double
scorefilter (void *space, Matchtype *m, IntSequence *a, IntSequence *b,
Uint *ptr, Uint len, Uint pos, void *info) {
Uint l;
double temp = 0;
double sum = 0;
imbissinfo *imbiss;
imbiss=(imbissinfo*) info;
m->count++;
m->pos = ALLOCMEMORY(space, m->pos, Uint, m->count);
m->org = ALLOCMEMORY(space, m->org, Uint, m->count);
m->pos[(m->count)-1]=pos;
m->org[(m->count)-1]=pos;
for (l=0; l < len; l++) {
temp = ((imbissinfo*)info)->score[(Uint)*ptr];
sum += temp;
m->score += temp;
ptr++;
}
m->blast = m->blast > sum ? m->blast : sum;
imbiss->consensus[pos] += (Uint) 1
/*((double)imbiss->lambda*sum)*/;
return sum > 0 ? sum : 0;
}
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;
}
void
constructchildtab(void *space, Suffixarray *s) {
Uint i;
int lastIndex = -1;
Stack *stack;
s->chldtab = ALLOCMEMORY(space, NULL, childtab, s->numofsuffixes);
memset(s->chldtab, 0, s->numofsuffixes*sizeof(childtab));
stack = ALLOCMEMORY(space, NULL, Stack, 1);
initStack(space, stack, 100000);
stackpush(space, stack, 1);
for(i=1; i < s->numofsuffixes; i++)
{
while(s->lcptab[i] < s->lcptab[stacktop(stack)]) {
lastIndex = stackpop(stack);
if(s->lcptab[i] <= s->lcptab[stacktop(stack)] &&
s->lcptab[stacktop(stack)] != s->lcptab[lastIndex])
{
s->chldtab[stacktop(stack)].down = lastIndex;
if (s->chldtab[stacktop(stack)].val != 0) printf("down conflict\n");
s->chldtab[stacktop(stack)].val = lastIndex;
}
}
if (lastIndex != -1) {
s->chldtab[i].up = lastIndex;
if (s->chldtab[i-1].val != 0) printf("up conflict\n");
s->chldtab[i-1].val = lastIndex;
lastIndex = -1;
}
stackpush(space, stack, i);
}
/*construction of nextlIndex value*/
destructStack(space, stack);
initStack(space, stack, 10000);
stackpush(space, stack,0);
for(i=1; i < s->numofsuffixes; i++) {
while(s->lcptab[i] < s->lcptab[stacktop(stack)]) {
stackpop(stack);
}
if (s->lcptab[i] == s->lcptab[stacktop(stack)]) {
lastIndex = stackpop(stack);
s->chldtab[lastIndex].nextlIndex = i;
s->chldtab[lastIndex].val = i;
}
stackpush(space, stack, i);
}
return;
}
void
constructLcp (void *space, Suffixarray *arr)
{
Uint i, j, k;
Uint s,t;
int l=0;
arr->lcptab = ALLOCMEMORY(space, NULL, Uint, arr->numofsuffixes);
for(i=0; i < arr->numofsuffixes; i++) {
j = arr->inv_suftab[i];
if (j > 0) {
k = arr->suftab[j-1];
s = arr->suffixptr[k]-arr->seq->sequences;
t = arr->suffixptr[i]-arr->seq->sequences;
l=l-1;
if (l < 0) l=0;
while ((s+l < arr->seq->totallength) && (t+l < arr->seq->totallength) && (arr->seq->sequences[s+l] == arr->seq->sequences[t+l])){
l++;
}
arr->lcptab[j] = l;
}
}
return;
}
Uint *quickSort(void *space, void* toSort, Uint size,
Uint (*cmp)(Uint, Uint, void *, void*),
void *info) {
int left, left2, right, right2;
PairSint ins, *lr;
Uint i, resc, *sorted, x;
VStack vstack;
sorted = ALLOCMEMORY(space, NULL, Uint, size);
for (i=0; i < size; i++) sorted[i]=i;
ins.a = 0;
ins.b = size-1;
bl_vstackInit(&vstack, 10000, sizeof(PairSint));
bl_vstackPush(&vstack, &ins);
while (!bl_vstackIsEmpty(&vstack)){
lr = (PairSint *) bl_vstackPop(&vstack, NULL);
left = lr->a;
right = lr->b;
free(lr);
while (left < right) {
x=sorted[(left+right)/2];
left2 = left;
right2 = right;
do {
while(cmp(sorted[left2], x, toSort, info)==2){
left2++;
}
while(cmp(sorted[right2], x, toSort, info)==1){
right2--;
}
if(left2 <= right2) {
resc = sorted[right2];
sorted[right2]=sorted[left2];
sorted[left2]=resc;
left2++;
right2--;
}
} while (right2 >= left2);
if ((left2-left) > (right-left2)) {
ins.a = left;
ins.b = right2;
bl_vstackPush(&vstack, &ins);
left = left2;
} else {
ins.a = left2;
ins.b = right;
bl_vstackPush(&vstack, &ins);
right = right2;
}
}
}
bl_vstackDestruct(&vstack, NULL);
return sorted;
}
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("md5: %s\n", MD5((unsigned char*)"f**k",4,NULL));
fprintf(stderr, "alphabet of size (%d): %s\n", mseq->mapsize, mseq->map);
//fprintf(stderr, "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);
fprintf(stderr, "constructing suftab.\n");
suffixptr = getSuffixPtr(space, mseq, (char)254, (char)127);
//mseq->sequences[numofsuffixes-1]=0;
sorted = alurusort(space, mseq->sequences, &(numofsuffixes));
// mseq->sequences[numofsuffixes-1]=save;
/* sorted = quickSortMultikey (space, suffixptr, numofsuffixes,
cmpCharSequence, numofsuffixes-1, NULL);
*/
fprintf(stderr, "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 *
readSuffixarray(void *space,
char *idxfilename,
CharSequence **seqs,
Uint len) {
FILE *fp;
char **suffixptr;
Uint nmemb = 0,
idvmemb = 0,
llvmemb = 0,
numofsuffixes,
*suftab = NULL,
*suflink = NULL;
childtab *chldtab = NULL;
unsigned char flags=0,
*lcpctab = NULL;
signed char *id = NULL;
PairUint *llvtab = NULL;
PairSint *idvtab = NULL;
MultiCharSeq *mseq;
Suffixarray *s;
mseq = concatCharSequences(space, seqs, len, (char)254, (char)127);
