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<!--
* Jalview - A Sequence Alignment Editor and Viewer (2.11.4.1)
* Copyright (C) 2024 The Jalview Authors
*
* 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/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#appletDeployment"> here </a> to view decorated page</b></div>
<!-- content start -->
<h2 name="appletDeployment"> Notes on applet deployment</h2>
<table width=80% border="1">
<tr><th colspan="2" align="center">Required Dependency Downloads</th></tr>
<tr>
<th>Dependency</th>
<th>Description</th>
</tr>
<tr>
<td><a href="http://www.jalview.org/builds/develop/examples/jalviewApplet.jar">JalviewApplet.jar</a> </td>
<td>Main Jalview Applet Jar</td>
</tr>
<tr>
<td><a href="http://www.jalview.org/builds/develop/examples/JmolApplet-14.6.4_2016.10.26.jar">JmolApplet-14.6.4_2016.10.26.jar</a> </td>
<td>Jmol Applet Jar</td>
</tr>
<tr>
<td><a href="http://www.jalview.org/builds/develop/examples/java-json.jar">java-json.jar</a></td>
<td>Required for BioJSON Generation</td>
</tr>
<tr>
<td><a href="http://www.jalview.org/builds/develop/examples/json_simple-1.1.jar">json_simple-1.1.jar</a></td>
<td>Required for BioJSON Generation</td>
</tr>
</table>
<p>To run Jalview applet in your web page download the Jars listed above. The snippet below shows a minimal code for embedding Jalview applet into a web page.
<pre><code>
<applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox" />
<param name="file" value="plantfdx.fa" />
<param name="features" value="plantfdx.features" />
<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF" />
<param name="showFullId" value="false" />
<param name="embedded" value="true" />
<param name="linkLabel_1" value="Uniprot" />
<param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$" />
<param name="linkLabel_2" value="EMBL-EBI Search" />
<param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$" />
<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp" />
</applet>
</code></pre>
<ul>
<li>View full list of <a href="javascript:doSubmit('appletParameters')"> supported applet parameters here.</a></li>
<li>Package all your data files into a single (or multiple) zip /
jar files. This is very useful to reduce download time of large data
files. The applet archive tag can take multiple entries separated by
commas, eg<br> <pre><applet code="jalview.bin.JalviewLite"<em><strong> archive="jalviewApplet.jar, mydata.zip"</strong></em>>
</pre>
</li>
<li>Use Jalview for input to a HTML form. For an example of how to
code this using Javascript, click <a
href="javascript:doSubmit('formComplete')">here</a>. <br>
</li>
<li>Embed Jalview into the web page, without the "Start
Jalview" button by setting the embed parameter to true;<br>
<param name="embedded" value="true">
</li>
<li>For more examples, see the links to the left.</li>
</ul>
<table border="1" width=80%>
<tr><th colspan="2">Applet Release History</th>
<tr>
<th>Release</th>
<th>New Features / required changes</th>
</tr>
<tr>
<td><strong>2.9<br>(Latest)</strong></td>
<td>
<ul>
<li>Split Views for cDNA and Protein alignments<br/>Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
</li>
<li>Jmol compatibility updated to Jmol 14.2.x series - <a href="JmolApplet-14.2.14_2015.06.11.jar">download the JmolApplet here </a></li>
<li>The Jmol jar must be updated from <b>'JmolApplet-12.2.4.jar'</b> to <b>'JmolApplet-14.2.14_2015.06.11.jar'</b> in the applet archive argument as highlighted in red below:<br>
<pre>archive="jalviewApplet.jar,<font color="red">JmolApplet-14.2.14_2015.06.11.jar,</font>java-json.jar,json_simple-1.1.jar"</pre>
</li>
<li>BioJson - A Json file format for representing a single multiple sequence alignment.
