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>
  98 </ul>
  99 </div>
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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="file" value="uniref50.fa">
 182         <param name="treeFile" value="ferredoxin.nw">
 183          <param name="userDefinedColour"
 184           value="C=yellow; R,K,H=FF5555; D,E=5555FF">
 185           <param name="showFullId" value="false">
 186        <param name="sortByTree" value="True">
 187         <param name="showSequenceLogo" value="true">
 188          <param name="showGroupConsensus" value="true">
 189           <param name="linkLabel_1" value="Uniprot">
 190            <param name="linkUrl_1"
 191             value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 192             <param name="linkLabel_2" value="Expasy">
 193              <param name="linkUrl_2"
 194               value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 195        <param name="APPLICATION_URL"
 196         value="http://www.jalview.org/services/launchApp">
 197        </applet></td>
 198       <td valign="center">User Defined Colours, loads an associated
 199        Newick format tree file which is used to sort the alignment, and
 200        group consensus and sequence logos are shown below the alignment.</td>
 201      </tr>
 202      <tr>
 203       <td width="10%" valign="center"><applet
 204         code="jalview.bin.JalviewLite" 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="linkLabel_1" value="Uniprot">
 215         <param name="linkUrl_1"
 216          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 217          <param name="linkLabel_2" value="Expasy">
 218           <param name="linkUrl_2"
 219            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 220            <param name="APPLICATION_URL"
 221             value="http://www.jalview.org/services/launchApp">
 222        </applet></td>
 223       <td valign="center">Displays a features file on the alignment</td>
 224      </tr>
 225      <tr>
 226       <td width="10%" valign="center"><applet
 227         code="jalview.bin.JalviewLite" width="140" height="35"
 228         archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 229        <param name="file" value="uniref50.fa">
 230         <!-- <param name="debug" value="true">
 231                         -->
 232         <param name="defaultColour" value="Strand Propensity">
 233          <param name="wrap" value="true">
 234           <param name="showAnnotation" value="false">
 235            <param name="windowHeight" value="500">
 236             <param name="windowWidth" value="650">
 237              <param name="showFullId" value="false">
 238        <param name="linkLabel_1" value="Uniprot">
 239         <param name="linkUrl_1"
 240          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 241          <param name="linkLabel_2" value="Expasy">
 242           <param name="linkUrl_2"
 243            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 244        <param name="APPLICATION_URL"
 245         value="http://www.jalview.org/services/launchApp">
 246         <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
 247        </applet></td>
 248       <td valign="center">Associates PDB file 1GAQ with sequence
 249        FER1_MAIZE</td>
 250      </tr>
 251      <tr>
 252       <td width="10%" valign="middle"><applet
 253         code="jalview.bin.JalviewLite" width="140" height="35"
 254         archive="jalviewApplet.jar">
 255        <param name="file" value="jpred_msa.fasta">
 256         <param name="jnetfile" value="jpred_msa.seq.concise">
 257          <param name="defaultColour" value="Clustal">
 258           <param name="showAnnotation" value="true">
 259            <param name="windowHeight" value="515">
 260             <param name="windowWidth" value="650">
 261              <param name="showConservation" value="false">
 262               <param name="showQuality" value="false">
 263                <param name="showConsensus" value="false">
 264                 <param name="showFullId" value="false">
 265        <param name="linkLabel_1" value="Uniprot">
 266         <param name="linkUrl_1"
 267          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 268          <param name="linkLabel_2" value="Expasy">
 269           <param name="linkUrl_2"
 270            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 271        <param name="APPLICATION_URL"
 272         value="http://www.jalview.org/services/launchApp">
 273        </applet></td>
 274       <td valign="center">Displays a Multiple Sequence Alignment
 275        Based JNet Prediction for a Sequence</td>
 276      </tr>
 277     </table>
 278     <p>
 279     <h2>RF00031 RFAM Alignment with per sequence secondary
 280      structure</h2>
 281     </p>
 282     <table width="90%">
 283      <tr>
 284       <td width="10%" valign="center"><applet
 285         code="jalview.bin.JalviewLite" width="140" height="35"
 286         archive="jalviewApplet.jar">
 287        <param name="file" value="RF00031_folded.stk">
 288         <param name="defaultColour" value="Purine/Pyrimidine">
 289          <param name="showAnnotation" value="true">
 290           <param name="windowHeight" value="515">
 291            <param name="windowWidth" value="650">
 292             <param name="showConservation" value="false">
 293              <param name="showQuality" value="false">
 294               <param name="showConsensus" value="true">
 295                <param name="showFullId" value="false">
 296        <param name="APPLICATION_URL"
 297         value="http://www.jalview.org/services/launchApp">
 298        </applet></td>
 299       <td valign="center">Displays an RFAM RNA fold family with
 300        secondary structure annotation</td>
 301      </tr>
 302     </table>
 303    </div>
 304   </div>
 305  </div>
 306
 307 <div id ="footer">
 308 <div id="innerFooter">
 309 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 310 <div id="cite">
 311 <p>
 312 If you use Jalview in your work, please cite this publication:
 313 </p>
 314 <br />
 315 <p>
 316 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 317 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 318 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 319 </p>
 320 </div>
 321 </div>
 322 </div>
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 325