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@@ -1,309 +0,0 @@
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-
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- <?php if ($picture) {
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- print $picture;
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- $feature = $node->feature;
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- $accession = $node->accession;
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- $organism = $node->organism;
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- }?>
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-
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- <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
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-
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- <?php if ($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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- <!-- theme_tripal_feature_feature_id -->
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- <!--<div id="feature_notice"><img src="sites/all/modules/tripal_analysis_blast/images/info-128x128.png"><br><i>Feature information and annotations have moved. See below</i></div>-->
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- <div id="feature-view">
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- <?php
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-
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- if($feature->is_obsolete == 't'){
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- drupal_set_message(t('This feature is obsolete and no longer used in analysis, but is here for reference.'));
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- }?>
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- <table class="tripal_table_vert">
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- <tr><th>Name</th><td><?php print $feature->featurename; ?></td></tr>
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- <tr><th nowrap>Unique Name</th><td><?php print $feature->uniquename; ?></td></tr>
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- <tr><th>Internal ID</th><td><?php print $accession; ?></td></tr>
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- <tr><th>Length</th><td><?php print $feature->seqlen ?></td></tr>
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- <tr><th>Type</th><td><?php print $feature->cvname; ?></td>
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- </tr>
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- <tr><th>Organism</th><td>
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- <?php
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- if ($node->org_nid) {
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- print"<a href=\"". url("node/$node->org_nid") ."\">$organism->genus $organism->species ($organism->common_name)</a>";
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- } else {
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- print"$organism->genus $organism->species ($organism->common_name)";
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- }
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- ?>
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- </td>
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- </tr>
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-
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- <!-- Add library information which this feature belongs to-->
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- <?php if ($node->lib_additions) { ?>
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- <tr><th>Library</th><td>
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- <?php
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- $libraries = $node->lib_additions;
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- foreach ($libraries as $lib_url => $lib_name) {
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- // Check if library exists as a node in drupal
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- if ($lib_url) {
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- ?>
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- <a href="<?php print $lib_url?>"><?php print $lib_name?></a><BR>
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- <?php
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- } else {
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- print $lib_name;
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- }
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- }
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- ?>
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- </td></tr>
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- <?php } ?>
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- <!-- End of library addition -->
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-
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- <!-- theme_tripal_feature_feature_synonyms -->
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- <?php
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- $synonyms = $node->synonyms;
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- if(count($synonyms) > 0){
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- ?>
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- <tr><th>Synonyms</th><td>
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- <?php
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- // iterate through each synonym
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- if (is_array($synonyms)) {
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- foreach ($synonyms as $result){
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- print $result->name."<br>";
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- }
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- } else {
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- print $synonyms;
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- }
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- ?>
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- </td></tr>
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- <?php } ?>
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- <!-- End of theme_tripal_feature_feature_synonyms -->
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- </table>
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- </div>
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- <!-- End of theme_tripal_feature_feature_id -->
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-
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- <?php endif; ?>
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-
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- <div class="content">
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- <?php if (!$teaser): ?>
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- <!-- Control link for the expandableBoxes -->
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- <br><a id="tripal_expandableBox_toggle_button" onClick="toggleExpandableBoxes()">[-] Collapse All</a><br><br>
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- <!-- End of Control link for the expandableBoxes -->
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-
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- <!-- Start of sequences -->
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- <div id="feature-sequence" class="tripal_feature-info-box">
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- <div class="tripal_expandableBox"><h3>Sequence</h3></div>
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- <div class="tripal_expandableBoxContent">
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- <?php print $feature->cvname; ?> sequence
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- <pre id="tripal_feature-sequence"><?php
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- if($feature->residues){
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- print ereg_replace("(.{100})","\\1<br>",$feature->residues);
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- } else {
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- print "sequence currently not available";
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- }
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- ?></pre>
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- </div></div>
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- <!-- End of sequences -->
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- <!-- Start of theme_tripal_feature_feature_references -->
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- <?php
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- $references = $node->references;
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- if(count($references) > 0){
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- ?>
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- <div id="feature-references" class="tripal_feature-info-box">
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- <div class="tripal_expandableBox"><h3>References</h3></div>
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- <div class="tripal_expandableBoxContent">
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- <table class="tripal_feature-references-table">
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- <tr>
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- <th>Dababase</th>
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- <th>Accession</th>
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- </tr>
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- <?php
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- foreach ($references as $result){
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- ?>
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- <tr>
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- <td><?php print $result->db_name?></td>
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- <td><?php if($result->urlprefix){ ?><a href="<?php print $result->urlprefix.$result->accession?>"><?php print $result->accession?></a><?php } else { print $result->accession; } ?></td>
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- </tr>
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- <?php } ?>
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- </table></div></div>
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- <?php } ?>
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- <!-- End of theme_tripal_feature_feature_references -->
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- <!-- Start of theme_tripal_feature_feature_featurelocs -->
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- <?php
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- $featurelocs = $node->featurelocs;
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- if(count($featurelocs) > 0){
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- ?>
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- <div id="feature-featurelocs" class="tripal_feature-info-box">
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- <div class="tripal_expandableBox"><h3><?php print $feature->featurename;?> is Located on These Features</h3></div>
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- <div class="tripal_expandableBoxContent">
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- <table class="tripal_feature-locations-table">
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- <tr>
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- <th>Name</th>
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- <th>Type</th>
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- <th>Position</th>
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- <th>Phase</th>
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- <th>Strand</th>
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- </tr>
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- <?php foreach ($featurelocs as $index => $loc){
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- $locname = $loc->src_name;
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- if($loc->nid){
