Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
<?php
/**
* @file
* BIPAA's theme implementation to display a single Drupal page.
*
* The doctype, html, head and body tags are not in this template. Instead they
* can be found in the html.tpl.php template normally located in the
* modules/system directory.
*
* Available variables:
*
* General utility variables:
* - $base_path: The base URL path of the Drupal installation. At the very
* least, this will always default to /.
* - $directory: The directory the template is located in, e.g. modules/system
* or themes/bipaa.
* - $is_front: TRUE if the current page is the front page.
* - $logged_in: TRUE if the user is registered and signed in.
* - $is_admin: TRUE if the user has permission to access administration pages.
*
* Site identity:
* - $front_page: The URL of the front page. Use this instead of $base_path,
* when linking to the front page. This includes the language domain or
* prefix.
* - $logo: The path to the logo image, as defined in theme configuration.
* - $site_name: The name of the site, empty when display has been disabled
* in theme settings.
* - $site_slogan: The slogan of the site, empty when display has been disabled
* in theme settings.
* - $hide_site_name: TRUE if the site name has been toggled off on the theme
* settings page. If hidden, the "element-invisible" class is added to make
* the site name visually hidden, but still accessible.
* - $hide_site_slogan: TRUE if the site slogan has been toggled off on the
* theme settings page. If hidden, the "element-invisible" class is added to
* make the site slogan visually hidden, but still accessible.
*
* Navigation:
* - $main_menu (array): An array containing the Main menu links for the
* site, if they have been configured.
* - $secondary_menu (array): An array containing the Secondary menu links for
* the site, if they have been configured.
* - $breadcrumb: The breadcrumb trail for the current page.
*
* Page content (in order of occurrence in the default page.tpl.php):
* - $title_prefix (array): An array containing additional output populated by
* modules, intended to be displayed in front of the main title tag that
* appears in the template.
* - $title: The page title, for use in the actual HTML content.
* - $title_suffix (array): An array containing additional output populated by
* modules, intended to be displayed after the main title tag that appears in
* the template.
* - $messages: HTML for status and error messages. Should be displayed
* prominently.
* - $tabs (array): Tabs linking to any sub-pages beneath the current page
* (e.g., the view and edit tabs when displaying a node).
* - $action_links (array): Actions local to the page, such as 'Add menu' on the
* menu administration interface.
* - $feed_icons: A string of all feed icons for the current page.
* - $node: The node object, if there is an automatically-loaded node
* associated with the page, and the node ID is the second argument
* in the page's path (e.g. node/12345 and node/12345/revisions, but not
* comment/reply/12345).
*
* Regions:
* - $page['header']: Items for the header region.
* - $page['featured']: Items for the featured region.
* - $page['highlighted']: Items for the highlighted content region.
* - $page['help']: Dynamic help text, mostly for admin pages.
* - $page['content']: The main content of the current page.
* - $page['sidebar_first']: Items for the first sidebar.
* - $page['triptych_first']: Items for the first triptych.
* - $page['triptych_middle']: Items for the middle triptych.
* - $page['triptych_last']: Items for the last triptych.
* - $page['footer_firstcolumn']: Items for the first footer column.
* - $page['footer_secondcolumn']: Items for the second footer column.
* - $page['footer_thirdcolumn']: Items for the third footer column.
* - $page['footer_fourthcolumn']: Items for the fourth footer column.
* - $page['footer']: Items for the footer region.
