Switch to embedded CViTjs mode to fix themeing issues + minor adjustments to results page for better flow.

theme/blast_report.tpl.php

@@ -62,7 +62,6 @@ $no_hits = TRUE;
 
 <div class="blast-report">
 
-  <div class="blast-job-info">
     <!-- Provide Information to the user about their blast job -->
     <div class="blast-job-info">
       <div class="blast-download-info"><strong>Download</strong>:
@@ -91,14 +90,14 @@ $no_hits = TRUE;
     ?>
       <!-- CViTjs image of BLAST hits, if enabled -->
       <div class="cvitjs">
-        <div id="title-div"></div>
+        <div id="title-div"><h2>Whole Genome Visualization of BLAST hits</h2></div>
         <div id="cvit-div"></div>
       </div>
+
     <?php
       }
     ?>
 
-  </div>
   <br />
 
   <div class="report-table">
@@ -111,6 +110,8 @@ $no_hits = TRUE;
     if ($xml) {
     ?>
 
+    <h2>Resulting BLAST hits</h2>
+
     <p>The following table summarizes the results of your BLAST.
     Click on a <em>triangle </em> on the left to see the alignment and a visualization of the hit,
     and click the <em>target name </em> to get more information about the target hit.</p>

theme/blast_ui.theme.inc

@@ -45,7 +45,7 @@ function blast_ui_preprocess_show_blast_report(&$vars) {
            . DIRECTORY_SEPARATOR . $cvitjs_location
            . DIRECTORY_SEPARATOR . 'js'
            . DIRECTORY_SEPARATOR . 'lib' . DIRECTORY_SEPARATOR;
-    drupal_add_css($base.'bootstrap/css/bootstrap.min.css',array('preprocess'=>FALSE));
+    drupal_add_css($base.'bootstrap_embed/css/bootstrap.min.css',array('preprocess'=>FALSE));
     drupal_add_css($base.'hopscotch/css/hopscotch.min.css',array('preprocess'=>FALSE));
     drupal_add_css($base.'../../css/cvit.css',array('preprocess'=> FALSE));
     drupal_add_js($base.'require/require.js',array('group'=>'JS_LIBRARY','type'=>'file'));

theme/css/blast_report.css

@@ -77,9 +77,15 @@ table#blast_report div.alignment-subrow{
 }
 .blast-job-info {
   float: left;
+  margin-bottom: 25px;
 }
 .cvitjs {
   float: left;
+  margin-top: 10px;
+  margin-bottom: 25px;
+}
+.cvitjs #cvit-div{
+  padding: 5px 0 0 0;
 }
 .report-table {
   clear: both;