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- $locname = "<a href=\"" . url("node/$loc->nid") . "\">$loc->src_name</a> ";
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- }
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- ?>
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- <tr>
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- <td><?php print $locname ?></td>
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- <td><?php print $loc->cvname ?></td>
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- <td><?php print $loc->src_name .":".$loc->fmin . ".." . $loc->fmax ?></td>
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- <td><?php print $loc->phase ?></td>
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- <td><?php print $loc->strand ?></td>
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- </tr>
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- <?php } ?>
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- </table></div></div>
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- <?php } ?>
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- <!-- End of theme_tripal_feature_feature_references -->
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- <!-- Start of theme_tripal_feature_feature_myfeaturelocs -->
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- <?php
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- $myfeaturelocs = $node->myfeaturelocs;
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- if(count($myfeaturelocs) > 0){
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- ?>
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- <div id="feature-myfeaturelocs" class="tripal_feature-info-box">
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- <div class="tripal_expandableBox"><h3>Features Located on <?php print $feature->featurename;?></h3></div>
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- <div class="tripal_expandableBoxContent">
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- <table class="tripal_feature-locations-table">
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- <tr>
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- <th>Name</th>
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- <th>Type</th>
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- <th>Position</th>
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- <th>Phase</th>
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- <th>Strand</th>
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- </tr>
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- <?php foreach ($myfeaturelocs as $index => $loc){
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- $locname = $loc->name;
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- if($loc->nid){
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- $locname = "<a href=\"" . url("node/$loc->nid") . "\">$loc->name</a> ";
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- }
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- ?>
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- <tr>
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- <td><?php print $locname ?></td>
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- <td><?php print $loc->cvname ?></td>
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- <td><?php print $loc->src_name .":".$loc->fmin . ".." . $loc->fmax ?></td>
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- <td><?php print $loc->phase ?></td>
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- <td><?php print $loc->strand ?></td>
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- </tr>
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- <?php } ?>
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- </table></div></div>
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- <?php } ?>
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- <!-- End of theme_tripal_feature_feature_references -->
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- <!-- Start of theme_tripal_feature_feature_relationships -->
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- <?php
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- print "<div id=\"feature-srelationships\" class=\"tripal_feature-info-box\">";
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- print "<div class=\"tripal_expandableBox\"><h3>Parent Relationships</h3></div>";
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- print "<div class=\"tripal_expandableBoxContent\">";
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- $srelationships = $node->subject_relationships;
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- if(count($srelationships) > 0){
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- print "
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- <table class=\"tripal_feature-relationships-subject-table\">
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- <tr>
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- <th>Relationship</th>
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- <th>Feature</th>
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- <th>Type</th>
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- </tr>
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- ";
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- foreach ($srelationships as $result){
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- print "<tr>";
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- print "<td><b>$result->rel_type</b></td>";
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- print "<td>";
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- if(isset($result->object_nid)){
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- print "<a href=\"" . url("node/$result->object_nid") . "\">$result->object_name</a> ";
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- } else {
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- print "$result->object_name ";
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- }
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- print "</td>";
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- print "<td>$result->object_type</td>";
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- }
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- print "</table>";
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- }
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- print "</div></div>";
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- ?>
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- <!-- End of theme_tripal_feature_feature_relationships -->
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- <!-- Start of theme_tripal_feature_feature_relationships -->
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- <?php
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- print "<div id=\"feature-srelationships\" class=\"tripal_feature-info-box\">";
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- print "<div class=\"tripal_expandableBox\"><h3>Child Relationships</h3></div>";
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- print "<div class=\"tripal_expandableBoxContent\">";
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- $orelationships = $node->object_relationships;
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- if(count($orelationships) > 0){
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- print "
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- <table class=\"tripal_feature-relationships-object-table\">
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- <tr>
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- <th>Name</th>
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- <th>Type</th>
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- <th>Relationship</th>
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- <th>Position</th>
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- </tr>
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- ";
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- foreach ($orelationships as $result){
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- $subject_name = $result->subject_name;
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- if(!$subject_name){
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- $subject_name = $result->subject_uniquename;
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- }
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- print "<tr>";
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- print "<td>";
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- if(isset($result->subject_nid)){
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- print "<a href=\"" . url("node/$result->subject_nid") . "\">$result->subject_name ($result->subject_type)</a> ";
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- } else {
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- print "$subject_name";
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- }
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- print "</td>";
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- print "<td>$result->subject_type</td>";
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- print "<td><b>$result->rel_type</b></td>";
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- print "<td>";
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- $featurelocs = $result->featurelocs;
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- if($featurelocs){
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- foreach($featurelocs as $src => $attrs){
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- print "$attrs->src_name ($attrs->src_cvname):$attrs->fmin $attrs->fmax</br>";
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- }
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- }
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- print "</td>";
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- print "</tr>";
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- }
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- print "</table>";
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-
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- print "</div></div>";
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- }
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- ?>
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-
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- <!-- End of theme_tripal_feature_feature_relationships -->
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- <!-- Start of theme_tripal_feature_feature_floc_sequences -->
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- <?php
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- $floc_sequences = $node->floc_sequences;
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- foreach($floc_sequences as $seq => $attrs){
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- print "<div id=\"feature-floc-squences\" class=\"tripal_feature-info-box\">";
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- print "<div class=\"tripal_expandableBox\"><h3>".$attrs['type']." Sequence </h3></div>";
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- print "<div class=\"tripal_expandableBoxContent\">";
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- print $attrs['formatted_seq'];
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- print "</div></div>";
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- }
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- ?>
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- <!-- End of theme_tripal_feature_feature_floc_sequences -->
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- <?php endif; ?>
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- <?php print $content?>
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- </div>
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-
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- <?php if (!$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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-
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- </div>
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spficklin