annotation.lisp

;;; Annotation
;;; Classes, generic functions, methods and functions for working
;;; with annotations of biological sequences
;;;
;;; 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)

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;; 
;;; Annotations. Annotations are themselves sequences, though not
;;; necessarily a sequence with residues.

(defclass qualifier ()
  ((name :initform nil :accessor name :initarg :name)
   (value :initform nil :accessor value :initarg :value)))

(defun make-qualifier (name value)
  (make-instance 'qualifier :name name :value value))

(defclass annotation (bio-sequence)
  ((length :accessor annotation-length :initarg :length)
   (type :accessor annotation-type :initarg :type)
   (note :accessor annotation-note :initarg :note)
   (qualifiers :initform nil :accessor annotation-qualifiers :initarg :qualifiers)))

(defclass exon (annotation)
  ((type :accessor annotation-type :initarg type :initform "exon")))

(defclass cds (annotation)
  ((type :accessor annotation-type :initarg type :initform "cds")))

(defclass sts (annotation)
  ((type :accessor annotation-type :initarg type :initform "sts")))

(defclass repeat-region (annotation)
  ((type :accessor annotation-type :initarg type :initform "repeat-region")))

(defclass source (annotation)
  ((type :accessor annotation-type :initarg type :initform "source")))

(defclass region (annotation)
  ((type :accessor annotation-type :initarg type :initform "region")))

(defclass site (annotation)
  ((type :accessor annotation-type :initarg type :initform "site")))


(defgeneric add-qualifier (annotation qualifier)
  (:method ((annotation annotation) (qualifier qualifier))
    (push (annotation-qualifiers annotation) qualifier)))