int z_pull_twos(z *n, int *j, z *p)
{
//n is overwritten
int c = 0;
z t1, t2;
fp_digit r;
zInit(&t1);
zInit(&t2);
while (!(n->val[0] & 1))
{
zShiftRight(n,n,1);
c = 1 - c;
}
zExp(2,p,&t2);
zSub(&t2,&zOne,&t1);
r = zShortDiv(&t1,16,&t2);
if ((c * r) == 8)
*j *= -1;
zFree(&t1);
zFree(&t2);
return c;
}
void zFreeGTFfeature (zGTFfeature *f) {
zFree(f->seqname);
zFree(f->source);
zFree(f->gene_id);
zFree(f->transcript_id);
zClearGTFfeature(f);
}
void zFreeBNTreeModel (zBNTreeModel *model) {
int i;
for (i = 0; i < model->submodels; i++) zFreeBNTreeModel(&model->submodel[i]);
if (model->submodel != NULL) zFree(model->submodel);
zFree(model->name);
/* free_bntree(model->bntree); Need to write this! */
}
void monty_init(z *n)
{
//for a input modulus n, initialize constants for
//montogomery representation
//this assumes that n is relatively prime to 2, i.e. is odd.
z g, b, q, r;
//global montyconst structure
zInit(&montyconst.nhat);
zInit(&montyconst.r);
zInit(&montyconst.rhat);
zInit(&montyconst.one);
if (abs(n->size) <= 16)
{
fp_montgomery_setup(n,&montyconst.nhat.val[0]);
fp_montgomery_calc_normalization(&montyconst.r,n);
montyconst.one.val[0] = 1;
montyconst.one.size = 1;
to_monty(&montyconst.one,n);
TFM_MONTY = 1;
return;
}
else
TFM_MONTY = 0;
zInit(&g);
zInit(&b);
zInit(&q);
zInit(&r);
b.val[1]=1; b.size=2;
//find r = b^t > N, where b = 2 ^32
if (montyconst.r.alloc < n->size + 1)
zGrow(&montyconst.r,n->size + 1);
zClear(&montyconst.r);
montyconst.r.size = n->size + 1;
montyconst.r.val[montyconst.r.size - 1] = 1;
//find nhat = -n^-1 mod b
//nhat = -(n^-1 mod b) mod b = b - n^-1 mod b
//since b is 2^32, this can be simplified, and made faster.
xGCD(n,&b,&montyconst.nhat,&montyconst.rhat,&g);
zSub(&b,&montyconst.nhat,&q);
zCopy(&q,&montyconst.nhat);
zCopy(&zOne,&montyconst.one);
to_monty(&montyconst.one,n);
zFree(&g);
zFree(&b);
zFree(&q);
zFree(&r);
return;
}
void monty_free(void)
{
zFree(&montyconst.nhat);
zFree(&montyconst.r);
zFree(&montyconst.rhat);
zFree(&montyconst.one);
return;
}
int main(int argc, char** argv) {
zHMM hmm;
char* seqname;
char* hmm_file;
char* zoe_file;
FILE* zoe_stream;
bool est_para_mode_bool = false;
zSFVec *sfv;
zGTFVec *gtfvec;
zSetProgramName(argv[0]);
zParseOptions(&argc, argv);
seqname = zOption("s");
if (argc != 3)
zDie(usage);
if (NULL == seqname)
zDie("must specify a sequence name (use -s=)\n%s", usage);
hmm_file = argv[1];
zoe_file = argv[2];
if(zOption("-pe")) {
est_para_mode_bool = true;
}
openHMM(&hmm, hmm_file, est_para_mode_bool);
if ((zoe_stream = fopen(zoe_file, "r")) == NULL) {
zDie("Couldn't open zoe file %s", zoe_stream);
}
sfv = zReadSFVec(zoe_stream);
fclose(zoe_stream);
if (sfv->size == 0) zWarn("Did not read any features");
gtfvec = zMalloc(sizeof(zGTFVec), "GTFVec");
zInitGTFVec(gtfvec, sfv->size);
zSFVec2GTFVec(&hmm, sfv, gtfvec, seqname, 0);
zSortGTFVec(gtfvec);
zWriteGTFVec(stdout, gtfvec);
zFreeGTFVec(gtfvec);
zFree(gtfvec);
zFreeSFVec(sfv);
zFree(sfv);
zFreeHMM(&hmm);
return 0;
}
void zHex2Dec(z *u, z *v)
{
//convert u[] in hex to v[] in decimal by repeatedly dividing
//u by 1e9 = 0x3b9aca00
//the remainder of the ith division is the ith decimal digit.
