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+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
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+
+ <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]>
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+<![endif]-->
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+
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+ closetimer = window.setTimeout(mclose, timeout);
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-function getEventTarget(e)
+
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- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" 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 class="jvlite-nav-small"><a href="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
+<div id="content" class="content">
<p>
<strong>Quick Links:<ul><li>Download the applet jar file from <a
href="jalviewApplet.jar">here</a>
<td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
</tr>
</table>
- <p align="center"> </p>
- <!-- InstanceEndEditable --></td>
- </tr>
- </table>
+</div>
+
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Copyright all rights reserved 2012</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 doi: 10.1093/bioinformatics/btp033
+</p>
+</div>
+</div>
</div>
</body>
-<!-- InstanceEnd --></html>
+</html>
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<!-- InstanceBeginEditable name="doctitle" -->
<TITLE>Jalview - Applets</TITLE>
-<!-- InstanceEndEditable -->
-<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">
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
-<style type="text/css">
+<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">
<!--
-td {
- font-family: Geneva, Arial, Helvetica, sans-serif;
- font-size: 12px;
-}
-.plain {
- font-family: Verdana, Arial, Helvetica, sans-serif;
- font-size: 14px;
- text-decoration: none;
+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';
+
}
-.plain:hover{
- background-color:#000000; color: #F2F2FF;
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
}
-
--->
-</style>
-<script language="JavaScript">
-function genHref()
+// go close timer
+function mclosetime()
{
-var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
-for(i=0; i<8; i++)
-{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
-window.location=href;
+ closetimer = window.setTimeout(mclose, timeout);
}
-function getEventTarget(e)
+
+// cancel close timer
+function mcancelclosetime()
{
-if(!e)
-e = window.event;
-if(e.target)
-return e.target;
-return e.srcElement;
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
+// close layer when click-out
+document.onclick = mclose;
+// -->
</script>
+
</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
-var gaJsHost = (("https:" == document.location.protocol) ?
-"https://ssl." : "http://www.");
-document.write(unescape("%3Cscript src='" + gaJsHost +
-"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-var pageTracker = _gat._getTracker("UA-9060947-1");
-pageTracker._trackPageview();
-} catch(err) {}
-</script>
-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <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>
- </tr>
- </table>
- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
-
- <div align="center">
- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
+<body>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <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
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" class="download-right">Download</a></li>
+</ul>
+<div style="clear:both"></div>
+</div>
+
+</div>
+
+
+<div id="pageWrap">
+
+<div id="sideNav">
+<ul>
+<li class="jvlite-nav-title"><a href="applets.html">JalviewLite Examples</a></li>
+<li><a href="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
+ <p>JalviewLite is a web based version of Jalview, which runs as a Java applet in or on a web page. It's one of the easiest ways of providing an 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
+ It lacks some functionality available in the Jalview Desktop, however, such
+ as making images, saving files, and running web service jobs. This is mostly 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
<li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
