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
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  20 <head>
  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>
  95 </div>
  96
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  99 <div id="navInner">
 100
 101 <ul id="sddm">
 102  <li><a href="#">Home</a></li>
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 105   <a href="#">Documentation</a>
 106   <a href="#">Publications</a>
 107   <a href="#">Credits</a>
 108   <a href="#">Screenshots</a>
 109   </div>
 110  </li>
 111  <li><a href="#">FAQ</a></li>
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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
 147       Examples</a></li>
 148     <li><a href="appletParameters.html">Applet Parameters</a></li>
 149     <li><a href="jalviewLiteJs.html">Javascript API</a></li>
 150     <li><a href="formComplete.html">in-page API demo</a></li>
 151     <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
 152     <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
 153    </ul>
 154   </div>
 155
 156   <div id="content" class="content">
 157    <p>JalviewLite is a web based version of Jalview, which runs as a
 158     Java applet in or on a web page. It's one of the easiest ways of
 159     providing an interactive display for precalculated alignments,
 160     features and annotations files. It lacks some functionality
 161     available in the Jalview Desktop, however, such as making images,
 162     saving files, and running web service jobs. This is mostly due to
 163     security restrictions imposed on applets.</p>
 164    <p align="left">
 165     For more information on how to use the applet in your website, see <a
 166      href="appletParameters.html"><strong>full list of
 167       applet
 168       <p>Pressing one of the buttons below will load up JalviewLite,
 169        a cut down version parameters.
 170     </strong></a>
 171    </p>
 172    of Jalview, which runs within your web browser.
 173    </p>
 174    <div align="center">
 175     <p>
 176      <h2>Ferredoxins, chloroplast precursor related UniRef50
 177       cluster</h2>
 178      <br /> (15 sequences x 150 residues)
 179     </p>
 180     <table width="90%">
 181      <tr>
 182       <td width="10%" valign="center"><applet
 183         code="jalview.bin.JalviewLite" width="140" height="35"
 184         archive="jalviewApplet.jar">
 185        <param name="file" value="uniref50.fa">
 186         <param name="treeFile" value="ferredoxin.nw">
 187          <param name="userDefinedColour"
 188           value="C=yellow; R,K,H=FF5555; D,E=5555FF">
 189           <param name="showFullId" value="false">
 190        <param name="sortByTree" value="True">
 191         <param name="showSequenceLogo" value="true">
 192          <param name="showGroupConsensus" value="true">
 193           <param name="linkLabel_1" value="Uniprot">
 194            <param name="linkUrl_1"
 195             value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 196             <param name="linkLabel_2" value="Expasy">
 197              <param name="linkUrl_2"
 198               value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 199        <param name="APPLICATION_URL"
 200         value="http://www.jalview.org/services/launchApp">
 201        </applet></td>
 202       <td valign="center">User Defined Colours, loads an associated
 203        Newick format tree file which is used to sort the alignment, and
 204        group consensus and sequence logos are shown below the alignment.</td>
 205      </tr>
 206      <tr>
 207       <td width="10%" valign="center"><applet
 208         code="jalview.bin.JalviewLite" width="140" height="35"
 209         archive="jalviewApplet.jar">
 210        <param name="file" value="uniref50.fa">
 211         <param name="features" value="exampleFeatures.txt">
 212          <param name="showFeatureSettings" value="true">
 213           <param name="wrap" value="true">
 214            <param name="showAnnotation" value="false">
 215             <param name="windowHeight" value="500">
 216              <param name="windowWidth" value="650">
 217               <param name="showFullId" value="false">
 218        <param name="linkLabel_1" value="Uniprot">
 219         <param name="linkUrl_1"
 220          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 221          <param name="linkLabel_2" value="Expasy">
 222           <param name="linkUrl_2"
 223            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 224            <param name="APPLICATION_URL"