//when the quotient = 0, stop
z a,b;
fp_digit r = 0;
int su = abs(u->size);
int approx_words = (int)((double)su * 1.5);
//because decimal takes more room than hex to store
zInit(&a);
zInit(&b);
if (v->alloc < approx_words)
zGrow(v,approx_words);
zClear(v);
if (a.alloc < approx_words)
{
zGrow(&a,approx_words);
zClear(&a);
}
if (b.alloc < approx_words)
{
zGrow(&b,approx_words);
zClear(&b);
}
zCopy(u,&a);
v->size = 1;
do
{
r = zShortDiv(&a,MAX_DEC_WORD,&b);
v->val[v->size - 1] = r;
v->size++;
zCopy(&b,&a);
} while (zCompare(&a,&zZero) != 0);
v->size--;
if (u->size < 0)
v->size *= -1;
zFree(&a);
zFree(&b);
return;
}
void zMemoryGroup_freeHostMemory(zMemoryGroup_t mem) {
if (mem && zMemoryGroup_hostMemoryAllocatedQ(mem) &&
zMemoryGroup_getHostMemory(mem) != NULL) {
zFree(zMemoryGroup_getHostMemory(mem));
zMemoryGroup_setHostMemoryStatus(mem, zMemoryStatus_unallocated);
}
}
void to_monty(z *x, z *n)
{
//given a number x in normal (hexadecimal) representation,
//find its montgomery representation
//this uses some precomputed monty constants
//xhat = (x * r) mod n
z t1,t2;
zInit(&t1);
zInit(&t2);
zMul(x,&montyconst.r,&t1);
zDiv(&t1,n,&t2,x);
zFree(&t1);
zFree(&t2);
return;
}
void zmModExp(z *a, z *b, z *u, z *nn)
{
//computes a^b mod m = u using the right to left binary method
//see, for instance, the handbook of applied cryptography
//uses monty arith
//a is already in monty rep, b doesn't need to be.
z n,bb,aa,t;
zInit(&aa);
zInit(&bb);
zInit(&n);
zInit(&t);
//overflow possibilities:
//t ranges to 2x input 'a'
//u needs at least as much space as modulus
zCopy(&montyconst.one,&n);
zCopy(a,&aa);
zCopy(b,&bb);
while (!isZero(&bb))
{
if (bb.val[0] & 0x1)
{
monty_mul(&n,&aa,&t,nn);
zCopy(&t,&n);
}
zShiftRight(&bb,&bb,1); //compute successive squares of a
monty_sqr(&aa,&t,nn);
zCopy(&t,&aa);
if (aa.size < 0)
aa.size *= -1;
}
zCopy(&n,u);
zFree(&aa);
zFree(&bb);
zFree(&n);
zFree(&t);
return;
}
void zFreeGTFVec (zGTFVec *vec) {
int i;
for (i = 0; i < vec->size; ++i) {
zFreeGTFfeature(&vec->elem[i]);
}
zFree(vec->elem);
vec->elem = NULL;
vec->size = 0;
vec->limit = 0;
vec->last = NULL;
}
void swap(z *a, z *b)
{
//do I actually have to physically copy here, or can I just swap pointers?
z tmp;
zInit(&tmp);
zCopy(a,&tmp);
zCopy(b,a);
zCopy(&tmp,b);
zFree(&tmp);
return;
}
int ndigits(z *n)
{
int i=0;
z nn,tmp;
fp_digit r;
//can get within one digit using zBits and logs, which would
//be tons faster. Any way to 'correct' the +/- 1 error?
zInit(&nn);
zInit(&tmp);
zCopy(n,&tmp);
while (tmp.size > 1)
{
zCopy(&tmp,&nn);
r = zShortDiv(&nn,MAX_DEC_WORD,&tmp);
i += DEC_DIGIT_PER_WORD;
}
i += ndigits_1(tmp.val[0]);
zFree(&nn);
zFree(&tmp);
return i;
}
int isSquare(z *n)
{
//thanks fenderbender @ mersenneforum.org
unsigned long m;
unsigned long largeMod;
z w2,w3;
int ans;
// start with mod 128 rejection. 82% rejection rate
// VERY fast, can read bits directly
m=n->val[0] & 127; // n mod 128
if ((m*0x8bc40d7d) & (m*0xa1e2f5d1) & 0x14020a) return 0;
//Other modulii share one BigInt modulus.
