Corrections for lots of themeing stuff

theme_tripal/css/tripal.css

@@ -5,6 +5,11 @@
 .tripal-table {
    width: 100%; 
 }
+.tripal-table th, 
+.tripal-table td {
+   padding-left: 5px;
+   padding-right: 5px;
+}
 .tripal-table-horz {
    border-top: 2px solid #999999;
    border-bottom: 2px solid #999999; 

theme_tripal/css/tripal_analysis_blast.css

@@ -1,21 +1,33 @@
-/*
- Copyright 2009 Clemson University
-*/
-
-.tripal_analysis_blast-box {
-
+#tripal_analysis_blast-table {
+   width: 100%;
+	overflow:auto;
 }
-
-.tripal_analysis_blast-table {
-   width:100%;
+#tripal_analysis_blast-table td {
+  text-align: left;
+}
+#tripal_analysis_blast-table .tripal-table-even-row {
+   border-top: 0px solid #CCCCCC;
+   border-bottom: 0px solid #CCCCCC;
 }
+#tripal_analysis_blast-table .tripal-table-odd-row {
+   border-top: 0px solid #CCCCCC;
+   border-bottom: 0px solid #CCCCCC;
+}
+#tripal_analysis_blast-table .tripal_analysis_blast-result-first-row {
+   border-top: 1px solid #CCCCCC;
+}
+#tripal_analysis_blast-table .tripal_analysis_blast-result-last-row {
+   border-bottom: 1px solid #CCCCCC;
+}
+
 .tripal_analysis_blast-info-hsp-desc {
-	background-color:#EEFEEE;
-	border:1px solid #CCC5AE;
+	background-color: #FFFFFF;
+	border:0px solid #CCC5AE;
 	display:none;
 	overflow:auto;
+   width: 100%;
 }
 .tripal_analysis_blast-info-hsp-desc pre{
-	background-color:#EEFEEE;
+	background-color: #FFFFFF;
    border:none;
-}
+}

theme_tripal/css/tripal_feature.css

@@ -1,7 +1,7 @@
 #tripal_feature-featureloc_sequence,
 #tripal_feature-sequence-residues {
-  height: 500px;
-  overflow: scroll;
+  /*height: 500px;*/
+  /*overflow: scroll;*/
   background-color: #FFFFFF;
   font-family: monospace;
 }

theme_tripal/js/tripal_analysis_blast.js

@@ -1,6 +1,3 @@
-//
-// Copyright 2009 Clemson University
-//
 
 if (Drupal.jsEnabled) {
    
@@ -10,8 +7,9 @@ if (Drupal.jsEnabled) {
 		   tripal_update_regex($("#edit-blastdb")[0]);
 		   tripal_set_genbank_style();
 	   }
-	   // Set blast hit alignment droppable box
-	   tripal_set_blast_subbox();
+      // hide the alignment information on the blast results box
+      $(".tripal_analysis_blast-info-hsp-desc").hide();
+
    });
   
    //------------------------------------------------------------
@@ -24,13 +22,34 @@ if (Drupal.jsEnabled) {
          type: 'POST',
          success: function(data){         
             $("#blast_db_" + db_id).html(data.update);
-            // make sure the newly added expandable boxes are closed
-            tripal_set_blast_subbox(db_id);
+            $(".tripal_analysis_blast-info-hsp-desc").hide();
             tripal_stopAjax();
          }
       });
       return false;
    }
+
+   //------------------------------------------------------------
+   // Update the blast results based on the user selection
+   function tripal_blast_toggle_alignment(analysis_id,hit_id){
+      var alignment_box = $("#tripal_analysis_blast-info-hsp-desc-"+analysis_id+"-"+hit_id);
+      var toggle_img = $("#tripal_analysis_blast-info-toggle-image-"+analysis_id+"-"+hit_id);
+	   var icon_url = toggle_img.attr("src");
+
+
+      if (alignment_box.is(':visible')) {
+         alignment_box.fadeOut('fast');
+	      var changed_icon_url = icon_url.replace(/arrow_d.png/,"arrow_r.png");
+	      toggle_img.attr("src", changed_icon_url);
+	   } else {
+         var width = alignment_box.parent().width();
+         alignment_box.css("width", width+'px');
+         alignment_box.fadeIn('slow');
+	      var icon_url = icon_url.replace(/arrow_r.png/,"arrow_d.png");
+	      toggle_img.attr("src", icon_url);
+	   }
+      return false;
+   }
    
