--- /dev/null
+/* qsufsort.c
+ Copyright 1999, N. Jesper Larsson, all rights reserved.
+
+ This file contains an implementation of the algorithm presented in "Faster
+ Suffix Sorting" by N. Jesper Larsson (jesper@@cs.lth.se) and Kunihiko
+ Sadakane (sada@@is.s.u-tokyo.ac.jp).
+
+ This software may be used freely for any purpose. However, when distributed,
+ the original source must be clearly stated, and, when the source code is
+ distributed, the copyright notice must be retained and any alterations in
+ the code must be clearly marked. No warranty is given regarding the quality
+ of this software.*/
+
+/*
+ Replaced int -> sint for massive data support and moved into namespace CSA.
+
+ - Jouni Siren 2009-03-16
+*/
+
+#include <climits>
+#include "qsufsort.h"
+
+
+namespace CSA
+{
+
+
+static sint *I, /* group array, ultimately suffix array.*/
+ *V, /* inverse array, ultimately inverse of I.*/
+ r, /* number of symbols aggregated by transform.*/
+ h; /* length of already-sorted prefixes.*/
+
+#define KEY(p) (V[*(p)+(h)])
+#define SWAP(p, q) (tmp=*(p), *(p)=*(q), *(q)=tmp)
+#define MED3(a, b, c) (KEY(a)<KEY(b) ? (KEY(b)<KEY(c) ? b : KEY(a)<KEY(c) ? c : (a)) : (KEY(b)>KEY(c) ? b : KEY(a)>KEY(c) ? c : (a)))
+
+/* Subroutine for select_sort_split and sort_split. Sets group numbers for a
+ group whose lowest position in I is pl and highest position is pm.*/
+
+static void update_group(sint *pl, sint *pm)
+{
+ sint g;
+
+ g=pm-I; /* group number.*/
+ V[*pl]=g; /* update group number of first position.*/
+ if (pl==pm)
+ *pl=-1; /* one element, sorted group.*/
+ else
+ do /* more than one element, unsorted group.*/
+ V[*++pl]=g; /* update group numbers.*/
+ while (pl<pm);
+}
+
+/* Quadratic sorting method to use for small subarrays. To be able to update
+ group numbers consistently, a variant of selection sorting is used.*/
+
+static void select_sort_split(sint *p, sint n) {
+ sint *pa, *pb, *pi, *pn;
+ sint f, v, tmp;
+
+ pa=p; /* pa is start of group being picked out.*/
+ pn=p+n-1; /* pn is last position of subarray.*/
+ while (pa<pn) {
+ for (pi=pb=pa+1, f=KEY(pa); pi<=pn; ++pi)
+ if ((v=KEY(pi))<f) {
+ f=v; /* f is smallest key found.*/
+ SWAP(pi, pa); /* place smallest element at beginning.*/
+ pb=pa+1; /* pb is position for elements equal to f.*/
+ } else if (v==f) { /* if equal to smallest key.*/
+ SWAP(pi, pb); /* place next to other smallest elements.*/
+ ++pb;
+ }
+ update_group(pa, pb-1); /* update group values for new group.*/
+ pa=pb; /* continue sorting rest of the subarray.*/
+ }
+ if (pa==pn) { /* check if last part is single element.*/
+ V[*pa]=pa-I;
+ *pa=-1; /* sorted group.*/
+ }
+}
+
+/* Subroutine for sort_split, algorithm by Bentley & McIlroy.*/
+
+static sint choose_pivot(sint *p, sint n) {
+ sint *pl, *pm, *pn;
+ sint s;
+
+ pm=p+(n>>1); /* small arrays, middle element.*/
+ if (n>7) {
+ pl=p;
+ pn=p+n-1;
+ if (n>40) { /* big arrays, pseudomedian of 9.*/
+ s=n>>3;
+ pl=MED3(pl, pl+s, pl+s+s);
+ pm=MED3(pm-s, pm, pm+s);
+ pn=MED3(pn-s-s, pn-s, pn);
