +</div><!--/#summarylists --> +<br> +<div class="ui-helper-reset" aria-live="assertive"> +<div aria-hidden="true" id="dbDetails" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> + <!-- multiple databases or subjects table --> +</div> +</div> <!-- aria end --> +<div class="ui-helper-reset" aria-live="assertive"> +<div aria-hidden="true" id="refInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> +<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9254694&dopt=Citation">Reference </a> +<div>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, +Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), +"Gapped BLAST and PSI-BLAST: a new generation of protein database search + programs", Nucleic Acids Res. 25:3389-3402.</div> + </div> <!-- refInfo --> +</div> <!-- aria end --> + +<div id="seealso"> +<label>Other reports:</label> + <a aria-expanded="false" role="button" aria-disabled="false" href="#" title="Show statistics" class="resArrowLinkB jtg jig-ncbitoggler ui-ncbitoggler ui-widget" data-ncbitoggler-toggles="resStat" id="showStat"><span class="ui-ncbitoggler-master-text">Search Summary</span><span class="ui-icon ui-icon-triangle-1-e"></span></a> + <span class="xgl"> + <a id="tax" class="hidden shown" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=PHWP1JNZ014&FORMAT_OBJECT=TaxBlast&NCBI_GI=off&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_BLOCK_ON_RESPAGE=Top&MASK_COLOR=1&MASK_CHAR=2" target="lnkPHWP1JNZ014" title="See results arranged by taxonomy">[Taxonomy reports]</a> + <a href="http://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&blastRID=PHWP1JNZ014&queryID=lcl%7C59987&entrezLim=&ex=&exl=&exh=&ns=100" class="" id="TreeViewlcl|59987" onclick="ViewTree('TreeViewlcl|59987');return false;" target="lnkPHWP1JNZ014" title="See a distance tree of these pairwise comparisons">[Distance tree of results]</a> + + + + </span> +</div> <!-- seealso --> + +<div class="ui-helper-reset" aria-live="assertive"> +<div aria-hidden="true" id="resStat" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> + <table id="params" class="dbInfo"> + <caption>Search Parameters</caption> + <tbody><tr><th><div>Search parameter name</div></th><th><div>Search parameter value</div></th></tr> + <tr><td>Program</td><td>blastn</td></tr><tr><td>Word size</td><td>7</td></tr><tr><td>Expect value</td><td>1000</td></tr><tr><td>Hitlist size</td><td>100</td></tr><tr><td>Match/Mismatch scores</td><td>1,-3</td></tr><tr><td>Gapcosts</td><td>5,2</td></tr><tr><td>Filter string </td><td>F</td></tr><tr><td>Genetic Code</td><td>1</td></tr> + </tbody></table> + <table id="dbStat" class="dbInfo"> + <caption>Database</caption> + <tbody><tr><th><div>Database parameter name</div></th><th><div>Database parameter value</div></th></tr> + <tr><td>Posted date</td><td>Apr 29, 2014 3:14 AM</td></tr> + <tr><td>Number of letters</td><td>885,284</td></tr> + <tr><td>Number of sequences</td><td>8,975</td></tr> + <tr><td>Entrez query</td><td>none</td></tr> + </tbody></table> + + <table id="Kappa" class="dbInfo show xgl"> +<caption>Karlin-Altschul statistics</caption> + <tbody><tr><th><div>Params</div></th><th><div>Ungapped</div></th><th><div>Gapped</div></th></tr> + <tr><td>Lambda</td><td>1.37406</td><td>1.37406</td></tr> + <tr><td>K</td><td>0.710603</td><td>0.710603</td></tr> + <tr><td>H</td><td>1.30725</td><td>1.30725</td></tr> + + </tbody></table> + + + <table class="dbInfo show"> + <caption>Results Statistics</caption> + <tbody><tr><th><div>Results Statistics parameter name</div></th><th><div>Results Statistics parameter value</div></th></tr> + <tr><td>Length adjustment</td><td> 11</td></tr><tr><td>Effective length of query</td><td> 5</td></tr><tr><td>Effective length of database</td><td> 786559</td></tr><tr><td>Effective search space</td><td> 3932795</td></tr><tr><td>Effective search space used</td><td> 3932795</td></tr> + </tbody></table> + <!-- Results statistics --> + </div> <!-- resStat --> + </div> <!-- aria end --> +</div><!--/#summary--> +</div><!--/#page--> + + +<div id="grView" class="hidden shown"> +<h2 class="resArr"> +<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showGraphic" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="graphicInfo" title="Show/hide Graphic Summary"> +<span class="ui-ncbitoggler-master-text">Graphic Summary</span> +<span class="ui-icon ui-icon-plus-minus-big-open"></span> +</a> +</h2> +<div class="ui-helper-reset" aria-live="assertive"> +<div aria-hidden="false" id="graphicInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler"> + + +<div id="graphic" class="hidden shown"> +<h3>Distribution of 45 Blast Hits on the Query Sequence +<a aria-expanded="false" role="button" aria-disabled="false" class="helplink jig-ncbitoggler ui-ncbitoggler ui-widget" title="Graphic summary help" id="grHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span> +<span class="ui-icon ui-icon-triangle-1-e"></span></a></h3> +<div class="ui-helper-reset" aria-live="assertive"> +<p aria-hidden="true" id="ovrInfo" class="helpbox ui-ncbitoggler-slave ui-ncbitoggler"> +An overview of the database sequences aligned to the query sequence is +shown. The score of each alignment is indicated by one of five +different colors, which divides the range of scores into five groups. +Multiple alignments on the same database sequence are connected +by a striped line. <span class="hl">Mousing over</span> a hit sequence causes the definition and score to be shown in the window at the top, +<span class="hl">clicking</span> on a hit sequence takes the user to the associated alignments. +New: +This graphic is an overview of database sequences aligned to the query sequence. +Alignments are color-coded by score, within one of five score ranges. +Multiple alignments on the same database sequence are connected by a dashed line. +<span class="hl">Mousing</span> over an alignment shows the alignment definition and score in the box at the top. +<span class="hl">Clicking</span> an alignment displays the alignment detail. +</p> +</div><!-- ARIA --> +<center><input name="defline" size="85" value="Mouse-over to show defline and scores, click to show alignments" type="text"><table bordercolordark="#0000FF" bordercolorlight="#0000FF" border="1" cellpadding="10" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/score.gif" height="40" width="500"></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="1"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/query_no_scale.gif" height="10" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="51"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/scale.gif" height="10" width="2"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="91"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/scale.gif" height="10" width="2"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="91"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/scale.gif" height="10" width="2"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="91"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/scale.gif" height="10" width="2"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="91"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/scale.gif" height="10" width="2"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="91"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/scale.gif" height="10" width="2"></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/1.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="83"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/3.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="83"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/6.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="83"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/9.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="73"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/1.gif" height="13" width="10"></td> +<td align="LEFT" valign="CENTER"><img alt="" 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S=32 E=0.00079'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="500"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#557804339" onclick='DisplayAlignFromGraphics("557804339",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J56_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="500"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#557804283" onclick='DisplayAlignFromGraphics("557804283",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J54_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="500"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#557804227" onclick='DisplayAlignFromGraphics("557804227",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J52_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="500"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#557804195" onclick='DisplayAlignFromGraphics("557804195",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J51_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="500"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#557804163" onclick='DisplayAlignFromGraphics("557804163",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J50_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="500"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#557804083" onclick='DisplayAlignFromGraphics("557804083",event)'><img alt="score 32" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J4X_A Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex I.. S=32 E=0.00079'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="500"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#485601478" onclick='DisplayAlignFromGraphics("485601478",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3F_5 Chain 5, Structure Of The H. 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Sapiens 60s Rrna S=16 E=47'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="124"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 14" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=14 E=1.9e+02'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="219"></a></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="6" width="1"></td> +<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=18 E=12'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="155"></a></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="6" width="1"></td> +<td align="LEFT" valign="CENTER"><a href="#485601474" onclick='DisplayAlignFromGraphics("485601474",event)'><img alt="score 16" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J3E_5 Chain 5, Structure Of The D. Melanogaster 60s Rrna S=16 E=47'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="124"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="50"></td> +<td align="LEFT" valign="CENTER"><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="94"></td> +<td align="LEFT" valign="CENTER"><a href="#357380483" onclick='DisplayAlignFromGraphics("357380483",event)'><img alt="score 18" onmouseout="document.overview0.defline.value='Mouse-over to show defline and scores, click to show alignments'" onmouseover="document.overview0.defline.value='3J0O_8 Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex .. S=18 E=12'" src="Blast%20output%20page%20example%20trimmed_files/black.gif" height="4" border="0" width="281"></a></td> +</tr></tbody></table> +<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td><img alt="" src="Blast%20output%20page%20example%20trimmed_files/white.gif" height="4" width="550"></td></tr></tbody></table> +</td></tr></tbody></table> +</center><hr> +</div><!--/#graphic--> +</div><!-- graphicInfo --> +</div><!-- ARIA --> +</div> +<!--HITMATRIX_VIEW - only for bl2seq --> + +<div id="dscrView" class="hidden shown"> +<h2 class="resArr"> +<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showDescr" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="descrInfo" title="Show/hide Descriptions"> +<span class="ui-ncbitoggler-master-text">Descriptions</span> +<span class="ui-icon ui-icon-plus-minus-big-open"></span> +</a> +</h2> +<div class="ui-helper-reset" aria-live="assertive"> +<div aria-hidden="false" id="descrInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler"> + <!-- legend to links to other resources --> +<a name="sort_mark"></a> + + +<div id="debug">, Reading indexes 1-5, displaying indexes 1-5</div> +<input id="Rid" value="PHWP1JNZ014" type="hidden"> +<input id="useAlignDB" name="useAlignDB" value="" type="hidden"> +<input id="dbType" value="GenBank" type="hidden"><!-- Indicates genbank, etc --> +<input id="serviceType" value="plain" type="hidden"> +<input id="clientType" value="web" type="hidden"> +<input id="currQuery" value="" type="hidden"> +<input id="minDispAlnLen" value="2000" type="hidden"> +<input id="maxDispAlnLen" value="20000" type="hidden"> +<div class="hidden" id="dynHspTmpl"><div class="alnParLinks moreHsps" id="@moreHspsID@"><a class="gbd toolsCtr navNext" title="Load matches @segs@ out of @totalHSP@ for @accs@" onmouseover="scan(this)" ref="range=@segs@&currseq=@alnSeqGi@" onclick="ReadNextHSPSet(@argstring@);"><span>Load next set</span></a><a class="gbd toolsCtr navPrev" title="Go to previous match #@aln_prev_num@ for @accs@" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a></div></div> +<div id="descriptions" class="blRes"> +<!--<pre> --> +<div class="cap">Sequences producing significant alignments:</div> +<a id="shcl" href="#" onclick="showAllCol(event,this)" class="shcl hidden"> +Show all columns <span class="accsb"> of the table presenting sequences producing significant alignments </span> +</a> +<span id="cntDesc"> +<span>Select:<a href="#" id="cntSelA" sel="all">All</a><a href="#" id="cntSelN" sel="n">None</a></span> +<span>Selected:<span id="slcNum">0</span></span> +</span> + +<div id="descTblCtrl" class="cnf"> +<a href="#alignInfo" id="alnNav" class="toolsCtr alnNav" title="Go to alignments"><span>Alignments</span></a> +<a aria-haspopup="true" aria-expanded="false" role="button" href="#dsDownload" minslct="1" class="jig-ncbipopper toolsCtr dnld dialog " data-jigconfig="hasArrow:'true',arrowDirection:'top'" id="dscDwnld" disabled="disabled" title="Download information for selected sequences"><span>Download</span></a> + +<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsDownload" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> +<div class=""><input name="dwn" checked="checked" id="dwFST" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST">FASTA (complete sequence)</label></div> +<div class=""><input name="dwn" id="dwFSTAl" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl">FASTA (aligned sequences)</label></div> +<div class=""><input name="dwn" id="dwGenBank" getgi="on" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class=" shownInl" for="dwGenBank">GenBank (complete sequence)</label></div> +<div><input name="dwn" id="dwHitText" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get" type="radio"><label class="shownInl" for="dwHitText">Hit Table (text)</label></div> +<div><input name="dwn" id="dwHitCsv" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=CSV&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get" type="radio"><label class="shownInl" for="dwHitCsv">Hit Table (CSV)</label></div> +<div><input name="dwn" id="dwText" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=Text&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwText">Text</label></div> +<div><input name="dwn" id="dwXML" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwXML">XML</label></div> +<div><input name="dwn" id="dwASN" url="Blast.cgi?RESULTS_FILE=on&RID=PHWP1JNZ014&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=Alignment&CMD=Get" type="radio"><label class="shownInl" for="dwASN">ASN.1</label></div> +<div> +<button class="cfg" id="dw_cont">Continue</button> +<button class="cfg cnc">Cancel</button> +</div> +</div> <!-- dsDownload --> + + + + + +<a href="#" class="toolsCtr" minslct="1" view="dflt" frm="submitterTop" seqlist="selSeqs" title="See genbank report for selected sequences" disabled="disabled">GenBank</a> <!-- genbank or Traces --> +<a href="#" class="toolsCtr " minslct="1" view="graph" title="See graphic representation for selected sequences" disabled="disabled">Graphics</a> +<a href="#" class="toolsCtr hidden shown" view="tree" minslct="1" frm="sbmtTreeView" seqlist="selSeqsTr" disabled="disabled" title="See a distance tree of pairwise comparisons for the selected sequences">Distance tree of results</a> +<a href="#" class="toolsCtr hidden " view="dflt" minslct="2" frm="sbmtMultiAln" seqlist="selSeqsMl" disabled="disabled" title="See multple alignment of query and target sequences for the selected sequences with expect value better than 0.001">Multiple alignment</a> + +<a aria-haspopup="true" aria-expanded="false" role="button" class="jig-ncbipopper button_config" title="Show/hide columns" id="button_config" href="#dsConfig"><span class="accsb">Show/hide columns of the table presenting sequences producing significant alignments </span></a> + +<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dsConfig" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> +<div class="tl">Available columns</div> +<input checked="checked" id="chkDs" value="2" type="checkbox"><label class="shownInl" for="chkDs">Description</label><br> +<input checked="checked" id="chkMS" value="3" type="checkbox"><label class="shownInl" for="chkMs">Max Score</label><br> +<input checked="checked" id="chkTS" value="4" type="checkbox"><label class="shownInl" for="chkTs">Total Score</label><br> +<input checked="checked" id="chkCov" value="5" type="checkbox"><label class="shownInl" for="chkCov">Coverage</label><br> +<input checked="checked" id="chkEval" value="6" type="checkbox"><label class="shownInl" for="chkEval">E-value</label><br> +<input checked="checked" id="chkIdnt" value="7" type="checkbox"><label class="shownInl" for="chkIdnt"><span class="">Ident</span><span class="hidden">N</span></label><br> +<input checked="checked" id="chkAcc" value="8" type="checkbox"><label class="shownInl" for="chkAcc">Accession</label><br> +<button class="cfg rdf" id="dscRsDf">Restore Defaults</button> +<button class="cfg" id="dscOk">Ok</button> +<button class="cfg cnc" id="dscCnc">Cancel</button> +</div> <!-- dsConfig --> + +<input id="cfcDsInf" defval="2,3,4,5,6,7,8" value="2,3,4,5,6,7,8" type="hidden"> +</div> +<div class="ui-ncbigrid-outer-div caption-exists"> +<div class="ui-ncbigrid-inner-div"> +<table id="dscTable" class="jig-ncbigrid ui-ncbigrid" data-jigconfig="" cellpadding="0" cellspacing="0"> +<caption class="hdnHeader">Sequences producing significant alignments:</caption> +<thead> +<tr class="first"> + <th class="c0" id="c0"><span>Select for downloading or viewing reports</span></th> + <th class="dflnDth c2" id="c2">Description</th> + <th class=" c3" id="c3"> + + <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=1&HSP_SORT=1" class="dcs" title="Sort by max score">Max score</a> + </th> + <th class=" c4" id="c4"> + <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=2&HSP_SORT=1" class="dcs" title="Sort by total score">Total score</a> + </th> + <th class=" c5" id="c5"> + <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=4&HSP_SORT=0" class="dcs" title="Sort by query coverage">Query cover</a> + </th> + <th class="sel c6" id="c6"> + <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&OLD_VIEW=false&DISPLAY_SORT=0&HSP_SORT=0" class="dcs" title="Sort by E value">E value</a> + </th> + <th class="c7" id="c7"> +<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&DYNAMIC_FORMAT=on&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&LINE_LENGTH=60&MASK_CHAR=2&MASK_COLOR=1&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=Nucleotides&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=PHWP1JNZ014&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&WORD_SIZE=7&DISPLAY_SORT=3&HSP_SORT=3" class="dcs" title="Sort by ident">Ident</a> +</th> + + <th class="c1" id="c8">Accession</th> +</tr> +</thead> +<tbody> +<tr id="dtr_557804451" ind="1" class="odd dflLnk"> +<td class="l c0"><span class="ind">1</span><input id="chk_1" class="cb" name="getSeqGi" value="557804451" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_1" class="accsb">Select seq pdb|3J5A|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="1" accs="pdb|3J5A|A" seqfsta="gi|557804451" gi="557804451" seqid="557804451" id="deflnDesc_1" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804451">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nucltop&blast_rank=1&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J5A_A">3J5A_A</a> +</td> +</tr><tr id="dtr_557804395" ind="2" class="even dflLnk"> +<td class="l c0"><span class="ind">2</span><input id="chk_2" class="cb" name="getSeqGi" value="557804395" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_2" class="accsb">Select seq pdb|3J58|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="2" accs="pdb|3J58|A" seqfsta="gi|557804395" gi="557804395" seqid="557804395" id="deflnDesc_2" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804395">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nucltop&blast_rank=2&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J58_A">3J58_A</a> +</td> +</tr><tr id="dtr_557804339" ind="3" class="odd dflLnk"> +<td class="l c0"><span class="ind">3</span><input id="chk_3" class="cb" name="getSeqGi" value="557804339" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_3" class="accsb">Select seq pdb|3J56|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="3" accs="pdb|3J56|A" seqfsta="gi|557804339" gi="557804339" seqid="557804339" id="deflnDesc_3" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804339">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nucltop&blast_rank=3&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J56_A">3J56_A</a> +</td> +</tr><tr id="dtr_557804283" ind="4" class="even dflLnk"> +<td class="l c0"><span class="ind">4</span><input id="chk_4" class="cb" name="getSeqGi" value="557804283" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_4" class="accsb">Select seq pdb|3J54|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="4" accs="pdb|3J54|A" seqfsta="gi|557804283" gi="557804283" seqid="557804283" id="deflnDesc_4" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804283">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nucltop&blast_rank=4&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J54_A">3J54_A</a> +</td> +</tr><tr id="dtr_557804227" ind="5" class="odd dflLnk"> +<td class="l c0"><span class="ind">5</span><input id="chk_5" class="cb" name="getSeqGi" value="557804227" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_5" class="accsb">Select seq pdb|3J52|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a stat="disp" title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="5" accs="pdb|3J52|A" seqfsta="gi|557804227" gi="557804227" seqid="557804227" id="deflnDesc_5" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804227">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nucltop&blast_rank=5&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J52_A">3J52_A</a> +</td> +</tr><tr id="dtr_557804195" ind="6" class="even dflLnk"> +<td class="l c0"><span class="ind">6</span><input id="chk_6" class="cb" name="getSeqGi" value="557804195" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_6" class="accsb">Select seq pdb|3J51|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="6" accs="pdb|3J51|A" seqfsta="gi|557804195" gi="557804195" seqid="557804195" id="deflnDesc_6" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804195">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804195?report=genbank&log$=nucltop&blast_rank=6&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J51_A">3J51_A</a> +</td> +</tr><tr id="dtr_557804163" ind="7" class="odd dflLnk"> +<td class="l c0"><span class="ind">7</span><input id="chk_7" class="cb" name="getSeqGi" value="557804163" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_7" class="accsb">Select seq pdb|3J50|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="7" accs="pdb|3J50|A" seqfsta="gi|557804163" gi="557804163" seqid="557804163" id="deflnDesc_7" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804163">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804163?report=genbank&log$=nucltop&blast_rank=7&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J50_A">3J50_A</a> +</td> +</tr><tr id="dtr_557804083" ind="8" class="even dflLnk"> +<td class="l c0"><span class="ind">8</span><input id="chk_8" class="cb" name="getSeqGi" value="557804083" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_8" class="accsb">Select seq pdb|3J4X|A</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)" class="deflnDesc" hsp="4" len="38" ind="8" accs="pdb|3J4X|A" seqfsta="gi|557804083" gi="557804083" seqid="557804083" id="deflnDesc_8" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_557804083">Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)</a> +</div> +</td> +<td class="c3">32.2</td> +<td class="c4">77.3</td> +<td class="c5">100%</td> +<td class="c6">8e-04</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804083?report=genbank&log$=nucltop&blast_rank=8&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J4X_A">3J4X_A</a> +</td> +</tr><tr id="dtr_485601478" ind="9" class="odd dflLnk"> +<td class="l c0"><span class="ind">9</span><input id="chk_9" class="cb" name="getSeqGi" value="485601478" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_9" class="accsb">Select seq pdb|3J3F|5</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain 5, Structure Of The H. Sapiens 60s Rrna" class="deflnDesc" hsp="8" len="63" ind="9" accs="pdb|3J3F|5" seqfsta="gi|485601478" gi="485601478" seqid="485601478" id="deflnDesc_9" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601478">Chain 5, Structure Of The H. Sapiens 60s Rrna</a> +</div> +</td> +<td class="c3">18.3</td> +<td class="c4"> 128</td> +<td class="c5">100%</td> +<td class="c6"> 12</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601478?report=genbank&log$=nucltop&blast_rank=9&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3F_5">3J3F_5</a> +</td> +</tr><tr id="dtr_485601474" ind="10" class="even dflLnk"> +<td class="l c0"><span class="ind">10</span><input id="chk_10" class="cb" name="getSeqGi" value="485601474" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_10" class="accsb">Select seq pdb|3J3E|5</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain 5, Structure Of The D. Melanogaster 60s Rrna" class="deflnDesc" hsp="4" len="31" ind="10" accs="pdb|3J3E|5" seqfsta="gi|485601474" gi="485601474" seqid="485601474" id="deflnDesc_10" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_485601474">Chain 5, Structure Of The D. Melanogaster 60s Rrna</a> +</div> +</td> +<td class="c3">18.3</td> +<td class="c4">63.4</td> +<td class="c5">100%</td> +<td class="c6"> 12</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/485601474?report=genbank&log$=nucltop&blast_rank=10&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J3E_5">3J3E_5</a> +</td> +</tr><tr id="dtr_357380483" ind="11" class="odd dflLnk"> +<td class="l c0"><span class="ind">11</span><input id="chk_11" class="cb" name="getSeqGi" value="357380483" onclick="configDescrLinks(event,this)" type="checkbox"><label for="chk_11" class="accsb">Select seq pdb|3J0O|8</label></td> +<td class="lim l c2"> +<div class="lim n"> +<a title="Go to alignment for Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2" class="deflnDesc" hsp="1" len="9" ind="11" accs="pdb|3J0O|8" seqfsta="gi|357380483" gi="357380483" seqid="357380483" id="deflnDesc_11" onclick="DisplayAlignFromDescription(this);" href="#alnHdr_357380483">Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2</a> +</div> +</td> +<td class="c3">18.3</td> +<td class="c4">18.3</td> +<td class="c5">56%</td> +<td class="c6"> 12</td><td class="c7">100%</td> +<td class="c1 l lim"> +<a href="http://www.ncbi.nlm.nih.gov/nucleotide/357380483?report=genbank&log$=nucltop&blast_rank=11&RID=PHWP1JNZ014" class="dflSeq" target="lnkPHWP1JNZ014" title="Show report for 3J0O_8">3J0O_8</a> +</td> +</tr> +</tbody> +</table> +</div></div> +<!--</pre> --> +</div><!--/#descriptions--> +</div><!-- descrInfo --> +</div><!--ARIA--> +</div> +</form><!-- this is the end tag for the <form in blastcgi templates --> + + + + + +<!-- used in redesign --> + +<div id="alignView" class=" "> +<h2 class="resArr"> +<a aria-expanded="true" role="button" aria-disabled="false" href="#" id="showAlign" class="jig-ncbitoggler-open ui-ncbitoggler-open ui-widget" data-jigconfig="indicator: 'plus-minus-big'" data-ncbitoggler-toggles="alignInfo" title="Show/hide Alignments"> +<span class="ui-ncbitoggler-master-text">Alignments</span> +<span class="ui-icon ui-icon-plus-minus-big-open"></span> +</a> +</h2> + +<div class="ui-helper-reset" aria-live="assertive"> +<div aria-hidden="false" id="alignInfo" class="resBox ui-ncbitoggler-slave-open ui-widget ui-ncbitoggler"> +<div id="alignments" class="blRes"> +<span id="alnStart"></span><div seqlist="gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227" indexes="1-5" id="alnShow_1" class="alnMsg"><div class="alnMsgS hidden" id="alnMsg_1">Loading alignment...<span class="db"> for sequences gi|557804451,gi|557804395,gi|557804339,gi|557804283,gi|557804227 Reading indexes 1-5</span></div><div id="alnShowReal_1" class="alnMsgR"><form name="getSeqAlignment1"> +<div class="alnHdr cnf" id="alnHdr_557804451" seqid="557804451" accs="pdb|3J5A|A"> +<a name="557804451"></a> +<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804451" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804451" title="Download information for pdb|3J5A|A"><span>Download</span></a> +<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804451" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> +<div><input seqfsta="gi|557804451" name="dwn_557804451" checked="checked" id="dwFST_557804451" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804451">FASTA (complete sequence)</label></div> +<div><input seqfsta="gi|557804451" name="dwn_557804451" id="dwFSTAl_557804451" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804451">FASTA (aligned sequences)</label></div> +<div class=""><input name="dwn_557804451" id="dwGenBank_557804451" getgi="557804451" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804451">GenBank (complete sequence)</label></div> +<div> +<button class="cfg" id="dw_cont_557804451">Continue</button> +<button class="cfg cnc">Cancel</button> +</div> +</div> <!-- dsDownload --> +<span class="csLinks" id="csLinks_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics">Graphics</a></span> + +<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> +<select id="sa_557804451" onchange="SortHSPAlnSel(event,this)"> +<option selected="selected" value="0">E value</option> +<option value="1"> Score</option> +<option value="3">Percent identity</option> +<option value="2">Query start position</option> +<option value="4">Subject start position</option> +</select> +</div> +<span class="alnSeqLinks"> +<a title="Go to next alignment for pdb|3J58|A" class="gbd toolsCtr navNext" ref="ordinalpos=1&currseq=557804451" id="alnNxt_557804451" onclick="goToNextAlign('dtr_557804451',true);"><span>Next</span></a> +<a disabled="disabled" class="gbd toolsCtr navPrev" ref="ordinalpos=1&currseq=557804451" id="alnPrv_557804451" onclick="goToNextAlign('dtr_557804451',false);"><span>Previous</span></a> +<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J5A|A" id="alnDsc_557804451" onclick="goToDefLine('dtr_557804451');" href="#dtr_557804451"><span>Descriptions</span></a> +</span> +</div> +<div class="oneSeqAln" id="aln_557804451"> +<div id="dln_557804451"> +<div class="dlfRow"> +Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit) +<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J5A|A">pdb|3J5A|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804451"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804451"><div id="hd_557804451_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> +<span id="hsp557804451_1" class="alnParLinks"> +<a init="on" class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack hidden" href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #1</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>32.2 bits(16)</td> +<td>8e-04<span class="sumN ">()</span></td> +<td>16/16(100%)</td> +<td>0/16(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804451_1"> +<pre>Query 1 CGTCCGTCGTGAAGAG 16 + |||||||||||||||| +Sbjct 961 CGTCCGTCGTGAAGAG 976 + + +</pre> +</div> +<div id="hd_557804451_2"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> +<span id="hsp557804451_2" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #2</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>16.4 bits(8)</td> +<td> 47<span class="sumN ">()</span></td> +<td>8/8(100%)</td> +<td>0/8(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804451_2"> +<pre>Query 5 CGTCGTGA 12 + |||||||| +Sbjct 2591 CGTCGTGA 2598 + + +</pre> +</div> +<div id="hd_557804451_3"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> +<span id="hsp557804451_3" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #3</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804451_3"> +<pre>Query 7 TCGTGAA 13 + ||||||| +Sbjct 839 TCGTGAA 845 + + +</pre> +</div> +<div id="hd_557804451_4"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804451"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J5A_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J5A_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> +<span id="hsp557804451_4" class="alnParLinks"> +<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804451" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J5A|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804451" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804451_1" title="Go to first match for pdb|3J5A|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #4</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804451_4"> +<pre>Query 9 GTGAAGA 15 + ||||||| +Sbjct 2027 GTGAAGA 2033 + + +</pre> +</div> +</div> <!-- alnAll_557804451 --> +</div> <!-- aln_557804451 --> +<div class="alnHdr cnf" id="alnHdr_557804395" seqid="557804395" accs="pdb|3J58|A"> +<a name="557804395"></a> +<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804395" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804395" title="Download information for pdb|3J58|A"><span>Download</span></a> +<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804395" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> +<div><input seqfsta="gi|557804395" name="dwn_557804395" checked="checked" id="dwFST_557804395" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804395">FASTA (complete sequence)</label></div> +<div><input seqfsta="gi|557804395" name="dwn_557804395" id="dwFSTAl_557804395" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804395">FASTA (aligned sequences)</label></div> +<div class=""><input name="dwn_557804395" id="dwGenBank_557804395" getgi="557804395" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804395">GenBank (complete sequence)</label></div> +<div> +<button class="cfg" id="dw_cont_557804395">Continue</button> +<button class="cfg cnc">Cancel</button> +</div> +</div> <!-- dsDownload --> +<span class="csLinks" id="csLinks_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics">Graphics</a></span> + +<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> +<select id="sa_557804395" onchange="SortHSPAlnSel(event,this)"> +<option selected="selected" value="0">E value</option> +<option value="1"> Score</option> +<option value="3">Percent identity</option> +<option value="2">Query start position</option> +<option value="4">Subject start position</option> +</select> +</div> +<span class="alnSeqLinks"> +<a title="Go to next alignment for pdb|3J56|A" class="gbd toolsCtr navNext" ref="ordinalpos=2&currseq=557804395" id="alnNxt_557804395" onclick="goToNextAlign('dtr_557804395',true);"><span>Next</span></a> +<a title="Go to previous alignment for pdb|3J5A|A" class="gbd toolsCtr navPrev" ref="ordinalpos=2&currseq=557804395" id="alnPrv_557804395" onclick="goToNextAlign('dtr_557804395',false);"><span>Previous</span></a> +<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J58|A" id="alnDsc_557804395" onclick="goToDefLine('dtr_557804395');" href="#dtr_557804395"><span>Descriptions</span></a> +</span> +</div> +<div class="oneSeqAln" id="aln_557804395"> +<div id="dln_557804395"> +<div class="dlfRow"> +Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit) +<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J58|A">pdb|3J58|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804395"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804395"><div id="hd_557804395_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> +<span id="hsp557804395_1" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack hidden" href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #1</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>32.2 bits(16)</td> +<td>8e-04<span class="sumN ">()</span></td> +<td>16/16(100%)</td> +<td>0/16(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804395_1"> +<pre>Query 1 CGTCCGTCGTGAAGAG 16 + |||||||||||||||| +Sbjct 961 CGTCCGTCGTGAAGAG 976 + + +</pre> +</div> +<div id="hd_557804395_2"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> +<span id="hsp557804395_2" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #2</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>16.4 bits(8)</td> +<td> 47<span class="sumN ">()</span></td> +<td>8/8(100%)</td> +<td>0/8(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804395_2"> +<pre>Query 5 CGTCGTGA 12 + |||||||| +Sbjct 2591 CGTCGTGA 2598 + + +</pre> +</div> +<div id="hd_557804395_3"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> +<span id="hsp557804395_3" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #3</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804395_3"> +<pre>Query 7 TCGTGAA 13 + ||||||| +Sbjct 839 TCGTGAA 845 + + +</pre> +</div> +<div id="hd_557804395_4"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804395"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804395?report=genbank&log$=nuclalign&blast_rank=2&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J58_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804395?report=graph&rid=PHWP1JNZ014[557804395]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J58_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> +<span id="hsp557804395_4" class="alnParLinks"> +<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804395" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J58|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804395" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804395_1" title="Go to first match for pdb|3J58|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #4</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804395_4"> +<pre>Query 9 GTGAAGA 15 + ||||||| +Sbjct 2027 GTGAAGA 2033 + + +</pre> +</div> +</div> <!-- alnAll_557804395 --> +</div> <!-- aln_557804395 --> +<div class="alnHdr cnf" id="alnHdr_557804339" seqid="557804339" accs="pdb|3J56|A"> +<a name="557804339"></a> +<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804339" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804339" title="Download information for pdb|3J56|A"><span>Download</span></a> +<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804339" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> +<div><input seqfsta="gi|557804339" name="dwn_557804339" checked="checked" id="dwFST_557804339" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804339">FASTA (complete sequence)</label></div> +<div><input seqfsta="gi|557804339" name="dwn_557804339" id="dwFSTAl_557804339" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804339">FASTA (aligned sequences)</label></div> +<div class=""><input name="dwn_557804339" id="dwGenBank_557804339" getgi="557804339" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804339">GenBank (complete sequence)</label></div> +<div> +<button class="cfg" id="dw_cont_557804339">Continue</button> +<button class="cfg cnc">Cancel</button> +</div> +</div> <!