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example applet and desktop application files that should be published
[jalview.git] / 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" -->
+<TITLE>Jalview - Applets</TITLE>
+<!-- InstanceEndEditable --> \r<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">\r<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r<style type="text/css">\r<!--\rtd {\r     font-family: Geneva, Arial, Helvetica, sans-serif;\r     font-size: 12px;\r}\r.plain {\r    font-family: Verdana, Arial, Helvetica, sans-serif;\r    font-size: 14px;\r       text-decoration: none;\r}\r.plain:hover{\r background-color:#000000; color: #F2F2FF;\r}\r \r-->\r</style>\r\r<script language="JavaScript">\rfunction genHref()\r{\rvar s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";\rfor(i=0; i<8; i++)\r{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);   }\rwindow.location=href;\r}\rfunction getEventTarget(e)\r{\rif(!e)\re = window.event;\rif(e.target)\rreturn e.target;\rreturn e.srcElement;\r}\r\r</script>\r</head>\r\r<body alink="#000000" vlink="#000000" link="#000000">\r<script type="text/javascript">\rvar gaJsHost = (("https:" == document.location.protocol) ? \r"https://ssl." : "http://www.");\rdocument.write(unescape("%3Cscript src='" + gaJsHost + \r"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r</script>\r<script type="text/javascript">\rtry{\rvar pageTracker = _gat._getTracker("UA-9060947-1");\rpageTracker._trackPageview();\r} catch(err) {}\r</script>\r<div align="left"> \r  <table width="805" height="100" cellpadding="5">\r    <tr>\r      <td background="../jalview.gif">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>\r    </tr>\r  </table>\r  <table width="805" border="0" cellpadding="5" cellspacing="5">\r    <tr> \r      <td width="183" valign="top" bgcolor="#F2F2FF" border="5"> \r       \r       <div align="center">\r          <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">\r            <tr> \r              <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="applets.html" class="plain">Applet \r                Version</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>\r            </tr>\r            <tr>\r              <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release \r                history</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source \r                Code</a></td>\r            </tr>\r                   <tr> \r              <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>\r            </tr>\r                   <tr> \r              <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>\r            </tr>\r            <tr> \r              <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News \r                Mailing List</a></td>\r            </tr>\r            <tr>\r              <td align="left" valign="middle"><a\r            href="http://www.jalview.org/mailman/listinfo/jalview-discuss"\r            class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and\r            bug reports to the discussion list.</em></td>\r            </tr>\r            <tr></tr>\r            <tr>\r              <!--<td align="left" valign="middle"><br>\r                Please send problems<br>and\r            bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->\r            </tr>\r          </table>\r\r        </div>\r\r        <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>\r          <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a> \r        </div>\r        </td>\r      <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
+        <p>Jalview comes in two distinct flavours.<br>
+          <br>
+          The main application allows connection to multiple web services provided
+          at the University of Dundee as well as a host of additional useful features
+          such as printing, making images from your alignment and annotating your
+          alignment. You need to download and install this software.</p>
+        <p>The applet version runs in web browsers and is a useful interactive
+          display for precalculated alignments, features and annotations files.
