Suffixarray*
constructSufArr(void *space, IntSequence **s, Uint len, FAlphabet* alphabet)
{
Uint i, numofsuffixes,
*sorted,
*inv_suftab,
**suffixptr;
MultiIntSeq *mseq;
Suffixarray *arr;
mseq = concatIntSequences(space, s, len, 4000, 4001);
numofsuffixes = (mseq->totallength - mseq->numofsequences)+1;
inv_suftab = ALLOCMEMORY(space, NULL, Uint , numofsuffixes);
arr = ALLOCMEMORY(space, NULL, Suffixarray, 1);
suffixptr = getSuffixPtr(space, mseq, 4000, 4001);
sorted = quickSortMultikey (space, suffixptr, numofsuffixes,
cmpIntSequence, numofsuffixes-1, NULL);
for (i=0; i < numofsuffixes; i++) {
inv_suftab[sorted[i]]=i;
}
arr->seq = mseq;
arr->numofsuffixes = numofsuffixes;
arr->suffixptr = suffixptr;
arr->suftab = sorted;
arr->inv_suftab = inv_suftab;
return arr;
}
Suffixarray*
constructSufArr(void *space,
CharSequence **s,
Uint len,
FAlphabet* alphabet)
{
Uint i, numofsuffixes,
*sorted,
*inv_suftab;
char **suffixptr;
MultiCharSeq *mseq;
Suffixarray *arr;
mseq = concatCharSequences(space, s, len, (char)254, (char)127);
numofsuffixes = (mseq->totallength - mseq->numofsequences)+1;
printf("allocating space for %d suffixes (%d bytes)\n", numofsuffixes, 2*numofsuffixes*sizeof(Uint));
inv_suftab = ALLOCMEMORY(space, NULL, Uint , numofsuffixes);
arr = ALLOCMEMORY(space, NULL, Suffixarray, 1);
printf("constructing suftab.\n");
suffixptr = getSuffixPtr(space, mseq, (char)254, (char)127);
sorted = quickSortMultikey (space, suffixptr, numofsuffixes,
cmpCharSequence, numofsuffixes-1, NULL);
printf("constructing inv_suftab.\n");
for (i=0; i < numofsuffixes; i++) {
inv_suftab[sorted[i]]=i;
}
arr->seq = mseq;
arr->numofsuffixes = numofsuffixes;
arr->suffixptr = suffixptr;
arr->suftab = sorted;
arr->inv_suftab = inv_suftab;
return arr;
}
Suffixarray*
constructSufArr(void *space,
CharSequence **s,
Uint len,
FAlphabet* alphabet,
unsigned char silent)
{
Uint i, numofsuffixes,
*sorted,
*inv_suftab;
MultiCharSeq *mseq;
Suffixarray *arr;
unsigned char *temp,
*mdfive=NULL;
mseq = concatCharSequences(space, s, len, (char)126, (char)127);
numofsuffixes = mseq->totallength;
mdfive = ALLOCMEMORY(space, NULL, char, 16);
temp = MD5R((unsigned char*)mseq->sequences, numofsuffixes, NULL);
memmove(mdfive, temp, 16);
if(!silent) NFO("alphabet of size (%d): %s\n", mseq->mapsize, mseq->map);
if(!silent) NFO("size of db sequence: %u\n", numofsuffixes);
inv_suftab = ALLOCMEMORY(space, NULL, Uint , numofsuffixes);
arr = ALLOCMEMORY(space, NULL, Suffixarray, 1);
if(!silent) MSG("constructing suftab.\n");
#ifdef SUF_MKQUICKSORT
sorted = quickSortMultikey (space, mseq->sequences, numofsuffixes,
cmpCharSequence, numofsuffixes-1, NULL);
#else
sorted = alurusort(space, mseq->sequences,
&(numofsuffixes));
#endif
if (!silent)NFO("constructing inv_suftab (%u).\n", numofsuffixes);
for (i=0; i < numofsuffixes; i++) {
if (sorted[i] > numofsuffixes) fprintf(stderr, "construction error? %u: %u\n",i, sorted[i]);
inv_suftab[sorted[i]]=i;
}
if (!silent)MSG("inv_suftab constructed.\n");
arr->seq = mseq;
arr->numofsuffixes = numofsuffixes;
arr->suftab = sorted;
arr->inv_suftab = inv_suftab;
arr->mdfive = mdfive;
arr->lcpctab = NULL;
arr->llvtab = NULL;
arr->id = NULL;
arr->idvtab = NULL;
arr->chldtab = NULL;
arr->bcktab = NULL;
arr->suflink = NULL;
arr->suflink_l = NULL;
arr->suflink_r = NULL;
arr->llint = 1;
return arr;
}