initial import

includes/blast_ui.custom.inc

@@ -0,0 +1,55 @@
+<?php
+/*
+ * customized for PeanutBase
+ *
+ */
+ 
+function tripal_custom_generate_linkout($url_prefix, $hit, $info, $options = array()) {
+// uncomment to see contents of hit object
+//echo "hit:<pre>";var_dump($hit);echo "</pre>";
+// uncomment to see contents of info object
+//echo "info:<pre>";var_dump($info);echo "</pre>";
+
+  $hit_name = $hit->{'Hit_def'};
+
+  if ($info['Target'] == 'All genomes') {
+    if (preg_match('/.*(aradu).*/i', $hit_name) == 1) {
+      $hit->{'linkout_id'} = $hit_name;
+      $url_prefix = "\gbrowse_aradu1.0?";   
+      $url = tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $options);
+    }
+    else if (preg_match('/.*(araip).*/i', $hit_name) == 1) {
+      $hit->{'linkout_id'} = $hit_name;
+      $url_prefix = "\gbrowse_araip1.0?";   
+      $url = tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $options);
+    }
+  }//handle All genomes BLAST target
+  
+  else {
+    if (preg_match('/.*(aradu).*/i', $hit_name) == 1) {
+      preg_match("/\w+\.(\w+\.\w+)/", $hit_name, $linkout_match);
+      $linkout_id = $linkout_match[1];
+      $hit->{'linkout_id'} = $linkout_id;
+      $url =   "/gbrowse_aradu1.0?query=q=$linkout_id;h_feat=$linkout_id";
+    }
+    else if(preg_match('/.*(araip).*/i', $hit_name) == 1) {
+      preg_match("/\w+\.(\w+\.\w+)/", $hit_name, $linkout_match);
+      $linkout_id = $linkout_match[1];
+      $hit->{'linkout_id'} = $linkout_id;
+      $url =  "/gbrowse_araip1.0?query=q=$linkout_id;h_feat=$linkout_id";
+    }
+    else if(preg_match('/.*(phytozome).*/i', $hit_name) == 1) {
+      preg_match("/(.*?)\s.*/", $hit_name, $linkout_match);
+      $linkout_id = $linkout_match[1];
+      $hit->{'linkout_id'} = $linkout_id;
+      $url = "http://legumeinfo.org/chado_phylotree/$linkout_id";
+    }
+    else {
+      // Don't know what to do with this hit
+      drupal_set_message("Don't know how to create linkout for $hit_name", 'error');
+      $url = false;
+    }  
+  }//handle remaining BLAST targets 
+    
+  return "$url";
+}