-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<html xmlns="http://www.w3.org/1999/xhtml">
<head>
+ <TITLE>Javascript API</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
- <title>JalviewLite API documentation</title>
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-
- <link href="css/reset.css" rel="stylesheet" type="text/css" />
- <link href="css/style.css" rel="stylesheet" type="text/css" />
-
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
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- <link rel="stylesheet" type="text/css" href="css/ie6.css" />
-<![endif]-->
-
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
-
-<!-- dd menu -->
-<script type="text/javascript">
-<!--
-var timeout = 500;
-var closetimer = 0;
-var ddmenuitem = 0;
-
-// open hidden layer
-function mopen(id)
-{
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
// cancel close timer
mcancelclosetime();
ddmenuitem = document.getElementById(id);
ddmenuitem.style.visibility = 'visible';
-}
-// close showed layer
-function mclose()
-{
+ }
+ // close showed layer
+ function mclose()
+ {
if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
+ }
-// go close timer
-function mclosetime()
-{
+ // go close timer
+ function mclosetime()
+ {
closetimer = window.setTimeout(mclose, timeout);
-}
+ }
-// cancel close timer
-function mcancelclosetime()
-{
+ // cancel close timer
+ function mcancelclosetime()
+ {
if(closetimer)
{
- window.clearTimeout(closetimer);
- closetimer = null;
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
-}
-// close layer when click-out
-document.onclick = mclose;
-// -->
-</script>
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
</head>
<body>
-<div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
-<ul id="buttons">
-<li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
-</ul>
-</div>
-
-
-<div id ="nav">
-<div id="navInner">
-
-<ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="#">Documentation</a>
- <a href="#">Publications</a>
- <a href="#">Credits</a>
- <a href="#">Screenshots</a>
- </div>
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
</li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="#">News Mailing List</a>
- <a href="#">Discussion Mailing List</a>
- <a href="#">Links</a>
- <a href="#">Community News</a>
- </div>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
</li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="#">Release History</a>
- <a href="#">Jalview Bug Tracker</a>
- <a href="#">Jalview Git Web</a>
- <a href="#">Development News</a>
- </div>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
</li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="#">Training Courses</a>
- <a href="#">Training News</a>
- </div>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
</li>
- <li><a href="#" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
-</div>
-
-</div>
-
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+ </div>
<div id="pageWrap">
<div id="sideNav">
-<ul>
-<li><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li class="jvlite-nav-small"><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li class="jvlite-nav-small"><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
</div>
-<div id="content" class="content">
+<div id="content" class="content">
+
+
+<!-- content start -->
+
+
<p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
</p>
<h3>Notes</h3>
</pre>
-</div>
+<!-- content end -->
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
-<div id="copyright"><p>Copyright all rights reserved 2012</p></div>
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
<div id="cite">
<p>
If you use Jalview in your work, please cite this publication:
<p>
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
</p>
</div>
</div>