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+<!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">
+ * 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/>.
+ -->
<head>
-<TITLE>Applet Parameters</TITLE>
+ <TITLE>Applet Parameters</TITLE>
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-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
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+ var closetimer = 0;
+ var ddmenuitem = 0;
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+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
- // close old layer
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+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
- // get new layer and show it
- ddmenuitem = document.getElementById(id);
- ddmenuitem.style.visibility = 'visible';
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
-}
-// close showed layer
-function mclose()
-{
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
-// go close timer
-function mclosetime()
-{
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-}
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
-// cancel close timer
-function mcancelclosetime()
-{
- if(closetimer)
- {
- window.clearTimeout(closetimer);
- closetimer = null;
- }
-}
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
-// close layer when click-out
-document.onclick = mclose;
-// -->
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+ document.onclick = mclose;
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+ <script>
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+ </script>
+
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<body>
-<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">
-
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- <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>
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- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
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- <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="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>
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- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
+ <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>
- </li>
- <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="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
-</div>
-</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="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="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="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="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="appletParameters.html">Applet Parameters</a></li>
-<li><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 ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li class="jvlite-nav-small"><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">
- <p>
- <strong>Quick Links:<ul><li>Download the applet jar file from <a
- href="jalviewApplet.jar">here</a>
- </li>
- <li>As of Jalview 2.8b1, the applet is signed, with 'sandbox' permissions</li>
- <li>Parameters are described <a href="#parameters">below</a></li>
- <li>The javascript API is described <a
- href="jalviewLiteJs.html">here</a></li>
- </ul></strong>
- </p>
- <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+
+
+<!-- content start -->
+<h2>JalviewLite Applet Parameter Documentation</h2>
+<p>
+The JalviewLite applet is configured through a series of applet parameters,
+which are described <a href="#parameters"> below</a>. Once initialised,
+the applet can be interacted with <em>via</em> its
+<a href="jalviewLiteJs.html">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
+</p>
+ <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
<p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
<a name="parameters"></a> <table width="97%" class="borderTable" align="center" >
<tr>
<param name="embedded"
value="true"> </li>
</ul>
- <p><strong>**APPLET SECURITY WARNINGS**</strong><ul><li>Since January 2014, only signed applets are allowed to run in the web page by default. We provide a range of different signed version of JalviewLite and JmolApplet that can be used in various situations.</li>
- <li>The default version of JalviewLite is signed for sandbox execution.</li>
- </ul></p>
<p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
<ul>
<li>Normalised sequence logo display
new line in an alignment file must be entered as a parameter)</li>
</ul>
-</div>
-</div>
+
+<!-- content end -->
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
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git://source.jalview.org / jalview.git / blobdiff