fix error with bipaa

color/color.inc

 <?php
 
 // Put the logo path into JavaScript for the live preview.
-drupal_add_js(array('color' => array('logo' => theme_get_setting('logo', 'bipaa'))), 'setting');
+drupal_add_js(array('color' => array('logo' => theme_get_setting('logo', 'abims'))), 'setting');
 
 $info = array(
   // Available colors and color labels used in theme.

color/preview.html

 <div id="preview">
 
   <div id="preview-header">
-    <div id="preview-logo"><img src="../../../themes/bipaa/logo.png" alt="Site Logo" /></div>
-    <div id="preview-site-name">Bipaa</div>
+    <div id="preview-logo"><img src="../../../themes/abims/logo.png" alt="Site Logo" /></div>
+    <div id="preview-site-name">ABiMS</div>
     <div id="preview-main-menu">
       <ul id="preview-main-menu-links">
         <li><a>Home</a></li>

templates/html.tpl.php

@@ -61,12 +61,12 @@
         <?php print $styles; ?>
         <?php print $scripts; ?>
     	<!--[if lt IE 9]>
-    	<script src="<?php echo $GLOBALS['base_url'].'/'.drupal_get_path('theme', 'bipaa');?>/js/html5.js"></script>
+    	<script src="<?php echo $GLOBALS['base_url'].'/'.drupal_get_path('theme', 'abims');?>/js/html5.js"></script>
     	<![endif]-->
     	<link rel="dns-prefetch" href="https://fonts.googleapis.com/">
         <link rel="dns-prefetch" href="https://s.w.org/">
         <!--[if lt IE 9]>
-        <link rel='stylesheet' id='twentythirteen-ie-css'  href='<?php echo $GLOBALS['base_url'].'/'.drupal_get_path('theme', 'bipaa');?>/css/bipaa/ie.css' type='text/css' media='all' />
+        <link rel='stylesheet' id='twentythirteen-ie-css'  href='<?php echo $GLOBALS['base_url'].'/'.drupal_get_path('theme', 'abims');?>/css/abims/ie.css' type='text/css' media='all' />
         <![endif]-->
     	<script>
     		(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){

templates/tripal_feature_alignments.tpl.php

@@ -56,7 +56,7 @@
 */
 $feature = $variables['node']->feature;
 $alignments = $feature->all_featurelocs;
-$genome_versions = bipaa_get_organisms_with_versions_from_chado();
+$genome_versions = abims_get_organisms_with_versions_from_chado();
 
 if(count($alignments) > 0){ ?>
   <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following features are aligned</div><?php