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-;;; "differ.scm" O(NP) Sequence Comparison Algorithm.
-;;; Copyright (C) 2001, 2002, 2003, 2004 Aubrey Jaffer
-
-;;;
-;;; Taken from Slib 3a2 and adapated by Ludovic Courtès
-;;; <ludovic.courtes@laas.fr> to use Guile's native API (March 2007).
-;;;
-
-(define-module (differ)
- :export (diff:longest-common-subsequence diff:edits
- diff:edit-length))
-
-;Permission to copy this software, to modify it, to redistribute it,
-;to distribute modified versions, and to use it for any purpose is
-;granted, subject to the following restrictions and understandings.
-;
-;1. Any copy made of this software must include this copyright notice
-;in full.
-;
-;2. I have made no warranty or representation that the operation of
-;this software will be error-free, and I am under no obligation to
-;provide any services, by way of maintenance, update, or otherwise.
-;
-;3. In conjunction with products arising from the use of this
-;material, there shall be no use of my name in any advertising,
-;promotional, or sales literature without prior written consent in
-;each case.
-
-;;@noindent
-;;@code{diff:edit-length} implements the algorithm:
-;;
-;;@ifinfo
-;;@example
-;;S. Wu, E. Myers, U. Manber, and W. Miller,
-;; "An O(NP) Sequence Comparison Algorithm,"
-;; Information Processing Letters 35, 6 (1990), 317-323.
-;; @url{http://www.cs.arizona.edu/people/gene/PAPERS/np_diff.ps}
-;;@end example
-;;@end ifinfo
-;;@ifset html
-;;S. Wu, <A HREF="http://www.cs.arizona.edu/people/gene/vita.html">
-;;E. Myers,</A> U. Manber, and W. Miller,
-;;<A HREF="http://www.cs.arizona.edu/people/gene/PAPERS/np_diff.ps">
-;;"An O(NP) Sequence Comparison Algorithm"</A>,
-;;Information Processing Letters 35, 6 (1990), 317-323.
-;;@end ifset
-;;
-;;@noindent
-;;The values returned by @code{diff:edit-length} can be used to gauge
-;;the degree of match between two sequences.
-;;
-;;@noindent
-;;@code{diff:edits} and @code{diff:longest-common-subsequence} combine
-;;the algorithm with the divide-and-conquer method outlined in:
-;;
-;;@ifinfo
-;;@example
-;;E. Myers and W. Miller,
-;; "Optimal alignments in linear space",
-;; Computer Application in the Biosciences (CABIOS), 4(1):11-17, 1988.
-;; @url{http://www.cs.arizona.edu/people/gene/PAPERS/linear.ps}
-;;@end example
-;;@end ifinfo
-;;@ifset html
-;;<A HREF="http://www.cs.arizona.edu/people/gene/vita.html">
-;;E. Myers,</A> and W. Miller,
-;;<A HREF="http://www.cs.arizona.edu/people/gene/PAPERS/linear.ps">
-;;"Optimal alignments in linear space"</A>,
-;;Computer Application in the Biosciences (CABIOS), 4(1):11-17, 1988.
-;;@end ifset
-;;
-;;@noindent
-;;If the items being sequenced are text lines, then the computed
-;;edit-list is equivalent to the output of the @dfn{diff} utility
-;;program. If the items being sequenced are words, then it is like the
-;;lesser known @dfn{spiff} program.
-
-
-;;; p-lim is half the number of gratuitous edits for strings of given
-;;; lengths.
-;;; When passed #f CC, fp:compare returns edit-distance if successful;
-;;; #f otherwise (p > p-lim). When passed CC, fp:compare returns #f.
-(define (fp:compare fp fpoff CC A M B N p-lim)
- (define Delta (- N M))
- ;;(if (negative? Delta) (slib:error 'fp:compare (fp:subarray A 0 M) '> (fp:subarray B 0 N)))
- ;;(set! compares (+ 1 compares)) ;(print 'fp:compare M N p-lim)
- (let loop ((p 0))
- (do ((k (- p) (+ 1 k)))
- ((>= k Delta))
- (fp:run fp fpoff k A M B N CC p))
- (do ((k (+ Delta p) (+ -1 k)))
- ((<= k Delta))
- (fp:run fp fpoff k A M B N CC p))
- (let ((fpval (fp:run fp fpoff Delta A M B N CC p)))
- ;; At this point, the cost to (fpval-Delta, fpval) is Delta + 2*p
- (cond ((and (not CC) (<= N fpval)) (+ Delta (* 2 p)))
- ((and (not (negative? p-lim)) (>= p p-lim)) #f)
- (else (loop (+ 1 p)))))))
-
-;;; Traces runs of matches until they end; then set fp[k]=y.
