chip.lisp

;;; Chip
;;; Classes, generic functions, methods and functions for working
;;; with chips such as Affymetrix GeneChips.
;;;
;;; Copyright (c) 2006 Cyrus Harmon (ch-lisp@bobobeach.com)
;;; All rights reserved.
;;;
;;; Redistribution and use in source and binary forms, with or without
;;; modification, are permitted provided that the following conditions
;;; are met:
;;;
;;;   * Redistributions of source code must retain the above copyright
;;;     notice, this list of conditions and the following disclaimer.
;;;
;;;   * Redistributions in binary form must reproduce the above
;;;     copyright notice, this list of conditions and the following
;;;     disclaimer in the documentation and/or other materials
;;;     provided with the distribution.
;;;
;;; THIS SOFTWARE IS PROVIDED BY THE AUTHOR 'AS IS' AND ANY EXPRESSED
;;; OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
;;; WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
;;; ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
;;; DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
;;; DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
;;; GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
;;; INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
;;; WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
;;; NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
;;; SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
;;;

(in-package :bio)

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;; 
;;; Probe

;;; probe protocol class
(defclass probe (bio-object)
  ((probe-id :accessor probe-id)))

(defclass xy-probe (probe)
  ((x :accessor x-pos)
   (y :accessor y-pos)))


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;; 
;;; Probe Set

;;; probe set protocol class
(defclass probe-set (bio-object)
  ((probes :accessor probes)
   (name :accessor name)))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;; 
;;; Chip

;;; probe set protocol class
(defclass chip ()
  ((name :accessor name)
   (unit-count :accessor unit-count)
   (probe-sets :accessor probe-sets)))

(defclass cdf ()
  ((chips :accessor chips)))