+ }
+ pm=MED3(pl, pm, pn); /* midsize arrays, median of 3.*/
+ }
+ return KEY(pm);
+}
+
+/* Sorting routine called for each unsorted group. Sorts the array of integers
+ (suffix numbers) of length n starting at p. The algorithm is a ternary-split
+ quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
+ Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
+ function is based on Program 7.*/
+
+static void sort_split(sint *p, sint n)
+{
+ sint *pa, *pb, *pc, *pd, *pl, *pm, *pn;
+ sint f, v, s, t, tmp;
+
+ if (n<7) { /* multi-selection sort smallest arrays.*/
+ select_sort_split(p, n);
+ return;
+ }
+
+ v=choose_pivot(p, n);
+ pa=pb=p;
+ pc=pd=p+n-1;
+ while (1) { /* split-end partition.*/
+ while (pb<=pc && (f=KEY(pb))<=v) {
+ if (f==v) {
+ SWAP(pa, pb);
+ ++pa;
+ }
+ ++pb;
+ }
+ while (pc>=pb && (f=KEY(pc))>=v) {
+ if (f==v) {
+ SWAP(pc, pd);
+ --pd;
+ }
+ --pc;
+ }
+ if (pb>pc)
+ break;
+ SWAP(pb, pc);
+ ++pb;
+ --pc;
+ }
+ pn=p+n;
+ if ((s=pa-p)>(t=pb-pa))
+ s=t;
+ for (pl=p, pm=pb-s; s; --s, ++pl, ++pm)
+ SWAP(pl, pm);
+ if ((s=pd-pc)>(t=pn-pd-1))
+ s=t;
+ for (pl=pb, pm=pn-s; s; --s, ++pl, ++pm)
+ SWAP(pl, pm);
+
+ s=pb-pa;
+ t=pd-pc;
+ if (s>0)
+ sort_split(p, s);
+ update_group(p+s, p+n-t-1);
+ if (t>0)
+ sort_split(p+n-t, t);
+}
+
+/* Bucketsort for first iteration.
+
+ Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
+ at least once. x[n] is 0. (This is the corresponding output of transform.) k
+ must be at most n+1. p is array of size n+1 whose contents are disregarded.
+
+ Output: x is V and p is I after the initial sorting stage of the refined
+ suffix sorting algorithm.*/
+
+static void bucketsort(sint *x, sint *p, sint n, sint k)
+{
+ sint *pi, i, c, d, g;
+
+ for (pi=p; pi<p+k; ++pi)
+ *pi=-1; /* mark linked lists empty.*/
+ for (i=0; i<=n; ++i) {
+ x[i]=p[c=x[i]]; /* insert in linked list.*/
+ p[c]=i;
+ }
+ for (pi=p+k-1, i=n; pi>=p; --pi) {
+ d=x[c=*pi]; /* c is position, d is next in list.*/
+ x[c]=g=i; /* last position equals group number.*/
+ if (d>=0) { /* if more than one element in group.*/
+ p[i--]=c; /* p is permutation for the sorted x.*/
+ do {
+ d=x[c=d]; /* next in linked list.*/
+ x[c]=g; /* group number in x.*/
+ p[i--]=c; /* permutation in p.*/
+ } while (d>=0);
+ } else
+ p[i--]=-1; /* one element, sorted group.*/
+ }
+}
+
+/* Transforms the alphabet of x by attempting to aggregate several symbols into
+ one, while preserving the suffix order of x. The alphabet may also be
+ compacted, so that x on output comprises all integers of the new alphabet
+ with no skipped numbers.
+
+ Input: x is an array of size n+1 whose first n elements are positive
+ integers in the range l...k-1. p is array of size n+1, used for temporary
+ storage. q controls aggregation and compaction by defining the maximum value
+ for any symbol during transformation: q must be at least k-l; if q<=n,
+ compaction is guaranteed; if k-l>n, compaction is never done; if q is
+ INT_MAX, the maximum number of symbols are aggregated into one.