numofsuffixes = (mseq->totallength - mseq->numofsequences)+1;
suffixptr = getSuffixPtr(space, mseq, (char)254, (char)127);
fp = fopen(idxfilename, "r");
if (fp == NULL) {
fprintf(stderr,"Couldn't open file '%s'. Exit forced.\n", idxfilename);
exit(-1);
}
fread(&nmemb, sizeof(Uint), 1, fp);
suftab = ALLOCMEMORY(NULL, NULL, Uint, nmemb);
fread(suftab, sizeof(Uint), nmemb, fp);
fread(&flags, sizeof(char), 1, fp);
if (flags & LCP_TAB_STORED) {
fprintf(stderr, "reading lcpc/vtab\n");
lcpctab = ALLOCMEMORY(space, NULL, unsigned char, nmemb);
fread(lcpctab, sizeof(unsigned char), nmemb, fp);
fread(&llvmemb, sizeof(Uint), 1, fp);
llvtab = ALLOCMEMORY(space, NULL, PairUint, nmemb);
fread(llvtab, sizeof(PairUint), llvmemb, fp);
}
Uint *quickSort(void *space, void* toSort, Uint size,
Uint (*cmp)(Uint, Uint, void *, void*),
void *info) {
Stackelement left, left2, right, right2;
Uint i, resc, *sorted, x;
Stack stack;
sorted = ALLOCMEMORY(space, NULL, Uint, size);
for (i=0; i < size; i++) sorted[i]=i;
initStack(space, &stack, 10000);
stackpush(space, &stack, 0);
stackpush(space, &stack, size-1);
while (!stackisempty(&stack)) {
right=stackpop(&stack);
left=stackpop(&stack);
while (left < right) {
x=sorted[(left+right)/2];
left2 = left;
right2 = right;
do {
while(cmp(sorted[left2], x, toSort, info)==2){
left2++;
}
while(cmp(sorted[right2], x, toSort, info)==1){
right2--;
}
if(left2 <= right2) {
resc = sorted[right2];
sorted[right2]=sorted[left2];
sorted[left2]=resc;
left2++;
right2--;
}
} while (right2 >= left2);
if ((left2-left) > (right-left2)) {
/*if ((right2-left) > (right-left2)) {*/
stackpush(space, &stack, left);
stackpush(space, &stack, right2);
left = left2;
} else {
stackpush(space, &stack, left2);
stackpush(space, &stack, right);
right = right2;
}
}
}
destructStack(space, &stack);
return sorted;
}
fasta_t*
initfasta(void *space) {
fasta_t *f;
f = ALLOCMEMORY(space, NULL, fasta_t, 1);
f->seqs = NULL;
f->noofseqs = 0;
return f;
}
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;
}
void
getimbissblast(void *space, IntSequence *query, IntSequence **seqs,
Uint noofseqs, FAlphabet *alphabet, imbissinfo *imbiss){
double *df, *sf, *scr;
double avgsum=0, inputscr=0, lambda=0, K=0;
Uint *sortind, i;
evdparam *evd;
/*frequency of query and database*/
df = dbfreq(space, seqs, noofseqs, alphabet, 1);
sf = seqfreq(space, query, alphabet);
scr = logoddscr(space, df, sf, alphabet);
for (i=0; i < alphabet->domainsize; i++) avgsum += df[i]*scr[i];
for (i=0; i < query->length; i++) inputscr += scr[query->sequence[i]];
sortind = quickSort(space, scr, alphabet->domainsize, cmp_dbl, NULL);
evd=ALLOCMEMORY (space, NULL, evdparam, 1);
evd->noofscores = alphabet->domainsize;
evd->probs = df;
evd->scores = scr;
lambda = uniroot(0, 1, score_evd, 0.0000001, evd);
FREEMEMORY(space, evd);
K = relentropy(space, sortind, scr, alphabet->domainsize, df, lambda);
if (K <= 0) K=1;
imbiss->score = scr;
imbiss->H = 0;
imbiss->K = K;
imbiss->lambda = lambda;
printf("\nBLAST statistics:\n-------------------\n");
printf("E(score): %f\n", avgsum);
printf("inputscr: %f\n", inputscr);
printf("lambda: %19.16e\n", lambda);
printf("check: %19.16e\n",
checklambda(scr, alphabet->domainsize, df, avgsum, lambda));
printf("K: %19.16e\n\n", K);
FREEMEMORY(space, sortind);
FREEMEMORY(space, df);
FREEMEMORY(space, sf);
return;
}
void
bl_radixSortKeyFirst(void *space, void *tosrt,
size_t size, size_t nelem,
Uint bits) {
char *p, *b, *src, *toSort;
Uint *cast;
Uint mask, offset=0, i, key;
Uint cntsize;
Uint *cnt;
toSort = (char*) tosrt;
cntsize = 1 << bits;
cnt = ALLOCMEMORY(space, NULL, Uint, cntsize);
memset(cnt, 0, sizeof(Uint)*cntsize);
b = src = malloc(size*nelem);
mask =~ (UINT_MAX<<bits);
for(; mask; mask <<= bits, offset+=bits) {
for(p=toSort; p < toSort+(nelem*size); p+=size) {
cast = (Uint*)p;
key = (*cast & mask) >> offset;
++cnt[key];
}
for(i=1; i < cntsize; ++i) {
cnt[i]+=cnt[i-1];
}
for(p=toSort+((nelem-1)*size); p >= toSort; p-=size) {
cast = (Uint*)p;
key = (*cast & mask) >> offset;
memmove(b+((cnt[key]-1)*size), p, size);
--cnt[key];
}
p=b; b=toSort; toSort=p;
memset(cnt, 0, sizeof(Uint)*cntsize);
}
if(toSort == src) memcpy(b, toSort, size*nelem);
FREEMEMORY(space, src);
FREEMEMORY(space, cnt);
return;
}
vector_t *decode_2tupel_cantor(void *space, Uint i) {
Uint j,y,x;
vector_t *v=NULL;
v=ALLOCMEMORY(space, v, vector_t, 1);
INITVECTOR(v);
j = q_cantor(i);
y = i-f_cantor(j);
x = j-y;
APPENDVEC(space, v, x);
APPENDVEC(space, v, y);
return v;
}
void
addinterval(void *space, List *list, Uint a, Uint b) {
PairUint *range;
range = ALLOCMEMORY(space, NULL, PairUint, 1);
range->a=a;
range->b=b;
if (list->length == 0) {
insertAfter(space, list, LISTNILVALUE, range);
} else {
insertAfter(space, list, list->lastNode, range);
}
return;
}
void
