/* ********************************************************
write lcp statistic to filename (plain ascii format)
******************************************************** */
void write_lcp(char *filename, UChar *x, int *p, int n)
{
FILE *lcp;
Int32 *stat, i, j, max_lcp=0, sum=0;
unsigned long long sum_lcp=0;
stat = (Int32 *) calloc(MAX_LCP_SIZE,sizeof(Int32)); // initialized to 0
if(stat==NULL) {
fprintf(stderr, "calloc failed (stat)\n");
exit(1);
}
if(_ds_Verbose)
fprintf(stderr,"Writing lcp stats to file %s\n",filename);
if((lcp = fopen(filename,"w"))==NULL)
perror(filename);
// computes lcp
for(i=0;i<n-1;i++) {
if (scmp3(x+p[i], x+p[i+1], & j, MIN(n-p[i], n-p[i+1]))>=0) {
fprintf(stderr,"Error in sa file!\n");
exit(1);
}
else {
max_lcp = MAX(max_lcp,j);
sum_lcp += j;
if(j<MAX_LCP_SIZE)
stat[j]++; // one more lcp of length j
}
}
// output lcp statistics
fprintf(lcp,"Average lcp: %.2f\n",((double) sum_lcp)/(n-1));
fprintf(lcp,"Maximum lcp: %d\n",max_lcp);
if(max_lcp<MAX_LCP_SIZE) {
for(i=0;i<=max_lcp;i++)
if(stat[i]) {
fprintf(lcp,"%10d %10d\n",i,stat[i]);
sum += stat[i];
}
if(sum+1!=n) {
fprintf(stderr,"Fatal error! Invalid lcp stats!\n");
exit(1);
}
}
else {
fprintf(stderr,"Unable to compute lcp stats. ");
fprintf(stderr,"Please set MAX_LCP_SIZE to %d\n",max_lcp+1);
exit(1);
}
fclose(lcp);
free(stat);
}
// function for checking the sa (very slow)
// if verbose>1 prints which suffixes are out of order
void check_sa_ordering(UChar *x, int *p, int n, int verbose)
{
int i,j,wrong=0;
printf("Checking...\n");
for (i=0; i<n-1; ++i) {
if (scmp3(x+p[i], x+p[i+1], & j, MIN(n-p[i], n-p[i+1]))>=0) {
wrong++;
if(verbose>1) {
printf("---> i=%d p[i]=%d p[i+1]=%d\n", i, p[i], p[i+1]);
}
}
}
if(wrong)
printf("%d suffixes out of order!\n",wrong);
else
printf("done.\n");
}
void build_sa(bwi_input *s)
{
int scmp3(unsigned char *p, unsigned char *q, int maxl);
void init_bit_buffer(void);
int fbit_read(FILE *,int);
int *larsson_sada_sufsort(uchar *, int, int);
int *suffixsort5n(uchar *, int);
void out_of_mem(char *s);
int int_log2(int);
int i, n, pointer_size,q,r,sa_size;
FILE *safile;
/* ------------ check sa file ---------------- */
n=0;
safile = fopen(Safile_name,"rb");
if(safile!=NULL) {
fseek(safile,0L,SEEK_END);
n=ftell(safile);
}
if (n==0) {
// ------- build sa using larsson-sada or 5n
if(Verbose) fprintf(stderr, " from scratch ");
if(Use_larsson_sada) {
if(Verbose) fprintf(stderr, "(using ls) ... ");
s->sa = larsson_sada_sufsort(s->text,s->text_size,s->alpha_size);
}
else {
if(Verbose) fprintf(stderr, "(using 5n) ... ");
s->sa = suffixsort5n(s->text,s->text_size);
}
}
else {
// ------ read sa from file --------
pointer_size = int_log2(s->text_size);
// --- compute sa_size = s->text_size * pointer_size + 7)/8
// --- use q and r to avoid overflow
q = s->text_size/8; r = s->text_size % 8;
sa_size = (q*pointer_size) + (r*pointer_size+7)/8;
if (n != sa_size)
fatal_error("Invalid .sa file\n");
if(Verbose) fprintf(stderr, " by reading it from file... ");
// allocate space for the suffix array
s->sa = (int *) malloc(s->text_size * sizeof(int));
if(s->sa==NULL) out_of_mem("build_sa");
rewind(safile);
init_bit_buffer();
for(i=0; i<s->text_size; i++)// read one suffix-array pointer at a time
s->sa[i] = fbit_read(safile,pointer_size);
fclose(safile);
}
// check the suffix array
#if 0
for (i=0; i<s->text_size-1; ++i)
if (scmp3(s->text+s->sa[i], s->text+s->sa[i+1],
MIN(s->text_size-s->sa[i], s->text_size-s->sa[i+1]))>=0) {
fprintf(stderr, "Suffix array check failed at position %d\n", i);
exit(1);
}
#endif
}