    //------------------------------------------------------------
    // Update regular expression for selected database
@@ -94,7 +113,7 @@ if (Drupal.jsEnabled) {
 		tripal_set_genbank_style();  
    }
    // ------------------------------------------------------------
-   // Use genbank style parser. Hid regular expression text feilds
+   // Use genbank style parser. Hide regular expression text feilds
    function tripal_set_genbank_style (){
 	  // Disable regular expressions if genbank style parser is used (checked)
 	  if ($("#edit-gb-style-parser").is(":checked")) {
@@ -125,55 +144,8 @@ if (Drupal.jsEnabled) {
 	        $(this).css("cursor", "pointer");
 	     }
 	  );
-	  if (!db_id){
-		 $('.tripal_expandableSubBoxContent').hide();
-	     $('.blast-hit-arrow-icon').click(
-	        function() {
-   	        // Find the width of the table column for the tripal_expandableSubBoxContent
-	           var width = $(this).parent().parent().width();
-	           width -= 40;
- 	           // Traverse through html DOM objects to find tripal_expandableSubBoxContent and change its settings
-              var subbox = $(this).parent().parent().next().children().children();
-	           subbox.css("width", width + 'px');
-	           subbox.slideToggle('fast', function () {
-              var image = $(this).parent().parent().prev().children().children().children();
-	        	  var icon_url = image.attr("src");
-	        	  if (subbox.is(':visible')) {
-	        		 var changed_icon_url = icon_url.replace(/arrow_r.png/,"arrow_d.png");
-	        		 image.attr("src", changed_icon_url);
-	        	  } else {
-	        		 var icon_url = icon_url.replace(/arrow_d.png/,"arrow_r.png");
-	        		 image.attr("src", icon_url);
-	        	  }
-	           });
-	        }
-	     );
-	  // Update only the part of DOM objects that have been changed by ajax. This is a solution
-	  // to solve the problem that droppable subbox opened then closed immediately.
-	  } else {
-		  $("#blast_db_" + db_id + ' div.tripal_expandableSubBoxContent').hide();
-		  var changedObject = $("#blast_db_" + db_id + " img.blast-hit-arrow-icon");
-		  changedObject.click(
-		     function() {
-		        // Find the width of the table column for the tripal_expandableSubBoxContent
-				var width = $(this).parent().parent().width();
-			    width -= 40;
-			    // Traverse through html DOM objects to find tripal_expandableSubBoxContent and change its settings
-		        var subbox = $(this).parent().parent().next().next().children().children();
-		        subbox.css("width", width + 'px');
-		        subbox.slideToggle('fast', function () {
-		        	var image = $(this).parent().parent().prev().prev().children().children();
-		        	var icon_url = image.attr("src");
-		        	if (subbox.is(':visible')) {
-		        		var changed_icon_url = icon_url.replace(/arrow_r.png/,"arrow_d.png");
-		        		image.attr("src", changed_icon_url);
-		        	} else {
-		        		var icon_url = icon_url.replace(/arrow_d.png/,"arrow_r.png");
-		        		image.attr("src", icon_url);
-		        	}
-		        });
-		     }
-		  );
-	  }
+     $('.blast-hit-arrow-icon').click(function() {
+	        
+     });
    }
 }

theme_tripal/node-chado_feature.tpl.php

@@ -90,6 +90,7 @@ if (Drupal.jsEnabled) {
   }
   #tripal_feature_toc_title {
      font-size: 1.5em;
+     line-height: 110%;
   }
   #tripal_feature_toc_desc {
     font-style: italic;
@@ -106,6 +107,7 @@ if (Drupal.jsEnabled) {
      padding: 20px;
      min-height: 500px;
      margin-right: 10px;
+     margin-bottom: 10px;
      border-style:solid;
      border-width:1px;
   }
@@ -155,7 +157,7 @@ if (Drupal.jsEnabled) {
 