bl_radixSortUint(void *space, Uint *toSort,
size_t nelem,
Uint bits) {
Uint *p, *b, *src;
Uint mask, offset=0, i, key;
Uint cntsize;
Uint *cnt;
cntsize = 1 << bits;
cnt = ALLOCMEMORY(space, NULL, Uint, cntsize);
memset(cnt, 0, sizeof(Uint)*cntsize);
b = src = malloc(sizeof(Uint)*nelem);
mask =~ (UINT_MAX<<bits);
for(; mask; mask <<= bits, offset+=bits) {
for(p=toSort; p < toSort+nelem; ++p) {
key = (*p & mask) >> offset;
++cnt[key];
}
for(i=1; i < cntsize; ++i) {
cnt[i]+=cnt[i-1];
}
for(p=toSort+((nelem-1)); p >= toSort; --p) {
key = (*p & mask) >> offset;
b[cnt[key]-1] = *p;
--cnt[key];
}
p=b; b=toSort; toSort=p;
memset(cnt, 0, sizeof(Uint)*cntsize);
}
if(toSort == src) memcpy(b, toSort, sizeof(Uint)*nelem);
FREEMEMORY(space, src);
FREEMEMORY(space, cnt);
return;
}
vector_t *decodeCantor(void *space, Uint code, Uint n) {
Uint i;
vector_t *v = NULL;
vector_t *r = NULL;
v=ALLOCMEMORY(space, v, vector_t, 1);
INITVECTOR(v);
for (i=0; i < (n-1); i++) {
r = decode_2tupel_cantor(space, code);
APPENDVEC(space, v, VECTOR(r,0));
code = VECTOR(r,1);
FREEMEMORY(space, r);
}
APPENDVEC(space, v, VECTOR(r,1));
return (v);
}
PairSint*
sufSubstring (void *space, Suffixarray *arr, Uint *pattern,
Uint len, Uint sublen)
{
Uint i;
PairSint *res, d;
if (len <= sublen)
{
return NULL;
}
res = ALLOCMEMORY(space, NULL, PairSint, len-sublen);
for(i=0; i < len-sublen; i++)
{
d=mmsearch(arr, &pattern[i], sublen, 0, 0, arr->numofsuffixes-1);
res[i].a=d.a;
res[i].b=d.b;
}
return res;
}
if(!silent) MSG("reading uint id.\n");
fread(idvutab, sizeof(PairUint), idvmemb, fp);
for(idvi=0; idvi < idvmemb; idvi++) {
idvtab[idvi].a = idvutab[idvi].a;
idvtab[idvi].b = idvutab[idvi].b;
}
free(idvutab);
}
}
if ((flags & MD5_STORED)) {
mdfive = ALLOCMEMORY(space, NULL, unsigned char, 16);
fread(mdfive, sizeof(unsigned char), 16, fp);
}
s = ALLOCMEMORY(space, NULL, Suffixarray, 1);
if ((flags & LINT_SUFLINKS))
s->llint = 1; else s->llint=0;
s->suftab = suftab;
s->seq = mseq;
s->numofsuffixes = numofsuffixes;
s->lcpctab = lcpctab;
s->llvtab = llvtab;
s->llvcnt = llvmemb;
s->inv_suftab=NULL;
s->chldtab = chldtab;
#ifdef SUFLINK_MMAP
s->suflink = (Uint*) &suflinkptr[pagediff_sl];
s->id = &id[pagediff_id];
int main(int argc, char** argv) {
char* content;
Uint contentlen, i, j, k, l, id, lines=0;
stringset_t *set, *set2, **csv, *que;
CharSequence **s;
Suffixarray *sarray;
MultiCharSeq *mseq;
PairSint d, *matches = NULL;
Uint totallength = 0;
Uint wsize=10;
Uint counter=0;
Uint all=0;
int *space = NULL;
char *pattern= "GGAAGAAAGCGTGGGGTTTG";
char *pattern2= "TGATTAGTGATTAGTGATTA";
char *pattern3= "ACAAACATAT";
char *start;
time_t startsuf, endsuf;
double difsuf;
Uint noofchildren;
List *list;
PairUint **childinterval;
gnuplot_ctrl *h;
double *genome;
//set = readfasta(&space, "HP26695.fasta");
//csv = readcsv(&space, "HP12_GCTC.inserts", "", &lines);
/*s = ALLOCMEMORY(&space, NULL, CharSequence *, set->noofstrings);
for(i=0; i < set->noofstrings/2; i++) {
totallength += set->strings[i].len;
s[i] = ALLOCMEMORY(&space, NULL, CharSequence, 1);
s[i]->sequence = set->strings[i].str;
s[i]->length = set->strings[i].len;
/ printf("%s,", set->strings[i].str);
printf("\n"); /
}*/
s = ALLOCMEMORY(&space, NULL, CharSequence *, 1);
s[0] = ALLOCMEMORY(&space, NULL, CharSequence, 1);
s[0]->sequence = pattern3;
s[0]->length = strlen(pattern3);
genome = ALLOCMEMORY(&space, NULL, double, totallength);
memset(genome, 0, sizeof(double)*totallength);
time (&startsuf);
sarray = constructSufArr(&space, s, 1/*set->noofstrings/2*/, NULL);
constructLcp(space, sarray);
dumplcptab(sarray);
constructchildtab(space, sarray);
time (&endsuf);
difsuf = difftime (endsuf, startsuf);
printf("noofsuffixes: %d\n", sarray->numofsuffixes);
dumpchildtab(sarray);
dumpSufArr(sarray);
list = getChildintervals(space, sarray, 0, 5);
childinterval = (PairUint**) dataList(space, list);
for(i=0; i < list->length; i++) {
printf("[%d,%d]\n", childinterval[i]->a, childinterval[i]->b);
}
constructsuflinks(space, sarray);
for(k=1; k < lines; k+=2) {
// printf("searching %s\n", csv[k]->strings[0].str);
if(csv[k]->strings[0].len > 8) {
if(wsize > csv[k]->strings[0].len) {
d=mmsearch(sarray, csv[k]->strings[0].str, csv[k]->strings[0].len, 0, 0, sarray->numofsuffixes-1);
// printf("suffixes were found at positions (%d, %d)\n",d.a, d.b);
for (j=d.a; j <= d.b; j++) {
genome[sarray->suftab[j]]++;
}
} else {
for(l=0; l < csv[k]->strings[0].len-wsize; l++) {
d=mmsearch(sarray, &csv[k]->strings[0].str[l], wsize, 0, 0, sarray->numofsuffixes-1);
// printf("suffixes were found at positions (%d, %d)\n",d.a, d.b);
for (j=d.a; j <= d.b; j++) {
genome[sarray->suftab[j]]++;
/* start = sarray->suffixptr[sarray->suftab[j]];
printf("pattern was: %s\n", &csv[k]->strings[0].str[l]);
printf("suffix found: ");
for (i=0; i < wsize; i++) {
