From a456e009f1cb0e05d74adac3ad8b3092a280b054 Mon Sep 17 00:00:00 2001 From: Ludovic Court`es Date: Thu, 8 Mar 2007 14:37:05 +0000 Subject: Added an experimental `diff' package. * src/guile/Makefile.am (dist_guilemodule_DATA): Added `differ.scm'. * src/guile/skribilo/package/Makefile.am (dist_guilemodule_DATA): Added `diff.scm'. git-archimport-id: lcourtes@laas.fr--2006-libre/skribilo--devo--1.2--patch-22 --- src/guile/differ.scm | 443 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 443 insertions(+) create mode 100644 src/guile/differ.scm (limited to 'src/guile/differ.scm') diff --git a/src/guile/differ.scm b/src/guile/differ.scm new file mode 100644 index 0000000..f8ff18b --- /dev/null +++ b/src/guile/differ.scm @@ -0,0 +1,443 @@ +;;; "differ.scm" O(NP) Sequence Comparison Algorithm. +;;; Copyright (C) 2001, 2002, 2003, 2004 Aubrey Jaffer + +;;; +;;; Taken from Slib 3a2 and adapated by Ludovic Courtès +;;; 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, +;;E. Myers, U. Manber, and W. Miller, +;; +;;"An O(NP) Sequence Comparison Algorithm", +;;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 +;; +;;E. Myers, and W. Miller, +;; +;;"Optimal alignments in linear space", +;;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 -- cgit v1.2.3