Tripal Search adheres to Drupal coding standards

tripal_search/tripal_search.module

@@ -5,9 +5,9 @@
 /*******************************************************************************
  * Tripal Search initiation
  ******************************************************************************/
-function tripal_search_init(){
+function tripal_search_init() {
    // Add javascript
-   drupal_add_js(drupal_get_path('theme', 'tripal').
+   drupal_add_js(drupal_get_path('theme', 'tripal') .
                                   '/js/tripal_search.js');
 }
 /*******************************************************************************
@@ -35,11 +35,11 @@ function tripal_search_form_alter(&$form, $form_state, $form_id) {
   if ($form_id == 'search_form' && arg(2)) {
     // for pagination etc.
     $get = drupal_query_string_encode($_GET, array('q'));
-    if(preg_match("/node/",arg(1))){
+    if (preg_match("/node/", arg(1))) {
       $form['basic']['inline']['fasta'] = array('#type' => 'markup',
           '#value' => "<br><br><a id=\"tripal_search_link\" href=\"".
                       url('tripal_search/'. arg(1) .'/'. urlencode(search_get_keys()),
-                      array('query' => trim($get)?$get:NULL)).
+                      array('query' => trim($get)?$get:NULL)) .
                       "\">Download features (multi-FASTA format)</a><br><br>");
 
     }
@@ -58,8 +58,8 @@ function tripal_search_view() {
     return drupal_not_found();
   }
 
-  if (trim($keys)) {  	
-    $results = tripal_do_search($keys,$type);    //var_dump($pager_total['0']);
+  if (trim($keys)) {
+    $results = tripal_do_search($keys, $type);    //var_dump($pager_total['0']);
     return tripal_search_file($type, $keys, $results);
   }
 }
@@ -71,24 +71,24 @@ function tripal_search_file($type, $keys, $results) {
 
   drupal_set_header('Content-Type: text');
   drupal_set_header('Content-Disposition: attachment; filename="searchresults.fasta"');
-	
+
   foreach ($results as $result) {
     // Get feature id from drupal database
     $sqld = "SELECT * FROM {chado_feature} CF INNER JOIN {node} N on N.nid = CF.nid WHERE CF.nid = %d";
-    if($f_objd = db_fetch_object(db_query($sqld, $result->sid))){
+    if ($f_objd = db_fetch_object(db_query($sqld, $result->sid))) {
 
        // Get sequence from chado database
        $previous_db = tripal_db_set_active('chado');  // use chado database
        $sqlc = "SELECT * FROM {feature} WHERE feature_id = '%s'";
-       $f_objc = db_fetch_object(db_query($sqlc,$f_objd->feature_id));
+       $f_objc = db_fetch_object(db_query($sqlc, $f_objd->feature_id));
        tripal_db_set_active($previous_db);  // now use drupal database
        print tripal_feature_return_fasta($f_objc, $desc);
-    } 
+    }
   }
 }
 
 /*******************************************************************************
- *  This code is a duplicate of the do_search function but with the paging 
+ *  This code is a duplicate of the do_search function but with the paging
  *  call replaced by a simle db_query call.
  */
 function tripal_do_search($keywords, $type, $join1 = '', $where1 = '1 = 1', $arguments1 = array(), $columns2 = 'i.relevance AS score', $join2 = '', $arguments2 = array(), $sort_parameters = 'ORDER BY score DESC') {
@@ -129,10 +129,10 @@ function tripal_do_search($keywords, $type, $join1 = '', $where1 = '1 = 1', $arg
   $select = "SELECT i.type, i.sid, $columns2 FROM {search_index} i $join $join2 WHERE $conditions GROUP BY i.type, i.sid HAVING COUNT(*) >= %d";
   $count_select =  "SELECT COUNT(*) FROM ($select) n1";
   $arguments = array_merge($arguments2, $arguments1, array($query[4]));
- 
+
   // Do actual search query
 //  $result = pager_query("$select $sort_parameters", 10, 0, $count_select, $arguments);
-  $result = db_query("$select $sort_parameters",$arguments);
+  $result = db_query("$select $sort_parameters", $arguments);
   $results = array();
   while ($item = db_fetch_object($result)) {
     $results[] = $item;