examples/applets.html

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  21   <TITLE>JalviewLite Examples</TITLE>
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  95     <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
  96     <ul id="buttons">
  97       <li id="applet"><a href="applets.html" title="applet"></a></li>
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 144 <div id="pageWrap">
 145
 146 <div id="sideNav">
 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>
 151       <li ><a href="embedded.html">Embedded Alignment</a></li>
 152       <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
 153       <li ><a href="formComplete.html">Access from Javascript</a></li>
 154       <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
 155       <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
 156   </ul>
 157 </div>
 158
 159 <div id="content" class="content">
 160
 161
 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
 345
 346
 347 </div> <!-- end content div -->
 348
 349 </div> <!-- content -->
 350 </div> <!-- pagewrap -->
 351 <div id ="footer">
 352 <div id="innerFooter">
 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>
 364 </div>
 365 </div>
 366 </div>
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