1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 <html lang="en" dir="ltr" version="HTML+RDFa 1.1"
23 xmlns:content="http://purl.org/rss/1.0/modules/content/"
24 xmlns:dc="http://purl.org/dc/terms/"
25 xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"
26 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
27 xmlns:sioc="http://rdfs.org/sioc/ns#"
28 xmlns:sioct="http://rdfs.org/sioc/types#"
29 xmlns:skos="http://www.w3.org/2004/02/skos/core#"
30 xmlns:xsd="http://www.w3.org/2001/XMLSchema#">
31 <head profile="http://www.w3.org/1999/xhtml/vocab">
32 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
33 <link rel="shortcut icon"
34 href="http://www.jalview.org/sites/all/themes/jalview/favicon.ico"
35 type="image/vnd.microsoft.icon" />
37 content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no" />
38 <meta content="" about="/About" property="dc:title" />
39 <link rel="shortlink" href="/node/18" />
40 <meta name="Generator" content="Drupal 7 (http://drupal.org)" />
41 <link rel="canonical" href="/About" />
42 <title>Development | jalview.org</title>
43 <link type="text/css" rel="stylesheet"
44 href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_pbm0lsQQJ7A7WCCIMgxLho6mI_kBNgznNUWmTWcnfoE.css"
46 <link type="text/css" rel="stylesheet"
47 href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_gUtVu-PFpNy2iKRzspQnPE665qK-eDx99tAc6O2EKBs.css"
49 <link type="text/css" rel="stylesheet"
50 href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_HByEx9XzXH_VOfr3lfyJmXRKhQdq8UyyslSu9odJFaw.css"
52 <link type="text/css" rel="stylesheet"
53 href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_Rj_Ai4KdTE0qt75bSUOfQPNak90tBSJRVjZIjglGhlM.css"
57 <link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie6.css?nqc8th" media="all" />
61 <link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie7.css?nqc8th" media="all" />
65 <link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie8.css?nqc8th" media="all" />
68 <!--[if (lt IE 9)&(!IEMobile)]>
69 <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" />
72 <!--[if gte IE 9]><!-->
73 <link type="text/css" rel="stylesheet"
74 href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_kD8qBi2CLfQkl16-SgdHuwlYq_NUjXsjCxmpeidlT0I.css"
77 <script type="text/javascript">
78 <!--//--><![CDATA[//><!--
79 document.cookie = 'adaptive_image=' + Math.max(screen.width, screen.height)
83 <script type="text/javascript"
84 src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_0gj6QcpfRH2jzTbCQqf7kEkm4MXY0UA_sRhwPc8jC1o.js"></script>
85 <script type="text/javascript"
86 src="http://www.jalview.org/sites/all/modules/lightbox2/js/lightbox.js?1434966756"></script>
87 <script type="text/javascript"
88 src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_SoFDHsgxDY2cLYbZ6HeW4SLlU_sLxsgGT6tSFwfsHGY.js"></script>
89 <script type="text/javascript"
90 src="http://www.jalview.org/sites/all/modules/mobile_navigation/js/mobile_menu.js?nqc8th"></script>
91 <script type="text/javascript"
92 src="http://www.jalview.org/sites/all/modules/mobile_navigation/mobile_navigation.js?nqc8th"></script>
93 <script type="text/javascript"
94 src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_IDBX5SzkJ9gGNq7x-qOE_2DZsexqguTJQGMKvi4w-Uw.js"></script>
95 <script type="text/javascript">
96 <!--//--><![CDATA[//><!--
97 var _gaq = _gaq || [];
98 _gaq.push([ "_setAccount", "UA-9060947-1" ]);
99 _gaq.push([ "_trackPageview" ]);
101 var ga = document.createElement("script");
102 ga.type = "text/javascript";
104 ga.src = ("https:" == document.location.protocol ? "https://ssl"
106 + ".google-analytics.com/ga.js";
107 var s = document.getElementsByTagName("script")[0];
108 s.parentNode.insertBefore(ga, s);
112 <script type="text/javascript"
113 src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_tnUY-Xr0uSK3E1mkrZ6ON7OmxH4PiVjShebnFJ8E-9c.js"></script>
114 <script type="text/javascript"
115 src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_43n5FBy8pZxQHxPXkf-sQF7ZiacVZke14b0VlvSA554.js"></script>
117 <script type="text/javascript">
118 <!--//--><![CDATA[//><!--
119 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)"}}}});
122 <!--[if lt IE 9]><script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script><![endif]-->
125 <script src="javascript/deployJava.js"></script>
126 <script src="jmol/Jmol2.js"></script>
127 <script src="javascript/jquery-1.4.4.min.js"></script>
128 <script src="javascript/jquery.timer.js"></script>
129 <script src="javascript/jquery.blockUI.js"></script>
130 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
131 <script src="javascript/jalview.js" language="javascript"></script>
132 <script src="javascript/jvcontroller.js"> </script>
140 <div id="header"></div>