<li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
</ul>
- <!-- InstanceEndEditable --></td>
- </tr>
- </table>
+</div>
+
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Copyright all rights reserved 2012</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 doi: 10.1093/bioinformatics/btp033
+</p>
+</div>
+</div>
</div>
</body>
-<!-- InstanceEnd --></html>
+</html>
+
\ No newline at end of file
--- /dev/null
+#nav #navInner
+{
+margin-top:0x;
+}
+
+
+#sddm
+{
+ position:relative;
+ top:0;
+}
+
+
+#sddm li a.download-right
+{
+position:absolute;
+top:28px;
+left:270px;
+}
+
+#sddm li
+{
+padding-top:30px;
+padding-bottom:30px;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ top:80px;
+ z-index:9999;
+ width:0;
+ display:none;
+}
+
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: left;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ z-index:100;
+ left:-1100px;
+ }
+
+
+#nav
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
+
+#content
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
--- /dev/null
+#sddm\r
+{\r
+ position:relative;\r
+ top:0;\r
+}\r
+\r
+\r
+#sddm li a.download-right\r
+{\r
+position:relative;\r
+left:0;\r
+}\r
+\r
+#sddm li\r
+{\r
+padding-top:30px;\r
+padding-bottom:30px;\r
+}\r
+\r
+#sddm div\r
+{ position: absolute;\r
+ visibility: hidden;\r
+ margin: 0;\r
+ padding: 0;\r
+ background: #555;\r
+ border: 1px solid #000000;\r
+ top:80px;\r
+ z-index:9999;\r
+ width:120px;\r
+}\r
+\r
+\r
+ #sddm div a\r
+ { position: relative;\r
+ display: block;\r
+ margin: 0;\r
+ padding:8px;\r
+ width: 200px;\r
+ white-space: nowrap;\r
+ text-align: left;\r
+ text-decoration: none;\r
+ background: #555;\r
+ color: #fff;\r
+ border: 1px solid #000000;\r
+ background: #555;\r
+ z-index:100;\r
+ left:-80px;\r
+ }\r
+ \r
+ \r
+#nav\r
+{\r
+position:relative;\r
+z-index:2;\r
+ clear:both;\r
+ float:left;\r
+ width:100%; /* width of whole page */\r
+}\r
+\r
+#content \r
+{\r
+position:relative;\r
+z-index:2;\r
+ clear:both;\r
+ float:left;\r
+ width:100%; /* width of whole page */\r
+}\r
--- /dev/null
+/* http://meyerweb.com/eric/tools/css/reset/
+
+ v2.0 | 20110126
+
+ License: none (public domain)
+
+*/
+
+
+
+html, body, div, span, applet, object, iframe,
+
+h1, h2, h3, h4, h5, h6, p, blockquote, pre,
+
+a, abbr, acronym, address, big, cite, code,
+
+del, dfn, em, img, ins, kbd, q, s, samp,
+
+small, strike, strong, sub, sup, tt, var,
+
+b, u, i, center,
+
+dl, dt, dd, ol, ul, li,
+
+fieldset, form, label, legend,
+
+table, caption, tbody, tfoot, thead, tr, th, td,
+
+article, aside, canvas, details, embed,
+
+figure, figcaption, footer, header, hgroup,
+
+menu, nav, output, ruby, section, summary,
+
+time, mark, audio, video {
+
+ margin: 0;
+
+ padding: 0;
+
+ border: 0;
+
+ font-size: 100%;
+
+ font: inherit;
+
+ vertical-align: baseline;
+
+}
+
+/* HTML5 display-role reset for older browsers */
+
+article, aside, details, figcaption, figure,
+
+footer, header, hgroup, menu, nav, section {
+
+ display: block;
+
+}
+
+body {
+
+ line-height: 1;
+
+}
+
+ol, ul {
+
+ list-style: none;
+
+}
+
+blockquote, q {
+
+ quotes: none;
+
+}
+
+blockquote:before, blockquote:after,
+
+q:before, q:after {
+
+ content: '';
+
+ content: none;
+
+}
+
+table {
+
+ border-collapse: collapse;
+
+ border-spacing: 0;
+
+}
\ No newline at end of file
--- /dev/null
+@import url(http://fonts.googleapis.com/css?family=Lato);
+@import url(http://fonts.googleapis.com/css?family=Oswald);
+
+/*****************
+HTML 5 Elements
+******************/
+new
+
+
+article, aside, details, figcaption, figure,
+footer, header, hgroup, menu, nav, section
+{
+ display: block;
+}
+
+
+.clearfix:after
+ {
+ visibility: hidden;
+ display: block;
+ font-size: 0;
+ content: " ";
+ clear: both;
+ height: 0;
+}
+
+
+/****************
+Body
+****************/
+
+body
+
+{
+ font: 76% arial,Helvetica,sans-serif;
+ text-align:left;
+ background:#fff;
+ color:#000;
+ border-top: 20px solid #555555;
+}
+
+
+
+/*********************
+Page Wrapper
+********************/
+
+#pageWrap
+
+{
+ width: 960px;
+ margin: 0 auto;
+ position:relative;
+}
+
+/**********************
+HEADER
+************************/
+
+#header
+{
+ display: block;
+ height: 180px;
+ margin: 0 auto 8px;
+ width: 960px;
+ position:relative;
