-<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\r
-<html xmlns="http://www.w3.org/1999/xhtml">\r
-<title>\r
-Embedded viewing of Alignments\r
-</title>\r
-<body>\r
-<h1>Embedded viewing of Alignments</h1>\r
-<p>The alignment below was generated from the following files:\r
-<ul>\r
- <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in\r
- FASTA format</li>\r
- <li><a href="plantfdx.features">plantfdx.features</a> - Jalview\r
- Format Sequence Features file</li>\r
- <li><a href="plantfdx.annotations">plantfdx.annotations</a> -\r
- Jalview Alignment Annotations File</li>\r
-</ul>\r
-<applet code="jalview.bin.JalviewLite"\r
- width="756" height="560" archive="../../jalviewApplet.jar">\r
- <param name="file" value="plantfdx.fa">\r
- <param name="annotations" value="plantfdx.annotations">\r
- <param name="features" value="plantfdx.features">\r
- <param name="embedded" value="true">\r
- <param name="userDefinedColour"\r
- value="C=yellow; R,K,H=FF5555; D,E=5555FF">\r
- <param name="showFullId" value="false">\r
- <param name="RGB" value="F2F2FF">\r
- <param name="linkLabel_1" value="SRS">\r
- <param name="linkUrl_1"\r
- value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">\r
- <param name="linkLabel_2" value="Uniprot">\r
- <param name="linkUrl_2"\r
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">\r
- <param name="APPLICATION_URL"\r
- value="http://www.jalview.org/services/launchApp">\r
- </applet>\r
-</p>\r
-</body>\r
-</html>\r
+<!--
+ * 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#embedded"> here</a> to view decorated page</b></div>
+
+<!-- boiler plate link to alternate demopage -->
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+</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>
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/embedded.html" target="_blank">View the source code for this example here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/embedded.html">this page</a> and viewing the page source manually).<p>
+ <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>
+</p>
+<!-- content template end -->
git://source.jalview.org / jalview.git / blobdiff