-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<!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
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * 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/>.
+-->
+<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<!-- InstanceBeginEditable name="doctitle" -->
-<TITLE>JalviewLite API documentation</TITLE>
-<!-- InstanceEndEditable -->
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
-<!-- InstanceBeginEditable name="head" -->
-<!-- InstanceEndEditable -->
-<style type="text/css">
+
+ <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" />
+
+ <!--[if IE 6]>
+ <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">
<!--
-td {
- font-family: Geneva, Arial, Helvetica, sans-serif;
- font-size: 12px;
-}
-.plain {
- font-family: Verdana, Arial, Helvetica, sans-serif;
- font-size: 14px;
- text-decoration: none;
+var timeout = 500;
+var closetimer = 0;
+var ddmenuitem = 0;
+
+// open hidden layer
+function mopen(id)
+{
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
}
-.plain:hover{
- background-color:#000000; color: #F2F2FF;
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
}
-
--->
-</style>
-<script language="JavaScript">
-function genHref()
+
+// go close timer
+function mclosetime()
{
-var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
-for(i=0; i<8; i++)
-{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
-window.location=href;
+ closetimer = window.setTimeout(mclose, timeout);
}
-function getEventTarget(e)
+
+// cancel close timer
+function mcancelclosetime()
{
-if(!e)
-e = window.event;
-if(e.target)
-return e.target;
-return e.srcElement;
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
</script>
+
</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
-var gaJsHost = (("https:" == document.location.protocol) ?
-"https://ssl." : "http://www.");
-document.write(unescape("%3Cscript src='" + gaJsHost +
-"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-var pageTracker = _gat._getTracker("UA-9060947-1");
-pageTracker._trackPageview();
-} catch(err) {}
-</script>
-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
- </tr>
- </table>
- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
-
- <div align="center">
- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p> </p>
- <strong>JalviewLite Javascript API<br></strong>
+
+
+<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>
+ </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>
+ <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>
+ <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>
+ <li><a href="#" 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">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<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>
<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>
+ <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 String getAlignmentFrom(AlignFrame alf, String format, String suffix)
// add the given features or annotation to the current alignment
+// if features are loaded, feature display is automatically enabled
public void loadAnnotation(String annotation)
// add the given features or annotation to the given alignment view
+// if features are loaded, feature display is automatically enabled
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
+// (v2.8)
+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
+// (v2.8)
+public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
+
// get the sequence features in the given format (Jalview or GFF)
public String getFeatures(String format)
public AlignFrame newViewFrom(AlignFrame alf, String name)
// load a new alignment
+// remember to store the AlignFrame object reference
+// if you want to manipulate the new alignment view.
public AlignFrame loadAlignment(String text, String title)
// debug flag - controls output to standard out
public static boolean debug
-</pre> <!-- InstanceEndEditable --></td>
- </tr>
- </table>
+</pre>
+
+</div>
+
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Copyright all rights reserved 2012</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 doi: 10.1093/bioinformatics/btp033
+</p>
+</div>
+</div>
</div>
</body>
-<!-- InstanceEnd --></html>
+</html>
git://source.jalview.org / jalview.git / blobdiff