(defun get-reaction-mapping (path)
  (let ((forms (read-taxonomy.log path)))
    (let ((equivalence-forms 
	   (remove-if-not 
	    (lambda(el) (and (listp el) (member ':= el) (some (lambda(s) (and (stringp s) (search "reaction" s))) el)))
	    forms )))
       equivalence-forms)))

(defun read-unmapped-reactions (path)
  (let ((table (make-hash-table :test 'equal)))
    (with-open-file (f  path)
      (loop for line = (read-line f nil :eof)
	 until (eq line :eof)
	 for fields = (split-at-char line #\tab)
	 do (setf (gethash (string-downcase (fifth fields)) table)
		  fields))
      table)))

(defun find-hits ()
  (let ((unmapped (read-unmapped-reactions "~/src/lsw/trunk/bug/unmapped-rxns-1.txt"))
	(count 0))
    (loop for mapping in (get-reaction-mapping "/usr/local/src/Fact++/Models.lisp/iJR904-no-compartment/Taxonomy.log")
       for mapped = (remove-if-not 'stringp mapping)
       for names = (mapcar (lambda(s) (string-downcase (regex-replace ".*[#/]" s ""))) mapped)
       do 
       (loop for name in names
	  for hit = (gethash name unmapped)
	    do 
	    (when (and hit (< (read-from-string (car hit)) 101) (> (read-from-string (car hit)) 49))
	       (format t "~a: ~a ~a~%" (read-from-string (car hit)) names (gethash name unmapped))
	       (incf count))
	    ))
    count))

(defun find-all-hits (unmapped-rxns-file taxonomy-file)
  (let ((unmapped (read-unmapped-reactions unmapped-rxns-file))
	(count 0))
    (loop for mapping in (get-reaction-mapping taxonomy-file)
       for mapped = (remove-if-not 'stringp mapping)
       for names = (mapcar (lambda(s) (string-downcase (regex-replace ".*[#/]" s ""))) mapped)
       do 
       (loop for name in names
	  for hit = (gethash name unmapped)
	    do 
	    (when hit
	      (format t "~a: ~a ~a~%" (read-from-string (car hit)) names (gethash name unmapped))
	       (incf count))))
    count))