examples/applets.html

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   3     * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
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  20   <TITLE>JalviewLite Examples</TITLE>
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  94     <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
  95     <ul id="buttons">
  96       <li id="applet"><a href="applets.html" title="applet"></a></li>
  97       <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
  98     </ul>
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 100
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 141
 142   </div>
 143 <div id="pageWrap">
 144
 145 <div id="sideNav">
 146   <ul>
 147       <li class="jvlite-nav-small"><a href="applets.html">JalviewLite Examples</a></li>
 148       <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
 149       <li ><a href="appletParameters.html">Applet Parameters</a></li>
 150       <li ><a href="embedded.html">Embedded Alignment</a></li>
 151       <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
 152       <li ><a href="formComplete.html">Access from Javascript</a></li>
 153       <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
 154       <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
 155   </ul>
 156 </div>
 157
 158 <div id="content" class="content">
 159
 160
 161 <!-- boiler plate link to alternate demopage -->
 162
 163 <div style="width: 100%">
 164 <div style="width:35%; align:left; float:right;">
 165 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
 166  Examples aren't working ?<br/>Try <a href="u_applets.html">the unsigned applet demos</a>
 167 </div>
 168 <div style="margin:8px; padding:10px; align: left;">
 169 <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>
 170 </p></div>
 171 </div>
 172 </div>
 173
 174 <!-- content template start -->
 175
 176 <p align="left">
 177 <h2>JalviewLite Button Examples</h2>
 178 Try out JalviewLite by pressing one of the buttons below.<br/>
 179  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>
 180 <p>&nbsp;</p><div align="center">
 181   <p align="center">
 182     <h2>Ferredoxins, chloroplast precursor related UniRef50
 183       cluster</h2>
 184     <br /> (15 sequences x 150 residues)
 185   </p>
 186   <table width="90%">
 187     <tr>
 188       <td width="10%" valign="center">
 189         <applet
 190    code="jalview.bin.JalviewLite" width="140" height="35"
 191    archive="jalviewApplet.jar">
 192 <param name="permissions" value="sandbox"/>
 193 <param name="file" value="uniref50.fa"/>
 194 <param name="treeFile" value="ferredoxin.nw"/>
 195 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
 196 <param name="sortByTree" value="True"/>
 197 <param name="showSequenceLogo" value="true"/>
 198 <param name="showGroupConsensus" value="true"/>
 199 <param name="showFullId" value="false"/>
 200    <param name="linkLabel_1" value="Uniprot"/>
 201    <param name="linkUrl_1"
 202      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 203    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 204    <param name="linkUrl_2"
 205      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 206    <param name="APPLICATION_URL"
 207      value="http://www.jalview.org/services/launchApp"/>
 208 </applet>
 209 </td>
 210       <td valign="center">User Defined Colours, loads an associated
 211         Newick format tree file which is used to sort the alignment, and
 212         group consensus and sequence logos are shown below the alignment.</td>
 213     </tr>
 214     <tr>
 215       <td width="10%" valign="center"><applet
 216    code="jalview.bin.JalviewLite" width="140" height="35"
 217    archive="jalviewApplet.jar">
 218 <param name="permissions" value="sandbox"/>
 219 <param name="file" value="uniref50.fa"/>
 220 <param name="features" value="exampleFeatures.txt"/>
 221 <param name="showFullId" value="false"/>
 222 <param name="windowHeight" value="500"/>
 223 <param name="windowWidth" value="650"/>
 224 <param name="showFeatureSettings" value="true"/>
 225 <param name="wrap" value="true"/>
 226 <param name="showAnnotation" value="false"/>
 227    <param name="linkLabel_1" value="Uniprot"/>
 228    <param name="linkUrl_1"
 229      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 230    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 231    <param name="linkUrl_2"
 232      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 233    <param name="APPLICATION_URL"
 234      value="http://www.jalview.org/services/launchApp"/>
 235 </applet>
 236 </td>
 237       <td valign="center">Displays a features file on the alignment</td>
 238     </tr>
 239     <tr>
 240       <td width="10%" valign="center"><applet
 241    code="jalview.bin.JalviewLite" width="140" height="35"
 242    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 243 <param name="permissions" value="sandbox"/>
 244 <param name="file" value="uniref50.fa"/>
 245 <param name="showFullId" value="false"/>
 246 <param name="windowHeight" value="500"/>
 247 <param name="windowWidth" value="650"/>
 248 <param name="wrap" value="true"/>
 249 <param name="showAnnotation" value="false"/>
 250 <param name="defaultColour" value="Strand Propensity"/>
 251 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
 252    <param name="linkLabel_1" value="Uniprot"/>
 253    <param name="linkUrl_1"
 254      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 255    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 256    <param name="linkUrl_2"
 257      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 258    <param name="APPLICATION_URL"
 259      value="http://www.jalview.org/services/launchApp"/>
 260 </applet>
 261 </td>
 262       <td valign="center">Associates PDB file 1GAQ with sequence
 263         FER1_MAIZE</td>
 264     </tr>
 265     <tr>
 266       <td width="10%" valign="center"><applet
 267    code="jalview.bin.JalviewLite" width="140" height="35"
 268    archive="jalviewApplet.jar">
 269 <param name="permissions" value="sandbox"/>
 270 <param name="file" value="jpred_msa.fasta"/>
 271 <param name="showFullId" value="false"/>
 272 <param name="windowHeight" value="515"/>
 273 <param name="windowWidth" value="650"/>
 274 <param name="showAnnotation" value="true"/>
 275 <param name="defaultColour" value="Clustal"/>
 276    <param name="linkLabel_1" value="Uniprot"/>
 277    <param name="linkUrl_1"
 278      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 279    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 280    <param name="linkUrl_2"
 281      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 282    <param name="APPLICATION_URL"
 283      value="http://www.jalview.org/services/launchApp"/>
 284 </applet>
 285                                                        </td>
 286       <td valign="middle">Displays a Multiple Sequence Alignment
 287         Based JNet Prediction for a Sequence</td>
 288     </tr>
 289   </table>
 290   <p>
 291     <h2>RF00031 RFAM Alignment with per sequence secondary
 292       structure</h2>
 293   </p>
 294   <table width="90%">
 295     <tr>
 296       <td width="10%" valign="center"><applet
 297    code="jalview.bin.JalviewLite" width="140" height="35"
 298    archive="jalviewApplet.jar">
 299 <param name="permissions" value="sandbox"/>
 300 <param name="file" value="RF00031_folded.stk"/>
 301 <param name="showFullId" value="false"/>
 302 <param name="windowHeight" value="515"/>
 303 <param name="windowWidth" value="650"/>
 304 <param name="showAnnotation" value="true"/>
 305 <param name="defaultColour" value="Purine/Pyrimidine"/>
 306    <param name="APPLICATION_URL"
 307      value="http://www.jalview.org/services/launchApp"/>
 308 </applet>
 309 </td>
 310       <td valign="center">Displays an RFAM RNA fold family with
 311         secondary structure annotation</td>
 312     </tr>
 313   </table>
 314 </div>
 315 <!-- content template end -->
 316
 317
 318
 319 </div> <!-- end content div -->
 320
 321 </div> <!-- content -->
 322 </div> <!-- pagewrap -->
 323 <div id ="footer">
 324 <div id="innerFooter">
 325 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 326 <div id="cite">
 327 <p>
 328 If you use Jalview in your work, please cite this publication:
 329 </p>
 330 <br />
 331 <p>
 332 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 333 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 334 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 335 </p>
 336 </div>
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