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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
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+ *
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+ *
+ * Jalview is free software: you can redistribute it and/or
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- <p> </p>
- <strong>JalviewLite Javascript API<br></strong>
+
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+
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+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
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+ </div>
+
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+ <div id="navInner">
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+ <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 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">
+
+
+<!-- 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>The best way to learn how to use the API is to see it in action on the demonstration pages below:</p>
- <ul>
- <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
- <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other.</a></li>
- <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page (EXPERIMENTAL! please provide feedback!).</a></li>
- <li><a href="javascriptLaunch.html">launch JalviewLite from a javascript button</a></li>
-
- </ul>
- <h4>Notes</h4>
+</p>
+ <h3>Notes</h3>
<ul>
<li>Unfortunately Javascript - Java communication is not possible
using Internet Explorer or Opera on Macs. Please use Safari or
</li>
</ul>
<a name="api">
- <h4>JalviewLite's Java API</h4></a>
+ <h1>JalviewLite's Javascript API</h1></a>
<p>The following public methods on the jalviewLite applet are available to be called from javascript:</p>
<pre>//get list of IDs of selected sequences
public String getSelectedSequences()
public void loadAnnotationFrom(AlignFrame alf, String annotation)
// parse the given string as a jalview or GFF features file and optionally enable feature display on the current alignment
-// (v2.7.1)
+// (v2.8)
public abstract void loadFeatures(String features, boolean autoenabledisplay)
// parse the given string as a jalview or GFF features file and optionally enable feature display on the given alignment
-// (v2.7.1)
+// (v2.8)
public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
// get the sequence features in the given format (Jalview or GFF)
// debug flag - controls output to standard out
public static boolean debug
-</pre> <!-- InstanceEndEditable --></td>
- </tr>
- </table>
+</pre>
+
+
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+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<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>
+<br />
+<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 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
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