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@@ -1,97 +1,165 @@
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<?php
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+// Purpose: This template provides the layout of the organism node (page)
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+// using the same templates used for the various feature content blocks.
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//
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-// Copyright 2009 Clemson University
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+// To Customize the Featture Node Page:
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+// - This Template: customize basic layout and which elements are included
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+// - Using Panels: Override the node page using Panels3 and place the blocks
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+// of content as you please. This method requires no programming. See
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+// the Tripal User Guide for more details
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+// - Block Templates: customize the content/layout of each block of stock
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+// content. These templates are found in the tripal_stock subdirectory
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//
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+// Variables Available:
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+// - $node: a standard object which contains all the fields associated with
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+// nodes including nid, type, title, taxonomy. It also includes stock
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+// specific fields such as stock_name, uniquename, stock_type, synonyms,
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+// properties, db_references, object_relationships, subject_relationships,
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+// organism, etc.
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+// NOTE: For a full listing of fields available in the node object the
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+// print_r $node line below or install the Drupal Devel module which
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+// provides an extra tab at the top of the node page labelled Devel
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?>
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- <?php if ($picture) {
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- print $picture;
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- }?>
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-
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- <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
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+<?php
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+ //uncomment this line to see a full listing of the fields avail. to $node
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+ //print '<pre>'.print_r($variables,TRUE).'</pre>';
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+
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+$node = $variables['node'];
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+$organism = $variables['node']->organism;
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+?>
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+
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+<?php if ($teaser) {
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+ include('tripal_analysis_blast/tripal_analysis_blast_teaser.tpl.php');
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+} else { ?>
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+
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+<script type="text/javascript">
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+if (Drupal.jsEnabled) {
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+ $(document).ready(function() {
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+ // hide all tripal info boxes at the start
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+ $(".tripal-info-box").hide();
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+
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+ // iterate through all of the info boxes and add their titles
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+ // to the table of contents
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+ $(".tripal-info-box-title").each(function(){
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+ var parent = $(this).parent();
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+ var id = $(parent).attr('id');
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+ var title = $(this).text();
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+ $('#tripal_analysis_blast_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_blast_toc_item">'+title+'</a></li>');
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+ });
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+
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+ // when a title in the table of contents is clicked, then
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+ // show the corresponding item in the details box
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+ $(".tripal_analysis_blast_toc_item").click(function(){
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+ $(".tripal-info-box").hide();
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+ href = $(this).attr('href');
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+ $(href).fadeIn('slow');
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+ // we want to make sure our table of contents and the details
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+ // box stay the same height
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+ $("#tripal_analysis_blast_toc").height($(href).parent().height());
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+ return false;
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+ });
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+
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+ // we want the base details to show up when the page is first shown
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+ // unless we're using the feature browser then we want that page to show
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+ if(window.location.href.match(/\?page=\d+/)){
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+ $("#tripal_analysis_blast-feature_browser-box").show();
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+ } else {
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+ $("#tripal_analysis_blast-base-box").show();
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+ }
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+ $("#tripal_analysis_blast_toc").height($("#tripal_analysis_blast-base-box").parent().height());
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+
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+ // we want to select the first GO/KEGG report by default
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+ $('.form-select').each(function() {
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+ var default_option = this.getElementsByTagName('option')[1];
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+ if (default_option) {
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+ this.selectedIndex =default_option.index ;
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+ if (this.onchange.toString().match('tripal_analysis_go_org_charts')) {
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+ tripal_analysis_go_org_charts(default_option.value);
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+ } else if (this.onchange.toString().match('tripal_analysis_kegg_org_report')) {
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+ tripal_analysis_kegg_org_report(default_option.value);
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+ }
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+ }
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+ });
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+
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+ });
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+}
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+</script>
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+
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+<style type="text/css">
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+ /* these styles are specific for this template and is not included
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+ in the main CSS files for the theme as it is anticipated that the
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+ elements on this page may not be used for other customizations */
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+ #tripal_analysis_blast_toc {
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+ float: left;
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+ width: 20%;
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+ background-color: #EEEEEE;
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+ -moz-border-radius: 15px;
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+ border-radius: 15px;
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+ -moz-box-shadow: 3px 3px 4px #000;
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+ -webkit-box-shadow: 3px 3px 4px #000;
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+ box-shadow: 3px 3px 4px #000;
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+ padding: 20px;
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+ min-height: 500px;
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+ border-style:solid;
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+ border-width:1px;
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+ }
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+ #tripal_analysis_blast_toc ul {
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+ margin-left: 0px;
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+ margin-top: 5px;
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+ padding-left: 15px;
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+ }
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+ #tripal_analysis_blast_toc_title {
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+ font-size: 1.5em;
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+ line-height: 110%;
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+ }
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+ #tripal_analysis_blast_toc_desc {
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+ /*font-style: italic; */
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+ }