+}
+
+#logo a
+{
+ background-image: url("../images/logo.jpg");
+ background-repeat: no-repeat;
+ height: 87px;
+ left: 0;
+ position: absolute;
+ top: 50px;
+ width: 361px;
+ margin-bottom:50px;
+}
+
+#buttons
+{
+height:88px;
+width:252px;
+float:right;
+ right: 0;
+ position: absolute;
+ top: 50px;
+}
+
+#buttons li
+{
+margin-bottom:10px;
+}
+
+#buttons #applet a
+{
+ background-image: url("../images/applet.jpg");
+ background-repeat: no-repeat;
+ height:50px;
+ width:250px;
+ position: absolute;
+ opacity: 1;
+ transition: opacity .25s ease-in-out;
+ -moz-transition: opacity .25s ease-in-out;
+ -webkit-transition: opacity .25s ease-in-out;
+ text-shadow: 2px 2px 10px #000000;
+}
+
+#buttons #desktop a
+{
+ background-image: url("../images/desk.jpg");
+ background-repeat: no-repeat;
+ height:50px;
+ width:250px;
+ position: absolute;
+ top:45px;
+ opacity: 1;
+ transition: opacity .25s ease-in-out;
+ -moz-transition: opacity .25s ease-in-out;
+ -webkit-transition: opacity .25s ease-in-out;
+ text-shadow: 2px 2px 10px #000000;
+}
+
+#buttons #applet a:hover
+{
+ opacity: 0.8;
+}
+
+#buttons #desktop a:hover
+{
+ opacity: 0.8;
+}
+
+/*****************************
+NAV
+*********************************/
+#nav
+{
+width:100%;
+max-width:100%;
+color:#fff;
+background:#555;
+height:80px;
+}
+
+#navInner
+{
+width:960px;
+margin:0 auto;
+position:relative;
+}
+
+
+#sddm
+{ margin: 0;
+ padding: 0;
+ z-index: 30;
+ position:relative;
+ top:27px;
+}
+
+#sddm li
+{ margin: 0;
+ padding:0;
+ list-style: none;
+ float: left;
+}
+
+#sddm li a
+{
+ color: #FFFFFF;
+ font-size: 13pt;
+ padding: 27px 15px 25px;
+ text-align: center;
+ text-decoration: none;
+ font-family: 'Lato',sans-serif;
+}
+
+#sddm li a.community:hover
+{
+background:#F78E1E;
+}
+
+#sddm li a.development:hover
+{
+background:#AEBF45;
+}
+
+#sddm li a.training:hover
+{
+background:#009DDC;
+}
+
+#sddm li a.download-right
+{
+float:right;
+position:relative;
+left:345px;
+display:block;
+clear:left;
+ margin-top: -27px;
+ padding: 27px 15px 25px;
+}
+
+
+ul#sddm li a:hover
+{
+ text-decoration: none;
+ background:#0083A9;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ background: #555;
+ border: 1px solid #000000;
+ top:50px;
+}
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: center;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ }
+
+
+
+/*****************************
+CONTENT
+*****************************/
+
+#content
+{
+ font-size: 10pt;
+ height: auto;
+ width: 710px;
+ padding-top:23px;
+ padding-bottom:23px;
+ overflow-x:auto;
+ overflow-y:hidden;
+}
+
+#sideNav
+{
+width:200px;
+float:left;
+padding-top:29px;
+margin-right:50px;
+}
+
+
+
+#sideNav li
+{
+ height: 40px;
+ list-style-image: none;
+ list-style-type: none;
+ margin-bottom: 20px;
+}
+
+#sideNav a
+{
+ color: #555555;
+ display: block;
+ font-size: 13pt;
+ padding: 8px 0 0 15px;
+ text-decoration: none;
+}
+
+#sideNav a:hover
+{
+ text-decoration: underline;
+}
+#sideNav .about-nav-title
+{
+background: url("../images/normal-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .jvlite-nav-title
+{
+background: url("../images/jvlite-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .jvlite-nav-small
+{
+background: url("../images/jvlite-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 0px;
+}
+
+#sideNav .com-nav-title
+{
+background: url("../images/com-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .dev-nav-title
+{
+background: url("../images/dev-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .train-nav-title
+{
+background: url("../images/train-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+/********************************
+FOOTER
+***********************************/
+
+#footer
+{
+max-width:100%;
+width:100%;
+color:#fff;
+background:#555;
+height:140px;
+padding-top:10px;
+clear:both;
+}
+
+#innerFooter
+{
+width:960px;
+margin:0 auto;
+height:140px;
+padding-top:10px;
+}
+
+
+#copyright
+{
+float:left;
+}
+
+#cite
+{
+float:right;
+width:555px;
+}
\ No newline at end of file
-<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
<html xmlns="http://www.w3.org/1999/xhtml">
-<title>
-Embedded viewing of Alignments
+<head>Embedded viewing of Alignments
</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>