-- dsDownload --> +<span class="csLinks" id="csLinks_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics">Graphics</a></span> + +<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> +<select id="sa_557804339" onchange="SortHSPAlnSel(event,this)"> +<option selected="selected" value="0">E value</option> +<option value="1"> Score</option> +<option value="3">Percent identity</option> +<option value="2">Query start position</option> +<option value="4">Subject start position</option> +</select> +</div> +<span class="alnSeqLinks"> +<a title="Go to next alignment for pdb|3J54|A" class="gbd toolsCtr navNext" ref="ordinalpos=3&currseq=557804339" id="alnNxt_557804339" onclick="goToNextAlign('dtr_557804339',true);"><span>Next</span></a> +<a title="Go to previous alignment for pdb|3J58|A" class="gbd toolsCtr navPrev" ref="ordinalpos=3&currseq=557804339" id="alnPrv_557804339" onclick="goToNextAlign('dtr_557804339',false);"><span>Previous</span></a> +<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J56|A" id="alnDsc_557804339" onclick="goToDefLine('dtr_557804339');" href="#dtr_557804339"><span>Descriptions</span></a> +</span> +</div> +<div class="oneSeqAln" id="aln_557804339"> +<div id="dln_557804339"> +<div class="dlfRow"> +Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit) +<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J56|A">pdb|3J56|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804339"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804339"><div id="hd_557804339_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> +<span id="hsp557804339_1" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack hidden" href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #1</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>32.2 bits(16)</td> +<td>8e-04<span class="sumN ">()</span></td> +<td>16/16(100%)</td> +<td>0/16(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804339_1"> +<pre>Query 1 CGTCCGTCGTGAAGAG 16 + |||||||||||||||| +Sbjct 961 CGTCCGTCGTGAAGAG 976 + + +</pre> +</div> +<div id="hd_557804339_2"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> +<span id="hsp557804339_2" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #2</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>16.4 bits(8)</td> +<td> 47<span class="sumN ">()</span></td> +<td>8/8(100%)</td> +<td>0/8(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804339_2"> +<pre>Query 5 CGTCGTGA 12 + |||||||| +Sbjct 2591 CGTCGTGA 2598 + + +</pre> +</div> +<div id="hd_557804339_3"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> +<span id="hsp557804339_3" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #3</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804339_3"> +<pre>Query 7 TCGTGAA 13 + ||||||| +Sbjct 839 TCGTGAA 845 + + +</pre> +</div> +<div id="hd_557804339_4"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804339"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804339?report=genbank&log$=nuclalign&blast_rank=3&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J56_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804339?report=graph&rid=PHWP1JNZ014[557804339]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J56_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> +<span id="hsp557804339_4" class="alnParLinks"> +<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804339" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J56|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804339" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804339_1" title="Go to first match for pdb|3J56|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #4</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804339_4"> +<pre>Query 9 GTGAAGA 15 + ||||||| +Sbjct 2027 GTGAAGA 2033 + + +</pre> +</div> +</div> <!-- alnAll_557804339 --> +</div> <!-- aln_557804339 --> +<div class="alnHdr cnf" id="alnHdr_557804283" seqid="557804283" accs="pdb|3J54|A"> +<a name="557804283"></a> +<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804283" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804283" title="Download information for pdb|3J54|A"><span>Download</span></a> +<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804283" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> +<div><input seqfsta="gi|557804283" name="dwn_557804283" checked="checked" id="dwFST_557804283" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804283">FASTA (complete sequence)</label></div> +<div><input seqfsta="gi|557804283" name="dwn_557804283" id="dwFSTAl_557804283" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804283">FASTA (aligned sequences)</label></div> +<div class=""><input name="dwn_557804283" id="dwGenBank_557804283" getgi="557804283" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804283">GenBank (complete sequence)</label></div> +<div> +<button class="cfg" id="dw_cont_557804283">Continue</button> +<button class="cfg cnc">Cancel</button> +</div> +</div> <!-- dsDownload --> +<span class="csLinks" id="csLinks_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics">Graphics</a></span> + +<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> +<select id="sa_557804283" onchange="SortHSPAlnSel(event,this)"> +<option selected="selected" value="0">E value</option> +<option value="1"> Score</option> +<option value="3">Percent identity</option> +<option value="2">Query start position</option> +<option value="4">Subject start position</option> +</select> +</div> +<span class="alnSeqLinks"> +<a title="Go to next alignment for pdb|3J52|A" class="gbd toolsCtr navNext" ref="ordinalpos=4&currseq=557804283" id="alnNxt_557804283" onclick="goToNextAlign('dtr_557804283',true);"><span>Next</span></a> +<a title="Go to previous alignment for pdb|3J56|A" class="gbd toolsCtr navPrev" ref="ordinalpos=4&currseq=557804283" id="alnPrv_557804283" onclick="goToNextAlign('dtr_557804283',false);"><span>Previous</span></a> +<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J54|A" id="alnDsc_557804283" onclick="goToDefLine('dtr_557804283');" href="#dtr_557804283"><span>Descriptions</span></a> +</span> +</div> +<div class="oneSeqAln" id="aln_557804283"> +<div id="dln_557804283"> +<div class="dlfRow"> +Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit) +<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J54|A">pdb|3J54|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804283"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804283"><div id="hd_557804283_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> +<span id="hsp557804283_1" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack hidden" href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #1</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>32.2 bits(16)</td> +<td>8e-04<span class="sumN ">()</span></td> +<td>16/16(100%)</td> +<td>0/16(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804283_1"> +<pre>Query 1 CGTCCGTCGTGAAGAG 16 + |||||||||||||||| +Sbjct 961 CGTCCGTCGTGAAGAG 976 + + +</pre> +</div> +<div id="hd_557804283_2"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> +<span id="hsp557804283_2" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #2</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>16.4 bits(8)</td> +<td> 47<span class="sumN ">()</span></td> +<td>8/8(100%)</td> +<td>0/8(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804283_2"> +<pre>Query 5 CGTCGTGA 12 + |||||||| +Sbjct 2591 CGTCGTGA 2598 + + +</pre> +</div> +<div id="hd_557804283_3"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> +<span id="hsp557804283_3" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #3</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804283_3"> +<pre>Query 7 TCGTGAA 13 + ||||||| +Sbjct 839 TCGTGAA 845 + + +</pre> +</div> +<div id="hd_557804283_4"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804283"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804283?report=genbank&log$=nuclalign&blast_rank=4&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J54_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804283?report=graph&rid=PHWP1JNZ014[557804283]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J54_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> +<span id="hsp557804283_4" class="alnParLinks"> +<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804283" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J54|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804283" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804283_1" title="Go to first match for pdb|3J54|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #4</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804283_4"> +<pre>Query 9 GTGAAGA 15 + ||||||| +Sbjct 2027 GTGAAGA 2033 + + +</pre> +</div> +</div> <!-- alnAll_557804283 --> +</div> <!-- aln_557804283 --> +<div class="alnHdr cnf" id="alnHdr_557804227" seqid="557804227" accs="pdb|3J52|A"> +<a name="557804227"></a> +<a aria-haspopup="true" aria-expanded="false" role="button" href="#dlgDwnl_557804227" class="jig-ncbipopper toolsCtr dnld dialog" data-jigconfig="hasArrow:'true',arrowDirection:'top',closeEvent: 'click', openEvent: 'click', destPosition: 'top center', triggerPosition: 'bottom right'" id="alnDwnld_557804227" title="Download information for pdb|3J52|A"><span>Download</span></a> +<div style="top: -100px; left: -100px; display: none;" aria-hidden="true" aria-live="assertive" id="dlgDwnl_557804227" class="popDl ui-helper-reset ui-ncbipopper-wrapper ui-ncbipopper-basic"> +<div><input seqfsta="gi|557804227" name="dwn_557804227" checked="checked" id="dwFST_557804227" fstadwtype="complete" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFST_557804227">FASTA (complete sequence)</label></div> +<div><input seqfsta="gi|557804227" name="dwn_557804227" id="dwFSTAl_557804227" fstadwtype="range" sbfunc="initDownLoadFSTA" type="radio"><label class="shownInl" for="dwFSTAl_557804227">FASTA (aligned sequences)</label></div> +<div class=""><input name="dwn_557804227" id="dwGenBank_557804227" getgi="557804227" sbname="id" url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&retmode=text" type="radio"><label class="shownInl" for="dwGenBank_557804227">GenBank (complete sequence)</label></div> +<div> +<button class="cfg" id="dw_cont_557804227">Continue</button> +<button class="cfg cnc">Cancel</button> +</div> +</div> <!-- dsDownload --> +<span class="csLinks" id="csLinks_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014" class="" target="lnkPHWP1JNZ014" title="Show genbank report for 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics">Graphics</a></span> + +<div class="seqlinks alnDflLn alnSortSeq"><label>Sort by:</label> +<select id="sa_557804227" onchange="SortHSPAlnSel(event,this)"> +<option selected="selected" value="0">E value</option> +<option value="1"> Score</option> +<option value="3">Percent identity</option> +<option value="2">Query start position</option> +<option value="4">Subject start position</option> +</select> +</div> +<span class="alnSeqLinks"> +<a title="Go to next alignment for pdb|3J51|A" class="gbd toolsCtr navNext" ref="ordinalpos=5&currseq=557804227" id="alnNxt_557804227" onclick="goToNextAlign('dtr_557804227',true);"><span>Next</span></a> +<a title="Go to previous alignment for pdb|3J54|A" class="gbd toolsCtr navPrev" ref="ordinalpos=5&currseq=557804227" id="alnPrv_557804227" onclick="goToNextAlign('dtr_557804227',false);"><span>Previous</span></a> +<a class="gbd toolsCtr navBack" title="Go to definition line for pdb|3J52|A" id="alnDsc_557804227" onclick="goToDefLine('dtr_557804227');" href="#dtr_557804227"><span>Descriptions</span></a> +</span> +</div> +<div class="oneSeqAln" id="aln_557804227"> +<div id="dln_557804227"> +<div class="dlfRow"> +Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit) +<div><label>Sequence ID: </label><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014" target="lnkPHWP1JNZ014" title="Show report for pdb|3J52|A">pdb|3J52|A</a><span class=" r"><label>Length: </label>2903<label>Number of Matches: </label>4</span></div> +</div> +</div> +<div class="relInf" id="relInf_557804227"><label>Related Information</label></div> +<!-- +<pre> +<@aln_gene_info@> +</pre> +--> +<div class="alnAll" id="alnAll_557804227"><div id="hd_557804227_1"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 1: 961 to 976</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=961&to=976" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 961 to 976 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=961:976&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 961 to 976 range">Graphics</a></span></span> +<span id="hsp557804227_1" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" disabled="disabled" title="Go to previous match #0 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=1&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack hidden" href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #1</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>32.2 bits(16)</td> +<td>8e-04<span class="sumN ">()</span></td> +<td>16/16(100%)</td> +<td>0/16(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804227_1"> +<pre>Query 1 CGTCCGTCGTGAAGAG 16 + |||||||||||||||| +Sbjct 961 CGTCCGTCGTGAAGAG 976 + + +</pre> +</div> +<div id="hd_557804227_2"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 2: 2591 to 2598</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=2591&to=2598" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2591 to 2598 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2591:2598&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2591 to 2598 range">Graphics</a></span></span> +<span id="hsp557804227_2" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #1 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=2&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #2</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>16.4 bits(8)</td> +<td> 47<span class="sumN ">()</span></td> +<td>8/8(100%)</td> +<td>0/8(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804227_2"> +<pre>Query 5 CGTCGTGA 12 + |||||||| +Sbjct 2591 CGTCGTGA 2598 + + +</pre> +</div> +<div id="hd_557804227_3"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 3: 839 to 845</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=839&to=845" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 839 to 845 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=839:845&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 839 to 845 range">Graphics</a></span></span> +<span id="hsp557804227_3" class="alnParLinks"> +<a class="gbd toolsCtr navNext" title="Go to next match #4 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a class="gbd toolsCtr navPrev" title="Go to previous match #2 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=3&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #3</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804227_3"> +<pre>Query 7 TCGTGAA 13 + ||||||| +Sbjct 839 TCGTGAA 845 + + +</pre> +</div> +<div id="hd_557804227_4"> +<div class="dflLnk hsp"><span class="alnRn"><label>Range 4: 2027 to 2033</label><span class="" id="rng_557804227"><a href="http://www.ncbi.nlm.nih.gov/nucleotide/557804227?report=genbank&log$=nuclalign&blast_rank=5&RID=PHWP1JNZ014&from=2027&to=2033" class="" target="lnkPHWP1JNZ014" title="Aligned region spanning positions 2027 to 2033 on 3J52_A">GenBank</a><a href="http://www.ncbi.nlm.nih.gov/nuccore/557804227?report=graph&rid=PHWP1JNZ014[557804227]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=2027:2033&appname=ncbiblast&link_loc=fromHSP" class="spr" target="lnkPHWP1JNZ014" title="Show alignment to 3J52_A in Nucleotide Graphics for 2027 to 2033 range">Graphics</a></span></span> +<span id="hsp557804227_4" class="alnParLinks"> +<a class="gbd toolsCtr navNext" disabled="disabled" title="Go to next match #5 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804227" onclick="goToNextHSP(this,true)"><span>Next Match</span></a> +<a init="on" class="gbd toolsCtr navPrev" title="Go to previous match #3 for pdb|3J52|A" onmouseover="scan(this)" ref="ordinalpos=4&currseq=557804227" onclick="goToNextHSP(this,false)"><span>Previous Match</span></a> +<a class="gbd toolsCtr navBack " href="#hsp557804227_1" title="Go to first match for pdb|3J52|A"><span>First Match</span></a> +</span> +</div> +<table class="alnParams"> +<caption class="hdnHeader">Alignment statistics for match #4</caption> +<tbody><tr> +<th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th><th class="aln_frame ">Frame</th> +</tr> +<tr> +<td>14.4 bits(7)</td> +<td> 186<span class="sumN ">()</span></td> +<td>7/7(100%)</td> +<td>0/7(0%)</td> +<td>Plus/Plus</td> +<td class="aln_frame "></td> +</tr></tbody></table> +<div class="dflLnk aln_feat hidden"><label>Features:</label><div></div></div> +</div> +<div id="ar_557804227_4"> +<pre>Query 9 GTGAAGA 15 + ||||||| +Sbjct 2027 GTGAAGA 2033 + + +</pre> +</div> +</div> <!-- alnAll_557804227 --> +</div> <!-- aln_557804227 --> +</form> + +</div></div> +<pre></pre> +</div><!--/#alignments--> +</div><!-- alignInfo --> +</div><!--ARIA--> + +</div><!-- alignView --> + + </div><!-- /#content --> + + + + + + </div><!-- /#content-wrap --> + + + + </div><!--/#wrap--> + +<script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/utils.js"></script> +<script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/toggle.js"></script> +<script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/remote_data_provider.js"></script> +<script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/results.js"></script><link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/firefox-descriptions.css" media="screen"><link rel="stylesheet" type="text/css" href="Blast%20output%20page%20example%20trimmed_files/firefox-descriptions_002.css" media="screen"> +<script type="text/javascript" src="Blast%20output%20page%20example%20trimmed_files/blast.js"></script> +<script type="text/javascript" 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/InstrumentPageStarterJS.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,86 @@ +(function(){if(typeof ncbi==="undefined")ncbi={};if(ncbi.sg)typeof console!=="undefined"&&console.error&&console.error("The logging JavaScript was added twice in the document. 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s=0;s<6&&u!==null;s++){(parId=u.id)&&c.push(parId);if(parClassName=u.className)v= +v.concat(parClassName.split(/\s/));u=u.parentNode}u=ncbi.sg.getInstance();var f=u.currentPageHitId||"";f=[];k.length>0&&f.push("link_id="+encodeURIComponent(k));j.length>0&&f.push("link_name="+encodeURIComponent(j));t.length>0&&f.push("link_sid="+encodeURIComponent(t));y.length>0&&f.push("link_href="+encodeURIComponent(y));A.length>0&&f.push("link_text="+encodeURIComponent(A));w.length>0&&f.push("link_class="+encodeURIComponent(w));s=u.getBrowserWidthHeight();s.width!==null&&f.push("browserwidth="+ +encodeURIComponent(s.width));s.height!==null&&f.push("browserheight="+encodeURIComponent(s.height));for(var i in e){s=e[i];s!==undefined&&f.push(i.toLowerCase()+"="+s.toString())}f.push("jsevent=hovernext");B.length>0&&f.push(B);if(typeof 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for those functions that are missing in window.console. +// (Safari implements some but not all of the firebug window.console methods--this implements the rest.) +(function() { + var names = [ "log", "debug", "info", "warn", "error", "assert", "dir", "dirxml", "group", + "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd" ]; + + if (typeof(console) === 'undefined' || typeof console === "function" ) { + //"typeof function" is needed see PP-769 + console = {}; + } + + for (var i = 0; i < names.length; ++i) { + if (typeof(console[names[i]]) === 'undefined') { + console[names[i]] = function() { return false; }; + } + } + ncbi.sg.getInstance().init(); +})();
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/blast.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,308 @@ + +function printfire() +{ + // Firefox + if (document.createEvent && window.dispatchEvent) { + printfire.args = arguments; + var ev = document.createEvent("Events"); + ev.initEvent("printfire", false, true); + window.dispatchEvent(ev); + } +} +//This functions handle setting defaults for protein or nulcleotide suite search page when +//one of blast program radio buttons is clicked - not used now +function AdjustMoreOptionsStyle() +{ + var optsEl = document.getElementById("moreopts"); + if(optsEl && optsEl.style.height != "0px") { + optsEl.style.height = optsEl.scrollHeight + "px"; + } +} + +//Strip (taxid:XXX) from organism list selection +//sgRunFunc="AdjustOrganism();" +function AdjustOrganism() +{ + var words = $("qorganism").value.split(" (taxid"); + $("qorganism").value = words[0]; +} + + +/* JS Common to all BLAST pages */ + + +function setResultsTarget() +{ + //var newWin = $("newwin"); + var newWin = this; + var searchFrm = $(newWin.getAttribute("form")); + if(newWin && newWin.checked == true) { + if(newWin.getAttribute("winType") == "random") { + searchFrm.target = "Blast_Results_for_" + Math.floor(Math.pow(10,10) *Math.random()); + } + else { + searchFrm.target = $("resPageTarget").value; + } + } + else { + searchFrm.target = ""; + } +} + +function diffFromDefault(elem) +{ + var currentVal = ""; + var ret = 0; + + if (!(elem)) return; + var defVal = elem.getAttribute("defVal"); //Default value + var elShowDiff = utils.getParent(elem); + if(!elem.type) {//div element for example + //Check if parent elem has "hide" class + if(utils.hasClass(utils.getParent(elem), "hide")) { + currentVal = "hide"; + } + else { + currentVal = "show"; + } + elShowDiff = elem; + } + else if(elem.type == "select-one") { + if(elem[elem.selectedIndex].value) currentVal = elem[elem.selectedIndex].value; + //If Default value is not specified - the first one in the selection list is the default + if (!defVal && elem[0].value) defVal = elem[0].value; + } + else if(elem.type == "select-multiple") { + currentVal = "";//for now + } + else if(elem.type == "checkbox") { + //alert("defVal1=" + elem.id + " " + defVal); + //var defVal = elem.defVal; //Default value + //alert("defVal2=" + defVal); + if(elem.checked == true) currentVal = "checked" + else currentVal = "unchecked"; + } + else { + currentVal = elem.value; + } + + + var numdiff = parseInt($("NUM_DIFFS").value,10); + var optsNumDiff = parseInt($("NUM_OPTS_DIFFS").value,10); + if(defVal != currentVal) { + if(!utils.hasClass(elShowDiff, "nondef")) { + utils.addClass(elShowDiff, "nondef"); + numdiff++; + if(utils.hasClass(elem,"opts")) optsNumDiff++; + } + ret = 1; + } + else { + if(utils.hasClass(elShowDiff, "nondef")) { + utils.removeClass(elShowDiff, "nondef"); + //alert("noDiff-" + elem.id); + if(numdiff != 0) numdiff--; + if(utils.hasClass(elem,"opts")) optsNumDiff--; + } + ret=0; + } + $("NUM_DIFFS").value = numdiff; + $("NUM_OPTS_DIFFS").value = optsNumDiff; + if(numdiff > 0) { + $("diffMes").style.display = "inline"; + } + else { + $("diffMes").style.display = "none"; + } + //alert(elem.id + " " + $("NUM_DIFFS").value); + return ret; +} + +function setDefalValue(elem) +{ + var currentVal; + var defVal = elem.getAttribute("defVal"); //Default value + if(elem.type == "select-one") { + //If Default value is not specified - the first one in the selection list is the default + if(!defVal) defVal = elem[0].value; + for(j=0; j < elem.options.length; j++) { + if(elem.options[j].value == defVal) { + elem.options[j].selected = true; + break; + } + } + } + else if(elem.type == "checkbox" || elem.type == "radio") { + if(!defVal) defVal = "checked"; + if(defVal == "checked") elem.checked = true + else elem.checked = false; + } + else { + if(!defVal) defVal = ""; + elem.value = defVal; + } + + var elShowDiff = utils.getParent(elem); + if(utils.hasClass(elShowDiff, "nondef")) { + utils.removeClass(elShowDiff, "nondef"); + } + //alert(elem.id + " " + $("NUM_DIFFS").value); +} + +function newResultsWinInit() { + jQuery("[class='newwin']").each(function(index) { + utils.addEvent(this, "click", setResultsTarget, false); + }); +} + +function resetOrganismSuggest(orgEntryElem) +{ + //suggestHint is in the hidden field used for SRA + var defaultMessage = ($("suggestHint")) ? $("suggestHint").value : "Enter organism name or id--completions will be suggested"; + var suggestHint = $("qorganism").getAttribute("suggestHint"); + if(suggestHint) defaultMessage = suggestHint; + if(orgEntryElem.value == "") { + orgEntryElem.value = defaultMessage; + } + if(orgEntryElem.value == defaultMessage) { + utils.addClass(orgEntryElem,"orgHint"); + } +} + +function setupOrganismSuggest(orgEntryElem) +{ + resetOrganismSuggest(orgEntryElem); + utils.addEvent(orgEntryElem, "focus", function() { + clearOrgSuggest(orgEntryElem); + }, false); +} + +function clearOrgSuggest(orgEntryElem) +{ + if(utils.hasClass(orgEntryElem,"orgHint")) { + orgEntryElem.value=""; + utils.removeClass(orgEntryElem,"orgHint"); + } +} + +function InitCustomButton(bn) +{ + utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false); + utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false); + utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false); + utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false); +} + +function showHideElem(id,hide) +{ + if($(id)) { + if(hide) { + if(!utils.hasClass($(id),"hidden")) utils.addClass($(id), "hidden"); + } + else { + if(utils.hasClass($(id),"hidden")) utils.removeClass($(id), "hidden"); + } + } +} + +function resetOrganismControls(orgEntryElem) { + resetOrganismSuggest(orgEntryElem); + if ($("orgExcl")) $("orgExcl").checked = false; + utils.replaceInHtml("", $("orgs")); + if ($("frOrgs")) utils.replaceInHtml("", $("frOrgs")); + if ($("numOrg")) $("numOrg").value = 1; +} + +function AddOrgRow(e,orgName,exclName) { + e = e || window.event; + utils.preventDefault(e); + var checkedExclude = new Array(); + var orgDict = jQuery($($("qorganism"))).ncbiautocomplete("option","dictionary"); + orgDict = (!orgDict || orgDict == "") ? "taxids_sg" : orgDict; + var len = $("qorganism").getAttribute("size"); + + var newOrgFieldID = "qorganism" + $("numOrg").value; + var newOrgField = " <div><input name=\"" + orgName + $("numOrg").value + "\" size=\"" + len + "\" id=\"" + newOrgFieldID + + "\" type=\"text\" data-jigconfig=\"dictionary:'" + orgDict + "'\" autocomplete=\"off\" class=\"jig-ncbiautocomplete multiOrg\" />"; + if (exclName != "") { + newOrgField += "<span class=\"orgExcl\">" + + "<input type=\"checkbox\" name=\"" + exclName + $("numOrg").value + "\" class=\"oExcl cb\" id=\"orgExcl" + $("numOrg").value + "\" />" + + "<label for=\"orgExcl" + $("numOrg").value + "\" class=\"right oExclRl\">Exclude</label></span>"; + } + newOrgField += "</div>"; + if (navigator.userAgent.match(/ie/i)) { + for (i = 1; i < $("numOrg").value; i++) { + if ($("orgExcl" + i)) checkedExclude[i] = $("orgExcl" + i).checked; + } + } + if (!navigator.userAgent.match(/firefox/i)) { + jQuery($($(orgs))).append(newOrgField,true); + } + else { + utils.insertInHtml(newOrgField, $("orgs")); + } + + if (navigator.userAgent.match(/ie/i)) { + for (i = 1; i < $("numOrg").value; i++) { + if ($("orgExcl" + i)) $("orgExcl" + i).checked = checkedExclude[i]; + } + } + setupOrganismSuggest($(newOrgFieldID)); + jQuery($($(newOrgFieldID))).ncbiautocomplete(); + $("numOrg").value++; +} + +function adjustOrgVal(orgEntryElem) +{ + //if (utils.hasClass($("searchForm").EQ_MENU, "orgHint")) $("searchForm").EQ_MENU.value = ""; + clearOrgSuggest(orgEntryElem); + if ($("numOrg")) { + for (i = 1; i < $("numOrg").value; i++) { + if ($("qorganism" + i)) { + clearOrgSuggest($("qorganism" + i)); + } + } + } +} + +function getUrlCompForEntryField(elem) { + var url = ""; + if (elem && elem.value != "") { + url = "&" + elem.name + "=" + escape(elem.value); + } + return url; +} + + +function getUrlCompForCheckedField(elem) { + var url = ""; + if (elem && elem.checked) { + url = "&" + elem.name + "=" + elem.value; + } + return url; + +} + +function getUrlCompForOptionsField(elem) { + var url = ""; + if (elem) { + url = "&" + elem.name + "=" + elem[elem.selectedIndex].value; + } + return url; +} + +function getUrlCompForMultiOptionsField(elem) { + var url = ""; + if (elem) { + for (i = 0; i < elem.options.length; i++) { + if (elem.options[i].selected) { + url += "&" + elem.name + "=" + elem.options[i].value; + } + } + } + return url; +} + + +utils.addEvent(window, 'load', newResultsWinInit, false); +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/blastReq.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,332 @@ +#msgR .info { +background-color: #dfd; +padding: 4px; +border: solid 1px green; +color: green; +} + +dl.summary dt { +float: left; +width: 8em; +clear:left; +margin: 0; +text-align: right; +padding-right: 1em; +color: #666; +} + +dl.summary dd { +padding-left: 0.5em; +display: block; +margin-left: 7em !important; +margin: 0; +} +dl.summary dt, dl.summary dd { +margin-bottom: 0.5em; +} +a.help +{ +float:right; +font-size: 110%; +} + +dl.summary label { +display: inline; +} + +dl.summary tr th label { +padding: 0; +margin-right:0; +} +table.options { +border: solid 1px #ccc; +border-right: solid 1px #ccc; +} + +table.options td, +table.options td.frh { +font-size: 90%; +_font-size: 85%; +} + +table.options label.rb { +border-right: solid 1px #ccc; +margin-right: 0.5em; +padding-right: 2.0em; +} + +table.options tr td { +_font-size: 90%; +padding-left: 0.5em; +} + +table.options { +/*border-collapse: collapse;*/ +margin-left: 0; +padding-left: 0; +width: 62em; +} + +table.options td label { +font-size: 90%; +} + +table.options th label, +table.options td label { +margin-right: 0; +_position: relative; +_top: -0.1em; +} + +table.options tr.hdr td, +table.options tr.hdr th { +padding: 2px; +border: solid 1px #ccc; +background-color: #ddd; +} + +table.options td, table.options td.frh { +padding: 0.25em 0; +vertical-align: center; +} + +table.options th { +padding-right: 1em; +text-align: right; +padding-left: 1em; +} + +/* +*:focus{ +background-color: white !important; +} +*/ + +table.options select,table.options input, #graphic input{ +border: solid 1px #888; +padding: 1px; +} + +select { +font-size: 90%; +} + +select option { +padding-right: 0.5em; +} + +input.cb, table.options input.cb { +border: none; +} + +select { +margin-right:1em; +} + +table.options tr { +background-color: #eee; +} + +table.options tr.odd { +background-color: #e0e0e0; +} + +table.options th { + +background-color: white; +} + +table.options tr.paramSet td +{ + border-top: solid 2px white; +} + + + + +.resetAll +{ +font-weight: normal; +padding: 0.5em; +font-size: 90%; +margin-left:5em; +} + +.button { +background-color: #ccc; +padding: 0.25em 0.25em; +color: black; +border: outset 3px #eee; +_border: outset 3px #eee; +font-size: 90%; +_padding:0; +font-weight: bold; +height:25px; +_height:22px; +} + +.fbtn { +margin-bottom: 0.5em; +} + +.note { +font-size: 80%; +color: green; +background-color: #ffc; +margin-left: 2em; +padding: 3px; +} +.instr { + margin-left: 1em; + color: #666; +font-size: 90%; +} +.smaller { +font-size: 90%; +font-weight: normal; +} + +/* Results Page styles */ + +#ridRes +{ + background-color: #FC9; + padding:5px 5px; +} + + +span dd.hidden,dt.hidden,dd.hidden span +{ + display:none; +} + +dl.query .query, +dl.title .title, +dl.entrez .entrez, +dl.db .db +{ + display:block; +} + + +dl.entrez span.entrez +{ + display:inline; +} + +.hidden { +display: none; +} +.hide { +display: none; +} +.shown { +display: block; +} + + + +table.megaBlast tr.psiBlast, +table.blastn tr.psiBlast, +table.blastx tr.psiBlast, +table.tblastn tr.psiBlast, +table.tblastx tr.psiBlast, +table.discoMegablast tr.psiBlast +{ +display: none; +} + + +table.GlobalAln .xgl, +body.GlobalAln div.xgl, +body.GlobalAln dt.xgl, +body.GlobalAln dd.xgl, +body.GlobalAln span.xgl, +body.GlobalAln table.xgl +{ +display: none; +} + +.dispType +{ + /*background-color:White; + border:solid 1px black;*/ + border-top:solid 2px gray; + border-left:solid 2px gray; + font-size:90%; + padding-left:2px; + +} + +.newwin { +border: none; +} + +table.options .helplink +{ + font-weight:bold; + position:absolute; + right:0; +} + +div#query label +{ + display: inline; + font-weight:bold; + padding-right:1em; +} +#NEW_VIEW +{ + _margin-left:-2px; +} + + +table.blastp *.blastn, +table.psiBlast *.blastn, +table.phiBlast *.blastn, +table.blastx *.blastn, +table.tblastn *.blastn, +table.tblastx *.blastn +{ +display: none; +} + +#formatTable th.col1 { +width: 8em; +vertical-align: top; +} +/* +#formatTable .helplink span { +position: relative; +} +*/ +#org +{ + margin-top:2em; +} +#qorganism +{ + /*display:block;*/ +} +.fi +{ + position:relative; +} + +a#organismHelp +{ + margin-top:-1.5em; +} + +table.options tr.paramSet td.hd { +padding-right: 1em; +text-align: right; +padding-left: 1em; +background-color:White; +font-weight:bold; +border-top:none; +} +.oExcl +{ + margin-left:2px; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/blastRes.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,262 @@ +a#refPage +{ + margin-left:3em; +} + +a.resLink +{ + margin-left:1em; + display:none; +} + +a.resLinkhidden +{ + display:none; +} + + +#cddResults +{ + float:right; + margin-top:-2em; + margin-right:1em; + color:#336699; + font-size:100%; +} + +#cddResults.showing { + background-image: url(images/down.gif); +} + + + +div.inlineDiv +{ + display:inline; +} + +span.reslink +{ + display:none; +} + +div.statPage *.statPage, +div.resPage *.resPage +{ + display:inline; +} + +div.resHeader *.hidden +{ + display:none; +} + +#cddInfo +{ + text-align:center; +} +#cddDesc +{ + font-weight:bold; +} +div#desctbl +{ +border: solid 1px #018aac; +/*min-width: 1000px;*/ +margin: none; +width: 100%; +background-color:White; +/*line-height:0; +_line-height:0;*/ +} + +table#descs +{ +font-family: Verdana, Sans-Serif; +font-size: 90%; +_font-size: 86%; +border-collapse: collapse; +/*min-width: 600px;*/ +width: 100%; +} + +table#descs th a { +text-decoration: none; +color: #00c; +} + +table#descs th a:visited { +color: #00c; +} + +table#descs th a:hover {position: relative; +text-decoration: underline; +} + +table#descs tr th.l, +table#descs tr td.l { +text-align: left; +} + +table#descs tr th.sp { +background-color: #def; +} + +table#descs tr th, +table#descs tr td { +text-align: center; +padding: 1px 4px; +} + +table#descs tr.first th { +padding-left:18px; +border-left: solid 1px #A0ceff; +border-top: solid 1px #A0ceff; +border-bottom: solid 1px #018aac; +border-right: solid 1px #018aac; +padding-right: 8px; +/*background-color: #01d5ff;*/ +background-color: #9cf; +/*font-size: 92%;*/ +white-space:normal; +line-height: 1.2em +} + + +table#descs td { +border: solid 1px #ccc; +border-width: 0px 1px; +white-space:nowrap; +overflow: hidden; +} + +.slink { +font-size: 90%; +font-weight: normal; +} + +table#descs tr.first th.sel { +background: #9cf url(images/up.gif) no-repeat center left; +padding-left: 18px; +padding-right: 18px; +} + +div.lim +{ +/*overflow: hidden;-this used to work in Firefox 2- comment for now and set the width */ +width: 35em; +display: inline-block; +height: 1.3em; +} + +table#descs tr:hover { +background-color: #def; +} + +pre +{ + font-size:110%; + _font-size:100%; + line-height:1; +} + +#msg +{ + white-space:normal; + border-color:#cccccc; + padding:0; + margin: 0; + margin-top:2px; +} +#msg li +{ + display:none; + padding:0; + margin: 0; + text-indent: 0; +} +#msg li.warning, #msg li.error ,#msg li.info +{ + display:block; +} + +#msg ul +{ + margin:0; + padding:0; +} + +table#statInfo +{ + border: solid 1px #ccc; + background-color: #eee; + width: 100%; +} + +table#statInfo tr.odd { +background-color: #e0e0e0; +} + +.READY, .UNKNOWN +{ + display:none; +} + +p.WAITING +{ + margin-top:1em; +} + +#frmPage +{ + margin-left:1em; +} + +span.Gene_PubMedLinks +{ + color: Green; font-weight: bold; +} + +ul.msg li p +{ + display:none; +} + +.msg li p.warning, .msg li p.error, .msg li p.success,.msg li p.info +{ + display:block; +} + +.mdlbox +{ + white-space:pre; + background-color:Transparent; + border:none; +} + +#blastErr +{ + white-space:normal; +} + + + +#RSIFrameNoRes,#RSIFrameDesc,#RSIFrameAln +{ + border:none; + width:519px; + height:35px; + margin:0px auto; +} + + +a.ui-ncbitoggler.hidden, a.ui-ncbitoggler-open.hidden +{ + display:none; +} + +.smn { + display: inline-block; + height: 16px; + width: 16px; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/dynFormatRes.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,623 @@ +/* style changes for redesign begin*/ +a.gbd +{ + text-decoration:none; +} + +tr.dflLnk td span +{ + font-size:78%; + display:none; + text-align:center; +} +a.dflSeq +{ + color:#369; + text-decoration:underline; + width:auto; +} +table.defln tr.dflLnk a +{ + margin-right:auto; + padding-left:0; +} + +.alnParLinks +{ + float:right; +} + +.alnSeqLinks +{ + float:right; + margin-right:1em; +} + + +.seqlinks select +{ + padding:0; +} + +.dlfRow div +{ + font-size:90%; +} + +.dlfRow +{ + display:inline; + font-size:110%; +} + +.dlfRow.hidden +{ + display:none; +} +.dlfRow label +{ + font-size:87%; + display:inline; + color:#606060; + font-weight:bold; +} + +.dlfRow span.r label +{ + padding-left:0.8em; +} + + +div.relInf +{ + font-family: Verdana, Sans-Serif; + font-size: 80%; + float:right; + width:21%; + border-top:solid 2px gray; + margin-top:-1em; + margin-right:3.5em; + left:3em; + max-width:25em; + padding-left:1em; + position:relative; + white-space:normal; +} + +div.relInf a +{ + padding-right:0.2em; +} + +.rlLink +{ + padding-left:0.2em; +} +.relInf label +{ + font-size:110%; + color:brown; + font-weight:bold; +} +div#content +{ + min-width:70em; +} + +.dflLnk a +{ + font-size:90%; +} +a.dflSeq +{ + width:auto; + font-weight:normal; +} + + +#cntDesc,#cntDesc_psiw +{ + margin-bottom:0.2em; + display:inline-block; + width:20em; +} +#cntDesc span,#cntDesc_psiw span +{ + margin-right:0.5em; +} + +#cntDesc a,#cntDesc input,#cntDesc_psiw a,#cntDesc_psiw input +{ + margin-left:0.5em; +} + +#cntSelNone,#cntShAll +{ + margin-left:0.2em; +} + +.toolsCtr +{ + color:Blue; +} + +table.ui-ncbigrid th span.slink a +{ + display:inline; + padding-right: 0; +} +table.ui-ncbigrid th.sp +{ + font-weight:bold; +} + +table.ui-ncbigrid th span.slink +{ + margin-left:0.2em; +} + +table.ui-ncbigrid td { + white-space:nowrap; +} +table.ui-ncbigrid td.c3 +{ + /*padding-left:0.8em;*/ +} +table.ui-ncbigrid caption +{ + font-size:0; + line-height:0; +} +#content h3.cap,#content h3.cap a.ui-ncbitoggler.ui-widget, #content h3.cap a.ui-ncbitoggler-open +{ + color:#4d4d4d; + text-align:left; + margin:0 0 0.5em 0; +} + +#content div.cap,#content div.cap a.ui-ncbitoggler.ui-widget, #content div.cap a.ui-ncbitoggler-open +{ + color:#4d4d4d; + text-align:left; + margin:0 0 0.5em 0; + letter-spacing:-1px; + font-size:110%; + font-weight:bold; +} + +#descriptions div.caption-exists { + margin: 0; +} + +/**********decrition toolbar styles *********/ + +div.cnf { + -moz-border-bottom-colors: none; + -moz-border-image: none; + -moz-border-left-colors: none; + -moz-border-right-colors: none; + -moz-border-top-colors: none; + background: url("images/cnf.png") repeat scroll 0 0 transparent; + border-style: solid none none; + border-width: 1px medium medium; + /*clear: left;*/ + height: 22px; + /*overflow: auto;*/ + width: 100%; +} + +ul.ui-ncbilocalnav li.has-child a.button_config { + background: url("/portal/portal3rc.fcgi/3493904/img/81796") no-repeat scroll right center transparent !important; + width: 22px; + height:22px; + margin-left:12em; +} + +#li-config +{ + float:right; + width:17em; +} +div#descTblCtrl ul.ui-ncbilocalnav li +{ + border-right:none; +} + + +.cfg +{ + font-size:90%; +} + + +.oneSeqAln .hsp label +{ + color:#606060; + font-size:95%; + padding-right:0.5em; +} + +.oneSeqAln pre +{ + margin-top:0.5em; +} + +.aln_feat label +{ + color: #606060; + font-size: 95%; + padding-right: 0.5em; +} +.oneSeqAln .dflLnk.aln_feat +{ + padding-bottom:1em; +} +div.oneSeqAln h4 +{ + border:none; + font-size:100%; + font-weight:normal; + letter-spacing:normal; + margin:0; +} + +.oneSeqAln .dflLnk +{ + width:56em; +} +.aln_feat a +{ + margin-left:1em; + display:block; +} +.dflLnk.aln_feat div +{ + /*display:inline-block; */ + margin-left:5em; + margin-top:-1em; +} +.aln_frame.shown +{ + display:block; +} +/*align params styles change */ + +table.alnParams +{ + border-left:none; + border-right:none; + margin-top:0.5em; + width:49em; +} + +table.alnParams th +{ + background-color:Transparent; + border:none; + text-align:left; +} + +table.alnParams td +{ + border:none; +} + + +.alnAll +{ + line-height:normal; + margin-top:1em; +} + +.alnAll div +{ + width:70%; +} + +/**new config staff begin**/ +.popDl +{ + display:none; +} +.popDl div +{ + margin-top:0.5em; +} +.popDl div.tl +{ + margin-top:0; + font-weight:bold; +} +a.button_config { + background: url("images/cnfButn.png") no-repeat scroll right center transparent !important; + width: 22px; + height:22px; + margin-left:12em; + float:right; +} + +a.toolsCtr,span.csLinks a +{ + margin-left:8px; + float:left; + cursor:pointer; +} + +a.toolsCtr[disabled] { + cursor: default; +} + + +a.toolsCtr SPAN +{ + color: #14376c; + /*line-height: 22px;*/ + padding-left: 15px; + background-repeat: no-repeat; + background-position:left center; +} + +a.toolsCtr[disabled] SPAN,a.toolsCtr[disabled] +{ + color:#C2C2C2; +} + +a.dnld span +{ + background-image: url("images/dndl.png"); +} + +a.dnld[disabled] span +{ + background-image: url("images/dndl_dsb.png"); +} + +a.dialog +{ + padding-right: 18px; + background:transparent url(images/dialog.png) no-repeat scroll right center; + text-decoration:none; +} + +a.dialog[disabled] { + background-image: url("images/dialog_dsb.png"); +} + + +a.alnNav span +{ + background-image: url("images/align_Normal.png"); +} + +a.alnNav +{ + text-decoration:none; +} + + +a.navNext span +{ + background-image: url("images/next_Normal.png"); +} + + +a.navNext[disabled] span +{ + background-image: url("images/next_Inactive.png"); +} + + +a.navPrev span +{ + background-image: url("images/prev_Normal.png"); +} + + +a.navPrev[disabled] span +{ + background-image: url("images/prev_Inactive.png"); +} + + +a.navBack span +{ + background-image: url("images/table_Normal.png"); +} + +.alnRn +{ + float:left; +} + + +/* styles to change per discusssion with Mark begin*/ +.dflLnk a +{ + padding-left:0; +} + + +table.ui-ncbigrid th { + padding-left:0.3em; + padding-right:0; + text-align:center; +} + +table.ui-ncbigrid td { + padding-left:0.4em; + padding-right:0.4em; + text-align:center; +} + +table.ui-ncbigrid td.c2,table.ui-ncbigrid td.c1 { + text-align:left; +} + +table.ui-ncbigrid td.c3{ + padding:0.363em 0.25em; +} + + +table.ui-ncbigrid th a { + padding-right: 5px; +} +table.ui-ncbigrid th.c0 +{ + width:25px; + padding:0; +} + +.dflnDth +{ + width:100%; +} +div.lim { + width: 14em; +} + +table.ui-ncbigrid th.c8,table.ui-ncbigrid th.c9 { + padding-right: 0.3em; +} +.c8,.c9 +{ + font-size:80%; +} + + +td.lim.l.c2,td.lim.l.c1 +{ + overflow:hidden; +} +a.spr +{ + border-right:none; +} + + +.psiInp +{ + margin-left:1em; + margin-top:0.5em; +} + + +.c8 input +{ + border:none; +} +table.ui-ncbigrid td.c8 +{ + padding-left:1.5em; +} + +tr.psi_new td +{ + background-color:#FFFF99; + border-top:solid 4px white; + border-spacing:3px; + border-collapse:collapse; + line-height:normal; +} +/* accessibility setting */ +tr.dflLnk td span.psiNw,tr.first th span,a.button_config span, a span.accsb,.dflLnk label.accsb +{ + display:inline; + position:absolute; + left:-9999px; +} + +div.tgl +{ + margin-top:-1em; +} +.shcl +{ + float:right; +} + +/* styles to change per discusssion with Mark end*/ + +.alnRn a +{ + padding-right:1em; +} +.alnAll .moreHsps +{ + font-family: Verdana, Sans-Serif; + font-size: 75%; + margin-top:-2.5em; + width:58%; +} +.erm +{ + background-color:#FFFFCC; + padding:0.5em; +} + +#debug,.ind,.alnMsgS .db,.erm .db +{ + display:none; +} + +.tmsAln label +{ + font-size:93%; + display:inline; + color:#606060; + font-weight:bold; +} +.alnAll .tmsAln, .tmsAln div +{ + width:100%; + margin-bottom:-1em; +} +.tmsAlnPar +{ + margin-top:-1em; +} +/*debug info styles begin */ + + +/* use those styles only in debug version + +.alnMsg +{ + border:solid 1px black; +} + +.alnMsgS.hidden,.alnMsgS .db +{ + display:block; +} + +.oneSeqAln +{ + border:1px solid #C8C8C8; +} + +#debug,tr.dflLnk td span.ind +{ + display:inline; +} +.c0 +{ + width:30px; +} +/*debug info styles end */ + + + +/**new config staff end**/ +/* +ul.ui-ncbilocalnav li, ul.ui-ncbilocalnav { + background-color: #F4F4F4; + background-image: -moz-linear-gradient(center top , #FFFFFF, #F4F4F4); +} +ul.ui-ncbilocalnav li { + border-right: 1px solid #C4C4C4; +} +*/ +/**********decrition toolbar styles end*********/ + + +/* style chenges for redesign end*/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/firefox-descriptions_002.