-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!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
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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+<html xmlns="http://www.w3.org/1999/xhtml">
<head>
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<TITLE>JalviewLite Applet API and Form Complete Example</TITLE>
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-<!-- InstanceBeginEditable name="head" -->
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-<style type="text/css">
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
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+<![endif]-->
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+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
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+<!-- dd menu -->
+<script type="text/javascript">
<!--
-td {
- font-family: Geneva, Arial, Helvetica, sans-serif;
- font-size: 12px;
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-.plain {
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- text-decoration: none;
+var timeout = 500;
+var closetimer = 0;
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+
+// open hidden layer
+function mopen(id)
+{
+ // cancel close timer
+ mcancelclosetime();
+
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+ closetimer = window.setTimeout(mclose, timeout);
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-function getEventTarget(e)
+
+// cancel close timer
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+
+// close layer when click-out
+document.onclick = mclose;
+// -->
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+
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-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
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-</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>
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- </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>
+
+
+<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()">
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+ <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><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li class="jvlite-nav-small"><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>
+</div>
+
+<div id="content" class="content">
<strong>Using the <a href="jalviewLiteJs.html">JalviewLite API</a> to fill out forms using data from JalviewLite<br></strong>
Click the Javascript buttons below to interact with the Applet
instance on the page.<br>
View the source in your browser to see how it has been done. <br>
<a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
- <applet code="jalview.bin.JalviewLite" width="140" height="35"
+ <applet code="jalview.bin.JalviewLite" width="0" height="0"
archive="jalviewApplet.jar" name="Jalview">
<param name="file" value="plantfdx.fa">
<param name="features" value="plantfdx.features">
<param name="windowHeight" value="500">
<param name="windowWidth" value="650">
<param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
- <param name="linkUrl_1"
- value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
- <param name="linkLabel_2" value="Uniprot">
- <param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="hidefeaturegroups" value="uniprot" />
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+<param name="hidefeaturegroups" value="uniprot" />
<param name="showbutton" value="false" />
</applet>
<form name="exampleForm"><br>
onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
value="Hide groups" /></div>
</form>
-
-<!-- InstanceEndEditable --></td>
- </tr>
- </table>
+ </div>
+</div>
+<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>
-</body>
-<!-- InstanceEnd --></html>
+</div>
+
+<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></body>
+</html>
+
\ No newline at end of file