printf("%c", start[i]);
}
printf("\n");
id = getMultiCharSeqIndex(sarray->seq, sarray->suffixptr[sarray->suftab[j]]);
printf("found in sequence: %d\n", id); */
}
}
}
if (d.a < d.b) counter++;
all++;}
}
destructStringset(&space, set);
writeY("out.xy", genome, totallength);
/*h = gnuplot_init();
gnuplot_setstyle(h, "points");
gnuplot_cmd(h, "set title 'IMBISS - seed statistics' -28,0 font'Helvetica,15'");
gnuplot_cmd(h, "set label 'seed length: %d' at graph 0.05,0.95 font 'Helvetica, 12'", totallength);
gnuplot_set_xlabel(h, "matches");
gnuplot_set_ylabel(h, "position");
gnuplot_plot_x(h, genome, totallength, "position");
*/
printf ("sliding windows of %d sequences (of %d) found\n", counter, all);
printf ("Building the suffixarray has taken %f seconds.\n", difsuf);
printf ("Total length of suffixarray was %d\n", totallength);
while(1);
return EXIT_SUCCESS;
}
Suffixarray *
readSuffixarray(void *space,
char *idxfilename,
CharSequence **seqs,
Uint len,
unsigned char silent) {
FILE *fp;
Uint nmemb = 0,
idvmemb = 0,
llvmemb = 0,
numofsuffixes,
*suftab = NULL,
idvi =0;
childtab *chldtab = NULL;
unsigned char flags=0,
*lcpctab = NULL;
unsigned char *mdfive=NULL,
*check=NULL;
PairUint *llvtab = NULL;
PairLSint *idvtab = NULL;
PairSint *idvutab = NULL;
MultiCharSeq *mseq;
Suffixarray *s;
#ifdef SUFLINK_MMAP
int fd;
signed char *id = NULL;
long curiopos, offset;
struct stat sb;
char *suflinkptr;
int pagediff_id;
int pagediff_sl;
#elif SUFLINK_DISKACC
int fd;
off_t off_sl;
off_t off_id;
#else
signed char *id = NULL;
Uint *suflink = NULL;
#endif
mseq = concatCharSequences(space, seqs, len, (char)126, (char)127);
numofsuffixes = mseq->totallength;
fp = fopen(idxfilename, "r");
if (fp == NULL) {
DBG("Couldn't open file '%s'. Exit forced.\n", idxfilename);
exit(-1);
}
fread(&nmemb, sizeof(Uint), 1, fp);
suftab = ALLOCMEMORY(NULL, NULL, Uint, nmemb);
fread(suftab, sizeof(Uint), nmemb, fp);
fread(&flags, sizeof(char), 1, fp);
if (flags & LCP_TAB_STORED) {
if (!silent) MSG("reading lcpc/vtab.\n");
lcpctab = ALLOCMEMORY(space, NULL, unsigned char, nmemb);
fread(lcpctab, sizeof(unsigned char), nmemb, fp);
fread(&llvmemb, sizeof(Uint), 1, fp);
llvtab = ALLOCMEMORY(space, NULL, PairUint, nmemb);
fread(llvtab, sizeof(PairUint), llvmemb, fp);
}
if (flags & CHLD_TAB_STORED) {
if(!silent) MSG("reading childtab.\n");
chldtab = ALLOCMEMORY(space, NULL, childtab, nmemb);
fread(chldtab, sizeof(childtab), nmemb, fp);
}
if ((flags & SUFLINK_TAB_STORED)) {
if(!silent) MSG("reading suflinks.\n");
#ifdef SUFLINK_MMAP
curiopos = ftell(fp);
fd = open(idxfilename, O_RDONLY);
if (fd == -1) {
perror("open");
exit(EXIT_FAILURE);
}
if (fstat(fd, &sb) == -1) {
perror("fstat");
exit(EXIT_FAILURE);
}
offset = curiopos & ~(sysconf(_SC_PAGE_SIZE) - 1);
if (curiopos >= sb.st_size) {
fprintf(stderr, "offset is past end of file\n");
exit(EXIT_FAILURE);
}
pagediff_sl = curiopos - offset;
suflinkptr = mmap(0, nmemb*sizeof(Uint) + pagediff_sl, PROT_READ, MAP_SHARED, fd, offset);
if (suflinkptr == MAP_FAILED) {
perror("mmap");
exit(EXIT_FAILURE);
}
#elif SUFLINK_DISKACC
sl_diskacc = 1;
off_sl = ftell(fp);
fd = open(idxfilename, O_RDONLY);
#else
suflink = ALLOCMEMORY(space, NULL, Uint, nmemb);
fread(suflink, sizeof(Uint), nmemb, fp);
#endif
#ifdef SUFLINK_MMAP
offset = (curiopos+(nmemb*sizeof(Uint))) & ~(sysconf(_SC_PAGE_SIZE) - 1);
if (curiopos >= sb.st_size) {
fprintf(stderr, "offset is past end of file\n");
exit(EXIT_FAILURE);
}
pagediff_id = (curiopos+(nmemb*sizeof(Uint))) - offset;
id = mmap(0, nmemb*sizeof(signed char) + pagediff_id, PROT_READ, MAP_SHARED, fd, offset);
if (id == MAP_FAILED) {
perror("mmap");
exit(EXIT_FAILURE);
}
fseek(fp, nmemb*(sizeof(Uint)+sizeof(signed char)), SEEK_CUR);
#elif SUFLINK_DISKACC
off_id = off_sl+(nmemb*sizeof(Uint));
fseek(fp, nmemb*(sizeof(Uint)+sizeof(signed char)), SEEK_CUR);
#else
id = ALLOCMEMORY(space, NULL, signed char, nmemb);
fread(id, sizeof(signed char), nmemb, fp);
#endif
fread(&idvmemb, sizeof(Uint), 1, fp);
idvtab = ALLOCMEMORY(space, NULL, PairLSint, idvmemb);
if ((flags & LINT_SUFLINKS)) {
if(!silent) MSG("reading lsint id.\n");
fread(idvtab, sizeof(PairLSint), idvmemb, fp);
} else {
idvutab = ALLOCMEMORY(space, NULL, PairSint, idvmemb);
if(!silent) MSG("reading uint id.\n");
fread(idvutab, sizeof(PairUint), idvmemb, fp);
for(idvi=0; idvi < idvmemb; idvi++) {
idvtab[idvi].a = idvutab[idvi].a;
idvtab[idvi].b = idvutab[idvi].b;
}
free(idvutab);
}
}
if ((flags & MD5_STORED)) {
mdfive = ALLOCMEMORY(space, NULL, unsigned char, 16);
fread(mdfive, sizeof(unsigned char), 16, fp);
}
void
matchkdseed( void *space,
Suffixarray *s,
fasta_t *reads,
Uint minsize,
char *outfile,
Uint *counter,
unsigned char silent,
Uint s_ext,
Uint p_mis,
Uint Xoff,
Uint k_p,
Uint rep_type,
Uint hitstrategy,
Uint bedist,
