JAL-1782 refactored JAL-1766 JAL-653 tests to TestNG
[jalview.git] / examples / u_embedded.html
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20 <head>
21   <TITLE>Embedded Alignment</TITLE>
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148       <li ><a href="u_applets.html">JalviewLite Examples</a></li>
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162 <!-- boiler plate link to alternate demopage -->
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166 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
167  Scary Java warnings ?<br/>Try <a href="embedded.html">the signed applet demos</a>
168 </div>
169 <div style="margin:8px; padding:10px; align: left;">
170 <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>
171 </p></div>
172 </div>
173 </div>
174
175 <!-- content template start -->
176 <h2>Embedded viewing of Alignments</h2>
177 <p>The alignment below was generated from the following files:
178   <ul>
179     <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
180       FASTA format</li>
181     <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
182       Format Sequence Features file</li>
183     <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
184       Jalview Alignment Annotations File</li>
185   </ul>
186   <applet
187    code="jalview.bin.JalviewLite" width="756" height="560"
188    archive="u_jalviewApplet.jar">
189 <param name="file" value="plantfdx.fa"/>
190 <param name="features" value="plantfdx.features"/>
191 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
192 <param name="showFullId" value="false"/>
193 <param name="embedded" value="true"/>
194    <param name="linkLabel_1" value="Uniprot"/>
195    <param name="linkUrl_1"
196      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
197    <param name="linkLabel_2" value="EMBL-EBI Search"/>
198    <param name="linkUrl_2"
199      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
200    <param name="APPLICATION_URL"
201      value="http://www.jalview.org/services/launchApp"/>
202 </applet>
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215 <div id="cite">
216 <p>
217 If you use Jalview in your work, please cite this publication:
218 </p>
219 <br />
220 <p>
221 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
222 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
223 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
224 </p>
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