-<!-- boiler plate link to alternate demopage -->
-
-<head>
-<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);})();
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
+<html lang="en" dir="ltr" version="HTML+RDFa 1.1"
+ xmlns:content="http://purl.org/rss/1.0/modules/content/"
+ xmlns:dc="http://purl.org/dc/terms/"
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+<head profile="http://www.w3.org/1999/xhtml/vocab">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<link rel="shortcut icon"
+ href="http://www.jalview.org/sites/all/themes/jalview/favicon.ico"
+ type="image/vnd.microsoft.icon" />
+<meta name="viewport"
+ content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no" />
+<meta content="" about="/About" property="dc:title" />
+<link rel="shortlink" href="/node/18" />
+<meta name="Generator" content="Drupal 7 (http://drupal.org)" />
+<link rel="canonical" href="/About" />
+<title>Development | jalview.org</title>
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_pbm0lsQQJ7A7WCCIMgxLho6mI_kBNgznNUWmTWcnfoE.css"
+ media="all" />
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_gUtVu-PFpNy2iKRzspQnPE665qK-eDx99tAc6O2EKBs.css"
+ media="all" />
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_HByEx9XzXH_VOfr3lfyJmXRKhQdq8UyyslSu9odJFaw.css"
+ media="all" />
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_Rj_Ai4KdTE0qt75bSUOfQPNak90tBSJRVjZIjglGhlM.css"
+ media="all" />
+
+<!--[if lte IE 6]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie6.css?nqc8th" media="all" />
+<![endif]-->
+
+<!--[if lte IE 7]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie7.css?nqc8th" media="all" />
+<![endif]-->
+
+<!--[if lte IE 8]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie8.css?nqc8th" media="all" />
+<![endif]-->
+
+<!--[if (lt IE 9)&(!IEMobile)]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_ybf1eloQwwauLFbDPh5-J2RvDVEM4Gsh1NsAC0ynfNs.css" media="all" />
+<![endif]-->
+
+<!--[if gte IE 9]><!-->
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_kD8qBi2CLfQkl16-SgdHuwlYq_NUjXsjCxmpeidlT0I.css"
+ media="all" />
+<!--<![endif]-->
+<script type="text/javascript">
+<!--//--><![CDATA[//><!--
+ document.cookie = 'adaptive_image=' + Math.max(screen.width, screen.height)
+ + '; path=/';
+ //--><!]]>
+</script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_0gj6QcpfRH2jzTbCQqf7kEkm4MXY0UA_sRhwPc8jC1o.js"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/all/modules/lightbox2/js/lightbox.js?1434966756"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_SoFDHsgxDY2cLYbZ6HeW4SLlU_sLxsgGT6tSFwfsHGY.js"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/all/modules/mobile_navigation/js/mobile_menu.js?nqc8th"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/all/modules/mobile_navigation/mobile_navigation.js?nqc8th"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_IDBX5SzkJ9gGNq7x-qOE_2DZsexqguTJQGMKvi4w-Uw.js"></script>
+<script type="text/javascript">
+<!--//--><![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 type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_tnUY-Xr0uSK3E1mkrZ6ON7OmxH4PiVjShebnFJ8E-9c.js"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_43n5FBy8pZxQHxPXkf-sQF7ZiacVZke14b0VlvSA554.js"></script>
+
+<script type="text/javascript">
+<!--//--><![CDATA[//><!--
+jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":{"theme":"jalview","theme_token":"wip-WGy4TPV1wdu4Sdq6IXFdriaYrLsrzHuYbaCEpD8","js":{"0":1,"sites\/all\/modules\/jquery_update\/replace\/jquery\/1.7\/jquery.min.js":1,"misc\/jquery.once.js":1,"misc\/drupal.js":1,"sites\/all\/modules\/lightbox2\/js\/lightbox.js":1,"sites\/all\/modules\/nice_menus\/superfish\/js\/superfish.js":1,"sites\/all\/modules\/nice_menus\/superfish\/js\/jquery.bgiframe.min.js":1,"sites\/all\/modules\/nice_menus\/superfish\/js\/jquery.hoverIntent.minified.js":1,"sites\/all\/modules\/nice_menus\/nice_menus.js":1,"sites\/all\/modules\/mobile_navigation\/js\/mobile_menu.js":1,"sites\/all\/modules\/mobile_navigation\/mobile_navigation.js":1,"sites\/all\/modules\/google_analytics\/googleanalytics.js":1,"1":1,"sites\/all\/themes\/jalview\/js\/jalview_ga_event_tracking.js":1,"sites\/all\/themes\/omega\/omega\/js\/jquery.formalize.js":1,"sites\/all\/themes\/omega\/omega\/js\/omega-mediaqueries.js":1},"css":{"modules\/system\/system.base.css":1,"modules\/system\/system.menus.css":1,"modules\/system\/system.messages.css":1,"modules\/system\/system.theme.css":1,"sites\/all\/modules\/adaptive_image\/css\/adaptive-image.css":1,"sites\/all\/modules\/date\/date_api\/date.css":1,"sites\/all\/modules\/date\/date_popup\/themes\/datepicker.1.7.css":1,"modules\/field\/theme\/field.css":1,"modules\/node\/node.css":1,"modules\/poll\/poll.css":1,"modules\/search\/search.css":1,"modules\/user\/user.css":1,"sites\/all\/modules\/views\/css\/views.css":1,"sites\/all\/modules\/ctools\/css\/ctools.css":1,"sites\/all\/modules\/lightbox2\/css\/lightbox.css":1,"sites\/all\/modules\/nice_menus\/nice_menus.css":1,"sites\/all\/modules\/nice_menus\/nice_menus_default.css":1,"sites\/all\/modules\/mobile_navigation\/mobile_navigation.css":1,"sites\/all\/themes\/omega\/alpha\/css\/alpha-reset.css":1,"sites\/all\/themes\/omega\/alpha\/css\/alpha-mobile.css":1,"sites\/all\/themes\/omega\/alpha\/css\/alpha-alpha.css":1,"sites\/all\/themes\/omega\/omega\/css\/formalize.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-text.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-branding.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-menu.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-forms.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-visuals.css":1,"sites\/all\/themes\/jalview\/css\/mobile.css":1,"sites\/all\/themes\/jalview\/css\/global.css":1,"sites\/all\/themes\/jalview\/css\/ie6.css":1,"sites\/all\/themes\/jalview\/css\/ie7.css":1,"sites\/all\/themes\/jalview\/css\/ie8.css":1,"ie::normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"ie::normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-normal.css":1,"ie::normal::sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/normal\/alpha-default-normal-12.css":1,"narrow::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"narrow::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-narrow.css":1,"sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/narrow\/alpha-default-narrow-12.css":1,"normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-normal.css":1,"sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/normal\/alpha-default-normal-12.css":1,"wide::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"wide::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-wide.css":1,"sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/wide\/alpha-default-wide-12.css":1}},"lightbox2":{"rtl":0,"file_path":"\/(\\w\\w\/)public:\/","default_image":"\/sites\/all\/modules\/lightbox2\/images\/brokenimage.jpg","border_size":10,"font_color":"000","box_color":"fff","top_position":"","overlay_opacity":"0.8","overlay_color":"000","disable_close_click":1,"resize_sequence":0,"resize_speed":100,"fade_in_speed":100,"slide_down_speed":100,"use_alt_layout":0,"disable_resize":0,"disable_zoom":0,"force_show_nav":0,"show_caption":1,"loop_items":0,"node_link_text":"View Image Details","node_link_target":0,"image_count":"Image !current of !total","video_count":"Video !current of !total","page_count":"Page !current of !total","lite_press_x_close":"press \u003Ca href=\u0022#\u0022 onclick=\u0022hideLightbox(); 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//--><!]]>
- </script>
+</script>
+<!--[if lt IE 9]><script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script><![endif]-->
+
+
<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="javascript/jalview.js" language="javascript"></script>
+<script src="javascript/jvcontroller.js"> </script>
+
+
+
+</head>
+
+
+
+<div id="header"></div>
+<section id="section-content" class="section section-content">
+ <div id="zone-content-wrapper"