-;;; If CC is supplied, set each CC[y] = min(CC[y], cost) for run.
-;;; Returns furthest y reached.
-(define (fp:run fp fpoff k A M B N CC p)
- (define cost (+ k p p))
- (let snloop ((y (max (+ (array-ref fp (+ -1 k fpoff)) 1)
- (array-ref fp (+ 1 k fpoff)))))
- (define x (- y k))
- (and CC (<= y N)
- (let ((xcst (- M x)))
- (cond ((negative? xcst))
- (else (array-set! CC
- (min (+ xcst cost) (array-ref CC y))
- y)))))
- ;;(set! tick (+ 1 tick))
- (cond ((and (< x M) (< y N)
- (eqv? (array-ref A x) (array-ref B y)))
- (snloop (+ 1 y)))
- (else (array-set! fp y (+ fpoff k))
- y))))
-
-;;; Check that only 1 and -1 steps between adjacent CC entries.
-;;(define (fp:step-check A M B N CC)
-;; (do ((cdx (+ -1 N) (+ -1 cdx)))
-;; ((negative? cdx))
-;; (case (- (array-ref CC cdx) (array-ref CC (+ 1 cdx)))
-;; ((1 -1) #t)
-;; (else (cond ((> 30 (car (array-dimensions CC)))
-;; (display "A: ") (print A)
-;; (display "B: ") (print B)))
-;; (slib:warn
-;; "CC" (append (list (max 0 (+ -5 cdx)) ': (min (+ 1 N) (+ 5 cdx))
-;; 'of)
-;; (array-dimensions CC))
-;; (fp:subarray CC (max 0 (+ -5 cdx)) (min (+ 1 N) (+ 5 cdx))))))))
-
-;;; Correct cost jumps left by fp:compare [which visits only a few (x,y)].
-;;(define (smooth-costs CC N)
-;; (do ((cdx (+ -1 N) (+ -1 cdx))) ; smooth from end
-;; ((negative? cdx))
-;; (array-set! CC (min (array-ref CC cdx) (+ 1 (array-ref CC (+ 1 cdx))))
-;; cdx))
-;; (do ((cdx 1 (+ 1 cdx))) ; smooth toward end
-;; ((> cdx N))
-;; (array-set! CC (min (array-ref CC cdx) (+ 1 (array-ref CC (+ -1 cdx))))
-;; cdx))
-;; CC)
-
-(define (diff:mid-split N RR CC cost)
- ;; RR is not longer than CC. So do for each element of RR.
- (let loop ((cdx (+ 1 (quotient N 2)))
- (rdx (quotient N 2)))
- ;;(if (negative? rdx) (slib:error 'negative? 'rdx))
- (cond ((eqv? cost (+ (array-ref CC rdx) (array-ref RR (- N rdx)))) rdx)
- ((eqv? cost (+ (array-ref CC cdx) (array-ref RR (- N cdx)))) cdx)
- (else (loop (+ 1 cdx) (+ -1 rdx))))))
-
-;;; Return 0-based shared array.
-;;; Reverse RA if END < START.
-(define (fp:subarray RA start end)
- (define n-len (abs (- end start)))
- (if (< end start)
- (make-shared-array RA (lambda (idx) (list (+ -1 (- start idx)))) n-len)
- (make-shared-array RA (lambda (idx) (list (+ start idx))) n-len)))
-
-(define (fp:init! fp fpoff fill mindx maxdx)
- (define mlim (+ fpoff mindx))
- (do ((idx (+ fpoff maxdx) (+ -1 idx)))
- ((< idx mlim))
- (array-set! fp fill idx)))
-
-;;; Split A[start-a..end-a] (shorter array) into smaller and smaller chunks.
-;;; EDX is index into EDITS.
