website/version2/examples/applets.html

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   5 <TITLE>JalView - Java alignment editor</TITLE>\r
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  24           <table width="550" border="0">\r
  25             <tr>\r
  26               <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
  27               <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
  28                   </font></strong></font> </div>\r
  29                 <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
  30                   multiple alignment editor</font> </div></td>\r
  31             </tr>\r
  32           </table>\r
  33           </center></td>\r
  34     </tr>\r
  35   </table>\r
  36  <br>\r
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  38     <tr> \r
  39       <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
  40         <ul>\r
  41           <li><a href="../index.html">Jalview</a></li>\r
  42         </ul>\r
  43         <strong>Examples</strong> <ul>\r
  44           <li><a href="applets.html">Applet</a></li>\r
  45           <li><a href="examples.html">Application</a></li>\r
  46         </ul>\r
  47         <strong>Reference</strong> <ul>\r
  48           <li> <a href="../../jalview.pdf" target="_blank">&quot;The Jalview Java<br>\r
  49             Alignment Editor,&quot;<br>\r
  50             </a></li>\r
  51           <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
  52         </ul>\r
  53         <strong>Source Code</strong> <ul>\r
  54           <li>Jalview 2</li>\r
  55         </ul>\r
  56         <p><strong>Feedback</strong></p>\r
  57         <p>&nbsp;&nbsp;&nbsp;<img src="../../help.gif" width="151" height="43"> </p>\r
  58         <p><br>\r
  59           <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
  60         </p></td>\r
  61       <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
  62         <p>Jalview2 comes in two distinct flavours.<br>\r
  63           <br>\r
  64           The main application allows connection to multiple web services provided\r
  65           at the University of Dundee as well as a host of additional useful features\r
  66           such as printing, making images from your alignment and annotating your\r
  67           alignment. <br>\r
  68           You need to download and install this software.</p>\r
  69         <p> Pressing one of the buttons below will load up a cut down version\r
  70           of Jalview2 multiple alignment editor, which runs within your web browser.</p>\r
  71         <H4>Alignment 1 - Serine proteases (6 sequences x 279 residues)</H4>\r
  72         <center>\r
  73 \r
  74                 <applet code="jalview.bin.JalviewLite"\r
  75                                 archive="jalviewlite.jar"\r
  76                                 width="200" height="40">\r
  77           <param name="file" value="serprot.msf">\r
  78         </applet>\r
  79 \r
  80                 </center>\r
  81         <H4>Alignment 2 - Lipases (16 sequences x 487 residues)</H4>\r
  82         <center>\r
  83                 <applet code="jalview.bin.JalviewLite"\r
  84                                 archive="jalviewlite.jar"\r
  85                                 width="200" height="40">\r
  86           <param name="file" value="lipase.msf">\r
  87                   <param name="defaultColour" value="Clustal">\r
  88                   <param name="showFullId" value="false">\r
  89         </applet></center>\r
  90         <H4>Alignment 3 - Glutathione S-transferases (61 sequences x 290 residues) With associated tree</H4>\r
  91                 <center>\r
  92           <applet code="jalview.bin.JalviewLite"\r
  93                                 archive="jalviewlite.jar"\r
  94                                 width="200" height="40">\r
  95             <param name="file" value="glut.msf">\r
  96                         <param name="defaultColour" value="Strand Propensity">\r
  97                         <param name="showConsensus" value="false">\r
  98                         <param name="showConservation" value="false">\r
  99                         <param name="treeFile" value="glut.newick">\r
 100           </applet>\r
 101                   </center>\r
 102         <p>The applet takes the following Parameters:</p>\r
 103         <table width="325" border="1" align="center" >\r
 104           <tr>\r
 105             <td width="103"><strong>name</strong></td>\r
 106             <td width="190"><strong>value</strong></td>\r
 107           </tr>\r
 108           <tr>\r
 109             <td>file</td>\r
 110             <td><em>fileName</em></td>\r
 111           </tr>\r
 112           <tr>\r
 113             <td>showFullId</td>\r
 114             <td>true false</td>\r
 115           </tr>\r
 116           <tr>\r
 117             <td>showAnnotation</td>\r
 118             <td>true false</td>\r
 119           </tr>\r
 120           <tr>\r
 121             <td>showConservation</td>\r
 122             <td>true false</td>\r
 123           </tr>\r
 124           <tr>\r
 125             <td>showQuality</td>\r
 126             <td>true false</td>\r
 127           </tr>\r
 128           <tr>\r
 129             <td>showConsensus</td>\r
 130             <td>true false</td>\r
 131           </tr>\r
 132           <tr>\r
 133             <td>defaultColour</td>\r
 134             <td>Clustal, Blosum62, % Identity, Zappo, Hydrophobic, Helix Propensity,\r
 135               Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>\r
 136           </tr>\r
 137         </table>\r
 138         <p align="center">&nbsp;</p>\r
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 140       </td>\r
 141     </tr>\r
 142   </table>\r
 143 </div>\r
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