anchor.diff:  
   (defmethod initialize-instance :after ((seq bio-sequence) &rest args)
     (declare (ignore args))
  -  (unless (slot-boundp seq 'upper-bound)
  -    (setf (upper-bound seq) (length (bio-sequence-seq seq)))))
  +  (unless (slot-boundp seq 'seq-end)
  +    (setf (seq-end seq) (length (bio-sequence-seq seq)))))
   
   
   (defclass nucleotide-sequence (bio-sequence)
  
positive.code:    (description :accessor bio-sequence-description
                  :initarg :description
                  :documentation "The descripitions of the object.")
     (lower-bound :accessor seq-start
                  :initarg :seq-start
                  :initform 1)
     (upper-bound :accessor seq-end
                  :initarg :seq-end))
     (:documentation "A biological sequence is a polymeric macromolecule
  of nucelic acids (with a phorsphor-sugar backbone) or of amino acids
  with various side-chaines. In daily routine, one does not use the full
  
negative.code:   (reduce #'+ (map 'vector #'* word scoring-word)))
  
  
  
  
  
  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
  ;;;; Sequence objects to closely model real world molecules.
  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
  
  ;; For now those are very similar to ensembl objects. maybe I will
  ;; change that later.
  (defclass transcript (nucleotide-sequence)
    ((exons :accessor exons
            :initarg :exons
            :initform #()
            :type sequence)
     (protein :accessor protein
              :initarg :protein
              :initarg :translation
              :documentation "The protein the transcript is coding for, if any."
              :initform nil))
     (:documentation "An transcript describes a RNA sequence that can be
  spliced into a mature mRNA.  Exons are the elements that make up the
  mRNA.  All sequence elements which are cut out in the splicing process
  are called introns and can be thought to be the relative complements of
  the exons within the transcript."))
  
  (defclass exon (nucleotide-sequence)
    ((transcript :accessor transcript
                 :initarg transcript
                 :documentation "The transcript corresponding to this exon.")
     (circular :allocation :class
               :initform nil)))
  
  (defclass protein (amino-acid-sequence)
    ((transcript :initarg :transcript
                 :accessor transcript
                 :documentation "The transcript which codes for this protein.")
     (features :initarg :features
               :accessor protein-features
               :documentation "Protein features")))
  
  (defclass protein-feature (feature)
    ((protein :initarg protein
              :accessor protein
              :accessor translation
              :documentation "the protein to which this feature belongs.")
     (feat-start :initarg :start
                 :accessor feat-start
                 :accessor lower-bound)
     (feat-end :initarg :end
               :accessor feat-end
               :accessor upper-bound)))
  
  (defclass transmembrane-helix (protein-feature)
    ())
  
  