-;;; EPO is insert/delete polarity (+1 or -1)
-(define (diff:divide-and-conquer fp fpoff CCRR A start-a end-a B start-b end-b edits edx epo p-lim)
- (define mid-a (quotient (+ start-a end-a) 2))
- (define len-b (- end-b start-b))
- (define len-a (- end-a start-a))
- (let ((tcst (+ p-lim p-lim (- len-b len-a))))
- (define CC (fp:subarray CCRR 0 (+ len-b 1)))
- (define RR (fp:subarray CCRR (+ len-b 1) (* 2 (+ len-b 1))))
- (define M2 (- end-a mid-a))
- (define M1 (- mid-a start-a))
- (fp:init! CC 0 (+ len-a len-b) 0 len-b)
- (fp:init! fp fpoff -1 (- (+ 1 p-lim)) (+ 1 p-lim (- len-b M1)))
- (fp:compare fp fpoff CC
- (fp:subarray A start-a mid-a) M1
- (fp:subarray B start-b end-b) len-b
- (min p-lim len-a))
- (fp:init! RR 0 (+ len-a len-b) 0 len-b)
- (fp:init! fp fpoff -1 (- (+ 1 p-lim)) (+ 1 p-lim (- len-b M2)))
- (fp:compare fp fpoff RR
- (fp:subarray A end-a mid-a) M2
- (fp:subarray B end-b start-b) len-b
- (min p-lim len-a))
- ;;(smooth-costs CC len-b) (smooth-costs RR len-b)
- (let ((b-splt (diff:mid-split len-b RR CC tcst)))
- (define est-c (array-ref CC b-splt))
- (define est-r (array-ref RR (- len-b b-splt)))
- ;;(set! splts (cons (/ b-splt (max .1 len-b)) splts))
- ;;(display "A: ") (array-for-each display (fp:subarray A start-a mid-a)) (display " + ") (array-for-each display (fp:subarray A mid-a end-a)) (newline)
- ;;(display "B: ") (array-for-each display (fp:subarray B start-b end-b)) (newline)
- ;;(print 'cc cc) (print 'rr (fp:subarray RR (+ 1 len-b) 0))
- ;;(print (make-string (+ 7 (* 2 b-splt)) #\-) '^ (list b-splt))
- (check-cost! 'CC est-c
- (diff2et fp fpoff CCRR
- A start-a mid-a
- B start-b (+ start-b b-splt)
- edits edx epo
- (quotient (- est-c (- b-splt (- mid-a start-a)))
- 2)))
- (check-cost! 'RR est-r
- (diff2et fp fpoff CCRR
- A mid-a end-a
- B (+ start-b b-splt) end-b
- edits (+ est-c edx) epo
- (quotient (- est-r (- (- len-b b-splt)
- (- end-a mid-a)))
- 2)))
- (+ est-c est-r))))
-
-;;; Trim; then diff sub-arrays; either one longer. Returns edit-length
-(define (diff2et fp fpoff CCRR A start-a end-a B start-b end-b edits edx epo p-lim)
- ;; (if (< (- end-a start-a) p-lim) (slib:warn 'diff2et 'len-a (- end-a start-a) 'len-b (- end-b start-b) 'p-lim p-lim))
- (do ((bdx (+ -1 end-b) (+ -1 bdx))
- (adx (+ -1 end-a) (+ -1 adx)))
- ((not (and (<= start-b bdx)
- (<= start-a adx)
- (eqv? (array-ref A adx) (array-ref B bdx))))
- (do ((bsx start-b (+ 1 bsx))
- (asx start-a (+ 1 asx)))
- ((not (and (< bsx bdx)
- (< asx adx)
- (eqv? (array-ref A asx) (array-ref B bsx))))
- ;;(print 'trim-et (- asx start-a) '+ (- end-a adx))
- (let ((delta (- (- bdx bsx) (- adx asx))))
- (if (negative? delta)
- (diff2ez fp fpoff CCRR B bsx (+ 1 bdx) A asx (+ 1 adx)
- edits edx (- epo) (+ delta p-lim))
- (diff2ez fp fpoff CCRR A asx (+ 1 adx) B bsx (+ 1 bdx)
- edits edx epo p-lim))))
- ;;(set! tick (+ 1 tick))
- ))
- ;;(set! tick (+ 1 tick))
- ))
-
-;;; Diff sub-arrays, A not longer than B. Returns edit-length
-(define (diff2ez fp fpoff CCRR A start-a end-a B start-b end-b edits edx epo p-lim)
