examples/applets.html

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   2 <TITLE>Jalview - Applets</TITLE>
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   4         <p>Jalview comes in two distinct flavours.<br>
   5           <br>
   6           The main application allows connection to multiple web services provided
   7           at the University of Dundee as well as a host of additional useful features
   8           such as printing, making images from your alignment and annotating your
   9           alignment. You need to download and install this software.</p>
  10         <p>The applet version runs in web browsers and is a useful interactive
  11           display for precalculated alignments, features and annotations files.
  12           It does not have the full functionality of the main application, such
  13           as making images, saving files, running web service jobs due to security
  14           restrictions imposed on applets.</p>
  15         <p align="left">For more information on how to use the applet in your
  16           website, see <a href="appletParameters.html"><strong>full list of applet
  17           parameters.</strong></a></p>
  18         <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
  19           of Jalview, which runs within your web browser. </p>
  20         <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
  21           cluster<br>
  22           (15 sequences x 150 residues)</H4>
  23         <div align="center"> </div>
  24         <div align="center">
  25           <table width="300" border="1" cellspacing="0" cellpadding="0">
  26             <tr>
  27               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
  28                   <tr>
  29                     <td width="100"> <applet code="jalview.bin.JalviewLite"
  30                                 width="140" height="35"
  31                                 archive="jalviewApplet.jar">
  32                                                 <param name="file" value="uniref50.fa">\r                        <param name="treeFile" value="ferredoxin.nw">
  33                         <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
  34                         <param name="showFullId" value="false">
  35                         <param name="RGB"  value="F2F2FF">\r                        <param name="sortByTree" value="True">\r                        <param name="showSequenceLogo" value="true">\r                        <param name="showGroupConsensus" value="true">\r                        <param name="linkLabel_1" value="SRS">
  36                         <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
  37                         <param name="linkLabel_2" value="Uniprot">
  38                         <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
  39                                                 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
  40                       </applet></td>
  41                     <td width="165">User Defined Colours, loads an associated Newick
  42                       format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
  43                   </tr>
  44                 </table></td>
  45             </tr>
  46           </table>
  47           <p>&nbsp;</p>
  48           <table width="300" border="1" cellspacing="0" cellpadding="0">
  49             <tr>
  50               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
  51                   <tr>
  52                     <td width="100"> <applet code="jalview.bin.JalviewLite"
  53                                 width="140" height="35"
  54                                 archive="jalviewApplet.jar">
  55                         <param name="file" value="uniref50.fa">
  56                         <param name="features" value="exampleFeatures.txt">
  57                         <param name="showFeatureSettings" value="true">
  58                         <param name="wrap" value="true">
  59                         <param name="showAnnotation" value="false">
  60                         <param name="windowHeight" value="500">
  61                         <param name="windowWidth" value="650">
  62                         <param name="showFullId" value="false">
  63                         <param name="RGB"  value="F2F2FF">
  64                         <param name="linkLabel_1" value="SRS">
  65                         <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
  66                         <param name="linkLabel_2" value="Uniprot">
  67                         <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
  68                                                 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
  69                       </applet> </td>
  70                     <td width="165">Displays a features file on the alignment</td>
  71                   </tr>
  72                 </table></td>
  73             </tr>
  74           </table>
  75             <p>&nbsp;</p>
  76           <table width="300" border="1" cellspacing="0" cellpadding="0">
  77             <tr>
  78               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
  79                   <tr>
  80                     <td width="100"> <applet code="jalview.bin.JalviewLite"
  81                                 width="140" height="35"
  82                                 archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
  83                         <param name="file" value="uniref50.fa">\r                        <!-- <param name="debug" value="true">
  84                         -->\r                        <param name="defaultColour" value="Strand Propensity">
  85                         <param name="wrap" value="true">
  86                         <param name="showAnnotation" value="false">
  87                         <param name="windowHeight" value="500">
  88                         <param name="windowWidth" value="650">
  89                         <param name="showFullId" value="false">
  90                         <param name="RGB"  value="F2F2FF">
  91                         <param name="linkLabel_1" value="SRS">
  92                         <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
  93                         <param name="linkLabel_2" value="Uniprot">
  94                         <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
  95                                                 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
  96                         <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
  97                       </applet> </td>
  98                     <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
  99                   </tr>
 100                 </table></td>
 101             </tr>
 102           </table>
 103           <p>&nbsp;</p>
 104           <table width="300" border="1" cellspacing="0" cellpadding="0">
 105             <tr>
 106               <td><table width="300" border="0" cellspacing="0" cellpadding="0">
 107                   <tr>
 108                     <td width="100"> <applet code="jalview.bin.JalviewLite"
 109                                 width="140" height="35"
 110                                 archive="jalviewApplet.jar">
 111                         <param name="file" value="jpred_msa.fasta">
 112                         <param name="jnetfile" value="jpred_msa.seq.concise">
 113                         <param name="defaultColour" value="Clustal">
 114                         <param name="showAnnotation" value="true">
 115                         <param name="windowHeight" value="515">
 116                         <param name="windowWidth" value="650">
 117                         <param name="showConservation" value="false">
 118                         <param name="showQuality" value="false">
 119                         <param name="showConsensus" value="false">
 120                         <param name="showFullId" value="false">
 121                         <param name="RGB"  value="F2F2FF">
 122                         <param name="linkLabel_1" value="SRS">
 123                         <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
 124                         <param name="linkLabel_2" value="Uniprot">
 125                         <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 126                         <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
 127                       </applet> </td>
 128                     <td width="165">Displays a Multiple Sequence Alignment Based
 129                       JNet Prediction for a Sequence</td>
 130                   </tr>
 131                 </table></td>
 132             </tr>
 133           </table>\r        </div>\r        <p>&nbsp;</p>\r          <p>For more JalviewLite examples, follow the links below.\r          <ul>\r          <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>\r          <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>\r          <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>\r          <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>\r          </ul>
 134         <!-- InstanceEndEditable --></td>\r    </tr>\r  </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r