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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 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>
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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     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
 166      href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
 167    <div align="center">
 168     <p>
 169      <h2>Ferredoxins, chloroplast precursor related UniRef50
 170       cluster</h2>
 171      <br /> (15 sequences x 150 residues)
 172     </p>
 173     <table width="90%">
 174      <tr>
 175       <td width="10%" valign="center"><applet
 176         code="jalview.bin.JalviewLite" 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"
 181           value="C=yellow; R,K,H=FF5555; D,E=5555FF">
 182           <param name="showFullId" value="false">
 183        <param name="sortByTree" value="True">
 184         <param name="showSequenceLogo" value="true">
 185          <param name="showGroupConsensus" value="true">
 186           <param name="linkLabel_1" value="Uniprot">
 187            <param name="linkUrl_1"
 188             value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 189             <param name="linkLabel_2" value="Expasy">
 190              <param name="linkUrl_2"
 191               value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 192        <param name="APPLICATION_URL"
 193         value="http://www.jalview.org/services/launchApp">
 194        </applet></td>
 195       <td valign="center">User Defined Colours, loads an associated
 196        Newick format tree file which is used to sort the alignment, and
 197        group consensus and sequence logos are shown below the alignment.</td>
 198      </tr>
 199      <tr>
 200       <td width="10%" valign="center"><applet
 201         code="jalview.bin.JalviewLite" width="140" height="35"
 202         archive="jalviewApplet.jar">
 203        <param name="file" value="uniref50.fa">
 204         <param name="features" value="exampleFeatures.txt">
 205          <param name="showFeatureSettings" value="true">
 206           <param name="wrap" value="true">
 207            <param name="showAnnotation" value="false">
 208             <param name="windowHeight" value="500">
 209              <param name="windowWidth" value="650">
 210               <param name="showFullId" value="false">
 211        <param name="linkLabel_1" value="Uniprot">
 212         <param name="linkUrl_1"
 213          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 214          <param name="linkLabel_2" value="Expasy">
 215           <param name="linkUrl_2"
 216            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 217            <param name="APPLICATION_URL"
 218             value="http://www.jalview.org/services/launchApp">
 219        </applet></td>
 220       <td valign="center">Displays a features file on the alignment</td>
 221      </tr>
 222      <tr>
 223       <td width="10%" valign="center"><applet
 224         code="jalview.bin.JalviewLite" width="140" height="35"
 225         archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 226        <param name="file" value="uniref50.fa">
 227         <!-- <param name="debug" value="true">
 228                         -->
 229         <param name="defaultColour" value="Strand Propensity">
 230          <param name="wrap" value="true">
 231           <param name="showAnnotation" value="false">
 232            <param name="windowHeight" value="500">
 233             <param name="windowWidth" value="650">
 234              <param name="showFullId" value="false">
 235        <param name="linkLabel_1" value="Uniprot">
 236         <param name="linkUrl_1"
 237          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 238          <param name="linkLabel_2" value="Expasy">
 239           <param name="linkUrl_2"
 240            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 241        <param name="APPLICATION_URL"
 242         value="http://www.jalview.org/services/launchApp">
 243         <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
 244        </applet></td>
 245       <td valign="center">Associates PDB file 1GAQ with sequence
 246        FER1_MAIZE</td>
 247      </tr>
 248      <tr>
 249       <td width="10%" valign="middle"><applet
 250         code="jalview.bin.JalviewLite" width="140" height="35"
 251         archive="jalviewApplet.jar">
 252        <param name="file" value="jpred_msa.fasta">
 253         <param name="jnetfile" value="jpred_msa.seq.concise">
 254          <param name="defaultColour" value="Clustal">
 255           <param name="showAnnotation" value="true">
 256            <param name="windowHeight" value="515">
 257             <param name="windowWidth" value="650">
 258              <param name="showConservation" value="false">
 259               <param name="showQuality" value="false">
 260                <param name="showConsensus" value="false">
 261                 <param name="showFullId" value="false">
 262        <param name="linkLabel_1" value="Uniprot">
 263         <param name="linkUrl_1"
 264          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 265          <param name="linkLabel_2" value="Expasy">
 266           <param name="linkUrl_2"
 267            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 268        <param name="APPLICATION_URL"
 269         value="http://www.jalview.org/services/launchApp">
 270        </applet></td>
 271       <td valign="center">Displays a Multiple Sequence Alignment
 272        Based JNet Prediction for a Sequence</td>
 273      </tr>
 274     </table>
 275     <p>
 276     <h2>RF00031 RFAM Alignment with per seqeunce secondary
 277      structure</h2>
 278     </p>
 279     <table width="90%">
 280      <tr>
 281       <td width="10%" valign="center"><applet
 282         code="jalview.bin.JalviewLite" width="140" height="35"
 283         archive="jalviewApplet.jar">
 284        <param name="file" value="RF00031_folded.stk">
 285         <param name="defaultColour" value="Purine/Pyrimidine">
 286          <param name="showAnnotation" value="true">
 287           <param name="windowHeight" value="515">
 288            <param name="windowWidth" value="650">
 289             <param name="showConservation" value="false">
 290              <param name="showQuality" value="false">
 291               <param name="showConsensus" value="true">
 292                <param name="showFullId" value="false">
 293        <param name="APPLICATION_URL"
 294         value="http://www.jalview.org/services/launchApp">
 295        </applet></td>
 296       <td valign="center">Displays an RFAM RNA fold family with
 297        secondary structure annotation</td>
 298      </tr>
 299     </table>
 300    </div>
 301   </div>
 302  </div>
 303
 304  <div id ="footer">
 305 <div id="innerFooter">
 306 <div id="copyright"><p>Copyright all rights reserved 2012</p></div>
 307 <div id="cite">
 308 <p>
 309 If you use Jalview in your work, please cite this publication:
 310 </p>
 311 <br />
 312 <p>
 313 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 314 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 315 Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
 316 </p>
 317 </div>
 318 </div>
 319 </div>
 320 </body>
 321 </html>
 322