-<!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 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
--->
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
+ * 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.
+ -->
+ <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" />
+
+<!--[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>
+<!--[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="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-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;
-}
+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',
+ 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',
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_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://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
APPLICATION_URL : "http://www.jalview.org/services/launchApp",
- PDBfile : "1gaq.txt FER1_MAIZE"
+ PDBfile : "1gaq.txt FER1_MAIZE",
+ permissions : "sandbox"
};
jmolSetCallback("hoverCallback","_jmolhover");
jmolSetCallback("pickCallback","_jmolpick");
modeltofiles+="1gaq.txt";
-</script>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+</script>
+<div style="width: 100%">
- <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]-->
+</div>
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
+<!-- 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>
-<!-- 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>
+<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>
-</head>
+</div>
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-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
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