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,3 @@ +table.dbInfo caption { + +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/format.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,270 @@ + +function UpdateDisplayTypes(displayTypes) { + dispMenu = displayTypes.options; + for(i=0; i < dispMenu.length; i++) { + //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") || + if($("stepNumber").value == "" || $("stepNumber").value < 2) { + if(dispMenu[i].value.indexOf("PSSM") != -1) { + dispMenu[i--] = null; + //break; + } + } + } +} + +function GetIndexByValue(selectElem,val) { + var idx = 0; + var opts = selectElem.options; + for(i=0; i < opts.length; i++) { + if(opts[i].value == val) { + idx = i; + break; + } + } + return idx; +} + +function resetAdvView(show) +{ + var advView = $("advView"); + if(show) { + if(utils.hasClass(advView, "hidden")) { + utils.removeClass(advView, "hidden"); + } + } + else { + utils.addClass(advView, "hidden"); + } +} + + +function ShowOrHide(hide,elem) +{ + if(hide) { + if(!utils.hasClass(elem, "hidden")) { + utils.addClass(elem, "hidden"); + } + } + else { + if(utils.hasClass(elem, "hidden")) { + utils.removeClass(elem, "hidden"); + } + } +} + +function UpdateFormatTypes(form) { + var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value; + var hideAdvView = false; + bioseqFormatHide = true; + pssmFormatHide = true; + pssmScFormatHide = true; + formatTypeHide = true; + if (selectedObjType == "Alignment") { + formatObjectSelectedIndex = 0; //HTML + formatTypeHide = false; + hideAdvView = true; + } + if (selectedObjType == "PSSM") { + formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text"); + pssmFormatHide = false; + } + if (selectedObjType == "PSSM_Scoremat") { + formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1"); + pssmScFormatHide = false; + } + else if (selectedObjType == "Bioseq") { + formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1"); + bioseqFormatHide = false; + } + form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex; + ShowOrHide(formatTypeHide,form.FORMAT_TYPE); + if ($("bioseqFormat")) { + ShowOrHide(bioseqFormatHide,$("bioseqFormat")); + $("bioseqFormat").readOnly=true; + } + if ($("pssmFormat")) { + ShowOrHide(pssmFormatHide,$("pssmFormat")); + $("pssmFormat").readOnly=true; + } + if ($("pssmScFormat")) { + ShowOrHide(pssmScFormatHide,$("pssmScFormat")); + $("pssmScFormat").readOnly=true; + } + resetAdvView(hideAdvView); +} + +function ResetForm() +{ + //var defValNodes = cssQuery(".reset"); + defValNodes = $("FormatForm").elements; + for(i=0; i < defValNodes.length; i++) { + if(utils.hasClass(defValNodes[i],"reset")) + setDefalValue(defValNodes[i]); + } + if ($("FormatForm").FORMAT_OBJECT.type == "select-one") { + UpdateFormatTypes($("FormatForm")); + UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT); + } + if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH) + else $("FormatForm").I_THRESH.value=""; + //resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM); + resetOrganismControls($("FormatForm").FORMAT_ORGANISM); + //TO DO: add threshold +} + +function LimitByHitlistSize(list) +{ + var listBreak = false; + var optSel = false; + for(i=0; i < list.options.length; i++) { + var optVal = parseInt(list.options[i].value ,10); + var hitListSize = parseInt($("maxNumSeq").value ,10); + if(list.options[i].selected) optSel = true; + if(optVal >= hitListSize) { + if(!optSel) {list.options[i].selected = true;} + list.options.length = i + 1; + break; + } + } +} + +function AddFormatOrgField(e) { + AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE"); +} + +function initSubmit() { + + +} + +function adjustFormatOptions() +{ + var alignView = $("FormatForm").ALIGNMENT_VIEW; + var formatType = $("FormatForm").FORMAT_TYPE; + var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities"); + var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch; + dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities"); + + UpdateDescriptions(dynFormatPW); + if (dynFormatPW) { + jQuery("#frmAln").addClass("hidden"); + if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT + jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE + jQuery("#scf").removeClass("hidden");//show CDS_FEAT + $("FormatForm").SHOW_LINKOUT.checked = true; + } + else { + if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex; + + jQuery("#frmAln").removeClass("hidden"); + if (dynFormatQA) { + if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT + } + else { + jQuery("#shl").removeClass("hidden"); + } + if (queryAnch) { + jQuery("#scf").addClass("hidden"); //hide CDS_FEAT + } + else {//pairwise old_view=false + jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT + } + jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE + } + if ($("blastSpec").value == "VecScreen") { + adjustVecscreen(dynFormatPW); + } +} + +function adjustVecscreen(dynFormatPW) +{ + var dfltDescrInd = 0; //0 + var dfltDynDescrInd = 5; //1000 + var dfltAlnInd = 6; //1000 + if (dynFormatPW) { + utils.addClass($("lr"), "hidden"); + $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd; + } + else { + utils.removeClass($("lr"), "hidden"); + $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd; + } + $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd; +} + + +function UpdateDescriptions(removeZero) +{ + if (removeZero) { + dispMenu = $("FormatForm").DESCRIPTIONS; + dispMenu.remove(0); + } + else { + dispMenu = $("FormatForm").DESCRIPTIONS; + if (dispMenu.options[0].value != "0") { + if (navigator.userAgent.match(/ie/i)) { + dispMenu.add(new Option("0", "0"), 0); + } + else { + dispMenu.add(new Option("0", "0"), dispMenu[0]); + } + } + } +} + +function InitDynFormatOptions() +{ + if ($("OLD_VIEW")) { + utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false); + utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false); + utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false); + adjustFormatOptions(); + } +} + +function InitFormatPage() +{ + if ($("FormatForm").FORMAT_OBJECT.type == "select-one") { + UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT); + UpdateFormatTypes($("FormatForm")); + list = $("FormatForm").FORMAT_OBJECT; + utils.addEvent(list, "change", function() { + UpdateFormatTypes($("FormatForm")); + }, + false); + } + utils.addEvent($("resetAll"), "click", ResetForm, false); + if($("maxNumSeq") != null) { + if($("maxNumSeq").value != "") { + LimitByHitlistSize($("FormatForm").DESCRIPTIONS); + LimitByHitlistSize($("FormatForm").ALIGNMENTS); + LimitByHitlistSize($("FormatForm").NUM_OVERVIEW); + } + } + setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM); + utils.addEvent($("FormatForm"), "submit", function() { + adjustOrgVal($("FormatForm").FORMAT_ORGANISM);}, + false); + + if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false); + InitDynFormatOptions(); + /* add this code if decide image for View Report + var imgButtons = jQuery("[class='viewReport']"); + for (var i = 0; i < imgButtons.length; i++) { + var l = imgButtons[i]; + utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false); + utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false); + utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false); + utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false); + utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false); + } + */ +} + +utils.addEvent(window, 'load', InitFormatPage, false); + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/formatRes.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1542 @@ +// JScript source code +/*************************new code begin *******************************************************/ + +function getHiddenFieldVal(elemName) { + var val; + var elem = document.getElementsByName(elemName); + if (elem) { + val = (elem.length > 1) ? elem[0].value : elem.value; + } + return val; +} + +function getHiddenFieldParamString(elemName) { + var ret = ""; + var val = getHiddenFieldVal(elemName); + if (val) { + ret = "&" + elemName + "=" + val; + } + return ret; +} + +function elementInViewport(el) { + if (!el) return; + var rect = el.getBoundingClientRect(); + + var myWidth = 0, myHeight = 0; + if (typeof (window.innerWidth) == 'number') { + //Non-IE + myWidth = window.innerWidth; + myHeight = window.innerHeight; + } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) { + //IE 6+ in 'standards compliant mode' + myWidth = document.documentElement.clientWidth; + myHeight = document.documentElement.clientHeight; + } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) { + //IE 4 compatible + myWidth = document.body.clientWidth; + myHeight = document.body.clientHeight; + } + //window.alert('Width = ' + myWidth); + //window.alert('Height = ' + myHeight); + + + //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth) + //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth) + return (rect.top >= 0 && rect.bottom <= myHeight); +} + +function DisplayAlignFromDescription(elem) { + var alignView = $("FormatForm").ALIGNMENT_VIEW; + if (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities") { + DisplayDynamicAlign(elem); + } + else { + location.href = "#" + elem.getAttribute("seqID"); + } +} + +//<a class="deflnDesc" hsp=<hsp_num> ind="<index>" gi="<gi>" id="deflnDesc_gi" href="#AlnHdrgi">desc</a> +//<div class="alnHdr" gi="<gi>" id="alnHdr_<index>"> +function DisplayDynamicAlign(elem) { + var currGi = elem.getAttribute("gi"); + var currInd = elem.getAttribute("ind"); + var stat = elem.getAttribute("stat"); + if (!currInd || !currGi) return; + + if (!stat || stat == "") { + //Get 4(5) aligns before currInd and 4(5) aligns after + ReadCurrentSeqAligns(currInd, 5); + } + else if (stat == "read") { + var indexes = getCurrIndexRange(currInd); + if (indexes) { + var msgID = "alnShow_" + indexes[0]; + location.href = "#" + msgID; + } + } + else { + //error status handling + } +} + + +function goToNextAlign(dtrID, next) { + var currInd = parseInt($(dtrID).getAttribute("ind")); + var rid = $("Rid").value; + nextInd = (next) ? currInd + 1 : currInd - 1; + + if ($("deflnDesc_" + nextInd)) { + currGi = $("deflnDesc_" + nextInd).getAttribute("seqID"); + scrollToGI = currGi; + if (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "") { + + if (!next) { + ReadPrevSeqAligns(currInd, 5, scrollToGI); + } + else { + //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!! + ReadNextSeqAligns(currInd, 5, scrollToGI); + } + + } + else { + location.href = "#" + scrollToGI; + } + } +} + +function goToDefLine(dtrID) { + if ($("psiInp")) { + var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table + togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1"; + jQuery($(togglerID)).ncbitoggler("open"); + } +} + +/* +readAln.rid = rid; +readAln.startIndex = parseInt(currInd); +readAln.numSeq = parseInt(maxNumAligns); + +readAln.insertAfterID = insertAfterID; +readAln.seqList = giList; +readAln.scrollToSeqID = scrollToGI; +*/ +function ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) { + var lastDispIdx = 0; + var rid = $("Rid").value; + + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + + currInd = parseInt(currInd); + + if (currInd != 0 && $("deflnDesc_" + currInd)) { + var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_<ind> + //alert(par.id); + if (par) par = utils.getParent(par); //"alnShow_<ind> + //alert(par.id); + if (par) readAln.insertAfterID = par.id; + } + else { + readAln.insertAfterID = "alnStart"; + } + + + + readAln.startIndex = currInd + 1; + readAln.numSeq = maxNumAligns; + + checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next"); + + readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : ""; + readAln.hspSort = 0; + ReadSeqAlignByIndex(readAln); +} + +function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) { + var lastDispIdx = 0; + var rid = $("Rid").value; + + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + + currInd = parseInt(currInd); + + + //sets readAln.insertAfterID and returns lastDispIdx; + //Find the index of the previously displayed alignment + lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln); + + readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1; + readAln.numSeq = currInd - readAln.startIndex; //stopIndex = currInd + + checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev"); + + readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID"); + readAln.hspSort = 0; + ReadSeqAlignByIndex(readAln); +} + +//When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd +function ReadCurrentSeqAligns(currInd, maxNumAligns) { + var rid = $("Rid").value; + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + + currInd = parseInt(currInd); + + + //sets readAln.insertAfterID and returns lastDispIdx; + //Find the index of the previously displayed alignment + var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln); + + //lastDispIdx = parseInt(lastDispIdx); + readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1; + readAln.numSeq = parseInt(maxNumAligns * 2); + + checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr"); + + readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID"); + readAln.hspSort = 0; + ReadSeqAlignByIndex(readAln); + g_DisableAutoCheck = true; + location.href = "#alnShow_" + readAln.startIndex; +} + + + + +function setupDynHSPParams(readAln) +{ + var currSeqInd = readAln.startIndex; + hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp")); + alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len")); + var maxDispLen = parseInt($("maxDispAlnLen").value);//20000 + var minDispLen = parseInt($("minDispAlnLen").value);//2000 + if (alnLen > maxDispLen) { + var lenPerMatch = alnLen / hspNum; + readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch); + readAln.AlignDbPageNum = 0; + $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize); + } +} + + + +function getCurrSeqsAlnLen(currSeqInd) +{ + var alnLen = 0; + if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") || $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) { + alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len"); + } + alnLen = (alnLen) ? parseInt(alnLen) : 0; + return alnLen; +} + +function checkTotalAlignLen(startIndex,stopIndex) +{ + var dispAlnLen = 0; + var maxDispLen = parseInt($("maxDispAlnLen").value); + for (var i = startIndex; i <= stopIndex; i++) { + alnLen = getCurrSeqsAlnLen(i); + if (alnLen == 0) break; + dispAlnLen += alnLen; + } + return dispAlnLen; +} +//Get total align length for seq currSeqInd and +//"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs +function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType) +{ + var startIndex = readAln.startIndex; + var stopIndex = readAln.startIndex + readAln.numSeq - 1; + if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current + startIndex = Math.max(startIndex, currSeqInd - countSeqs); + stopIndex = Math.min(stopIndex, currSeqInd + countSeqs); + } + else if(dispType == "prev") { + startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs); + stopIndex = currSeqInd - 1; + } + else {//next + stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1); + } + var totAlnLen = checkTotalAlignLen(startIndex,stopIndex); + return totAlnLen; +} + +function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType) +{ + var maxDispLen = parseInt($("maxDispAlnLen").value); + var totAlnLen = 0; + var exc = false; + for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) { + totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType); + if(totAlnLen > maxDispLen) { + break; + } + } + if (totAlnLen > maxDispLen) { + if (numSeq != 0) numSeq--; + if (dispType == "curr") { + readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq); + //prev + 1(curr) + next + readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq; + } + else if (dispType == "prev") { + readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq); + readAln.numSeq = numSeq + 1; + } + else { //"next" - readAln.startIndex stays + readAln.numSeq = numSeq + 1; + } + + if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") { + setupDynHSPParams(readAln); + } + + exc = true; + } + return exc; +} + + +//readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set +function ReadSeqAlignByIndex(readAln) { + var numAligns = 0; + for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) { + + if (!$("deflnDesc_" + i)) { + break; + } + if (!$("deflnDesc_" + i).getAttribute("stat") || $("deflnDesc_" + i).getAttribute("stat") == "") { + currGi = $("deflnDesc_" + i).getAttribute("seqFSTA"); + if (readAln.seqList != "") readAln.seqList += ","; + readAln.seqList += currGi; + numAligns++; + } + else { + break; + } + } + if (readAln.seqList != "") { + readAln.numSeq = parseInt(numAligns); + ReadSeqAlignForSeqList(readAln); + } +} + + +var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2... +//Find the range of indexes of displayed alignments for currAlnInd +//Returns array of 2 startIndex, stopIndex +function getCurrIndexRange(currAlinInd) { + var currRange; + var ranges = g_DisplayeAlignsRanges.split(","); + for (var i = 0; i < ranges.length; i++) { + var indexes = ranges[i].split("-"); + if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) { + currRange = indexes; + break; + } + } + return currRange; +} + + +//Find the index of the previous displayed alignment +function getPrevDisplyedAlignInfo(currInd, readAln) { + readAln.insertAfterID = "alnStart"; + lastDispIdx = 0; + for (var i = currInd - 1; i >= 1; i--) { + indexes = getCurrIndexRange(i); + if (indexes) { + lastDispIdx = indexes[1]; + readAln.insertAfterID = "alnShow_" + indexes[0]; + break; + } + } + return parseInt(lastDispIdx); +} + + +//setReadStatus +function setSeqAlnReadStatus(readAln, status) { + for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) { + if ($("deflnDesc_" + i)) { + jQuery($($("deflnDesc_" + i))).attr("stat", status); + if (status == "disp") { + g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex; + } + } + } +} + +/* +readAln.rid = rid; +readAln.seqList = giList; +readAln.startIndex = parseInt(idx); +readAln.insertAfterID = insertAfterID; +readAln.numSeq = parseInt(numSeq); +readAln.scrollToSeqID = scrollToGI; +*/ +function SendReadSeqAlinRequest(readAln) { + blastUrl = "t2g.cgi"; + + var rp = new RemoteDataProvider(blastUrl); + + + rp.onSuccess = function(obj) { + if ($("alignView")) utils.removeClass($("alignView"), "hidden"); + + if ($("alnShow_" + readAln.startIndex)) { + var moreHspsLink = getNextHspsLink(readAln); + jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, { + 'widgets': ['ncbipopper', 'ncbitoggler'], + 'configs': { + 'ncbipopper': { hasArrow: true, arrowDirection: 'top' } + } + }); + setSeqAlnReadStatus(readAln, "disp"); + jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden"); + //Saves start and stop indexes of loaded alignments in global variables + saveIdxesForAutomaticLoad(readAln); + jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) { + var seqID = this.getAttribute("seqID"); + if(seqID) initAlignBatch(seqID); + }); + + } + + if (readAln.scrollToSeqID) { + location.href = "#" + readAln.scrollToSeqID; + } + + }; + rp.onError = function(obj) { + if ($("alignView")) utils.removeClass($("alignView"), "hidden"); + jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden"); + $("alnShowReal_" + readAln.startIndex).innerHTML = "<div class=\"erm\" id=\"erm_" + readAln.startIndex + "\">Error loading alignment ...<span class=\"db\">requests:" + this.iActiveRequests + " status:" + obj.status + + "</span><a class=\"gbd\" href=\"#\" onclick=\"ReSubmitReadSeqAligns(event," + readAln.startIndex + ")\">Try again<\a></div>"; + } + var params = constructURLParams(readAln); + if (readAln.numSeq == 1) { + params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); + } + params += "&SEQ_LIST_START=" + readAln.startIndex; + + var formatParams = constructFormatParams(); + params += formatParams; + + //alert(params); + rp.Request(params); +} + + +function constructURLParams(readAln) { + var params; + + if ($("useAlignDB") && $("useAlignDB").value == "true") { + + var alignDbParams = "&USE_ALIGNDB=true"; + var batchID = document.getElementsByName("ALIGNDB_BATCH_ID"); + if (batchID) { + alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID"); + alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS"); + alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST"); + alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH"); + } + alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList; + alignDbParams += "&HSP_SORT=" + readAln.hspSort; + + if (readAln.hasOwnProperty("AlignDbPageNum")) { + alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum; + alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize; + alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum; + } + + params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams; + } + else { + params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort; + } + if ($("phiPtInd")) { + params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value; + } + return params; +} + +/* +readAln.rid = rid; +readAln.seqList = giList; +readAln.startIndex = parseInt(idx); +readAln.insertAfterID = insertAfterID; +readAln.numSeq = parseInt(numSeq); +readAln.scrollToSeqID = scrollToGI; +*/ +/*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes +2. Insert another div with id="alnShowReal_index and class="alnMsgR" +3. For "alnShow_index" set atrr indexes="startInd-stopInd" +4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this +5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes +6. Send read request +*/ + +function ReadSeqAlignForSeqList(readAln) { + var text = "<div id=\"alnShow_" + readAln.startIndex + "\" class=\"alnMsg\"><div class=\"alnMsgS\" id=\"alnMsg_" + readAln.startIndex + "\">Loading alignment...<span class=\"db\"> for sequences " + readAln.seqList; + var stopIndex = readAln.startIndex + readAln.numSeq - 1; + var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : ""; + text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "</span></div>"; + text += "<div id=\"alnShowReal_" + readAln.startIndex + "\" class=\"alnMsgR\"></div></div>"; + var debugControl = "<div id=\"debug\"></div>"; + if (!$("debug")) { + jQuery($($("descriptions"))).before(debugControl); + } + if (!$("alnShow_" + readAln.startIndex)) { + jQuery($($(readAln.insertAfterID))).after(text); + jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex); + jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList); + g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex; + setSeqAlnReadStatus(readAln, "read"); + $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex; + + if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ","; + g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex; + + SendReadSeqAlinRequest(readAln); + } + else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) { + jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden"); + jQuery($("erm_" + readAln.startIndex)).remove(); + SendReadSeqAlinRequest(readAln); + } +} + + +function ReSubmitReadSeqAligns(e,currInd) { + var rid = $("Rid").value; + if ($("alnShow_" + currInd)) { + var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes"); + var range = indexRange.split("-"); + + + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist"); + readAln.startIndex = parseInt(range[0]); + readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1; + readAln.hspSort = 0; + ReadSeqAlignForSeqList(readAln); + utils.preventDefault(e); + } +} + + +var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read" +var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N +var g_DisableAutoCheck = false; + +var g_autoStartIdx = new Array(); +var g_autoStopIdx = new Array(); + +function saveIdxesForAutomaticLoad(readAln) { + var stopIndex = readAln.startIndex + readAln.numSeq - 1; + g_autoStartIdx.push(readAln.startIndex); //1,20,25 + g_autoStopIdx.push(stopIndex); //4,24,29 + $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex; +} + +function getNextHspsLink(readAln) +{ + var moreHspsLink = "" + if (readAln.hasOwnProperty("AlignDbPageNum")) { + var nextPageNum = readAln.AlignDbPageNum + 1; + var currHspInd = readAln.AlignDbPageSize * nextPageNum; + var argstring = readAln.startIndex + "," + currHspInd; + var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId"); + var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs"); + var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); + var prevHspInd = readAln.AlignDbPageSize * nextPageNum; + var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize); + var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1); + + moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID); + moreHspsLink = moreHspsLink.replace(/@accs@/g, accs); + moreHspsLink = moreHspsLink.replace("@argstring@", argstring); + moreHspsLink = moreHspsLink.replace(/@segs@/g, segs); + moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps); + moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize); + moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd); + moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi); + } + return moreHspsLink; +} + + +function ReadNextHSPSet(currSeqInd, currHSPNum) { + var readAln = new Object(); + + readAln.rid = $("Rid").value; + readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA"); + readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId"); + dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps"); + readAln.startIndex = currSeqInd; + readAln.numSeq = 1; + if (dynHsps) { + readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps); + readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve + } + if (currHSPNum != 0) { + readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1); + readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum; + } + var sortLink = $("sa_" + readAln.gi); + readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0; + SendReadSeqAlinSortHSPRequest(readAln); +} + +function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) { + ReadNextHSPSet(currSeqInd, currHSPNum); + utils.preventDefault(e); +} + + + +function checkAutoAlignArray() { + var stop = false; + var start = false; + var currAlignViewPos = $("alignView").getBoundingClientRect().top; + if (currAlignViewPos < g_alignViewPos) {//scrolling down + g_alignViewPos = currAlignViewPos; + if (g_DisableAutoCheck) { + g_DisableAutoCheck = false; + return; + } + for (i = 0; i < g_autoStopIdx.length; i++) { + if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) { + //alert("Reading more aligns scrolling down!"); + var nextInd = parseInt(g_autoStopIdx[i] + 1); + var currInd = g_autoStopIdx[i]; + if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "")) { + ReadNextSeqAligns(currInd, 5); + stop = true; + break; + } + } + } + if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array + } + else if (currAlignViewPos > g_alignViewPos) {//scrolling up + g_alignViewPos = currAlignViewPos; + //here maybe return if autoStop found!!! + /* commenting automic read when scroll up */ + for (i = 0; i < g_autoStartIdx.length; i++) { + if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) { + //alert("Reading more aligns scrolling up!"); + var currInd = g_autoStartIdx[i]; + //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!! + if (currInd > 1) { + ReadPrevSeqAligns(currInd, 5); + start = true; + break; + } + } + } + if (start) g_autoStartIdx.splice(i, 1); + } + /*end of comment*/ +} + +var g_alignViewPos = 0; + +function checkAutoAlignLoad() { + + + checkAutoAlignArray(); + + if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) { + //alert("bottom!"); + + if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") { + //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex + ReadNextSeqAligns(g_MaxDisplayedIndex, 5); + } + } +} + + +function GetPatternLocResults() +{ + form = $("results"); + if (!form.PHI_PTTRN_INDEX) { + var el = document.createElement("input"); + el.name = "PHI_PTTRN_INDEX"; + el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value; + form.appendChild(el); + } + else { + form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value; + } + form.submit(); +} + +function goToNextHSP(elem, next) { + var par = jQuery(elem).parent(); //parent span with class="alnParLinks" + var parts = par[0].id.split("_"); //"hsp<seqid>_hspnum "hsp207524544_2" + if (parts[0].indexOf("nxHsp") != -1) { + parts[0] = parts[0].replace("nxHsp", "hsp"); + } + nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1) + + gotoElem = jQuery($(nextID)); + if (gotoElem[0]) { + a = jQuery(gotoElem).offset(); + window.scroll(0, a.top); + } + + else { + retrieveNextHSP(parts[0],parts[1]); + } + +} + + +//parts[0]//hsp<seqid>, parts[1] hspnum +function retrieveNextHSP(currLinkID, currHSPNum) +{ + var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id + var currSeqInd, totalHsps; + jQuery($($(desLineID))).find(".deflnDesc").each(function(index) { + currSeqInd = parseInt(this.getAttribute("ind")); + totalHsps = parseInt(this.getAttribute("hsp")); + dynHsps = this.getAttribute("dynHsps"); + }); + currHSPNum = parseInt(currHSPNum); + if (currHSPNum < totalHsps && dynHsps) { + ReadNextHSPSet(currSeqInd, currHSPNum); + } +} +/********Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error********************************/ +function getUrlCompForEntryField(elem) { + var url = ""; + if (elem && elem.value != "") { + url = "&" + elem.name + "=" + escape(elem.value); + } + return url; +} + + +function getUrlCompForCheckedField(elem) { + var url = ""; + if (elem && elem.checked) { + url = "&" + elem.name + "=" + elem.value; + } + return url; + +} + +function getUrlCompForOptionsField(elem) { + var url = ""; + if (elem) { + url = "&" + elem.name + "=" + elem[elem.selectedIndex].value; + } + return url; +} +/****************************************/ + +function constructFormatParams() { + var formatParams = ""; + + if ($("queryList")) { + formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value; + } + + + formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT); + formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE); + formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI); + formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW); + formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR); + formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR); + formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW); + formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH); + formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW); + formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH); + formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH); + + + formatParams += getHiddenFieldParamString("BUILD_NAME"); + + var serviceType = ""; + if ($("serviceType").value == "sra") { + serviceType = "sra"; + } + else if ($("clientType").value == "TMSmart_restricted") { + serviceType = "restricted"; + } + if (serviceType != "") { + formatParams += "&BOBJSRVC=" + serviceType; + } + if ($("currQuery").value != "") { + formatParams += "&CURR_QUERY_ID=" + $("currQuery").value; + } + + return formatParams; +} + +//readAln.seqList contains one gi only for this +function SendReadSeqAlinSortHSPRequest(readAln) { + blastUrl = "t2g.cgi"; + var rp = new RemoteDataProvider(blastUrl); + + + rp.onSuccess = function(obj) { + var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : ""; + var alnHtml = obj.responseText + moreHspsLink; + initHSPRequest(readAln, obj.responseText + moreHspsLink,false); + if (readAln.scrollToSeqID) { + location.href = "#" + readAln.scrollToSeqID; + } + }; + rp.onError = function(obj) { + var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0; + var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1); + if (!$(msgID)) { + var msg = "<div class=\"erm\" att=\"1\" id=\"" + msgID + "\">Error loading alignment ...<span class=\"db\">status:" + obj.status + + "</span><a class=\"gbd\" href=\"#\" onclick=\"ReadNextHSPSetEvt(event," + readAln.startIndex + "," + currHspInd + + ")\">Try again <span class=\"attmt\"></span> <\a></div>"; + initHSPRequest(readAln, msg, true); + } + else { + var attNum = parseInt($(msgID).getAttribute("att")) + 1; + $(msgID).setAttribute("att", attNum); + jQuery($(msgID)).find(".attmt").each(function(index) { + jQuery(this).html(", attempt " + attNum); + }); + } + } + + var params = constructURLParams(readAln); + if (readAln.AlignDbPageSize) { + params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); + } + params += "&SORT_ONE_ALN=on"; + var formatParams = constructFormatParams(); + + params += formatParams; + + //alert(params); + rp.Request(params); +} +function initHSPRequest(readAln, alnHtml, err) { + var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0; + if (currHspInd != 0) { + readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd; + jQuery($(readAln.insertAfterID)).after(alnHtml); + moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1); + jQuery($(moreHspsID)).remove(); + if (!err) { + errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1); + jQuery($(errMsgID)).remove(); + } + } + else { + jQuery($("alnAll_" + readAln.gi)).html(alnHtml); + } +} + +function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544" + var readAln = new Object(); + + + var desLineID = sortLink.id.replace("sa", "dtr"); //tr id + var seqInd; + + jQuery($($(desLineID))).find(".deflnDesc").each(function(index) { + seqInd = this.getAttribute("ind"); + }); + + ReadNextHSPSet(parseInt(seqInd), 0); +} + + +function configDescriptions(e,btn,dlgId) +{ + var suffix = PsiBelowThresh(dlgId); + var colmnsInfId = "cfcDsInf" + suffix; + var tblID = "dscTable" + suffix; //"dscTable[_psiw]" + var showAllColId = "shcl" + suffix; + var chkBoxes = $C("checkbox", "type", $(dlgId), "input"); + if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = ""; + for (i = 0; i < chkBoxes.length; i++) { + var check; + if (utils.hasClass(btn, "cnc")) {//cancel + if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) { + check = true; + } + else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) { + check = false; + } + } + else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) { + check = true; + } + if (typeof (check) != 'undefined') { + chkBoxes[i].checked = check; + showHideCol(tblID,parseInt(chkBoxes[i].value), !check); + } + if (!utils.hasClass(btn, "cnc")) { + if (chkBoxes[i].checked) { //OK + if ($(colmnsInfId).value != "") $(colmnsInfId).value += ","; + $(colmnsInfId).value += chkBoxes[i].value; + } + } + } + if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8" + jQuery($(showAllColId)).removeClass("hidden"); + } + else { + jQuery($(showAllColId)).addClass("hidden"); + } + + var chConfig = $("cfcDsSave").value != $(colmnsInfId).value; + + var cfds = document.getElementsByName("CONFIG_DESCR"); + if (cfds) { + for (i = 0; i < cfds.length; i++) { + cfds[i].value = $(colmnsInfId).value; + } + } + $("cfcDsSave").value = $(colmnsInfId).value; + if (chConfig) SaveConfigTable(); + jQuery(document.body).click(); + utils.preventDefault(e); +} + + + +function initDescConfig() +{ + initConfigColumns("dsConfig"); + if ($("psiw") && utils.hasClass($("psiw"), "shown")) { + initConfigColumns("dsConfig_psiw"); + } +} + + +function initConfigColumns(cnfDlgID) +{ + var suffix = PsiBelowThresh(cnfDlgID); + //cnfDlgID is "dsConfig[_psiw]" + var colmnsInfId = "cfcDsInf" + suffix; + var tblID = "dscTable" + suffix; //"dscTable[_psiw]" + var showAllColId = "shcl" + suffix; + + if (navigator.userAgent.match(/ie/i)) { + if ($("FormatForm").NCBI_GI.checked || $("serviceType").value == "sra") { + jQuery($(tblID)).find("th.c1").each(function(index) { + db = getHiddenFieldVal("DATABASE"); + var width = (db.match(/WGS/i) || db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em"; + jQuery(this).css("width", width); + }); + } + } + + jQuery($(tblID)).find("tr.first").each(function(index) { + jQuery(this).find("a.dcs").each(function(index) { + jQuery(this).bind("click", function(e) { checkConfig(this); }); + }); + }); + + jQuery($(cnfDlgID)).find("button").each(function(index) { + jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); }); + }); + + + jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); }); + + $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR"); + if ($(colmnsInfId).value == "" || $(colmnsInfId).value == "undefined") { + $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval"); + } + if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8" + jQuery($(showAllColId)).removeClass("hidden"); + } + else { + jQuery($(showAllColId)).addClass("hidden"); + } + var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input") + for (i = 0; i < chkBoxes.length; i++) { + jQuery(chkBoxes[i]).bind("click", configColumn); + if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) { + chkBoxes[i].checked = true; + } + else { + //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value); + showHideCol($(tblID), chkBoxes[i].value, true); + } + } +} +function showAllCol(e,elem) +{ + var suffix = PsiBelowThresh(elem.id); + var rdf = "dscRsDf" + suffix; + jQuery($(rdf)).click();//click "restore defaults' + utils.preventDefault(e); +} + + +function configColumn() { + var suffix = PsiBelowThresh(this.id); + var tblID = "dscTable" + suffix; //"dscTable[_psiw]" + + cCls = "c" + this.value; + if (this.checked) {//show + showHideCol(tblID,parseInt(this.value), false); + } + else { + showHideCol(tblID,parseInt(this.value), true); + } +} + +function showHideCol(tblID, columnIndex, hide) { + + if ($("Transcr")) { + colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden"); + hide = hide && !colHidden; + show = !hide && colHidden; + } + else { + show = !hide; + } + if (hide) { + jQuery($(tblID)).ncbigrid("hideColumn", columnIndex); + } + else if (show) { + jQuery($(tblID)).ncbigrid("showColumn", columnIndex); + } + if ($("Transcr") && (hide || show) ) { + var colsp = parseInt($("Transcr").getAttribute("colspan")); + colsp = (hide) ? colsp - 1 : colsp + 1; + $("Transcr").setAttribute("colSpan", colsp); + if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp); + } +} + +function checkConfig(lnk) { + var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value; + lnk.href = lnk.href + cnfCol + "#sort_mark"; +} + +function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists +{ + var dflLineLinks = $C(seqID, "gi", document, "a"); + for (i = 0; i < dflLineLinks.length; i++) { + jQuery(dflLineLinks[i]).click(); + break; + } + location.href = dflLineLinks[i].href; +} + + + +function initDescSelect() +{ + + jQuery("#cntDesc").find("a").each(function(index) { + jQuery(this).bind("click", configDescrSelect); + }); + jQuery("#cntSelN").click(); + jQuery("#descTblCtrl").find("a[view]").each(function(index) { + jQuery(this).bind("click", DisplaySelectedView); + }); + if ($("psiw") && utils.hasClass($("psiw"), "shown")) { + jQuery("#cntDesc_psiw").find("a").each(function(index) { + jQuery(this).bind("click", configDescrSelect); + }); + jQuery("#cntSelN_psiw").click(); + jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) { + jQuery(this).bind("click", DisplaySelectedView); + }); + } + + + //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });?? + +} + +function DisplaySelectedView(e) { + if (this.getAttribute("view") == "graph") { //seqviewer + ViewSelectedSeqViewer(e,this); + } + else { + if (this.getAttribute("view") == "tree") { //seqviewer + $("scrWidth").value = screen.width; + $("scrHeight").value = screen.height; + } + ViewSelectedSeqsEx(e, this); + } +} + +function PsiBelowThresh(elemID) +{ + var suffix = ""; + if (elemID.indexOf("_psiw") != -1) { + suffix = "_psiw"; + } + return suffix; +} + +function ViewSelectedSeqsEx(e,elem) { + var sbmForm = elem.getAttribute("frm"); + var seqList = elem.getAttribute("seqList"); + + var cnfElem = utils.getParent(elem); //.cnf div + var suffix = PsiBelowThresh(cnfElem.id); + var tblID = "dscTable" + suffix; + + $(seqList).value = createSelseqString(tblID,true); + $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces + if ($(seqList).value.indexOf("dbSNP") != -1) { + $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp + elem.href = $(sbmForm).action + $(seqList).value; + elem.target = "new"; + } + else { + $(sbmForm).submit(); + utils.preventDefault(e); + } +} + +function ViewSelectedSeqsTree(e) { + $("scrWidth").value = screen.width; + $("scrHeight").value = screen.height; +} + +function initSeqViewerGet(seqList) { + if (seqList.length >= 2000) { + seqList = seqList.substr(0,2000); + lastComma = seqList.lastIndexOf(","); + seqList = seqList.substr(0,lastComma); + } + $("seqViewParams").name = "RID"; + $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]"; +} + +function ViewSelectedSeqViewer(e, elem) +{ + var cnfElem = utils.getParent(elem); //.cnf div + var suffix = PsiBelowThresh(cnfElem.id); + var tblID = "dscTable" + suffix; + + //change to false when new verison of seqVier is installed in production + var seqList = createSelseqString(tblID, false); + $("sbmtGraphics").action = $("seqViewUrl").value; + + var rp = new RemoteDataProvider("url2nc.cgi"); + rp.onSuccess = function(obj) { + var jsnResp = JSON.parse(obj.responseText); + ncid = jsnResp.ncid; + + if (ncid != "") { + $("seqViewParams").name = "rkey"; + $("seqViewParams").value = ncid; + } + else { + initSeqViewerGet(seqList); + } + $("sbmtGraphics").submit(); + }; + rp.onError = function(obj) { + initSeqViewerGet(seqList); + $("sbmtGraphics").submit(); + utils.preventDefault(e); + } + var params = $("ridParam").value + "[" + seqList + "]"; + rp.Request(params, "POST"); + utils.preventDefault(e); +} + +function configDescrSelect(e) { + var sel = this.getAttribute("sel"); + if (sel) { + var selNum = 0; + var check = (sel == "all") ? true : false; + + var suffix = PsiBelowThresh(this.id); + var tblID = "dscTable" + suffix; + var toolbarID = "descTblCtrl" + suffix; + var selElID = "slcNum" + suffix; + + jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) { + jQuery(this)[0].checked = check; + if (check) selNum++; + }); + enableDescrLinks(selNum, toolbarID, selElID); + } + utils.preventDefault(e); +} + + + +function enableDescrLinks(selNum, toolbarID, selElID) { + jQuery($(toolbarID)).find("a[minSlct]").each(function(index) { + var minSelected = this.getAttribute("minSlct"); + minSelected = parseInt(minSelected); + if (selNum >= minSelected) { + this.removeAttribute("disabled"); + } + else { + this.setAttribute("disabled", "disabled"); + } + }); + $(selElID).innerHTML = selNum; +} + + + +function configDescrLinks(e, elem) +{ + + ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false"); + var par = jQuery(elem).parents(".jig-ncbigrid");//parent table + if (par) { + var suffix = PsiBelowThresh(par[0].id); + var tblID = "dscTable" + suffix; + var toolbarID = "descTblCtrl" + suffix; + var selElID = "slcNum" + suffix; + + var currSelNum = parseInt($(selElID).innerHTML); + var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1; + enableDescrLinks(selNum, toolbarID, selElID); + } +} +/***Download code begin****/ + +function initDownLoadPopup(dwnDialog) { + + jQuery(dwnDialog).find("button").each(function(index) { + jQuery(this).bind("click", execDownLoad); + }); + + jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); }); +} + +function initDescDownLoad() { + initDownLoadPopup($("dsDownload")); + + if ($("psiw") && utils.hasClass($("psiw"), "shown")) { + initDownLoadPopup($("dsDownload_psiw")); + } +} + +function initAlignDownLoad(navObj) +{ + var seqID = navObj.seqID; + var dwnDialog = $("dlgDwnl_" + seqID); + jQuery(dwnDialog).find("button").each(function(index) { + jQuery(this).bind("click", execDownLoad); + }); + + var dwnFSTW = $("dwFST_" + seqID);//whole seq + var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions + + if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID); + if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID); + + jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); }); +} + + +function execDownLoad(e) { + if (!utils.hasClass(this, "cnc")) { + par = utils.getParent(this); + dwnDialog = utils.getParent(par); //parent dialog with popDl class + var descr = (this.id == "dw_cont" || this.id == "dw_cont_psiw") ? true : false; + jQuery(dwnDialog).find("input").each(function(index) { + if (this.checked) { + submitDownLoad(this, descr); + } + }); + } + jQuery(document.body).click(); + utils.preventDefault(e); +} + +function submitDownLoad(radioElem, descr) { + var toolURL = radioElem.getAttribute("url"); + if (toolURL) { + if (descr) { + var getGi = radioElem.getAttribute("getGi"); + getGi = (getGi) ? true : false; + + var tblID = "dscTable"; + var suffix = PsiBelowThresh(radioElem.id); + tblID += suffix; + + $("selDnSeqs").value = createSelseqString(tblID,getGi); + } + else { + var seqfsta = radioElem.getAttribute("seqfsta"); + $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi"); + } + var addParams = ""; + if (radioElem.getAttribute("addParam")) { + addParams = addDwnlParams(); + } + var submitName = radioElem.getAttribute("sbName") + $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST"; + $("dwdlSubmit").action = toolURL + addParams; + $("dwdlSubmit").submit(); + } + else { + var sbFunction = radioElem.getAttribute("sbFunc"); + if (sbFunction) { + eval(sbFunction + "(radioElem, descr)"); + } + } +} + + +function initDownLoadFSTA(radioElem, descr) +{ + if (descr) { + + var tblID = "dscTable"; + var suffix = PsiBelowThresh(radioElem.id); + tblID += suffix; + + $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false); + } + else { + $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta"); + } + $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType"); + + $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE"); + if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox + var batchID = document.getElementsByName("ALIGNDB_BATCH_ID"); + if (batchID) { + $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID"); + $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS"); + $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST"); + $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH"); + } + } + $("sbmtFASTA").submit(); +} + +function createSelseqString(tblID,getGi) { + var selSeqs = ""; + jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) { + if (jQuery(this)[0].checked) { + if (selSeqs != "") selSeqs += ","; + if (getGi) { + selSeqs += jQuery(this)[0].value; + } + else { + var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc"); + selSeqs += $(linkID).getAttribute("seqFSTA"); + } + } + }); + return selSeqs; +} + +/***Download code end****/ + +/***Init navigation code begin **/ + +function initNavigation(navObj) { + initNextAlnLink(navObj, true); + initNextAlnLink(navObj, false); +} + + +function initNavInfo(navObj) { + var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind")); + nextInd = currInd + 1; + prevInd = currInd - 1; + + navObj.currSeqID = ""; + navObj.nextSeqID = ""; + navObj.prevSeqID = ""; + + if ($("deflnDesc_" + nextInd)) { + navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs"); + if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA"); + } + if ($("deflnDesc_" + prevInd)) { + navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs"); + if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA"); + } + if ($("deflnDesc_" + currInd)) { + navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA"); + } +} + + +function initNextAlnLink(navObj, next) { + + var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID); + var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID; + + if (nextLinkEl) { + if (nextSeqid != "") { + var text = (next) ? "next" : "previous"; + nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid); + } + else { + nextLinkEl.setAttribute("disabled", "disabled"); + } + } +} +function scan(link) { + var init = link.getAttribute("init"); + if (!init) { + ncbi.sg.scanLinks(link); + link.setAttribute("init","on"); + } +} + +function initWidth(seqID) { + var lineLengthElem = $("FormatForm").LINE_LENGTH; + var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value); + if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return; + + var relWidth = (lineLength > 90) ? "12%" : "15%"; + var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7; + lineLength = (lineLength + parseInt(17)) * charWidth; + var width = lineLength + "px"; + jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) { + jQuery(this).css("width", width); + }); + jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) { + jQuery(this).css("width", width); + }); + jQuery($("relInf_" + seqID)).css("width", relWidth); +} + + +/***Init navigation code end **/ +function initAlignBatch(seqID) +{ + var navObj = new Object(); + navObj.seqID = seqID; + initNavInfo(navObj); + + initAlignDownLoad(navObj); + initNavigation(navObj); + ncbi.sg.scanLinks($("alnNxt_" + seqID)); + ncbi.sg.scanLinks($("alnPrv_" + seqID)); + if ($("serviceType").value == "vecscreen") { + utils.addClass($("alnDsc_" + seqID), "hidden"); + } + ncbi.sg.scanLinks($("alnDwnld_" + seqID)); + jQuery($("csLinks_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("relInf_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("rng_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("dln_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + initWidth(seqID); +/* + jQuery($("alnHdr_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("aln_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); +*/ +} + +function SaveConfigTable() { + blastUrl = "fmtsave.cgi"; + + + var rp = new RemoteDataProvider(blastUrl); + + + rp.onSuccess = function(obj) { + //alert("success"); + }; + rp.onError = function(obj) { + //alert("error"); + } + + var program = getHiddenFieldVal("PROGRAM"); + var rid = getHiddenFieldVal("RID"); + var blastSpec = getHiddenFieldVal("BLAST_SPEC"); + var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value; + if(blastSpec) { + params += "&BLAST_SPEC=" + blastSpec; + } + rp.Request(params,"POST"); +} + +function removeRID() { + var rid = document.getElementsByName("RID"); + for (var i = 0; i <= rid.length; i++) { + jQuery(rid[i]).remove(); + } +} + +function initAdvancedView() +{ + if ($("dsConfig")) { + + var alnView = getHiddenFieldVal("ALIGNMENT_VIEW"); + if (alnView == "Pairwise" || alnView == "PairwiseWithIdentities") { + var rid = getHiddenFieldVal("RID"); + ReadNextSeqAligns(0, 5); + g_alignViewPos = $("alignView").getBoundingClientRect().top; + utils.addEvent(window, "scroll", checkAutoAlignLoad, false); + } + list = $("phiPtInd"); + if (list) { + utils.addEvent(list, "change", GetPatternLocResults, false); + } + initDescConfig(); + initDescSelect(); + initDescDownLoad(); + if ($("psiInp")) { + var nextIter = document.getElementsByName("NEXT_I"); + for (var i = 0; i < nextIter.length; i++) { + utils.addEvent(nextIter[i], "click", removeRID, false); + } + } + } +} + +//takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4" +function initjQry() +{ + var oldCreate = jQuery.ui.ncbipopper.prototype._create; + jQuery.ui.ncbipopper.prototype._create = function() { + var destSelector = this.options.destSelector || this.options.sourceSelector || this.element.prop("hash"); + this.options.destSelector = destSelector.replace(/\./g, "\\."); + oldCreate.apply(this, arguments); + } +} +utils.addEvent(window, + "load", initAdvancedView, + false); + +initjQry() + +/* If user agent has "safari" in it, include safari-specific stylesheet. */ +if (navigator.userAgent.match(/ie/i)) { + document.write("<link rel='stylesheet' type='text/css' href='css/ie-descriptions.css' media='screen'/>"); +} +/*****************************new code end*********************************************************************/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jig.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +.ui-helper-hidden{display:none;}.ui-helper-hidden-accessible{position:absolute;left:-99999999px;}.ui-helper-reset{margin:0;padding:0;border:0;outline:0;line-height:1.3;text-decoration:none;font-size:100%;list-style:none;}.ui-helper-clearfix:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-helper-clearfix{display:inline-block;}/* required comment for clearfix to work in Opera \*/ * html .ui-helper-clearfix{height:1%;}.ui-helper-clearfix{display:block;}/* end clearfix */ 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,11 @@ +jQuery.widget("ui.ncbimenu",{options:{isSubMenuLimited:false,delayTimeout:500,useHoverEvents:true},_create:function(){this._addClasses();this._addAria();this._createMenus();this._addListeners();this._addEvents();this._addAjaxEvents()},rescan:function(){this._destroyListeners();this._destroyEvents();this._addAria();this._createMenus();this._addListeners();this._addEvents()},destroy:function(){this._destroyEvents();this._destroyClasses();this._destroyAria();this._destroyListeners();this._destroyMenus()}, +_addClasses:function(){this.element.addClass("ui-ncbimenu")},_destroyClasses:function(){this.element.removeClass("ui-ncbimenu")},_addAria:function(){this.element.attr("role","menubar").find("li").filter(":has(ul)").find("a").attr("aria-haspopup","true").end().find("ul").attr("aria-hidden","true")},_destroyAria:function(){this.element.removeAttr("role").find("li").removeAttr("role").filter(":has(ul)").find("a").removeAttr("aria-haspopup").removeAttr("role").end().find("ul").removeAttr("aria-hidden").removeAttr("role")}, +_createMenus:function(){this.element.ncbibasicmenu({orientation:"horizontal"});var a=this.element.find(">li:has(>ul)");a.find(">a").addClass("expandDown");a.find(">ul").ncbibasicmenu({nested:true});if(!this.options.isSubMenuLimited){a.find(">ul ul").ncbibasicmenu({nested:true});a.find(">ul ul").parent().find(">a").addClass("expandRight")}},_destroyMenus:function(){this.element.removeClass("jig-ncbimenu cf ui-ncbibasicmenu orientation_hort").find("ul").andSelf().show().ncbibasicmenu("destroy")},_addEvents:function(){var a= +this;this._windowClickFnc=function(b){b=b.target||b.srcElement;a.element[0]===b||a.element.find(b).length===1||a.closeSub(a.element.find("ul"))};jQuery(window).on("click",this._windowClickFnc);this._unselectEverythingFnc=function(){a._unselectEverything()};this.element.find("li").not(":has(ul)").find("a").on("click",this._unselectEverythingFnc);this._blurFnc=function(){a._checkFocus()};this.element.on("blur","a",this._blurFnc);if(this.options.useHoverEvents){var d={timeout:this.options.delayTimeout, +over:function(){if(a._isActive){var b=jQuery(this),c=b.parent();if(c.has("ul").length===0){c=c.siblings("li.selected").removeClass("selected");a.closeSub(c);b.focus()}else c.hasClass("selected")||b.focus().click()}},out:function(){}};this.element.find(">li:not(:has(ul))>a,li:has(ul)>a").hoverIntent(d)}},_destroyEvents:function(){jQuery(window).off("click",this._windowClickFnc);this._windowClickFnc=null;this.element.off("blur","a",this._blurFnc);this._blurFnc=null;this.element.find(">li:not(:has(ul))>a,li:has(ul)>a").unbind("mouseover mouseoff"); +this.element.find("li").not(":has(ul)").find("a").off("click",this._unselectEverythingFnc)},_addAjaxEvents:function(){if(this.element.find(">li:has(a.expandDown)").not(":has(ul)").length>0){var a=this;this._ajaxEnterFnc=function(){a._loadAjaxContent()};this.element.on("mouseenter",this._ajaxEnterFnc)}},_loadAjaxContent:function(){var a=this;this.element.off("mouseenter",this._ajaxEnterFnc);this._ajaxEnterFnc=null;var d=this.element.find("a.expandDown"),b=d.eq(0).prop("href").split("#");jQuery("<div/>").load(b[0], +function(){a._handleAjaxLoadCallback(this,d)})},_handleAjaxLoadCallback:function(a,d){var b=jQuery(a);d.each(function(){var c=jQuery(this),e=c.prop("href").split("#")[1];e=b.find("#"+e);if(e[0].tagName.toLowerCase()==="li")e=e.find(">ul");c.parent().append(e)});this._createMenus();this._addEvents()},_checkFocus:function(){function a(){d.element.find("a:focus").length===0&&d._unselectEverything()}var d=this;window.setTimeout(a,10)},_addListeners:function(){var a=this;this.element.find(">ul").andSelf().on("ncbibasicmenuunselected", +function(d,b,c,e){e==="click"&&a.closeSub(c)}).on("ncbibasicmenuselected",function(d,b,c,e){if(e==="click")a.openSub(c);else{d=c.siblings().find("ul:visible");if(d.length>0){d.each(function(){a.closeSub(jQuery(this))});c.parent("ul").hasClass("ui-ncbimenu")&&a.openSub(c)}}}).on("ncbibasicmenuactiondown ncbibasicmenuactionright",function(d,b){b=jQuery(b);var c=b.find(">ul");if(b.hasClass("selected"))c.length===1&&c.not(":visible")&&a.openSub(b);else b.find(">a").click();c.length===1&&window.setTimeout(function(){c.ncbibasicmenu("selectFirstItem")}, +10)}).on("ncbibasicmenuactionup ncbibasicmenuactionleft ncbibasicmenuescape",function(d,b){b=jQuery(b);d=b.find(">ul");if(d.length>0&&d.is(":visible"))a.closeSub(jQuery(b));else{b=b.parent("ul").parent("li");b.find(">a").focus();a.closeSub(b)}})},_destroyListeners:function(){this.element.find("ul").andSelf().off("ncbibasicmenuunselected").off("ncbibasicmenuselected")},openSub:function(a){var d=a.find(">ul");if(d.length===1){this._isActive=true;var b=a.parent().find("li:has(ul:visible)");b.length> +0&&this.closeSub(b);if(a.parent().hasClass("orientation_hort")){b="left bottom";var c="fit flip"}else{b="right center";c="flip fit"}d.show().position({of:a,my:"left top",at:b,collision:c}).attr("aria-hidden","false")}},closeSub:function(a){(a.is("li")?a.find("ul"):a).find("ul").andSelf().not(".ui-ncbimenu").hide().attr("aria-hidden","true").end().ncbibasicmenu("removeAllSelections").find("li.selected").removeClass("selected")},_unselectEverything:function(){this.closeSub(this.element.find("ul:visible").andSelf()); +this._isActive=false}});
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_002.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +.ui-ncbigrid-outer-div{min-width:300px;}table.ui-ncbigrid td{padding:.363em .637em;}table.ui-ncbigrid th{padding:.308em .539em;text-align:left;border-left:0;border-top:0;font-weight:normal;}table.ui-ncbigrid thead th{border-bottom:1px solid #d4dfe9;border-right:1px solid #cfcfcf;background:#F0F0F0;background:-moz-linear-gradient(top,#FFF 0,#F0F0F0 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#F0F0F0));}table.ui-ncbigrid tbody th{line-height:1.333em;color:#333;font-size:.923em;border-bottom:1px solid #d4dfe9;border-right:1px solid #cfcfcf;background:#FAFAFA;background:-moz-linear-gradient(top,#FFF 0,#FAFAFA 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#FAFAFA));}table.ui-ncbigrid th:last-child{border-right:0;*margin-right:-1px;}table.ui-ncbigrid td{border:0;}table.ui-ncbigrid td input[type="checkbox"]{margin:0;}table.ui-ncbigrid thead,table.ui-ncbigrid tbody,table.ui-ncbigrid colgroup,table.ui-ncbigrid col,table.ui-ncbigrid tr{border:0!important;}table.ui-ncbigrid,table.ui-ncbigrid thead,table.ui-ncbigrid caption{margin:0;}.ui-ncbigrid-outer-div{position:relative;zoom:1;margin:1em 0 2.8em 0;}div.caption-exists,div.filterToolbar-exists{margin:3em 0;}table.ui-ncbigrid{border-width:0;}.ui-ncbigrid-inner-div{border-color:#97b0c8;border-style:solid;}.ui-ncbigrid-inner-div{border-width:0 0 1px 0;clear:both;}.ui-ncbigrid-outer-div{border:1px solid #97b0c8;}.ui-ncbigrid-outer-div:after{clear:both;content:'.';display:block;height:0;visibility:hidden;font-size:0;}.ui-ncbigrid-header-wrapper{height:auto;max-width:100%;}.ui-ncbigrid-header-wrapper table.ui-ncbigrid{border:0;height:auto;}.ui-ncbigrid-header-wrapper thead{border-width:1px 0 0 0;}table.ui-ncbigrid caption{color:#4D4D4D;font-size:.923em;font-weight:bold;padding:0;position:absolute;text-align:left;top:-2.077em;zoom:1;}.ui-ncbigrid-filter-toolbar{clear:both;display:block;font-size:.923em;line-height:27px;position:absolute;right:0;text-align:right;top:-2.417em;width:auto;}.ui-ncbigrid-filter-toolbar input[type="text"]{font-size:inherit!important;height:1.091em;padding:0;margin-right:-1px;}.ui-ncbigrid-paged-toolbar{display:block;clear:both;width:100%;}.ui-ncbigrid-paged-countItems,.ui-ncbigrid-checkbox-toolbar{font-size:.923em;}.ui-ncbigrid-paged-toolbar div{float:left;display:inline-block;width:auto;margin-right:1em;}.ui-ncbigrid-paged-toolbar .ui-ncbigrid-paged-pageControl{margin-right:0;}.ui-ncbigrid-paged-countItems{text-align:center;}.ui-ncbigrid-paged-pageControl{text-align:right;font-size:.923em;}.ui-ncbigrid-paged-pageControl .prev{margin-left:.2em;margin-right:.6em;}.ui-ncbigrid-paged-pageControl .next{margin-left:.6em;margin-right:.2em;}.ui-ncbigrid-paged-toolbar-bottom{border-top:0;}.ui-ncbigrid-select-question{clear:both;text-align:center;display:none;padding:.385em 0 .308em;border-style:solid;border-color:#d4dfe9;border-width:1px 0;background:-moz-linear-gradient(top,#FFF 0,#F5F5F5 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0%,#FFF),color-stop(100%,#F5F5F5));font-size:.923em;}.ui-ncbigrid-select-question-footer{background:#fff;border-bottom:0;}.ui-ncbigrid-select-question .ui-ncbigrid-select-row-count{font-weight:bold;}.ui-ncbigrid-select-question a{margin-left:.583em;}.ui-ncbigrid-checkbox-toolbar label{margin-left:1em;}.ui-ncbigrid-checkbox-toolbar label:first-child{margin-left:0;}.ui-ncbigrid-checkbox-toolbar a,.ui-ncbigrid-checkbox-toolbar a:visited{color:#369;}.ui-ncbigrid-checkbox-toolbar,.ui-ncbigrid-paged-toolbar{width:auto;}.ui-ncbigrid-checkbox-toolbar{float:left;clear:left;padding:.416em .416em .416em .583em;line-height:1.75em;}.ui-ncbigrid-paged-toolbar{float:right;clear:right;padding:.385em .385em .385em .539em;line-height:1.615em;}table.ui-ncbigrid{border-collapse:separate;width:100%;}div.ui-ncbigrid-scroll{height:20em;overflow-y:auto;overflow-x:hidden;}div.ui-ncbigrid-scroll table.ui-ncbigrid{border-top:0;border-bottom:0;width:100%;}div.ui-ncbigrid-scroll table.ui-ncbigrid caption,div.ui-ncbigrid-scroll>table.ui-ncbigrid>thead>tr>th{visibility:hidden;line-height:0;border-bottom:0;border-top:0;padding-top:0;padding-bottom:0;}div.ui-ncbigrid-scroll table.ui-ncbigrid tbody tr:first-child td{border-top:0;}div.ui-ncbigrid-header-wrapper{width:100%;overflow:hidden;}div.ui-ncbigrid-hort-scroll{overflow-x:auto;}tr.ui-ncbigrid-rowHidden{display:none;}table.ui-ncbigrid th.sortAsc a,table.ui-ncbigrid th.sortDsc a,table.ui-ncbigrid th.sortNone a{padding-right:21px;background-repeat:no-repeat;background-position:right center;color:#333;}table.ui-ncbigrid th.sortAsc,table.ui-ncbigrid th.sortDsc{background:#fff;}table.ui-ncbigrid th.sortAsc a{background-image:url('../img/sorted_asc.gif');}table.ui-ncbigrid th.sortDsc a{background-image:url('../img/sorted_dsc.gif');}table.ui-ncbigrid th.sortNone a{background-image:none;color:#14376c;}table.ui-ncbigrid th.sortNone a:hover{background-image:url('../img/sorted_non.gif');color:#985735;}table.ui-ncbigrid th a{display:block;text-decoration:none;_width:100%;padding-right:21px;border:0;}table.ui-ncbigrid th a:hover,table.ui-ncbigrid th a,table.ui-ncbigrid th a:active{border:0!important;}table.ui-ncbigrid th,table.ui-ncbigrid th a{color:#14376c;}table.ui-ncbigrid tbody tr.ui-ncbigrid-checkbox-selected td,table.ui-ncbigrid tr.ui-ncbigrid-row-selected td{background-color:#eaf0f4;}table.ui-ncbigrid tbody tr.ui-ncbigrid-checkbox-hover td,table.ui-ncbigrid tr.ui-ncbigrid-row-hover>td{background-color:#D5DEE3;}table.ui-ncbigrid tr.ncbigrid-row-filtered{display:none;}td.ui-ncbigrid-column-hidden,th.ui-ncbigrid-column-hidden{display:none;}table.ui-ncbigrid tbody tr.ui-ncbigrid-high>td{background-color:#eaf0f4;}.ui-ncbigrid-paged-pageControl{margin-top:0;}.ui-ncbigrid-paged-pageControl input[type="text"]{height:1.091em;font-size:inherit!important;padding:0;}.ui-ncbigrid-paged-pageControl span.page_link{color:#ccc;padding:1px 7px;}.ui-ncbigrid-paged-pageControl a.page_link{border:1px solid #ddd;padding:2px 6px;*padding:0 4px;white-space:nowrap;text-decoration:none;}.ui-ncbigrid-paged-pageControl a.page_link:hover{color:#985735;}.ui-ncbigrid tbody tr.collapsed{display:none;}.ui-ncbigrid tbody tr th span.collapsableTbodyIcon{float:left;margin-right:.833em;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big{background-position:left -30px;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big-open{background-position:left 0;}.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big,.ui-ncbigrid tbody tr th span.ui-icon-plus-minus-big-open{background-color:transparent;background-image:url("../img/ncbitoggler-plus-minus-big.gif");background-repeat:no-repeat;margin-left:-0.1em;top:.2em;}.ui-ncbigrid-collapsable,.ui-ncbigrid-collapsable span{cursor:pointer;}table.ui-ncbigrid .ignoreCollapse{cursor:default;}.ui-ncbigrid-outer-div .ui-ncbigrid-outer-div{margin:0;*position:static;} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_002.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,22 @@ +(function(e){e.widget("ui.ncbitoggler",{styles:{ariaWrapper:"ui-ncbitoggler-live",groupMasterReplaceNode:"span.ui-ncbitoggler-group-replace-txt",groupMasterStateClose:"ui-ncbitoggler-group-master-to-close",groupMasterStateOpen:"ui-ncbitoggler-group-master-to-open",master:"ui-ncbitoggler",masterOpen:"ui-ncbitoggler-open",target:"ui-ncbitoggler-slave",targetOpen:"ui-ncbitoggler-slave-open",icon:"ui-icon-triangle-1-e",iconOpen:"ui-icon-triangle-1-s",iconPlusMinusBig:"ui-icon-plus-minus-big",iconPlusMinusBigOpen:"ui-icon-plus-minus-big-open", +iconArrowStop:"ui-icon-arrowthickstop-1-s",iconArrowStopOpen:"ui-icon-arrowthickstop-1-n"},options:{animation:"slide",closedAppendText:"",cookieNamePrefix:"jig-tog-rem-",indicator:"small-arrow",initOpen:false,isIcon:true,liveRegions:true,openedAppendText:"",remember:false,speed:50,targets:""},_cachedTargetData:{},_create:function(){this._setOption("disabled",false);this.appendTextNode=this.initTargetsClass=this.iconSpan=this.startOpen=this.rememberCookie=this.remember=this.cookieName=this.addedHref= +null;var a=this.element,b=a[0],c=this.styles,d=this,f=this.options.isIcon;a.data("isOpen",false);a.addClass("ui-widget ui-ncbitoggler");f||a.addClass("ui-ncbitoggler-no-icon");var g=a.attr("href");!g?(this.addedHref=true):(this.addedHref=false);this._validate(g);a.children("span.ui-ncbitoggler-master-text").length===0&&a.contents().filter(function(){return this.nodeType===3}).each(function(){var h=e(this);jQuery.trim(this.nodeValue).length>0&&h.wrap('<span class="ui-ncbitoggler-master-text"></span>')}); +if(this.options.openedAppendText!==""||this.options.closedAppendText!==""){this.appendTextNode=a.children("span.ui-ncbitoggler-appended-text");if(this.appendTextNode.length===0)if(!this.initOpen){this.appendTextNode=e('<span class="ui-ncbitoggler-appended-text">'+this.options.closedAppendText+"</span>");a.find(".ui-ncbitoggler-master-text").after(this.appendTextNode)}}if(this.remember=this.options.remember||false){g=this.element.attr("id");if(!g){window.console&&console.error&&console.error("ncbitoggler: master node "+ +b+" must have a unique id attribute when remembering state");return}this.cookieName=this.options.cookieNamePrefix+g;this.rememberCookie=e.cookie(this.cookieName)}if(this.startOpen=this.rememberCookie?this.rememberCookie==="open"?true:false:a.hasClass("jig-ncbitoggler-open")||a.hasClass(c.masterOpen)||this.options.initOpen?true:false){this.element.data("isOpen",true);a.removeClass(this.styles.master);a.addClass(c.masterOpen);this._targetsOpen=true}else{this.element.data("isOpen",false);a.removeClass(this.styles.masterOpen); +a.addClass(c.master)}f&&this._initMasterIcon();this.targets=this._getTargets();this.targets.addClass("ui-ncbitoggler").removeClass("ui-ncbitoggler-disabled ui-state-disabled");if(this.startOpen){this.targets.removeClass(c.target);this.targets.addClass(c.targetOpen);this.initTargetsClass=c.targetOpen}else{this.targets.removeClass(c.targetOpen);this.targets.addClass(c.target);this.initTargetsClass=c.target}this._initAria();this._doGrouping();a.click(function(h){d.toggle(h,d)});this._saveReferences()}, +_getGroupMaster:function(){for(var a=this.styles,b=this.element[0].className.split(/\s+/),c=0;c<b.length;c++){var d=b[c].match(/ui-ncbitoggler-group-(.+)$/);if(d){d=d[1];var f=e("a.ui-ncbitoggler-group-open-"+d+", a.ui-ncbitoggler-group-close-"+d,this.options.contextNode);if(f.length===1){f.hasClass("ui-ncbitoggler-group-open-"+d)&&f.addClass(a.groupMasterStateOpen);f.hasClass("ui-ncbitoggler-group-close-"+d)&&f.addClass(a.groupMasterStateClose);return f}}}},_doGrouping:function(){var a=this._getGroupMaster(); +if(a){var b=this,c=this.styles,d=a.data("togglers");this.element.id||e.ui.jig._generateId(this.widgetName);if(!this.element[0].id)this.element[0].id=e.ui.jig._generateId(this.widgetName);if(typeof d==="undefined"){a.data("togglers",[]);a.data("togglers").push(this.element)}else d.push(this.element);var f=a.find(c.groupMasterReplaceNode);a.click(function(g){g.preventDefault();g=a.data("togglers");g=g[g.length-1][0];if(a.hasClass(c.groupMasterStateOpen)){b.open();f.length>0&&f.text(b.options.groupMasterCloseReplaceText); +b.element[0]===g&&a.removeClass(c.groupMasterStateOpen).addClass(c.groupMasterStateClose)}else{b.close();f.length>0&&f.text(b.options.groupMasterOpenReplaceText);b.element[0]===g&&a.removeClass(c.groupMasterStateClose).addClass(c.groupMasterStateOpen)}})}},_initAria:function(){var a=this.startOpen;this.element.attr({role:"button","aria-expanded":a});this.options.liveRegions&&this.targets.each(function(){var b=e(this);b.find("table").length===0&&!b.parent("div").hasClass("ui-helper-reset")&&b.wrap('<div class="ui-helper-reset" aria-live="assertive">'); +b.attr("aria-hidden",a?"false":"true")})},_validate:function(a){var b=this.element,c=["a"],d=b[0].tagName.toLowerCase();if(e.inArray(d,c)===-1)throw new Error("ncbitoggler: master node must be one of the following elements: "+c.toString());a||b.attr("href","#")},_initMasterIcon:function(){var a=this.element,b=this.styles;if(this.options.indicator=="plus-minus-big"){this.iconOpenClass=b.iconPlusMinusBigOpen;this.iconCloseClass=b.iconPlusMinusBig}else if(this.options.indicator=="arrow-stop"){this.iconOpenClass= +b.iconArrowStopOpen;this.iconCloseClass=b.iconArrowStop}else{this.iconOpenClass=b.iconOpen;this.iconCloseClass=b.icon}this.iconSpan=a.find("span.ui-icon");if(this.iconSpan.length===0){this.iconSpan=e('<span class="ui-icon"></span>');this.startOpen?this.iconSpan.addClass(this.iconOpenClass):this.iconSpan.addClass(this.iconCloseClass);a.append(this.iconSpan)}else if(this.startOpen){this.iconSpan.removeClass(this.iconCloseClass);this.iconSpan.addClass(this.iconOpenClass)}},getSlaves:function(){return this._targets}, +getTargets:function(){return this.getSlaves()},_getTargets:function(){var a=this.element,b=a.attr("toggles")||a.attr("data-ncbitoggler-toggles");if(b)jQuery.ui.jig._isConsole("warn")&&console.warn('The attributes "toggles" and "data-ncbitoggler-toggles" are deprecated. Please use the "targets" attribute instead (see documentation).');else b=this.options.targets;if(b&&typeof b=="object"){b=b;a="";for(var c in b)a+=c+", ";a=a.replace(/,\s$/,"");c=e(a)}else if(b){c=e(b);if(c.length===0){this.isSibling= +false;c=b.split(/ +/);b="";for(a=0;a<c.length;a++)b+=a!==c.length-1?"#"+c[a]+",":"#"+c[a];c=e(b)}}else if(a.parent(":header").length>0){a.parent(":header").parent().css("zoom","1");this.isSibling=true;c=a.parent(":header").css("zoom","1").next()}else{this.isSibling=true;c=a.next()}return this._targets=this._normalizeTargets(c)},_normalizeTargets:function(a){var b=[];a.each(function(){var c=this,d=e(this);if(d.hasClass("ui-helper-reset"))c=d.children().get(0);b.push(c)});return ret=e(b)},_getCachedTargetData:function(a){return this._cachedTargetData[a]}, +_cacheTargetData:function(a,b){this._cachedTargetData[a]=b},_openAjaxTarget:function(a,b){var c=this,d=this._getCachedTargetData(a);d?e(a).html(d):e.get(b,function(f){c._cacheTargetData(a,f);e(a).html(f)})},_openTargets:function(){if(!(this._targetsOpening||this._targetsClosing||this._targetOpen)){this._targetsOpening=true;var a=this.targets,b=this.styles;a.removeClass(b.target).addClass(b.targetOpen).attr("aria-hidden","false");var c=this.options.targets;if(typeof c=="object"){var d=this;for(targetSel in c)(function(f){d._openAjaxTarget(f, +c[f])})(targetSel)}b=this.options.openedAppendText;b!==""&&this.appendTextNode.html(b);a.css("display","");this._targetsOpening=false;this._targetsOpen=true}},_closeTargets:function(){if(!(this._targetsOpening||this._targetsClosing||!this._targetsOpen)){this._targetsClosing=true;var a=this.targets,b=this.styles;a.removeClass(b.targetOpen).addClass(b.target).attr("aria-hidden","true");b=this.options.closedAppendText;b!==""&&this.appendTextNode.html(b);a.css("display","");this._targetsOpen=this._targetsClosing= +false}},_fixHasLayout:function(a){window.setTimeout(function(){a.targets.addClass("foo").removeClass("foo")},1)},open:function(a){var b=this.element,c=this;if(!b.hasClass(this.styles.master))return b;this.updateState("open");if(this.options.animation==="slide")this.targets.slideToggle(this.options.speed,function(){c._openTargets();e.browser.msie&&c._fixHasLayout(c);b.data("isOpen",true);b.trigger("ncbitoggleropen");a&&a()});else{this._openTargets();e.browser.msie&&c._fixHasLayout(c);b.data("isOpen", +true);b.trigger("ncbitoggleropen");a&&a()}this._updateReferences("open");return b},close:function(a){var b=this.element,c=this;if(!b.hasClass(this.styles.masterOpen))return b;this.updateState("closed");if(this.options.animation==="slide")this.targets.slideToggle(this.options.speed,function(){c._closeTargets();b.trigger("ncbitogglerclosed").trigger("ncbitogglerclose");b.data("isOpen",false);a&&a()});else{this._closeTargets();b.data("isOpen",false);b.trigger("ncbitogglerclosed");a&&a()}this._updateReferences("closed"); +return b},toggle:function(a,b,c){var d=arguments.length;if(d===0||d===1){b=this;if(d===1)c=arguments[0]}else a.preventDefault();this.element.hasClass(this.styles.master)?b.open(c):b.close(c)},updateState:function(a){var b=this.element;a||(a=b.hasClass(styles.master)?"open":"closed");var c=this.styles.master,d=this.styles.masterOpen,f=this.iconCloseClass,g=this.iconOpenClass;if(a=="closed"){c=this.styles.masterOpen;d=this.styles.master;f=this.iconOpenClass;g=this.iconCloseClass}b.removeClass(c).addClass(d).attr("aria-expanded", +a=="closed"?"false":"true");this.options.isIcon&&this.iconSpan.removeClass(f).addClass(g);this.remember&&e.cookie(this.cookieName,a)},_removeHandlers:function(){this.element.unbind("click")},destroy:function(){e.Widget.prototype.destroy.apply(this,arguments);var a=this.element,b=this.styles;a.removeClass(b.master+" "+b.masterOpen+" ui-state-disabled ui-widget ui-ncbitoggler-disabled").removeAttr("role").removeAttr("aria-expanded");this.targets.removeClass("ui-ncbitoggler ui-ncbitoggler-slave ui-ncbitoggler-slave-open ui-state-disabled ui-ncbitoggler-disabled"); +this.targets.removeAttr("aria-hidden");if(this.options.isIcon){b=a.find("span.ui-icon")[0];a[0].removeChild(b)}this.targets.each(function(){var d=jQuery(this),f=d.parent("div.ui-helper-reset");if(f.length>0){d.insertBefore(f);f.remove()}});b=a.find("span.ui-ncbitoggler-master-text");var c=b.html();b.remove();a.html(c);this._removeHandlers();return this},disable:function(){e.Widget.prototype.disable.apply(this,arguments);this._removeHandlers();this.targets.addClass("ui-ncbitoggler-disabled ui-state-disabled"); +return this},enable:function(){e.Widget.prototype.enable.apply(this,arguments);this.targets.removeClass("ui-ncbitoggler-disabled ui-state-disabled");var a=this;this.element.click(function(b){a.toggle(b,a)});return this},_saveReferences:function(){var a=this;this._targets.each(function(){typeof e(this).data("ncbitoggler-masters")==="undefined"&&e(this).data("ncbitoggler-masters",[]);e(this).data("ncbitoggler-masters").push(a.element)})},_updateReferences:function(a){var b=this;e.each(this._targets.data("ncbitoggler-masters"), +function(){b.element!=this&&e(this).ncbitoggler("updateState",a)})}})})(jQuery);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_003.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +.ui-ncbibasicmenu{list-style-type:none;min-width:200px;}.ui-ncbibasicmenu,.ui-ncbibasicmenu>li{padding:0;margin:0;}.ui-ncbibasicmenu li ul li{background-color:#FFF;}.ui-ncbibasicmenu li ul li a:hover,.ui-ncbibasicmenu li ul li.selected a:hover{background-color:#4C96DF;color:#FFF;}.oneLevel li a,.ui-ncbibasicmenu li a{display:block;text-decoration:none;background-color:#FCFCFC;border:1px solid #FCFCFC;border-width:1px 0;color:#14376C;font-size:13px;font-weight:normal;margin:0;padding:.2em .9em;text-decoration:none;}.oneLevel li a:hover,.ui-ncbibasicmenu>li>a:hover{background-color:#E3F8FF;}.oneLevel li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbibasicmenu>li.ui-ncbimenu-item-no-hlt>a:hover,.oneLevel li.ui-ncbimenu-item-skip a:hover,.ui-ncbibasicmenu>li.ui-ncbimenu-item-skip>a:hover{background-color:#FCFCFC;}.oneLevel li a:focus,.ui-ncbibasicmenu>li>a:focus{outline:1px dashed #000;}.oneLevel li.selected a,.ui-ncbibasicmenu>li.selected>a{color:#FFF;background-color:#4C96DF;}.oneLevel li.selected a:hover,.ui-ncbibasicmenu>li.selected>a:hover{color:#FFF;}.oneLevel li.selected.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbibasicmenu>li.selected.ui-ncbimenu-item-no-hlt>a:hover,.oneLevel li.selected.ui-ncbimenu-item-skip a:hover,.ui-ncbibasicmenu>li.selected.ui-ncbimenu-item-skip>a:hover{color:inherit;background-color:#FCFCFC;}.orientation_hort>li{display:inline;float:left;} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_003.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +(function(){jQuery.widget("ui.ncbilocalnav",jQuery.ui.ncbimenu,{_create:function(){this.options.isSubMenuLimited=true;jQuery.ui.ncbimenu.prototype._create.apply(this,arguments)},_addClasses:function(){this.element.addClass("ui-ncbilocalnav");jQuery.ui.ncbimenu.prototype._addClasses.apply(this,arguments)},_destroyClasses:function(){this.element.removeClass("ui-ncbilocalnav");jQuery.ui.ncbimenu.prototype._destroyClasses.apply(this,arguments)}})})();
