Cleaning up themeing

theme_tripal/css/tripal_organism.css

@@ -12,7 +12,6 @@
 
 #tripal_organism-base-box {
    float: left;
-   width: 300px;
 }
 #tripal_organism-description-box {
    clear: left;

theme_tripal/tripal_analysis_blast/tripal_analysis_blast_results.tpl.php

@@ -5,9 +5,11 @@ $blast_object_array = $variables['blast_object'];
 	<div id="loadingText">Loading...</div>
 	<img src="sites/all/themes/theme_tripal/images/ajax-loader.gif">
 </div>
-<?php foreach ($blast_object_array AS $blast_object) {
-					$hits_array = $blast_object->hits_array;
-					$db = $blast_object->db;
+<?php 
+if($blast_object_array){
+   foreach ($blast_object_array as $blast_object) {
+	  $hits_array = $blast_object->hits_array;
+	  $db = $blast_object->db;
 ?>
 <div id="tripal_analysis_blast-results-box" class="tripal_analysis_blast-box tripal-info-box">
 	<div class="tripal_analysis_blast-info-box-title tripal-info-box-title"><h3><?php print $blast_object->title ?></h3></div>
@@ -83,4 +85,5 @@ $blast_object_array = $variables['blast_object'];
 	</span>
 	</div>
 </div>
-<?php } ?>
+  <?php } ?>
+<?php } ?>

theme_tripal/tripal_analysis_interpro/tripal_analysis_interpro_results.tpl.php

@@ -2,7 +2,7 @@
 $results = $variables['tripal_analysis_interpro']['results'];
 ?>
 <div id="tripal_analysis_interpro-results-box" class="tripal_analysis_interpro-box tripal-info-box">
-  <div class="tripal_analysis_interpro-info-box-title tripal-info-box-title">Blast Results</div>
+  <div class="tripal_analysis_interpro-info-box-title tripal-info-box-title">InterProScan Analysis Results</div>
   <div class="tripal_analysis_interpro-info-box-desc tripal-info-box-desc"></div>
   <?php print $results ?>
 </div>

theme_tripal/tripal_feature/tripal_feature_base.tpl.php

@@ -13,7 +13,7 @@ $org_nid = $variables['node']->org_nid;
    <?php if($feature->is_obsolete == 't'){ ?>
       <div class="tripal_feature-obsolete">This feature is obsolete and no longer used in analysis, but is here for reference</div>
    <?php }?>
-   <table class="tripal_feature-table tripal-table tripal-table-vert">
+   <table id="tripal_feature-base-table" class="tripal_feature-table tripal-table tripal-table-vert">
       <tr class="tripal_feature-table-odd-row tripal-table-even-row">
         <th>Name</th>
         <td><?php print $feature->featurename; ?></td>

theme_tripal/tripal_feature/tripal_feature_featurelocs_as_child.tpl.php

@@ -7,7 +7,7 @@ $feature = $variables['node']->feature;
 <div id="tripal_feature-featurelocs_as_child-box" class="tripal_feature-info-box tripal-info-box">
   <div class="tripal_feature-info-box-title tripal-info-box-title">Locations where <?php print $feature->featurename;?> is found</div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The <?php print $feature->featurename;?> feature is located relative to the following features:</div>
-  <table class="tripal_feature-table tripal-table tripal-table-horz">
+  <table id="tripal_feature-featurelocs_as_child-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Name</th>
       <th>Type</th>

theme_tripal/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php

@@ -7,7 +7,7 @@ $feature = $variables['node']->feature;
 <div id="tripal_feature-featurelocs_as_parent-box" class="tripal_feature-info-box tripal-info-box">
   <div class="tripal_feature-info-box-title tripal-info-box-title">Features located relative to <?php print $feature->featurename;?></div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The features shown below are located relative to <?php print $feature->featurename;?></div>
-  <table class="tripal_feature-table tripal-table tripal-table-horz">
+  <table id="tripal_feature-featurelocs_as_parent-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Name</th>
       <th>Type</th>

theme_tripal/tripal_feature/tripal_feature_properties.tpl.php

@@ -6,7 +6,7 @@ $feature = $variables['node']->feature;
   <div class="tripal_feature-info-box-title tripal-info-box-title">Properties</div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' has these properties</div>
   <?php if(count($properties) > 0){ ?>
-  <table class="tripal_feature-table tripal-table tripal-table-horz">
+  <table id="tripal_feature-properties-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Synonym</th>
     </tr>

theme_tripal/tripal_feature/tripal_feature_references.tpl.php

@@ -20,7 +20,6 @@ These variables are avaliable for each reference in the array:
   dbxref_id
 
 */
-
 $references = $variables['tripal_feature']['references'];
 $feature = $variables['node']->feature;
 