unsigned char showalignment,
double maxevalue,
int acc,
Uint M,
unsigned char matchingstat,
FILE *dev,
FILE *nomatchdev) {
double H,
K,
lambda;
char *buffer,
*curseq;
Uint k,
curlen,
dim,
wordno;
bitvector *D,
*Mv;
Gmap map;
gread_t read;
gmatch_t *mmatches=NULL,
*pmatches=NULL;
matchstem_t *V;
int plusdiff, minusdiff, noofmatches=0;
pthread_mutex_t *mtx=NULL;
pthread_mutex_t *mtx2=NULL;
Uint *enctab, i,j, nmmatch, npmatch;
int bmscr, bpscr;
unsigned char uninformative = 0,
beststrand = 0,
best = 0;
if (hitstrategy == 2) {
beststrand = 1;
best = 1;
} else if (hitstrategy == 1) {
beststrand = 1;
}
/*build alignment matrix*/
enctab = encodetab(s->seq->map, s->seq->mapsize);
dim = reads->maxlen + 2*((reads->maxlen-ceil((acc*reads->maxlen)/100))+4);
wordno = reads->maxlen/BITVECTOR_WORDSIZE;
// wordno += ((reads->maxlen & (BITVECTOR_WORDSIZE-1)) > 0) ? 1 : 0;
wordno++;
D = ALLOCMEMORY(space, NULL, bitvector, 2*(dim+1));
Mv = &D[dim+1];
for(i=0; i <= dim; i++) {
D[i] = initbitvector(space, wordno*BITVECTOR_WORDSIZE);
Mv[i] = initbitvector(space, wordno*BITVECTOR_WORDSIZE);
}
if (counter == NULL) {
initProgressBarVT();
} else {
mtx = &mutex1;
mtx2 = &mutex2;
}
karlinunitcostpp(space, &lambda, &H, &K);
for (k=0; k < reads->noofseqs; k++) {
plusdiff = 0;
minusdiff = 0;
noofmatches = 0;
if (!silent) {
if (counter == NULL) {
progressBarVT("reads matched.", reads->noofseqs, k, 25);
} else {
(*counter)++;
}
}
curseq = reads->seqs[k]->sequence;
curlen = reads->seqs[k]->length;
npmatch = 0;
nmmatch = 0;
if(curlen >= minsize) {
initGmap(&map, s->seq, 1);
initRead(&read, reads->seqs[k]);
bpscr = 0;
bmscr = 0;
V=kdseeds(space, s, curseq, curlen, s_ext, p_mis, Xoff, k_p);
#ifdef KDUNINFORMATIVE
if(V[0].branches[0].r > V[0].branches[0].l && V[0].branches[0].r-V[0].branches[0].l > M) {
uninformative = 1;
plusdiff = V[0].branches[0].r - V[0].branches[0].l;
} else
#endif
if(!matchingstat) {
uninformative = 0;
pmatches = alignkdmatches(space, s, V, reads->seqs[k], curseq, curlen, M, enctab, beststrand,
bedist, lambda, H, K, maxevalue, acc, D, dim, &npmatch, &bpscr);
if(npmatch > 0) {
setMatches(&read, pmatches, npmatch, PLUSSTRAND);
}
} else {
printf("#%d %s\n",curlen, reads->seqs[k]->description);
dumpkdseeds(s, V, curlen, '+', M);
}
for(j=0; j < curlen; j++) {
if (V[j].noofbranches > 0) {
FREEMEMORY(space, V[j].branches);
}
}
FREEMEMORY(space, V);
/*search the complement*/
buffer = charDNAcomplement(space, curseq, curlen);
V=kdseeds(space, s, buffer, curlen, s_ext, p_mis, Xoff, k_p);
#ifdef KDUNINFORMATIVE
if(uninformative && V[0].branches[0].r > V[0].branches[0].l && V[0].branches[0].r-V[0].branches[0].l > M) {
minusdiff = V[0].branches[0].r - V[0].branches[0].l;
uninformative = 1;
} else
#endif
if(!matchingstat) {
uninformative = 0;
mmatches = alignkdmatches(space, s, V, reads->seqs[k], buffer, curlen, M, enctab, beststrand,
bedist, lambda, H, K, maxevalue, acc, D, dim, &nmmatch, &bmscr);
if(nmmatch > 0) {
setMatches(&read, mmatches, nmmatch, MINUSSTRAND);
}
if (best) {
bpscr = MIN(bmscr, bpscr);
bmscr = bpscr;
} else if (!beststrand) {
bpscr = bmscr = curlen-ceil((acc*curlen)/100);
}
setReads(&map, &read, 1);
reportMatch(dev, &map, rep_type, showalignment, mtx, bpscr, bmscr);
FREEMEMORY(space, pmatches);
FREEMEMORY(space, mmatches);
pmatches = NULL;
mmatches = NULL;
} else {
dumpkdseeds(s, V, curlen, '-', M);
}
for(j=0; j < curlen; j++) {
if (V[j].noofbranches > 0) {
FREEMEMORY(space, V[j].branches);
}
}
FREEMEMORY(space, V);
FREEMEMORY(space, buffer);
}
if(nomatchdev && nmmatch == 0 && npmatch == 0) {
if (mtx2 != NULL) pthread_mutex_lock(mtx2);
fprintf(nomatchdev, "%s\n%s\n", reads->seqs[k]->description, reads->seqs[k]->sequence);
fflush(nomatchdev);
if (mtx2 != NULL) pthread_mutex_unlock(mtx2);
}
}
wrapBitmatrix(space, D, 2*(dim+1));
FREEMEMORY(space, D);
FREEMEMORY(space, enctab);
return;
}
gmatch_t*
alignkdmatches(void *space,
Suffixarray *s,
matchstem_t *M,
CharSequence *query,
char *curseq,
Uint m,
Uint t,
Uint *enctab,
unsigned char bestonly,
Uint bedist,
double lambda,
double H,
double K,
double maxevalue,
int acc,
bitvector* D,
Uint dim,
Uint* nmatch,
int* bscr) {
Uint k,j,l,r,q,noofmatches=0, mat, mis, ins, del;
Lint pos, margin, schr, echr, sstart, slen, i ;
char *sseq;
unsigned int idx;
Alignment *al=NULL;
bitvector *peq;
PairSint result;
#ifdef ALIGNDBG
PairSint result2;
CharSequence *checkseq;
#endif
double E;
int scr;
int maxedist = 0;
int bestscr = 0;
gmatch_t *matches=NULL;
margin = bestscr = maxedist = m-ceil((acc*m)/100);
peq = getpeq(NULL, curseq, m, s->seq->map, s->seq->mapsize, enctab);
for(i=0; i < m; i++) {
for(q=0; q < M[i].noofbranches; q++) {
l = M[i].branches[q].l; r = M[i].branches[q].r;
scr = M[i].branches[q].mat - (M[i].branches[q].mis+M[i].branches[q].ins+M[i].branches[q].del);
