JAL-1782 refactored JAL-1766 JAL-653 tests to TestNG
[jalview.git] / examples / applets.html
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21   <TITLE>JalviewLite Examples</TITLE>
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147   <ul>
148       <li class="jvlite-nav-small"><a href="applets.html">JalviewLite Examples</a></li>
149       <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
150       <li ><a href="appletParameters.html">Applet Parameters</a></li>
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154       <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
155       <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
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162 <!-- boiler plate link to alternate demopage -->
163
164 <div style="width: 100%">
165 <div style="width:35%; align:left; float:right;">
166 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
167  Examples aren't working ?<br/>Try <a href="u_applets.html">the unsigned 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="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
171 </p></div>
172 </div>
173 </div>
174
175 <!-- content template start -->
176
177 <p align="left">
178 <h2>JalviewLite Button Examples</h2>
179 Try out JalviewLite by pressing one of the buttons below.<br/>
180  For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
181 <p>&nbsp;</p><div align="center">
182   <p align="center">
183     <h2>Ferredoxins, chloroplast precursor related UniRef50
184       cluster</h2>
185     <br /> (15 sequences x 150 residues)
186   </p>
187   <table width="90%">
188     <tr>
189       <td width="10%" valign="center">
190         <applet
191    code="jalview.bin.JalviewLite" width="140" height="35"
192    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
193 <param name="permissions" value="sandbox"/>
194 <param name="file" value="uniref50.fa"/>
195 <param name="treeFile" value="ferredoxin.nw"/>
196 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
197 <param name="sortByTree" value="True"/>
198 <param name="showSequenceLogo" value="true"/>
199 <param name="showGroupConsensus" value="true"/>
200 <param name="showFullId" value="false"/>
201    <param name="linkLabel_1" value="Uniprot"/>
202    <param name="linkUrl_1"
203      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
204    <param name="linkLabel_2" value="EMBL-EBI Search"/>
205    <param name="linkUrl_2"
206      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
207    <param name="APPLICATION_URL"
208      value="http://www.jalview.org/services/launchApp"/>
209 </applet>
210 </td>
211       <td valign="center">User Defined Colours, loads an associated
212         Newick format tree file which is used to sort the alignment, and
213         group consensus and sequence logos are shown below the alignment.</td>
214     </tr>
215     <tr>
216       <td width="10%" valign="center"><applet
217    code="jalview.bin.JalviewLite" width="140" height="35"
218    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
219 <param name="permissions" value="sandbox"/>
220 <param name="file" value="uniref50.fa"/>
221 <param name="features" value="exampleFeatures.txt"/>
222 <param name="showFullId" value="false"/>
223 <param name="windowHeight" value="500"/>
224 <param name="windowWidth" value="650"/>
225 <param name="showFeatureSettings" value="true"/>
226 <param name="wrap" value="true"/>
227 <param name="showAnnotation" value="false"/>
228    <param name="linkLabel_1" value="Uniprot"/>
229    <param name="linkUrl_1"
230      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
231    <param name="linkLabel_2" value="EMBL-EBI Search"/>
232    <param name="linkUrl_2"
233      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
234    <param name="APPLICATION_URL"
235      value="http://www.jalview.org/services/launchApp"/>
236 </applet>
237 </td>
238       <td valign="center">Displays a features file on the alignment</td>
239     </tr>
240     <tr>
241       <td width="10%" valign="center"><applet
242    code="jalview.bin.JalviewLite" width="140" height="35"
243    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
244 <param name="permissions" value="sandbox"/>
245 <param name="file" value="uniref50.fa"/>
246 <param name="showFullId" value="false"/>
247 <param name="windowHeight" value="500"/>
248 <param name="windowWidth" value="650"/>
249 <param name="wrap" value="true"/>
