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new and restructured javascript examples and documentation (JAL-816,
[jalview.git] / examples / linkedapplets_ng.html
diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.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>Linked Jalview Applets Demo</title>\r
+<!-- 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" -->\r
+<script src="http://www.java.com/js/deployJava.js"></script>\r
+<script src="javascript/jalview.js" language="javascript"></script>\r
+<script>  //deployJava.debug="true";\r
+  \r
+  function lJvApp() {\r
+    var jvapp = document.getElementById("jvapp");\r
+    var jvfollower = document.getElementById("jvfollower");\r
+    setConsole(document.getElementById("stdout"));\r
+    //jvapp.setSeparator(""+jvapp.getSeparator());\r
+    linkJvJmol(jvapp);\r
+  };\r
+\r
+  function lJvFollow() {\r
+    var jvapp = document.getElementById("jvapp");\r
+    var jvfollower = document.getElementById("jvfollower");\r
+    //jvfollower.setSeparator(""+jvfollower.getSeparator());\r
+    linkJvJmol(jvfollower);\r
+  };\r
+</script>\r
+\r
+<!-- InstanceEndEditable --> \r
+<style type="text/css">\r
+<!--\r
+td {\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
+<script language="JavaScript">\r
+function genHref()\r
+{\r
+var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";\r
+for(i=0; i<8; i++)\r
+{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);  }\r
+window.location=href;\r
+}\r
+function getEventTarget(e)\r
+{\r
+if(!e)\r
+e = window.event;\r
+if(e.target)\r
+return e.target;\r
+return e.srcElement;\r
+}\r
+</script>\r
+</head>\r
+<body alink="#000000" vlink="#000000" link="#000000">\r
+<script type="text/javascript">\r
+var gaJsHost = (("https:" == document.location.protocol) ? \r
+"https://ssl." : "http://www.");\r
+document.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">\r
+try{\r
+var pageTracker = _gat._getTracker("UA-9060947-1");\r
+pageTracker._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
+        </div>\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" -->\r
+    <p>&nbsp;</p>\r
+    <strong>JalviewLite Linked Applets Demo<br></strong>\r
+    <p>The two applets below use <a href="JalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.\r
+    </p>\r
+    <p>See the other demonstration pages below to see the API in action:</p>\r
+    <ul>\r
+          <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>\r
+          <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>\r
+          <li><a href="javascriptLaunch.html">launch JalviewLite from a javascript button</a></li>\r
+          \r
+    </ul>\r
+       <script> \r
+  var attributes = {\r
+    code : 'jalview.bin.JalviewLite',\r
+    archive : 'jalviewApplet.jar',\r
+    width : 800,\r
+    height : 300,\r
+    mayscript : 'True', scriptable: 'True',\r
+    id : 'jvapp'\r
+  };\r
+  var parameters = {\r
+    oninit : "lJvApp",\r
+    automaticScrolling : "true",\r
+    file : "plantfdx.fa",\r
+    annotations : "plantfdx.annotations",\r
+    debug : "true",\r
+    wrap : "false",\r
+    // separator : "^",\r
+    showAnnotation : "true",\r
+    embedded : "true",\r
+    showFullId : "false",\r
+    RGB : "F2F2FF",\r
+    linkLabel_1 : "SRS",\r
+    linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"\r
+ \r
+    ,\r
+    linkLabel_2 : "Uniprot"\r
+ \r
+    ,\r
+    linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",\r
+    APPLICATION_URL : "http://www.jalview.org/services/launchApp"\r
+  };\r
+ \r
+  deployJava.runApplet(attributes, parameters, '1.6');\r
+</script>\r
+<script> \r
+  var attributes = {\r
+    code : 'jalview.bin.JalviewLite',\r
+    archive : 'jalviewApplet.jar',\r
+    width : 800,\r
+    height : 300,\r
+    mayscript : 'True', scriptable: 'True',\r
+    id : "jvfollower"\r
+  };\r
+  var parameters = {\r
+    oninit : "lJvFollow",\r
+    file : "plantfdx.fa",\r
+    annotations : "plantfdx.annotations",\r
+    automaticScrolling : "true",\r
+    debug : "true",\r
+    wrap : "false",\r
+    // separator : "^",\r
+    showAnnotation : "true",\r
+    embedded : "true",\r
+    showFullId : "false",\r
+    RGB : "F2F2FF",\r
+    linkLabel_1 : "SRS",\r
+    linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"\r
+ \r
+    ,\r
+    linkLabel_2 : "Uniprot"\r
+ \r
+    ,\r
+    linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",\r
+    APPLICATION_URL : "http://www.jalview.org/services/launchApp"\r
+  };\r
+  deployJava.runApplet(attributes, parameters, '1.6');\r
+</script>\r
+    <p>\r
+<!--      <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>\r
+      <br>\r
+       --><form name="console" id="console"><textarea name="output"\r
+        id="stdout" rows="20" cols="80">Messages  will appear here.</textarea></form>\r
+      <br>\r
+</p>\r
+\r
+</body>\r
+</html>
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