X-Git-Url: http://git.kpe.io/?p=umlisp.git;a=blobdiff_plain;f=composite.lisp;h=1c453e1805c31b9cf8823a9f642703cdf6c6842f;hp=f440ac07d7192c881f9e101e93d0bb13509ef2ec;hb=HEAD;hpb=8f58bdf5056ba1925a973a3353d329a9a1e72ad2

diff --git a/composite.lisp b/composite.lisp
index f440ac0..1c453e1 100644
--- a/composite.lisp
+++ b/composite.lisp
@@ -2,23 +2,19 @@
 ;;;; *************************************************************************
 ;;;; FILE IDENTIFICATION
 ;;;;
-;;;; Name:          composite.lisp
-;;;; Purpose:       Composite Classes for UMLisp
-;;;; Programmer:    Kevin M. Rosenberg
-;;;; Date Started:  Apr 2000
-;;;;
-;;;; $Id: composite.lisp,v 1.15 2002/11/24 19:03:34 kevin Exp $
+;;;; Name:     composite.lisp
+;;;; Purpose:  Composite Classes for UMLisp
+;;;; Author:   Kevin M. Rosenberg
+;;;; Created:  Apr 2000
 ;;;;
 ;;;; This file, part of UMLisp, is
-;;;;    Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
+;;;;    Copyright (c) 2000-2010 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)))
-
+(in-package #:umlisp)
 
 ;;; Semantic type constants
 
@@ -30,7 +26,7 @@
 
 (defun tui-disease-or-syndrome ()
   (find-tui-word "disease or syndrome"))
-(defun tui-sign-or-symptom () 
+(defun tui-sign-or-symptom ()
   (find-tui-word "sign or symptom"))
 (defun tui-finding ()
   (find-tui-word "finding"))
@@ -44,21 +40,20 @@
 
 (defun find-ucon2-tui (ucon tui cui2-func related-con-func)
   "Returns a list of related ucons that have specific tui"
-  (remove-duplicates 
+  (remove-duplicates
    (filter
-    #'(lambda (c) 
-	(aif (funcall cui2-func c)
-	     (let ((ucon2 (find-ucon-cui it)))
- 	       (when (ucon-is-tui? ucon2 tui)
-		 ucon2))
-	     nil))
+    #'(lambda (c)
+        (aif (funcall cui2-func c)
+             (let ((ucon2 (find-ucon-cui it)))
+               (when (ucon-is-tui? ucon2 tui)
+                 ucon2)) nil))
     (funcall related-con-func ucon))
    :key #'cui))
 
-(defun find-ucon2-coc-tui (ucon tui)
+#+mrcoc (defun find-ucon2-coc-tui (ucon tui)
   "Return list of ucon's that have co-occuring concepts of semantic type tui"
   (find-ucon2-tui ucon tui #'cui2 #'s#coc))
-  
+
 (defun find-ucon2-rel-tui (ucon tui)
   "Return list of ucon's that have related concepts to ucon and semantic type tui"
   (find-ucon2-tui ucon tui #'cui2 #'s#rel))
@@ -66,50 +61,53 @@
 ;;; Composite Objects
 
 (defclass freq (hyperobject)
-  ((freq :type integer :initarg :freq :accessor freq :print-formatter fmt-comma-integer))
+  ((freq :value-type integer :initarg :freq :accessor freq
+         :print-formatter fmt-comma-integer))
   (:metaclass hyperobject-class)
   (:default-initargs :freq 0)
-  (:title "Frequency class")
-  (:print-slots freq)
+  (:user-name "Frequency class" "Frequency classes")
+  (:default-print-slots freq)
   (:description "Base class containing frequency slot, used for multi-inherited objects"))
 
 (defclass ucon_freq (ucon freq)
   ()
   (:metaclass hyperobject-class)
-  (:title "Concept and Count")
-  (:print-slots cui freq pfstr)
+  (:user-name "Concept and Count" "Concepts and Counts")
+  (:default-print-slots cui freq pfstr)
   (:description "Composite object of ucon/freq"))
 
 (defclass ustr_freq (ustr freq)
   ()
   (:metaclass hyperobject-class)
-  (:title "String and Count")
-  (:print-slots sui freq stt lrl str)
+  (:user-name "String and Count" "Strings and Counts")
+  (:default-print-slots sui freq stt lrl str)
   (:description "Composite object of ustr/freq"))
 
