examples/applets.html

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   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   4  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
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  21 <TITLE>Jalview - Applets</TITLE>
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  89 <div id="header">
  90 <div id="logo"><a href="/" title="Home"></a></div>
  91 <ul id="buttons">
  92 <li id="applet"><a href="applets.html" title="applet"></a></li>
  93 <li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
  94 </ul>
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 108   <a href="#">Screenshots</a>
 109   </div>
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 135 </ul>
 136 <div style="clear:both"></div>
 137 </div>
 138
 139 </div>
 140
 141
 142 <div id="pageWrap">
 143
 144 <div id="sideNav">
 145 <ul>
 146 <li class="jvlite-nav-title"><a href="applets.html">JalviewLite Examples</a></li>
 147 <li><a href="appletParameters.html">Applet Parameters</a></li>
 148 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
 149 <li><a href="formComplete.html">in-page API demo</a></li>
 150 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
 151 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
 152 </ul>
 153 </div>
 154
 155 <div id="content" class="content">
 156         <p>JalviewLite is a web based version of Jalview, which runs as a Java applet in or on a web page. It's one of the easiest ways of providing an interactive
 157           display for precalculated alignments, features and annotations files.
 158           It lacks some functionality available in the Jalview Desktop, however, such
 159           as making images, saving files, and running web service jobs. This is mostly due to security
 160           restrictions imposed on applets.</p>
 161         <p align="left">For more information on how to use the applet in your
 162           website, see <a href="appletParameters.html"><strong>full list of applet
 163           parameters.</strong></a></p>
 164         <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
 165           of Jalview, which runs within your web browser. </p>
 166         <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
 167           cluster<br>
 168           (15 sequences x 150 residues)</H4>
 169         <div align="center"> </div>
 170         <div align="center">
 171           <table width="300" border="1" cellspacing="0" cellpadding="0">
 172             <tr>
 173               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
 174                   <tr>
 175                     <td width="100"> <applet code="jalview.bin.JalviewLite"
 176                                 width="140" height="35"
 177                                 archive="jalviewApplet.jar">
 178                                                 <param name="file" value="uniref50.fa">
 179                         <param name="treeFile" value="ferredoxin.nw">
 180                         <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
 181                         <param name="showFullId" value="false">
 182                         <param name="RGB"  value="F2F2FF">
 183                         <param name="sortByTree" value="True">
 184                         <param name="showSequenceLogo" value="true">
 185                         <param name="showGroupConsensus" value="true">
 186                         <param name="linkLabel_1" value="SRS">
 187                         <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
 188                         <param name="linkLabel_2" value="Uniprot">
 189                         <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 190                                                 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
 191                       </applet></td>
 192                     <td width="165">User Defined Colours, loads an associated Newick
 193                       format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
 194                   </tr>
 195                 </table></td>
 196             </tr>
 197           </table>
 198           <p>&nbsp;</p>
 199           <table width="300" border="1" cellspacing="0" cellpadding="0">
 200             <tr>
 201               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
 202                   <tr>
 203                     <td width="100"> <applet code="jalview.bin.JalviewLite"
 204                                 width="140" height="35"
 205                                 archive="jalviewApplet.jar">
 206                         <param name="file" value="uniref50.fa">
 207                         <param name="features" value="exampleFeatures.txt">
 208                         <param name="showFeatureSettings" value="true">
 209                         <param name="wrap" value="true">
 210                         <param name="showAnnotation" value="false">
 211                         <param name="windowHeight" value="500">
 212                         <param name="windowWidth" value="650">
 213                         <param name="showFullId" value="false">
 214                         <param name="RGB"  value="F2F2FF">
 215                         <param name="linkLabel_1" value="SRS">
 216                         <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
 217                         <param name="linkLabel_2" value="Uniprot">
 218                         <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 219                                                 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
 220                       </applet> </td>
 221                     <td width="165">Displays a features file on the alignment</td>
 222                   </tr>
 223                 </table></td>
 224             </tr>
 225           </table>
 226             <p>&nbsp;</p>
 227           <table width="300" border="1" cellspacing="0" cellpadding="0">
 228             <tr>
 229               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
 230                   <tr>
 231                     <td width="100"> <applet code="jalview.bin.JalviewLite"
 232                                 width="140" height="35"
 233                                 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 234                         <param name="file" value="uniref50.fa">
 235                         <!-- <param name="debug" value="true">
 236                         -->
 237                         <param name="defaultColour" value="Strand Propensity">
 238                         <param name="wrap" value="true">
 239                         <param name="showAnnotation" value="false">
 240                         <param name="windowHeight" value="500">
 241                         <param name="windowWidth" value="650">
 242                         <param name="showFullId" value="false">
 243                         <param name="RGB"  value="F2F2FF">
 244                         <param name="linkLabel_1" value="SRS">
