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: skribilo@sv.gnu.org--2006/skribilo--devo--1.2--patch-63

1 files changed, 443 insertions, 0 deletions

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
+;;; <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