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-<TITLE>Applet Parameters</TITLE>
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- <p>\r <strong>Quick Links:<ul><li>Download the applet jar file from <a\r href="jalviewApplet.jar">here</a>\r </li>\r <li>Parameters are described <a href="#parameters">below</a></li>\r <li>The javascript API is described <a\r href="jalviewLiteJs.html">here</a></li>\r </ul></strong>\r </p>\r
- <h3 align="left">Useful to know!!</h3>
- <ul>
- <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>
- <font face="Courier New, Courier, mono" align="left"><applet code="jalview.bin.JalviewLite"<em><strong>
- archive="jalviewApplet.jar, mydata.zip"</strong></em>><br>
- </font></li>
- <li> Use Jalview for input to a HTML form. For an example of how to
- code this using Javascript, click <a href="formComplete.html">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>
- </ul>\r <p><strong><font size="2">** NEW FEATURES ** in Jalview 2.7.1</font></strong></p>\r <ul><li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.16452.jar">download the JmolApplet here</a></font></li>\r<li>To use Jmol as the structure viewer for Jalview, you must include \r the jar file in the applet archive argument thus:<br>\r <pre>archive="jalviewApplet.jar,Jmol-12.2.16452.jar"</pre></font>\r </li>\r <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have \r Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the \r original Jalview structure viewer will still be available. <br>\r </li>\r \r </ul>\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>\r <ul>\r <li><font size="2">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>\r <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></font>\r </li>\r <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.\r </font></li></ul>\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>\r <ul>\r <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series</font></li>\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from \r the Jmol binary distribution available at the Jmol Sourceforge site, \r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>\r <li><font size="2">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).</font></li>\r </ul>
- <br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>\r <ul>\r <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>\r </ul> \r <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
- <ul>
- <li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>
- <li><font size="2">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.</font>
- </li>
- <li><font size="2">Regular expressions can be used in URL links for sequence IDs.</font></li>
- <li><font size="2">"debug" parameter to control verbosity of the applet's console output.</font></li>
- <li><font size="2">"showbutton" parameter to disable launch button and open JalviewLite immediatly.</font></li>
- <li><font size="2">"nojmol" parameter to disable check for Jmol classes.</font></li>
- </ul><br>
- <strong><font size="2">**NEW FEATURES** in Jalview 2.3</font></strong></p>
- <ul>
- <li><font size="2">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>
- <param name="PDBFile" value="First.pdb SeqA SeqB
- SeqC"> </font><br>
- <font size="2"><param name="PDBFile2" value="Second.pdb
- A=SeqA B=SeqB C=SeqC"> </font><br>
- <font size="2"><param name="PDBFile3" value="Third.pdb
- D=SeqX B=SeqY C=SeqZ"> </font> <br>
- </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>
- <p> </p>
- </li>
- </ul>
- <strong><font size="2">**NEW FEATURES** in Jalview 2.1</font></strong>
- <ul>
- <li>Jalview Applet can read and display JNet secondary structure annotation
- directly via the <strong>jnetfile</strong> parameter. <br>
- </li>
- <li>Param <font face="Courier New, Courier, mono">UserDefinedColour</font><em>
- </em>- 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>
- <font face="Courier New, Courier, mono"><param name="userDefinedColour"
- value="D,E=red; K,R,H=0022FF; C=yellow"></font><br>
- </li>
- <li>Param <font face="Courier New, Courier, mono">showFeatureSettings</font>
- - this will display the feature settings window when the applet starts.<br>
- </li>
- <li>Param <font face="Courier New, Courier, mono">Application_URL value="http://www.jalview.org/services/launchApp"<br>
- </font>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>
- </li>
- <li>Alignment file can be a series of parameters using eg PFAM format
- <br>
- <font face="Courier New, Courier, mono"><param name="sequence1"
- value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI"><br>
- <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><br>
- </font>(All the usual Jalview File formats are valid, however each
- new line in an alignment file must be entered as a parameter)<font face="Courier New, Courier, mono"><br>
- </font> </li>
- </ul>
- <a name="parameters"></a> <table width="97%" border="1" align="center" >
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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#appletParameters"> here</a> to view decorated page</b></div>
+
+<!-- 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="javascript:doSubmit('jalviewLiteJs')">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 may not be compatible with these settings. </p>
+ <p>For additional deployment notes, <a href="javascript:doSubmit('appletDeployment')">see Applet Deployment</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" >