+
+</head>
+
+
<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" 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="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li class="jvlite-nav-small"><a href="embedded.html">Embedded applet demo</a></li>
+<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<h1>Embedded viewing of Alignments</h1>
<p>The alignment below was generated from the following files:
<ul>
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<!-- InstanceBeginEditable name="doctitle" -->
<TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
-<!-- InstanceEndEditable -->
-<meta http-equiv="content-type" content="text/html; charset=UTF-8">
-<meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">
-<!-- InstanceBeginEditable name="head" -->
<script src="javascript/deployJava.js"></script>
<script src="jmol/Jmol.js"></script>
<script src="javascript/jquery-1.4.4.min.js"></script>
jmolInitialize("","JmolApplet-12.2.4.jar");
function genHref()
{
- var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
- for(i=0; i<11; i++)
- { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
- }
- window.location=href;
+ var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
+ for(i=0; i<11; i++)
+ { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
+ }
+ window.location=href;
}
</script>
<script>
- var loglevel=1;
- function dbg(lvl,string) {
- if (_console && lvl<=loglevel) {_console.value += string + "\n";}
- }
- var _lastTime=new Date();
- var _path;
- var _datazip;
- var _zip;
- var alignA;
- var alignB;
- var featuresA;
- var featuresB;
- var pairs;
- var atompairs;
- var structdata;
- var jmolview;
- var jvstructassoc;
- var modeltofiles = new Array();
+ var loglevel=1;
+ function dbg(lvl,string) {
+ if (_console && lvl<=loglevel) {_console.value += string + "\n";}
+ }
+ var _lastTime=new Date();
+ var _path;
+ var _datazip;
+ var _zip;
+ var alignA;
+ var alignB;
+ var featuresA;
+ var featuresB;
+ var pairs;
+ var atompairs;
+ var structdata;
+ var jmolview;
+ var jvstructassoc;
+ var modeltofiles = new Array();
- function lJvA() {
- jvfollower = document.getElementById("jvA");
- setConsole(document.getElementById("stdout"));
-
- sep = jvfollower.getSeparator();
- //jvapp.setSeparator(""+jvapp.getSeparator());
- linkJvJmol(jvfollower, "jmolView", modeltofiles);
- };
+ function lJvA() {
+ jvfollower = document.getElementById("jvA");
+ setConsole(document.getElementById("stdout"));
+
+ sep = jvfollower.getSeparator();
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ };
- var _jvA=new Object();
- _jvA.attributes = {
- code : 'jalview.bin.JalviewLite',
- archive : 'jalviewApplet.jar',
- width : '500',
- height : '350',
- mayscript : 'True',
- scriptable: 'True',
- id : 'jvA'
- };
- _jvA.parameters = {
- java_arguments : "-Xmx256m",
- externalstructureviewer : "true",
- oninit : "lJvA",
- automaticScrolling : "true",
-// <!-- defaultColour : "Strand Propensity", -->
- file : "uniref50_mz.fa",
-
- relaxedidmatch : "true",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "false",
- embedded : "true",
- showFullId : "false",
- RGB : "F2F2FF",
- linkLabel_1 : "SRS",
- linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
- ,
- linkLabel_2 : "Uniprot"
- ,
- linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
- APPLICATION_URL : "http://www.jalview.org/services/launchApp",
- PDBfile : "1gaq.txt FER1_MAIZE"
- };
- jmolSetCallback("hoverCallback","_jmolhover");
+ var _jvA=new Object();
+ _jvA.attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'jalviewApplet.jar',
+ width : '500',
+ height : '350',
+ mayscript : 'True',
+ scriptable: 'True',
+ id : 'jvA'
+ };
+ _jvA.parameters = {
+ java_arguments : "-Xmx256m",
+ externalstructureviewer : "true",
+ oninit : "lJvA",
+ automaticScrolling : "true",
+// <!-- defaultColour : "Strand Propensity", -->
+ file : "uniref50_mz.fa",
+
+ relaxedidmatch : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "false",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "SRS",
+ linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp",
+ PDBfile : "1gaq.txt FER1_MAIZE"
+ };
+ jmolSetCallback("hoverCallback","_jmolhover");
jmolSetCallback("pickCallback","_jmolpick");
modeltofiles+="1gaq.txt";
</script>
-<!-- InstanceEndEditable -->
