-;;;; $Id: composite.lisp,v 1.1 2002/10/08 22:08:56 kevin Exp $
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: composite.lisp
+;;;; Purpose: Composite Classes for UMLisp
+;;;; Programmer: Kevin M. Rosenberg
+;;;; Date Started: Apr 2000
+;;;;
+;;;; $Id: composite.lisp,v 1.7 2002/10/16 16:09:55 kevin Exp $
+;;;;
+;;;; This file, part of UMLisp, is
+;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
+;;;;
+;;;; UMLisp users are granted the rights to distribute and use this software
+;;;; as governed by the terms of the GNU General Public License.
+;;;; *************************************************************************
(in-package :umlisp)
+(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
;;; Semantic type constants
(defun find-tui-word (words)
- (gu:aif (car (find-usty-word words))
- (tui gu::it)
+ (kmrcl:aif (car (find-usty-word words))
+ (tui kmrcl::it)
nil))
-(gu:memoize 'find-tui-word)
+(kmrcl:memoize 'find-tui-word)
(defun tui-disease-or-syndrome ()
(find-tui-word "disease or syndrome"))
(remove-duplicates
(filter
#'(lambda (c)
- (gu:aif (funcall cui2-func c)
- (let ((ucon2 (find-ucon-cui gu::it)))
+ (kmrcl:aif (funcall cui2-func c)
+ (let ((ucon2 (find-ucon-cui kmrcl::it)))
(when (ucon-is-tui? ucon2 tui)
ucon2))
nil))
(defclass ucon_freq (umlsclass)
((ucon :type ucon :initarg :ucon :reader ucon)
(freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
+ (:metaclass kmrcl:ml-class)
(:default-initargs :cui nil :pfstr nil :freq nil)
(:title "Concept and Count")
(:fields (cui :string fmt-cui) (freq :fixnum) (pfstr :cdata))
(defclass ustr_freq (umlsclass)
((ustr :type ustr :initarg :ustr :reader ustr)
(freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
+ (:metaclass kmrcl:ml-class)
(:default-initargs :cui nil :pfstr nil :freq nil)
(:title "String and Count")
(:fields (sui :string fmt-sui) (freq :fixnum) (stt :string) (lrl :fixnum) (str :cdata))
(defclass usty_freq (umlsclass)
((usty :type usty :initarg :usty :reader usty)
(freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
+ (:metaclass kmrcl:ml-class)
(:default-initargs :usty nil :freq nil)
(:title "Semantic Type and Count")
- (:ref-fields (tui find-ucon-tui "subobjects=no"))
+;; (:ref-fields (tui find-ucon-tui "subobjects=no"))
+ (:ref-fields (tui find-ucon-tui))
(:fields (tui :string fmt-tui) (freq :fixnum) (sty :string))
(:documentation "Composite object of usty/freq"))
-(defun usty_freq-tui (s)
+(defmethod tui ((s usty_freq))
(tui (usty s)))
-
-(defun usty_freq-sty (s)
+
+(defmethod sty ((s usty_freq))
(sty (usty s)))
+
+(defun find-usty_freq-all ()
+ (let ((usty_freqs '()))
+ (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
+ (let* ((tui (car tuple))
+ (freq (ensure-integer
+ (caar (mutex-sql-query
+ (format nil "select count(*) from MRSTY where TUI=~a" tui))))))
+ (push (make-instance 'usty_freq :usty (find-usty-tui tui) :freq freq) usty_freqs)))
+ (sort usty_freqs #'> :key #'freq)))
+
+
(defclass usrl_freq (umlsclass)
((usrl :type usrl :initarg :usrl :reader usrl)
(freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
+ (:metaclass kmrcl:ml-class)
(:default-initargs :usrl nil :freq nil)
(:title "Source and Count")
(:ref-fields (sab find-ustr-sab))
(:fields (sab :string) (freq :commainteger) (srl :fixnum))
(:documentation "Composite object of usrl/freq"))
-(defun usrl_freq-sab (s)
+(defmethod sab ((s usrl_freq))
(sab (usrl s)))
-(defun usrl_freq-srl (s)
+(defmethod srl ((s usrl_freq))
(srl (usrl s)))
;; Frequency finding functions
+
+(defun find-usrl_freq-all ()
+ (let ((freqs '()))
+ (dolist (usrl (find-usrl-all))
+ (let ((freq (ensure-integer
+ (caar (mutex-sql-query
+ (format nil "select count(*) from MRSO where SAB='~a'"
+ (sab usrl)))))))
+ (push (make-instance 'usrl_freq :usrl usrl :freq freq) freqs)))
+ (sort freqs #'> :key #'usrl_freq-freq)))
+
(defun find-ucon2_freq-coc-tui (ucon tui)
"Return sorted list of tuples with ucon and freq that have co-occuring concepts of semantic type tui"
(let ((ucon_freqs '()))
(dolist (ucoc (s#coc ucon))
- (gu:aif (cui2 ucoc)
- (let ((ucon2 (find-ucon-cui gu::it)))
+ (kmrcl:aif (cui2 ucoc)
+ (let ((ucon2 (find-ucon-cui kmrcl::it)))
(when (ucon-is-tui? ucon2 tui)
(push (make-instance 'ucon_freq :ucon ucon2 :freq (cof ucoc))
ucon_freqs)))))
(let ((ucon_freqs (make-array (1+ (find-cui-max)) :initial-element nil)))
(dolist (ucon (find-ucon-tui tui)) ;; for all disease-or-syn
(dolist (ucon2 (funcall ucon2-tui-func ucon tui)) ;; for each related disease
- (gu:aif (aref ucon_freqs (cui ucon2))
- (setf (freq gu::it) (1+ (freq gu::it)))
+ (kmrcl:aif (aref ucon_freqs (cui ucon2))
+ (setf (freq kmrcl::it) (1+ (freq kmrcl::it)))
(setf (aref ucon_freqs (cui ucon2))
(make-instance 'ucon_freq :ucon ucon2 :freq 1)))))
(let ((ucon_freq-list '()))
(dotimes (i (find-cui-max))
(declare (fixnum i))
- (gu:awhen (aref ucon_freqs i)
- (push gu::it ucon_freq-list)))
+ (kmrcl:awhen (aref ucon_freqs i)
+ (push kmrcl::it ucon_freq-list)))
(sort ucon_freq-list #'> :key #'freq))))
(defun find-ucon2_freq-rel-tui-all (tui)
(defun find-ucon2_freq-coc-tui-all (tui)
(find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
+#+cmu
+(dolist (c '(ucon_freq ustr_freq usty_freq usrl_freq))
+ (let ((cl #+cmu (pcl:find-class c)
+ #+sbcl (sb-pcl:find-class c)))
+ #+cmu (pcl:finalize-inheritance cl)
+ #+sbcl (sb-pcl:finalize-inheritance cl)))
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