 <!-- Table of contents -->
 <div id="tripal_feature_toc">
-   <div id="tripal_feature_toc_title"><?php print $feature->featurename ?> Resources</div>
+   <div id="tripal_feature_toc_title">Resources for <?php print $feature->cvname?><br><?php print $feature->featurename ?></div>
    <span id="tripal_feature_toc_desc">Select a link below for more information</span>
    <ul id="tripal_feature_toc_list">
 

theme_tripal/node-chado_organism.tpl.php

@@ -96,6 +96,7 @@ if (Drupal.jsEnabled) {
   }
   #tripal_organism_toc_title {
      font-size: 1.5em;
+     line-height: 110%;
   }
   #tripal_organism_toc_desc {
     font-style: italic;
@@ -139,7 +140,7 @@ if (Drupal.jsEnabled) {
 
 <!-- Table of contents -->
 <div id="tripal_organism_toc">
-   <div id="tripal_organism_toc_title"><?php print $organism->genus ?> <?php print $organism->species ?> Resources</div>
+   <div id="tripal_organism_toc_title">Resources for <br><?php print $organism->genus ?> <?php print $organism->species ?></div>
    <span id="tripal_organism_toc_desc">Select a link below for more information</span>
    <ul id="tripal_organism_toc_list">
 

theme_tripal/tripal_analysis_blast/tripal_analysis_blast_results.tpl.php

@@ -1,89 +0,0 @@
-<?php
-$blast_object_array = $variables['blast_object'];
-?>
-<div id="tripal_ajaxLoading" style="display:none">
-	<div id="loadingText">Loading...</div>
-	<img src="sites/all/themes/theme_tripal/images/ajax-loader.gif">
-</div>
-<?php 
-if($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 $blast_object->title ?></h3></div>
-	<div class="tripal_analysis_blast-info-box-desc tripal-info-box-desc" id="blast_db_<?php print "$db->db_id" ?>">
-	<strong>Analysis Date: </strong><?php print "$blast_object->ana_time (<a href=node/$blast_object->ana_nid>$blast_object->ana_name</a>)"?><br>
-	Query: <?php print "$blast_object->xml_tag"?><br>
-	
-	<?php 	if($blast_object->max != 10){ ?>
-		<span><a onclick="return tripal_update_blast(this,<?php print $db->db_id?>)" href="tripal_top_blast/<?php print "$blast_object->feature_id/$db->db_id/10" ?>>Show Best 10 Hits</a></span>";
-	<?php } else { ?>
-		<span>Best 10 Hits Shown</span>
-	<?php } ?>
-	
-	<?php if($blast_object->number_hits <= 10){ ?>
-	<?php } else if ($blast_object->max != 25) { ?>
-		<span> | <a onclick="return tripal_update_blast(this,<?php print"$db->db_id"?>)" href="tripal_top_blast/<?php print "$blast_object->feature_id/$db->db_id/25"?>">Show Best 25 Hits</a></span>
-	<?php }else { ?>
-		<span> | Best 25 Hits Shown</span>
-	<?php } ?>
-	
-	<?php if($blast_object->number_hits <= 25){ ?>
-	<?php } else if ($blast_object->max != 0) {
-						$url = url("tripal_top_blast/$feature_id/$db->db_id/0");
-		?>		
-		<span> | <a onclick="return tripal_update_blast(this, <?php print $db->db_id ?>)" href="<?php print "tripal_top_blast/$blast_object->feature_id/$db->db_id/0"?>">Show All Hits</a> </span>
-	<?php } else { ?>
-		<span> | All Hits Shown</span>
-	<?php } ?>
-	
-	<br><span><i>Note:</i> Click a description for more details</span>
-		<span>
-		<table class="tripal_analysis_blast-table">
-			<tr>
-				<th nowrap>Match Name</th>
-				<th nowrap>E value</th>
-				<th nowrap>Identity</th>
-				<th nowrap>Description</th>
-			</tr>
-			
-			<?php 
-			foreach($hits_array AS $hit) {
-			?>
-			<tr>
-			<?php if ($hit['hit_url']) { ?>
-				<td><a href="<?php print $hit['hit_url']?>" target="_blank"><?php print $hit['hit_name']?></a></td>
-			<?php } else {?>
-				<td><?php print $hit['hit_name'] ?></td>
-			<?php } ?>
-				<td nowrap><?php print $hit['best_evalue']?></td>
-				<td nowrap><?php  print $hit['percent_identity']?></td>
-				<td nowrap><?php print $hit['description']?></td>
-			</tr>
-		<tr>
-			<td colspan=4>
-				<a class="blast-hit-arrow-icon"><img src=<?php print $hit['arrowr_url']?> align="top"> View Alignment</a>
-				<div class="tripal_analysis_blast-info-hsp-title"></div>
-			</td>
-		</tr>
-		<tr>
-			<td colspan=4>
-			<?php 
-			$hsps_array = $hit['hsp'];
-			foreach ($hsps_array AS $hsp) { ?>
-				<div class="tripal_analysis_blast-info-hsp-desc">
-					<b>HSP <?php  print $hsp['hsp_num'] ?></b>
-					<pre>Score: <?php print $hsp['bit_score'] ?> bits (<?php print $hsp['score'] ?>), Expect = <?php print $hsp['evalue'] ?><br>Identity = <?php print sprintf("%d/%d (%.2f%%)", $hsp['identity'], $hsp['align_len'], $hsp['identity']/$hsp['align_len']*100) ?>, Postives = <?php print sprintf("%d/%d (%.2f%%)", $hsp['positive'], $hsp['align_len'], $hsp['positive']/$hsp['align_len']*100)?>, Query Frame = <?php print $hsp['query_frame']?></a><br><br></a>Query: <?php print sprintf("%4d", $hsp['query_from'])?> <?php print $hsp['qseq'] ?> <?php print sprintf("%d", $hsp['query_to']); ?><br>            <?php print $hsp['midline'] ?><br>Sbjct: <?php print sprintf("%4d", $hsp['hit_from']) ?> <?php print $hsp['hseq']?> <?php print sprintf("%d",$hsp['hit_to']) ?></pre><br>
-				</div>
-			<?php } ?>
-			</td>
-		</tr>		
-		<?php	} ?>
-		</table>
-	</span>
-	</div>
-</div>
-  <?php } ?>
-<?php } ?>