+ class="zone-wrapper zone-content-wrapper clearfix">
+
+ <div id="zone-content" class="zone zone-content clearfix container-12">
+ <!— — — — — — — — — — — side bar — — — — — — — — — — —>
+ <aside class="grid-3 region region-sidebar-first"
+ id="region-sidebar-first">
+ <div class="region-inner region-sidebar-first-inner">
+ <section
+ class="block block-menu-block block-1 block-menu-block-1 odd"
+ id="block-menu-block-1">
+ <div class="block-inner clearfix">
+ <h2 class="block-title">
+ <a href="/development" class="development active-trail">Development</a>
+ </h2>
+ <div class="content clearfix">
+ <div class="menu-block-wrapper menu-block-1 menu-name-main-menu parent-mlid-0 menu-level-2">
+ <div id="nav" class="nav">nav</div>
+ </div>
+ </div>
+ </div>
+ </section>
+ <section
+ class="block block-menu-block block-2 block-menu-block-2 even"
+ id="block-menu-block-2">
+ <div class="block-inner clearfix">
+ <h2 class="block-title">
+ <a href="/About" class="active-trail active">About</a>
+ </h2>
+
+ <div class="content clearfix">
+ <div
+ class="menu-block-wrapper menu-block-2 menu-name-main-menu parent-mlid-0 menu-level-2">
+ <div id="nav" class="nav">nav</div>
+ </div>
+ </div>
+ </div>
+ </section>
+ </div>
+ </aside>
+ <!- — - - - - - - - - - - - - end of sidebar — — — — —>
+
+ <div class="grid-9 region region-content" id="region-content">
+ <div class="region-inner region-content-inner">
+ <a id="main-content"></a>
+ <div
+ class="block block-system block-main block-system-main odd block-without-title"
+ id="block-system-main">
+ <div class="block-inner clearfix">
+ <div class="content clearfix">
+ <article about="/About" typeof="sioc:Item foaf:Document"
+ class="node node-basic-page node-published node-not-promoted node-not-sticky author-admin odd clearfix"
+ id="node-basic-page-18">
+ <div class="content clearfix">
+ <div
+ class="field field-name-body field-type-text-with-summary field-label-hidden">
+ <div class="field-items">
+ <div class="field-item even" property="content:encoded">
+ <div id="content">
+
+
+
+
+
+
+
+<div>
+
+
<script language="JavaScript">
-// instead of this, we use a custom JmolApplet spec
-// jmolInitialize('jmol');
jmolInitialize("","JmolApplet-12.2.4.jar");
function genHref()
{
var jvstructassoc;
var modeltofiles = new Array();
- function lJvA() {
- jvfollower = document.getElementById("jvA");
- setConsole(document.getElementById("stdout"));
+ //function lJvA() {
+ //jvfollower = document.getElementById("jvA");
+ //setConsole(document.getElementById("stdout"));
- sep = jvfollower.getSeparator();
+ //sep = jvfollower.getSeparator();
//jvapp.setSeparator(""+jvapp.getSeparator());
- linkJvJmol(jvfollower, "jmolView", modeltofiles);
- };
+// linkJvJmol(jvfollower, "jmolView", modeltofiles);
+// };
var _jvA=new Object();
_jvA.attributes = {
jmolSetCallback("pickCallback","_jmolpick");
modeltofiles+="1gaq.txt";
</script>
-</head>
-
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
<!-- 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>
+
+
+<div>
<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 -->
\ No newline at end of file
+</div>
+<div>
+<applet
+ code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="permissions" value="sandbox"/>
+<param name="java_arguments" value="-Xmx256m"/>
+<param name="externalstructureviewer" value="true"/>
+<param name="oninit" value="lJvA"/>
+<param name="automaticScrolling" value="true"/>
+<param name="file" value="uniref50_mz.fa"/>
+<param name="relaxedidmatch" value="true"/>
+<param name="debug" value="true"/>
+<param name="wrap" value="false"/>
+<param name="showAnnotation" value="false"/>
+<param name="embedded" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="RGB" value="F2F2FF"/>
+<param name="linkLabel_1" value="EMBL-EBI Search"/>
+<param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+<param name="linkLabel_2" value="Uniprot"/>
+<param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
+</applet>
+
+</div>
+
+<!-- content template end -->
