-<!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"> <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> </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>
\ No newline at end of file
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>Linked JalviewLites</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+<![endif]-->
+
+<!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+<![endif]-->
+
+<!-- dd menu -->
+<script type="text/javascript">
+<!--
+var timeout = 500;
+var closetimer = 0;
+var ddmenuitem = 0;
+
+// open hidden layer
+function mopen(id)
+{
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+}
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+}
+
+// go close timer
+function mclosetime()
+{
+ closetimer = window.setTimeout(mclose, timeout);
+}
+
+// cancel close timer
+function mcancelclosetime()
+{
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
+</script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+
+</head>
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+<ul id="buttons">
+<li id="applet"><a href="applets.html" title="applet"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+</ul>
+</div>
+
+
+<div id ="nav">
+<div id="navInner">
+
+<ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+</ul>
+<div style="clear:both"></div>
+</div>
+
+</div>
+
+
+<div id="pageWrap">
+
+<div id="sideNav">
+<ul>
+<li><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li class="jvlite-nav-small"><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_linkedapplets_ng.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+<script src="http://www.java.com/js/deployJava.js"></script>
+<script src="javascript/jalview.js" language="javascript"></script>
+<script> //deployJava.debug="true";
+
+ function lJvApp() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ setConsole(document.getElementById("stdout"));
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvapp);
+ };
+
+ function lJvFollow() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ //jvfollower.setSeparator(""+jvfollower.getSeparator());
+ linkJvJmol(jvfollower);
+ };
+</script>
+ <h2>JalviewLite Linked Applets Demo</h2>
+ <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.
+ </p>
+ <script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'jalviewApplet.jar',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : 'jvapp'
+ };
+ var parameters = {
+ oninit : "lJvApp",
+ automaticScrolling : "true",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'sandbox',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+
+ deployJava.runApplet(attributes, parameters, '1.6');
+</script>
+<script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'jalviewApplet.jar',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : "jvfollower"
+ };
+ var parameters = {
+ oninit : "lJvFollow",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ automaticScrolling : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot",
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'sandbox',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+ deployJava.runApplet(attributes, parameters, '1.6');
+</script>
+ <p>
+<!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
+ <br>
+ -->
+<form name="console" id="console">
+<textarea name="output"
+ id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
+ <br>
+</p>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff