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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  93   <div id="header">
  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
 101
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 140     </div>
 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 JalviewLite applets</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="float:left;">
 165 </div><div style="border: 2px solid black; align: left; float:right;">
 166  Working on Snow Leopard or Java out of date ? Try <a href="u_applets.html">the unsigned applet demos</a>
 167 </div>
 168 </div>
 169
 170 <!-- content template start -->
 171
 172 <p align="left">
 173 <h2>JalviewLite Button Examples</h2>
 174 Try out JalviewLite by pressing one of the buttons below.<br/>
 175  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>
 176 <div align="center">
 177   <p>
 178     <h2>Ferredoxins, chloroplast precursor related UniRef50
 179       cluster</h2>
 180     <br /> (15 sequences x 150 residues)
 181   </p>
 182   <table width="90%">
 183     <tr>
 184       <td width="10%" valign="center">
 185         <applet
 186    code="jalview.bin.JalviewLite" width="140" height="35"
 187    archive="jalviewApplet.jar">
 188 <param name="permissions" value="sandbox"/>
 189 <param name="file" value="uniref50.fa"/>
 190 <param name="treeFile" value="ferredoxin.nw"/>
 191 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
 192 <param name="sortByTree" value="True"/>
 193 <param name="showSequenceLogo" value="true"/>
 194 <param name="showGroupConsensus" value="true"/>
 195 <param name="showFullId" value="false"/>
 196    <param name="linkLabel_1" value="Uniprot"/>
 197    <param name="linkUrl_1"
 198      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 199    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 200    <param name="linkUrl_2"
 201      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 202    <param name="APPLICATION_URL"
 203      value="http://www.jalview.org/services/launchApp"/>
 204 </applet>
 205 </td>
 206       <td valign="center">User Defined Colours, loads an associated
 207         Newick format tree file which is used to sort the alignment, and
 208         group consensus and sequence logos are shown below the alignment.</td>
 209     </tr>
 210     <tr>
 211       <td width="10%" valign="center"><applet
 212    code="jalview.bin.JalviewLite" width="140" height="35"
 213    archive="jalviewApplet.jar">
 214 <param name="permissions" value="sandbox"/>
 215 <param name="file" value="uniref50.fa"/>
 216 <param name="features" value="exampleFeatures.txt"/>
 217 <param name="showFullId" value="false"/>
 218 <param name="windowHeight" value="500"/>
 219 <param name="windowWidth" value="650"/>
 220 <param name="showFeatureSettings" value="true"/>
 221 <param name="wrap" value="true"/>
 222 <param name="showAnnotation" value="false"/>
 223    <param name="linkLabel_1" value="Uniprot"/>
 224    <param name="linkUrl_1"
 225      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 226    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 227    <param name="linkUrl_2"
 228      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 229    <param name="APPLICATION_URL"
 230      value="http://www.jalview.org/services/launchApp"/>
 231 </applet>
 232 </td>
 233       <td valign="center">Displays a features file on the alignment</td>
 234     </tr>
 235     <tr>
 236       <td width="10%" valign="center"><applet
 237    code="jalview.bin.JalviewLite" width="140" height="35"
 238    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 239 <param name="permissions" value="sandbox"/>
 240 <param name="file" value="uniref50.fa"/>
 241 <param name="showFullId" value="false"/>
 242 <param name="windowHeight" value="500"/>
 243 <param name="windowWidth" value="650"/>
 244 <param name="wrap" value="true"/>
 245 <param name="showAnnotation" value="false"/>
 246 <param name="defaultColour" value="Strand Propensity"/>
 247    <param name="linkLabel_1" value="Uniprot"/>
 248    <param name="linkUrl_1"
 249      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 250    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 251    <param name="linkUrl_2"
 252      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 253    <param name="APPLICATION_URL"
 254      value="http://www.jalview.org/services/launchApp"/>
 255 </applet>
 256 </td>
 257       <td valign="center">Associates PDB file 1GAQ with sequence
 258         FER1_MAIZE</td>
 259     </tr>
 260     <tr>
 261       <td width="10%" valign="center"><applet
 262    code="jalview.bin.JalviewLite" width="140" height="35"
 263    archive="jalviewApplet.jar">
 264 <param name="permissions" value="sandbox"/>
 265 <param name="file" value="jpred_msa.fasta"/>
 266 <param name="showFullId" value="false"/>
 267 <param name="windowHeight" value="515"/>
 268 <param name="windowWidth" value="650"/>
 269 <param name="showAnnotation" value="true"/>
 270 <param name="defaultColour" value="Clustal"/>
 271    <param name="linkLabel_1" value="Uniprot"/>
 272    <param name="linkUrl_1"
 273      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 274    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 275    <param name="linkUrl_2"
 276      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 277    <param name="APPLICATION_URL"
 278      value="http://www.jalview.org/services/launchApp"/>
 279 </applet>
 280                                                        </td>
 281       <td valign="middle">Displays a Multiple Sequence Alignment
 282         Based JNet Prediction for a Sequence</td>
 283     </tr>
 284   </table>
 285   <p>
 286     <h2>RF00031 RFAM Alignment with per sequence secondary
 287       structure</h2>
 288   </p>
 289   <table width="90%">
 290     <tr>
 291       <td width="10%" valign="center"><applet
 292    code="jalview.bin.JalviewLite" width="140" height="35"
 293    archive="jalviewApplet.jar">
 294 <param name="permissions" value="sandbox"/>
 295 <param name="file" value="RF00031_folded.stk"/>
 296 <param name="showFullId" value="false"/>
 297 <param name="windowHeight" value="515"/>
 298 <param name="windowWidth" value="650"/>
 299 <param name="showAnnotation" value="true"/>
 300 <param name="defaultColour" value="Purine/Pyrimidine"/>
 301    <param name="APPLICATION_URL"
 302      value="http://www.jalview.org/services/launchApp"/>
 303 </applet>
 304 </td>
 305       <td valign="center">Displays an RFAM RNA fold family with
 306         secondary structure annotation</td>
 307     </tr>
 308   </table>
 309 </div>
 310 <!-- content template end -->
 311
 312
 313
 314 </div> <!-- end content div -->
 315
 316 </div> <!-- content -->
 317 </div> <!-- pagewrap -->
 318 <div id ="footer">
 319 <div id="innerFooter">
 320 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 321 <div id="cite">
 322 <p>
 323 If you use Jalview in your work, please cite this publication:
 324 </p>
 325 <br />
 326 <p>
 327 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 328 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 329 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 330 </p>
 331 </div>
 332 </div>
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