theme_tripal/tripal_feature/tripal_feature_blast_results.tpl.php

@@ -0,0 +1,104 @@
+<?php
+$feature  = $variables['node']->feature;
+$blast_results_list = $variables['tripal_analysis_blast']['blast_results_list'];
+
+?>
+<div id="tripal_ajaxLoading" style="display:none">
+	<div id="loadingText">Loading...</div>
+	<img src="sites/all/themes/theme_tripal/images/ajax-loader.gif">
+</div>
+
+<?php 
+if(count($blast_results_list) > 0){
+   foreach ($blast_results_list as $blast_result) {
+	  $hits_array = $blast_result->hits_array;
+	  $db = $blast_result->db;
+     $analysis = $blast_result->analysis;
+?>
+<div id="blast_db_<?php print $db->db_id ?>">
+<div id="tripal_analysis_blast-results-<?php print "$db->db_id" ?>-box" class="tripal_analysis_blast-box tripal-info-box">
+	<div class="tripal-info-box-title tripal_analysis_blast-info-box-title">Blast vs. <?php print $db->name ?></div>
+	<div class="tripal-info-box-desc tripal_analysis_blast-info-box-desc">
+	<strong>Analysis Date: </strong><?php print "$blast_result->ana_time (<a href=".url("node/$blast_result->ana_nid").">$blast_result->ana_name</a>)"?><br>
+	Query: <?php print "$blast_result->xml_tag"?><br>
+	
+	<?php 
+   if($blast_result->max != 10){    
+      $url = url("tripal_top_blast/$feature->feature_id/$db->db_id/10");
+		?><span><a onclick="return tripal_update_blast(this,<?php print $db->db_id?>)" href="<?php print $url ?>">Show Best 10 Hits</a></span><?php
+	} else { 
+		?><span>Best 10 Hits Shown</span><?php
+	} 
+	
+	if($blast_result->number_hits <= 10){ 
+	} 
+   else if ($blast_result->max != 25) { 
+  	   $url = url("tripal_top_blast/$feature->feature_id/$db->db_id/25"); 	
+		?><span> | <a onclick="return tripal_update_blast(this,<?php print"$db->db_id"?>)" href="<?php print $url ?>">Show Best 25 Hits</a></span><?php
+	}else {
+		?><span> | Best 25 Hits Shown</span><?php
+	} 
+	
+	if($blast_result->number_hits <= 25){
+	} 
+   else if ($blast_result->max != 0) {
+	   $url = url("tripal_top_blast/$feature->feature_id/$db->db_id/all"); 		
+		?><span> | <a onclick="return tripal_update_blast(this, <?php print $db->db_id ?>)" href="<?php print $url ?>">Show All Hits</a> </span><?php
+	} else {
+		?><span> | All Hits Shown</span><?php
+	} 
+   ?>
+	<br><br><span>Click a description for more details</span>
+   </div>
+	<table id="tripal_analysis_blast-table" class="tripal-table tripal-table-horz tripal_analysis_blast-table">
+		<tr>
+         <th>&nbsp;</th>
+			<th nowrap>Match Name</th>
+			<th nowrap>E value</th>
+			<th nowrap>Identity</th>
+			<th nowrap>Description</th>
+		</tr>
+		
+		<?php 
