X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=composite.lisp;h=b49eec4867e2bd1443d57622f9fb66773af6050f;hb=5a80d916816131a1d56a60790cd1e4b5e9c88810;hp=d31c51321494f3cb4b9422e2085c3d1dfe660a80;hpb=cd8b476663925be5a1ebbeb569a056e2e5b93aba;p=umlisp.git

diff --git a/composite.lisp b/composite.lisp
index d31c513..b49eec4 100644
--- a/composite.lisp
+++ b/composite.lisp
@@ -1,15 +1,32 @@
-;;;; $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 1.4 2002/10/14 09:25:20 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"))
@@ -30,8 +47,8 @@
   (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))
@@ -51,7 +68,7 @@
 (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))
@@ -67,7 +84,7 @@
 (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))
@@ -89,13 +106,23 @@
 (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"))
   (:fields (tui :string fmt-tui) (freq :fixnum) (sty :string))
   (:documentation "Composite object of usty/freq"))
 
+(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)))
+
 (defun usty_freq-tui (s)
   (tui (usty s)))
  
@@ -105,7 +132,7 @@
 (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))
@@ -124,8 +151,8 @@
 "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)))))
@@ -157,15 +184,15 @@
   (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)
@@ -175,3 +202,8 @@
 (defun find-ucon2_freq-coc-tui-all (tui)
   (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
 
+(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)))