;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: classes-support.lisp
-;;;; Purpose: Support for UMLisp classes
-;;;; Author: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
+;;;; Name: classes-support.lisp
+;;;; Purpose: Support for UMLisp classes
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
;;;;
-;;;; $Id: class-support.lisp,v 1.18 2003/07/21 00:53:27 kevin Exp $
+;;;; $Id$
;;;;
;;;; This file, part of UMLisp, is
-;;;; Copyright (c) 2000-2003 by Kevin M. Rosenberg, M.D.
+;;;; Copyright (c) 2000-2006 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)
-
;;; Formatting routines
(defgeneric fmt-cui (c))
(defmethod fmt-cui ((c ucon))
(fmt-cui (cui c)))
-(defmethod fmt-cui ((c fixnum))
- (prefixed-fixnum-string c #\C 7))
+(when *has-fixnum-class*
+ (defmethod fmt-cui ((c fixnum))
+ (prefixed-fixnum-string c #\C 7)))
+
+(defmethod fmt-cui ((c integer))
+ (prefixed-integer-string c #\C 7))
(defmethod fmt-cui ((c string))
(if (eql (aref c 0) #\C)
(defmethod fmt-lui ((l uterm))
(fmt-lui (lui l)))
-(defmethod fmt-lui ((l fixnum))
- (prefixed-fixnum-string l #\L 7))
+(when *has-fixnum-class*
+ (defmethod fmt-lui ((l fixnum))
+ (prefixed-fixnum-string l #\L 7)))
+
+(defmethod fmt-lui ((l integer))
+ (prefixed-integer-string l #\L 7))
(defmethod fmt-lui ((l string))
(if (eql (aref l 0) #\L)
(defmethod fmt-sui ((s ustr))
(fmt-sui (sui s)))
-(defmethod fmt-sui ((s fixnum))
- (prefixed-fixnum-string s #\S 7))
+(when *has-fixnum-class*
+ (defmethod fmt-sui ((s fixnum))
+ (prefixed-fixnum-string s #\S 7)))
+
+(defmethod fmt-sui ((s integer))
+ (prefixed-integer-string s #\S 7))
(defmethod fmt-sui ((s string))
(if (eql (aref s 0) #\S)
(fmt-sui (parse-integer s))))
(defgeneric fmt-tui (tui))
-(defmethod fmt-tui ((tui fixnum))
- (prefixed-fixnum-string tui #\T 3))
+(when *has-fixnum-class*
+ (defmethod fmt-tui ((tui fixnum))
+ (prefixed-fixnum-string tui #\T 3)))
+
+(defmethod fmt-tui ((tui integer))
+ (prefixed-integer-string tui #\T 3))
(defmethod fmt-tui ((tui string))
(if (eql (aref tui 0) #\T)
tui
- (fmt-tui (parse-integer tui))))
+ (fmt-tui (parse-integer tui))))
+
+(defgeneric fmt-aui (aui))
+(when *has-fixnum-class*
+ (defmethod fmt-aui ((aui fixnum))
+ (if (>= aui 10000000)
+ (prefixed-fixnum-string aui #\A 8)
+ (prefixed-fixnum-string aui #\A 7))))
+
+(defmethod fmt-aui ((aui integer))
+ (if (>= aui 10000000)
+ (prefixed-integer-string aui #\A 8)
+ (prefixed-integer-string aui #\A 7)))
+
+(defmethod fmt-aui ((aui string))
+ (if (eql (aref aui 0) #\A)
+ aui
+ (fmt-aui (parse-integer aui))))
+
+(defgeneric fmt-rui (rui))
+(when *has-fixnum-class*
+ (defmethod fmt-rui ((rui fixnum))
+ (prefixed-fixnum-string rui #\A 8)))
+
+(defmethod fmt-rui ((rui integer))
+ (prefixed-integer-string rui #\A 8))
+
+(defmethod fmt-rui ((rui string))
+ (if (eql (aref rui 0) #\R)
+ rui
+ (fmt-rui (parse-integer rui))))
(defgeneric fmt-eui (e))
-(defmethod fmt-eui ((e fixnum))
- (prefixed-fixnum-string e #\E 7))
+(when *has-fixnum-class*
+ (defmethod fmt-eui ((e fixnum))
+ (prefixed-fixnum-string e #\E 7)))
+
+(defmethod fmt-eui ((e integer))
+ (prefixed-integer-string e #\E 7))
(defmethod fmt-eui ((e string))
(if (eql (aref e 0) #\E)
"Return the string for a ulo object"
(find-string-sui (sui lo)))