+      $i = 0; 
+		foreach($hits_array AS $hit) { 
+         $class = 'tripal-table-odd-row tripal_analysis_blast-table-odd-row';
+         if($i % 2 == 0 ){
+            $class = 'tripal-table-even-row tripal_analysis_blast-table-odd-row';
+         }?>
+         <tr class="<?php print $class ?> tripal_analysis_blast-result-first-row">
+            <td><?php print $i+1 ?>.</td>
+		      <?php if ($hit['hit_url']) { ?>
+			      <td><a href="<?php print $hit['hit_url']?>" target="_blank"><?php print $hit['hit_name']?></a></td>
+		      <?php } else {?>
+			      <td><?php print $hit['hit_name'] ?></td>
+		      <?php } ?>
+			   <td nowrap><?php print $hit['best_evalue']?></td>
+			   <td nowrap><?php  print $hit['percent_identity']?></td>
+			   <td><?php print $hit['description']?></td>
+		   </tr>
+	      <tr class="<?php print $class ?>">
+		      <td colspan=5>
+			      <a class="blast-hit-arrow-icon" onclick="return tripal_blast_toggle_alignment(<?php print $analysis->aid ?>,<?php print $i?>)"><img id="tripal_analysis_blast-info-toggle-image-<?php print $analysis->aid ?>-<?php print $i?>" src=<?php print $hit['arrowr_url']?> align="top"> View Alignment</a>
+			      <div class="tripal_analysis_blast-info-hsp-title"></div>
+		      </td>
+	      </tr>
+	      <tr class="<?php print $class ?> tripal_analysis_blast-result-last-row">
+		      <td colspan=5>
+		      <?php 
+		      $hsps_array = $hit['hsp'];
+		      foreach ($hsps_array AS $hsp) { ?>
+			      <div class="tripal_analysis_blast-info-hsp-desc" id="tripal_analysis_blast-info-hsp-desc-<?php print $analysis->aid ?>-<?php print $i?>">
+				      &nbsp;HSP <?php  print $hsp['hsp_num'] ?>
+				      <pre>Score: <?php print $hsp['bit_score'] ?> bits (<?php print $hsp['score'] ?>), Expect = <?php print $hsp['evalue'] ?><br>Identity = <?php print sprintf("%d/%d (%.2f%%)", $hsp['identity'], $hsp['align_len'], $hsp['identity']/$hsp['align_len']*100) ?>, Postives = <?php print sprintf("%d/%d (%.2f%%)", $hsp['positive'], $hsp['align_len'], $hsp['positive']/$hsp['align_len']*100)?>, Query Frame = <?php print $hsp['query_frame']?></a><br><br></a>Query: <?php print sprintf("%4d", $hsp['query_from'])?> <?php print $hsp['qseq'] ?> <?php print sprintf("%d", $hsp['query_to']); ?><br>            <?php print $hsp['midline'] ?><br>Sbjct: <?php print sprintf("%4d", $hsp['hit_from']) ?> <?php print $hsp['hseq']?> <?php print sprintf("%d",$hsp['hit_to']) ?></pre><br>
+			      </div>
+		      <?php } ?>
+		      </td>
+	      </tr>		
+         <?php $i++;
+	   } ?>
+	</table>
+</div>
+</div>
+  <?php } ?>
+<?php } ?>