+
+
+</div>
+
+
+
+
+
+
+
+
+
+
+</div>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div class="clearfix">
+ <nav class="links node-links clearfix"></nav>
+ </div>
+ </article>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+</section>
+
+<div id="footer"></div>
+
+
*/
- //var currentPage = (readCookie("current_page")) ? readCookie("current_page") : "applets";
+
var currentPage = "applets";
- var signedJars = "jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar";
- var unsignedJars = "u_jalviewApplet.jar,u_JmolApplet-12.2.4.jar,u_java-json.jar,u_json_simple-1.1.jar";
- setOrUpdateCookie('jv_applet_mode', 'false', '1');
- //var isSignedAppletMode = readCookie("jv_applet_mode");
- //var appletJars = (isSignedAppletMode === 'true') ? signedJars : unsignedJars;
- //alert(unsigned);
-
function createAppletTag(code, name, archive, width, height, params){
var app = document.createElement('applet');
var newPage = url.substring(start + 1, end);
var page = ((start === -1) ? currentPage : newPage);
//alert("page:" + page);
- $('#header').load("includes/header_jv.html");
- $('#content').load(page+".html");
- $('#nav').load("includes/nav_jv.html");
- $('#footer').load("includes/footer_jv.html");
- $('#'+ currentPage).addClass('active-trail active');
+ if(page === "embeddedWJmol"){
+ // do nothing embeddedWJmol page already include
+
+ $('#header').load("includes/header_jv.html");
+ //$('#content').load(page + ".html");
+ $('#nav').load("includes/nav_jv.html");
+ $('#footer').load("includes/footer_jv.html");
+ $('#'+ currentPage).addClass('active-trail active');
+ }else{
+ $('#header').load("includes/header_jv.html");
+ $('#content').load(page + ".html");
+ $('#nav').load("includes/nav_jv.html");
+ $('#footer').load("includes/footer_jv.html");
+ $('#'+ currentPage).addClass('active-trail active');
+ }
});
- $(document).ready(function(){
- //var currentPage = (readCookie("current_page")) ? readCookie("current_page") : "applets.html";
- //updateLinks(currentPage);
- var params = [["file","uniref50.fa"],
- ["treeFile","ferredoxin.nw"],
- ["userDefinedColour","C=yellow; R,K,H=FF5555; D,E=5555F"],
- ["sortByTree","True"],
- ["showSequenceLogo","true"],
- ["showGroupConsensus","true"],
- ["showFullId","false"],
- ["linkLabel_1","Uniprot"],
- ["linkUrl_1","http://www.uniprot.org/uniprot/$SEQUENCE_ID$"],
- ["linkLabel_2","EMBL-EBI Search"],
- ["linkUrl_2","http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"],
- ["APPLICATION_URL","http://www.jalview.org/services/launchApp"]];
- var app = createAppletTag('jalview.bin.JalviewLite','',appletJars,'140','35', params);
- console.log('—————————> app ———————> ' + app);
- //var appDiv = document.getElementById("applet_div");
- //var appDiv = document.getElementById("applet_div");
- //appDiv.appendChild(app);
- $("<div class='newbox'>I'm new box by appendTo</div>").appendTo('.applet_div');
- //$(‘.applet_div').append(app);
- });
function doSubmit(target){
- //setOrUpdateCookie('current_page', target, '1');
- //alert('current page : ' + readCookie("current_page"));
var currentPage = target+'.html';
- $('#content').load(currentPage);
+ //alert("page:" + target);
+ if(target == "embeddedWJmol"){
+ //loadJMolPage();
+ window.location.href = 'embeddedWJmol.html#' + target;
+ $('#content').load(currentPage);
+ }else{
+ window.location.href = 'index.html#' + target;
+ $('#content').load(currentPage);
+ }
updateLinks(target);
}
+
+
function updateLinks(target) {
var ul = document.getElementById("menu");
var items = ul.getElementsByTagName("li");
ele.className=ele.className.replace(reg,' ');
}
}
+
</div>
</div>
+
+
+
+
<!-- content template start -->
-<script src="javascript/deployJava.js"></script>
-<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
-<script src="javascript/jalview.js" language="javascript"></script>
-<script> //deployJava.debug="true";
-
- function lJvApp() {
- var jvapp = document.getElementById("jvapp");
- var jvfollower = document.getElementById("jvfollower");
