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[jalview.git] / website / version2 / examples / applets.html
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
-       font-family: Geneva, Arial, Helvetica, sans-serif;\r
-       font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
-  <table border="0">\r
-    <tr> \r
-      <td width="700" ><center>\r
-          <table width="550" border="0">\r
-            <tr>\r
-              <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0"  align="absmiddle"></a></div></td>\r
-              <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
-                  </font></strong></font> </div>\r
-                <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
-                  multiple alignment editor</font> </div></td>\r
-            </tr>\r
-          </table>\r
-          </center></td>\r
-    </tr>\r
-  </table>\r
- <br>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
-        <ul>\r
-          <li><a href="../index.html">Jalview</a></li>\r
-        </ul>\r
-        <strong>Examples</strong> <ul>\r
-          <li><a href="applets.html">Applet</a></li>\r
-          <li><a href="examples.html">Application</a></li>\r
-        </ul>\r
-        <strong>Reference</strong> <ul>\r
-          <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
-            Alignment Editor,&quot;<br>\r
-            </a></li>\r
-          <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
-        </ul>\r
-        <strong>Source Code</strong> <ul>\r
-          <li>Jalview 2</li>\r
-        </ul>\r
-        <p><strong>Feedback</strong></p>\r
-        <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
-        <p><br>\r
-          <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
-        </p></td>\r
-      <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
-        <p>Jalview2 comes in two distinct flavours.<br>\r
-          <br>\r
-          The main application allows connection to multiple web services provided\r
-          at the University of Dundee as well as a host of additional useful features\r
-          such as printing, making images from your alignment and annotating your\r
-          alignment. <br>\r
-          You need to download and install this software.</p>\r
-        <p> Pressing one of the buttons below will load up a cut down version\r
-          of Jalview2 multiple alignment editor, which runs within your web browser.</p>\r
-        <H4>Alignment 1 - Serine proteases (6 sequences x 279 residues)</H4>\r
-        <center>\r
-\r
-               <applet code="jalview.bin.JalviewLite"\r
-                               archive="jalviewlite.jar"\r
-                               width="200" height="40">\r
-          <param name="file" value="serprot.msf">\r
-        </applet>\r
-\r
-               </center>\r
-        <H4>Alignment 2 - Lipases (16 sequences x 487 residues)</H4>\r
-        <center>\r
-               <applet code="jalview.bin.JalviewLite"\r
-                               archive="jalviewlite.jar"\r
-                               width="200" height="40">\r
-          <param name="file" value="lipase.msf">\r
-                 <param name="defaultColour" value="Clustal">\r
-                 <param name="showFullId" value="false">\r
-        </applet></center>\r
-        <H4>Alignment 3 - Glutathione S-transferases (61 sequences x 290 residues) With associated tree</H4>\r
-               <center>\r
-          <applet code="jalview.bin.JalviewLite"\r
-                               archive="jalviewlite.jar"\r
-                               width="200" height="40">\r
-            <param name="file" value="glut.msf">\r
-                       <param name="defaultColour" value="Strand Propensity">\r
-                       <param name="showConsensus" value="false">\r
-                       <param name="showConservation" value="false">\r
-                       <param name="treeFile" value="glut.newick">\r
-          </applet>\r
-                 </center>\r
-        <p>The applet takes the following Parameters:</p>\r
-        <table width="325" border="1" align="center" >\r
-          <tr>\r
-            <td width="103"><strong>name</strong></td>\r
-            <td width="190"><strong>value</strong></td>\r
-          </tr>\r
-          <tr>\r
-            <td>file</td>\r
-            <td><em>fileName</em></td>\r
-          </tr>\r
-          <tr>\r
-            <td>showFullId</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showAnnotation</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showConservation</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showQuality</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>showConsensus</td>\r
-            <td>true false</td>\r
-          </tr>\r
-          <tr>\r
-            <td>defaultColour</td>\r
-            <td>Clustal, Blosum62, % Identity, Zappo, Hydrophobic, Helix Propensity,\r
-              Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>\r
-          </tr>\r
-        </table>\r
-        <p align="center">&nbsp;</p>\r
-        <!-- InstanceEndEditable --> \r
-      </td>\r
-    </tr>\r
-  </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r