Biojson uses the following external libraries: java-json and json_simple-1.1. <br>Hence the jar files highlighted in red must be included in the applet archive argument as follows:<br>
<pre>archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,<font color="red">java-json.jar,json_simple-1.1.jar</font>"</pre>
</li>
</ul>
</td>
</tr>
<tr>
<td><strong>2.8</strong></td>
<td><ul>
<li>Normalised sequence logo display
</li>
<li>RNA secondary structure annotation row
</li>
<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></li>
<li>To use Jmol as the structure viewer for Jalview, you must include
the jar file in the applet archive argument thus:<br>
<pre>archive="jalviewApplet.jar,Jmol-12.2.4.jar"</pre>
</li>
<li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
original Jalview structure viewer will still be available. <br>
</li>
</ul></td>
</tr>
<tr>
<td><strong>2.7</strong></td>
<td><ul>
<li>Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
<li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul>
</li>
<li>New <a href="javascript:doSubmit('jalviewLiteJs')">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
</li></ul>
<p><strong>**NEW FEATURES** in Jalview 2.6</strong></p>
<ul>
<li>Jmol compatibility updated to Jmol 12.1.x series</li>
<li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
the Jmol binary distribution available at the Jmol Sourceforge site,
or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
<li>Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</li>
</ul></td>
</tr>
<tr>
<td><strong>2.5</strong></td>
<td><ul>
<li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li> </ul>
</td>
</tr>
<tr>
<td><strong>2.4</strong></td>
<td><ul>
<li>New applet API methods for feature display control, views, and obtaining current selection via javascript.</li>
<li>Group show and hide parameters:
"showfeaturegroups" and
"hidefeaturegroups". Both take a list
of feature group names (separarated by "|" by default) to hide or show on the displayed
alignment.
</li>
<li>Regular expressions can be used in URL links for sequence IDs.</li>
<li>"debug" parameter to control verbosity of the applet's console output.</li>
<li>"showbutton" parameter to disable launch button and open JalviewLite immediatly.</li>
<li>"nojmol" parameter to disable check for Jmol classes.</li>
</ul></td>
</tr>
<tr>
<td><strong>2.3</strong></td>
<td><ul>
<li>Note that Parameter "PDBFile" now takes
the PDB file followed by a space separated list of alignment sequence
ids to associate the structure to. It is also possible to associate
multiple PDB files by adding an incremental value to PDBFile (up to
10). It is also possible to map specific sequences to specific chains
by using the following notation:<br>
<br>
<pre>
<param name="PDBFile" value="First.pdb SeqA SeqB
SeqC"><br>
<param name="PDBFile2" value="Second.pdb
A=SeqA B=SeqB C=SeqC"><br>
<param name="PDBFile3" value="Third.pdb
D=SeqX B=SeqY C=SeqZ"><br>
</pre>
</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="/development">versions archive if you want to download the old Jmol applet</a>.</li>
</ul></td>
</tr>
<tr>
<td><strong>2.1</strong></td>
<td><ul>
<li>Jalview Applet can read and display JPred secondary structure annotation
directly via the <strong>jnetfile</strong> parameter. <br>
</li>
<li>Param "UserDefinedColour" - specify your own colours for each residue using a semi colon
separated list. Multiple residues can be assigned the same colour
using commas. eg:<br>
<pre><param name="userDefinedColour"
value="D,E=red; K,R,H=0022FF; C=yellow"></pre>
</li>
<li>Param "showFeatureSettings"
- this will display the feature settings window when the applet starts.
</li>
<li>Param "Application_URL" value="http://www.jalview.org/services/launchApp"<br/>
This calls a servlet which creates a JNLP file with the alignment
file, annotations file and features file of the applet as arguments.
If the user has Java installed, the returned JNLP file should start
up the full Jalview Application. BUT this does not currently work
for alignment files added to the applet in a zip file.
<br/>Look at the XML comments in the file downloaded from <a href="http://www.jalview.org/services/launchApp">The LaunchApp page</a> for full documentation.
</li>
<li>Alignment file can be a series of parameters using eg PFAM format
<br>
<pre><param name="sequence1"
value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI"><br>
<param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><br>
</pre>(All the usual Jalview File formats are valid, however each
new line in an alignment file must be entered as a parameter)</li>
</ul></td>
</tr>
</table>
<!-- content end -->
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