theme_tripal/tripal_feature/tripal_feature_featureloc_sequences.tpl.php

@@ -1,6 +1,6 @@
 <?php
 $featureloc_sequences =  $variables['tripal_feature']['featureloc_sequences'];
-if($featureloc_sequences){
+if(count($featureloc_sequences) > 0){
    foreach($featureloc_sequences as $seq => $attrs){ ?>
      <div id="tripal_feature-floc_seq-<?php print $attrs['type']?>-box" class="tripal_feature-info-box tripal-info-box">
        <div class="tripal_feature-info-box-title tripal-info-box-title">Formatted <?php print $attrs['type']?> sequence </div>

theme_tripal/tripal_feature/tripal_feature_featurelocs_as_child.tpl.php

@@ -7,6 +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 $feature->featurename;?> feature is located relative to the following features:</div>
+  <?php if(count($featurelocs_as_child) > 0){ ?>
   <table id="tripal_feature-featurelocs_as_child-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Name</th>
@@ -38,6 +39,9 @@ $feature = $variables['node']->feature;
          $i++;  
       } ?>
     </table>
+  <?php } else { ?>
+    <div class="tripal-no-results">There are no locations where this feature is found</div> 
+  <?php }?>
 </div>
 
 

theme_tripal/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php

@@ -7,6 +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 $feature->featurename;?></div>
+  <?php if(count($featurelocs_as_parent) > 0){ ?>
   <table id="tripal_feature-featurelocs_as_parent-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>
       <th>Name</th>
@@ -37,7 +38,10 @@ $feature = $variables['node']->feature;
          <?php
          $i++;  
       } ?>
-    </table>
+  </table>
+  <?php } else { ?>
+    <div class="tripal-no-results">There are no features located relative to <?php print $feature->featurename;?></div> 
+  <?php }?>
 </div>
 
 

