--- comment_notify.module.orig	2009-03-08 00:52:51.000000000 +0530
+++ comment_notify.module	2009-04-03 16:20:25.000000000 +0530
@@ -418,12 +418,35 @@
     drupal_mail('comment_notify', 'comment_notify_mail', $author->mail, $language, $message);
     $sent_to[] = $author->mail;
   }
+  $thread = db_result(db_query("SELECT thread FROM {comments} WHERE cid = %d", $cid));
+  //This array contains the nodeid and parent threads.
+  $parent_thread_ids = array();
+  $parent_thread_ids[] = $nid;
+  $format_string = NULL;
+  $thread_arr = explode('.', $thread);
+  // $thread_arr contains the exploded thread value.
+  // Get values from the string thread, 3 at a time and replace the third value(.) from substring
+  // and then attach / at the end. keep the value in the array $parent_thread_ids[].
+  // Format string is formed according to the number of thread id's.
+  for ($i = count($thread_arr) - 1, $j = 3; $i > 0; $i--, $j+=3)  {
+    $thread_id = mb_substr($thread, 0, $j);
+    $thread_id = substr_replace($thread_id, "", -1, 1 ) ."/";
+    $parent_thread_ids[] = $thread_id;
+    $format_string .= "'%s',";
+  }
 
-  //Get the list of commenters to notify
-  $result = db_query("SELECT DISTINCT c.cid, c.uid, c.name, c.nid, c.mail AS cmail, u.mail AS umail, u.init AS uinit, c.uid, c.name, cn.notify, cn.notify_hash
-    FROM {comments} c INNER JOIN {comment_notify} cn on c.cid = cn.cid LEFT OUTER JOIN {users} u ON c.uid = u.uid
-    WHERE nid = %d AND cn.notify > 0 AND c.status = 0 AND (u.status = 1 OR u.uid = 0)", $nid
-  );
+  // Replace the last comma from $format_string
+  $format_string = substr_replace($format_string, "", -1, 1 );
+
+  if (count($thread_arr) > 1) {
+    $conditional_expr = " AND (c.thread IN (". $format_string .") OR cn.notify = 1) ";
+  }
+  else{
+    $conditional_expr = "OR cn.notify = 1";
+  }
+
+  // Get the list of commenters to notify
+  $result = db_query("SELECT DISTINCT c.cid, c.uid, c.name, c.nid, c.mail AS cmail, u.mail AS umail, u.init AS uinit, c.uid, c.name, cn.notify,   cn.notify_hash FROM {comments} c INNER JOIN {comment_notify} cn ON c.cid = cn.cid LEFT OUTER JOIN {users} u ON c.uid = u.uid WHERE nid = %d  AND c.status = 0 AND (u.status = 1 OR u.uid = 0)  ". $conditional_expr, $parent_thread_ids);
   // TODO? the original big query had stuff making sure the mail was populated and contained .+@.+ Perhaps check for that here and set notify = 0 if that is the case for this cid
 
   while ($alert = db_fetch_object($result)) {