theme_tripal/css/tripal_analysis_go.css

@@ -1,6 +1,3 @@
-/*
- Copyright 2009 Clemson University
-*/
 
 .tripal_go-info-box, .tripal_go_summary-info-box {
    margin-top: 10px;
@@ -17,4 +14,4 @@
 
 .tripal_go_summary-info-box .tripal_cv_tree {
    border-collapse: separate;
-}
+}

theme_tripal/node-chado_feature.tpl.php

@@ -144,6 +144,8 @@ if (Drupal.jsEnabled) {
 
    <!-- InterProScan Results -->
    <?php include('tripal_analysis_interpro/tripal_analysis_interpro_results.tpl.php'); ?>
+
+   <?php print $content ?>
 </div>
 
 <!-- Table of contents -->

theme_tripal/node-chado_organism.tpl.php

@@ -24,6 +24,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($variables,TRUE).'</pre>';
+$node = $variables['node'];
 $organism = $variables['node']->organism;
 ?>
 <script type="text/javascript">
@@ -122,6 +123,10 @@ if (Drupal.jsEnabled) {
    <!-- Basic Details Theme -->
    <?php include('tripal_organism/tripal_organism_base.tpl.php'); ?>
 
+   <!-- Feature Browser -->
+   <?php include('tripal_organism/tripal_organism_feature_browser.tpl.php'); ?>
+
+   <?php print $content ?>
 </div>
 
 <!-- Table of contents -->
@@ -132,3 +137,5 @@ if (Drupal.jsEnabled) {
 
    </ul>
 </div>
+
+

theme_tripal/tripal_feature/tripal_feature_references.tpl.php

@@ -22,7 +22,6 @@ These variables are avaliable for each reference in the array:
 */
 $references = $variables['tripal_feature']['references'];
 $feature = $variables['node']->feature;
-
 ?>
 <div id="tripal_feature-references-box" class="tripal_feature-info-box tripal-info-box">
   <div class="tripal_feature-info-box-title tripal-info-box-title">References</div>

theme_tripal/tripal_organism/tripal_organism_description.tpl.php

@@ -2,8 +2,8 @@
 $organism = $variables['node']->organism;
 ?>
 <div id="tripal_organism-description-box" class="tripal_organism-info-box tripal-info-box">
-  <div id="tripal_organism-table-description" class="tripal_organism-info-box-title tripal-info-box-title">Organism Description</div>
-   <table class="tripal_organism-table tripal-table tripal-table-horz">
+  <div class="tripal_organism-info-box-title tripal-info-box-title">Organism Description</div>
+   <table id="tripal_organism-table-description" class="tripal_organism-table tripal-table tripal-table-horz">
       <tr class="tripal_organism-table-odd-row tripal-table-even-row">
         <td><?php print $organism->description; ?></td>
       </tr>        	                                

theme_tripal/tripal_organism/tripal_organism_feature_browser.tpl.php

@@ -0,0 +1,45 @@
+<?php
+$organism = $variables['node']->organism;
+$features = $variables['tripal_feature']['browser']['features'];
+$pager = $variables['tripal_feature']['browser']['pager'];
+?>
+<div id="tripal_organism-feature_browser-box" class="tripal_organism-info-box tripal-info-box">
+  <div class="tripal_organism-info-box-title tripal-info-box-title">Feature Browser</div>
+   <?php if(count($features) > 0){ ?>
+   <table id="tripal_organism-table-feature_browser" class="tripal_organism-table tripal-table tripal-table-horz">     
+      <tr class="tripal_organism-table-odd-row tripal-table-even-row">
+        <th>Feature Name</th>
+        <th>Unique Name</th>
+        <th>Type</th>
+      </tr>
+      <?php
+      foreach ($features as $feature){ 
+      $class = 'tripal_organism-table-odd-row tripal-table-odd-row';
+      if($i % 2 == 0 ){
+         $class = 'tripal_organism-table-odd-row tripal-table-even-row';
+      }
+      ?>
+      <tr class="<?php print $class ?>">
+        <td><?php 
+           if($feature->nid){    
+              $link =   url("node/$feature->nid");        
+              print "<a href=\"$link\">$feature->name</a>";
+           } else {
+              print $feature->name;
+           }
+           ?>
+        </td>
+        <td><?php print $feature->uniquename?></td>
+        <td><?php print $feature->cvname?></td>
+      </tr>
+      <?php
+      $i++;  
+    } ?>
+   </table>
+  <?php } ?>
+  <?php print $pager ?>
+
+</div>
+
+
+

theme_tripal/tripal_organism/tripal_organism_go_summary.tpl.php

@@ -0,0 +1,25 @@
+<?php
+  $form = $variables['tripal_analysis_go']['form']['value'];
+  $form_status = $variables['tripal_analysis_go']['form']['status'];
+?>
+<div id="tripal_organism-go_summary-box" class="tripal_organism-info-box tripal-info-box">
+  <div  class="tripal_organism-info-box-title tripal-info-box-title">GO Analysis Reports</div>
+  <?php 
+     if($form_status){
+        print $form;
+     } else {
+       ?><div class="tripal-no-results"><?php print $form?></div><?php
+     }
+  ?>
+  <div id="tripal_analysis_go_org_charts"></div>    
+  <div id="tripal_cv_cvterm_info_box">
+      <a href="#" onclick="$('#tripal_cv_cvterm_info_box').hide()" style="float: right">Close [X]</a>
+      <div>Term Information</div>
+      <div id="tripal_cv_cvterm_info"></div>
+   </div>
+   <div id="tripal_ajaxLoading" style="display:none">
+     <div id="loadingText">Loading...</div>
+   </div>   
+</div>
+
+