@@ -29,7 +28,7 @@ $feature = $variables['node']->feature;
   <div class="tripal_feature-info-box-title tripal-info-box-title">References</div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' is also available at these locations</div>
   <?php if(count($references) > 0){ ?>
-  <table class="tripal_feature-table tripal-table tripal-table-horz">
+  <table id="tripal_feature-references-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Dababase</th>
       <th>Accession</th>

theme_tripal/tripal_feature/tripal_feature_relationships_as_object.tpl.php

@@ -4,11 +4,11 @@ $object_relationships = $variables['tripal_feature']['object_relationships'];
 $feature = $variables['node']->feature;
 
 ?>
-<div id="tripal_feature-subject_relationships-box" class="tripal_feature-info-box tripal-info-box">
+<div id="tripal_feature-object_relationships-box" class="tripal_feature-info-box tripal-info-box">
   <div class="tripal_feature-info-box-title tripal-info-box-title">Object Relationships</div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' has an object relationship with the following</div>
   <?php if(count($object_relationships) > 0){ ?>
-  <table class="tripal_feature-table tripal-table tripal-table-horz">
+  <table id="tripal_feature-object_relationships-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Name</th>
       <th>Type</th>

theme_tripal/tripal_feature/tripal_feature_relationships_as_subject.tpl.php

@@ -8,7 +8,7 @@ $feature = $variables['node']->feature;
   <div class="tripal_feature-info-box-title tripal-info-box-title">Subject Relationships</div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' has a subject relationship with the following</div>
   <?php if(count($subject_relationships) > 0){ ?>
-  <table class="tripal_feature-table tripal-table tripal-table-horz">
+  <table id="tripal_feature-subject_relationships-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Relationship</th>
       <th>Feature</th>

theme_tripal/tripal_feature/tripal_feature_synonyms.tpl.php

@@ -1,12 +1,13 @@
 <?php
 $synonyms = $variables['tripal_feature']['synonyms'];
 $feature = $variables['node']->feature;
+
 ?>
 <div id="tripal_feature-synonyms-box" class="tripal_feature-info-box tripal-info-box">
   <div class="tripal_feature-info-box-title tripal-info-box-title">Synonyms</div>
   <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' has the following synonyms</div>
   <?php if(count($synonyms) > 0){ ?>
-  <table class="tripal_feature-table tripal-table tripal-table-horz">
+  <table id="tripal_feature-synonyms-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Synonym</th>
     </tr>

theme_tripal/tripal_organism/tripal_organism_base.tpl.php

@@ -4,7 +4,8 @@ $organism = $variables['node']->organism;
 <div id="tripal_organism-base-box" class="tripal_organism-info-box tripal-info-box">
   <div class="tripal_organism-info-box-title tripal-info-box-title">Organism Details</div>
   <div class="tripal_organism-info-box-desc tripal-info-box-desc"></div>
-   <table class="tripal_organism-table tripal-table tripal-table-vert">
+   <img src=<?php print file_create_url(file_directory_path() . "/tripal/tripal_organism/images/".$organism->genus."_".$organism->species.".jpg")?>>
+   <table id="tripal_organism-table-base" class="tripal_organism-table tripal-table tripal-table-vert">
       <tr class="tripal_organism-table-odd-row tripal-table-even-row">
         <th>Common Name</th>
         <td><?php print $organism->common_name; ?></td>
@@ -22,4 +23,9 @@ $organism = $variables['node']->organism;
         <td><?php print $organism->abbreviation; ?></td>
       </tr>         	                                
    </table>
+   <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>        	                                
+   </table>
 </div>

theme_tripal/tripal_organism/tripal_organism_description.tpl.php

@@ -2,7 +2,7 @@
 $organism = $variables['node']->organism;
 ?>
 <div id="tripal_organism-description-box" class="tripal_organism-info-box tripal-info-box">
-  <div class="tripal_organism-info-box-title tripal-info-box-title">Organism Description</div>
+  <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">
       <tr class="tripal_organism-table-odd-row tripal-table-even-row">
         <td><?php print $organism->description; ?></td>

theme_tripal/tripal_organism/tripal_organism_image.tpl.php

@@ -2,5 +2,7 @@
 $organism = $variables['node']->organism;
 ?>
 <div id="tripal_organism-image-box" class="tripal_organism-info-box tripal-info-box">
+  <div class="tripal_analysis_interpro-info-box-title tripal-info-box-title"><?php $organism->genus." ".$organism->species?> Image</div>
+  <div class="tripal_analysis_interpro-info-box-desc tripal-info-box-desc"></div>
   <img src=<?php print file_create_url(file_directory_path() . "/tripal/tripal_organism/images/".$organism->genus."_".$organism->species.".jpg")?>>
 </div>