+          It does not have the full functionality of the main application, such
+          as making images, saving files, running web service jobs due to security
+          restrictions imposed on applets.</p>
+        <p align="left">For more information on how to use the applet in your
+          website, see <a href="appletParameters.html"><strong>full list of applet
+          parameters.</strong></a></p>
+        <p> Pressing one of the buttons below will load up a cut down version
+          of Jalview, which runs within your web browser. </p>
+        <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
+          cluster<br>
+          (15 sequences x 150 residues)</H4>
+        <div align="center"> </div>
+        <div align="center">
+          <table width="300" border="1" cellspacing="0" cellpadding="0">
+            <tr>
+              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+                  <tr>
+                    <td width="100"> <applet code="jalview.bin.JalviewLite"
+                               width="140" height="35"
+                               archive="jalviewApplet.jar">
+                        <param name="file" value="uniref50.fa">
+                        <param name="treeFile" value="ferredoxin.nw">
+                        <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
+                        <param name="showFullId" value="false">
+                        <param name="RGB"  value="F2F2FF">
+                        <param name="linkLabel_1" value="SRS">
+                        <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+                        <param name="linkLabel_2" value="Uniprot">
+                        <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+                                               <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+                      </applet></td>
+                    <td width="165">User Defined Colours, loads an associated Newick
+                      format tree file</td>
+                  </tr>
+                </table></td>
+            </tr>
+          </table>
+          <p>&nbsp;</p>
+          <table width="300" border="1" cellspacing="0" cellpadding="0">
+            <tr>
+              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+                  <tr>
+                    <td width="100"> <applet code="jalview.bin.JalviewLite"
+                               width="140" height="35"
+                               archive="jalviewApplet.jar">
+                        <param name="file" value="uniref50.fa">
+                        <param name="features" value="exampleFeatures.txt">
+                        <param name="showFeatureSettings" value="true">
+                        <param name="wrap" value="true">
+                        <param name="showAnnotation" value="false">
+                        <param name="windowHeight" value="500">
+                        <param name="windowWidth" value="650">
+                        <param name="showFullId" value="false">
+                        <param name="RGB"  value="F2F2FF">
+                        <param name="linkLabel_1" value="SRS">
+                        <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+                        <param name="linkLabel_2" value="Uniprot">
+                        <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+                                               <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+                      </applet> </td>
+                    <td width="165">Displays a features file on the alignment</td>
+                  </tr>
+                </table></td>
+            </tr>
+          </table>
+          <p>&nbsp;</p>
+          <table width="300" border="1" cellspacing="0" cellpadding="0">
+            <tr>
+              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+                  <tr>
+                    <td width="100"> <applet code="jalview.bin.JalviewLite"
+                               width="140" height="35"
+                               archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
+                        <param name="file" value="uniref50.fa">
+                        <param name="defaultColour" value="Strand Propensity">
+                        <param name="wrap" value="true">
+                        <param name="showAnnotation" value="false">
+                        <param name="windowHeight" value="500">
+                        <param name="windowWidth" value="650">
+                        <param name="showFullId" value="false">
+                        <param name="RGB"  value="F2F2FF">
+                        <param name="linkLabel_1" value="SRS">
+                        <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+                        <param name="linkLabel_2" value="Uniprot">
+                        <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+                                               <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+                        <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
+                      </applet> </td>
+                    <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
+                  </tr>
+                </table></td>
+            </tr>
+          </table>
+          <p>&nbsp;</p>
+          <table width="300" border="1" cellspacing="0" cellpadding="0">
+            <tr>
+              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+                  <tr>
+                    <td width="100"> <applet code="jalview.bin.JalviewLite"
+                               width="140" height="35"
+                               archive="jalviewApplet.jar">
+                        <param name="file" value="jpred_msa.fasta">
+                        <param name="jnetfile" value="jpred_msa.seq.concise">
+                        <param name="defaultColour" value="Clustal">
+                        <param name="showAnnotation" value="true">
+                        <param name="windowHeight" value="515">
+                        <param name="windowWidth" value="650">
+                        <param name="showConservation" value="false">
+                        <param name="showQuality" value="false">
+                        <param name="showConsensus" value="false">
+                        <param name="showFullId" value="false">
+                        <param name="RGB"  value="F2F2FF">
+                        <param name="linkLabel_1" value="SRS">
+                        <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+                        <param name="linkLabel_2" value="Uniprot">
+                        <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+                        <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+                      </applet> </td>
+                    <td width="165">Displays a Multiple Sequence Alignment Based
+                      JNet Prediction for a Sequence</td>
+                  </tr>
+                </table></td>
+            </tr>
+          </table>
+        </div>
+        <!-- InstanceEndEditable --></td>\r    </tr>\r  </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
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