examples/applets.html

   1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   4  * Copyright (C) 2014 The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <head>
  21   <TITLE>JalviewLite Examples</TITLE>
  22   <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
  23
  24   <link href="css/reset.css" rel="stylesheet" type="text/css" />
  25   <link href="css/style.css" rel="stylesheet" type="text/css" />
  26
  27   <!--[if IE 6]>
  28       <link rel="stylesheet" type="text/css" href="css/ie6.css" />
  29       <![endif]-->
  30
  31   <!--[if IE 7]>
  32       <link rel="stylesheet" type="text/css" href="css/ie7.css" />
  33       <![endif]-->
  34
  35   <!-- dd menu -->
  36   <script type="text/javascript">
  37     <!--
  38         var timeout         = 500;
  39         var closetimer  = 0;
  40         var ddmenuitem      = 0;
  41
  42         // open hidden layer
  43         function mopen(id)
  44         {
  45         // cancel close timer
  46         mcancelclosetime();
  47
  48         // close old layer
  49         if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
  50
  51         // get new layer and show it
  52         ddmenuitem = document.getElementById(id);
  53         ddmenuitem.style.visibility = 'visible';
  54
  55         }
  56         // close showed layer
  57         function mclose()
  58         {
  59         if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
  60         }
  61
  62         // go close timer
  63         function mclosetime()
  64         {
  65         closetimer = window.setTimeout(mclose, timeout);
  66         }
  67
  68         // cancel close timer
  69         function mcancelclosetime()
  70         {
  71         if(closetimer)
  72         {
  73         window.clearTimeout(closetimer);
  74         closetimer = null;
  75         }
  76         }
  77
  78         // close layer when click-out
  79         document.onclick = mclose;
  80         // -->
  81   </script>
  82   <script>
  83     <!--//--><![CDATA[//><!--
  84 var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
  85 //--><!]]>
  86   </script>
  87
  88 </head>
  89
  90
  91 <body>
  92
  93
  94   <div id="header">
  95     <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
  96     <ul id="buttons">
  97       <li id="applet"><a href="applets.html" title="applet"></a></li>
  98       <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
  99     </ul>
 100   </div>
 101
 102
 103   <div id ="nav">
 104     <div id="navInner">
 105
 106       <ul id="sddm">
 107         <li><a href="http://www.jalview.org">Home</a></li>
 108         <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
 109           <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 110             <a href="http://www.jalview.org/about/documentation">Documentation</a>
 111             <a href="http://www.jalview.org/about/citation">Publications</a>
 112             <a href="http://www.jalview.org/about/credits">Credits</a>
 113           </div>
 114         </li>
 115         <li><a href="http://www.jalview.org/faq">FAQ</a></li>
 116         <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
 117           <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 118             <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
 119             <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
 120             <a href="http://www.jalview.org/community/links">Links</a>
 121             <a href="http://www.jalview.org/community/community-news">Community News</a>
 122           </div>
 123         </li>
 124         <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
 125           <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 126             <a href="http://www.jalview.org/development/release-history">Release History</a>
 127             <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
 128             <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
 129             <a href="http://www.jalview.org/development/development-news">Development News</a>
 130           </div>
 131         </li>
 132         <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
 133           <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 134             <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
 135             <a href="http://www.jalview.org/training/training-news">Training News</a>
 136           </div>
 137         </li>
 138         <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 139       </ul>
 140       <div style="clear:both"></div>
 141     </div>
 142
 143   </div>
 144 <div id="pageWrap">
 145
 146 <div id="sideNav">
 147   <ul>
 148       <li class="jvlite-nav-small"><a href="applets.html">JalviewLite Examples</a></li>
 149       <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
 150       <li ><a href="appletParameters.html">Applet Parameters</a></li>
 151       <li ><a href="embedded.html">Embedded Alignment</a></li>
 152       <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
 153       <li ><a href="formComplete.html">Access from Javascript</a></li>
 154       <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
 155       <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
 156   </ul>
 157 </div>
 158
 159 <div id="content" class="content">
 160
 161
 162 <!-- boiler plate link to alternate demopage -->
 163
 164 <div style="width: 100%">
 165 <div style="width:35%; align:left; float:right;">
 166 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
 167  Examples aren't working ?<br/>Try <a href="u_applets.html">the unsigned applet demos</a>
 168 </div>
 169 <div style="margin:8px; padding:10px; align: left;">
 170 <p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a>, <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>,
 171 and <a href="VARNAv3-91.jar">VARNAv3-91.jar</a>
 172 </p></div>
 173 </div>
 174 </div>
 175
 176 <!-- content template start -->
 177
 178 <p align="left">
 179 <h2>JalviewLite Button Examples</h2>
 180 Try out JalviewLite by pressing one of the buttons below.<br/>
 181  For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
 182 <p>&nbsp;</p><div align="center">
 183   <p align="center">
 184     <h2>Ferredoxins, chloroplast precursor related UniRef50
 185       cluster</h2>
 186     <br /> (15 sequences x 150 residues)
 187   </p>
 188   <table width="90%">
 189     <tr>