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+ #tripal_analysis_blast_details {
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+ float: left;
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+ width: 70%;
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+ background-color: #FFFFFF;
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+ -moz-border-radius: 15px;
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+ border-radius: 15px;
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+ -moz-box-shadow: 3px 3px 4px #000;
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+ -webkit-box-shadow: 3px 3px 4px #000;
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+ box-shadow: 3px 3px 4px #000;
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+ padding: 20px;
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+ min-height: 500px;
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+ margin-right: 10px;
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+ margin-bottom: 10px;
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+ border-style:solid;
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+ border-width:1px;
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+ }
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+ #tripal_analysis_blast-base-box img {
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+ float: left;
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+ margin-bottom: 10px;
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+ }
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+ #tripal_analysis_blast-table-base {
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+ float: left;
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+ width: 100%;
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+ margin-left: 0px;
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+ margin-bottom: 10px;
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+ }
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+</style>
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+
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+
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+<div id="tripal_analysis_blast_details">
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+
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+ <!-- Basic Details Theme -->
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+ <?php include('tripal_analysis_blast/tripal_analysis_blast_base.tpl.php'); ?>
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+
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+ <?php print $content ?>
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+</div>
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+
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+<!-- Table of contents -->
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+<div id="tripal_analysis_blast_toc">
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+ <div id="tripal_analysis_blast_toc_title">Resources</i></div>
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+ <span id="tripal_analysis_blast_toc_desc">Select a link below for more information</span>
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+ <ul id="tripal_analysis_blast_toc_list">
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+
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+ </ul>
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+</div>
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- <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
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- <?php global $base_url;
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- if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
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- </h2><?php }; ?>
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-
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- <?php if (!$teaser): ?>
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- <?php if ($submitted): ?>
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- <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
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- <?php endif; ?>
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- <div>
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- <!-- tripal_analysis_blast theme -->
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- <table>
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- <tr><th>Name</th><td><?php print $node->analysisname;?></td></tr>
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- <tr><th>Program (version)</th><td><?php print $node->program.' ('.$node->programversion.')';?></td></tr>
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- <?php
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- $ver = $node->sourceversion;
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- if ($node->sourceversion) {
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- $ver = "($node->sourceversion)";
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- }
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- $date = preg_replace("/^(\d+-\d+-\d+) .*/","$1",$node->timeexecuted);
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- ?>
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- <tr><th>Source (version)</th><td><?php print $node->sourcename.' '.$ver;?></td></tr>
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- <tr><th>Source URI</th><td><?php print $node->sourceuri;?></td></tr>
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- <tr><th>Executed</th><td><?php print $date?></td></tr>
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- <tr><th>Description</th><td><?php print $node->description?></td></tr>
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- <tr><th>Blast Settings</th>
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- <td>
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- <b>Database:</b>
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- <?php
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- // We want to show database name instead of database id
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- $previous_db = db_set_active('chado');
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- $sql = "SELECT name FROM db WHERE db_id = %d";
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- $dbname = db_result(db_query($sql, $node->blastdb));
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- print $dbname;
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- db_set_active($previous_db);
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- ?><br>
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- <b>File:</b>
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- <?php print preg_replace("/.*\/(.*)/", "$1", $node->blastfile); ?><br>
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- <b>Parameters:</b>
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- <?php print $node->blastparameters?><br>
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- <?php if ($node->blastjob) {
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- print "A job for parsing blast xml output will be submitted.";
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- }
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- ?>
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- </td>
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- </tr>
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- <tr><th>Report</th>
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- <?php
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- $sql = "SELECT AFP.analysisfeature_id
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- FROM {analysisfeature} AF
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- INNER JOIN {analysisfeatureprop} AFP ON AF.analysisfeature_id = AFP.analysisfeature_id
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- WHERE analysis_id = %d
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- AND AFP.type_id = (SELECT cvterm_id FROM {cvterm} WHERE name = '%s' AND cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal'))";
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- $previous_db = db_set_active('chado');
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- $exists = db_result(db_query($sql, $node->analysis_id, 'analysis_blast_besthit_query'));
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- db_set_active($previous_db);
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- if ($exists) {
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- $report_url = url("tripal_blast_report/".$node->analysis_id."/1/0/0/20");
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- print "<td><a href=$report_url>View the best hit homology report</a></td>";
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- } else {
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- print "<td>The homology report is not available. Please submit a job to parse the best hit first.</td>";
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- }
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- ?>
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-
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- </tr>
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- </table>
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- <!-- End of tripal_analysis_blast theme-->
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- </div>
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-
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- <?php endif; ?>
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-
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- <div class="content"><?php print $content?></div>
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-
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- <?php if (!$teaser): ?>
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- <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
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- <?php endif; ?>
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-
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- <?php if ($teaser): ?>
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- <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
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- <?php endif; ?>
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-
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- <?php if (!$teaser): ?>
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- <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
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- <?php endif; ?>
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- </div>
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+<?php } ?>
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spficklin