E = evalue(lambda, K, spacemult(m, s->numofsuffixes, H, K), scr);
if(l <= r && E <= maxevalue && (r-l) <= t) {
for(j=l; j <= r; j++) {
pos = s->suftab[j];
/*skip marginal matches*/
for(k=0; k < noofmatches; k++)
if (abs((signed int)matches[k].p-(pos-(i+margin))) <= margin) break;
if (k == noofmatches) {
idx = getMultiCharSeqIndex(s->seq, &s->seq->sequences[pos]);
schr = (idx > 0) ? s->seq->markpos[idx-1]+1 : 0;
echr = s->seq->markpos[idx];
assert(echr >= pos);
sstart = MAX(schr, pos-(i+margin));
slen = (echr > sstart+m+2*(margin+1)) ? m+2*(margin+1) : (echr-sstart)+1;
sseq = &s->seq->sequences[sstart];
/*
if(echr == pos) {
fprintf(stderr, "\n\n sstart:%lld, slen:%lld, ssend:%lld, echr:%lld\n\n",
sstart, slen, sstart+slen-1, echr);
}
*/
myersbitmatrix(NULL, curseq, m, sseq, slen, s->seq->map,
s->seq->mapsize, enctab, m-bestscr, peq, &result, D, slen);
#ifdef ALIGNDBG
result2 = myersbitvector(NULL, curseq, m, sseq, slen,
s->seq->map, s->seq->mapsize, enctab, m-bestscr, peq);
assert(result.a == result2.a && result.b == result2.b);
#endif
if (result.a != -1 && result.b <= maxedist
&& result.b <= bestscr && result.a < slen) {
al = ALLOCMEMORY(space, NULL, Alignment, 1);
initAlignment(al, curseq, m, 0, sseq, slen, 0);
bitvectorbacktrack(al, D, slen, m, result.a);
#ifdef ALIGNDBG
assert(getEdist(al) == result.b);
checkseq = (CharSequence*) s->seq->ref[idx].ref;
assert(strncmp(& checkseq->sequence[pos-schr],
&s->seq->sequences[pos], slen) == 0);
#endif
countEops(al, &mat, &mis, &del, &ins);
/*skip identical matches*/
for(k=0; k < noofmatches; k++) {
if (matches[k].p == sstart+al->voff) break;
}
if (k == noofmatches) {
matches=realloc(matches, sizeof(gmatch_t)*(noofmatches+1));
matches[noofmatches].p = sstart+al->voff;
matches[noofmatches].q = sstart+result.a-1;
matches[noofmatches].edist = result.b;
matches[noofmatches].i = i;
matches[noofmatches].j = i+M[i].branches[q].mat+
M[i].branches[q].mis+M[i].branches[q].ins-1;
matches[noofmatches].scr = scr;
matches[noofmatches].evalue = E;
matches[noofmatches].mat = mat;
matches[noofmatches].mis = mis;
matches[noofmatches].ins = ins;
matches[noofmatches].del = del;
matches[noofmatches].subject = idx;
matches[noofmatches].checklen = matches[noofmatches].j;
matches[noofmatches].al = al;
noofmatches++;
if(bestonly) {
bestscr = MIN(maxedist, (result.b+bedist));
}
} else {
wrapAlignment(al);
FREEMEMORY(space, al);
}
}
}
}
}
}
}
for(i=0; i < s->seq->mapsize; i++) {
FREEMEMORY(space, peq[i]);
}
FREEMEMORY(space, peq);
(*bscr) = bestscr;
(*nmatch) = noofmatches;
return matches;
}
int
main (int argc, char** argv)
{
Sint optindex, c;
unsigned char depictsw=0;
unsigned char wurst=1;
unsigned char gnuplot=0;
Uint i, j, noofseqs=0, nooffreqs=0, noofqueries=0;
Uint noofhits=100;
Uint substrlen = 10;
Uint minseeds = 5;
Uint maxmatches = 10000;
char *seq, *vec, *bin;
imbissinfo *imbiss;
void *space = NULL;
double *scores = NULL;
int swscores[2]={3,-2};
char *pveclistfile=NULL;
char *alphabetfile=NULL;
char *inputfile=NULL;
char *batchfile = NULL;
char *subfile=NULL;
char *reportfile = NULL;
int (*handler)
(void *, Matchtype *, IntSequence **, Uint,
Uint, void *) = allscores;
double (*filter)
(void *, Matchtype *, IntSequence *, IntSequence *,
Uint *, Uint, Uint, void *) = swconstfilter;
Matchtype* (*select)
(void *, Matchtype *, Uint k,
IntSequence *, IntSequence **, void *) = selectSW;
stringset_t **fn, **freq, *queryurl, **queries=NULL;
Suffixarray *arr = NULL;
IntSequence **sequences = NULL;
IntSequence *input = NULL;
FAlphabet *alphabet = NULL;
PairSint *matches=NULL;
Uint percent=0;
time_t startsuf, endsuf;
double difsuf, difmatch, difrank;
#ifdef MEMMAN_H
Spacetable spacetab;
initmemoryblocks(&spacetab, 100000);
space = &spacetab;
#endif
while(1)
{
c=getopt_long(argc, argv, "SAghFGBLM:D:r:m:x:n:p:b:s:a:q:l:c:dvw",
long_options, &optindex);
if (c==-1) break;
switch(c) {
case 'r':
reportfile=optarg;
break;
case 'v':
verbose_flag=1;
break;
case 'd':
depictsw = 1;
break;
case 's':
pveclistfile = optarg;
break;
case 'a':
alphabetfile = optarg;
break;
case 'q':
inputfile = optarg;
noofqueries = 1;
break;
case 'l':
substrlen = atoi(optarg);
break;
case 'c':
minseeds = atoi(optarg);
break;
case 'b':
batchfile = optarg;
break;
case 'p':
percent = atoi(optarg);
break;
case 'x':
subfile = optarg;
break;
case 'n':
noofhits = atoi(optarg);
break;
case 'w':
wurst = 0;
break;
case 'B':
filter = scorefilter;
select = selectBlastScore;
break;
case 'S':
filter = scorefilter;
select = selectScore;
break;
case 'A':
filter = swconstfilter;
select = selectSW;
break;
case 'F':
filter = scorefilter;
select = selectScoreSWconst;
break;
case 'G':
filter = scorefilter;
select = selectBlastScoreSWconst;
break;
case 'M':
swscores[0]=atoi(optarg);
break;
case 'L':
handler = latexscores;
break;