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_004.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +div.ui-ncbiautocomplete-holder{position:absolute;top:0;left:0;border:1px solid #5a5a5a;display:none;font-family:Arial,helvetica,sans-serif;font-size:inherit;border-style:solid;border-color:#777;border-width:1px;}ul.ui-ncbiautocomplete-options{height:218px;overflow:auto;overflow-x:hidden;overflow-y:auto;width:100%;margin:0;padding:0;list-style-type:none;font-weight:normal;cursor:pointer;background-color:#FFF;}ul.ui-ncbiautocomplete-options li span{font-weight:normal;}ul.ui-ncbiautocomplete-options li{padding:.2em;padding-left:.8em;padding:.231em .461em;white-space:nowrap;overflow:hidden;width:100%;color:#14376c;text-overflow:ellipsis;}ul.ui-ncbiautocomplete-options li:last-child{padding-bottom:.6em;}ul.ui-ncbiautocomplete-options li.ui-ncbiautocomplete-options-high{background-color:#DAEEF4;text-decoration:none;color:#015;}.ui-ncbiautocomplete-actions{background-color:#CECECE;line-height:inherit;padding:5px;border:1px solid #777;*zoom:1;*display:block;margin:1px -1px 0 -1px;min-height:15px;}.ui-ncbiautocomplete-actions:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-ncbiautocomplete-actions{display:inline-block;}.ui-ncbiautocomplete-actions a{display:inline;float:left;color:#015;text-decoration:none;}.ui-ncbiautocomplete-actions .ui-ncbiautocomplete-link-pref-right{text-align:right;float:right;}.ui-ncbiautocomplete-link-pref{text-indent:-9999px;background:url("../img/gear.png") no-repeat;width:15px;height:16px;}a.ui-ncbiautocomplete-link-off:hover,a.ui-ncbiautocomplete-link-pref:hover{text-decoration:underline;color:#015;}li.ui-ncbiautocomplete-show-more{width:100%!important;background:#C3D2DB!important;border-top:1px solid #5A5A5A;}li.ui-ncbiautocomplete-show-more.ui-ncbiautocomplete-options-high{text-decoration:underline!important;}iframe.ui-ncbiautocomplete-iframe{position:absolute;top:0;left:0;height:200px;z-index:1000;display:none;filter:alpha(opacity=1);}.shadow{-webkit-box-shadow:.4em .4em .5em rgba(153,153,153,.9);-moz-box-shadow:.4em .4em .5em rgba(153,153,153,.9);box-shadow:.4em .4em .5em rgba(153,153,153,.9);} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_004.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,53 @@ +jQuery.widget("ui.ncbiautocomplete",{options:{webserviceUrl:"/portal/utils/autocomp.fcgi",isUrlRelative:false,dictionary:"",responseFormat:"old",disableUrl:null,prefUrl:null,zIndex:1001,isEnabled:true,hasRelatedMatches:false,minLength:2,expandPauseTime:400,maxListLimit:null,isCrossDomain:false,disableCache:false,requireValidation:false,queryParameter:"q"},_create:function(){if(this.options.localData&&!this.options.dictionary)this.options.dictionary="local";this._storeTitleAttribute();this._createOptionsBox(); +this._addAttributes();this._setHandlers();this._setWebServicePath();this._lastEnteredTerm="";this._setSGData()},_storeTitleAttribute:function(){this.element.data("ncbiautocompleteOriginalTitle",this.element.attr("title"))},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);this.element.removeAttr("title");this._destroyAria();this._destroyHandlers();var a=this.element.data("ncbiautocompleteOriginalTitle");a&&this.element.attr("title",a)},_destroyOptionsBox:function(){jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox!= +null&&jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox.remove()},_destroyHandlers:function(){this.element.off("keypress keydown keyup cut paste")},_destroyAria:function(){this.element.removeAttr("aria-haspopup").removeAttr("aria-autocomplete").removeAttr("role").removeAttr("autocomplete")},_activeRequest:null,_keys:{up:38,down:40,enter:13,escape:27,tab:9,shift:16},_setSGData:function(){this.sgData={jsevent:"autocomplete",userTyped:"",hasScrolled:false,usedArrows:false,selectionAction:"",optionSelected:"", +optionIndex:-1,optionsCount:-1}},_addAttributes:function(){this.element.attr({title:"Use up and down arrows to choose an item from the autocomplete.","aria-haspopup":true,"aria-autocomplete":"list",role:"textbox"})},_setHandlers:function(){var a=this;jQuery(this.element).focus(function(){a._focused()}).keypress(function(c){a._keyPress(c,"press")}).keydown(function(c){a._keyPress(c,"down")}).keyup(function(c){a._keyUp(c)}).bind("cut paste",function(){a._changeFired()}).attr("AUTOCOMPLETE","OFF");var b= +jQuery(this.element)[0];b.autocomplete="off";b.AUTOCOMPLETE="OFF";jQuery(window).resize(function(){a._isActive&&a._positionOptionsBox()});jQuery(document).click(function(c){a._checkClickEvent(c)});jQuery(this._gol.optionsBox).hover(function(){if(a._isActive)a._isOptionsBoxFocused=true},function(){if(a._isActive)a._isOptionsBoxFocused=false})},_isOptionsBoxFocused:false,_createOptionsBox:function(){if(jQuery.ui.ncbiautocomplete._globalOptionsList===null){jQuery.ui.ncbiautocomplete._globalOptionsList= +{};var a=jQuery("div.grid");a=a.length===1?a:jQuery(document.body);jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox=jQuery("<div class='ui-ncbiautocomplete-holder shadow' aria-live='assertive'></div>").appendTo(a);jQuery.ui.ncbiautocomplete._globalOptionsList.optionsList=jQuery("<ul class='ui-ncbiautocomplete-options' role='listbox' aria-activedescendant=''></ul>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox));jQuery.ui.ncbiautocomplete._globalOptionsList.optionsActions= +jQuery("<div class='ui-ncbiautocomplete-actions shadow'></div>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox));jQuery.ui.ncbiautocomplete._globalOptionsList.prefLink=jQuery("<a href='#' class='ui-ncbiautocomplete-link-pref'>Preferences</a>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsActions));jQuery.ui.ncbiautocomplete._globalOptionsList.turnOffLink=jQuery("<a href='#' class='ui-ncbiautocomplete-link-off'>Turn off</a>").appendTo(jQuery(jQuery.ui.ncbiautocomplete._globalOptionsList.optionsActions)); +jQuery.ui.ncbiautocomplete._globalOptionsList.isIE6=jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<7;if(jQuery.ui.ncbiautocomplete._globalOptionsList.isIE6)jQuery.ui.ncbiautocomplete._globalOptionsList.optionsBox.iframe=jQuery("<iframe src='javascript:\"\";' class='ui-ncbiautocomplete-iframe' marginwidth='0' marginheight='0' align='bottom' scrolling='no' frameborder='0'></iframe>").appendTo(document.body)}this._gol=jQuery.ui.ncbiautocomplete._globalOptionsList},_positionOptionsBox:function(){if(this._gol.activeElement){var a= +jQuery(this.element),b=jQuery(this._gol.activeElement);a=a.attr("id")||a[0];b=b.attr("id")||b[0];a!==b&&this._hideOptions()}var c=this;if(this._gol.activeElement!==this.element){b=this.options.prefUrl!==null?"block":"none";a=this.options.disableUrl!==null?"block":"none";var e=b==="block"||a==="block"?"block":"none";jQuery(this._gol.prefLink).css("display",b).attr("href",this.options.prefUrl).unbind("click").click(function(){c._prefLinkClick()});jQuery(this._gol.turnOffLink).css("display",a).unbind("click").click(function(m){c.turnOff(); +m.preventDefault()});jQuery(this._gol.optionsActions).css("display",e);jQuery(this._gol.optionsActions).children(":nth-child(2)").addClass("ui-ncbiautocomplete-link-pref-right")}else this._gol.activeElement=this.element;e=this.element;var d=jQuery(this._gol.optionsBox),f=false;if(e.parent().hasClass("jig-ncbiclearbutton-wrap")){e=e.parent();f=true;d.addClass("ui-ncbiautocomplete-holder-clearfix")}else d.removeClass("ui-ncbiautocomplete-holder-clearfix");b=e.outerWidth();a=e.outerHeight();e=e.offset(); +var i,k,h;if(jQuery.browser.msie)h=k=i=0;else{i=parseInt(d.css("borderLeftWidth"),10);k=parseInt(d.css("borderRightWidth"),10);h=f?0:-1}d.css("top",e.top+a+(f?-1:-2)+"px").css("left",e.left+"px").width(b-i-k+h+"px");f=parseInt(this.options.zIndex,10);d.css("zIndex",f);d=jQuery(this._gol.optionsList);d[0].onscroll=function(){};d.scrollTop(0);d[0].onscroll=function(){c.sgData.hasScrolled=true};if(this._gol.isIE6){d=jQuery(this._gol.optionsBox.iframe);d.css("top",e.top+a+"px").css("left",e.left+"px").width(b- +i-k+h+"px");d.css("zIndex",f-1)}},_isActive:false,_focused:function(){this._gol.activeElement!==this.element&&this._hideOptions();this._setActivedescendant();this._positionOptionsBox();if(this.options.isEnabled){this._isActive=true;this._hasBeenEscaped=false}this.options.minLength===0&&this.options.localData&&this._keyUp({})},_lastEnteredTerm:null,_isCached:false,_hasBeenEscaped:false,_lastKeyPressDwnUpScroll:new Date,_lastFoundMatch:null,_findMatchInCache:function(a){this._lastFoundMatch=null;if(typeof this._localCache[this.options.dictionary]=== +"undefined")return false;var b="l"+(this.options.maxListLimit||"n");if(typeof this._localCache[this.options.dictionary][b]==="undefined")return false;for(var c=0;a.length>1||c<10;){a=a.substr(0,a.length-1);var e=this._localCache[this.options.dictionary][b][a];if(e)if(e.isCompleteList){this._lastFoundMatch=a;return true}else break;c++}return false},_cloneMatchObject:function(a){var b={};b.matchedText=a.matchedText.toString();b.matches=a.matches?a.matches.slice():[];b.isCompleteList=a.isCompleteList=== +true;return b},_timerTriggerEnterEvent:null,_clearTriggerEnterEvent:function(){this._timerTriggerEnterEvent=null},_triggerEnterEvent:function(){var a=this;if(!this._timerTriggerEnterEvent){this._timerTriggerEnterEvent=window.setTimeout(function(){a._clearTriggerEnterEvent()},50);this.element.trigger("ncbiautocompleteenter",this.sgData);this.element.trigger("ncbiautocompletechange",this.sgData);this._sgSend()}},_triggerTabEvent:function(){this.element.trigger("ncbiautocompletetab",this.sgData);this.element.trigger("ncbiautocompletechange", +this.sgData);this._sgSend()},_keyPress:function(a,b){var c=false,e=this;if(a.keyCode===this._keys.enter||a.keyCode===this._keys.tab){var d=a.keyCode===this._keys.enter,f=false;if(this._isActive&&this.isOptionsBoxOpen())if(this._currIndex===this.options.maxListLimit&&jQuery("li:eq("+this._currIndex+")",this._gol.optionsList).hasClass("ui-ncbiautocomplete-show-more")){this._hideOptions(true);this._gotoShowAll()}else if(this.sgData.optionSelected===jQuery(this.element).val()){f=d;if(!this._timerTriggerEnterEvent){this.sgData.selectionAction= +d?"enter":"tab";this.element.attr("valueId",this.element.attr("_optValue")||null);if(d)this._triggerEnterEvent();else{this._sentTab||this._triggerTabEvent();this._sentTab=true;window.setTimeout(function(){e._sentTab=false},10)}}this._hideOptions(true);if(d){a.stopPropagation();a.preventDefault();return false}}else a.keyCode===this._keys.tab&&this._hideOptions(true);else if(a.keyCode===this._keys.tab)if(!this._tabCalled){this._hideOptions(true);this._tabCalled=true;window.setTimeout(function(){e._tabCalled= +false},10)}if(d&&!f){this._hideOptions(true);this._triggerEnterEvent()}}else if(jQuery(this.element).val().length===0&&!this.options.localData)this._hideOptions(true);else if(a.keyCode===this._keys.up){c=true;this._scrollUpDownRateLimiter(-1)}else if(a.keyCode===this._keys.down&&!a.shiftKey){if(jQuery(this.element).val().length>=this.options.minLength&&!this.isOptionsBoxOpen()){this._reopenOptions=true;c=false;return}this._reopenOptions=false;c=true;this._scrollUpDownRateLimiter(1)}if(!this._lastKeyAction|| +b===this._lastKeyAction){this._lastKeyAction=b;this._prevWasArrow=this._usedArrow;this._usedArrow=c}},_scrollUpDownRateLimiter:function(a){if(!(new Date-this._lastKeyPressDwnUpScroll<90)){this._moveSelection(a);this._lastKeyPressDwnUpScroll=new Date}},_checkArrowSelection:function(a){if(this._prevWasArrow&&a.keyCode!==this._keys.down&&a.keyCode!==this._keys.up&&a.keyCode!==this._keys.tab&&a.keyCode!==this._keys.enter&&this._isActive&&this.isOptionsBoxOpen()){this.sgData.selectionAction="arrows";typeof ncbi!== +"undefined"&&ncbi.sg&&ncbi.sg.ping&&ncbi.sg.ping(this.sgData,false);this._usedArrow=this._prevWasArrow=false}},_keyUp:function(a){if(!(!this.options.isEnabled||this._hasBeenEscaped)){this._checkArrowSelection(a);var b=jQuery(this.element).val().toLowerCase().replace(/^\s+/,"").replace(/\s+$/," "),c="l"+(this.options.maxListLimit||"n");if(!((a.keyCode===this._keys.up||a.keyCode===this._keys.down||a.keyCode===this._keys.enter)&&!this._reopenOptions))if(a.keyCode===this._keys.tab&&this._isOptionsBoxFocused){this._isActive= +this._isOptionsBoxFocused=false;a.type!=="keyup"&&this._hideOptions(true)}else if(a.keyCode===this._keys.escape){this._isActive=this._isOptionsBoxFocused=false;this._hasBeenEscaped=true;this._hideOptions(true)}else if(!(this._lastEnteredTerm===b||a.keyCode===this._keys.shift))if(this._localCache[this.options.dictionary]&&this._localCache[this.options.dictionary][c]&&this._localCache[this.options.dictionary][c][b]){this._isActive=true;this._resetValueId(b);this._lastEnteredTerm=b;this._displayOptions(this._localCache[this.options.dictionary][c][b])}else if(this._isCached&& +this._findMatchInCache(b)){this._isActive=true;this._localCache[this.options.dictionary][c][b]=this._cloneMatchObject(this._localCache[this.options.dictionary][c][this._lastFoundMatch]);this._resetValueId(b);this._lastEnteredTerm=b;this._filteredCache(b)}else if(b.length>=this.options.minLength&&this.options.localData){if(!this._localCache||!this._localCache[this.options.dictionary]||!this._localCache[this.options.dictionary][c]||!this._localCache[this.options.dictionary][c]["*_*_local_*_*"])this._putInCache({matchedText:"*_*_local_*_*", 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false});jQuery(a).mouseleave(function(){e._removeHighlight("mouse");e._resetCurrentIndex()});this._resetCurrentIndex();c=jQuery("li",c);b=jQuery(this._gol.optionsBox).width(); +var l=jQuery.browser.msie&&!this._gol.isIE6||jQuery.browser.safari||jQuery.browser.opera;d=c.eq(0);parseFloat(d.css("padding-left"));k=d.html();d.html("<span>MMMMMMMMM.</span>");i=d.children("span:first").width()/10;d.html("<span>…<span>");d.children("span:first").width();d.html(k);var r=a.width(),y=Math.floor(b/i);c.each(function(){var j=jQuery(this);j.css("white-space","nowrap");var n=j.html();j.attr("fullText",n).attr("acValue",n.replace(/<\/?span>/gi,""));if(j.width()/j.attr("acValue").length< +9)if(l)j.attr("partialText",j.html()).attr("isIEExpand",true).css("width",r-28+"px");else{var t=n.toLowerCase().indexOf("<span>"),u=n.toLowerCase().indexOf("</span>"),z=function(g){var 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Date-this._lastKeyPressDwnUpScroll>100){this._resetCurrentIndex();this._currIndex=jQuery(a).prevAll("li").length;this._addHightlight(a)}},_addHightlight:function(a){this._removeHighlight();jQuery(a).addClass("ui-ncbiautocomplete-options-high");var b=this;this._expandTimer&&window.clearTimeout(this._expandTimer);this._expandTimer=window.setTimeout(function(){b._expandOption(a)},this.options.expandPauseTime)},_expandOption:function(a){if(jQuery(a).hasClass("ui-ncbiautocomplete-options-high")){a= +jQuery(a).attr("isExpanded",true);var b=a.attr("fullText");if(a.html()!==b||a.attr("isIEExpand")){a.html(b).css("text-overflow","").css("white-space","normal").css("-o-text-overflow","");this._scrollIntoView()}}},_collapseOption:function(a){a=jQuery(a);a.attr("isIEExpand")?a.css("text-overflow","ellipsis").css("white-space","nowrap").css("-o-text-overflow","ellipsis"):a.css("white-space","nowrap").html(a.attr("partialText"))},_optionClicked:function(a){a=jQuery(a);if(a.hasClass("ui-ncbiautocomplete-show-more"))this._gotoShowAll(); +else{var b=this._cleanUpSelectionText(a);a=a.attr("valueId")||null;this.sgData.optionSelected=b;this.sgData.optionIndex=this._currIndex;this.sgData.valueId=a;this.sgData.selectionAction="click";this._sgSend();b=jQuery(this.element).val(b);b.attr("valueid",a);b.trigger("ncbiautocompleteoptionclick",this.sgData);b.trigger("ncbiautocompletechange",this.sgData)}this._isOptionsBoxFocused=false;this._hideOptions()},isOptionsBoxOpen:function(){return jQuery(this._gol.optionsBox).css("display")==="block"}, +_hideOptions:function(a){this._gol.activeElement=null;if(!(this._isOptionsBoxFocused&&!a)){var b=jQuery(this._gol.optionsBox);a&&jQuery(this._gol.optionsBox).css("display","none");b.attr("aria-activedescendant")===this.element.attr("id")&&b.attr("aria-activedescendant","");this._gol.isIE6&&jQuery(this._gol.optionsBox.iframe).css("display","none");this._resetCurrentIndex();this._isActive=false;this._lastEnteredTerm=null;b=jQuery(this._gol.optionsBox);var c=jQuery(this._gol.optionsList);b.css("display", +"none");c.html("");this._lastTextInTextbox=b=this.element.val();if(this.options.requireValidation&&b.length>0&&this.options.isEnabled&&(!this.element.is(":focus")||a))this._trigger((b.length<this.options.minLength?false:this.isInDictionary(b))?"validselection":"invalidselection")}},_setTextCursorToEnd:function(a){var b=this.element;jQuery(b).val(a);if(b.createTextRange){a=b.createTextRange();a.moveStart("character",b.value.length);a.collapse();a.select()}},_resetCurrentIndex:function(){this._currIndex= +-1},_cleanUpSelectionText:function(a){return jQuery.trim(a.attr("acValue")).replace(/&/gi,"&").replace(/\\"/g,'"')},_currIndex:-1,_moveSelection:function(a){if(this._isActive){this.sgData.usedArrows=true;var b=jQuery("li",this._gol.optionsList).length;this._currIndex+=a;this._removeHighlight();a=this._lastEnteredTerm;var c="";if(!(a===null||a.length<this.options.minLength)){if(this._currIndex<0||this._currIndex>=b)this._currIndex=this._currIndex===-2?b-1:-1;if(this._currIndex!==-1){b=jQuery("li:eq("+ +this._currIndex+")",this._gol.optionsList);this._addHightlight(b);if(this._currIndex===this.options.maxListLimit){this.sgData.optionSelected="";this.sgData.valueId=""}else{a=this._cleanUpSelectionText(b);c=b.attr("valueId")||null;this.sgData.optionSelected=a;this.sgData.valueId=c}}else{this.sgData.optionSelected="";this.sgData.valueId=""}this.element.attr("_optValue",c);this.element.attr("valueId",c);this._setTextCursorToEnd(a);this._scrollIntoView();this.sgData.optionIndex=this._currIndex}}},_scrollIntoView:function(){var a= +jQuery("li:eq("+this._currIndex+")",this._gol.optionsList);if(a.length!==0){var b=jQuery(this._gol.optionsList),c=b.height(),e=b.scrollTop(),d=a[0].offsetTop;a=a.height();if(d-c+a>e){e=jQuery("li:eq("+(this._currIndex+1)+")",this._gol.optionsList);b.scrollTop((e.length===1?e[0].offsetTop:d+a+10)-c)}else d<e&&b.scrollTop(d)}},enableAutocomnplete:function(){this.options.isEnabled=true},disableAutocomnplete:function(){this.disableAutocomplete()},disableAutocomplete:function(){this._isOptionsBoxFocused= +this.options.isEnabled=false;this._hideOptions()},turnOff:function(a){this.disableAutocomplete();var b=this.element.data("ncbiautocompleteOriginalTitle");b&&this.element.attr("title",b);if(!a){typeof ncbi!=="undefined"&&ncbi.sg&&ncbi.sg.ping&&ncbi.sg.ping(this.element[0],"autocompleteoffclick","dictionary="+this.options.dictionary);this.element.trigger("ncbiautocompletedisableclicked");a=this.options.disableUrl;if(a!==null&&a.length>0){b=jQuery.ui.jig._getFncFromStr(a);typeof b==="function"?b():jQuery.get(a)}}}, +_prefLinkClick:function(){typeof ncbi!=="undefined"&&ncbi.sg&&ncbi.sg.ping&&ncbi.sg.ping(this.element[0],"autocompleteprefclick","dictionary="+this.options.dictionary)},_checkClickEvent:function(a){if(this._isActive)if(jQuery(this.element)[0]!=a.target){this._isActive=this._isOptionsBoxFocused=false;this._hideOptions()}},_sgSend:function(){typeof ncbi!=="undefined"&&typeof ncbi.sg!=="undefined"&&typeof ncbi.sg.ping!=="undefined"&&ncbi.sg.ping(this.sgData,false)},getSgData:function(){return this.sgData}, +_gotoShowAll:function(){var a=jQuery(this.element),b=a.val();a.trigger("ncbiautocompleteshowall",{value:b,dictionary:this.options.dictionary})},_hideOptionsIfOffPage:function(){if(this.options.maxListLimit){var a=this,b=jQuery(".ui-ncbiautocomplete-options li"),c=b.eq(0).outerHeight()||20,e=jQuery(this._gol.optionsBox),d=jQuery(window).height(),f=e.position().top,i=f+e.outerHeight()-(document.body.scrollTop||document.documentElement.scrollTop||window.pageYOffset||0);if(b.last().hasClass("ui-ncbiautocomplete-show-more")){var k= +f+"-"+d+"-"+i;if(!this.choppedDetails)this.choppedDetails={};var h=this.choppedDetails[k],m=0,q=function(){i=f+e.outerHeight()-(document.body.scrollTop||document.documentElement.scrollTop||window.pageYOffset||0);if(i>d){b=jQuery(".ui-ncbiautocomplete-options li");var r=b.length-2;if(r>=0){b.eq(r).remove();sz=c*(b.length-1);b.closest(".ui-ncbiautocomplete-holder").height(sz).css("min-height",sz+"px");b.closest(".ui-ncbiautocomplete-options").height(sz).css("overflow-y","hidden");m++;q()}}else a.choppedDetails[k].count= +m};if(h){var l=h.count;if(l>0){h=2*h.length-l-b.length-2;b.filter(":lt("+(b.length-1)+")").filter(":gt("+h+")").remove();b=jQuery(".ui-ncbiautocomplete-options li");sz=c*b.length;b.closest(".ui-ncbiautocomplete-holder").height(sz).css("min-height",sz+"px");b.closest(".ui-ncbiautocomplete-options").height(sz).css("overflow-y","hidden")}m=l}else this.choppedDetails[k]={count:0,length:b.length};q()}else{l=Math.floor((d-f)/c)*c;h=b.length*c;if(l>h)l=h;b.closest(".ui-ncbiautocomplete-holder").height(l).css("min-height", +l+"px");b.closest(".ui-ncbiautocomplete-options").height(l).css("overflow-y","auto")}}},isValid:function(){return this.isInDictionary(this.element.val())},isInDictionary:function(a){var b=false;if(a&&a.length>=this.options.minLength&&this.options.dictionary&&this.options.dictionary.length>0&&this.options.isEnabled){var c=false,e="l"+(this.options.maxListLimit||"n"),d=a.toLowerCase();if(this._localCache[this.options.dictionary]&&this._localCache[this.options.dictionary][e]){e=this._localCache[this.options.dictionary][e]; +c=true;if(e[d])b=this._isValidCheck(d,e[d].matches);else for(var f in e)if(b=this._isValidCheck(d,e[f].matches))break}if(!b&&!c)b=this._validSeverCall(a)}return b},_isValidCheck:function(a,b){var c=false;if(b){c=jQuery.inArray(a.toLowerCase(),b)>-1;if(!c){var e=new RegExp("(^|@)("+a.toLowerCase()+")(@|$)","i");jQuery.each(b,function(d,f){if(f.match(e)){c=true;return false}})}}return c},_customFormat:function(a){if(typeof this.options.responseProcessor==="string")this.options.responseProcessor=jQuery.ui.jig._getFncFromStr(this.options.responseProcessor); +this._displayOptions({matchedText:this._lastEnteredTerm,matches:this.options.responseProcessor.call(this,a),isCompleteList:0})}});jQuery.ui.ncbiautocomplete._globalOptionsList=null;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_005.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +a.ui-ncbitoggler{color:#22c;}a.ui-ncbitoggler,a.ui-ncbitoggler-open{padding-left:16px;position:relative;display:block;}a.ui-ncbitoggler-no-icon{padding-left:0;}a.ui-ncbitoggler span.ui-icon-plus-minus-big,a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open{background-color:transparent;background-image:url(../img/ncbitoggler-plus-minus-big.gif);background-repeat:no-repeat;top:.2em;margin-left:-0.1em;}a.ui-ncbitoggler span.ui-icon-plus-minus-big{background-position:left -30px;}a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open{background-position:left 0;}.ui-ncbitoggler-slave,.ui-ncbitoggler-slave-open{margin:.2em 0 0 16px;}.ui-ncbitoggler-slave{display:none;}.ui-ncbitoggler-slave-open{display:block;}a.ui-ncbitoggler span.ui-icon,a.ui-ncbitoggler-open span.ui-icon{display:inline;position:absolute;left:0;_left:-1em;}a.ui-ncbitoggler-disabled{outline:none;}a.ui-ncbitoggler-disabled:active{outline:none;color:#551A8B;} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_005.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,2 @@ +(function(){var d=jQuery.ui.button.prototype._create;jQuery.ui.button.prototype.options.color="ui-ncbibutton-gray";jQuery.ui.button.validColors=["ui-ncbibutton-gray","ui-ncbibutton-copper","ui-ncbibutton-blue"];jQuery.ui.button.classColors=["jig-ncbibutton-gray","jig-ncbibutton-copper","jig-ncbibutton-blue"];var e=function(){d.apply(this,arguments);this._addClasses()};jQuery.widget("ui.ncbibutton",jQuery.ui.button,{_create:function(){e.apply(this,arguments)},_getColor:function(){for(var a=this.options.color, +f=this.element[0].className,c=jQuery.ui.button.classColors,b=0;b<c.length;b++)if(f.indexOf(c[b])!==-1){a=jQuery.ui.button.validColors[b];break}if(a.indexOf("ui-ncbibutton-")!==0)a="ui-ncbibutton-"+a;if(jQuery.inArray(a,jQuery.ui.button.validColors)===-1){typeof console!=="undefined"&&console.warn&&console.warn("The color you picked: "+this.options.color+" is not a valid color choice.\n Valid colors: "+jQuery.ui.button.validColors.join(", "));a=jQuery.ui.button.validColors[0]}return a},_addClasses:function(){this.buttonElement.addClass("ui-ncbibutton").addClass(this._getColor()).removeClass("ui-button ui-widget")}})})();
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_006.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +.ui-ncbipopper-wrapper{position:fixed;top:0;left:0;z-index:11;display:none;}.ui-ncbipopper-wrapper-relative-parent{position:fixed!important;}.ui-ncbipopper-basic{border:3px solid #3e72a6;background-color:#fff;color:#303030;padding:1em;text-align:left;-moz-border-radius:6px;-webkit-border-radius:6px;border-radius:6px;}button.ui-ncbipopper-close-button-generated{display:block;float:right;margin:-1.25em -1.3em 0 0;font-size:small;width:1.7em;text-align:center;padding:0;border:0;}button.ui-ncbipopper-close-button-generated,button.ui-ncbipopper-close-button-generated:active{margin:-0.615em;height:14px;width:13px;background-image:url(../img/ui-popper-closebutton.png);background-color:transparent;background-repeat:no-repeat;}button.ui-ncbipopper-close-button-generated .ui-button-text{color:transparent;text-shadow:none;}div.ui-ncbipopper-arrow-image{position:absolute;top:100px;left:100px;width:7px;height:7px;z-index:11;display:none;background-image:url(../img/ncbipopper-arrow.png);background-repeat:no-repeat;}div.ui-ncbipopper-arrow-left{background-position:center left;height:28px;}div.ui-ncbipopper-arrow-right{background-position:center right;height:28px;}div.ui-ncbipopper-arrow-top{background-position:top center;width:28px;}div.ui-ncbipopper-arrow-bottom{background-position:bottom center;width:28px;}.brieflinkpopdesc{font-size:.846em;margin-top:.4em;}.portlet .brieflinkpop{width:350px;}.portlet .brieflinkpop a{font-size:1em;}.portlet .brieflinkpopperctrl{display:inline-block;} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_006.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,75 @@ +jQuery.widget("ui.ncbigrid",{options:{isScrollable:false,height:"10em",hortScrollbarEnabled:false,width:null,isPageable:false,currentPage:1,isPageToolbarHideable:true,pageSize:10,isSortable:false,columnTypes:[],sortFunctions:[],isPresorted:false,sortColumn:-1,sortColumnDir:1,sortRowIndex:0,titleAscending:"sort ascending",titleDescending:"sort descending",ariaLabelAscending:"activate to sort column ascending",ariaLabelDescending:"activate to sort column descending",regExp:false,checkboxToolbarEnabled:false, +filterToolbarEnabled:false,filterToolbarIsCaseInsensitive:null,filterToolbarColumnIndex:null,filterToolbarIsInverse:null,isLoadingMessageShown:true,loadingText:"Loading",collapseRowsEnabled:false,addCommas:false},_init:function(){},_create:function(){this._isStartPageOne=this.options.currentPage===1;this._wrapTable();this._addBasicStyles();this._checkIfCSSIsScrollable();this._attachLoadingMessageListener();if(this.options.isScrollable||this.options.isSortable||this.options.isPageable||this.options.checkboxToolbarEnabled|| +this.options.filterToolbarEnabled)this._addAriaRolesAndStates();this._addRowClickWatcher();this.options.isScrollable&&this._createScrollable();if(this.options.isPageable||this.options.isPagable){this.options.isPageable=true;this._createPageGrid()}if(this.options.isSortable){this._createSortGrid();this.updateAriaTH()}else this._enableCollapseTbodyRows();this.options.checkboxToolbarEnabled&&this._createCheckboxSelectors();this.options.filterToolbarEnabled&&this._createFilterBarControl();this._addRowHoverEvent(); +this._addContentsAdjustmentEvent();this._adjustContents()},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);this.options.isScrollable&&this._destroyScrollable();if(this.options.isPageable||this.options.isPagable)this._destroyPageGrid();this._destroyRowHoverEvent()},_addBasicStyles:function(){this.element.addClass("ui-ncbigrid").attr("cellpadding","0").attr("cellspacing","0")},_checkIfCSSIsScrollable:function(){if(this.element.hasClass("jig-ncbigrid-scroll"))this.options.isScrollable= +true},_wrapTable:function(){var a=this.element.parent().parent();if(!a.hasClass("ui-ncbigrid-outer-div")){this.element.wrap('<div class="ui-ncbigrid-outer-div"><div class="ui-ncbigrid-inner-div"></div></div>');a=this.element.parent().parent()}this.element.find("caption").length>0&&a.addClass("caption-exists");var b=this.options.width;b&&a.css("width",b)},_addRowHoverEvent:function(){jQuery(this.element).on("mouseenter","tbody > tr",function(){var a=jQuery(this);a.hasClass("ignoreHoverHighlight")|| +a.addClass("ui-ncbigrid-row-hover")}).on("mouseleave","tbody > tr",function(){jQuery(this).removeClass("ui-ncbigrid-row-hover")})},_destroyRowHoverEvent:function(){jQuery(this.element).off("mouseenter mouseleave","tr")},_addContentsAdjustmentEvent:function(){var a=this;this.element.on("ncbigridupdated",function(){a._adjustContents()})},_getNumCommaIndices:function(){var a=this.options.columnTypes;if(!a)return[];for(var b=[],c=0;c<a.length;c++)if(a[c]=="numComma"||a[c]=="numberComma")b.push(c);return b}, +_getCommaSeparatedValue:function(a){var b=parseInt(a);if(isNaN(b))return a;else{a=a.split(".");b=a[0].replace(/(\d)(?=(\d\d\d)+(?!\d))/g,"$1,");return a[1]?b+"."+a[1]:b}},_adjustContentsForCommas:function(){var a=this._getNumCommaIndices();if(a.length){var b=this;jQuery(this.element).find("tbody td").each(function(){var c=jQuery(this),d=c.parent().find("td").index(c);jQuery.inArray(d,a)!=-1&&c.html(b._getCommaSeparatedValue(c.html()))})}},_adjustContents:function(){this.options.addCommas&&this._adjustContentsForCommas()}, +_addAriaRolesAndStates:function(){var a=this.element;a.attr("id")||a.attr("id",jQuery.ui.jig._generateId(this.widgetName));a.parent().parent().attr("role","grid").attr("tabindex","0");a.children("thead").children("tr").attr("role","row").children("th").attr({"aria-controls":a.attr("id"),role:"columnheader",tabindex:"0"});a.children("tbody").attr({role:"alert","aria-live":"polite","aria-relevant":"text"})},updateAriaTH:function(){if(this.options.isSortable){var a=this;this.element.parent().parent().find("div, table").attr("tabindex", +"0").end().find("thead").find("th").each(function(b,c){b="";var d=a.options.ariaLabelAscending;if(jQuery(c).is(".sortDsc")){b="descending";d=a.options.ariaLabelAscending}else if(jQuery(c).is(".sortAsc")){b="ascending";d=a.options.ariaLabelDescending}c=jQuery(c).children("a");jQuery(c).attr("aria-label",jQuery(c).text()+": "+d);b==""?jQuery(c).removeAttr("aria-sort"):jQuery(c).attr("aria-sort",b)})}},_createScrollable:function(){this._storeRefs();this._addScrollClasses();this._copyCaptionHeader(); +this._setWidthHeight();this._setWidths();this._registerScrollableListeners()},_destroyScrollable:function(){this._removeScrollClasses();if(this.parts){this.parts.scrollWrapper.removeClass("ui-ncbigrid-scroll");this.parts.headerWrapper.remove();for(var a in this.parts)this.parts[a]=null;this.parts=null}this._windowResize&&jQuery(window).unbind("resize",this._windowResize)},_storeRefs:function(){var a=this.element;this.parts={table:a,ths:a.find("> thead th")}},_addScrollClasses:function(){var a=this.element, +b=a.parent().addClass("ui-ncbigrid-scroll");this.parts.scrollWrapper=b;if(jQuery.browser.webkit){var c=navigator.userAgent;c.indexOf("AppleWebKit")>0&&c.indexOf("Chrome")==-1&&a.addClass("safari")}this.options.hortScrollbarEnabled&&b.addClass("ui-ncbigrid-hort-scroll")},_removeScrollClasses:function(){this.element.removeClass("ui-ncbigrid").removeClass("safari").parent().removeClass("ui-ncbigrid-scroll")},_copyCaptionHeader:function(){var a=this.element,b=a.parent();b.parent();var c=a.find("caption").clone(); +a=a.find("> thead").clone();c=jQuery("<div class='ui-ncbigrid-header-wrapper'></div>").append("<table cellpadding='0' cellspacing='0' class='ui-ncbigrid ui-ncbigrid-header'></table>").find("table").append(c).append(a).end();c.insertBefore(b);b=c.find("caption");b.wrapInner("<div></div>");this.parts.captionDiv=b.find("div");this.parts.headerWrapper=c;this.parts.headerThs=c.find("thead th")},_setWidthHeight:function(){this.options.height!==null&&this.parts.scrollWrapper.height(this.options.height)}, +_setWidths:function(){function a(j){jQuery(this).width(h[j])}var b=this.parts,c=b.table,d=b.ths,e=b.scrollWrapper,g=b.headerWrapper;b=b.headerThs;var f=jQuery.browser.msie;if(!this.options.hortScrollbarEnabled&&c.data("isMinSet")!==true&&this.element.is(":visible")){var i=c.outerWidth();if(c.width()>e.width()){e.css("min-width",i+16);c.data("isMinSet",true)}}var h=[];d.each(function(){var j=0;if(jQuery(this).is(":visible"))j=jQuery(this).width()+0;h.push(j)});d=c.height()>e.height()?16:0;f=this.options.isSortable&& +f&&parseInt(jQuery.browser.version,10)<8?d:0;c.parent().parent().find("table.ui-ncbigrid-header").width(c.width()+2-f);c=e.width()-d;g.width(c);this.parts.captionDiv&&this.parts.captionDiv.width(c);b.each(a)},_handleScroll:function(a,b,c){function d(){g._handleScroll(a,b,true)}var e=a.scrollLeft;b.scrollLeft=e;this.parts.captionDiv&&this.parts.captionDiv.css("margin-left",e+"px");var g=this;if(!c){window.setTimeout(d,1);window.setTimeout(d,5)}},_registerScrollableListeners:function(){var a=this;this._windowResize= +function(){a._setWidths()};jQuery(window).resize(this._windowResize);var b=this.element.parent().parent().find(".ui-ncbigrid-header-wrapper")[0];this.element.parent().scroll(function(){a._handleScroll(this,b)});this.element.bind("ncbigridupdated",function(){a._setWidths()});this.element.bind("resetScroll",function(){a._resetScrollToTop()})},_resetScrollToTop:function(){this.parts.scrollWrapper.scrollTop(0)},_createPageGrid:function(){this._createPageBars();this._addPagingEvents();this._gotoPage(this.options.currentPage)}, +_destroyPageGrid:function(){if(this._pageBars){this._removePagingEvents();this._removePageBars()}},_pagingControlsHTML:' <div class="ui-ncbigrid-paged-toolbar"> <div class="ui-ncbigrid-paged-countItems">Items <span class="ui-ncbigrid-paged-startRow">1</span> - <span class="ui-ncbigrid-paged-endRow">10</span> of <span class="ui-ncbigrid-paged-totalRows">10</span></div> <div class="ui-ncbigrid-paged-pageControl pagination"> <a href="#" class="ui-ncbigrid-paged-pageControl-first page_link" title="Goto First Page"><< First</a> <span class="ui-ncbigrid-paged-pageControl-first page_link" title="Inactive Goto First Page"><< First</span> <a href="#" class="ui-ncbigrid-paged-pageControl-previous page_link prev" title="Goto Previous Page">< Prev</a> <span class="ui-ncbigrid-paged-pageControl-previous page_link prev" title="Inactive Goto Previous Page">< Prev</span> <label>Page</label> <input type="text" value="1" size="2" title="current page number"/> of <span class="ui-ncbigrid-paged-endPage">2</span> <a href="#" class="ui-ncbigrid-paged-pageControl-next next page_link" title="Goto Next Page">Next ></a> <span class="ui-ncbigrid-paged-pageControl-next next page_link" title="Inactive Goto Next Page">Next ></span> <a href="#" class="ui-ncbigrid-paged-pageControl-last page_link" title="Goto Last Page">Last >></a> <span class="ui-ncbigrid-paged-pageControl-last page_link" title="Inactive Goto Last Page">Last >></span> </div> </div>', +_createPageBars:function(){this._pageToolBar_top=jQuery(this._pagingControlsHTML).addClass("ui-ncbigrid-paged-toolbar-top");this._pageToolBar_bottom=jQuery(this._pagingControlsHTML).addClass("ui-ncbigrid-paged-toolbar-bottom");var a=this.element,b=a.parent().parent();b.prepend(this._pageToolBar_top);b.append(this._pageToolBar_bottom);b.children(".ui-ncbigrid-paged-toolbar-top").children(".ui-ncbigrid-paged-countItems").attr("id",jQuery.ui.jig._generateId("ui-ncbigrid-paged-countItems"));a.attr("aria-describedby", +this._pageToolBar_top.children(".ui-ncbigrid-paged-countItems").attr("id"));this._pageBars=this._pageToolBar_top.add(this._pageToolBar_bottom);this._pageBars.find(":input").each(function(c,d){jQuery(d).attr("id",jQuery.ui.jig._generateId("ui-ncbigrid-paged-current-page")).prev().attr("for",jQuery(d).attr("id"))})},_removePageBars:function(){this._pageToolBar_top.remove();this._pageToolBar_top=null;this._pageToolBar_bottom.remove();this._pageBars=this._pageToolBar_bottom=null;this.element.removeAttr("aria-describedby")}, +_addPagingEvents:function(){var a=this,b=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-first"),c=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-previous"),d=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-next"),e=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-last"),g=this._pageBars.find("input");b.click(function(f){a.gotoFirstPage();f.preventDefault()});c.click(function(f){a.gotoPrevPage();f.preventDefault()});d.click(function(f){a.gotoNextPage();f.preventDefault()});e.click(function(f){a.gotoLastPage(); +f.preventDefault()});g.keypress(function(f){if(f.keyCode===13){a.gotoPage(this.value.replace(/,/g,""));f.preventDefault()}})},_removePagingEvents:function(){this._pageBars.find("a").unbind("click").end().find("input").unbind("keypress")},_showHidePageToolbar:function(){if(this._pageBars)if(this.options.isPageToolbarHideable)parseInt(this.getRowCount())<=parseInt(this.options.pageSize)?this._pageBars.hide():this._pageBars.show()},_setPage:function(){this.element.trigger("resetScroll");this.element.trigger("pagechanged"); +var a=this._getCurrentPage(),b=this.getMaxPage();this._showHidePageToolbar();this._updateRows(a,b);this._updateButtons(a,b);this._updatePagingText(a,b);this._updateGoto(a,b);this._updateItemRange(a,b);this._pageBars.find(".ui-ncbigrid-paged-pageControl").attr({"aria-valuemin":"1","aria-controls":this.element.attr("id"),"aria-valuemax":b,"aria-valuenow":a});this._notifyGridUpdated()},_updateRows:function(a){var b=this.options.pageSize,c=this.getRowCount();a=(a-1)*b;var d=a+b;b=this.element.find("> tbody > tr:not(.ncbigrid-row-filtered)"); +var e=this.element.find("> tbody").length>1,g=0;if(e&&a>0)g=b.filter(":lt("+a+")").filter(":has(th)").length;var f="";if(d<c)f+=":lt("+(d+g)+")";if(a>0)f+=":gt("+(a-1+g)+")";c=b;if(f.length>0){b.not(".ui-ncbigrid-rowHidden").addClass("ui-ncbigrid-rowHidden");c=b.filter(f)}c.removeClass("ui-ncbigrid-rowHidden");if(e){a=c.filter(":has(th)").length;if(a>0){b=0;for(c=c.last().next();b<a&&c.length===1;){if(!c.hasClass("ncbigrid-row-filtered")){c.has("th")||b++;c.removeClass("ui-ncbigrid-rowHidden")}c= +c.next()}}}this._notifyGridUpdated()},_updateButtons:function(a,b){var c=b===2,d=a===1,e=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-previous,a.ui-ncbigrid-paged-pageControl-first").css("display",d?"none":"inline").filter("a.ui-ncbigrid-paged-pageControl-first");d=this._pageBars.find("span.ui-ncbigrid-paged-pageControl-previous,span.ui-ncbigrid-paged-pageControl-first").css("display",d?"inline":"none").filter("span.ui-ncbigrid-paged-pageControl-first");b=a===b||b==0;a=this._pageBars.find("a.ui-ncbigrid-paged-pageControl-next,a.ui-ncbigrid-paged-pageControl-last").css("display", +b?"none":"inline").filter("a.ui-ncbigrid-paged-pageControl-last");b=this._pageBars.find("span.ui-ncbigrid-paged-pageControl-next,span.ui-ncbigrid-paged-pageControl-last").css("display",b?"inline":"none").filter("span.ui-ncbigrid-paged-pageControl-last");c&&e.add(d).add(a).add(b).css("display","none")},_updatePagingText:function(a,b){if(b<1)b=1;if(this.options.addCommas)b=this._getCommaSeparatedValue(""+b);this._pageBars.find("div.ui-ncbigrid-paged-pageControl").find("span.ui-ncbigrid-paged-endPage").html(b)}, +_updateGoto:function(a){if(this.options.addCommas)a=this._getCommaSeparatedValue(""+a);this._pageBars.find("input").val(a)},_updateItemRange:function(a){var b=parseInt(this.options.pageSize,10),c=this.getRowCount();a=(a-1)*b+1;b=a+b-1;if(b>c)b=c;if(c==0)a=0;if(this.options.addCommas){c=this._getCommaSeparatedValue(""+c);a=this._getCommaSeparatedValue(""+a);b=this._getCommaSeparatedValue(""+b)}var d=this._pageBars.find("div.ui-ncbigrid-paged-countItems");d.find("span.ui-ncbigrid-paged-startRow").html(a); +d.find("span.ui-ncbigrid-paged-endRow").html(b);d.find("span.ui-ncbigrid-paged-totalRows").html(c)},_getCurrentPage:function(){return this.options.currentPage},getCurrentPage:function(){return this._getCurrentPage()},getMaxPage:function(){return Math.ceil(this.getRowCount()/this.options.pageSize)},getRowCount:function(){return jQuery(this.element).find("> tbody > tr:not(.ncbigrid-row-filtered):not(:has(> th))").length},getHeaderRowCount:function(){return jQuery(this.element).find("tbody > tr:has(th)").length}, +gotoFirstPage:function(){this._gotoPage(1)},gotoLastPage:function(){this._gotoPage(this.getMaxPage())},gotoNextPage:function(){this._gotoPage(this._getCurrentPage()+1)},gotoPrevPage:function(){this._gotoPage(this._getCurrentPage()-1)},gotoPage:function(a){this._gotoPage(parseInt(a,10))},_gotoPage:function(a){if(isNaN(a)||a<1)a=1;else if(a>this.getMaxPage()){a=this.getMaxPage();if(a<1)a=1}this.options.currentPage=a;this._pagingSelectAllQuestions&&this._pagingSelectAllQuestions.hide();this._setPage()}, +_createSortGrid:function(){var a=this.options.sortColumn;if(this.options.sortColumn!==-1){a=a-1;this.options.sortColumn=a!==-1?a:0}this._indexGrid();this._addSortEvents();this._setSortHeaders();this._checkInitialState();this._notifyGridUpdated()},_destroySortGrid:function(){},reindex:function(){for(var a=0;a<this.element.find("tbody tr:eq(0) td").length;a++)this.element.data("sort_order_col_"+a,null);this.element.data("rows",null);this._indexGrid()},_indexGrid:function(){var a=this,b=this.element.find("> tbody"); +if(b.length===0)this._isIndexed=false;else for(var c=0;c<b.length;c++)(function(d,e){function g(){for(var o=0;o<50&&k<m;o++){var p=l[k],q=a.getRowValues_DOM(p);if(q.length==0){a._enableCollapseTbodyRows(p);i.push(p);j++}else{q.unshift(k-j,p);f.push(q);h.push(q)}k++}if(k<m)window.setTimeout(g,0);else{a.element.data("tbody"+e+"-rows",h);a.element.data("tbody"+e+"-header",i);a._presort(f,e)}}var f=[],i=[],h=[],j=0,l=jQuery(d).find("> tr"),k=0,m=l.length;if(m===0)a._isIndexed=false;else{a._isIndexed= +true;g()}})(b[c],c)},_presort:function(a,b){function c(h){var j=g.options.sortFunctions[h-2];j||(j=g.element.find("> thead th:eq("+(h-2)+")").data("sortfunc"));if(j)if(typeof j==="function")return j;else if(j.indexOf("fnc:")===0){j=j.substr(4,j.length).split(".");for(var l=window[j[0]],k=1;k<j.length;k++)l=l[j[k]];return g.options.sortFunctions[h]=l}return null}function d(h,j,l){function k(n){if(n.length<2)return n;var r=parseInt(n.length/2),s=n.slice(0,r);n=n.slice(r,n.length);return m(k(s),k(n))} +function m(n,r){for(var s=[];n.length&&r.length;){var u=false;(u=o?-g.options.sortColumnDir==o.call(g,{data:n[0][j],row:jQuery(n[0][1])},{data:r[0][j],row:jQuery(r[0][1])}):n[0][j]<=r[0][j])?s.push(n.shift()):s.push(r.shift())}for(;n.length;)s.push(n.shift());for(;r.length;)s.push(r.shift());return s}var o=c(j),p=jQuery.browser.msie?100:1E3,q=0,t=[];(function(){for(var n=0;n<p&&q<h.length;n++){t.push(h[q]);q++}q<h.length?setTimeout(arguments.callee,0):l(k(t),j)})()}function e(h,j){var l=0,k=[];(function(){for(var m= +0;m<50&&l<h.length;m++){k.push(h[l][0]);l++}l<h.length?setTimeout(arguments.callee,0):g.element.data("tbody"+b+"-sort_order_col_"+(j-2),k)})()}for(var g=this,f=a[0].length,i=2;i<f;i++)this._getColumnType(i-2)!=="none"&&d(a,i,e)},_getColumnType:function(a){var b=this.options.columnTypes[a];b||(b=this.element.find("> thead th:eq("+a+")").data("columntype"));return b||"str"},getColumnType:function(a){return this._getColumnType(a-1)},getRowValues:function(a){if(typeof a==="number")a=this.element.find("tbody tr:eq("+ +a+")");var b=[];a=a[0].getElementsByTagName("td");for(var c=a.length,d=0;d<c;d++)b.push(this._getCellValueHelper(a[d].innerHTML,d));return b},getRowValues_DOM:function(a){var b=[];a=jQuery(a).children("td");for(var c=a.length,d=0;d<c;d++)b.push(this._getCellValueHelper(a[d].textContent||a[d].innerText||"",d));return b},_getCellValue:function(a,b){return this._getCellValueHelper(a.html(),b)},_getCellValueHelper:function(a,b){var c=this._getColumnType(b);switch(c){case "num":case "number":case "float":return a!== +undefined&&a.length>0?parseFloat(a):Number.POSITIVE_INFINITY;case "int":return a!==undefined&&a.length>0?parseInt(a,10):Number.POSITIVE_INFINITY;case "numberComma":case "numComma":a=(a||"").replace(/[, ]/g,"");return a.length>0?parseFloat(a):Number.POSITIVE_INFINITY;case "date":return new Date(a);case "str-insensitive":return a.toLowerCase();case "str":default:if(typeof c==="function")return c(a);else if(c.indexOf("fnc:")===0){c=c.substr(4,c.length).split(".");for(var 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tr:"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h);h="ui-ncbigrid-high";if(e)h=i.hasClass("ui-ncbigrid-row-even")?"ui-ncbigrid-row-even-high-IE6":"ui-ncbigrid-row-odd-high-IE6";i.addClass(h);g.push(i)});this.element.trigger("ncbigridhighlightapplied",[a,b,c,g]).trigger("ncbigridhideloadingbar");return{highlightedRows:g}}},removeHighlightRows:function(a,b,c,d){var e=jQuery.browser.msie&&parseFloat(jQuery.browser.version)< +7;if(typeof a!="undefined"&&a.length>0){var g=[],f=b?"-insensitive":"";d=d?"not-":"";if(a.constructor&&a.constructor.toString().indexOf("RegExp")>0){f="-regexp";d=""}typeof c!="undefined"?jQuery("tbody tr td"+(":nth-child("+c+")")+":"+d+"contains"+f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).parent().removeClass("ui-ncbigrid-high");e&&i.removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6");jQuery.inArray(i,g)===-1&&g.push(i)}):jQuery("tbody tr:"+d+"contains"+ +f+"("+a+")",this.element).each(function(i,h){i=jQuery(h).removeClass("ui-ncbigrid-high");e&&i.removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6");g.push(i)})}else{jQuery(".ui-ncbigrid-high",this.element).removeClass("ui-ncbigrid-high");e&&jQuery(".ui-ncbigrid-row-odd-high-IE6, .ui-ncbigrid-row-even-high-IE6",this.element).removeClass("ui-ncbigrid-row-odd-high-IE6").removeClass("ui-ncbigrid-row-even-high-IE6")}this.element.trigger("ncbigridhighlightremoved",[a, +b,c])},setCellData:function(a,b,c,d){jQuery("tbody"+(d!==undefined?":eq("+d+")":"")+" tr:nth-child("+a+") td:nth-child("+b+")",this.element).text(c);this.element.trigger("ncbigridcellchange",[a,b,this.getCellData(a,b)]);this._notifyGridUpdated();this._notifyGridContentChanged()},setRowData:function(a,b,c){jQuery("tbody"+(c!==undefined?":eq("+c+")":"")+" tr:nth-child("+a+") td",this.element).each(function(d,e){jQuery(e).text(b[d])});this.element.trigger("ncbigridrowchange",[a,this.getRowData(a,c)]); +this._notifyGridUpdated();this._notifyGridContentChanged()},_enableCollapseTbodyRows:function(a){if(this.options.collapseRowsEnabled){a||(a=jQuery(this.element).find("tbody tr:has(th)"));var b=this;jQuery(a).each(function(){jQuery(this).addClass("ui-ncbigrid-collapsable").find("th").eq(0).prepend('<span class="collapsableTbodyIcon ui-icon ui-icon-plus-minus-big-open"></span>').find("span").click(function(c){c.stopPropagation();b._collapseTbodyRows(this.parentNode.parentNode)}).end().end().not(".ignoreCollapse").click(function(){b._collapseTbodyRows(this.parentNode)})})}}, +_collapseTbodyRows:function(a){jQuery(a).find("th span.collapsableTbodyIcon").toggleClass("ui-icon-plus-minus-big").toggleClass("ui-icon-plus-minus-big-open").end().siblings().toggleClass("collapsed")}});jQuery.extend(jQuery.expr[":"],{"contains-insensitive":function(a,b,c){return(a.textContent||a.innerText||"").toLowerCase().indexOf((c[3]||"").toLowerCase())>=0}}); +jQuery.extend(jQuery.expr[":"],{"contains-regexp":function(a,b,c){a=jQuery.trim(a.textContent||a.innerText||"");c=c[3];b=c.match(/\/([gi]+)$/);b=b!==null?b[1]:"";c=c.replace(/\/[gi]?$/,"").replace(/^\//,"");return a.match(new RegExp(c,b))!==null}});jQuery.extend(jQuery.expr[":"],{"contains-functionTest":function(a,b,c){a=a.textContent||a.innerText||"";return jQuery.ui.jig._getFncFromStr(c[3])(a)}}); +jQuery.extend(jQuery.expr[":"],{"not-contains":function(a,b,c){return(a.textContent||a.innerText||"").indexOf(c[3]||"")===-1}});jQuery.extend(jQuery.expr[":"],{"not-contains-insensitive":function(a,b,c){return(a.textContent||a.innerText||"").toLowerCase().indexOf((c[3]||"").toLowerCase())===-1}});
