descriptor.lisp

;;; Descriptors
;;; Classes, generic functions, methods and functions for identifying
;;; bioloigcal sequences and features
;;;
;;; 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)

(defclass descriptor () ())

(defclass described-object ()
  ((descriptors :accessor descriptors :initform nil)))

(defgeneric get-descriptors (described &key type))
(defgeneric add-descriptor (described descriptor))
(defgeneric remove-descriptor (described descriptor))

(defmethod get-descriptors ((described described-object) &key type)
  (if type
      (loop for descr in (descriptors described)
         when (typep descr type)
         collect descr)
      (descriptors described)))

(defmethod add-descriptor ((described described-object)
                           (desc descriptor))
  (pushnew desc (descriptors described)))

(defmethod remove-descriptor ((described described-object)
                           (desc descriptor))
  (setf (descriptors described)
        (delete desc (descriptors described))))