*
* @see template_preprocess()
* @see template_preprocess_page()
* @see template_process()
* @see bipaa_process_page()
* @see html.tpl.php
*/
if (isset($node) && $node->type == "chado_feature") {
if ($node->feature->type_id->name == "mRNA" && isset($node->feature->all_relationships['object']['derives from']['polypeptide'][0]->record->subject_id->nid)) {
$feat_nav = "You are viewing an mRNA, more information available on the corresponding ".l("polypeptide page", "node/".$node->feature->all_relationships['object']['derives from']['polypeptide'][0]->record->subject_id->nid);
else if ($node->feature->type_id->name == "polypeptide" && isset($node->feature->all_relationships['subject']['derives from']['mRNA'][0]->record->object_id->nid)) {
$feat_nav = "You are viewing a polypeptide, more information available on the corresponding ".l("mRNA page", "node/".$node->feature->all_relationships['subject']['derives from']['mRNA'][0]->record->object_id->nid);
?>
<header id="masthead" class="site-header" role="banner">
<a class="home-link" href="<?php echo $GLOBALS['base_url']; ?>" title="BIPAA" rel="home">
</a>
<div id="navbar" class="navbar">
<nav id="site-navigation" class="navigation main-navigation" role="navigation">
<button class="menu-toggle">Menu</button>
<a class="screen-reader-text skip-link" href="#content" title="Skip to content">Skip to content</a>
<div class="menu-main-container">
<ul id="primary-menu" class="nav-menu">
<?php if (getenv('ENABLE_ORTHOLOGY')): ?>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/search/phylotree">Gene families</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/organism">Organisms</a></li>
<?php elseif (getenv('ENABLE_NO_CHADO_DATA')): ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-home menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']; ?>">
<?php
if (getenv('SITE_NAME'))
echo getenv('SITE_NAME');
else
echo "Home";
?>
</a>
</li>
<?php else: ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-home menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']; ?>">
<?php
if (getenv('SITE_NAME'))
echo getenv('SITE_NAME');
else
echo "Home";
?>
</a>
<ul class="sub-menu">
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/analysis">Analyses</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/feature">Features</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/chado/organism">Organisms</a></li>
<!--li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="<?php echo $GLOBALS['base_url']; ?>/elastic_search">Advanced search</a></li-->
</ul>
<?php if (count($page['organisms']) > 1): ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46">
<a href="#">GO Reports</a>
<ul class="sub-menu">
<?php endif; ?>
<?php foreach ($page['organisms'] as $org_id => $org): ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']."/organism/".str_replace(' ', '-', $org->genus)."/".str_replace(' ', '-', $org->species)."?pane=GO"; ?>">
<?php if (count($page['organisms']) > 1): ?>
<?php echo "$org->genus $org->species"; ?>
<?php else: ?>
GO Report
<?php endif; ?>
</a></li>
<?php endforeach; ?>
<?php if (count($page['organisms']) > 1): ?>
</ul>
</li>
<?php endif; ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Blast</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_JBROWSE')): ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url'].$url; ?>">JBrowse</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_APOLLO')): ?>
if (getenv('ENABLE_APOLLO') == "1") {
$url = $GLOBALS['base_url'] . '/apollo';
$url_report = $GLOBALS['base_url'] . '/apollo_report';
}
else {
foreach ($page['organisms'] as $org_id => $org) {
if (isset($org->version)) {
$apollo_org = $org->genus . ' ' . $org->species . ' ' . $org->version;
if (strpos($url, '?') !== false)
$url .= '&organism=' . $apollo_org;
else
$url .= 'annotator/loadLink?organism=' . $apollo_org;
break;
}
}
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Apollo</a>
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="<?php echo $url_report; ?>">Annotation report</a></li>
<?php if (getenv('ENABLE_CIRCOS')): ?>
<?php
if (getenv('ENABLE_CIRCOS') == "1")
$url = $GLOBALS['base_url'].'/circos';
else
$url = getenv('ENABLE_CIRCOS');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Synteny</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_AUREME')): ?>
<?php
if (getenv('ENABLE_AUREME') == "1")
$url = $GLOBALS['base_url'].'/aureme';
else
