+++ /dev/null
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-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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- *
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- * Jalview is free software: you can redistribute it and/or
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- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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--->
-<head>
- <TITLE>Embedded Alignment</TITLE>
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- </div>
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- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
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- <div style="clear:both"></div>
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-<div id="pageWrap">
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-<div id="sideNav">
- <ul>
- <li ><a href="u_applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li class="jvlite-nav-small"><a href="u_embedded.html">Embedded Alignment</a></li>
- <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="u_formComplete.html">Access from Javascript</a></li>
- <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Scary Java warnings ?<br/>Try <a href="embedded.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
-<h2>Embedded viewing of Alignments</h2>
-<p>The alignment below was generated from the following files:
- <ul>
- <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
- FASTA format</li>
- <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
- Format Sequence Features file</li>
- <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
- Jalview Alignment Annotations File</li>
- </ul>
- <applet
- code="jalview.bin.JalviewLite" width="756" height="560"
- archive="u_jalviewApplet.jar">
-<param name="file" value="plantfdx.fa"/>
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-<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>
-</p>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<div id ="footer">
-<div id="innerFooter">
-<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
-<div id="cite">
-<p>
-If you use Jalview in your work, please cite this publication:
-</p>
-<br />
-<p>
-Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
-"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
-</p>
-</div>
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git://source.jalview.org / jalview.git / blobdiff