-<style type="text/css">
+<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">
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- text-decoration: none;
+var timeout = 500;
+var closetimer = 0;
+var ddmenuitem = 0;
+
+// open hidden layer
+function mopen(id)
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+ // cancel close timer
+ mcancelclosetime();
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+ // close old layer
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-.plain:hover{
- background-color:#000000; color: #F2F2FF;
+// close showed layer
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-<script language="JavaScript">
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+
+// go close timer
+function mclosetime()
{
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-{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
-window.location=href;
+ closetimer = window.setTimeout(mclose, timeout);
}
-function getEventTarget(e)
+
+// cancel close timer
+function mcancelclosetime()
{
-if(!e)
-e = window.event;
-if(e.target)
-return e.target;
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+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
</script>
+
</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
-var gaJsHost = (("https:" == document.location.protocol) ?
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-try{
-var pageTracker = _gat._getTracker("UA-9060947-1");
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-} catch(err) {}
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-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <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>
- </tr>
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- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
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- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
-<!-- <a onclick="colourStructs();">Colour from jalviews</a>
- -->
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" 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="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li class="jvlite-nav-small"><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<center>
<script>
jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
</script>
</center>
- </td>
- </tr>
- </table>
-<!-- <form name="console" id="console">
- <textarea name="output" id="stdout" rows="3" cols="80"
- >Messages will appear here.</textarea></form>
- --></div>
- <!-- InstanceEndEditable --></td>
- </tr>
- </table>
+</div>
+
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Copyright all rights reserved 2012</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 doi: 10.1093/bioinformatics/btp033
+</p>
+</div>
+</div>
</div>
</body>
-<!-- InstanceEnd --></html>
-
+</html>
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<!-- InstanceBeginEditable name="doctitle" -->
<TITLE>JalviewLite Applet API and Form Complete Example</TITLE>
-<!-- InstanceEndEditable -->
-<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">
-<!-- InstanceBeginEditable name="head" -->
-<!-- InstanceEndEditable -->
-<style type="text/css">
+<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">
<!--
-td {
- font-family: Geneva, Arial, Helvetica, sans-serif;
- font-size: 12px;
+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';
+
}
-.plain {
- font-family: Verdana, Arial, Helvetica, sans-serif;
- font-size: 14px;
- text-decoration: none;
-}
-.plain:hover{
- background-color:#000000; color: #F2F2FF;
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
}
-
--->
-</style>
-<script language="JavaScript">
-function genHref()
+
+// go close timer
+function mclosetime()
{
-var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
-for(i=0; i<8; i++)
-{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
-window.location=href;
+ closetimer = window.setTimeout(mclose, timeout);
}
-function getEventTarget(e)
+
+// cancel close timer
+function mcancelclosetime()
{
-if(!e)
-e = window.event;
-if(e.target)
-return e.target;
-return e.srcElement;
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
</script>
+
</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
-var gaJsHost = (("https:" == document.location.protocol) ?