$url = getenv('ENABLE_AUREME');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Metabolic model</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_APHIDCYC')): ?>
<?php
if (getenv('ENABLE_APHIDCYC') == "1")
$url = 'http://aphidcyc.cycadsys.org/';
else
$url = getenv('ENABLE_APHIDCYC');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">AphidCyc</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_WIKI')): ?>
<?php
if (getenv('ENABLE_WIKI') == "1")
$url = $GLOBALS['base_url'].'/wiki/';
else
$url = getenv('ENABLE_WIKI');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Wiki</a></li>
<?php endif; ?>
<?php if (getenv('ENABLE_DOWNLOAD')): ?>
<?php
if (getenv('ENABLE_DOWNLOAD') == "1")
$url = '/download';
else
$url = getenv('ENABLE_DOWNLOAD');
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url'].$url; ?>">Download</a></li>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="http://bipaa.genouest.org/is/">BIPAA</a>
<ul class="sub-menu">
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="https://bipaa.genouest.org/is/aphidbase/">AphidBase</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/parwaspdb/">ParWaspDB</a></li>
<li id="menu-item-78" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-78"><a href="https://bipaa.genouest.org/is/lepidodb/">LepidoDB</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/coleoptera/">Coleoptera</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/crustacea/">Crustacea</a></li>
<li id="menu-item-130" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-130"><a href="https://bipaa-galaxy.genouest.org/">Galaxy</a></li>
<li id="menu-item-138" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-138"><a href="https://bipaa.genouest.org/account/">BIPAA account</a></li>
<?php if (!getenv('ENABLE_ORTHOLOGY')): ?>
<?php print render($page['header']["tripal_elasticsearch_elasticsearch_website_search_box"]); ?>
<?php endif; ?>
</nav><!-- #site-navigation -->
</div><!-- #navbar -->
</header><!-- #masthead -->
<div id="main" class="site-main">
<div id="primary" class="content-area">
<div id="content" class="site-content" role="main">
<article class="page type-page status-publish hentry">
<div class="entry-content">
<?php if ($page['highlighted']): ?><div id="highlighted"><?php print render($page['highlighted']); ?></div><?php endif; ?>
<a id="main-content"></a>
<header class="entry-header">
<?php print render($title_prefix); ?>
<?php if ($title): ?>
<h1 class="entry-title" id="page-title">
<?php print $title; ?>
</h1>
<?php endif; ?>
<?php if (!empty($feat_nav)): ?>
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
<?php print render($title_suffix); ?>
</header>
<?php if ($tabs): ?>
<div class="tabs">
<?php print render($tabs); ?>
</div>
<?php endif; ?>
<?php print render($page['help']); ?>
<?php if ($action_links): ?>
<ul class="action-links">
<?php print render($action_links); ?>
</ul>
<?php endif; ?>
<?php print render($page['content']); ?>
<?php if ($page['sidebar_second']): ?>
<div id="sidebar-second" class="column sidebar"><div class="section">
<?php print render($page['sidebar_second']); ?>
</div></div> <!-- /.section, /#sidebar-second -->
<?php endif; ?>
</div><!-- #entry-content -->
</article>
</div><!-- #content -->
</div><!-- #primary -->
<div id="tertiary" class="sidebar-container" role="complementary">
<div class="sidebar-inner">
<div class="widget-area">
</div><!-- .widget-area -->
</div><!-- .sidebar-inner -->
</div><!-- #tertiary -->
</div><!-- #main -->
<footer id="colophon" class="site-footer" role="contentinfo">
<div id="secondary" class="sidebar-container" role="complementary">
<div class="widget-area masonry" style="position: relative; height: 250px;">
<aside id="meta-2" class="widget widget_meta masonry-brick" style="position: absolute; left: 248px; top: 0px;"><h3 class="widget-title">Links</h3> <ul>
<?php if (!$logged_in): ?>
<li><a href="<?php echo $GLOBALS['base_url']."/user" ?>">Log in</a></li>
<?php endif; ?>
<li><a href="<?php echo $GLOBALS['base_url']."/rss.xml" ?>">Content <abbr title="Really Simple Syndication">RSS</abbr></a></li>
<li><a href="https://bipaa.genouest.org/">BIPAA website</a></li>
</aside>
<aside id="text-4" class="widget widget_text masonry-brick" style="position: absolute; left: 496px; top: 0px;">
<div class="textwidget"><img src="<?php echo $GLOBALS['base_url']."/".drupal_get_path('theme', 'bipaa');?>/images/bipaa/bipaa.png"></div>
</aside>
</div><!-- .widget-area -->
</div><!-- #secondary -->