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_007.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +html .ui-ncbimenu>li>a{color:#fff;}.jig-ncbimenu li.offscreen_noflow{position:absolute;left:-1000px;}.jig-ncbimenu{clear:both;}.jig-ncbimenu ul{display:none;}.jig-ncbimenu>li{display:inline;float:left;}ul.ui-ncbibasicmenu li{display:block;margin:0;}.ui-ncbimenu li>a{background-color:transparent;border:0;}.ui-ncbimenu ul{-moz-border-radius:6px;-webkit-border-radius:6px;border-radius:6px;border:1px solid #CCC;-webkit-box-shadow:.4em .4em .5em rgba(0,0,0,.3);-moz-box-shadow:.4em .4em .5em rgba(0,0,0,.3);box-shadow:.4em .4em .5em rgba(0,0,0,.3);}.ui-ncbimenu li.active a{background-color:#4c96df;}.ui-ncbimenu>li a:focus{outline:0;}.ui-ncbimenu li a.expandDown{padding-right:20px;background:url("../img/arrow-sprite.png") no-repeat scroll 96% -6% #FFF;}.ui-ncbimenu li a.expandRight{background:url("../img/arrow-sprite.png") no-repeat scroll 96% 106% #FFF;}.ui-ncbimenu>li>a.expandDown,.ui-ncbimenu>li>a.expandRight{background-color:transparent;}.ui-ncbimenu li>a:hover.expandRight{background:url("../img/arrow-sprite.png") no-repeat scroll 96% 106% #4C96DF;}.ui-ncbimenu li.ui-ncbimenu-item-no-hlt>a:hover.expandRight,.ui-ncbimenu li.ui-ncbimenu-item-skip>a:hover.expandRight{background-color:transparent;}.ui-ncbimenu li ul{display:none;z-index:200;}ul.ui-ncbimenu li ul li a{background-color:#fff;}.ui-ncbimenu ul{position:absolute;display:none;}.ui-ncbimenu>li a:hover,.ui-ncbimenu li.selected>a{background-color:#4C96DF;color:#fff;}.ui-ncbimenu li ul.ncbibasicmenu li.ui-ncbimenu-item-no-hlt,.ui-ncbimenu li ul.ncbibasicmenu li.ui-ncbimenu-item-skip{background-color:#FFF;}.ui-ncbimenu li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu li.selected.ui-ncbimenu-item-no-hlt>a,.ui-ncbimenu li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu li.selected.ui-ncbimenu-item-skip>a{color:#fff;}.ui-ncbimenu li ul li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu li ul li.selected.ui-ncbimenu-item-no-hlt>a,.ui-ncbimenu li ul li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu li ul li.selected.ui-ncbimenu-item-skip>a{color:#14376C;background-color:transparent;}.ui-ncbimenu .oneLevel li.ui-ncbimenu-item-no-hlt a:hover,.ui-ncbimenu.ui-ncbibasicmenu>li.ui-ncbimenu-item-no-hlt>a:hover,.ui-ncbimenu .oneLevel li.ui-ncbimenu-item-skip a:hover,.ui-ncbimenu.ui-ncbibasicmenu>li.ui-ncbimenu-item-skip>a:hover{background-color:transparent;}.ui-ncbimenu .ui-ncbimenu-item-leaf{margin:0 .75em 0 0;}.ui-ncbimenu .ui-ncbimenu-item-leaf>a:hover{background-color:transparent;}.ui-ncbimenu:before,.ui-ncbimenu:after{content:"";display:table;}.ui-ncbimenu{*zoom:1;} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_007.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,14 @@ +jQuery.widget("ui.ncbibasicmenu",{options:{defaultSelection:-1,allowMultipleSelections:false,orientation:"vertical",preventDefaultCheck:true,stopPropagationCheck:true,normalizeSubsToOneLevel:false,disableSelect:false},styles:{itemNoHilite:"ui-ncbimenu-item-no-hlt",itemSkip:"ui-ncbimenu-item-skip"},_init:function(){this._loadedOnce&&this.rescan();this._loadedOnce=true},_create:function(){this._setSelectorString();this._addClasses();this._formatList();this._addEvents();this._setUpDefaults();this._setTabIndex(); +this._addAria()},rescan:function(){this._addClasses();this._setTabIndex();this._addAria();this._destroyFocusEvents();this._setUpFocusEvents()},destroy:function(){this._destroyTabIndex();this._destroyClasses();this._destroyEvents();this._destroyAria();this._destroyFormatList()},_setSelectorString:function(){var a=">";if(this.options.normalizeSubsToOneLevel){a="";this.element.addClass("oneLevel")}this._liSelector=a+"li:not(.ui-ncbimenu-item-skip)"},_addClasses:function(){this.isVert=this.options.orientation=== +"vertical";var a="ui-ncbibasicmenu";this.isVert||(a+=" orientation_hort");this.element.addClass(a)},_destroyClasses:function(){this.element.removeClass("ui-ncbibasicmenu")},_setUpDefaults:function(){this.selectedOption=this.options.defaultSelection;if(this.selectedOption!==-1){var a=this.element.find(this._liSelector+">a");if(this.options.allowMultipleSelections)for(var b=0;b<this.selectedOption.length;b++)this._makeSelection(a.eq(this.selectedOption[b]),"load");else this._makeSelection(a.eq(this.selectedOption), +"load")}},_formatList:function(){},_destroyFormatList:function(){},_setTabIndex:function(){var a=this.element.find(this._liSelector+">a").attr("tabindex","-1"),b=this.element.find(this._liSelector+".selected>a");if(b.length>0)b=b.eq(0);else{var c=0;for(b=a.eq(0);b.is("."+this.styles.itemSkip+" a")&&c<a.length-1;){c+=1;b=a.eq(c)}}this.options.nested||b.removeAttr("tabindex")},_destroyTabIndex:function(){this.element.find(this._liSelector+">a").removeAttr("tabindex")},_addEvents:function(){this._setUpKeyListener(); +this._setUpClickEvents();this._setUpFocusEvents();this._setUpHoverEvents()},_destroyEvents:function(){this._destroyKeyListener();this._destroyClickEvents();this._destroyFocusEvents();this._destroyHoverEvents()},_setUpKeyListener:function(){if(!this._menuKeyListener){var a=this;this._menuKeyListener=function(b){if(a.element.is(":visible"))if(a._keyPressDetected(b.keyCode)){b.preventDefault();a.options.stopPropagationCheck&&b.stopPropagation()}};jQuery(document).keydown(this._menuKeyListener)}},_destroyKeyListener:function(){if(this._menuKeyListener){jQuery(window).unbind("keydown", +this._menuKeyListener);this._menuKeyListener=null}},_setUpClickEvents:function(){var a=this;this._ulClickEvent=function(b){var c=b.srcElement||b.target;if(c){a.options.disableSelect||a._makeSelection(jQuery(c),"click");a.options.stopPropagationCheck&&b.stopPropagation();a.options.preventDefaultCheck&&jQuery(c).siblings("ul").length===1&&b.preventDefault()}};this.element.on("click.ncbibasicmenu",this._ulClickEvent)},_destroyClickEvents:function(){this.element.off("click",this._ulClickEvent)},_setUpFocusEvents:function(){var a= +this;this._focusFnc=function(){a._menuFocused(this)};this._blurFnc=function(){a._menuBlured(this)};this.element.find(this._liSelector+">a").on("blur",this._blurFnc).on("focus",this._focusFnc)},_destroyFocusEvents:function(){this.element.find(this._liSelector+">a").off("blur",this._blurFnc).off("focus",this._focusFnc)},focus:function(){this._menuFocused(null)},_menuFocused:function(a){this._lastAnchor=a;this._isFocused=true},_menuBlured:function(a){if(this._lastAnchor==a)this._isFocused=false},removeFocus:function(){this._menuBlured()}, +_setUpHoverEvents:function(){var a=this;this._mouseEnterFnc=function(b){b=jQuery(b.target).closest("li");!b.hasClass(a.styles.itemNoHilite)&&!b.hasClass(a.styles.itemSkip)&&b.addClass("hover")};this.mouseLeaveFnc=function(){jQuery(this).removeClass("hover")};this.element.on("mouseenter","li",this._mouseEnterFnc).on("mouseleave","li",this.mouseLeaveFnc)},_destroyHoverEvents:function(){this.element.off("mouseenter",this._mouseEnterFnc).off("mouseleave",this.mouseLeaveFnc);this.mouseLeaveFnc=this._mouseEnterFnc= +null},_makeSelection:function(a,b){var c=a.parent("li");if(c.length===1){var d=c.hasClass("selected");this.options.allowMultipleSelections||this._removeAllSelections();if(!c.hasClass(this.styles.itemSkip)){c.hasClass(this.styles.itemNoHilite)||c[d?"removeClass":"addClass"]("selected");var e=d?"unselected":"selected";b!=="menunav"&&this._trigger(e,"x",[a,c,b]);if(b==="click"||b==="load")this.selectedOption=this.element.find(this._liSelector+".selected").index();else d||c.find(">a").focus()}}this._setTabIndex()}, +_keys:{up:38,down:40,left:37,right:39,enter:13,escape:27,tab:9},_keyPressDetected:function(a){var b=this._keys,c=false;if(this._isFocused&&this.element.has(this._liSelector+">a:focus"))switch(a){case b.up:this._upDownPressed(-1);c=true;break;case b.down:this._upDownPressed(1);c=true;break;case b.left:this._leftRightPressed(-1);c=true;break;case b.right:this._leftRightPressed(1);c=true;break;case b.enter:this._enterSelected();c=false;break;case b.escape:this._escapeTyped();c=false;break;case b.tab:this._trigger("tab"); +default:c=false}return c},_upDownPressed:function(a){this.isVert?this._moveSelection(a):this._trigger(a===1?"actiondown":"actionup","x",this.focusedElement())},_leftRightPressed:function(a){this.isVert?this._trigger(a===1?"actionright":"actionleft","x",this.focusedElement()):this._moveSelection(a)},focusedElement:function(){return this.selectedOption!==-1?this.element.find(this._liSelector).eq(this.selectedOption):this.element.find(this._liSelector+":has(>a:focus)")},moveSelection:function(a){this._moveSelection(a)}, +_getNextIndex:function(a,b,c){a=a+b;if(a<0)a=c-1;else if(a>c-1)a=0;return a},_moveSelection:function(a){for(var b=this.element.find(this._liSelector+">a"),c=this._getNextIndex(this.selectedOption,a,b.length);b.eq(c).closest("li").hasClass(this.styles.itemSkip);)c=this._getNextIndex(c,a,b.length);this.selectedOption=c;this._makeSelection(b.eq(c),"keyboard")},removeAllSelections:function(){this.selectedOption=-1;this._removeAllSelections();this._setTabIndex()},_removeAllSelections:function(){this.element.find(this._liSelector).removeClass("selected")}, +_enterSelected:function(){this._trigger("enter")},_escapeTyped:function(){this._trigger("escape","x",this.focusedElement())},_addAria:function(){var a=this.element.parents('[role="menubar"]'),b=this.element.find(this._liSelector),c=b.find(">a");this.element.attr("role",a.length===0?"menubar":"menu");b.attr("role","presentation");c.attr("role","menuitem")},_destroyAria:function(){var a=this.element.find(this._liSelector),b=a.find(">a");this.element.removeAttr("role");a.removeAttr("role");b.removeAttr("role")}, +selectFirstItem:function(){this.selectedOption=0;this._moveSelection(0)}});
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_008.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1 @@ +ul.jig-ncbilocalnav,ul.ui-ncbilocalnav{list-style:none;margin:0;padding:0;width:100%;}ul.jig-ncbilocalnav:after,ul.ui-ncbilocalnav:after{content:".";display:block;height:0;clear:both;visibility:hidden;*zoom:1;*display:block;}ul.jig-ncbilocalnav li,ul.ui-ncbilocalnav li{float:left;position:relative;list-style:none;display:block;}ul.jig-ncbilocalnav li a,ul.ui-ncbilocalnav li a{color:#444;text-decoration:none;display:block;padding:.15em 1em .15em 1em;zoom:1;}ul.jig-ncbilocalnav ul{display:none;}ul.ui-ncbilocalnav ul{margin:0;margin-left:0!important;display:none;border-width:1px 0 0 1px;width:200px;padding-left:0;-moz-box-shadow:.4em .4em .5em #999;-webkit-box-shadow:.4em .4em .5em #999;box-shadow:.4em .4em .5em #999;_margin-top:1px;}ul.ui-ncbilocalnav li.open ul{display:block;position:absolute;left:-1px;}ul.ui-ncbilocalnav li:first-child{margin-left:1.333em;}ul.ui-ncbilocalnav ul li:first-child{margin-left:0;}ul.ui-ncbilocalnav ul li{float:none;display:block;position:relative;*line-height:125%;zoom:1;}ul.ui-ncbilocalnav li.has-child ul{z-index:1003;}ul.ui-ncbilocalnav li:first-child{border-left:1px solid #b0b0b0;}ul.ui-ncbilocalnav ul li:first-child{border-left:0;}ul.ui-ncbilocalnav{border-top:1px solid #c4c4c4;border-bottom:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul{border-left:1px solid #b0b0b0;}ul.ui-ncbilocalnav li{border-right:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul li{border-bottom:1px solid #c4c4c4;}ul.ui-ncbilocalnav ul li:first-child{border-top:1px solid #b0b0b0;}ul.ui-ncbilocalnav li.active{border-right:1px solid #c4c4c4;*z-index:1005;}ul.ui-ncbilocalnav li.active ul li{*z-index:1006;}ul.ui-ncbilocalnav li.active,ul.ui-ncbilocalnav li.active ul li,ul.ui-ncbilocalnav li.hover,ul.ui-ncbilocalnav li.hover ul li{*z-index:1006;}ul.ui-ncbilocalnav li.selected>ul>li a{margin:0 .75em;padding:.15em 1.5em .15em .25em;}ul.ui-ncbilocalnav li.selected a{color:#444!important;background-color:transparent!important;}ul.ui-ncbilocalnav li.hover>a,ul.ui-ncbilocalnav li.hover.selected>a,ul.ui-ncbilocalnav li.selected>a{background-color:transparent!important;color:#444!important;}ul.ui-ncbilocalnav,ul.ui-ncbilocalnav li{background-color:#F4F4F4;background-image:-webkit-gradient(linear,left top,left bottom,from(#fff),to(#F4F4F4));background-image:-webkit-linear-gradient(top,#fff,#F4F4F4);background-image:-moz-linear-gradient(top,#fff,#F4F4F4);background-image:-ms-linear-gradient(top,#fff,#F4F4F4);background-image:-o-linear-gradient(top,#fff,#F4F4F4);background-image:linear-gradient(top,#fff,#F4F4F4);}ul.ui-ncbilocalnav li.hover,ul.ui-ncbilocalnav li.selected{background-color:#E0E0E0;background-image:-webkit-gradient(linear,left top,left bottom,from(#F2F2F2),to(#E0E0E0));background-image:-webkit-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-moz-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-ms-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:-o-linear-gradient(top,#F2F2F2,#E0E0E0);background-image:linear-gradient(top,#F2F2F2,#E0E0E0);}ul.ui-ncbilocalnav li li.hover{background-color:#EDEDED;background-image:-webkit-gradient(linear,left top,left bottom,from(#DEDEDE),to(#EDEDED));background-image:-webkit-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-moz-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-ms-linear-gradient(top,#DEDEDE,#EDEDED);background-image:-o-linear-gradient(top,#DEDEDE,#EDEDED);background-image:linear-gradient(top,#DEDEDE,#EDEDED);}.ui-ncbilocalnav>li>a.expandDown{background:url(../img/ncbilocalnav-arrow.png) no-repeat right 8px!important;_background-position:right 11px!important;padding:.15em 1.5em .15em .25em;margin:0 .75em;color:#444;}ul.ui-ncbilocalnav li.selected ul li a{background-image:none!important;zoom:1;} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_008.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,14 @@ +(function(b){var h,i,j,g,l=function(){var a=b(this).find(":ui-button");setTimeout(function(){a.button("refresh")},1)},k=function(a){var c=a.name,e=a.form,f=b([]);if(c)f=e?b(e).find("[name='"+c+"']"):b("[name='"+c+"']",a.ownerDocument).filter(function(){return!this.form});return f};b.widget("ui.button",{options:{disabled:null,text:true,label:null,icons:{primary:null,secondary:null}},_create:function(){this.element.closest("form").unbind("reset.button").bind("reset.button",l);if(typeof this.options.disabled!== +"boolean")this.options.disabled=this.element.propAttr("disabled");this._determineButtonType();this.hasTitle=!!this.buttonElement.attr("title");var a=this,c=this.options,e=this.type==="checkbox"||this.type==="radio",f="ui-state-hover"+(!e?" ui-state-active":"");if(c.label===null)c.label=this.buttonElement.html();if(this.element.is(":disabled"))c.disabled=true;this.buttonElement.addClass("ui-button ui-widget ui-state-default ui-corner-all").attr("role","button").bind("mouseenter.button",function(){if(!c.disabled){b(this).addClass("ui-state-hover"); +this===h&&b(this).addClass("ui-state-active")}}).bind("mouseleave.button",function(){c.disabled||b(this).removeClass(f)}).bind("click.button",function(d){if(c.disabled){d.preventDefault();d.stopImmediatePropagation()}});this.element.bind("focus.button",function(){a.buttonElement.addClass("ui-state-focus")}).bind("blur.button",function(){a.buttonElement.removeClass("ui-state-focus")});if(e){this.element.bind("change.button",function(){g||a.refresh()});this.buttonElement.bind("mousedown.button",function(d){if(!c.disabled){g= +false;i=d.pageX;j=d.pageY}}).bind("mouseup.button",function(d){if(!c.disabled)if(i!==d.pageX||j!==d.pageY)g=true})}if(this.type==="checkbox")this.buttonElement.bind("click.button",function(){if(c.disabled||g)return false;b(this).toggleClass("ui-state-active");a.buttonElement.attr("aria-pressed",a.element[0].checked)});else if(this.type==="radio")this.buttonElement.bind("click.button",function(){if(c.disabled||g)return false;b(this).addClass("ui-state-active");a.buttonElement.attr("aria-pressed","true"); +var d=a.element[0];k(d).not(d).map(function(){return b(this).button("widget")[0]}).removeClass("ui-state-active").attr("aria-pressed","false")});else{this.buttonElement.bind("mousedown.button",function(){if(c.disabled)return false;b(this).addClass("ui-state-active");h=this;b(document).one("mouseup",function(){h=null})}).bind("mouseup.button",function(){if(c.disabled)return false;b(this).removeClass("ui-state-active")}).bind("keydown.button",function(d){if(c.disabled)return false;if(d.keyCode==b.ui.keyCode.SPACE|| +d.keyCode==b.ui.keyCode.ENTER)b(this).addClass("ui-state-active")}).bind("keyup.button",function(){b(this).removeClass("ui-state-active")});this.buttonElement.is("a")&&this.buttonElement.keyup(function(d){d.keyCode===b.ui.keyCode.SPACE&&b(this).click()})}this._setOption("disabled",c.disabled);this._resetButton()},_determineButtonType:function(){this.type=this.element.is(":checkbox")?"checkbox":this.element.is(":radio")?"radio":this.element.is("input")?"input":"button";if(this.type==="checkbox"||this.type=== +"radio"){var a=this.element.parents().filter(":last"),c="label[for='"+this.element.attr("id")+"']";this.buttonElement=a.find(c);if(!this.buttonElement.length){a=a.length?a.siblings():this.element.siblings();this.buttonElement=a.filter(c);if(!this.buttonElement.length)this.buttonElement=a.find(c)}this.element.addClass("ui-helper-hidden-accessible");(a=this.element.is(":checked"))&&this.buttonElement.addClass("ui-state-active");this.buttonElement.attr("aria-pressed",a)}else this.buttonElement=this.element}, +widget:function(){return this.buttonElement},destroy:function(){this.element.removeClass("ui-helper-hidden-accessible");this.buttonElement.removeClass("ui-button ui-widget ui-state-default ui-corner-all ui-state-hover ui-state-active ui-button-icons-only ui-button-icon-only ui-button-text-icons ui-button-text-icon-primary ui-button-text-icon-secondary ui-button-text-only").removeAttr("role").removeAttr("aria-pressed").html(this.buttonElement.find(".ui-button-text").html());this.hasTitle||this.buttonElement.removeAttr("title"); +b.Widget.prototype.destroy.call(this)},_setOption:function(a,c){b.Widget.prototype._setOption.apply(this,arguments);if(a==="disabled")c?this.element.propAttr("disabled",true):this.element.propAttr("disabled",false);else this._resetButton()},refresh:function(){var a=this.element.is(":disabled");a!==this.options.disabled&&this._setOption("disabled",a);if(this.type==="radio")k(this.element[0]).each(function(){b(this).is(":checked")?b(this).button("widget").addClass("ui-state-active").attr("aria-pressed", +"true"):b(this).button("widget").removeClass("ui-state-active").attr("aria-pressed","false")});else if(this.type==="checkbox")this.element.is(":checked")?this.buttonElement.addClass("ui-state-active").attr("aria-pressed","true"):this.buttonElement.removeClass("ui-state-active").attr("aria-pressed","false")},_resetButton:function(){if(this.type==="input")this.options.label&&this.element.val(this.options.label);else{var a=this.buttonElement.removeClass("ui-button-icons-only ui-button-icon-only ui-button-text-icons ui-button-text-icon-primary ui-button-text-icon-secondary ui-button-text-only"), +c=b("<span></span>",this.element[0].ownerDocument).addClass("ui-button-text").html(this.options.label).appendTo(a.empty()).text(),e=this.options.icons,f=e.primary&&e.secondary,d=[];if(e.primary||e.secondary){if(this.options.text)d.push("ui-button-text-icon"+(f?"s":e.primary?"-primary":"-secondary"));e.primary&&a.prepend("<span class='ui-button-icon-primary ui-icon "+e.primary+"'></span>");e.secondary&&a.append("<span class='ui-button-icon-secondary ui-icon "+e.secondary+"'></span>");if(!this.options.text){d.push(f? +"ui-button-icons-only":"ui-button-icon-only");this.hasTitle||a.attr("title",c)}}else d.push("ui-button-text-only");a.addClass(d.join(" "))}}});b.widget("ui.buttonset",{options:{items:":button, :submit, :reset, :checkbox, :radio, a, :data(button)"},_create:function(){this.element.addClass("ui-buttonset")},_init:function(){this.refresh()},_setOption:function(a,c){a==="disabled"&&this.buttons.button("option",a,c);b.Widget.prototype._setOption.apply(this,arguments)},refresh:function(){var a=this.element.css("direction")=== +"rtl";this.buttons=this.element.find(this.options.items).filter(":ui-button").button("refresh").end().not(":ui-button").button().end().map(function(){return b(this).button("widget")[0]}).removeClass("ui-corner-all ui-corner-left ui-corner-right").filter(":first").addClass(a?"ui-corner-right":"ui-corner-left").end().filter(":last").addClass(a?"ui-corner-left":"ui-corner-right").end().end()},destroy:function(){this.element.removeClass("ui-buttonset");this.buttons.map(function(){return b(this).button("widget")[0]}).removeClass("ui-corner-left ui-corner-right").end().button("destroy"); +b.Widget.prototype.destroy.call(this)}})})(jQuery);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/jquery_009.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,46 @@ +document.times=0; +jQuery.widget("ui.ncbipopper",{destTextCallbackCalledCount:0,options:{openMethod:"",openEvent:"mouseover",openAnimation:"slideDown",openAnimationTime:290,closeMethod:"",closeEvent:"mouseout",closeAnimation:"slideUp",closeAnimationTime:150,isEscapeKeyClose:true,isSourceElementCloseClick:false,isTriggerElementCloseClick:true,isTargetElementCloseClick:false,isDestElementCloseClick:false,isDocumentCloseClick:true,addCloseButton:false,adjustFit:"autoAdjust",delayTimeout:300,sourcePosition:"",destPosition:"top left", +sourceSelector:"",destSelector:"",targetPosition:"",triggerPosition:"bottom right",sourceText:null,destText:null,multipleHandlesSelector:"",openAtTarget:false,hasArrow:false,arrowDirection:"left",groupName:null,width:null,height:null,cssClass:null,excludeBasicCssStyles:false,wrapElement:false,loadingText:"loading...",showLoadingMessage:true,isDestTextCacheable:true,resizable:false,openAtMousePosition:false},_create:function(){this._setUpDestElem();this._addEventHandlers();this._addEscapeListener(); +this._addDocumentClickListener();this._addResizeListener();this._addCloseButton();this._addSharingDetails();this._addPopperHover();this.addTriggerAria()},updateTriggers:function(){this._addEventHandlers();this._addDocumentClickListener();this.addTriggerAria()},destroy:function(){jQuery.Widget.prototype.destroy.apply(this,arguments);var a=this.isPopperShared();this._destroyDestAria();this._destroyTriggerAria();this._removeSharingDetails();this._destroyCloseButton(a);this._destroyResizeListener();this._destroyDocumentClickListener(); +this._destroyEscapeListener();this._removeEventHandlers();this._destroyDestElem(a)},getDestElement:function(a){var b=this.destElem;if(!this.origDestElem)this.origDestElem=b;if(b){if(a&&this._isWaitingToBeAddedToDom){a=jQuery("div.grid");a=a.length===1?a:jQuery(document.body);b.appendTo(a);this._isWaitingToBeAddedToDom=true;this._getActualText(b)}}else{b=this.options.destSelector||this.options.sourceSelector||this.element.prop("hash");a=this.options.destText||this.options.sourceText;if(b){b=jQuery(b); +if(b.length===0)b=this._createTextHolder()}else if(a)b=this._createTextHolder();else throw"The popper can not find the popper element or text to display";if(this.options.wrapElement){if(!b.parent().hasClass("ui-ncbipopper-wrapper")){b.wrap('<div style="display:none"></div>');b.show()}if(!this.origDestElem)this.origDestElem=b;b=b.parent()}this.destElem=b;this._addDestAria()}if(!this.origDestElem)this.origDestElem=this.destElem;return b},_createTextHolder:function(){var a=jQuery('<div><div class="ui-ncbipopper-content"></div></div>'); +this._isWaitingToBeAddedToDom=true;return a},_getActualText:function(a){if(!this.isFunctionResultCached){var b=this.options.destText||this.options.sourceText,c=this._getFunction(b);if(typeof c==="function")b=this._getText(c);a.css("display","none").attr("generated","true").find(".ui-ncbipopper-content").html(b)}},_getFunction:function(a){var b=null;if(jQuery.ui.jig&&jQuery.ui.jig._getFncFromStr)b=jQuery.ui.jig._getFncFromStr(a);else if(typeof a==="function")b=a;return b},getDestTextCallbackCalledCount:function(){return this.destTextCallbackCalledCount}, +_getText:function(a){if(!(this.options.isDestTextCacheable&&this.getTextCalled||this.callbackInProgress)){this.getTextCalled=true;a||(a=this._getFunction(this.options.destText||this.options.sourceText));var b=this;this.callbackInProgress=true;a=a.call(this.element[0],function(c){b._setHTML(c);b.destTextCallbackCalledCount++;b.callbackInProgress=false})||this.options.loadingText;if(a!==this.options.loadingText)this.isFunctionResultCached=this.options.isDestTextCacheable;return a}},reloadContent:function(){var a= +this._getText(),b=this.getDestElement().find(".ui-ncbipopper-content");b&&b.html(a);return this.element},_setHTML:function(a){var b=this.getDestElement().find(".ui-ncbipopper-content");if(b){b.html(a);this.isFunctionResultCached=this.options.isDestTextCacheable;!this.options.showLoadingMessage&&!this.isPopperDisplayed&&this._openAnimation()}},_setUpDestElem:function(){var a=this.getDestElement().addClass("ui-ncbipopper-wrapper");this.options.excludeBasicCssStyles||a.addClass("ui-ncbipopper-basic"); +this.options.resizable&&a.resizable();var b=this.options.cssClass;b&&a.addClass(b);this.options.width!==null&&a.width(this.options.width);this.options.height!==null&&a.height(this.options.height);this._resetElementPosition(a);a.removeClass("offscreen_noflow").hide();a.data("isOpen",false)},_setArrowDirection:function(){if(this.options.hasArrow){var a=this.options.arrowDirection;this._arrow&&this._arrow.removeClass("ui-ncbipopper-arrow-top ui-ncbipopper-arrow-bottom ui-ncbipopper-arrow-left ui-ncbipopper-arrow-right").addClass("ui-ncbipopper-arrow-"+ +a)}},_setUpArrow:function(a,b,c){if(this.options.hasArrow){var d=this.options.arrowDirection;if(this._arrow)this._arrow.removeClass("ui-ncbipopper-arrow-top ui-ncbipopper-arrow-bottom ui-ncbipopper-arrow-left ui-ncbipopper-arrow-right").addClass("ui-ncbipopper-arrow-"+d);else this._arrow=jQuery('<div class="ui-ncbipopper-arrow-image ui-ncbipopper-arrow-'+d+'"> </div>').appendTo(document.body);a=this._getPositionSettings(a,"arrow",c);this._arrow.show().position({my:a.dest,of:this._activeTrigger|| +a.triggerElement||this.element,at:a.trigger,offset:a.offset,collision:"none"});if(b||this._arrowOverlapsPopper())this._arrow.hide()}},_destroyDestElem:function(a){a||this.getDestElement().removeClass("ui-ncbipopper-wrapper ui-ncbipopper-basic ui-ncbipopper-wrapper-relative-parent").attr("style","").show();this.options.wrapElement&&this.origDestElem.unwrap();this.destElem=null},_addEventHandlers:function(){var a=this,b=this.element,c=this.options.multipleHandlesSelector;if(c&&c.length>0)b=b.add(c); +var d=this.options.openMethod||this.options.openEvent,e=this.options.closeMethod||this.options.closeEvent;if(d===e&&e==="click"){this._openFunction=function(f){a._toggle(f,f.currentTarget);f.preventDefault()};b.on("click",this._openFunction)}else{c={timeout:this.options.delayTimeout};if(d==="mouseover")c.over=function(f){a._isOverTrigger=true;a.open(f,this)};else{c.over=function(){a._isOverTrigger=true};this._openFunction=function(f){if(d==="click")if(a.option.isTriggerElementCloseClick){a._toggle(f, +this);f.preventDefault()}else{a.isOpen(this)||f.preventDefault();a.open(f,this)}else a.open(f,this)};b.on(d,this._openFunction)}if(e==="mouseout")c.out=function(){a._isOverTrigger=false;a.isOpen(this)&&!a._isOverPopper&&a.close()};else{c.out=function(){};this._closeFunction=function(f){a.close();e==="click"&&f.preventDefault()};b.on(e,this._closeFunction)}if(d==="mouseover"||e==="mouseout")b.hoverIntent(c);if(this.options.isTriggerElementCloseClick&&e!=="click"&&d!=="click"){this._closeFunction2= +function(f){a.isOpen(b)&&a.close();f.preventDefault()};b.on("click",this._closeFunction2)}}if(this.options.isDestElementCloseClick){this._closeFunctionPopper=function(f){a.isOpen(b)&&a.close();f.preventDefault()};this.getDestElement().on("click",this._closeFunctionPopper)}},_removeEventHandlers:function(){var a=this.element,b=this.getDestElement(),c=this.options.multipleHandlesSelector;if(c&&c.length>0)a=a.add(c);a.off("mouseover mouseout");if(this._openFunction){a.off(this.options.openMethod||this.options.openEvent, +this._openFunction);this._openFunction=null}if(this._closeFunction){a.off(this.options.closeMethod||this.options.closeEvent,this._closeFunction);this._closeFunction=null}if(this._closeFunction2){a.off("click",this._closeFunction2);this._closeFunction2=null}if(this._closeFunctionPopper){b.off("click",this._closeFunctionPopper);this._closeFunctionPopper=null}},_toggle:function(a,b){this.isOpen(b)?this.close():this.open(a,b);a&&a.preventDefault&&a.preventDefault();return this.element},_arrowOverlapsPopper:function(){var a= +this.getDestElement(),b=Math.floor(a.position().top),c=Math.floor(a.position().left),d=Math.floor(c+a.outerWidth());a=Math.floor(b+a.height());var e=this._arrow,f=Math.floor(e.position().top),g=Math.floor(e.position().left);Math.floor(g+e.width());var h=Math.floor(f+e.height());c=g>c&&g<d||g+e.css("width")>c&&g+e.css("width")<d;b=f>b&&f<a||f+e.css("height")>b&&h+e.css("height")<a;return c&&b?true:false},_openAnimation:function(a){function b(){var k=d.outerHeight(),l=jQuery(window).height();k>l&&d.css({"max-height":l- +45+"px",overflow:"auto"});jQuery(window).trigger("resize")}var c=this,d=this.getDestElement().data("isOpening",this.element).stop(true,true),e=this._arrow,f=this.options.openAnimation,g=function(){c._trigger("opencomplete");c.getDestElement().data("isOpening",null);jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<=7&&c._positionPopper(a,false,true);b()},h=function(k){e.fadeTo(0,0);window.setTimeout(function(){e.stop(true,true).show();c._arrowOverlapsPopper()||e.css("opacity",1)},k)};if(f=== +"none"||this.isOpen()){d.show();e&&h(0);g()}else{var j=this.options.openAnimationTime;if(e){var i=0;if(e==="top")i=0;else if(e==="bottom")i=j;else{i=parseInt(e.css("top"),10)-parseInt(d.css("top"),10);var m=d.height()||i;i=i/m*j;if(i>j)i=j}h(i)}d[f](j,g)}},open:function(a,b){if(!b)b=this.element;if(this.options.openAtTarget){if(this._activeTrigger!==b){this.getDestElement().hide();this.getDestElement().data("isOpen",false)}this._activeTrigger=b}else this._activeTrigger=this.element;b=this.getDestElement(); +var c=b.data("isOpening");if(c&&c[0]!==this.element[0])(b.data("closeFnc")||function(){})(true);this._handleSharedPoppersOpen();this._handleGroupsOpen();b.data("isOpening",this.element);this._setUpArrow(a,true,true);jQuery.browser.msie&&this._positionPopper(a,true,true);this._setParentsZIndex(11);this._positionPopper(a,true,true);this._trigger("open");this.options.destText&&!this.options.showLoadingMessage&&!this.isFunctionResultCached||this._openAnimation(a);this._setAriaState(true);this.getDestElement().data("isOpen", +true);return this.element},_handleGroupsOpen:function(){var a=this.options.groupName;if(a){this.closeGroup(a);jQuery.ui.ncbipopper.openGroups[a]=this.element}},_closeAnimation:function(a){var b=this,c=function(){b._setParentsZIndex(1);b._trigger("closecomplete")},d=this.getDestElement().data("isOpening");if(d&&this.element[0]!=d[0])c();else{d=this.getDestElement().stop(true,true);var e=this.options.closeAnimation;if(e==="none"||a){d.hide();this._resetElementPosition(d);c()}else{var f=d;d[e](this.options.closeAnimationTime, +function(){b._resetElementPosition(f);c()})}}a=this.getDestElement().data("popperTriggers");for(e=0;e<a.length;e++){d=jQuery.ui.jig.getElementWidgets(a[e],"ncbipopper")[0];var g=d._arrow;if(g){g.stop(true,true).hide();d._resetElementPosition(g)}}},close:function(a){if(this.isOpen(this._activeTrigger)){this._handleGroupsClose(a);this._trigger("close");this._activeTrigger=null;this._closeAnimation(a);this._setAriaState(false);this.getDestElement().data("isOpen",false);return this.element}},closeGroup:function(a){if(a= +a||this.options.groupName)(a=jQuery.ui.ncbipopper.openGroups[a])&&jQuery.ui.jig.getElementWidgets(a,"ncbipopper")[0].close(true);return this.element},_handleGroupsClose:function(a){var b=this.options.groupName;if(!a&&b)jQuery.ui.ncbipopper.openGroups[b]=null},_determineAutoPosition:function(a){var b=jQuery(this._activeTrigger||this.element),c=b.offset(),d=this.getDestElement(true),e=jQuery(window);if(a){a=e.width();d=d.outerWidth();b=b.width();e=e.scrollLeft();if(d+b+c.left<a+e){c="right";b=e="left"}else{c= +"left";b=e="right"}}else{a=e.height();d=d.outerHeight();b=b.height();e=e.scrollTop();if(d+b+c.top<a+e){c="bottom";b=e="top"}else{c="top";b=e="bottom"}}return{posT:c,posP:e,arrow:b}},_getPositionSettings:function(a,b,c){var d=this.options.sourcePosition||this.options.destPosition,e=this.options.targetPosition||this.options.triggerPosition;d=d.split(/\s/);e=e.split(/\s/);if(d[0]==="middle")d[0]="center";if(d[1]==="middle")d[1]="center";if(e[0]==="middle")e[0]="center";if(e[1]==="middle")e[1]="center"; +this.options.sourcePosition=null;this.options.destPosition=d.join(" ");this.options.targetPosition=null;this.options.triggerPosition=e.join(" ");var f;if(d[0]==="auto"){f=this._determineAutoPosition(false);d[0]=f.posP;e[0]=f.posT;this.options.arrowDirection=f.arrow;this._setArrowDirection(f.arrow)}if(d[1]==="auto"){f=this._determineAutoPosition(true);d[1]=f.posP;e[1]=f.posT;this.options.arrowDirection=f.arrow;this._setArrowDirection(f.arrow)}f=d[1]+" "+d[0];var g=e[1]+" "+e[0],h="0px 0px";if(this.options.hasArrow)h= +b==="popper"?this._getPopperOffsets(d[0],d[1]):this._getArrowOffsets(d[0],d[1]);if(this.options.openAtMousePosition&&c){h.xOffset=a.pageX-jQuery(a.target).offset().left+(h.xOffset-0)+1;h.yOffset=a.pageY-jQuery(a.target).offset().top+(h.yOffset-0)}if(this._isArea===undefined)this._isArea=((this._activeTrigger?this._activeTrigger[0]:false)||this.element[0]).nodeName.toUpperCase()==="AREA";if(this._isArea){a=this._areaElementAdjustment(h,e);triggerElement=a.positionElement;h=a.offset;g="left top"}else triggerElement= +null;if(this.options.openAtMousePosition&&c)g="left top";return{dest:f,trigger:g,offset:typeof h=="string"?h:h.xOffset+"px "+h.yOffset+"px",triggerElement:triggerElement}},_getArrowOffsets:function(a,b){var c="0",d="0";switch(this.options.arrowDirection){case "left":case "right":switch(a){case "top":d="-13";break;case "center":d="0";break;case "bottom":d="13";break;default:d="0";break}break;case "top":case "bottom":switch(b){case "left":c="-13";break;case "center":c="0";break;case "right":c="13"; +break;default:c="0";break}break;default:throw"Valid arrow directions are top, bottom, left, right";}return{xOffset:c,yOffset:d}},_getPopperOffsets:function(a,b){var c="0",d="0";c=this.options.arrowDirection;switch(c){case "left":case "right":c=c==="left"?"7":"-7";switch(a){case "top":d="-13";break;case "center":d="0";break;case "bottom":d="13";break;default:d="0";break}break;case "top":case "bottom":d=c==="top"?"7":"-7";switch(b){case "left":c="-13";break;case "center":c="0";break;case "right":c= +"13";break;default:c="0";break}break;default:throw"Valid arrow directions are top, bottom, left, right";}return{xOffset:c,yOffset:d}},_areaElementAdjustment:function(a,b){a=typeof a=="string"?a.split(" "):[a.xOffset,a.yOffset];var c=parseInt(a[0],10);a=parseInt(a[1],10);var d=jQuery(this._activeTrigger||this.element).parent(),e=jQuery(this._activeTrigger||this.element[0])[0];d=jQuery("img[usemap='#"+(d[0].name||d[0].id)+"']");var f=e.shape||"rect";e=(e.coords||"").split(/\s?,\s?