+++ /dev/null
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>Jalview and Jmol</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>
-<script src="javascript/deployJava.js"></script>
-<script src="jmol/Jmol.js"></script>
-<script src="javascript/jquery-1.4.4.min.js"></script>
-<script src="javascript/jquery.timer.js"></script>
-<script src="javascript/jquery.blockUI.js"></script>
-<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
-<!-- <script src="archive-min.js" language="javascript"></script>
--->
-<script src="javascript/jalview.js" language="javascript"></script>
-<script language="JavaScript">
-// instead of this, we use a custom JmolApplet spec
-// jmolInitialize('jmol');
-jmolInitialize("","u_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;
-}
-</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();
-
- 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 : 'u_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 : "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/$SEQUENCE_ID$",
- APPLICATION_URL : "http://www.jalview.org/services/launchApp",
- PDBfile : "1gaq.txt FER1_MAIZE",
- permissions : "sandbox"
- };
- jmolSetCallback("hoverCallback","_jmolhover");
- jmolSetCallback("pickCallback","_jmolpick");
- modeltofiles+="1gaq.txt";
-</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="u_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="u_embedded.html">Embedded Alignment</a></li>
- <li class="jvlite-nav-small"><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="u_formComplete.html">Access from Javascript</a></li>
- <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="u_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;">
- Scary Java warnings ?<br/>Try <a href="embeddedWJmol.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
-<h2>Structure and Alignment</h2>
-<p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
-<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");
- </script>
- <script>
- deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
- </script>
-</center>
-<!-- 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