- setConsole(document.getElementById("stdout"));
- //jvapp.setSeparator(""+jvapp.getSeparator());
- linkJvJmol(jvapp);
- };
- function lJvFollow() {
- var jvapp = document.getElementById("jvapp");
- var jvfollower = document.getElementById("jvfollower");
- //jvfollower.setSeparator(""+jvfollower.getSeparator());
- linkJvJmol(jvfollower);
- };
-</script>
<h2>JalviewLite Linked Applets Demo</h2>
<p>The two applets below use <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
</p>
- <script>
- var attributes = {
- code : 'jalview.bin.JalviewLite',
- archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
- width : 800,
- height : 300,
- mayscript : 'True', scriptable: 'True',
- id : 'jvapp'
- };
- var parameters = {
- oninit : "lJvApp",
- automaticScrolling : "true",
- file : "plantfdx.fa",
- annotations : "plantfdx.annotations",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "true",
- embedded : "true",
- showFullId : "false",
- RGB : "F2F2FF",
- linkLabel_1 : "EMBL-EBI Search",
- linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
- ,
- linkLabel_2 : "Uniprot"
- ,
- linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
- permissions : 'sandbox',
- APPLICATION_URL : "http://www.jalview.org/services/launchApp"
- };
-
- deployJava.runApplet(attributes, parameters, '1.6');
-</script>
-<script>
- var attributes = {
- code : 'jalview.bin.JalviewLite',
- archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
- width : 800,
- height : 300,
- mayscript : 'True', scriptable: 'True',
- id : "jvfollower"
- };
- var parameters = {
- oninit : "lJvFollow",
- file : "plantfdx.fa",
- annotations : "plantfdx.annotations",
- automaticScrolling : "true",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "true",
- embedded : "true",
- showFullId : "false",
- RGB : "F2F2FF",
- linkLabel_1 : "EMBL-EBI Search",
- linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
- ,
- linkLabel_2 : "Uniprot",
- linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
- permissions : 'sandbox',
- APPLICATION_URL : "http://www.jalview.org/services/launchApp"
- };
- deployJava.runApplet(attributes, parameters, '1.6');
-</script>
+
+
+<applet
+ code="jalview.bin.JalviewLite" width="800" height="300" id="jvapp" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="oninit" value="lJvApp"/>
+<param name="automaticScrolling" value="true"/>
+<param name="file" value="plantfdx.fa"/>
+<param name="annotations" value="plantfdx.annotations"/>
+<param name="debug" value="true"/>
+<param name="wrap" value="false"/>
+<param name="showAnnotation" value="true"/>
+<param name="embedded" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="RGB" value="F2F2FF"/>
+<param name="linkLabel_1" value="EMBL-EBI Search"/>
+<param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+<param name="linkLabel_2" value="Uniprot"/>
+<param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+<param name="permissions" value="sandbox"/>
+<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+</applet>
+
+
+
+
+<applet
+ code="jalview.bin.JalviewLite" width="800" height="300" id="jvfollower" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="oninit" value="lJvFollow"/>
+<param name="file" value="plantfdx.fa"/>
+<param name="annotations" value="plantfdx.annotations"/>
+<param name="automaticScrolling" value="true"/>
+<param name="debug" value="true"/>
+<param name="wrap" value="false"/>
+<param name="showAnnotation" value="true"/>
+<param name="embedded" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="RGB" value="F2F2FF"/>
+<param name="linkLabel_1" value="EMBL-EBI Search"/>
+<param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+<param name="linkLabel_2" value="Uniprot"/>
+<param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+<param name="permissions" value="sandbox"/>
+<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+</applet>
+
+
<p>
<!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
<br>
git://source.jalview.org / jalview.git / commitdiff