/g);d=d;var g=0,h= +0;if(f==="circle"){if(b[0]=="top")h=parseFloat(e[1])-parseFloat(e[2]);else if(b[0]=="bottom")h=e[3]+parseFloat(e[2]);else if(b[0]=="center")h=parseFloat(e[1]);if(b[1]==="left")g=e[0]-parseFloat(e[2]);else if(b[1]==="right")g=e[2]+parseFloat(e[2]);else if(b[1]==="center")g=parseFloat(e[0])}else{if(b[0]=="top")h=parseFloat(e[1]);else if(b[0]=="bottom")h=parseFloat(e[3]);else if(b[0]=="center")h=(parseFloat(e[1])+parseFloat(e[3]))/2;if(b[1]==="left")g=parseFloat(e[0]);else if(b[1]==="right")g=parseFloat(e[2]); +else if(b[1]==="center")g=(parseFloat(e[0])+parseFloat(e[2]))/2}g+=c;h+=a;return{positionElement:d,offset:g+"px "+h+"px"}},_getCollisionSetting:function(){var a=this.options.adjustFit;return a=a==="autoAdjust"||a==="slide"?"fit":"none"},_resetElementPosition:function(a){a.css("top","-100px").css("left","-100px")},_positionPopper:function(a,b,c){a=this._getPositionSettings(a,"popper",c);c=this._getCollisionSetting();var d=a.triggerElement||this.options.openAtTarget&&this._activeTrigger||this.element; +a=this.getDestElement(true).stop().show().position({my:a.dest,of:d,at:a.trigger,offset:a.offset,collision:c}).data("attached-to",d);b&&a.hide();document.times++},_addEscapeListener:function(){if(this.options.isEscapeKeyClose){this._registerGlobalEscapeListener();var a=this;this._ncbipopperescapepressedFunction=function(){a.close()};jQuery(document).bind("ncbipopperescapepressed",this._ncbipopperescapepressedFunction)}},_destroyEscapeListener:function(){if(this._ncbipopperescapepressedFunction){jQuery(document).unbind("ncbipopperescapepressed", +this._ncbipopperescapepressedFunction);this._ncbipopperescapepressedFunction=null}},_registerGlobalEscapeListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalEscapeRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalEscapeRegistered=true;var a=document,b="keypress";if(!jQuery.browser.msie&&!jQuery.browser.mozilla){a=window;b="keydown"}jQuery(a)[b](function(c){c.keyCode===27&&jQuery(document).trigger("ncbipopperescapepressed")})}},_addDocumentClickListener:function(){if(this.options.isDocumentCloseClick){this._registerGlobalClickListener(); +var a=this;this._ncbipopperdocumentclickFunction=function(b,c){a._checkDocumentClick(b,c)};jQuery(document).bind("ncbipopperdocumentclick",this._ncbipopperdocumentclickFunction)}},_destroyDocumentClickListener:function(){this._ncbipopperdocumentclickFunction&&jQuery(document).unbind("ncbipopperdocumentclick",this._ncbipopperdocumentclickFunction)},_registerGlobalClickListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalClickRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalClickRegistered= +true;jQuery(document).click(function(a){jQuery(document).trigger("ncbipopperdocumentclick",[a.srcElement||a.target])})}},_checkDocumentClick:function(a,b){if(b&&this.isOpen()){b=jQuery(b);if(!(this._isSameElementOrChild(jQuery(this.element),b)||this._isSameElementOrChild(this.getDestElement(),b)))if(!(jQuery.ui.jig.getElementWidgets(jQuery(b),"ncbipopper")[0]&&this.getDestElement()[0]==jQuery.ui.jig.getElementWidgets(jQuery(b),"ncbipopper")[0].getDestElement()[0])){if(a=this.options.multipleHandlesSelector){var c= +false,d=this;jQuery(a).each(function(){if(d._isSameElementOrChild(jQuery(this),b))c=true});if(c)return}this.close()}}},_isSameElementOrChild:function(a,b){return a[0]==b[0]||jQuery(a).has(b).length===1},_addResizeListener:function(){this._registerGlobalResizeListener();var a=this;this.ncbipopperdocumentresizeFunction=function(b){a._pageResized(b)};jQuery(window).bind("ncbipopperdocumentresize",this.ncbipopperdocumentresizeFunction)},_destroyResizeListener:function(){if(this.ncbipopperdocumentresizeFunction){jQuery(window).unbind("ncbipopperdocumentresize", +this.ncbipopperdocumentresizeFunction);this.ncbipopperdocumentresizeFunction=null}},_registerGlobalResizeListener:function(){if(!jQuery.ui.ncbipopper.globalEvents.isGlobalResizeRegistered){jQuery.ui.ncbipopper.globalEvents.isGlobalResizeRegistered=true;jQuery(window).on("resize scroll",function(){jQuery(window).trigger("ncbipopperdocumentresize")})}},_pageResized:function(a){if(this.isOpen()){this._positionPopper(a);this._setUpArrow(a)}},_addCloseButton:function(){if(this.options.addCloseButton){var a= +this.getDestElement(),b=a.find(".ui-ncbipopper-close-button, .ncbipopper-close-button");if(b.length===0){b=jQuery("<button class='ui-ncbipopper-close-button ui-ncbipopper-close-button-generated'>x</button>").attr("generated","true").prependTo(a);b.ncbibutton({color:"blue"})}if(b){var c=this;this._closeButtonFunction=function(d){c.close();d.preventDefault()};b.on("click",this._closeButtonFunction)}}},_destroyCloseButton:function(a){this._closeButtonFunction&&this.getDestElement().find(".ui-ncbipopper-close-button, .ncbipopper-close-button").off("click", +this._closeButtonFunction).filter(function(){return!a}).filter(".ui-ncbipopper-close-button-generated").ncbibutton("destroy").remove()},isPopperShared:function(){return(this.getDestElement().data("popperTriggers")||[]).length>1},_addSharingDetails:function(){var a=this.getDestElement(),b=a.data("popperTriggers")||[];b.push(this.element);a.data("popperTriggers",b)},_removeSharingDetails:function(){for(var a=this.getDestElement(),b=a.data("popperTriggers"),c=this.element[0],d=0;d<b.length;d++)if(b[d][0]== +c){b.slice(d,1);break}b.length===0?a.removeData("popperTriggers"):a.data("popperTriggers",b)},_handleSharedPoppersOpen:function(){if(this.isPopperShared())for(var a=this.getDestElement().data("popperTriggers"),b=this.element[0],c=0;c<a.length;c++)if(a[c][0]!=b&&jQuery.ui.jig.getElementWidgets(a[c],"ncbipopper")[0].isOpen()){jQuery.ui.jig.getElementWidgets(a[c],"ncbipopper")[0].close(true);break}},_addPopperHover:function(){if((this.options.closeMethod||this.options.closeEvent)==="mouseout"){var a= +this.getDestElement();if(this._arrow)a=a.add(this._arrow);var b=this,c={timeout:this.options.delayTimeout,over:function(){},out:function(){b._overPopper(false)}};jQuery(a).hoverIntent(c);jQuery(a).mouseenter(function(){b._overPopper(true);b._lastOver=new Date});jQuery(a).mouseleave(function(){new Date-b._lastOver<b.options.delayTimeout&&b._overPopper(false)}).mouseout(function(d){var e=jQuery(d.target||d.srcElement);if(e.hasClass("ui-ncbipopper-wrapper")||e.hasClass("ui-ncbipopper-arrow-image"))if(e.find(d.relatedTarget).length=== +0){b._isOverPopper=false;b._outTimer=window.setTimeout(function(){b._overPopper(false)},200)}})}},_destroyPopperHover:function(){var a=jQuery(this.getDestElement());a.unbind("mouseenter").unbind("mouseleave");a.removeProp("hoverIntent_t");a.removeProp("hoverIntent_s")},_overPopper:function(a){this._outTimer&&window.clearInterval(this._outTimer);if(a)this._pTimer=new Date;this._isOverPopper=a;if(!a)if(this._isOverTrigger){var b=this;window.setTimeout(function(){!b._isOverPopper&&!b._isOverTrigger&& +b._overPopper(false)},300)}else this.close()},isOpen:function(a){if(!a)a=this._activeTrigger;a=jQuery(a);var b=jQuery(this._activeTrigger),c=this.getDestElement().data("popperTriggers");a=this.options.openAtTarget||c.length>1?a&&a.length&&b&&b.length&&b[0]===a[0]:true;return this.getDestElement().data("isOpen")&&a?true:false},_setParentsZIndex:function(a){if(jQuery.browser.msie&&parseInt(jQuery.browser.version,10)<=7){var b=this.getDestElement().parents(),c=0;if(b.length>1){b.each(function(e){if(jQuery(this).css("position")=== +"relative"){c=e===0?0:e+1;return false}});b=b.eq(c);var d=b.css("position");b.data("orgPosition")||b.data("orgPosition",d);if(d==="static"||d==="relative"){d=a===1?b.data("orgPosition"):"relative";b.css({position:d,"z-index":a})}}}},addTriggerAria:function(a){var b=a;if(!a){b=this.element;if((a=this.options.multipleHandlesSelector)&&a.length>0)b=b.add(a)}b.attr("role","button").attr("aria-expanded",false).attr("aria-haspopup",true)},_destroyTriggerAria:function(){var a=this.element,b=this.options.multipleHandlesSelector; +if(b&&b.length>0)a=a.add(b);a.removeAttr("role aria-expanded aria-haspopup")},_addDestAria:function(){this.getDestElement().attr("aria-live","assertive").attr("aria-hidden",true).addClass("ui-helper-reset")},_destroyDestAria:function(){this.getDestElement().removeAttr("aria-live aria-hidden").removeClass("ui-helper-reset")},_setAriaState:function(a,b,c){b=b?b:this.element;c=c?c:this.getDestElement();b.attr("aria-expanded",a);c.attr("aria-hidden",!a)}});jQuery.ui.ncbipopper.openGroups={}; +jQuery.ui.ncbipopper.globalEvents={isGlobalEscapeRegistered:false,isGlobalClickRegistered:false,isGlobalResizeRegistered:false};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/main.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,337 @@ +/* +LEGAL +===== +Copyright: Daemon Pty Limited 1995-2006, http://www.daemon.com.au & http://www.mollio.org/ +License: Released Under the "Common Public License 1.0", http://www.opensource.org/licenses/cpl.php +Version: 010306 +*/ +body {padding: 0 0 10px;background: #fff url("images/body_bg-ncbi.gif") repeat-x 0 100%;color:#333;font:83%/1.5 arial,tahoma,verdana,sans-serif;} +body { margin: 0; padding: 0; } +/* LINKS */ +a,a:link,a:link,a:link,a:hover {text-decoration:underline;cursor:pointer} +a:link {color:#369} +/* Original: a:visited {color:#999} */ +a:visited {color:#664E99;} +a:hover,a:active {color:#069} +/* FORMS */ +form {margin: 0 0 1.5em} +input {font-family: arial,tahoma,verdana,sans-serif;margin: 2px 0 0} +label {display:block;padding: 5px 0} +label br {clear:left} +#desc {font-weight: bold;margin-bottom: 5px;} +#desc a {font-weight: normal;} +#logolink, #logolink img {float: left;border: 0;margin: 0;} + +/* TYPOGRAPHY */ +p, ul, ol {margin: 0 0 1.5em} +/* Original: h1, h2, h3, h4, h5, h6 {letter-spacing: -1px;font-family: arial,verdana,sans-serif;margin: 1.2em 0 .3em;color:#000;border-bottom: 1px solid #eee;padding-bottom: .1em}*/ +h1, h2, h3, h4, h5, h6 { letter-spacing: -1px;font-family: arial,verdana,sans-serif;margin: 1.2em 0 .3em;color:#2A6979;border-bottom: 1px solid #ccc;padding-bottom: .1em} +h1 {font-size: 196%;margin-top:.6em} +h2 {font-size: 136%} +h3 {font-size: 126%} +h4 {font-size: 116%} +h5 {font-size: 106%} +h6 {font-size: 96%} +.highlight {color:#4E8999; padding: 3px; border: solid 1px #ccc;} +.featured { background-color: #ffc; padding: 0.25em 0.5em;margin:0; } +.subdued {color:#999} + +small {font-size:11px} + +/* LISTS */ +ul {margin: .3em 0 1.5em 0;list-style-type:none} +ul.related {margin-top: -1em} +ol {margin: .5em .5em 1.5em} +ol li {margin-left: 1.4em;padding-left: 0;background: none; list-style-type: decimal} +.section li {line-height: 1.4em;padding-left: 25px;background: transparent url("images/sprites-ncbi.gif") no-repeat 0 0}*/ +li.doc {background-position: 3px -500px} +ul.nomarker li {background:none;padding-left:0} +dl {margin: 0 0 1em 0} +dt {font-weight:bold;margin-top: 1.3em} +dl dl {margin: 0 0 1.5em 30px} + +/* GENERAL */ +/*img {border:none} */ +hr {margin: 1em 0;background:#f2f2f2;height:1px;color:#f2f2f2;border:none;clear:both} +.clear {clear:both;position:relative;font-size:0px;height:0px;line-height:0px} +/* LAYOUT - HEADER */ +#header {background: #204174 url("images/sprites-ncbi.gif") repeat-x 0 100%;margin: 0 0 3px;padding: 0 0 8px;white-space:nowrap;} +#header #site-name {font: 120% arial;letter-spacing: -.05em;margin: 0 ;padding:3px 0; color:#ffffff;font-weight: bold;} +#header #site-name h1 {font-style: italic; letter-spacing: 0; color: #68a; margin:0 0 0 5em; position: relative; left: 200px;font-size:85%;border:none;padding-bottom:0;display:inline;} +#header {min-width:770px;position:relative;} +/* NAV - top horizontal nav */ +#nav, #nav ul {padding: 0;margin: 0;list-style: none} +#nav {font-weight:bold;height:2.09em;font: bold 95% arial;margin: 0 105px 0 40px; width: 430px;} +#nav li {background: #999;float: left;width: auto;display:block;margin: 0;border-bottom: 3px solid #666;border-right: 3px solid #252525;padding:0} +#nav a, #nav a:link, #nav a:visited, #nav a:hover, #nav a:active {text-decoration:none;cursor:pointer;color:#fff;display: block;padding: 4px 10px 2px} +#nav a:hover {color:#000} +#nav li ul {border-left: 1px solid #ccc;background: #eee;width:22.8em;font-size:90%;margin-top:3px;position: absolute;font-weight:normal;left: -999em} +#nav li:hover ul, #nav li.sfhover ul {left: 0;z-index:99999;} +#nav li li {background:none;float:none;border:none;border: 1px solid #999;border-top:1px solid #fff;border-right:solid 1px #ccc;border-left:none;padding-left:0} +#nav li li.last {border-bottom:solid 1px #ccc;} +#nav li li a, #nav li li a:link, #nav li li a:visited, #nav li li a:hover {color:#000;padding: 3px 10px 2px;width:21em} +#nav li li a:hover {color:#fff;background:#4E8999} +#nav li.active {background: #4E8999;border-bottom: 3px solid #4E8999} +#nav li.active a:link, #nav li.active a:visited, #nav li.active a:hover, #nav li.active a:active {} +#nav li.active a:hover {color:#000} +#nav li.active li {border:none;border-top: 1px solid #ccc;border-bottom: 1px solid #ccc;} +#nav li.active li {border: solid 1px #ccc;border-right: solid 1px #4E8999;border-left: solid 1px #4E8999;} +#nav li.active li.last {border-bottom: solid 1px #4E8999;} +#nav li.active li a:link, #nav li.active li a:visited, #nav li.active li a:hover, #nav li.active li a:active {color:#000} +#nav li.active li a:hover {background: #666 url("images/sprites-ncbi.gif") repeat-x 0 99%;color:#fff; filter:progid:DXImageTransform.Microsoft.AlphaImageLoader (src='images/sprites-ncbi.gif', sizingMethod='crop');} +#nav li.active li.active a:link, #nav li.active li.active a:visited, #nav li.active li.active a:hover, #nav li.active li.active a:active {color:#fff;font-weight:bold;background: #666 url("images/sprites-ncbi.gif") repeat-x 0 99%; filter:progid:DXImageTransform.Microsoft.AlphaImageLoader (src='images/sprites-ncbi.gif', sizingMethod='crop');} + +/* hide from IE mac \*/ +#nav li {width:auto} +/* end hiding from IE5 mac */ + +/* SEARCH */ +#search {color:#fff;font-weight:bold;position:absolute;top:10px;right:4em} +#search form {margin:0} +#search input {width:8em;margin: 0 0 -1px;height:1.2em} +#search label {padding:5px 0 0;display:inline} +#search input.f-submit {width:auto;font-size:81%;margin:0 0 -.15em;height:1.95em} +#content {margin: 0;} +#type-d #content {margin: 0 0 0 40px;} +#breadcrumb {margin-top:-5px;font-size:93%;font-weight:bold; margin-left: 1em; margin-bottom: 0; padding: 0 6px 0 12px;; background: url("images/right-arrow.gif") no-repeat center left;display:inline;} +#breadcrumb strong{font-weight:bold;} +#breadcrumb a:link, #breadcrumb a:visited {text-decoration:none} +#breadcrumb a:hover, #breadcrumb a:active {text-decoration:underline} +/* CODE - formatting for code inserted into body - more here: http://dizque.lacalabaza.net/temp/lipt/ */ +ol.code {font-family: monospace;position:relative} +ol.code li {color: #666;margin-bottom: 1px} +ol.code code {color: #000;display: block} +ol.code .cmt {color: #4077d2} +li.tab0 code {padding-left: 4em} +li.tab1 code {padding-left: 8em} +li.tab2 code {padding-left: 12em} +li.tab3 code {padding-left: 16em} +li.tab4 code {padding-left: 20em} +li.tab5 code {padding-left: 24em} +ol.code li {background: #f3f3f3} +p.note {margin: 1em;border: 1px solid #ddd;background: #f0f0f0;padding: 1em} + +/* LAYOUT TYPE A */ +#type-a #content-wrap { width: 100%; margin: 0; padding: 0; white-space:nowrap;margin-top:-0.3em;} +#type-a #content { margin: 0 40px; } +/* LAYOUT - FOOTER */ +#footer p {margin:0; padding: 0;padding-bottom:1.5em;} + +#footer a:link {color:#999} +#footer {clear:both;border-top: 1px solid #E3E8EE;padding: 4px 10px 0 10px;font-size:86%;color:#999; margin: 0;} +#breadcrumb a.help {margin-left: 1em;font-weight:normal;text-decoration: underline;} +div#search {border: solid 1px #aaa;} +div#search td{padding: 1px;} +/* Mozilla-only rule */ +html > body div#search td{padding: 2px;font-weight: bold;font-size: 80%;} +div#search {background-color: white;position: absolute;right: 4px;top: 4px;color: #369; /* new rule: text by default is white */} +#jtitle{margin-left:1em;} +.hidden {display: none;} +.shown {display: block;} +a#moreHelp {font-weight:bold;text-decoration:underline;font-size:80%;padding-left:5px;background:none;} +/* These next two rules replace the text of <a class="helplink"><span>[?]</span></a> + * with a 16x16 help link image with transparent background + */ +.helpbox, .resBox {font-size: 95%;color: #666;border: solid 1px #ccc;background-color: #def;margin-left: 1em;padding: 0.5em;margin-bottom: 0.5em;zoom:1;} +.help, .helpbox, .resBox {font-size: 95%;color: #666;white-space:normal;} +.helplink {padding-left: 16px;background:transparent url(images/help.gif) center left no-repeat;list-style: none;} +.helplink span {visibility: hidden;} +a.helplink {text-decoration: none;} +.helpbox a {background:none;text-decoration:underline;font-size:90%;} +a.arrowlink:hover {text-decoration: underline;} +a.arrowlink{ + padding-left: 16px; + background-image: url(images/right.gif); + background-repeat: no-repeat; + background-position: center left; + -moz-outline-style: none; + text-decoration: none; + text-decoration: underline; +} + +#orgns {float: right;} + +ul.msg, ul.msg li { +padding:0; +text-indent:0; +margin: 0; +} + +ul.msg { +margin-top: 1em; +} + +ul.msg li { +margin-bottom: 3px; +display: none; +font-weight: bold; +background: transparent url(images/gradient30down.png) repeat-x top left; +} +/* IE6 doesn't have alpha transparency, so hack it out */ +* html ul.msg li { +background-image: none; +} + +ul.msg li p, ul.msg li div.msInf { +padding: 3px; +padding-left: 28px; +margin:0; +white-space:normal; +} + +ul.msg li a.small { +font-weight: normal; +font-size: 90%; +} + +ul.msg li.error { +background-color: #fbb; +border: solid 1px #c00; +color: #c00; +} + +ul.msg li.error p, ul.msg li.error div.msInf{ +background: transparent url(images/error.png) no-repeat 6px center; +} + +ul.msg li.warning { +background-color: #ffc; +border: solid 1px #cc0; +color: #444; +} + +ul.msg li.warning p, ul.msg li.warning div.msInf { +background: transparent url(images/warn.png) no-repeat 6px center; +} + +ul.msg li.success { +background-color: #dfd; +border: solid 1px #0d0; +color: #060; +} + +ul.msg li.success p,ul.msg li.success div.msInf { +background: transparent url(images/ok.png) no-repeat 6px center; +} + +ul.msg li.info { +background-color: #ace; +color: #444; +border: solid 1px #369; +padding: 1px; +} + +ul.msg li.info p,ul.msg li.info div.msInf { +background: transparent url(images/info.png) no-repeat 6px center; +} + +ul.msg li.warning,ul.msg li.error,ul.msg li.success,ul.msg li.info +{ + display:block; +} +ul.msg li p +{ + display:block; +} + +ul.msg li.error p.warning { +background: transparent url(images/warn.png) no-repeat 6px center; +} + +ul.msg li .helpbox +{ + font-weight:normal; + margin-left:0; +} + +a.errorHelp +{ +/*float:right; +margin-right:2em; +margin-top:-2em;*/ +margin-left:0.5em; +} + +.msInf a.shown +{ + display:inline; +} + +#tryNew +{ + color:Red; +} +.orgHint +{ + color:#AAAAAA; +} + + +span.acPromt,.skp +{ + position:absolute; + left:-9999px; +} + + + +#rgs +{ + margin-left:35em; + white-space:nowrap; +} + +#trdm +{ + vertical-align:super; + font-size:small; +} + +.print-log-res { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; } +.print-log-res li { list-style-image: none; } + +/* jig toggler adjustments */ +#content .ui-ncbitoggler.ui-widget, #content a.ui-ncbitoggler-open, #content a.ui-ncbitoggler-slave-open +{ + font-size:100%; +} + +.helplink.ui-widget +{ + display:inline; +} + + +#content a.ui-ncbitoggler.ui-widget, #content a.ui-ncbitoggler-open +{ +color:#336699; +} + +#moreHelp span +{ + visibility:visible; +} + + +#content #moreHelp.ui-ncbitoggler, #content #moreHelp.ui-ncbitoggler-open +{ + font-size:80%; +} + +#content .ui-ncbitoggler-slave-open +{ + line-height:1.4em; +} + +div.ui-ncbiautocomplete-holder { + font-size: 80%; +} +ul.ui-ncbiautocomplete-options li span{ color: red;} +.ytb,.section a.ytb +{ + margin-bottom:-5px; + background: url("/core/assets/guide/images/YouTube.png") no-repeat scroll left center transparent !important; + height:22px; + padding-left:55px; + font-weight:normal; +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/print.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,305 @@ +/* +LEGAL +===== +Copyright: Daemon Pty Limited 1995-2006, http://www.daemon.com.au & http://www.mollio.org/ +License: Released Under the "Common Public License 1.0", http://www.opensource.org/licenses/cpl.php +Version: 010306 +*/ + + +body {font: 10pt arial,tahoma,verdana,sans-serif} +h1, h2, h3, h4, h5, h6 {margin: 1em 0 .2em;font-family: arial,tahoma,verdana,sans-serif} + +* {float:none;position:static;background:#fff} +p {margin: 0 0 1em} +dt {font-weight:bold} + +#nav, #search, #nav-secondary, #poweredby {display:none} + +/* =LINKS */ +a {border:none} +a,a:link,a:link,a:link,a:hover {background:transparent;text-decoration:underline;cursor:pointer} +a:link {color:#5291c4} +a:visited {color:#666} +a:hover {color:#ff9900;border:none} +a:active {color:#0066cc} + +.teaserBox {clear:both;margin: 0 0 1em} + +.sponsors img {margin: .5em 0} + +#footer {margin: 1em 0} + +#jtitle { +border-bottom:2px solid black; +margin-top:0.25em;; +margin-left:-1.5em;; +margin-bottom: 2em;; +font-size: 110%;; +padding-bottoM:0.5em;; +} + +/* TABLES */ +table {font-size: 9pt;margin: 0 0 1em;border-collapse:collapse;} + + table th {border-bottom: 3px solid #000;vertical-align:top;padding: 1.5em 3px 3px;line-height:1.1;font: bold 145% arial;letter-spacing:0;text-align:left} + .table1 th.time {border-bottom: none;font: bold 89% verdana;color:#ff9c00;vertical-align:top;padding: 3px} + .table1 td {border: 1px solid #ddd;font-size: 9pt;padding: 3px;vertical-align:top} + .table1 td a {display:block;width:auto;font-weight:bold} + .table1 td a:link, .table1 td a:visited, .table1 td a:hover, .table1 td a:active {border:none;text-decoration:none} + .table1 th.sub {background: #aaa} + .table1 th.sub2 {background: #bbb;color:#000} + .table1 td ul li {background: #fff} + + +#logolink img { +display: none; +} + +#site-name { +font-size: 140%; +font-weight: bold; +padding: 3px; +text-align:center; +} + +div.resHeader { +display: none; +} + +#content-wrap { +margin : 0 0.25in; +} + +#blHeader pre, #query pre { +white-space: normal; +} + +#blHeader pre p { +display: none; /* Get rid of pointer to BLAST FAQs */ +} + +#graphic input { +display: none; +} + +#descs td { vertical-align: top; } +td.lim { white-space: normal; padding-bottom: 0.5em;} +#descs td { vertical-align: top; border-bottom: solid 1px #888; border-collapse: collapse; padding-top: 0;} + +#descs a { +text-decoration: none; +color: black; +padding: 0; +margin: 0; +} + +#descs th { +font-size: 110%; +} + +#graphic table { +margin: 0; +} + +input { +display: none; +} + +#graphic h3 a { +border-bottom:2px solid black; +color:black; +display:block; +margin-bottom:2em; +margin-top:3em; +text-align:left; +text-decoration:none; +margin-left: -1.5em; +} + + +#graphic {page-break-after: always; } + +td.l a { padding: 0; margin-right: 1em !important; font-weight:bold;} +#descs td {color: black;} + +/* Get rid of stupid long headers */ +#desctbl { margin-top: 1em; border-top: solid 1px #ccc; page-break-after: always;} +#desctbl table thead { display: none; margin-top: 1em;} +#desctbl table tr td { width: 4em; } +#desctbl table td.lim { width: 40em; } + +#alignments { line-height: 0.9em; } +#alignments center b { + display: block; z-index: 100; position: relative; +} +#alignments center b font { color: black; display: block; text-align: left; font-size: 120%; padding: 0 0 3px; border-bottom: solid 2px #444; margin-left: -1.5em; } + +div#alignments.blRes a { text-decoration: none; color: black; font-weight: bold; } + +#footer { +display: none; +} + +h1 +{ +font-size:120%; +font-weight:bold; +} +#FormatForm,#FormatDownload,#showDetails,#queryHelp,#dbDetails,.reslink +{ + display:none; +} +#multipleSeqs,#queryInfo,.skp,.resLink,.seqlinks,.msg +{ + display:none; +} + +#dbDetails,#refInfo,#seealso,#resStat,#showRefs,dd.hidden +{ + display:none; +} +/* +#querysummary dl +{ + line-height:1.4em; +} + +#querysummary dd +{ + margin-left:20%; + margin-top:-1.2em; +} + +#querysummary dd a +{ + display:none; +} +*/ + +#summary { +font-size:1.2em; +} +#summary { +margin-top:0pt; +padding-bottom:1em; +padding-top:0.5em; +font-family:Verdana,Arial,Sans-Serif; +font-size:90%; + +} +#summarylists { +margin:1em 0pt 0pt; +overflow:hidden; +} +#querysummary { +float:left; +padding:0pt; +width:49%; +} + +#dbsummary { +margin-left:51%; +padding:0pt; +} +#summary dl { +margin:0pt 0pt 0.5em; +padding:0pt; +} +#summary dt, #summary dd { +line-height:1.4em; +} +#summary dt { +float:left; +font-weight:bold; +text-align:right; +width:10em; +margin-top:0; +} +#summary dd { +margin-left:11em; +white-space:normal !important; +} +#summary h3 { +color:#444444; +font-style:italic; +margin-bottom:-0.5em; +margin-top:0pt; +text-align:center; +} +#ht,#graphic,#cddDesc +{ + text-align:center; +} + +#ht +{ + font-weight:bold; +} + +#graphic h3 a,#ovrInfo,#showCDD,.psiInp,.defln caption,#grView.hidden,#RSIFrameDesc +{ + display:none; +} + + +#grView.hidden.shown +{ + display:block; +} + +.print-log-res { position:absolute;left:-10000px;top:auto;width:1px;height:1px;overflow:hidden; } +.print-log-res li { list-style-image: url("images/img_blast_results_gif"); } + +#SwitchDesign,#ytb,.fdb,#debug,.moreHsps,.shcl,#cntDesc,#descTblCtrl,.hdnHeader,td.c0,th.c0,.alnMsgS,.alnHdr,.relInf +{ + display:none; +} + +h3.cap,#RSIFrameAln,.alnRn span, div.hsp .alnParLinks,.ui-ncbiautocomplete-link-pref,.ui-ncbiautocomplete-link-off +{ + display:none; +} + +.alnAll +{ + margin-top:0.5emem; +} +.dlfRow +{ + line-height:1.5em; +} + +span.r label +{ + margin-left:0.5em; +} +td.l a.deflnDesc +{ + font-weight:normal; + text-decoration:none; + color:inherit; +} + +table.alnParams +{ + width:50em; +} +table.alnParams th +{ + font-size:100%; +} + +table.alnParams td +{ + font-size:110%; + padding-top:0.5em; +} + +.oneSeqAln +{ + border-top:1px solid gery; + margin-top:1em; + padding-top:1em; + width:60em; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/remote_data_provider.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,79 @@ +//========================================================================================================= +function RemoteDataProvider(sUrl) { + this.iActiveRequests = 0; + this.sUrl = sUrl; +} + +//------------------------------------------------------------------------------------------------------------- +RemoteDataProvider.prototype.GetHttpObj = function() { + var oHttpObj = null; + try { + oHttpObj = new ActiveXObject("Msxml2.XMLHTTP"); + } catch(e) { + try { + oHttpObj = new ActiveXObject("Microsoft.XMLHTTP") + } catch(oc) { + oHttpObj = null; + } + } + if (!oHttpObj && typeof XMLHttpRequest != "undefined") { + oHttpObj = new XMLHttpRequest(); + } + return oHttpObj; +} + +//------------------------------------------------------------------------------------------------------------- +RemoteDataProvider.prototype.Request = function(sRequest, method) { + var oHttpObj = this.GetHttpObj(); + if (null == oHttpObj) return; + + method = (!method) ? "GET" : "POST"; + var sURL = (method == "GET") ? this.sUrl + "?" + sRequest : this.sUrl; //alert(sURL); + this.iActiveRequests++; + var oThis = this; + oHttpObj.onreadystatechange = function () { + if (oHttpObj.readyState == 4 && oHttpObj.status == 200) { + oThis.onSuccess(oHttpObj); + oThis.iActiveRequests--; + oThis.onStop(); + } else if(oHttpObj.readyState == 4 && oHttpObj.status != 200) { + oThis.onError(oHttpObj); + oThis.iActiveRequests--; + oThis.onStop(); + } + }; + + if (oHttpObj.readyState != 0) oHttpObj.abort(); + this.onStart(); + oHttpObj.open(method, sURL, true); +// oHttpObj.setRequestHeader('Cache-Control', 'no-cache'); + var params = (method == "GET") ? null : sRequest; + if (params) { + oHttpObj.setRequestHeader("Content-type", "application/x-www-form-urlencoded"); + oHttpObj.setRequestHeader("Content-length", params.length); + oHttpObj.setRequestHeader("Connection", "close"); + } + oHttpObj.send(params); +} + +//------------------------------------------------------------------------------------------------------------- +RemoteDataProvider.prototype.onSuccess = function(obj) { + alert(["success:", this.iActiveRequests, obj.responseText]); +} + +//------------------------------------------------------------------------------------------------------------- +RemoteDataProvider.prototype.onStart = function() { +// alert(["start:", this.iActiveRequests]); +} + +//------------------------------------------------------------------------------------------------------------- +RemoteDataProvider.prototype.onStop = function() { +// alert(["start:", this.iActiveRequests]); +} + +//------------------------------------------------------------------------------------------------------------- +RemoteDataProvider.prototype.onError = function(obj) { + //alert(["error:", this.iActiveRequests, obj.status]); +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/results.css Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1224 @@ +#summary { +font-size:1.2em; +} +#summary { +margin-top:0pt; +padding-bottom:1em; +padding-top:0.5em; +font-family:Verdana,Arial,Sans-Serif; +font-size:90%; + +} +#summarylists { +margin:1em 0pt 0pt; +overflow:hidden; +} +#seealso { +margin-left:2em; +} +#querysummary { +float:left; +padding:0pt; +width:49%; +} +#dbsummary { +margin-left:51%; +padding:0pt; +} +#summary dl { +margin:0pt 0pt 0.5em; +padding:0pt; +} +#summary dt, #summary dd { +line-height:1.4em; +} +#summary dt { +float:left; +font-weight:bold; +text-align:right; +width:10em; +margin-top:0; +} +#summary dd { +margin-left:11em; +white-space:normal !important; +overflow:hidden; +} +#summary h3 { +color:#444444; +font-style:italic; +margin-bottom:-0.5em; +margin-top:0pt; +text-align:center; +} + +#multipleSeqs { +font-weight: bold; +} +#multipleSeqs a { +font-size:80%; +font-weight:normal; +} +#breadcrumb { +background:transparent url(images/right-arrow.gif) no-repeat scroll left center; +font-size:93%; +font-weight:bold; +margin-top:-5px; +padding:0pt 6px 0pt 12px; +} +#breadcrumb a { +color:#336699; +} + +#jobTitle +{ +color:#669; +/*color:#2A6980;*/ +font-weight:bold; +margin-bottom:-0.5em; +} + +#type-a #content-wrap {white-space:normal; padding-bottom:2em;} + +#statInfo +{ + font-size:100%; +} + + +#resMsg +{ +background-color:#FFFFCC; +font-size:110%; +/*margin-top:4em; +padding-left:0.5em;*/ +text-align:center; +} + +#seealso label +{ + display:inline; +} + +#seealso a +{ + padding: 0,4px; +} + +a.shown +{ + display:inline; +} + + +table.dbInfo +{ + width:50%; + border:solid 1px gray; + font-size:100%; + border-collapse:collapse; + margin-top:1em; +} +table.dbInfo td, +table.dbInfo caption +{ + border:solid 1px gray; + padding: 1px 4px; +} +table.dbInfo caption { + background-color:#acf; + text-align:center; + border-bottom:none; + margin-bottom:-0.2em; + font-weight:bold; + margin-top:1em; +} +#resStat, #dbDetails +{ + padding-left:25%; +} + +table.dbInfo td +{ + text-align:left; +} + +table.dbInfo th { +visibility:hidden; +/*padding:0;*/ +} + + +table.dbInfo th div { +height:0; +} + +table#Kappa pre +{ + font-size:120%; +} + + +/****** Mark new rules ************/ +/* override main.css rules */ +#type-a #content { +margin: 0 2em; +} + +#type-a h1 { +font-size: 150%; +margin-bottom: 1em; +border-top: solid 1px #ccc; +} + +#type-a h2 { +font-size: 125%; +color: #666; +} + +#type-a h3 { +border: none; +font-size: 110%; +} +#graphic { +text-align: center; +margin: auto; +} + +#multipleSeqs label { +width: 9em; +height: 1em; +text-align: right; +margin-right: 0; +padding: 0 1em; +float: left; +} +#multipleSeqs select { +margin-right: 1em; +font-size: 95%; +} +#multipleSeqs input { +font-size: 95%; +margin-top: -0.25em; +margin-right: 1em; +} +label.other { +font-size: 110%; +font-weight: bold; +} +form#results +{ + display:none; +} + +#hdLink +{ + margin-top:-1.2em; + float:right; +} + +#hdTitle +{ + margin-left:5em; +} +.shownInl +{ + display:inline; +} + +#psiHd +{ + margin-top:1em; +} + +#phiInfo +{ + text-align:center; + color:Green; + font-size:110%; + margin-top:1em; +} +#ht +{ +font-weight:bold; +margin-bottom:-0.9em; +margin-top:0.2em; +text-align:center; +} + +.psiThresh +{ + text-align:center; + color:Green; + font-weight:bold; +} + +#psiThreshA span.shown,#psiThreshB span.shown +{ + display:inline; +} + +a.resArr +{ + color:#666; + font-size:120%; + font-weight:bold; +} + +a.arrowlink.showing +{ + background-image: url(images/down.gif); +} + +#graphic table +{ + background-color:White; +} + +#type-a #content +{ + background-color:#D3DFF5; + border:1px solid #888888; + padding:0 0.5em; + zoom:1; +} + +.resBox +{ + background-color:#eee; + margin-right:1em; + color:#222; + zoom:1; +} + +.resBox1 +{ + background-color:white; +} + +#tryNew,.hl +{ + color:Red; +} + +/*#tryNew +{ + margin-right:20em; +}*/ + + +div#vecSrceen { +margin-bottom:0pt; +margin-left:17%; +margin-top:0pt; +padding-left:2em; +white-space:pre; +width:64%; +zoom:1; +} + +.psiInp +{ + white-space:normal; + margin-bottom:1.5em; +} + +.seqlinks label +{ + display:inline; +} + +.seqlinks input +{ + margin-left:1em; +} +.seqlinks a.ln +{ + margin-left:2em; +} + +.seqlinks a.lnt +{ + margin-left:0.5em; +} + +form.getseq +{ + margin:0; +} + +#queryList option.nohits +{ + color:Gray; +} + +#queryList +{ + float:left; +} + +p#qb +{ + margin-top:0; + margin-bottom:0; +} + +#dn +{ + margin-left:5em; +} + +#dnf +{ + font-size:80%; +} + +/*#FormatForm +{ + margin-left:2em; +}*/ +table.options +{ + width:80%; + margin-top:0.5em; + margin-left:10%; + border-collapse:collapse; + max-width:70em; +} + +form.resbox label +{ + display:inline; +} + +#onPageReformat +{ + position:absolute; + right:0.5em; + border:none; + padding-bottom:1px; + bottom:0.1em; +} + +table.dwnl +{ + width:60%; + margin-left:20%; + height:3em; +} +table.dwnl td +{ + padding-right:0.5em; +} +/* +a#showStat +{ + margin-left:-0.4em; +} +*/ +a.resArrowLinkB:hover,a.resArrowLinkW:hover {text-decoration: underline;} +a.resArrowLinkB,a.resArrowLinkW{ + padding-left: 12px; + background-image: url(images/rightSmallArrow.gif); + background-repeat: no-repeat; + background-position: center left; + -moz-outline-style: none; + text-decoration: none; + text-decoration: underline; +} +a.resArrowLinkB.showing +{ + background-image: url(images/downSmallArrow.gif); +} + +a.resArrowLinkW{ + background-image: url(images/rightSmallWArrow.gif); +} + +a.resArrowLinkW.showing +{ + background-image: url(images/downSmallWArrow.gif); +} +td.dnl +{ + border-left:solid 1px gray; +} +.dnLinks a +{ + margin-left:1em; +} + +.dnLinks +{ + text-align:center; +} +#tdal +{ + width:30em; +} + +.dnHeader +{ + font-size:100%; + font-weight:bold; + text-align:center; +} +#dnHelp +{ + display:inline; + position:relative; + padding-left:0; +} + +table td.frh +{ + background-color:#E0E0E0; + color:Gray; + text-align:center; +} + +#type-a h3.tb,#type-a div.tb +{ + display:inline; + color:Gray; + letter-spacing:normal; + font-size:120%; + font-weight:bold; +} + +#content a.resLink +{ + display:inline; +} + +#content a.resLink.hide +{ + display:none; +} + +ul.msg li p.info { +background: transparent url(images/info.png) no-repeat 6px center; +} + +.blRes +{ + background-color:White; + border:solid 1px #CCCCCC; + padding: 1em; + margin:1em; + /*font-size:110%;*/ + zoom:1; +} +/* Check this for many results */ +div#content +{ + min-width:80em; +} +#hitmtImg +{ + + padding:1em; + border:solid 2px gray; + padding-bottom:2em; +} +#qgr +{ + margin-top:-1.8em; + /*writing-mode:tb-rl;*/ +} +#htmb +{ + margin-top:-2em; + margin-left:11em; + border:solid 1px gray; +} + +#hitMatrixView +{ + margin-top:1em; +} + +#hitMatrixInfo +{ + text-align:center; +} + +#bl2ovrInfo +{ + text-align:left; +} + +.newMln +{ + height:12px; + margin-left:-0.5em; +} + +/***** New staff neew to remove all table#descs from blastRes.css, a.resArr, .psiThresh after formatter upadte *******/ + +h2.resArr a +{ + color:#666; + font-size:105%; + font-weight:bold; + font-family:arial,tahoma,verdana,sans-serif; + white-space:nowrap; +} + +h2.resArr +{ + border-bottom:none; + letter-spacing:normal; + margin:0; + padding:0; + width:15%; +} + +.psiThresh h3 +{ + text-align:center; + color:Green; + font-weight:bold; +} + +/*#alignments +{ + font-size:115%; + font-family:Monospace; + white-space:pre; + line-height:1; +} +*/ +table.defln +{ +font-family: Verdana, Sans-Serif; +font-size: 80%; +_font-size: 86%; +border-collapse: collapse; +width: 100%; +border-bottom:1px solid #018AAC; +} + +table.defln caption +{ +font-weight:bold; +text-align:left; +} + +table.hideCap caption +{ +visibility:hidden; +height:0; +font-size:1%; +} + +table.defln th a { +/*text-decoration: none;*/ +color: #00c; +} + +table.defln th a:visited { +color: #00c; +} + +table.defln th a:hover {position: relative; +text-decoration: underline; +} + +table.defln tr th.l, +table.defln tr td.l { +text-align: left; +} + +table.defln tr th.sp { +background-color: #def; +} + +table.defln tr th, +table.defln tr td { +text-align: center; +padding: 1px 4px; +} + +table.defln tr.first th { +padding-left:18px; +border-left: solid 1px #A0ceff; +border-top: solid 1px #A0ceff; +border-bottom: solid 1px #018aac; +border-right: solid 1px #018aac; +border-top: 1px solid #018AAC; +padding-right: 8px; +padding-bottom: 3px; +background-color: #9cf; +white-space:normal; +line-height: 1.2em +} + + +table.defln td { +border: solid 1px #ccc; +border-width: 0px 1px; +white-space:nowrap; +overflow: hidden; +} + +table.defln tr.first th.sel { +background: #9cf url(images/up.gif) no-repeat center left; +padding-left: 18px; +padding-right: 18px; +} + +table.defln tr:hover { +/*background-color: #def;*/ +} + +/* accessebility styles */ +table.defln.noCaption caption +{ + display:none; +} + + +/* accessebility styles */ +.hdnHeader { +/*visibility:hidden;*/ +font-size:0; +height:0; +} + +div.chs +{ + margin-bottom: -1em; +} + +.psiInp label +{ + display:inline; +} + +h3.tgl +{ + letter-spacing:normal; + margin:0; +} +h3.tgl a +{ + font-size:80%; + color:#222222; + font-family:Verdana,Sans-Serif; +} +div.tgl +{ + margin-top:0; + background-color:White; + border:none; +} +div.tgl table.defln a +{ + font-size:100%; +} + +/************ new alignment styles ************/ + +.sumN, .aln_frame +{ + display: none; +} + +table.alnParams +{ + border:solid 1px #a0a0a0; + border-collapse:collapse; + font-family:Verdana,Arial,Sans-Serif; + font-size:87%; + width:60%; + margin-bottom:1em; +} + +table.alnParams th +{ + background-color:#e8e8e8; + color:#606060; + border:solid 1px #a0a0a0; + padding: 1px 4px; + font-size:86%; +} + +table.alnParams td +{ + border:solid 1px #a0a0a0; + padding: 1px 4px; + white-space:nowrap; +} + + +.aln_feat.hidden +{ +width:0; +padding:0; +} + +a.sortAlnArrowLinkB +{ + padding-left: 12px; + background-image: url(images/downSmallArrow.gif); + background-repeat: no-repeat; + background-position: center left; +} + +a.sortAlnArrowLinkW +{ + padding-left: 12px; + background-image: url(images/downSmallWArrow.gif); + background-repeat: no-repeat; + background-position: center left; +} + +.seqlinks span +{ + margin-left:1em; +} + +.alnSortSeq +{ + margin-bottom:2em; + display:inline; +} + +.alnSortSeq a +{ + font-size:90%; +} +table.alnParams a +{ + display:block; + padding:3px 3px; + font-size:90%; +} + +table.alSeqInf td +{ +vertical-align:top; +} +td.alSeq +{ +padding-left:1em; +} + +td.alSeq.alFirst +{ +white-space:nowrap; +padding-left:0; +} + +td.alTitle +{ +font-size:90%; +} + +img.imn +{ +/* width:30px; + height:15px; +*/ +} + +img.imc +{ + width:15px; + height:15px; +} +td.l img.hidden +{ + display:inline; + visibility:hidden; +} + + +.dflLnk a +{ + padding-left:1em; + font-size:110%; +} + +table.defln td.dflLnk +{ + text-align:left; + padding-bottom:0.5em; + font-size:11px; +} + +.dflLnk label +{ + font-weight:bold; + display:inline; +} +.oneSeqAln .dflLnk +{ +font-family: Verdana, Sans-Serif; +font-size: 80%; +padding-bottom:1em; +width:60%; +} + +table.alnDefln tr td.l +{ + text-align:left; +} + +table.alnDefln td +{ + /*overflow:hidden;*/ + white-space:nowrap; + vertical-align:top; +} + +table.alnDefln td.lim +{ + white-space:normal; + font-size:98%; +} + +/* check specific browser file */ +table.alnDefln div.lim +{ + width:35em; +} + +table.defln tr.dflnAln.shown +{ + display:table-row; +} + +table.alnDefln tr.shown +{ + display:table-row; +} + +.alnDflLn label +{ + font-weight:bold; + display:inline; + font-size:80%; + color:#444444; + padding-right:3px; + padding-left:3px; +} + +.alnDflLn +{ + margin-left:2em; +} + +.alnSortSeq.alnDflLn +{ + margin-left:0.5em; + float:left; + position:absolute; +} + +.alnDflLn input +{ + margin-left:1em; + border:none; +} +.alnDflLn label.hidden +{ + display:none; +} + +h3.sAlnHdr +{ + color:#444444; + display:inline; + letter-spacing:normal; +} + +h3.sAlnHdr a +{ + color:#444444; + text-decoration:none; + margin-left:2em; + font-size:85%; +} + +.alnHdr +{ + padding-top:0.1em; + padding-bottom:0.1em; +} + +.oneSeqAln +{ + padding-left:1em; + padding-top:0.2em; +} + +table.defln tr.dflnAln td +{ + text-align:left; + border:none; + background-color:White; +} + +table.defln tr.dflnAln td input.ch,table.defln tr.dflnAln td h3 +{ + display:none; +} + + +tr.dflnAln .oneSeqAln +{ + font-size:120%; +} + +tr.dflnAln .alnDflLn{ + + margin-left:0; +} + +tr.dflnAln .alnHdr +{ + padding:0; +} + +tr.dflnAln .alnHdr label +{ + font-size:90%; +} +.hil +{ +background-color: #def; +} + + +table.defln tr.odd +{ + background-color:#f8f8f8; +} + +table.defln tr.even +{ + background-color:#e8e8e8; +} +a.dflSeq +{ + color:Gray; + font-weight:bold; + text-decoration:none; + padding-left:0; + display:inline-block; + width:13em; +} +a.dflSeq.nogi +{ + color:#336699; + text-decoration:underline; +} +td.lim +{ + font-size:13px; +} + +.ldsb +{ + padding-left:1em; + color:Gray; + font-size:110%; +} + +a.spr +{ + padding-right:3px; + border-right:solid 1px; +} + + + +#hlp11 +{ + width:60%; + margin-left:22%; + margin-top:0.5em; +} + +/* jig toggler styles */ +a.resLink.ui-ncbitoggler, a.jtg.ui-ncbitoggler,a.resLink.ui-ncbitoggler-open, a.jtg.ui-ncbitoggler-open +{ +padding-left:13px; +color:#336699; +} + +a.resLink.ui-ncbitoggler,a.resLink.ui-ncbitoggler-open +{ + font-size:100%; +} + + +table.options .helplink +{ + font-size:100%; + display:inline; +} + + +span.ui-icon.ui-icon-triangle-1-e,span.ui-icon.ui-icon-triangle-1-s +{ + padding-left: 12px; + background-repeat: no-repeat; + -moz-outline-style: none; + text-decoration: underline; + /*height:18px; + width:20px; */ +} + + + +span.ui-icon.ui-icon-triangle-1-e +{ + background-image: url(images/rightSmallArrow.gif); +} + +span.ui-icon.ui-icon-triangle-1-s +{ + background-position: center left; + background-image: url(images/downSmallArrow.gif); +} + +table.dbInfo.shown +{ + display:table; +} + +#seealso a.hidden +{ + display:none; +} + +#seealso a, #seealso a.hidden.shown +{ + display:inline-block; +} + + +a.ui-ncbitoggler.hidden.shown.jtg, a.ui-ncbitoggler-open.hidden.shown.jtg +{ + display:inline; +} +/**Comment those line to display ncbi-toggler native icon - begin * +a.ui-ncbitoggler span.ui-icon-plus-minus-big, a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open +{ + padding-left: 16px; + background-image: url(images/down.gif); + background-repeat: no-repeat; + background-position: center left; + -moz-outline-style: none; + text-decoration: none; + text-decoration: underline; +} + +a.ui-ncbitoggler span.ui-icon-plus-minus-big +{ + background-image: url(images/right.gif); +} + +a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open +{ + background-image: url(images/down.gif); +} +*Comment those line to diplay ncbi-toggler native icon - end **/ + +a.ui-ncbitoggler span.ui-icon-plus-minus-big, a.ui-ncbitoggler-open span.ui-icon-plus-minus-big-open { + background-image: url("images/ncbitoggler-plus-minus-big.gif"); +} +a.helplink{display:inline} +#summary .ui-widget +{ +font-family:Verdana,Arial,Sans-Serif !important; +font-size:100%; +} +.resBox.ui-widget,.resbox.ui-widget +{ + font-size:100%; +} + +.resetAll +{ + position:absolute; + padding:0; + right:0; + margin-right:5em; +} + +#nft +{ + padding-right:1em; + vertical-align:baseline; +} +#advView +{ + margin-left:3em; +} +#SwitchDesign, a.fdb +{ + color:Red; +} +a.fdb +{ + margin-top: -1.5em; + float:right; + margin-right:5%; +} +#SwitchDesign +{ + left:50em; + right:10em; + position:absolute; + white-space:nowrap; +} + + +#brFtp +{ + margin-left:1em; +} + +#hnr +{ + float:right; +} + +#topLinks +{ + float:left; +} +#topLinksLeft +{ + float:right; +} + +#summary h1 +{ + border-top:none; +} + +#dbPlusSpecies > div { + width: 50%; + margin-top:0.5em; + padding-bottom:0.1em; +} + +#nextDbSet,#lastDbSet { + float: right; +} +#prevDbSet,#lastDbSet { + padding-left:0.5em; +} +#dbSpecies,#dbSpecies caption +{ + margin-top:auto; +} +.cpAdd +{ + font-size:80%; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/results.