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-<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>
+<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>
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-<h2><a name="appletdeploymentnotes"/>Notes on applet deployment</h2>
- <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>
- <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><a href="javascript:doSubmit('appletParameters')">View full list of supported parameters here.</a> </li>
- </ul>
-
- <p><strong>**NEW FEATURES** in Jalview 2.9</strong></p>
+<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>
<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>
- </p>
- <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
- <ul>
+ </td>
+ </tr>
+ <tr>
+ <td><strong>2.8</strong></td>
+ <td><ul>
<li>Normalised sequence logo display
</li>
<li>RNA secondary structure annotation row
original Jalview structure viewer will still be available. <br>
</li>
- </ul>
- <p><strong>**NEW FEATURES** in Jalview 2.7</strong></p>
- <ul>
+ </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>
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>
- <br><strong>**NEW FEATURES** in Jalview 2.5</strong></p>
- <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>
- <br><strong>**NEW FEATURES** in Jalview 2.4</strong></p>
- <ul>
+ </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
<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><br>
- <strong>**NEW FEATURES** in Jalview 2.3</strong></p>
- <ul>
+ </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
<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>
- <p> </p>
- </li>
- </ul>
- <strong>**NEW FEATURES** in Jalview 2.1</strong>
- <ul>
- <li>Jalview Applet can read and display JNet secondary structure annotation
+
+ </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
<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>
+ </ul></td>
+ </tr>
+</table>
+
+
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git://source.jalview.org / jalview.git / blobdiff