Had to comment-out linkout code for now. Need to resolve Lacey's and Deepak's approaches to linkouts for hits.

blast_ui.module

@@ -9,7 +9,7 @@
 require_once 'includes/blast_ui.form_common.inc';
 require_once 'includes/blast_ui.form_advanced_options.inc';
 // NOTE: The forms themeselves are included using hook_menu to ensure they
-// are only inlcuded when needed.
+// are only included when needed.
 
 // BLAST DB Node functionality
 require_once 'includes/blast_ui.node.inc';
@@ -252,7 +252,7 @@ function show_blast_output($job_id) {
  *
  */
 function ajax_blast_ui_example_sequence_callback($form, $form_state) {
-
+//eksc- get this out of here!
   // First, set a default example sequence in case administrators have not yet
   // bothered to set their own.
   $sequence_type = $form_state['values']['query_type'];

includes/blast_ui.form_advanced_options.inc

@@ -367,7 +367,7 @@ function blast_ui_blastx_advanced_options_form_validate($form, $form_state) { }
 function blast_ui_blastx_advanced_options_form_submit($form, $form_state) {
 
   // Same as blastp form submit
-  return blast_ui_blastp_advanced_options_form(&$form, $form_state);
+  return blast_ui_blastp_advanced_options_form($form, $form_state);
 
 }
 

includes/blast_ui.form_per_program.inc

@@ -217,7 +217,6 @@ attempting to submit your BLAST.</strong>',
  */
 function blast_ui_per_blast_program_form_validate($form, &$form_state) {
 
-
   $blast_program = $form_state['values']['blast_program'];
 
   $type = $form_state['values']['query_type'];

includes/blast_ui.node.inc

@@ -187,7 +187,7 @@ function blastdb_form($node, &$form_state) {
   //  '#required' => TRUE,
     '#default_value' => isset($node->gbrowse_path) ? $node->gbrowse_path : '',
   );
-
+/*eksc- linkout vs gbrowse
   $types = module_invoke_all('blast_linkout_info');
   $options = array();
   foreach ($types as $machine_name => $details) {
@@ -200,6 +200,7 @@ function blastdb_form($node, &$form_state) {
     '#options' => $options,
     '#default_value' => (isset($node->linkout->type)) ? $node->linkout->type : 'link'
   );
+*/
 
   return $form;
 }
@@ -322,7 +323,7 @@ function blastdb_delete($node) {
 function blastdb_load($nodes) {
 
 //eksc- linkout vs gbrowse
-  $result = db_query('SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id, dbxref_linkout_type FROM {blastdb} WHERE nid IN (:nids)', array(':nids' => array_keys($nodes)));
+//  $result = db_query('SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id, dbxref_linkout_type FROM {blastdb} WHERE nid IN (:nids)', array(':nids' => array_keys($nodes)));
   $result = db_query('SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id, gbrowse_path FROM {blastdb} WHERE nid IN (:nids)', array(':nids' => array_keys($nodes)));
 
   foreach ($result as $record) {
@@ -346,6 +347,7 @@ function blastdb_load($nodes) {
       $nodes[$record->nid]->linkout->db_id = tripal_get_db(array('db_id' => $record->dbxref_db_id));
       $nodes[$record->nid]->linkout->none = FALSE;
 
+/*eksc- linkouts vs gbrowse
       // Support complex link-outs.
       $nodes[$record->nid]->linkout->type = $record->dbxref_linkout_type;
       $types = module_invoke_all('blast_linkout_info');
@@ -361,6 +363,7 @@ function blastdb_load($nodes) {
           array('%type' => $record->dbxref_linkout_type)
         );
       }
+*/
     }
     else {
       $nodes[$record->nid]->linkout = new stdClass();

theme/blast_user_menupage.tpl.php

@@ -8,15 +8,14 @@
 ?>
 
 <h1> BLAST Search </h1>
-<p>  Search for one or more of your sequences (using BLAST) against the
-available wild peanut genome sequences. First pick a query type
-(nucleotide or protein). You will be able to set search parameters on
-the next page. (We will be adding additional BLAST targets in the coming
-months).
+<p>
+  Search for one or more of your sequences (using BLAST). First pick 
+  a query type (nucleotide or protein). You will be able to set search 
+  parameters on the next page.
 </p>
 <p>
-Choose the appropriate program based on the Query type and Target
-database type. Please click on the program name to view the search form.
+  Choose the appropriate program based on the Query type and Target
+  database type. Please click on the program name to view the search form.
 <p>
 
 <table>