+
+ Output: Returns an integer j in the range 1...q representing the size of the
+ new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
+ set to the number of old symbols grouped into one. Only x[n] is 0.*/
+
+static sint transform(sint *x, sint *p, sint n, sint k, sint l, sint q)
+{
+ sint b, c, d, e, i, j, m, s;
+ sint *pi, *pj;
+
+ for (s=0, i=k-l; i; i>>=1)
+ ++s; /* s is number of bits in old symbol.*/
+ e=INT_MAX>>s; /* e is for overflow checking.*/
+ for (b=d=r=0; r<n && d<=e && (c=d<<s|(k-l))<=q; ++r) {
+ b=b<<s|(x[r]-l+1); /* b is start of x in chunk alphabet.*/
+ d=c; /* d is max symbol in chunk alphabet.*/
+ }
+ m=(1<<(r-1)*s)-1; /* m masks off top old symbol from chunk.*/
+ x[n]=l-1; /* emulate zero terminator.*/
+ if (d<=n) { /* if bucketing possible, compact alphabet.*/
+ for (pi=p; pi<=p+d; ++pi)
+ *pi=0; /* zero transformation table.*/
+ for (pi=x+r, c=b; pi<=x+n; ++pi) {
+ p[c]=1; /* mark used chunk symbol.*/
+ c=(c&m)<<s|(*pi-l+1); /* shift in next old symbol in chunk.*/
+ }
+ for (i=1; i<r; ++i) { /* handle last r-1 positions.*/
+ p[c]=1; /* mark used chunk symbol.*/
+ c=(c&m)<<s; /* shift in next old symbol in chunk.*/
+ }
+ for (pi=p, j=1; pi<=p+d; ++pi)
+ if (*pi)
+ *pi=j++; /* j is new alphabet size.*/
+ for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
+ *pi=p[c]; /* transform to new alphabet.*/
+ c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
+ }
+ while (pi<x+n) { /* handle last r-1 positions.*/
+ *pi++=p[c]; /* transform to new alphabet.*/
+ c=(c&m)<<s; /* shift right-end zero in chunk.*/
+ }
+ } else { /* bucketing not possible, don't compact.*/
+ for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
+ *pi=c; /* transform to new alphabet.*/
+ c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
+ }
+ while (pi<x+n) { /* handle last r-1 positions.*/
+ *pi++=c; /* transform to new alphabet.*/
+ c=(c&m)<<s; /* shift right-end zero in chunk.*/
+ }
+ j=d+1; /* new alphabet size.*/
+ }
+ x[n]=0; /* end-of-string symbol is zero.*/
+ return j; /* return new alphabet size.*/
+}
+
+/* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
+ n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
+ contents of x[n] is disregarded, the n-th symbol being regarded as
+ end-of-string smaller than all other symbols.*/
+
+void suffixsort(sint *x, sint *p, sint n, sint k, sint l)
+{
+ sint *pi, *pk;
+ sint i, j, s, sl;
+
+ V=x; /* set global values.*/
+ I=p;
+
+ if (n>=k-l) { /* if bucketing possible,*/
+ j=transform(V, I, n, k, l, n);
+ bucketsort(V, I, n, j); /* bucketsort on first r positions.*/
+ } else {
+ transform(V, I, n, k, l, INT_MAX);
+ for (i=0; i<=n; ++i)
+ I[i]=i; /* initialize I with suffix numbers.*/
+ h=0;
+ sort_split(I, n+1); /* quicksort on first r positions.*/
+ }
+ h=r; /* number of symbols aggregated by transform.*/
+
+ while (*I>=-n) {
+ pi=I; /* pi is first position of group.*/
+ sl=0; /* sl is negated length of sorted groups.*/
+ do {
+ if ((s=*pi)<0) {
+ pi-=s; /* skip over sorted group.*/
+ sl+=s; /* add negated length to sl.*/
+ } else {
+ if (sl) {
+ *(pi+sl)=sl; /* combine sorted groups before pi.*/
+ sl=0;
+ }
+ pk=I+V[s]+1; /* pk-1 is last position of unsorted group.*/
+ sort_split(pi, pk-pi);
+ pi=pk; /* next group.*/
+ }
+ } while (pi<=I+n);
+ if (sl) /* if the array ends with a sorted group.*/
+ *(pi+sl)=sl; /* combine sorted groups at end of I.*/
+ h=2*h; /* double sorted-depth.*/
+ }
+
+ for (i=0; i<=n; ++i) /* reconstruct suffix array from inverse.*/
+ I[V[i]]=i;
+}
+
+
+} // namespace CSA
projects / SXSI / TextCollection.git / blobdiff