141 <section id="section-content" class="section section-content">
142 <div id="zone-content-wrapper"
143 class="zone-wrapper zone-content-wrapper clearfix">
145 <div id="zone-content" class="zone zone-content clearfix container-12">
146 <!— — — — — — — — — — — side bar — — — — — — — — — — —>
147 <aside class="grid-3 region region-sidebar-first"
148 id="region-sidebar-first">
149 <div class="region-inner region-sidebar-first-inner">
151 class="block block-menu-block block-1 block-menu-block-1 odd"
152 id="block-menu-block-1">
153 <div class="block-inner clearfix">
154 <h2 class="block-title">
155 <a href="/development" class="development active-trail">Development</a>
157 <div class="content clearfix">
158 <div class="menu-block-wrapper menu-block-1 menu-name-main-menu parent-mlid-0 menu-level-2">
159 <div id="nav" class="nav">nav</div>
165 class="block block-menu-block block-2 block-menu-block-2 even"
166 id="block-menu-block-2">
167 <div class="block-inner clearfix">
168 <h2 class="block-title">
169 <a href="/About" class="active-trail active">About</a>
172 <div class="content clearfix">
174 class="menu-block-wrapper menu-block-2 menu-name-main-menu parent-mlid-0 menu-level-2">
175 <div id="nav" class="nav">nav</div>
182 <!- — - - - - - - - - - - - - end of sidebar — — — — —>
184 <div class="grid-9 region region-content" id="region-content">
185 <div class="region-inner region-content-inner">
186 <a id="main-content"></a>
188 class="block block-system block-main block-system-main odd block-without-title"
189 id="block-system-main">
190 <div class="block-inner clearfix">
191 <div class="content clearfix">
192 <article about="/About" typeof="sioc:Item foaf:Document"
193 class="node node-basic-page node-published node-not-promoted node-not-sticky author-admin odd clearfix"
194 id="node-basic-page-18">
195 <div class="content clearfix">
197 class="field field-name-body field-type-text-with-summary field-label-hidden">
198 <div class="field-items">
199 <div class="field-item even" property="content:encoded">
211 <script language="JavaScript">
212 // instead of this, we use a custom JmolApplet spec
213 // jmolInitialize('jmol');
214 jmolInitialize("","JmolApplet-14.6.4_2016.10.26.jar");
218 function dbg(lvl,string) {
219 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
221 var _lastTime=new Date();
234 var modeltofiles = new Array();
237 jvfollower = document.getElementById("jvA");
238 setConsole(document.getElementById("stdout"));
239 linkJvJmol(jvfollower, "jmolView", modeltofiles);
242 var _jvA=new Object();
244 code : 'jalview.bin.JalviewLite',
245 archive : 'jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar',
253 java_arguments : "-Xmx256m",
254 externalstructureviewer : "true",
256 automaticScrolling : "true",
257 // <!-- defaultColour : "Strand Propensity", -->
258 file : "uniref50_mz.fa",
260 relaxedidmatch : "true",
264 showAnnotation : "false",
266 showFullId : "false",
268 linkLabel_1 : "EMBL-EBI Search",
269 linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
271 linkLabel_2 : "Uniprot"
273 linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
274 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
275 PDBfile : "1gaq.txt FER1_MAIZE",
276 permissions : "sandbox"
278 jmolSetCallback("hoverCallback","_jmolhover");
279 jmolSetCallback("pickCallback","_jmolpick");
280 modeltofiles+="1gaq.txt";
282 <div style="width: 100%">
286 <!-- content template start -->
287 <h2>Structure and Alignment</h2>
288 <p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
293 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");
298 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">
299 <param name="permissions" value="sandbox"/>
300 <param name="java_arguments" value="-Xmx256m"/>
301 <param name="externalstructureviewer" value="true"/>
302 <param name="oninit" value="lJvA"/>
303 <param name="automaticScrolling" value="true"/>
304 <param name="file" value="uniref50_mz.fa"/>
305 <param name="relaxedidmatch" value="true"/>
306 <param name="debug" value="true"/>
307 <param name="wrap" value="false"/>
308 <param name="showAnnotation" value="false"/>
309 <param name="embedded" value="true"/>
310 <param name="showFullId" value="false"/>
311 <param name="RGB" value="F2F2FF"/>
312 <param name="linkLabel_1" value="EMBL-EBI Search"/>
313 <param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
314 <param name="linkLabel_2" value="Uniprot"/>
315 <param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
316 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
317 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
322 <!-- content template end -->
341 <div class="clearfix">
342 <nav class="links node-links clearfix"></nav>
354 <div id="footer"></div>