theme_tripal/tripal_feature/tripal_feature_go_terms.tpl.php

@@ -0,0 +1,36 @@
+<?php
+$terms = $variables['tripal_analysis_go']['terms'];
+$feature = $variables['node']->feature;
+
+?>
+<div id="tripal_feature-go_terms-box" class="tripal_feature-info-box tripal-info-box">
+  <div class="tripal_feature-info-box-title tripal-info-box-title">GO Assignments</div>
+  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' is annotated with the following GO terms. Hover your mouse over the term name for a popup description.</div>
+  <?php if(count($terms) > 0){ ?>
+  <table id="tripal_feature-go_terms-table" class="tripal_feature-table tripal-table tripal-table-horz">
+    <tr>
+      <th>Category</th>
+      <th>Term Accession</th>
+      <th>Term Name</th>
+    </tr>
+    <?php
+    $i = 0; 
+    foreach ($terms as $term){
+      $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
+      if($i % 2 == 0 ){
+         $class = 'tripal_feature-table-odd-row tripal-table-even-row';
+      }
+      ?>
+      <tr class="<?php print $class ?>">
+        <td><?php print $term->cvname ?></td>
+        <td>GO:<?php print $term->accession?></td>
+        <td><span title="<?php print $term->definition ?>"><?php print $term->goterm ?></span></td>
+      </tr>
+      <?php
+      $i++;  
+    } ?>
+  </table>
+  <?php } else { ?>
+    <div class="tripal-no-results">There are no GO terms for this feature</div> 
+  <?php }?>
+</div>

theme_tripal/tripal_feature/tripal_feature_relationships_as_object.tpl.php

@@ -48,6 +48,8 @@ $feature = $variables['node']->feature;
       </tr>
     <?php } ?>
   </table>
-  <?php }?>
+  <?php } else {?>
+    <div class="tripal-no-results">There are no object relationships for this feature</div>
+  <?php } ?> 
 </div>
 

theme_tripal/tripal_feature/tripal_feature_relationships_as_subject.tpl.php

@@ -36,6 +36,8 @@ $feature = $variables['node']->feature;
       $i++;  
     }?>
   </table>
-  <?php } ?> 
+  <?php } else { ?>
+    <div class="tripal-no-results">There are no subject relationships for this feature</div> 
+  <?php }?>
 </div>
 

theme_tripal/tripal_organism/tripal_organism_feature_browser.tpl.php

@@ -8,6 +8,7 @@ if($enabled){
 ?>
 <div id="tripal_organism-feature_browser-box" class="tripal_organism-info-box tripal-info-box">
   <div class="tripal_organism-info-box-title tripal-info-box-title">Feature Browser</div>
+  <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following browser provides a quick view for new visitors.  Use the searching mechanism to find specific features.</div>
    <?php if(count($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">

theme_tripal/tripal_organism/tripal_organism_feature_counts.tpl.php

@@ -15,7 +15,7 @@ if (Drupal.jsEnabled) {
 </script>
 <div id="tripal_organism-feature_counts-box" class="tripal_organism-info-box tripal-info-box">
   <div class="tripal_organism-info-box-title tripal-info-box-title">Feature Type Summary</div>
-  <div class="tripal_organism-info-box-desc tripal-info-box-desc">Hold your mouse over the feature type for a popup of the description.</div>
+  <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following types of features are currently present in this database. Hold your mouse over the feature type for a popup with a description.</div>
    <?php if(count($types) > 0){ ?>
    <table id="tripal_organism-table-feature_counts" class="tripal_organism-table tripal-table tripal-table-horz">     
       <tr class="tripal_organism-table-odd-row tripal-table-even-row">

theme_tripal/tripal_organism/tripal_organism_go_summary.tpl.php

@@ -1,14 +1,14 @@
 <?php
-  $form = $variables['tripal_analysis_go']['form']['value'];
-  $form_status = $variables['tripal_analysis_go']['form']['status'];
+  $form = $variables['tripal_analysis_go']['select_form']['form'];
+  $has_results = $variables['tripal_analysis_go']['select_form']['has_results'];
 ?>
 <div id="tripal_organism-go_summary-box" class="tripal_organism-info-box tripal-info-box">
   <div  class="tripal_organism-info-box-title tripal-info-box-title">GO Analysis Reports</div>
   <?php 
-     if($form_status){
+     if($has_results){
         print $form;
      } else {
-       ?><div class="tripal-no-results"><?php print $form?></div><?php
+       ?><div class="tripal-no-results">There are no GO reports avaialble</div><?php
      }
   ?>
   <div id="tripal_analysis_go_org_charts"></div>