- (define len-a (- end-a start-a))
- (define len-b (- end-b start-b))
- ;;(if (> len-a len-b) (slib:error 'diff2ez len-a '> len-b))
- (cond ((zero? p-lim) ; B inserts only
- (if (= len-b len-a)
- 0 ; A = B; no edits
- (let loop ((adx start-a)
- (bdx start-b)
- (edx edx))
- (cond ((>= bdx end-b) (- len-b len-a))
- ((>= adx end-a)
- (do ((idx bdx (+ 1 idx))
- (edx edx (+ 1 edx)))
- ((>= idx end-b) (- len-b len-a))
- (array-set! edits (* epo (+ 1 idx)) edx)))
- ((eqv? (array-ref A adx) (array-ref B bdx))
- ;;(set! tick (+ 1 tick))
- (loop (+ 1 adx) (+ 1 bdx) edx))
- (else (array-set! edits (* epo (+ 1 bdx)) edx)
- ;;(set! tick (+ 1 tick))
- (loop adx (+ 1 bdx) (+ 1 edx)))))))
- ((<= len-a p-lim) ; delete all A; insert all B
- ;;(if (< len-a p-lim) (slib:error 'diff2ez len-a len-b 'p-lim p-lim))
- (do ((idx start-a (+ 1 idx))
- (jdx start-b (+ 1 jdx)))
- ((and (>= idx end-a) (>= jdx end-b)) (+ len-a len-b))
- (cond ((< jdx end-b)
- (array-set! edits (* epo (+ 1 jdx)) edx)
- (set! edx (+ 1 edx))))
- (cond ((< idx end-a)
- (array-set! edits (* epo (- -1 idx)) edx)
- (set! edx (+ 1 edx))))))
- (else (diff:divide-and-conquer
- fp fpoff CCRR A start-a end-a B start-b end-b
- edits edx epo p-lim))))
-
-(define (check-cost! name est cost)
- (if (not (eqv? est cost))
- (slib:warn name "cost check failed" est '!= cost)))
-
-;;;; Routines interfacing API layer to algorithms.
-
-(define (diff:invert-edits! edits)
- (define cost (car (array-dimensions edits)))
- (do ((idx (+ -1 cost) (+ -1 idx)))
- ((negative? idx))
- (array-set! edits (- (array-ref edits idx)) idx)))
-
-;;; len-a < len-b
-(define (edits2lcs! lcs edits A)
- (define cost (car (array-dimensions edits)))
- (define len-a (car (array-dimensions A)))
- (let loop ((edx 0)
- (sdx 0)
- (adx 0))
- (let ((edit (if (< edx cost) (array-ref edits edx) 0)))
- (cond ((>= adx len-a))
- ((positive? edit)
- (loop (+ 1 edx) sdx adx))
- ((zero? edit)
- (array-set! lcs (array-ref A adx) sdx)
- (loop edx (+ 1 sdx) (+ 1 adx)))
- ((>= adx (- -1 edit))
- (loop (+ 1 edx) sdx (+ 1 adx)))
- (else
- (array-set! lcs (array-ref A adx) sdx)
- (loop edx (+ 1 sdx) (+ 1 adx)))))))
-
-;; A not longer than B (M <= N)
-(define (diff2edits! edits fp CCRR A B)
- (define N (car (array-dimensions B)))
- (define M (car (array-dimensions A)))
- (define est (car (array-dimensions edits)))
- (let ((p-lim (quotient (- est (- N M)) 2)))
- (check-cost! 'diff2edits!
- est
- (diff2et fp (+ 1 p-lim)
- CCRR A 0 M B 0 N edits 0 1 p-lim))))
-
-;; A not longer than B (M <= N)
-(define (diff2editlen fp A B p-lim)
- (define N (car (array-dimensions B)))
- (define M (car (array-dimensions A)))
- (let ((maxdx (if (negative? p-lim) (+ 1 N) (+ 1 p-lim (- N M))))
- (mindx (if (negative? p-lim) (- (+ 1 M)) (- (+ 1 p-lim)))))
- (fp:init! fp (- mindx) -1 mindx maxdx)
- (fp:compare fp (- mindx) #f A M B N p-lim)))
-
-
-;;;
-;;; Public API.
-;;;
-
-;;@args array1 array2 p-lim
-;;@args array1 array2
-;;@1 and @2 are one-dimensional arrays.