+(defgeneric pf-ustr (obj))
+(defmethod pf-ustr ((ucon ucon))
+ "Return the preferred ustr for a ucon"
+ (pf-ustr
+ (find-if (lambda (uterm) (string= "P" (ts uterm))) (s#term ucon))))
+
+(defmethod pf-ustr ((uterm uterm))
+ "Return the preferred ustr for a uterm"
+ (find-if (lambda (ustr) (string= "PF" (stt ustr))) (s#str uterm)))
+
+(defgeneric mesh-number (obj))
+(defmethod mesh-number ((con ucon))
+ (mesh-number (pf-ustr con)))
+
+(defmethod mesh-number ((ustr ustr))
+ (let ((codes
+ (map-and-remove-nils
+ (lambda (sat)
+ (when (and (string-equal "MSH" (sab sat))
+ (string-equal "MN" (atn sat)))
+ (atv sat)))
+ (s#sat ustr))))
+ (if (= 1 (length codes))
+ (car codes)
+ codes)))
+
+(defun ucon-ustrs (ucon)
+ "Return lists of strings for a concept"
+ (let (res)
+ (dolist (term (s#term ucon) (nreverse res))
+ (dolist (str (s#str term))
+ (push str res)))))
+
+
(defmethod pfstr ((uterm uterm))
"Return the preferred string for a uterm"
(dolist (ustr (s#str uterm))
(defun rel-abbr-info (rel)
(nth-value 0 (gethash (string-downcase rel) *rel-info-table*)))
-
-
-#+(or scl)
+(defun filter-urels-by-rel (urels rel)
+ (remove-if-not (lambda (urel) (string-equal rel (rel urel))) urels))
+
+
+(defvar +language-abbreviations+
+ '(("BAQ" . "Basque")
+ ("CZE" . "Chech")
+ ("DAN" . "Danish")
+ ("DUT" . "Dutch")
+ ("ENG" . "English")
+ ("FIN" . "Finnish")
+ ("FRE" . "French")
+ ("GER" . "German")
+ ("HEB" . "Hebrew")
+ ("HUN" . "Hungarian")
+ ("ITA" . "Italian")
+ ("JPN" . "Japanese")
+ ("NOR" . "Norwegian")
+ ("POR" . "Portuguese")
+ ("RUS" . "Russian")
+ ("SPA" . "Spanish")
+ ("SWE" . "Swedish")))
+
+(defvar *lat-info-table* (make-hash-table :size 30 :test 'equal))
+(defvar *is-lat-table-init* nil)
+(unless *is-lat-table-init*
+ (dolist (latinfo +language-abbreviations+)
+ (setf (gethash (string-downcase (car latinfo)) *lat-info-table*)
+ (cdr latinfo)))
+ (setq *is-lat-table-init* t))
+
+(defun lat-abbr-info (lat)
+ (aif (nth-value 0 (gethash (string-downcase lat) *lat-info-table*))
+ it
+ lat))
+
+
+
+(defun stt-abbr-info (stt)
+ (when (string-equal "PF" stt)
+ (return-from stt-abbr-info "Preferred"))
+ (when (char-equal #\V (schar stt 0))
+ (setq stt (subseq stt 1)))
+ (loop for c across stt
+ collect
+ (cond
+ ((char-equal #\C c)
+ "Upper/lower case")
+ ((char-equal #\W c)
+ "Word order")
+ ((char-equal #\S c)
+ "Singular")
+ ((char-equal #\P c)
+ "Plural")
+ ((char-equal #\O c)
+ "Other"))))
+
+
+(defun ucon-parents (ucon &key sab include-rb)
+ (ucon-ancestors ucon :sab sab :include-rb include-rb
+ :ancestors nil))
+
+(defun is-ucon-in-ancestors (ucon ancestors)
+ (cond
+ ((null ancestors) nil)
+ ((atom ancestors) (eql (cui ucon) (cui ancestors)))
+ ((listp (car ancestors))
+ (or (is-ucon-in-ancestors ucon (car ancestors))
+ (is-ucon-in-ancestors ucon (cdr ancestors))))
+ (t
+ (or (eql (cui ucon) (cui (car ancestors)))
+ (is-ucon-in-ancestors ucon (cdr ancestors))))))
+
+
+(defun ucon-ancestors (ucon &key sab include-rb ancestors)
+ "Returns a list of ancestor lists for a concept"
+ (let* ((parent-rels (append (filter-urels-by-rel (s#rel ucon) "par")
+ (when include-rb
+ (filter-urels-by-rel (s#rel ucon) "rb"))))
+ (parents nil))
+ (when sab
+ (setq parent-rels (delete-if-not
