-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
<!--
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
+ * 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/>.
+ * 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" />
+ -->
+ <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/"
+ xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:sioc="http://rdfs.org/sioc/ns#"
+ xmlns:sioct="http://rdfs.org/sioc/types#"
+ xmlns:skos="http://www.w3.org/2004/02/skos/core#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#">
+<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" />
- <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);})();
+<!--[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(); return FALSE;\u0022\u003E\u003Ckbd\u003Ex\u003C\/kbd\u003E\u003C\/a\u003E to close","download_link_text":"","enable_login":false,"enable_contact":false,"keys_close":"c x 27","keys_previous":"p 37","keys_next":"n 39","keys_zoom":"z","keys_play_pause":"32","display_image_size":"original","image_node_sizes":"()","trigger_lightbox_classes":"","trigger_lightbox_group_classes":"","trigger_slideshow_classes":"","trigger_lightframe_classes":"","trigger_lightframe_group_classes":"","custom_class_handler":0,"custom_trigger_classes":"","disable_for_gallery_lists":true,"disable_for_acidfree_gallery_lists":true,"enable_acidfree_videos":true,"slideshow_interval":5000,"slideshow_automatic_start":true,"slideshow_automatic_exit":true,"show_play_pause":true,"pause_on_next_click":false,"pause_on_previous_click":true,"loop_slides":false,"iframe_width":600,"iframe_height":400,"iframe_border":1,"enable_video":0},"nice_menus_options":{"delay":"800","speed":"fast"},"mobile_navigation":{"breakpoint":"all and (min-width: 740px) and (min-device-width: 740px), (max-device-width: 800px) and (min-width: 740px) and (orientation:landscape)","menuSelector":".primary-nav","menuPlugin":"accordion","showEffect":"expand_down","showItems":"all","tabHandler":1,"menuWidth":"100","specialClasses":0,"mainPageSelector":"#page","useMask":1,"menuLabel":"","expandActive":1},"googleanalytics":{"trackOutbound":1,"trackMailto":1,"trackDownload":1,"trackDownloadExtensions":"7z|aac|arc|arj|asf|asx|avi|bin|csv|doc|exe|flv|gif|gz|gzip|hqx|jar|jpe?g|js|mp(2|3|4|e?g)|mov(ie)?|msi|msp|pdf|phps|png|ppt|qtm?|ra(m|r)?|sea|sit|tar|tgz|torrent|txt|wav|wma|wmv|wpd|xls|xml|z|zip"},"omega":{"layouts":{"primary":"normal","order":["narrow","normal","wide"],"queries":{"narrow":"all and (min-width: 740px) and (min-device-width: 740px), (max-device-width: 800px) and (min-width: 740px) and (orientation:landscape)","normal":"all and (min-width: 980px) and (min-device-width: 980px), all and (max-device-width: 1024px) and (min-width: 1024px) and (orientation:landscape)","wide":"all and (min-width: 1220px)"}}}});
//--><!]]>
- </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/Jmol2.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 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-14.2.14_2015.06.11.jar");
+jmolInitialize("","JmolApplet-14.6.4_2016.10.26.jar");
</script>
<script>
var loglevel=1;
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,JmolApplet-14.2.14_2015.06.11.jar',
+ archive : 'jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar',
width : '500',
height : '350',
mayscript : 'True',
jmolSetCallback("hoverCallback","_jmolhover");
jmolSetCallback("pickCallback","_jmolpick");
modeltofiles+="1gaq.txt";
-</script>
+</script>
+<div style="width: 100%">
-</head>
+</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>
-<body>
+<div>
+ <script>
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; background black; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;set hoverDelay 0.001; select 0","jmolView");
+ </script>
+</div>
+<div>
+<applet
+ code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="mayscript" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.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>
- <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>
+<!-- content template end -->
-
- <div id ="nav">
- <div id="navInner">
-
- <ul id="sddm">
- <li><a href="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li ><a href="applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
+
</div>
-<div id="content" class="content">
-<!-- boiler plate link to alternate demopage -->
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Examples aren't working ?<br/>Try <a href="u_embeddedWJmol.html">the unsigned applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-<!-- content template start -->
-<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>
+ </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>
+
+
git://source.jalview.org / jalview.git / blobdiff