-"https://ssl." : "http://www.");
-document.write(unescape("%3Cscript src='" + gaJsHost +
-"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-var pageTracker = _gat._getTracker("UA-9060947-1");
-pageTracker._trackPageview();
-} catch(err) {}
-</script>
-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <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>
- </tr>
- </table>
- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
-
- <div align="center">
- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p> </p>
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" 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="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li class="jvlite-nav-small"><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<strong>Using the <a href="jalviewLiteJs.html">JalviewLite API</a> to fill out forms using data from JalviewLite<br></strong>
Click the Javascript buttons below to interact with the Applet
instance on the page.<br>
onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
value="Hide groups" /></div>
</form>
-
-<!-- InstanceEndEditable --></td>
- </tr>
- </table>
+ </div>
+
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Copyright all rights reserved 2012</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 doi: 10.1093/bioinformatics/btp033
+</p>
+</div>
+</div>
</div>
</body>
-<!-- InstanceEnd --></html>
+</html>
+
\ No newline at end of file
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<!-- InstanceBeginEditable name="doctitle" -->
-<TITLE>JalviewLite API documentation</TITLE>
-<!-- InstanceEndEditable -->
-<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">
-<!-- InstanceBeginEditable name="head" -->
-<!-- InstanceEndEditable -->
-<style type="text/css">
+
+ <title>JalviewLite API documentation</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">
<!--
-td {
- font-family: Geneva, Arial, Helvetica, sans-serif;
- font-size: 12px;
-}
-.plain {
- font-family: Verdana, Arial, Helvetica, sans-serif;
- font-size: 14px;
- text-decoration: none;
+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';
+
}
-.plain:hover{
- background-color:#000000; color: #F2F2FF;
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
}
-
--->
-</style>
-<script language="JavaScript">
-function genHref()
+
+// go close timer
+function mclosetime()
{
-var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
-for(i=0; i<8; i++)
-{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
-window.location=href;
+ closetimer = window.setTimeout(mclose, timeout);
}
-function getEventTarget(e)
+
+// cancel close timer
+function mcancelclosetime()
{
-if(!e)
-e = window.event;
-if(e.target)
-return e.target;
-return e.srcElement;
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
</script>
+
</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
-var gaJsHost = (("https:" == document.location.protocol) ?