-;;
-;;The non-negative integer @3, if provided, is maximum number of
-;;deletions of the shorter sequence to allow. @0 will return @code{#f}
-;;if more deletions would be necessary.
-;;
-;;@0 returns a one-dimensional array of length @code{(quotient (- (+
-;;len1 len2) (diff:edit-length @1 @2)) 2)} holding the longest sequence
-;;common to both @var{array}s.
-(define (diff:longest-common-subsequence A B . p-lim)
- (define M (car (array-dimensions A)))
- (define N (car (array-dimensions B)))
- (set! p-lim (if (null? p-lim) -1 (car p-lim)))
- (let ((edits (if (< N M)
- (diff:edits B A p-lim)
- (diff:edits A B p-lim))))
- (and edits
- (let* ((cost (car (array-dimensions edits)))
- (lcs (make-typed-array (array-type A) *unspecified*
- (/ (- (+ N M) cost) 2))))
- (edits2lcs! lcs edits (if (< N M) B A))
- lcs))))
-
-;;@args array1 array2 p-lim
-;;@args array1 array2
-;;@1 and @2 are one-dimensional arrays.
-;;
-;;The non-negative integer @3, if provided, is maximum number of
-;;deletions of the shorter sequence to allow. @0 will return @code{#f}
-;;if more deletions would be necessary.
-;;
-;;@0 returns a vector of length @code{(diff:edit-length @1 @2)} composed
-;;of a shortest sequence of edits transformaing @1 to @2.
-;;
-;;Each edit is an integer:
-;;@table @asis
-;;@item @var{k} > 0
-;;Inserts @code{(array-ref @1 (+ -1 @var{j}))} into the sequence.
-;;@item @var{k} < 0
-;;Deletes @code{(array-ref @2 (- -1 @var{k}))} from the sequence.
-;;@end table
-(define (diff:edits A B . p-lim)
- (define M (car (array-dimensions A)))
- (define N (car (array-dimensions B)))
- (set! p-lim (if (null? p-lim) -1 (car p-lim)))
- (let ((fp (make-typed-array 's32 0
- (if (negative? p-lim)
- (+ 3 M N)
- (+ 3 (abs (- N M)) p-lim p-lim)))))
- (define est (if (< N M)
- (diff2editlen fp B A p-lim)
- (diff2editlen fp A B p-lim)))
- (and est
- (let ((edits (make-typed-array 's32 0 est))
- (CCRR (make-typed-array 's32 0 (* 2 (+ (max M N) 1)))))
- (cond ((< N M)
- (diff2edits! edits fp CCRR B A)
- (diff:invert-edits! edits))
- (else
- (diff2edits! edits fp CCRR A B)))
- ;;(diff:order-edits! edits est)
- edits))))
-
-;;@args array1 array2 p-lim
-;;@args array1 array2
-;;@1 and @2 are one-dimensional arrays.
-;;
-;;The non-negative integer @3, if provided, is maximum number of
-;;deletions of the shorter sequence to allow. @0 will return @code{#f}
-;;if more deletions would be necessary.
-;;
-;;@0 returns the length of the shortest sequence of edits transformaing
-;;@1 to @2.
-(define (diff:edit-length A B . p-lim)
- (define M (car (array-dimensions A)))
- (define N (car (array-dimensions B)))
- (set! p-lim (if (null? p-lim) -1 (car p-lim)))
- (let ((fp (make-typed-array 's32 0
- (if (negative? p-lim)
- (+ 3 M N)
- (+ 3 (abs (- N M)) p-lim p-lim)))))
- (if (< N M)
- (diff2editlen fp B A p-lim)
- (diff2editlen fp A B p-lim))))
-
-;;@example
-;;(diff:longest-common-subsequence "fghiejcklm" "fgehijkpqrlm")
-;;@result{} "fghijklm"
-;;
-;;(diff:edit-length "fghiejcklm" "fgehijkpqrlm")
-;;@result{} 6
-;;
-;;(diff:edits "fghiejcklm" "fgehijkpqrlm")
-;;@result{} #A:fixZ32b(3 -5 -7 8 9 10)
-;; ; e c h p q r
-;;@end example
-
-;;(trace-all "/home/jaffer/slib/differ.scm")(set! *qp-width* 333)(untrace fp:run fp:subarray)
-
-
-;;;arch-tag: 8e80eb1d-fb11-4872-895a-8adcee26580d
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-09 16:33:54 +0000