better jbrowse links

templates/tripal_feature_alignments.tpl.php

@@ -102,36 +102,69 @@ if(count($alignments) > 0){ ?>
 
     if ($alignment->type == 'contig' && getenv('ENABLE_JBROWSE')) {
         $links = getenv(JBROWSE_LINKS);
+        $found_link = false;
         if ($links) {
             $dlist = explode(';', $links);
 
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
                 if (substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
-                    $dataset = "data=data/".$d[1]."&";
+                    $url = "/jbrowse?data=data/".$d[1]."&";
+                    $found_link = true;
                     break;
                 }
             }
         }
-        $feature_loc = "<a href='".$GLOBALS['base_url']."/../jbrowse?".$dataset."loc=".$alignment->name."%3A".($alignment->fmin + 1)."..".$alignment->fmax."'>".$feature_loc."</a>";
+
+        if (!$found_link) {
+            if (getenv('ENABLE_JBROWSE') == "1")
+                $url = '/jbrowse?';
+            else {
+                // Some url was given
+                $url = getenv('ENABLE_JBROWSE');
+                if (strpos($url, '?') !== false)
+                    $url .= '&';
+                else
+                    $url .= '?';
+            }
+        }
+        $feature_loc = "<a href='".$GLOBALS['base_url'].$url."loc=".$alignment->name."%3A".($alignment->fmin + 1)."..".$alignment->fmax."'>".$feature_loc."</a>";
     }
 
     if ($alignment->type == 'contig' && getenv('ENABLE_APOLLO')) {
         $links = getenv(APOLLO_LINKS);
         if (!$links && getenv(JBROWSE_LINKS))
             $links = getenv(JBROWSE_LINKS);
+
+        $links = getenv(JBROWSE_LINKS);
+        $found_link = false;
         if ($links) {
             $dlist = explode(';', $links);
 
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
                 if (substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
-                    $dataset = "data=data/".$d[1]."&";
+                    $url = "/apollo/jbrowse?data=data/".$d[1]."&";
+                    $found_link = true;
                     break;
                 }
             }
         }
-        $feature_loc .= " <a href='".$GLOBALS['base_url']."/../apollo/jbrowse?".$dataset."loc=".$alignment->name."%3A".($alignment->fmin + 1)."..".$alignment->fmax."'>Apollo</a>";
+
+        if (!$found_link) {
+            if (getenv('ENABLE_JBROWSE') == "1")
+                $url = '/apollo/jbrowse?';
+            else {
+                // Some url was given
+                $url = getenv('ENABLE_JBROWSE');
+                if (strpos($url, '?') !== false)
+                    $url .= '&';
+                else
+                    $url .= '?';
+            }
+        }
+
+        $feature_loc .= " <a href='".$GLOBALS['base_url'].$url."loc=".$alignment->name."%3A".($alignment->fmin + 1)."..".$alignment->fmax."'>Apollo</a>";
     }
 
     $rows[] = array(