examples/applets.html

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  22 <TITLE>Jalview - Applets</TITLE>
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  80       <td background="../jalview.gif">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
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  98             <tr>
  99               <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
 100                 Version</a></td>
 101             </tr>
 102             <tr>
 103               <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
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 113                 history</a></td>
 114             </tr>
 115             <tr>
 116               <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
 117                 Code</a></td>
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 119                         <tr>
 120               <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
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 142
 143         </div>
 144
 145         <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
 146           <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
 147         </div>
 148         </td>
 149       <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
 150         <p>Jalview comes in two distinct flavours.<br>
 151           <br>
 152           The main application allows connection to multiple web services provided
 153           at the University of Dundee as well as a host of additional useful features
 154           such as printing, making images from your alignment and annotating your
 155           alignment. You need to download and install this software.</p>
 156         <p>The applet version runs in web browsers and is a useful interactive
 157           display for precalculated alignments, features and annotations files.
 158           It does not have the full functionality of the main application, such
 159           as making images, saving files, running web service jobs 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         <p>&nbsp;</p>
 317           <p>For more JalviewLite examples, follow the links below.
 318           <ul>
 319           <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>
 320           <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
 321           <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
 322           <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
 323           </ul>
 324         <!-- InstanceEndEditable --></td>
 325     </tr>
 326   </table>
 327 </div>
 328 </body>
 329 <!-- InstanceEnd --></html>