 225             value="http://www.jalview.org/services/launchApp">
 226        </applet></td>
 227       <td valign="center">Displays a features file on the alignment</td>
 228      </tr>
 229      <tr>
 230       <td width="10%" valign="center"><applet
 231         code="jalview.bin.JalviewLite" width="140" height="35"
 232         archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 233        <param name="file" value="uniref50.fa">
 234         <!-- <param name="debug" value="true">
 235                         -->
 236         <param name="defaultColour" value="Strand Propensity">
 237          <param name="wrap" value="true">
 238           <param name="showAnnotation" value="false">
 239            <param name="windowHeight" value="500">
 240             <param name="windowWidth" value="650">
 241              <param name="showFullId" value="false">
 242        <param name="linkLabel_1" value="Uniprot">
 243         <param name="linkUrl_1"
 244          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 245          <param name="linkLabel_2" value="Expasy">
 246           <param name="linkUrl_2"
 247            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 248        <param name="APPLICATION_URL"
 249         value="http://www.jalview.org/services/launchApp">
 250         <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
 251        </applet></td>
 252       <td valign="center">Associates PDB file 1GAQ with sequence
 253        FER1_MAIZE</td>
 254      </tr>
 255      <tr>
 256       <td width="10%" valign="middle"><applet
 257         code="jalview.bin.JalviewLite" width="140" height="35"
 258         archive="jalviewApplet.jar">
 259        <param name="file" value="jpred_msa.fasta">
 260         <param name="jnetfile" value="jpred_msa.seq.concise">
 261          <param name="defaultColour" value="Clustal">
 262           <param name="showAnnotation" value="true">
 263            <param name="windowHeight" value="515">
 264             <param name="windowWidth" value="650">
 265              <param name="showConservation" value="false">
 266               <param name="showQuality" value="false">
 267                <param name="showConsensus" value="false">
 268                 <param name="showFullId" value="false">
 269        <param name="linkLabel_1" value="Uniprot">
 270         <param name="linkUrl_1"
 271          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 272          <param name="linkLabel_2" value="Expasy">
 273           <param name="linkUrl_2"
 274            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 275        <param name="APPLICATION_URL"
 276         value="http://www.jalview.org/services/launchApp">
 277        </applet></td>
 278       <td valign="center">Displays a Multiple Sequence Alignment
 279        Based JNet Prediction for a Sequence</td>
 280      </tr>
 281     </table>
 282     <p>
 283     <h2>RF00031 RFAM Alignment with per seqeunce secondary
 284      structure</h2>
 285     </p>
 286     <table width="90%">
 287      <tr>
 288       <td width="10%" valign="center"><applet
 289         code="jalview.bin.JalviewLite" width="140" height="35"
 290         archive="jalviewApplet.jar">
 291        <param name="file" value="RF00031_folded.stk">
 292         <param name="defaultColour" value="Purine/Pyrimidine">
 293          <param name="showAnnotation" value="true">
 294           <param name="windowHeight" value="515">
 295            <param name="windowWidth" value="650">
 296             <param name="showConservation" value="false">
 297              <param name="showQuality" value="false">
 298               <param name="showConsensus" value="true">
 299                <param name="showFullId" value="false">
 300        <param name="APPLICATION_URL"
 301         value="http://www.jalview.org/services/launchApp">
 302        </applet></td>
 303       <td valign="center">Displays an RFAM RNA fold family with
 304        secondary structure annotation</td>
 305      </tr>
 306     </table>
 307    </div>
 308   </div>
 309  </div>
 310
 311  <div id ="footer">
 312 <div id="innerFooter">
 313 <div id="copyright"><p>Copyright all rights reserved 2012</p></div>
 314 <div id="cite">
 315 <p>
 316 If you use Jalview in your work, please cite this publication:
 317 </p>
 318 <br />
 319 <p>
 320 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 321 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 322 Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
 323 </p>
 324 </div>
 325 </div>
 326 </div>
 327 </body>
 328 </html>
 329