-<!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">
<!--
-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" -->
-<!-- <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>
git://source.jalview.org / jalview.git / blobdiff