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,649 @@ +// JScript source code + +//Display Reformat page button only after the whole page is loaded + +function ReformatPageEvent() +{ + var refPageLink = document.getElementById("refPage"); + + //alert(refPageLink); + //alert(refPageLink.getAttribute("submitForm")); + var submitForm = refPageLink.getAttribute("submitForm"); + alert(submitForm); + if(refPageLink && submitForm) { + utils.addEvent(refPageLink, + "click", + function() { + document.getElementById(submitForm).submit(); + }, + false); + } +} + + +function SubmitEvent(linkID) +{ + + var link = document.getElementById(linkID); + //alert(link.getAttribute("submitForm")); + var submitForm = link.getAttribute("submitForm"); + if(link && submitForm) { + utils.addEvent(link, + "click", + function() { + document.getElementById(submitForm).submit(); + }, + false); + } +} + + +function SubmitEventSave(linkID) +{ + + var link = document.getElementById(linkID); + //alert(link.getAttribute("submitForm")); + var submitForm = link.getAttribute("submitForm"); + if(link && submitForm) { + utils.addEvent(link, + "click", + function() { + //$(submitForm).CMD.value = "GetSaved"; + document.getElementById(submitForm).submit(); + }, + false); + } +} + + + + +//This function creates submit form event on click +//form submitted is defined in submitForm attribute +//It also copies params from forms[0] (search paramateres) created by formatter +function SubmitEventNew(linkID) +{ + + var link = document.getElementById(linkID); + //alert(link.getAttribute("submitForm")); + if(!link) return; + var submitForm = link.getAttribute("submitForm"); + if(link && submitForm) { + utils.addEvent(link, + "click", + function() { + document.forms[0].CMD.value = ""; + if(document.forms[0].PAGE_TYPE) { + document.forms[0].PAGE_TYPE.value = ""; + } + var s = document.forms[0].innerHTML; + var form = $(submitForm); + form.innerHTML = s + form.innerHTML; + form.submit(); + }, + false); + } +} + +function GetResults() +{ + form = $("results"); + form.QUERY_INDEX.value = $("queryList")[$("queryList").selectedIndex].value; + form.submit(); +} + +function isIdIn(id, idArray){ + var idSeen=false; + + for(i=0; i<idArray.length; i++){ + if(id==idArray[i]){ + idSeen=true; + break; + } + } + return idSeen; +} + +function GetSelectedSeqString(formName) +{ + var selSeqs = ""; + var idArray=new Array(); + forms = document.getElementsByName(formName); + for(var j=0; j < forms.length; j++){ + for(var i=0; i < forms[j].elements.length; i++){ + var theElem=forms[j].elements[i]; + if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"&&theElem.checked){ + if(!isIdIn(theElem.value, idArray)){ + idArray[idArray.length]=theElem.value; + } + } + } + } + selSeqs = idArray.join(); + return selSeqs; +} + +function ViewSelectedSeqs(e) +{ + var submitForm = $("submitterTop"); + var targetForm = submitForm.getAttribute("seqsForm"); + $("selSeqs").value = GetSelectedSeqString(targetForm); + submitForm.submit(); + utils.preventDefault(e); +} + + +function ViewSelectedSeqTree() +{ + var submitForm = $("treesubmitterTop"); + var targetForm = submitForm.getAttribute("seqsForm"); + $("seqSet").value = GetSelectedSeqString(targetForm); + $("scrWidth").value = screen.width; + $("scrHeight").value = screen.height; + submitForm.submit(); +} + +function ViewTree(linkID) { + link = document.getElementById(linkID); + var target = link.target; + winRef = window.open(link.href + "&screenWidth=" + screen.width + "&screenHeight=" + screen.height, target); +} + +function ViewSelectedSeqMultiAlign() +{ + var submitForm = $("multisubmitterTop"); + var targetForm = submitForm.getAttribute("seqsForm"); + $("seqSetM").value = GetSelectedSeqString(targetForm); + submitForm.submit(); +} + + + +function selectAllSeqs() +{ + var formName = this.getAttribute("seqsForm"); + forms = document.getElementsByName(formName); + for(var j=0; j < forms.length; j++){ + for(var i=0; i < forms[j].elements.length; i++){ + //for(var i=0; i < document.forms[formName].elements.length; i++){ + var theElem=forms[j].elements[i]; + if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"){ + theElem.checked=this.checked; + } + } + } + links = document.getElementsByName("selectAll"); + for(var i=0; i < links.length;i++) { + if(links[i] != this) links[i].checked = this.checked; + } +} + + +function InitSeqAlignLinks() +{ + var links = document.getElementsByName("getSeqs"); + for(var i=0; i < links.length;i++) { + utils.addEvent(links[i],"click",ViewSelectedSeqs,false); + } + links = document.getElementsByName("treeView"); + for(var i=0; i < links.length;i++) { + utils.addEvent(links[i],"click",ViewSelectedSeqTree,false); + } + links = document.getElementsByName("mltiAln"); + for(var i=0; i < links.length;i++) { + utils.addEvent(links[i],"click",ViewSelectedSeqMultiAlign,false); + } + links = document.getElementsByName("selectAll"); + for(var i=0; i < links.length;i++) { + utils.addEvent(links[i],"click",selectAllSeqs,false); + } + + if($("showAlign")) + utils.addEvent($("showAlign"),"click",showHideLinks,false); +} + +function InitDownLoad() +{ + var deltaBlast = ($("diThresh") && $("diThresh").value != "") ? true : false; + if (!deltaBlast && ($("stepNumber").value == "" || $("stepNumber").value < 2)) { + utils.addClass($("dnPSSMPar"),"hidden"); + } +} +function Reformat() +{ + if(utils.hasClass($("FormatForm").FORMAT_ORGANISM,"orgHint")) $("FormatForm").FORMAT_ORGANISM.value = ""; + + $("FormatForm").submit(); +} +function InitCustomButton(bn) +{ + utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false); + utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false); + utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false); + utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false); +} + +function InitAllCustomButtons() +{ + if($("go")) InitCustomButton($("go")); + if($("dn")) InitCustomButton($("dn")); + if($("onPageReformat")) InitCustomButton($("onPageReformat")); +} +function showHideLinks() +{ + var links = document.getElementsByName("selectAll"); + for(var i=0; i < links.length;i++) { + //This is done since IE does not recognize getElementsByName for span elem + var allLinks = utils.getParent(links[i]); + var removeClass,addClass; + if(utils.hasClass(allLinks,"shownInl")) { + removeClass="shownInl"; + addClass="hidden"; + } + else { + removeClass="hidden"; + addClass="shownInl"; + } + utils.removeClass(allLinks,removeClass); + utils.addClass(allLinks,addClass); + } +} +/*remove this function */ +function InitHelpLinks() +{ + for(var i=1; i <= 11;i++) { + InitToggleEvent($("hlp" + i)); + } +} +//This function is used for collapsible deflines onmouseover="showInfo(this)" +//Initialized in showdefline.cpp +function showInfo(elem) +{ + var targetElem = $("info_" + elem.id); + if(!targetElem) return; + if(elem.getAttribute("init") == "on") return; + + Toggle.addTarget(elem, targetElem); + elem.setAttribute("init","on"); +} + +function InitPsiBlast() +{ + //utils.addEvent($("ttt"),"keyup",SetHitlistSize,false); + var hts = document.getElementsByName("HITLIST_SIZE"); + for(var i=0; i < hts.length;i++) { + utils.addEvent(hts[i],"keyup",SetHitlistSize,false); + } + if($("psiInp")) { + var numSubsets = $("psiInp").getAttribute("numSubsets"); + for(var i=1; i <= numSubsets;i++) { + if ($("alnPos" + i)) InitToggleEvent($("alnPos" + i)); + if ($("deflnG" + i)) InitToggleEvent($("deflnG" + i)); + if ($("deflnB" + i)) InitToggleEvent($("deflnB" + i)); + } + } +} + +function SetHitlistSize() +{ + var hts = document.getElementsByName("HITLIST_SIZE"); + for(var i=0; i < hts.length;i++) { + if(this != hts[i]) { + hts[i].value = this.value; + } + } +} +function InitToggleEvent(toggleNode) +{ + if(toggleNode) { + var srcid = toggleNode.getAttribute("toggle"); + if(srcid) Toggle.addTarget(srcid, toggleNode); + } +} + +function InitIFrameLinks() +{ + CheckIframe($("RSIFrameNoRes"),"prlink"); + CheckIframe($("RSIFrameDesc"),"prlink"); + CheckIframe($("RSIFrameAln"),"prlink"); +} + +function CheckIframe(iframe,contentElemID) +{ + if(!iframe) return; + + var iframeDoc; + + if(iframe.contentDocument) {//Firefox + iframeDoc = iframe.contentDocument; + } + else if (iframe.contentWindow) {//IE + iframeDoc = iframe.contentWindow.document; + } + else if(iframe.document) { + iframeDoc = iframe.document; + } + if(iframeDoc){ + if(iframeDoc.getElementById(contentElemID)) { + utils.addClass(iframe,"shown"); + utils.removeClass(iframe,"hidden"); + } + } +} + + +function InitHitMatrix() +{ + if($("bl2seImg")) { + + utils.addEvent($("hitmtImg"),"load", + function() { + utils.addClass($("bl2seImg"),"shown"); + utils.removeClass($("bl2seImg"),"hidden"); + + }, + false); + utils.addEvent($("showHitMatrix"),"click", + function() { + $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc"); + if(utils.hasClass($("htmb"),"shown")) { + utils.addClass($("htmb"),"hidden"); + utils.removeClass($("htmb"),"shown"); + } + else { + utils.addClass($("htmb"),"shown"); + utils.removeClass($("htmb"),"hidden"); + } + }, + false); + + if($("blastSpec") && $("blastSpec").value=="GlobalAln") { + $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc"); + } + } +} + + + + + +function SetFormSubmitEvent() +{ + var el = $("refPage"); + if(el) { + SubmitEventNew("refPage"); + } + SubmitEventNew("frmPage"); + el = $("searchOptions"); + if(el) { + SubmitEventNew("searchOptions"); + } + el = $("saveSearchOptions"); + if(el) { + SubmitEventNew("saveSearchOptions"); + } + //SubmitEventNew("breadCrSearchOptions"); + list = $("queryList"); + if(list) { + utils.addEvent(list,"change",GetResults,false); + } + + list = $("go"); + if(list) { + utils.addEvent(list,"click",GetResults,false); + } + + + list= $("onPageReformat"); + if(list) { + utils.addEvent(list,"click",Reformat,false); + } + + if ($("cddResults") && $("statInfo")) { + jQuery($("cddResults")).ncbitoggler('toggle'); + } + //New design still uses toggle + if ($("showCDD")) { + InitToggleEvent($("cddInfo")); + } + InitToggleEvent($("refInfo")); + InitToggleEvent($("resStat")); + InitToggleEvent($("dbDetails")); + InitToggleEvent($("graphicInfo")); + InitToggleEvent($("descrInfo")); + InitToggleEvent($("alignInfo")); + InitToggleEvent($("ovrInfo")); + InitToggleEvent($("queryInfo")); + InitToggleEvent($("hitMatrixInfo")); + InitToggleEvent($("bl2ovrInfo")); + //Init only for PSI blastfse + if($("prevRID")) InitPsiBlast(); + InitSeqAlignLinks(); + InitAllCustomButtons(); + if($("dnPSSMPar")) InitDownLoad(); + InitHitMatrix(); + if($("noRes")) { + if($("hitCvs")) utils.addClass($("hitCvs"),"hidden"); + if($("hitText")) utils.addClass($("hitText"),"hidden"); + } + InitIFrameLinks(); + showDbDetails(); //fill behind the scene + if ($("showDetails") && utils.hasClass($("showDetails"), "shown")) { + utils.addEvent($("showDetails"), "click", showDbDetails, false); + } + initContentWidth(); +} + +function initContentWidth() { + var lineLengthElem = $("FormatForm").LINE_LENGTH; + if (lineLengthElem) { + var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value); + if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return; + + var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7; + var minWidth = (lineLength + parseInt(17)) * charWidth; + + + var alignView = $("FormatForm").ALIGNMENT_VIEW; + var formatType = $("FormatForm").FORMAT_TYPE; + var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities"); + + var addWidth = ($("FormatForm").OLD_VIEW.checked || queryAnch) ? 250 : 350; + + minWidth = minWidth + parseInt(addWidth) + "px"; + jQuery($("content")).css("min-width", minWidth); + } + +} + + + + + +function ShowHideAlnDeflines(alnID, checkbx) { + var dflTableID = "dln_" + alnID; + if ($(dflTableID)) { + var rmClass, addClass; + if (checkbx.checked) { + rmClass = "hidden"; + addClass = "shown"; + } + else { + rmClass = "shown"; + addClass = "hidden"; + } + var elems = $C(rmClass, "class", $(dflTableID), "tr"); + if (elems) { + //alert(elems.length); + for (var i = 0; i < elems.length; i++) { + utils.removeClass(elems[i], rmClass); + utils.addClass(elems[i], addClass); + } + } + } +} + +function SortAln(e, sortLink, sortItem) { + var p = utils.getParent(sortLink); + var p = utils.getParent(p); + p_TD = utils.getParent(p); + p_TR = utils.getParent(p_TD); + if (utils.hasClass(p_TR, "dflnAln")) { + p_TD.innerHTML = "Reading seqaligns..."; + var gi = p_TD.id.substr(2); + var rid = p_TD.getAttribute("rid"); + getAlignSort(rid, gi, p_TD, sortItem); + e = e || window.event; + utils.preventDefault(e); + return; + } + var links = document.getElementsByName("alnSort"); + if (links.length >= sortItem) { + var href = links[sortItem].href.replace(new RegExp("selectAllTop.*(&|$)"), ""); + var hrefLn = sortLink.href.replace(new RegExp(".*#"), ""); + sortLink.href = href + hrefLn; + } +} + + + +var fullArr; +var numDbs; +function showDbDetails(e,dbSetIndex) +{ + if (!($("dbPlusSpecies"))) return; //No org display + if ($("dbPlusSpecies").getAttribute("init") == "on" && dbSetIndex == null) return; + $("dbPlusSpecies").setAttribute("init", "on"); + + dbInfoUrl = "getDBInfo.cgi"; + var rp = new RemoteDataProvider(dbInfoUrl); + rp.minArr = 10; + + if (!fullArr) { + var arr = $("results").DATABASE.value.split(" "); + numDbs = arr.length; + if (arr.length > rp.minArr) { + fullArr = new Array(); + while (arr.length > 1) { + var arrNew = arr.splice(0, rp.minArr); //does not include stopindex + fullArr.push(arrNew); + } + if (!dbSetIndex) dbSetIndex = 0; + } + } + + rp.onSuccess = function(obj) { + var navDB = document.createElement("div"); + if (fullArr) { + var prevLink, nextLink, firstLink, lastLink; + if (this.currDbSetIndex >= 1) { + var firstStart = 1; + var firstEnd = firstStart + fullArr[0].length - 1; + firstLink = document.createElement("a"); + jQuery(firstLink).attr("href", "#"); + jQuery(firstLink).attr("id", "firstDbSet"); + jQuery(firstLink).attr("onclick", "showDbDetails(event,0);"); + jQuery(firstLink).attr("title", "Databases " + firstStart + "-" + firstEnd); + jQuery(firstLink).html("First " + this.minArr + " dbs"); + + } + if (this.currDbSetIndex >= 1) { + var prevStart = (this.currDbSetIndex - 1) * this.minArr + 1; + var prevEnd = prevStart + fullArr[this.currDbSetIndex - 1].length - 1; + prevLink = document.createElement("a"); + jQuery(prevLink).attr("href", "#"); + jQuery(prevLink).attr("id", "prevDbSet"); + jQuery(prevLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex - 1) + ");"); + jQuery(prevLink).attr("title", "Databases " + prevStart + "-" + prevEnd); + jQuery(prevLink).html("Prev " + this.minArr + " dbs"); + } + + if (this.currDbSetIndex < fullArr.length - 1) { + var nextStart = (this.currDbSetIndex + 1) * this.minArr + 1; + var nextEnd = nextStart + fullArr[this.currDbSetIndex + 1].length - 1; + nextLink = document.createElement("a"); + jQuery(nextLink).attr("href", "#"); + jQuery(nextLink).attr("id", "nextDbSet"); + jQuery(nextLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex + 1) + ");"); + jQuery(nextLink).attr("title", "Databases " + nextStart + "-" + nextEnd); + jQuery(nextLink).html("Next " + this.minArr + " dbs"); + } + if (this.currDbSetIndex < fullArr.length - 1) { + var lastInd = fullArr.length - 1; + var lastStart = numDbs - fullArr[lastInd].length; + var lastEnd = numDbs; + lastLink = document.createElement("a"); + jQuery(lastLink).attr("href", "#"); + jQuery(lastLink).attr("id", "lastDbSet"); + jQuery(lastLink).attr("onclick", "showDbDetails(event," + lastInd + ");"); + jQuery(lastLink).attr("title", "Databases " + lastStart + "-" + lastEnd); + jQuery(lastLink).html("Last " + this.minArr + " dbs"); + } + + + jQuery(navDB).attr("id", "addDbSet"); + if (firstLink) jQuery(navDB).append(firstLink); + if (prevLink) jQuery(navDB).append(prevLink); + if (lastLink) jQuery(navDB).append(lastLink); + if (nextLink) jQuery(navDB).append(nextLink); + } + + jQuery($("dbPlusSpecies")).html(navDB); + jQuery(navDB).after(obj.responseText); + if (fullArr) { + var cap = jQuery($("dbSpecies")).find("caption"); + if (cap) { + var currStart = (this.currDbSetIndex) * this.minArr + 1; + var currEnd = currStart + fullArr[this.currDbSetIndex].length - 1; + var capText = cap.html() + "<div class=\"cpAdd\"> Databases " + currStart + "-" + currEnd; + cap.html(capText); + } + } + }; + rp.onError = function(obj) { + $("dbPlusSpecies").innerHTML += "error, requests:" + this.iActiveRequests + " status:" + obj.status; + } + var dbs; + if (fullArr) { + rp.currDbSetIndex = dbSetIndex; + var currArr = fullArr[dbSetIndex]; + dbs = currArr.join(","); + } + else { + dbs = $("results").DATABASE.value.replace(/ /g, ","); + } + + rp.Request("CMD=getDBOrg&DATABASE=" + dbs, "POST"); + if(e) utils.preventDefault(e); +} + +function synchronizeCheck(id, formName, inputName, isChecked) { + + for (var i = 0; i < document.forms[formName].elements.length; i++) { + var theElem = document.forms[formName].elements[i]; + if (theElem.type == "checkbox" && theElem.name == inputName && id == theElem.value) { + theElem.checked = isChecked; + + } + } + +} + +utils.addEvent(window, + "load", SetFormSubmitEvent, + false); + + +/* If user agent has "safari" in it, include safari-specific stylesheet. */ +if (navigator.userAgent.match(/safari/i) || navigator.userAgent.match(/opera/i)) { +document.write("<link rel='stylesheet' type='text/css' href='css/safari-descriptions.css' media='screen'/>"); +} +if (navigator.userAgent.match(/opera/i)) { +document.write("<link rel='stylesheet' type='text/css' href='css/opera-descriptions.css' media='screen'/>"); +} +if (navigator.userAgent.match(/firefox/i) || navigator.userAgent.match(/safari/i)) { +document.write("<link rel='stylesheet' type='text/css' href='css/firefox-descriptions.css' media='screen'/>"); +} + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/toggle.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,174 @@ + +Toggle = function(node) { + this.init(node); +} + +/** +* @class Creates a new Toggle class with "node" as src +* @return Reutrns a new toggle instance +*/ +Toggle.prototype = { + + init: function(node) { + + // Subclass instance? + if (typeof(arguments[0]) == 'undefined') return; + + var oThis = this; + this.node = node; + + // Initialize "showing" variable based on presence of "showing" or + // "hiding" class. If neither, then showing. Be sure class is + // set to reflect variable value + node.showing = + utils.hasClass(node, "showing") || !utils.hasClass(node, "hiding"); + utils.addClass(node, node.showing ? "showing" : "hiding"); + + // Set notifier for node + utils.addEvent(node, "click", function(e) { + e = e || window.event; + utils.preventDefault(e); + + var theNode = utils.getTargetObj(e); + + // Send message to global notifier, if one exists + if (typeof(Notifier) != 'undefined') { + var notifier = Notifier.getInstance(); + // Notify before change + notifier.Notify(oThis, "change:" + theNode.id, !this.showing); + } + + // Hide or show based on current state + if (this.showing) { + oThis.hide(); + } else { + oThis.show(); + } + + }, false); + + utils.addEvent(node, "selectstart", function(e) { utils.preventDefault(e); }, true); + utils.addEvent(node, "drag", function(e) { utils.preventDefault(e); }, true); + + // Cache "this" for ID lookup + if (!node.id) { + node.id = utils.createNewId(); + } + var m = Toggle.getSrcs(); + m[node.id] = this; + }, + + // Hide targets, and set self to hiding. + hide: function() { + var oThis = this; + + oThis.setHiding(); + if (oThis.listeners) { + forEach(oThis.listeners, function(l) { + oThis.hideTarget(l); + }); + } + }, + + // Show targets, and set self to showing. + show: function() { + var oThis = this; + + oThis.setShowing(); + if (oThis.listeners) { + forEach(oThis.listeners, function(l) { + oThis.showTarget(l); + }); + } + }, + + // Set own presentation to "showing" + setShowing: function() { + utils.addClass(this.node, "showing"); + utils.removeClass(this.node, "hiding"); + this.node.showing = true; + }, + + // Set own presentation to "hiding" + setHiding: function() { + utils.addClass(this.node, "hiding"); + utils.removeClass(this.node, "showing"); + this.node.showing = false; + }, + + // Show a target + showTarget: function(l) { + utils.addClass(l, "shown"); + utils.removeClass(l, "hidden"); + }, + + // Hide a target + hideTarget: function(l) { + utils.addClass(l, "hidden"); + utils.removeClass(l, "shown"); + }, + + // Add a target to this toggle. + add: function(target) { + if (!this.listeners) { + this.listeners = new Array(); + } + this.listeners[this.listeners.length] = target; + + if (utils.hasClass(target, "hidden")) { + this.setHiding(); + this.node.showing = false; + } else { + this.setShowing(); + this.node.showing = true; + } + } +} + +// Show/hide a "target" (a node controlled by the node with the given ID) +Toggle.addTarget = function(srcid, target) { + var tn = Toggle.findOrMake(srcid); + tn.add(target); +} + +// Assoc array of srcs indexed by their ids +Toggle.getSrcs = function() { + if (!Toggle.srcs) { + Toggle.srcs = new Object(); + } + return Toggle.srcs; +} + +// Find or make toggle for given id +Toggle.findOrMake = function(srcid) { + var ts = Toggle.getSrcs(); + var tn = ts[srcid]; + if (!tn) { + tn = new Toggle($(srcid)); + } + return tn; +} + +// This dispatches the call to Toggle.onload, which may be +// overridden by instances (subclasses) +Toggle._onload = function() { + Toggle.onload(); +} + +// A toggle source node controls other nodes that reference it by id using +// their toggle= attribute. A node may be both a toggle source and destination. +Toggle.onload = function() { +//alert("toggle start"); + if(utils.hasClass(document.body,"noToggleCheck")) return; + + shnodes = jQuery("[toggle]"); + // Now hook up dst nodes + forEach(shnodes, function(node) { + // Link toggle node to its source + var srcid = node.getAttribute("toggle"); + Toggle.addTarget(srcid, node); + }); + //alert("toggle 2 end"); +} + +utils.addEvent(window, 'load', Toggle._onload, false);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed_files/utils.js Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,633 @@ +// $Id: utils.js,v 1.4 2014/02/26 14:47:32 zaretska Exp $ + +utils = { + +KeyCode_TAB: 9, +KeyCode_DELETE: 46, +KeyCode_BACKSPACE: 8, +KeyCode_LEFT_ARROW: 37, +KeyCode_RIGHT_ARROW: 39, +KeyCode_HOME: 36, +KeyCode_END: 35, +KeyCode_PAGE_UP: 33, +KeyCode_PAGE_DOWN: 34, +KeyCode_UP_ARROW: 38, +KeyCode_DOWN_ARROW: 40, +KeyCode_ESC: 27, +KeyCode_ENTER: 13, +KeyCode_SPACE: 32, +KeyCode_SHIFT_KEY: 16, +KeyCode_CTRL_KEY: 17, +KeyCode_ALT_KEY: 18, +KeyCode_LEFT_MS_WINDOWS_KEY: 91, +KeyCode_RIGHT_MS_WINDOWS_KEY: 92, +KeyCode_MS_MENU_KEY: 93, + +isObject: function(a) { return (a && typeof a == 'object'); }, + +isArray: function(a) { return this.isObject(a) && a.constructor == Array; }, + +insertInHtml: function(text, obj) { + if (document.all) { + obj.innerHTML += text; + } else { + var range = document.createRange(); + range.setStartAfter(obj); + var docFrag = range.createContextualFragment(text); + obj.appendChild(docFrag); + } + +}, + +replaceInHtml: function(text, obj) { + if (document.all) { + obj.innerHTML = text; + } else { + while (obj.hasChildNodes()) obj.removeChild(obj.firstChild); + var range = document.createRange(); + range.setStartAfter(obj); + var docFrag = range.createContextualFragment(text); + obj.appendChild(docFrag); + } +}, + + +getTargetObj: function(eEvent) { + var oTarget; + var e = eEvent || window.event; + if (e == null) return null; + if (e.srcElement == null) { + oTarget = e.target; + } else { + oTarget = e.srcElement; + } + while ( oTarget && oTarget.nodeType != 1 ) oTarget = oTarget.parentNode; + return oTarget; +}, + + + + +getParent: function(obj) { + if (obj) { + var result = obj.parentNode; + while (result && result.nodeType != 1) result = result.nextSibling; + if (result) return result; + } + return null; +}, + +getFirstChild: function(obj) { + if (obj) { + var result = obj.firstChild; + while (result && result.nodeType != 1) result = result.nextSibling; + if (result) return result; + } + return null; +}, + +getNextSibling: function(obj, tagName) { + if (obj) { + var result = obj.nextSibling; + if (tagName) { + var tn = tagName.toUpperCase(); + while (result && result.tagName != tn) result = result.nextSibling; + } else { + while (result && result.nodeType != 1) result = result.nextSibling; + } + return result; + } + return null; +}, + +getPreviousSibling: function(obj, tagName) { + if (obj) { + var result = obj.previousSibling; + if (tagName) { + var tn = tagName.toUpperCase(); + while (result && result.tagName != tn) result = result.previousSibling; + } else { + while (result && result.nodeType != 1) result = result.previousSibling; + } + return result; + } + return null; +}, + +removeChildren: function(oObj) { + if (!oObj || typeof oObj != "object") return; + while(oObj.hasChildNodes()) oObj.removeChild(oObj.firstChild) +}, + +insertAfter: function(parent, node, referenceNode) { + parent.insertBefore(node, referenceNode.nextSibling); +}, + +nextItem: function(item, nodeName) { + if (item == null) return; + var next = item.nextSibling; + while (next != null) { + if (next.nodeName == nodeName) return next; + next = next.nextSibling; + } + return null; +}, + +previousItem: function(item, nodeName) { + var previous = item.previousSibling; + while (previous != null) { + if (previous.nodeName == nodeName) return previous; + previous = previous.previousSibling; + } + return null +}, + +moveBefore: function(item1, item2) { + var parent = item1.parentNode; + parent.removeChild(item1); + parent.insertBefore(item1, item2); +}, + +moveAfter: function(item1, item2) { + var parent = item1.parentNode; + parent.removeChild(item1); + parent.insertBefore(item1, item2 ? item2.nextSibling : null); +}, + + + + +createCookie: function(name, value, days) { + if (days) { + var date = new Date(); + date.setTime(date.getTime() + (days * 24 * 60 * 60 * 1000)); + var expires = '; expires=' + date.toGMTString(); + } else expires = ''; + document.cookie = name + '=' + value + expires + '; path=/'; +}, + +readCookie: function(name) { + var nameEQ = name + '='; + var ca = document.cookie.split(';'); + for (var i = 0; i < ca.length; i++) { + var c = ca[i]; + while (c.charAt(0)==' ') c = c.substring(1, c.length); + if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length, c.length); + } + return ""; +}, + +eraseCookie: function(name) { + document.cookie = name + "=null; expires=Thu, 01-Jan-1970 00:00:01 GMT; domain=nih.gov; path=/"; + document.cookie = name + "; expires=Thu, 01-Jan-1970 00:00:01 GMT; domain=nih.gov; path=/"; +}, + +addClass: function(element, className) { + if (!this.hasClass(element, className)) { + if (element.className) element.className += " " + className; + else element.className = className; + } +}, + +removeClass: function(element, className) { + var regexp = new RegExp("(^|\\s)" + className + "(\\s|$)"); + element.className = element.className.replace(regexp, "$2"); +}, + +hasClass: function(element, className) { + var regexp = new RegExp("(^|\\s)" + className + "(\\s|$)"); + return regexp.test(element.className); +}, + + +getXY: function (obj){ + /* + +------------- w ---- + | (x,y) + | + h + | + */ + var b={x:0, y:0, w:obj.offsetWidth, h:obj.offsetHeight}; + + if (obj.offsetParent) { + while(obj) { + b.x += obj.offsetLeft; + b.y += obj.offsetTop; + obj = obj.offsetParent; + } + } else if (obj.x) { + b.x = obj.x; + b.y = obj.y; + } + return b; +}, + +/* Based on ppk (untested) */ +getEventXY: function(e) { + var xpos = 0; + var ypos = 0; + e = e || window.event; + xpos = e.pageX || (e.clientX + document.body.scrollLeft + + document.documentElement.scrollLeft); + ypos = e.pageY || (e.clientY + document.body.scrollTop + + document.documentElement.scrollTop); + return {x: xpos, y: ypos}; +}, + +drawText: function (sText, sId, add) { + if (!sId) sId = "debug"; + var obj = document.getElementById(sId); + if (obj) { + if (add) + this.insertInHtml("<br/>" + sText, obj); + else + this.replaceInHtml(sText, obj); + } +}, + + +selectRange: function (oObj /*:object*/, iStart /*:int*/, iLength /*:int*/) { + if (!(oObj && oObj.value)) return; + + if (oObj.createTextRange) { + //use text ranges for Internet Explorer + var oRange = oObj.createTextRange(); + oRange.moveStart("character", iStart); + oRange.moveEnd("character", iLength - oObj.value.length); + oRange.select(); + } else if (oObj.setSelectionRange) { + //use setSelectionRange() for Mozilla + oObj.setSelectionRange(iStart, iLength); + } + //set focus back to the textbox + oObj.focus(); +}, + +getSelection: function() { + var text = ""; + if (window.getSelection) { + text += window.getSelection(); + } else if (document.getSelection) { + text += document.getSelection(); + } else if (document.selection){ //IE + text += document.selection.createRange().text; + } + return text; +}, + + + + +// http://ejohn.org/apps/jselect/event.html +addEvent: function(obj, type, fn, b) { + if (obj.attachEvent) { + var name = "" + type + fn; +// name = name.substring(0, name.indexOf("\n")); // IE This doesn't work + obj["e" + name] = fn; + obj[name] = function(){ obj["e" + name](window.event);} + obj.attachEvent("on" + type, obj[name]); + } else { + obj.addEventListener(type, fn, b); + return true; + } +}, + + +removeEvent: function(obj, type, fn, b) { + if (obj.detachEvent) { + var name = "" + type + fn; +// name = name.substring(0, name.indexOf("\n")); //IE This doesn't work + if ("function" == typeof obj[name]) { + obj.detachEvent("on" + type, obj[name]); + obj[name] = null; + obj["e" + name] = null; + } + } else { + obj.removeEventListener(type, fn, b); + return true; + } +}, + +noBubbleEvent: function(e) { + if (e && e.stopPropagation) e.stopPropagation(); + else window.event.cancelBubble = true; +}, + +targetEvent: function(e) { + if (e.srcElement == null) { + return e.target; + } else { + return window.event.srcElement; + } +}, + +preventDefault: function(e) { + if (e.preventDefault) e.preventDefault(); + else window.event.returnValue = false; +}, + +relatedTarget: function(e) { + if (!e) var e = window.event; + if (e.relatedTarget) return e.relatedTarget; + else if (e.toElement) return e.toElement; + else if (e.fromElement) return e.fromElement; +}, + +readStyle: function(element, property) { + if (element.style[property]) { + return element.style[property]; + } else if (element.currentStyle) { + return element.currentStyle[property]; + } else if (document.defaultView && document.defaultView.getComputedStyle) { + var style = document.defaultView.getComputedStyle(element, null); + if (style) return style.getPropertyValue(property); + } + return ""; +}, + + +printObj: function (oObj, iLevel) { + var s = ""; + var sIdent = ""; + if (!iLevel) iLevel = 0; + for (var i = 0; i < iLevel; i++) { + sIdent += "__"; + } + for (var i in oObj) { + var ss = []; + if ("string" == typeof oObj[i]) { + ss = oObj[i].split("<"); + } + s += sIdent + " " + i + " : [" + (typeof oObj[i]) + "] : " + ss.join("<") + "<br/>"; + // if (oObj[i] && "object" == typeof oObj[i] && iLevel < 2) { + // s+= "<br/>-----" + typeof oObj[i] + " --- " + iLevel + "</br>"; + // s += this.printObj(oObj[i], iLevel + 1); + // } + } + return s; +}, + +jsLoader: { + sBase: "", /* Base is this directory */ + oLoaded: [], + load: function (aScripts) { + + var oS = document.getElementsByTagName("script"); + var k = 0; + for (var j = 0; j < oS.length; j++) { + if (oS[j].src == "") continue; + this.oLoaded[k++] = oS[j].src; + } + + var oHead = document.getElementsByTagName("head")[0]; + + for (var i = 0; i < aScripts.length; i++) { + var sNewSrc = this.sBase + aScripts[i]; + var oS = document.getElementsByTagName("script"); + var b = true; + for (var j = 0; j < this.oLoaded.length; j++) { + if (sNewSrc == this.oLoaded[j]) { +// alert(sNewSrc + " : already loaded"); + b = false; + } + } + + if (b) { + var oScript = document.createElement("script"); + oScript.src = sNewSrc; + oScript.setAttribute("type", "text/javascript"); + oHead.appendChild(oScript); + this.oLoaded[this.oLoaded.length] = sNewSrc; + } + } + } +}, + +// Create an id that doesn't exist in this document +createNewId: function() +{ + var newid = null + + while (!newid || document.getElementById(newid)) { + newid = "XID" + Math.round(Math.random() * 65536).toString(16) + } + return newid +} + +}; + + +String.prototype.trimSpaces = function(trimMode) { + // 0 = trim begin and end + // 1 = trim begin only + // 2 = trim after only + + var targetString = this; + var iPos = 0; + if (!trimMode) trimMode = 0; + + if (trimMode==0 || trimMode==1) { + if (targetString.charAt(iPos)==" ") { + while(targetString.charAt(iPos)==" ") iPos++; + targetString = targetString.substr(iPos); + } + } + + iPos = targetString.length-1; + if (trimMode==0 || trimMode==2) { + if (targetString.charAt(iPos) == " ") { + while(targetString.charAt(iPos) == " ") iPos--; + targetString = targetString.substr(0, iPos + 1); + } + } + return targetString; +} + + + + +/* Shortcuts */ + +// Get elements by Id's +function $() { + var elements = new Array(); + + for (var i = 0; i < arguments.length; i++) { + var element = arguments[i]; + if (typeof element == 'string') + element = document.getElementById(element); + + if (arguments.length == 1) + return element; + + elements.push(element); + } + + return elements; +} + +// Get elements by AttributeValue for Attributename +// http://www.dustindiaz.com/top-ten-javascript/ (but has some errors) +function $C(attrValue, attrName, node, tag) { + //alert([attrValue, attrName, node, tag]) + if ("*" == attrValue) { + return $AN(attrName, node, tag); + } + var oElements = new Array(); + if (!node) node = document; + if (!tag) tag = '*'; + if (!attrName) attrName = 'class'; + + var els = node.getElementsByTagName(tag); + var elsLen = els.length; + var pattern = new RegExp("(^|\\s)" + attrValue + "(\\s|$)"); + var j = 0; + for (i = 0; i < elsLen; i++) { + if (attrName == "class" && pattern.test(els[i].className)) { + // IE behavior +// oElements.push(els[i]); + oElements[j++] = els[i]; + } else if (pattern.test(els[i].getAttribute(attrName))) { + oElements[j++] = els[i]; +// oElements.push(els[i]); + } + } + return oElements; +} + + +function $AN(attrName, node, tag) { + var oElements = new Array(); + if (node == null) node = document; + if (tag == null)tag = '*'; + var els = node.getElementsByTagName(tag); + for (i = 0; i < els.length; i++) { + if (els[i].getAttribute(attrName) != null) { + oElements.push(els[i]); + } + } + return oElements; +} + +function dump(aMessage) { + var consoleService = Components.classes["@mozilla.org/consoleservice;1"] + .getService(Components.interfaces.nsIConsoleService); + consoleService.logStringMessage(aMessage); +} + + +// forEach iterators from Dean Edwards: http://dean.edwards.name/weblog/2006/07/enum/ +// generic enumeration +Function.prototype.forEach = function(object, block, context) { + for (var key in object) { + if (typeof this.prototype[key] == "undefined") { + block.call(context, object[key], key, object); + } + } +}; + +// globally resolve forEach enumeration +var forEach = function(object, block, context) { + if (object) { + var resolve = Object; // default + if (object instanceof Function) { + // functions have a "length" property + resolve = Function; + } else if (object.forEach instanceof Function) { + // the object implements a custom forEach method so use that + object.forEach(block, context); + return; + } else if (typeof object.length == "number") { + // the object is array-like + resolve = Array; + } + resolve.forEach(object, block, context); + } +}; + +// +// Update Array class to JS 1.5 if not yet there. +// + +// array-like enumeration +if (!Array.forEach) { // mozilla already supports this + Array.forEach = function(object, block, context) { + for (var i = 0; i < object.length; i++) { + block.call(context, object[i], i, object); + } + }; +} + +if (!Array.prototype.indexOf) + Array.prototype.indexOf = function(item, startIndex) { + var len = this.length; + if (startIndex == null) + startIndex = 0; + else if (startIndex < 0) { + startIndex += len; + if (startIndex < 0) + startIndex = 0; + } + for (var i = startIndex; i < len; i++) { + var val = this[i] || this.charAt && this.charAt(i); + if (val == item) + return i; + } + return -1; + }; + +if (!Array.prototype.lastIndexOf) + Array.prototype.lastIndexOf = function(item, startIndex) { + var len = this.length; + if (startIndex == null || startIndex >= len) + startIndex = len - 1; + else if (startIndex < 0) + startIndex += len; + for (var i = startIndex; i >= 0; i--) { + var val = this[i] || this.charAt && this.charAt(i); + if (val == item) + return i; + } + return -1; + }; + +if (!Array.prototype.map) + Array.prototype.map = function(func, thisVal) { + var len = this.length; + var ret = new Array(len); + for (var i = 0; i < len; i++) + ret[i] = func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this); + return ret; + }; + +if (!Array.prototype.filter) + Array.prototype.filter = function(func, thisVal) { + var len = this.length; + var ret = new Array(); + for (var i = 0; i < len; i++) { + var val = this[i] || this.charAt && this.charAt(i); + if(func.call(thisVal, val, i, this)) + ret[ret.length] = val; + } + return ret; + }; + +if (!Array.prototype.every) + Array.prototype.every = function(func, thisVal) { + var len = this.length; + for (var i = 0; i < len; i++) + if (!func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this)) + return false; + return true; + }; + +if (!Array.prototype.some) + Array.prototype.some = function(func, thisVal) { + var len = this.length; + for (var i = 0; i < len; i++) + if (func.call(thisVal, this[i] || this.charAt && this.charAt(i), i, this)) + return true; + return false; + }; +