case 'D':
swscores[1]=atoi(optarg);
break;
case 'g':
gnuplot = 1;
break;
case 'm':
maxmatches=atoi(optarg);
break;
case 'h':
default:
usage(argv[0]);
exit (EXIT_FAILURE);
}
}
if (pveclistfile==NULL || (inputfile == NULL && batchfile==NULL)
|| alphabetfile == NULL) {
usage(argv[0]);
exit (EXIT_FAILURE);
}
imbiss = ALLOCMEMORY(space, NULL, imbissinfo, 1);
imbiss->reportfile = reportfile;
imbiss->swscores = swscores;
imbiss->noofhits = noofhits;
imbiss->minseeds = minseeds;
imbiss->wurst = wurst;
/*read batch file*/
if (batchfile) {
queries = readcsv(space, batchfile, "", &noofqueries);
}
/*read substitution matrix*/
if (subfile) {
freq=readcsv(space, subfile,",", &nooffreqs);
scores = ALLOCMEMORY(space, NULL, double, ((nooffreqs-1)*(nooffreqs-1)) );
for(i=1; i < nooffreqs; i++) {
for(j=1; j < nooffreqs; j++) {
if(strcmp(SETSTR(freq[i],j),"inf")==0){
MATRIX2D(scores, nooffreqs-1, i, j)=0;
}else{
MATRIX2D(scores, nooffreqs-1, i, j)=atof(SETSTR(freq[i],j));
}
}
}
}
/*read alphabet*/
if (alphabetfile != NULL) {
alphabet = loadCSValphabet(space, alphabetfile);
sortMapdomain(space, alphabet);
}
/*load sequence database*/
fn=readcsv(space, pveclistfile, "", &noofseqs);
sequences = ALLOCMEMORY(space, NULL, IntSequence *, noofseqs);
for(i=0; i < noofseqs; i++)
{
sequences[i] = loadSequence(space, SETSTR(fn[i],0));
}
for (i=0; i < noofseqs; i++) {
destructStringset(space, fn[i]);
}
FREEMEMORY(space, fn);
/*construct the suffix array*/
time (&startsuf);
arr = constructSufArr(space, sequences, noofseqs, NULL);
constructLcp(space, arr);
time (&endsuf);
difsuf = difftime (endsuf, startsuf);
/*do search*/
for (i=0; i < noofqueries; i++) {
/*get query form batchfile*/
if (queries) {
inputfile = SETSTR(queries[i],0);
}
/*typically only used with batchfile*/
if (percent != 0) {
substrlen =
((double)((double)input->length/100)*(double) percent);
}
input = loadSequence(space, inputfile);
//seq = printSequence (space, input, 60);
printf(">IMBISS order delivered\n");
//printf("%s\n",seq);
printf("%s\n", input->url);
//FREEMEMORY(space, seq);
time (&startsuf);
matches=sufSubstring(space, arr, input->sequence, input->length, substrlen);
time (&endsuf);
difmatch = difftime (endsuf, startsuf);
/*get prob vector url for salami/wurst*/
//printf("%.*s\n", 5, input->url + 58);
vec = malloc(sizeof(char)*66);
sprintf(vec, "/smallfiles/public/no_backup/bm/pdb_all_vec_6mer_struct/%5s.vec\0", input->url+56);
bin = malloc(sizeof(char)*54);
sprintf(bin, "/smallfiles/public/no_backup/bm/pdb_all_bin/%5s.bin\0", input->url+56);
queryurl = initStringset(space);
addString(space, queryurl, bin, strlen(bin));
addString(space, queryurl, vec, strlen(vec));
getimbissblast(space, input, sequences, noofseqs, alphabet, imbiss);
imbiss->query = queryurl;
imbiss->substrlen = substrlen;
imbiss->alphabet = alphabet;
/*if a substition file was given ...*/
if (subfile) {
imbiss->sub = createsubmatrix(scores, imbiss->score, nooffreqs-1);
}
/*match 'n' report*/
time (&startsuf);
imbiss->consensus = ALLOCMEMORY(space, NULL, Uint, (input->length-substrlen));
memset(imbiss->consensus, 0, (sizeof(Uint)*(input->length-substrlen)));
rankSufmatch(space, arr, matches, input->length-substrlen,
maxmatches, substrlen,
sequences, noofseqs, filter, select, handler,
input, imbiss, scores, depictsw);
if (gnuplot) {
consensus (space, imbiss->consensus, input->length-substrlen,
input, substrlen, imbiss);
}
time (&endsuf);
difrank = difftime (endsuf, startsuf);
printf ("Building the suffixtree has taken %f seconds.\n", difsuf);
printf ("Match the suffixtree has taken %f seconds.\n", difmatch);
printf ("Rank the suffixtree has taken %f seconds.\n", difrank);
/*partial cleanup*/
//destructStringset(space, queryurl);
destructSequence(space, input);
if(subfile) {
FREEMEMORY(space, imbiss->sub);
}
FREEMEMORY(space, imbiss->consensus);
FREEMEMORY(space, imbiss->score);
FREEMEMORY(space, matches);
free(bin);
free(vec);
}
/*final cleanup*/
for (i=0; i < noofseqs; i++) {
destructSequence(space, sequences[i]);
}
FREEMEMORY(space, sequences);
destructSufArr(space, arr);
#ifdef MEMMAN_H
activeblocks(space);
#endif
printf("Goodbye.\n");
return EXIT_SUCCESS;
}
Uint *
quickSortMultikey (void *space, void* toSort, Uint size,
Uint (*cmp)(Uint, Uint, Uint, void *, void*),
Uint sentinel, void *info)
{
Sint a, b, c, d, v, n, r;
TripleSint ins;
Uint *sorted = NULL, offset;
Uint depth = 0;
VStack vstack;
if (size == 0) return NULL;
sorted = ALLOCMEMORY(space, NULL, Uint, size);
if (size<=1) {
sorted[0]=0;
}
for (r=0; r < size; r++) sorted[r]=r;
bl_vstackInit(&vstack, 100, sizeof(TripleSint));
n = size;
offset=0;
while (1) {
a = rand() % n;
SWAPUINT(sorted, offset, a+offset);
v = sorted[offset];
a = b = 1;
c = d = n-1;
for(;;) {
while(b<=c&&((r=cmp(sorted[b+offset],v,depth,toSort,info))==2||r==0))