 190       <td width="10%" valign="center">
 191         <applet
 192    code="jalview.bin.JalviewLite" width="140" height="35"
 193    archive="jalviewApplet.jar,VARNAv3-91.jar">
 194 <param name="permissions" value="sandbox"/>
 195 <param name="file" value="uniref50.fa"/>
 196 <param name="treeFile" value="ferredoxin.nw"/>
 197 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
 198 <param name="sortByTree" value="True"/>
 199 <param name="showSequenceLogo" value="true"/>
 200 <param name="showGroupConsensus" value="true"/>
 201 <param name="showFullId" value="false"/>
 202    <param name="linkLabel_1" value="Uniprot"/>
 203    <param name="linkUrl_1"
 204      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 205    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 206    <param name="linkUrl_2"
 207      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 208    <param name="APPLICATION_URL"
 209      value="http://www.jalview.org/services/launchApp"/>
 210 </applet>
 211 </td>
 212       <td valign="center">User Defined Colours, loads an associated
 213         Newick format tree file which is used to sort the alignment, and
 214         group consensus and sequence logos are shown below the alignment.</td>
 215     </tr>
 216     <tr>
 217       <td width="10%" valign="center"><applet
 218    code="jalview.bin.JalviewLite" width="140" height="35"
 219    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,VARNAv3-91.jar">
 220 <param name="permissions" value="sandbox"/>
 221 <param name="file" value="uniref50.fa"/>
 222 <param name="features" value="exampleFeatures.txt"/>
 223 <param name="showFullId" value="false"/>
 224 <param name="windowHeight" value="500"/>
 225 <param name="windowWidth" value="650"/>
 226 <param name="showFeatureSettings" value="true"/>
 227 <param name="wrap" value="true"/>
 228 <param name="showAnnotation" value="false"/>
 229    <param name="linkLabel_1" value="Uniprot"/>
 230    <param name="linkUrl_1"
 231      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 232    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 233    <param name="linkUrl_2"
 234      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 235    <param name="APPLICATION_URL"
 236      value="http://www.jalview.org/services/launchApp"/>
 237 </applet>
 238 </td>
 239       <td valign="center">Displays a features file on the alignment</td>
 240     </tr>
 241     <tr>
 242       <td width="10%" valign="center"><applet
 243    code="jalview.bin.JalviewLite" width="140" height="35"
 244    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,VARNAv3-91.jar">
 245 <param name="permissions" value="sandbox"/>
 246 <param name="file" value="uniref50.fa"/>
 247 <param name="showFullId" value="false"/>
 248 <param name="windowHeight" value="500"/>
 249 <param name="windowWidth" value="650"/>
 250 <param name="wrap" value="true"/>
 251 <param name="showAnnotation" value="false"/>
 252 <param name="defaultColour" value="Strand Propensity"/>
 253 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
 254    <param name="linkLabel_1" value="Uniprot"/>
 255    <param name="linkUrl_1"
 256      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 257    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 258    <param name="linkUrl_2"
 259      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 260    <param name="APPLICATION_URL"
 261      value="http://www.jalview.org/services/launchApp"/>
 262 </applet>
 263 </td>
 264       <td valign="center">Associates PDB file 1GAQ with sequence
 265         FER1_MAIZE</td>
 266     </tr>
 267     <tr>
 268       <td width="10%" valign="center"><applet
 269    code="jalview.bin.JalviewLite" width="140" height="35"
 270    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,VARNAv3-91.jar">
 271 <param name="permissions" value="sandbox"/>
 272 <param name="file" value="jpred_msa.fasta"/>
 273 <param name="jnetfile" value="jpred_msa.seq.concise"/>
 274 <param name="showFullId" value="false"/>
 275 <param name="windowHeight" value="515"/>
 276 <param name="windowWidth" value="650"/>
 277 <param name="showAnnotation" value="true"/>
 278 <param name="defaultColour" value="Clustal"/>
 279    <param name="linkLabel_1" value="Uniprot"/>
 280    <param name="linkUrl_1"
 281      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 282    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 283    <param name="linkUrl_2"
 284      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 285    <param name="APPLICATION_URL"
 286      value="http://www.jalview.org/services/launchApp"/>
 287 </applet>
 288                                                        </td>
 289       <td valign="middle">Displays a Multiple Sequence Alignment
 290         Based JNet Prediction for a Sequence</td>
 291     </tr>
 292   </table>
 293   <p>
 294     <h2>RF00031 RFAM Alignment with per sequence secondary
 295       structure</h2>
 296   </p>
 297   <table width="90%">
 298     <tr>
 299       <td width="10%" valign="center"><applet
 300    code="jalview.bin.JalviewLite" width="140" height="35"
 301    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,VARNAv3-91.jar">
 302 <param name="permissions" value="sandbox"/>
 303 <param name="file" value="RF00031_folded.stk"/>
 304 <param name="showFullId" value="false"/>
 305 <param name="windowHeight" value="515"/>
 306 <param name="windowWidth" value="650"/>
 307 <param name="showAnnotation" value="true"/>
 308 <param name="defaultColour" value="Purine/Pyrimidine"/>
 309    <param name="APPLICATION_URL"
 310      value="http://www.jalview.org/services/launchApp"/>
 311 </applet>
 312 </td>
 313       <td valign="center">Displays an RFAM RNA fold family with
 314         secondary structure annotation</td>
 315     </tr>
 316   </table>
 317 </div>
 318 <!-- content template end -->
 319
 320
 321
 322 </div> <!-- end content div -->
 323
 324 </div> <!-- content -->
 325 </div> <!-- pagewrap -->
 326 <div id ="footer">
 327 <div id="innerFooter">
 328 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 329 <div id="cite">
 330 <p>
 331 If you use Jalview in your work, please cite this publication:
 332 </p>
 333 <br />
 334 <p>
 335 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 336 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 337 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 338 </p>
 339 </div>
 340 </div>
 341 </div>
 342 </body>
 343 </html>