+ (lambda (rel) (string-equal sab (sab rel)))
+ parent-rels)))
+ (dolist (rel parent-rels)
+ (let ((parent (find-ucon-cui (cui2 rel))))
+ ;; (format t "~S ~S ~S ~S~%" rel ucon parent ancestors)
+ (unless (is-ucon-in-ancestors parent ancestors)
+ (push
+ (list*
+ parent
+ (ucon-ancestors parent :sab (sab rel) :ancestors (append (list parent) ancestors)))
+ parents))))
+ (nreverse parents)))
+
+
+(defun find-minimum-distance (anc1 anc2 &key (distance 0) (minimum 0) path)
+ (cond
+ ((or (null anc1) (null anc2) nil)
+ ((and (atom (car anc1)) (atom (car anc2)))
+ (when (eql (cui ucon1) (cui ucon2))
+ (return-from find-minimum-distance (values distance path)))
+ (incf distance)
+ (when (> distance minimum)
+ (return-from find-minimum-distance nil))
+ (multiple-value-bind (dist1 path1)
+ (find-minimum-distance anc1 (cdr anc2)
+ :distance distance :minimum minimum
+ :path (list* anc1 path))
+ (when (and dist1 (< dist1 minimum))
+ (setf minimum dist1
+ path path1)))
+ (multiple-value-bind (dist2 path2)
+ (find-minimum-distance (cdr anc1) anc2
+ :distance distance :minimum minimum
+ :path (list* anc2 path))
+ (when (and dist2 (< dist2 minimum))
+ (setf minimum dist2
+ path path2)))
+ (return-from find-minimum-distance (values distance path))
+
+
+ (min2 (find-minimum-distance
+ (cdr anc1) anc2
+ :distance distance :minimum minimum
+ :path (list* anc2 path))))
+
+ (when (and min2 (< min2 minimum))
+ (setf minimum min2
+ path (list* anc2 path)))))
+
+
+ )
+
+(defun ucon-cdist (ucon1 ucon2 &key include-rb sab)
+ "Compute James Cimino's CDist metric"
+ (let ((anc1 (ucon-ancestors ucon1 :include-rb include-rb :sab sab))
+ (anc2 (ucon-ancestors ucon2 :include-rb include-rb :sab sab)))
+ (find-minimum-distance (list ucon1 anc1) (list ucon2 anc2))))
+
+
+(defgeneric cxt-ancestors (obj))
+(defmethod cxt-ancestors ((con ucon))
+ (loop for term in (s#term con)
+ append (cxt-ancestors term)))
+
+
+(defmethod cxt-ancestors ((term uterm))
+ (loop for str in (s#str term)
+ append (cxt-ancestors str)))
+
+(defmethod cxt-ancestors ((str ustr))
+ "Return the ancestory contexts of a ustr"
+ (let* ((anc (remove-if-not
+ (lambda (cxt) (string-equal "ANC" (cxl cxt)))
+ (s#cxt str)))
+ (num-contexts (if anc
+ (apply #'max (mapcar (lambda (cxt) (cxn cxt)) anc))
+ 0))
+ (anc-lists '()))
+ (dotimes (i num-contexts (nreverse anc-lists))
+ (let* ((anc-this-cxn (remove-if-not
+ (lambda (cxt) (= (1+ i) (cxn cxt))) anc)))
+ (push
+ (sort anc-this-cxn (lambda (a b) (< (rank a) (rank b))))
+ anc-lists)))))
+
+(defun uso-unique-codes (usos)
+ (let ((sab-codes (make-hash-table :test 'equal)))
+ (dolist (uso usos)
+ (setf (gethash (sab uso) sab-codes) (code uso)))
+ (loop for key being the hash-key in sab-codes
+ collect (list key (gethash key sab-codes)))))
+
+
+(defun ucon-has-sab (ucon sab)
+ (and (find-if (lambda (uso) (string-equal sab (sab uso))) (s#so ucon)) t))
+
+
+#+scl
(dolist (c '(urank udef usat uso ucxt ustr ulo uterm usty urel ucoc uatx ucon uxw uxnw uxns lexterm labr lagr lcmp lmod lnom lprn lprp lspl ltrm ltyp lwd sdef sstr sstre1 sstre2 usrl))
- #+cmu
- (let ((cl (pcl:find-class c)))
- (pcl:finalize-inheritance cl))
- #+scl
(let ((cl (find-class c)))
(clos:finalize-inheritance cl)))
+
+
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