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+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
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- <a href="#">Documentation</a>
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+ <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>
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- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <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>
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- <a href="#">News Mailing List</a>
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+ <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>
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+ <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="#">Release History</a>
- <a href="#">Jalview Bug Tracker</a>
- <a href="#">Jalview Git Web</a>
- <a href="#">Development News</a>
+ <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>
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- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
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- <a href="#">Training Courses</a>
- <a href="#">Training News</a>
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
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</li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
</ul>
<div style="clear:both"></div>
</div>
<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>
<td width="80" ><strong>value=""></strong></td>
<td width="100%"><strong>Description</strong></td>
</tr>
+ <tr>
+ <td>permissions</td>
+ <td>sandbox</td>
+ <td><strong>This parameter is necessary, and must have the value <em>sandbox</em> to allow the JalviewLite applet to run.</strong></td>
+ </tr>
<tr>
<td>file</td>
<td>fileName</td>
</tr>
<tr>
<td>linkLabel_1</td>
- <td>Uniprot</td>
+ <td>EMBL-EBI Search</td>
<td rowspan="2"><p>Right click on sequence id to see list of available
links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
value. For multiple links, increment the label and url name by
<br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
</tr>
<tr>
- <td> <p><br>
+ <td> <p>
+ <br>
linkUrl_1<br>
</p></td>
<td><p><br>
- http://us.expasy.org/cgi-bin/<br>
- niceprot.pl?$SEQUENCE_ID$</p>
+ http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
</td>
</tr>
<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
</li>
<li>Note parameter "PDBSeq" is no longer required.<br>
</li>
- <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li>
+ <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li>
<p> </p>
</li>
</ul>
</div>
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git://source.jalview.org / jalview.git / blobdiff