 (defclass usty_freq (usty freq)
-  ((freq :type fixnum :initarg :freq :accessor freq))
+  ()
   (:metaclass hyperobject-class)
-  (:title "Semantic Type and Count")
-  (:print-slots tui freq sty)
+  (:user-name "Semantic Type and Count" "Semantic Types and Counts")
+  (:default-print-slots tui freq sty)
   (:description "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)))
+             (freq (ensure-integer
+                     (caar (mutex-sql-query
+                            (format nil "select count(*) from MRSTY where TUI=~a" tui)))))
+             (usty (find-usty-tui tui)))
+        (push (make-instance 'usty_freq :sty (sty usty)
+                             :tui (tui usty) :freq freq) usty_freqs)))
     (sort usty_freqs #'> :key #'freq)))
 
 
 (defclass usrl_freq (usrl freq)
   ()
   (:metaclass hyperobject-class)
-  (:title "Source and Count")
-  (:print-slots sab freq srl)
+  (:user-name "Source and Count" "Sources and Counts")
+  (:default-print-slots sab freq srl)
   (:description "Composite object of usrl/freq"))
 
 ;; Frequency finding functions
@@ -117,35 +115,37 @@
 (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)) 
-      (aif (cui2 ucoc) 
-           (let ((ucon2 (find-ucon-cui it))) 
+      (let ((freq (ensure-integer
+                   (caar (mutex-sql-query
+                          (format nil "select count(*) from MRSO where SAB='~a'"
+                                  (sab usrl)))))))
+        (push (make-instance 'usrl_freq :sab (sab usrl) :srl (srl usrl)
+                             :freq freq)
+              freqs)))
+    (sort freqs #'> :key #'freq)))
+
+#+mrcoc (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))
+      (aif (cui2 ucoc)
+           (let ((ucon2 (find-ucon-cui it)))
              (when (ucon-is-tui? ucon2 tui)
-	       (push (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
-				    :pfstr (pfstr ucon2) :freq (cof ucoc)) 
-		     ucon_freqs)))))
+               (push (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
+                                    :pfstr (pfstr ucon2) :freq (cof ucoc))
+                     ucon_freqs)))))
     (setq ucon_freqs (delete-duplicates ucon_freqs :key #'cui))
     (sort ucon_freqs #'> :key #'freq)))
- 
+
 (defun find-ucon2-str&sty (str sty lookup-func)
   "Call lookup-func for ucon and usty for given str and sty"
   (let ((ucon (car (find-ucon-str str)))
-	(usty (car (find-usty-word sty))))
+        (usty (car (find-usty-word sty))))
     (if (and ucon usty)
-	(funcall lookup-func ucon (tui usty))
+        (funcall lookup-func ucon (tui usty))
       nil)))
-  
-(defun find-ucon2-coc-str&sty (str sty)
+
+#+mrcoc (defun find-ucon2-coc-str&sty (str sty)
   "Find all ucons that are a co-occuring concept for concept named str
    and that have semantic type of sty"
   (find-ucon2-str&sty str sty #'find-ucon2-coc-tui))
@@ -162,28 +162,28 @@
   (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
-	(aif (aref ucon_freqs (cui ucon2))
-	     (setf (freq it) (1+ (freq it)))
-	     (setf (aref ucon_freqs (cui ucon2)) 
-	       (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
-			      :pfstr (pfstr ucon2) :freq 1)))))
+        (aif (aref ucon_freqs (cui ucon2))
+             (setf (freq it) (1+ (freq it)))
+             (setf (aref ucon_freqs (cui ucon2))
+               (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
+                              :pfstr (pfstr ucon2) :freq 1)))))
     (let ((ucon_freq-list '()))
       (dotimes (i (find-cui-max))
-	(declare (fixnum i))
-	(awhen (aref ucon_freqs i)
-	     (push it ucon_freq-list)))
+        (declare (fixnum i))
+        (awhen (aref ucon_freqs i)
+             (push it ucon_freq-list)))
       (sort ucon_freq-list #'> :key #'freq))))
 
 (defun find-ucon2_freq-rel-tui-all (tui)
   "Sorted list of ucon_freq with semantic type tui that are rel's of ucons with semantic type tui"
   (find-ucon2_freq-tui-all tui #'find-ucon2-rel-tui))
 
-(defun find-ucon2_freq-coc-tui-all (tui)
+#+mrcoc (defun find-ucon2_freq-coc-tui-all (tui)
   (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
 
-#+(or cmu scl)
+#+(or scl)
 (dolist (c '(ucon_freq ustr_freq usty_freq usrl_freq))
   (let ((cl #+cmu (pcl:find-class c)
-	    #+scl (find-class c)))
+            #+scl (find-class c)))
     #+cmu (pcl:finalize-inheritance cl)
     #+scl (clos:finalize-inheritance cl)))