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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  21 <TITLE>Jalview - Applets</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>
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 143
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 145  <div id="pageWrap">
 146
 147   <div id="sideNav">
 148    <ul>
 149     <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
 150       Examples</a></li>
 151     <li><a href="appletParameters.html">Applet Parameters</a></li>
 152     <li><a href="jalviewLiteJs.html">Javascript API</a></li>
 153     <li><a href="formComplete.html">in-page API demo</a></li>
 154     <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
 155     <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
 156    </ul>
 157   </div>
 158
 159   <div id="content" class="content">
 160    <p>JalviewLite is a web based version of Jalview, which runs as a
 161     Java applet in or on a web page. It's one of the easiest ways of
 162     providing an interactive display for precalculated alignments,
 163     features and annotations files. It lacks some functionality
 164     available in the Jalview Desktop, however, such as making images,
 165     saving files, and running web service jobs. This is mostly due to
 166     security restrictions imposed on applets.</p>
 167    <p align="left">
 168     Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
 169      href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
 170    <div align="center">
 171     <p>
 172      <h2>Ferredoxins, chloroplast precursor related UniRef50
 173       cluster</h2>
 174      <br /> (15 sequences x 150 residues)
 175     </p>
 176     <table width="90%">
 177      <tr>
 178       <td width="10%" valign="center"><applet
 179         code="jalview.bin.JalviewLite" width="140" height="35"
 180         archive="jalviewApplet.jar">
 181 <param name="permissions" value="all-permissions">
 182        <param name="file" value="uniref50.fa">
 183         <param name="treeFile" value="ferredoxin.nw">
 184          <param name="userDefinedColour"
 185           value="C=yellow; R,K,H=FF5555; D,E=5555FF">
 186           <param name="showFullId" value="false">
 187        <param name="sortByTree" value="True">
 188         <param name="showSequenceLogo" value="true">
 189          <param name="showGroupConsensus" value="true">
 190           <param name="linkLabel_1" value="Uniprot">
 191            <param name="linkUrl_1"
 192             value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 193             <param name="linkLabel_2" value="EMBL-EBI Search">
 194              <param name="linkUrl_2"
 195               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
 196        <param name="APPLICATION_URL"
 197         value="http://www.jalview.org/services/launchApp">
 198        </applet></td>
 199       <td valign="center">User Defined Colours, loads an associated
 200        Newick format tree file which is used to sort the alignment, and
 201        group consensus and sequence logos are shown below the alignment.</td>
 202      </tr>
 203      <tr>
 204       <td width="10%" valign="center"><applet
 205         code="jalview.bin.JalviewLite" width="140" height="35"
 206         archive="jalviewApplet.jar">
 207 <param name="permissions" value="all-permissions">
 208        <param name="file" value="uniref50.fa">
 209         <param name="features" value="exampleFeatures.txt">
 210          <param name="showFeatureSettings" value="true">
 211           <param name="wrap" value="true">
 212            <param name="showAnnotation" value="false">
 213             <param name="windowHeight" value="500">
 214              <param name="windowWidth" value="650">
 215               <param name="showFullId" value="false">
 216        <param name="linkLabel_1" value="Uniprot">
 217         <param name="linkUrl_1"
 218          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 219                      <param name="linkLabel_2" value="EMBL-EBI Search">
 220              <param name="linkUrl_2"
 221               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
 222         <param name="APPLICATION_URL"
 223             value="http://www.jalview.org/services/launchApp">
 224        </applet></td>
 225       <td valign="center">Displays a features file on the alignment</td>
 226      </tr>
 227      <tr>
 228       <td width="10%" valign="center"><applet
 229         code="jalview.bin.JalviewLite" width="140" height="35"
 230         archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 231 <param name="permissions" value="all-permissions">
 232        <param name="file" value="uniref50.fa">
 233         <!-- <param name="debug" value="true">
 234                         -->
 235         <param name="defaultColour" value="Strand Propensity">
 236          <param name="wrap" value="true">
 237           <param name="showAnnotation" value="false">
 238            <param name="windowHeight" value="500">
 239             <param name="windowWidth" value="650">
 240              <param name="showFullId" value="false">
 241        <param name="linkLabel_1" value="Uniprot">
 242         <param name="linkUrl_1"
 243          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 244             <param name="linkLabel_2" value="EMBL-EBI Search">
 245              <param name="linkUrl_2"
 246               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
 247        <param name="APPLICATION_URL"
 248         value="http://www.jalview.org/services/launchApp">
 249         <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
 250        </applet></td>
 251       <td valign="center">Associates PDB file 1GAQ with sequence
 252        FER1_MAIZE</td>
 253      </tr>
 254      <tr>
 255       <td width="10%" valign="middle"><applet
 256         code="jalview.bin.JalviewLite" width="140" height="35"
 257         archive="jalviewApplet.jar">
 258 <param name="permissions" value="all-permissions">
 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="EMBL-EBI Search">
 273              <param name="linkUrl_2"
 274               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
 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 sequence 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="permissions" value="all-permissions">
 292        <param name="file" value="RF00031_folded.stk">
 293         <param name="defaultColour" value="Purine/Pyrimidine">
 294          <param name="showAnnotation" value="true">
 295           <param name="windowHeight" value="515">
 296            <param name="windowWidth" value="650">
 297             <param name="showConservation" value="false">
 298              <param name="showQuality" value="false">
 299               <param name="showConsensus" value="true">
 300                <param name="showFullId" value="false">
 301        <param name="APPLICATION_URL"
 302         value="http://www.jalview.org/services/launchApp">
 303        </applet></td>
 304       <td valign="center">Displays an RFAM RNA fold family with
 305        secondary structure annotation</td>
 306      </tr>
 307     </table>
 308    </div>
 309   </div>
 310  </div>
 311
 312 <div id ="footer">
 313 <div id="innerFooter">
 314 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 315 <div id="cite">
 316 <p>
 317 If you use Jalview in your work, please cite this publication:
 318 </p>
 319 <br />
 320 <p>
 321 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 322 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 323 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 324 </p>
 325 </div>
 326 </div>
 327 </div>
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 330