JAL-3210 Barebones gradle/buildship/eclipse. See README
[jalview.git] / examples / index.html
diff --git a/examples/index.html b/examples/index.html
deleted file mode 100644 (file)
index 37edb8e..0000000
+++ /dev/null
@@ -1,217 +0,0 @@
-<!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
- * 
- * 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.
- -->
- <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(); 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>
-<!--[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">
-                                                       <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>        
-                                                                                               </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>
-
-