{
if (r==0) {
SWAPUINT(sorted, a+offset, b+offset);
a++;
}
b++;
}
while(b<=c&&((r=cmp(sorted[c+offset],v,depth,toSort,info))==1||r==0))
{
if (r==0) {
SWAPUINT(sorted, c+offset, d+offset);
d--;
}
c--;
}
if (b > c) break;
SWAPUINT(sorted, b+offset, c+offset);
b++;
c--;
}
r = MIN(a, (b-a));
vecswap(offset, (b-r)+offset, r, sorted);
r = MIN((d-c), (n-d-1));
vecswap(b+offset, (n-r)+offset, r, sorted);
/*sort lesser*/
r = b-a;
if (r > 1) {
ins.a = offset;
ins.b = r;
ins.c = depth;
bl_vstackPush(&vstack, &ins);
}
/*sort equal*/
if ((a+n-d-1) > 1 && cmp(sorted[r+offset], sentinel, depth, toSort, info) != 0)
/*if (r > 1 && sorted[r+offset]!=sentinel)*/
{
ins.a = r+offset;
ins.b = (a+n-d-1);
ins.c = depth+1;
bl_vstackPush(&vstack, &ins);
}
/*sort greater*/
r=d-c;
if (r > 1) {
ins.a = (n-r)+offset;
ins.b = r;
ins.c = depth;
bl_vstackPush(&vstack, &ins);
}
if (!bl_vstackIsEmpty(&vstack)){
ins = *((TripleSint *) bl_vstackPop(&vstack, NULL));
offset = ins.a;
r = ins.b;
depth = ins.c;
} else {
break;
}
}
bl_vstackDestruct(&vstack, NULL);
return sorted;
}
Uint *
quickSortMultikey (void *space, void* toSort, Uint size,
Uint (*cmp)(Uint, Uint, Uint, void *, void*),
Uint sentinel, void *info)
{
Sint a, b, c, d, v, n, r;
Uint *sorted = NULL, offset;
Uint depth = 0;
Stack stack;
if (size == 0) return NULL;
sorted = ALLOCMEMORY(space, NULL, Uint, size);
if (size<=1) {
sorted[0]=0;
}
for (r=0; r < size; r++) sorted[r]=r;
initStack(space, &stack, 100);
n = size;
offset=0;
while (1) {
a = rand() % n;
SWAPUINT(sorted, offset, a+offset);
v = sorted[offset];
a = b = 1;
c = d = n-1;
for(;;) {
while(b<=c&&((r=cmp(sorted[b+offset],v,depth,toSort,info))==2||r==0))
{
if (r==0) {
SWAPUINT(sorted, a+offset, b+offset);
a++;
}
b++;
}
while(b<=c&&((r=cmp(sorted[c+offset],v,depth,toSort,info))==1||r==0))
{
if (r==0) {
SWAPUINT(sorted, c+offset, d+offset);
d--;
}
c--;
}
if (b > c) break;
SWAPUINT(sorted, b+offset, c+offset);
b++;
c--;
}
r = MIN(a, (b-a));
vecswap(offset, (b-r)+offset, r, sorted);
r = MIN((d-c), (n-d-1));
vecswap(b+offset, (n-r)+offset, r, sorted);
/*sort lesser*/
r = b-a;
if (r > 1) {
stackpush(space, &stack, offset);
stackpush(space, &stack, r);
stackpush(space, &stack, depth);
}
/*sort equal*/
if ((a+n-d-1) > 1 && cmp(sorted[r+offset], sentinel, depth, toSort, info) != 0)
/*if (r > 1 && sorted[r+offset]!=sentinel)*/
{
stackpush(space, &stack, r+offset);
stackpush(space, &stack, (a+n-d-1));
stackpush(space, &stack, depth+1);
}
/*sort greater*/
r=d-c;
if (r > 1) {
stackpush(space, &stack, (n-r)+offset);
stackpush(space, &stack, r);
stackpush(space, &stack, depth);
}
if (!stackisempty(&stack)) {
depth = stackpop(&stack);
n = stackpop(&stack);
offset = stackpop(&stack);
} else {
break;
}
}
destructStack(space, &stack);
return sorted;
}
void
constructsuflinks(void *space, Suffixarray *s) {
Uint i,
j,
a,
b,
k,
nooflists,
lcp,
pos;
Stack istack;
Stack jstack;
List *children,
**lists;
PairUint **data,
slinkinterval;
nooflists = maxlcp(s) +1;
lists = ALLOCMEMORY(space, NULL, List*, nooflists);
memset(lists, 0, sizeof(List*)*nooflists);
initStack(space, &istack, 1000);
initStack(space, &jstack, 1000);
stackpush(space, &istack, 0);
stackpush(space, &jstack, s->numofsuffixes-1);
while(!stackisempty(&istack)) {
i = stackpop(&istack);
j = stackpop(&jstack);
lcp = getlcpval(s, i, j);
/*printf("adding list %d\n", lcp);*/
if (lists[lcp] == NULL) {
lists[lcp] = initList(space, 10);
}
addinterval(space, lists[lcp], i, j);
/*printf("lcp: %d-[%d,%d]\n", lcp, i, j);*/
children = getChildintervals(space, s, i, j);
data = (PairUint**) dataList(space, children);
for(k=children->length; k > 0; k--) {
a = data[k-1]->a;
b = data[k-1]->b;
FREEMEMORY(space, data[k-1]);
if(a != b) {
stackpush(space, &istack, a);
stackpush(space, &jstack, b);
}
}
FREEMEMORY(space, data);
wrapList(space, children, NULL);
}
destructStack(space, &istack);
destructStack(space, &jstack);
s->suflink_l = ALLOCMEMORY(space, NULL, Uint, s->numofsuffixes);
s->suflink_r = ALLOCMEMORY(space, NULL, Uint, s->numofsuffixes);
memset(s->suflink_l, 0, sizeof(Uint)*s->numofsuffixes);
memset(s->suflink_r, 0, sizeof(Uint)*s->numofsuffixes);
for(i=1; i < nooflists; i++) {
if(lists[i] != NULL && lists[i-1] !=NULL) {
for(j=0; j < lists[i]->length; j++) {
/*printf("looking at interval [%d,%d], list %d\n", ((PairUint*)lists[i]->nodes[j].data)->a, ((PairUint*)lists[i]->nodes[j].data)->b, i);*/
slinkinterval = findslinkinterval(space, s, lists, i, j);
pos = getfirstlindex(s, ((PairUint*)lists[i]->nodes[j].data)->a, ((PairUint*)lists[i]->nodes[j].data)->b);
/*printf("store at %d: [%d,%d]\n", pos, slinkinterval.a, slinkinterval.b);*/
s->suflink_l[pos]=slinkinterval.a;
s->suflink_r[pos]=slinkinterval.b;
}
}
wrapList(space, lists[i-1], destructinterval);
}
FREEMEMORY(space, lists);
return;
}