250 <param name="showAnnotation" value="false"/>
251 <param name="defaultColour" value="Strand Propensity"/>
252 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
253    <param name="linkLabel_1" value="Uniprot"/>
254    <param name="linkUrl_1"
255      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
256    <param name="linkLabel_2" value="EMBL-EBI Search"/>
257    <param name="linkUrl_2"
258      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
259    <param name="APPLICATION_URL"
260      value="http://www.jalview.org/services/launchApp"/>
261 </applet>
262 </td>
263       <td valign="center">Associates PDB file 1GAQ with sequence
264         FER1_MAIZE</td>
265     </tr>
266     <tr>
267       <td width="10%" valign="center"><applet
268    code="jalview.bin.JalviewLite" width="140" height="35"
269    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
270 <param name="permissions" value="sandbox"/>
271 <param name="file" value="jpred_msa.fasta"/>
272 <param name="jnetfile" value="jpred_msa.seq.concise"/>
273 <param name="showFullId" value="false"/>
274 <param name="windowHeight" value="515"/>
275 <param name="windowWidth" value="650"/>
276 <param name="showAnnotation" value="true"/>
277 <param name="defaultColour" value="Clustal"/>
278    <param name="linkLabel_1" value="Uniprot"/>
279    <param name="linkUrl_1"
280      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
281    <param name="linkLabel_2" value="EMBL-EBI Search"/>
282    <param name="linkUrl_2"
283      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
284    <param name="APPLICATION_URL"
285      value="http://www.jalview.org/services/launchApp"/>
286 </applet>
287                                                        </td>
288       <td valign="middle">Displays a Multiple Sequence Alignment
289         Based JNet Prediction for a Sequence</td>
290     </tr>
291   </table>
292   <p>
293     <h2>RF00031 RFAM Alignment with per sequence secondary
294       structure</h2>
295   </p>
296   <table width="90%">
297     <tr>
298       <td width="10%" valign="center"><applet
299    code="jalview.bin.JalviewLite" width="140" height="35"
300    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
301 <param name="permissions" value="sandbox"/>
302 <param name="file" value="RF00031_folded.stk"/>
303 <param name="showFullId" value="false"/>
304 <param name="windowHeight" value="515"/>
305 <param name="windowWidth" value="650"/>
306 <param name="showAnnotation" value="true"/>
307 <param name="defaultColour" value="Purine/Pyrimidine"/>
308    <param name="APPLICATION_URL"
309      value="http://www.jalview.org/services/launchApp"/>
310 </applet>
311 </td>
312       <td valign="center">Displays an RFAM RNA fold family with
313         secondary structure annotation</td>
314     </tr>
315   </table>
316   <p>
317     <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
318   </p>
319   <table width="90%">
320     <tr>
321       <td width="10%" valign="center"><applet
322    code="jalview.bin.JalviewLite" width="140" height="35"
323    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
324 <param name="permissions" value="sandbox"/>
325 <param name="file" value="estrogenReceptorCdna.fa"/>
326 <param name="file2" value="estrogenReceptorProtein.fa"/>
327 <param name="enableSplitFrame" value="true"/>
328 <param name="scaleProteinAsCdna" value="true"/>
329 <param name="showFullId" value="false"/>
330 <param name="windowHeight" value="300"/>
331 <param name="windowWidth" value="800"/>
332 <param name="showAnnotation" value="true"/>
333 <param name="showSequenceLogo" value="true"/>
334 <param name="defaultColour" value="Purine/Pyrimidine"/>
335    <param name="APPLICATION_URL"
336      value="http://www.jalview.org/services/launchApp"/>
337 </applet>
338 </td>
339       <td valign="center">Displays a split window view of protein and its related cDNA</td>
340     </tr>
341   </table>
342 </div>
343 <!-- content template end -->
344
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353 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
354 <div id="cite">
355 <p>
356 If you use Jalview in your work, please cite this publication:
357 </p>
358 <br />
359 <p>
360 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
361 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
362 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
363 </p>
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