 245                         <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
 246                         <param name="linkLabel_2" value="Uniprot">
 247                         <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 248                                                 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
 249                         <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
 250                       </applet> </td>
 251                     <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
 252                   </tr>
 253                 </table></td>
 254             </tr>
 255           </table>
 256           <p>&nbsp;</p>
 257                                                 <table width="300" border="1" cellspacing="0" cellpadding="0">
 258                                                         <tr>
 259                                                                 <td><table width="300" border="0" cellspacing="0"
 260                                                                                 cellpadding="0">
 261                                                                                 <tr>
 262                                                                                         <td width="100"><applet code="jalview.bin.JalviewLite"
 263                                                                                                         width="140" height="35" archive="jalviewApplet.jar">
 264                                                                                                         <param name="file" value="jpred_msa.fasta">
 265                                                                                                         <param name="jnetfile" value="jpred_msa.seq.concise">
 266                                                                                                         <param name="defaultColour" value="Clustal">
 267                                                                                                         <param name="showAnnotation" value="true">
 268                                                                                                         <param name="windowHeight" value="515">
 269                                                                                                         <param name="windowWidth" value="650">
 270                                                                                                         <param name="showConservation" value="false">
 271                                                                                                         <param name="showQuality" value="false">
 272                                                                                                         <param name="showConsensus" value="false">
 273                                                                                                         <param name="showFullId" value="false">
 274                                                                                                         <param name="RGB" value="F2F2FF">
 275                                                                                                         <param name="linkLabel_1" value="SRS">
 276                                                                                                         <param name="linkUrl_1"
 277                                                                                                                 value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
 278                                                                                                         <param name="linkLabel_2" value="Uniprot">
 279                                                                                                         <param name="linkUrl_2"
 280                                                                                                                 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 281                                                                                                         <param name="APPLICATION_URL"
 282                                                                                                                 value="http://www.jalview.org/services/launchApp">
 283                                                                                                 </applet></td>
 284                                                                                         <td width="165">Displays a Multiple Sequence Alignment
 285                                                                                                 Based JNet Prediction for a Sequence</td>
 286                                                                                 </tr>
 287                                                                         </table></td>
 288                                                         </tr>
 289                                                 </table>
 290                                                 <p>&nbsp;</p>
 291                                                 <table width="300" border="1" cellspacing="0" cellpadding="0">
 292             <tr>
 293               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
 294                   <tr>
 295                     <td width="100"> <applet code="jalview.bin.JalviewLite"
 296                                 width="140" height="35"
 297                                 archive="jalviewApplet.jar">
 298                         <param name="file" value="RF00031_folded.stk">
 299                         <param name="defaultColour" value="Purine/Pyrimidine">
 300                         <param name="showAnnotation" value="true">
 301                         <param name="windowHeight" value="515">
 302                         <param name="windowWidth" value="650">
 303                         <param name="showConservation" value="false">
 304                         <param name="showQuality" value="false">
 305                         <param name="showConsensus" value="true">
 306                         <param name="showFullId" value="false">
 307                         <param name="RGB"  value="F2F2FF">
 308                         <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
 309                       </applet> </td>
 310                     <td width="165">Displays an RFAM RNA fold family with secondary structure annotation</td>
 311                   </tr>
 312                 </table></td>
 313             </tr>
 314           </table>
 315         </div>
 316 </div>
 317
 318 <div id ="footer">
 319 <div id="innerFooter">
 320 <div id="copyright"><p>Copyright all rights reserved 2012</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 doi: 10.1093/bioinformatics/btp033
 330 </p>
 331 </div>
 332 </div>
 333 </div>
 334 </body>
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 336