-"https://ssl." : "http://www.");
-document.write(unescape("%3Cscript src='" + gaJsHost +
-"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-var pageTracker = _gat._getTracker("UA-9060947-1");
-pageTracker._trackPageview();
-} catch(err) {}
-</script>
-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <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>
- </tr>
- </table>
- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
-
- <div align="center">
- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p> </p>
- <strong>JalviewLite Javascript API<br></strong>
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" 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="appletParameters.html">Applet Parameters</a></li>
+<li class="jvlite-nav-small"><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
+</p>
<p>The best way to learn how to use the API is to see it in action on the demonstration pages below:</p>
<ul>
<li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
<li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other.</a></li>
<li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page (EXPERIMENTAL! please provide feedback!).</a></li>
<li><a href="javascriptLaunch.html">launch JalviewLite from a javascript button</a></li>
-
</ul>
- <h4>Notes</h4>
+ <h3>Notes</h3>
<ul>
<li>Unfortunately Javascript - Java communication is not possible
using Internet Explorer or Opera on Macs. Please use Safari or
</li>
</ul>
<a name="api">
- <h4>JalviewLite's Java API</h4></a>
+ <h1>JalviewLite's Javascript API</h1></a>
<p>The following public methods on the jalviewLite applet are available to be called from javascript:</p>
<pre>//get list of IDs of selected sequences
public String getSelectedSequences()
public void loadAnnotationFrom(AlignFrame alf, String annotation)
// parse the given string as a jalview or GFF features file and optionally enable feature display on the current alignment
-// (v2.7.1)
+// (v2.8)
public abstract void loadFeatures(String features, boolean autoenabledisplay)
// parse the given string as a jalview or GFF features file and optionally enable feature display on the given alignment
-// (v2.7.1)
+// (v2.8)
public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
// get the sequence features in the given format (Jalview or GFF)
// debug flag - controls output to standard out
public static boolean debug
-</pre> <!-- InstanceEndEditable --></td>
- </tr>
- </table>
+</pre>
+
+</div>
+
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Copyright all rights reserved 2012</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 doi: 10.1093/bioinformatics/btp033
+</p>
+</div>
+</div>
</div>
</body>
-<!-- InstanceEnd --></html>
+</html>
-<html>
+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
<head><title>Opening JalviewLite from Javascript</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>
+
</head>
- <body>
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" 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="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a><ul><li class="jvlite-nav-small"><a href="javascriptLaunch.html">JalviewLite Button</a></li></ul></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<SCRIPT type="text/javascript">
/* <![CDATA[ // */
// From http://snipplr.com/view.php?codeview&id=1272
</form>
- </body>
-</html>
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!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)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<!-- InstanceBeginEditable name="doctitle" -->
<title>Linked Jalview Applets Demo</title>
-<!-- InstanceEndEditable -->
-<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">
-<!-- InstanceBeginEditable name="head" -->
+ <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" />
<script src="http://www.java.com/js/deployJava.js"></script>
<script src="javascript/jalview.js" language="javascript"></script>
<script> //deployJava.debug="true";
linkJvJmol(jvfollower);
};
</script>
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+<![endif]-->
-<!-- InstanceEndEditable -->
-<style type="text/css">
+<!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+<![endif]-->
+
+<!-- dd menu -->
+<script type="text/javascript">
<!--
-td {
- font-family: Geneva, Arial, Helvetica, sans-serif;
- font-size: 12px;
-}
-.plain {
- font-family: Verdana, Arial, Helvetica, sans-serif;
- font-size: 14px;
- text-decoration: none;
+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';
+
}
-.plain:hover{
- background-color:#000000; color: #F2F2FF;
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
}
-
--->
-</style>
-<script language="JavaScript">
-function genHref()
+
+// go close timer
+function mclosetime()
{
-var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
-for(i=0; i<8; i++)
-{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
-window.location=href;
+ closetimer = window.setTimeout(mclose, timeout);
}
-function getEventTarget(e)
+
+// cancel close timer
+function mcancelclosetime()
{
-if(!e)
-e = window.event;
-if(e.target)
-return e.target;
-return e.srcElement;
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
</script>
+
</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
-var gaJsHost = (("https:" == document.location.protocol) ?
-"https://ssl." : "http://www.");
-document.write(unescape("%3Cscript src='" + gaJsHost +
-"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-var pageTracker = _gat._getTracker("UA-9060947-1");
-pageTracker._trackPageview();
-} catch(err) {}
-</script>
-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <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>
- </tr>
- </table>
- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
-
- <div align="center">
- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p> </p>
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" 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="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" 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="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li class="jvlite-nav-small"><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<strong>JalviewLite Linked Applets Demo<br></strong>
<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>
git://source.jalview.org / jalview.git / commitdiff