largeMod=zShortMod(n,(63UL*25*11*17*19*23*31)); // SLOW, bigint modulus
// residues mod 63. 75% rejection
m=largeMod%63; // fast, all 32-bit math
if ((m*0x3d491df7) & (m*0xc824a9f9) & 0x10f14008) return 0;
// residues mod 25. 56% rejection
m=largeMod%25;
if ((m*0x1929fc1b) & (m*0x4c9ea3b2) & 0x51001005) return 0;
// residues mod 31. 48.4% rejection
// Bloom filter has a little different form to keep it perfect
m=0xd10d829a*(largeMod%31);
if (m & (m+0x672a5354) & 0x21025115) return 0;
// residues mod 23. 47.8% rejection
m=largeMod%23;
if ((m*0x7bd28629) & (m*0xe7180889) & 0xf8300) return 0;
// residues mod 19. 47.3% rejection
m=largeMod%19;
if ((m*0x1b8bead3) & (m*0x4d75a124) & 0x4280082b) return 0;
// residues mod 17. 47.1% rejection
m=largeMod%17;
if ((m*0x6736f323) & (m*0x9b1d499) & 0xc0000300) return 0;
// residues mod 11. 45.5% rejection
m=largeMod%11;
if ((m*0xabf1a3a7) & (m*0x2612bf93) & 0x45854000) return 0;
// Net nonsquare rejection rate: 99.92%
// We COULD extend to another round, doing another BigInt modulus and
// then followup rejections here, using
// primes of 13 29 37 41 43 53. That'd give 98% further rejection.
// Empirical timing shows this second round would be useful for n>10^100 or so.
// VERY expensive final definitive test
zInit(&w2);
zInit(&w3);
zNroot(n,&w2,2); //w2 = sqrt(w1)
zSqr(&w2,&w3); //w3 = w2^2
ans = zCompare(n,&w3);
zFree(&w2);
zFree(&w3);
return (ans == 0);
}
void fp_mul_comba(z *A, z *B, z *C)
{
int ix, iy, iz, tx, ty, pa, sA, sB;
fp_digit c0, c1, c2, *tmpx, *tmpy;
z *dst;
z loc;
COMBA_START;
COMBA_CLEAR;
/* get size of output and trim */
sA = abs(A->size);
sB = abs(B->size);
pa = sA + sB;
if (A == C || B == C) {
zInit(&loc);
//dst = &atmp1;
dst = &loc;
} else {
dst = C;
}
if (dst->alloc < pa)
zGrow(dst,pa + LIMB_BLKSZ);
zClear(dst);
for (ix = 0; ix < pa; ix++) {
/* get offsets into the two bignums */
ty = MIN(ix, sB-1);
tx = ix - ty;
/* setup temp aliases */
tmpx = A->val + tx;
tmpy = B->val + ty;
/* this is the number of times the loop will iterrate, essentially its
while (tx++ < a->used && ty-- >= 0) { ... }
*/
iy = MIN(sA-tx, ty+1);
/* execute loop */
COMBA_FORWARD;
for (iz = 0; iz < iy; ++iz) {
MULADD(*tmpx++, *tmpy--);
}
/* store term */
COMBA_STORE(dst->val[ix]);
}
COMBA_FINI;
dst->size = pa;
if ((A->size * B->size) < 0)
dst->size *= -1;
fp_clamp(dst);
if (dst != C) {
zCopy(dst, C);
zFree(&loc);
}
}
void zDec2Hex(z *u, z *v)
{
//convert u[] in dec to v[] in hex by multiplying the ith digit by (1e9)*i
//and adding to the previous digits
z a,b,vv;
int i,su = abs(u->size);
zInit(&a);
zInit(&b);
zInit(&vv);
if (v->alloc < su)
zGrow(v,su);
if (a.alloc < su)
{
zGrow(&a,su);
zClear(&a);
}
if (b.alloc < su)
{
zGrow(&b,su);
zClear(&b);
}
if (vv.alloc < su)
{
zGrow(&vv,su);
zClear(&vv);
}
vv.size = su;
//a holds the value of (1e9)*i
a.size = 1;
a.val[0] = 1;
for (i=0;i<su;i++)
{
zShortMul(&a,u->val[i],&b);
zAdd(&vv,&b,&vv);
zShortMul(&a,MAX_DEC_WORD,&a);
}
//v may have unused high order limbs
for (i=su-1;i>=0;i--)
{
if (vv.val[i] != 0)
break;
}
vv.size = i+1;
if (u->size < 0)
vv.size *= -1;
if (vv.size == 0)
vv.size = 1;
zCopy(&vv,v);
zFree(&vv);
zFree(&a);
zFree(&b);
return;
}
char *z2decstr(z *n, str_t *s)
{
//pass in a pointer to a string. if necessary, this routine will
//reallocate space for the string to accomodate its size. If this happens
//the pointer to the string's (likely) new location is automatically
//updated and returned.
z a;
int i,sza;
char *tmp;
//for really long inputs, a significant amount of time is spent here.
//for instance, in computing 10000!, 0.047sec is spent on actually
//computing the factorial, while ~.5 sec is needed for the Hex2Dec conversion
//and ~.8 sec is required to print it to a string.
//maybe try to unroll the loop a bit?
strcpy(s->s,"");
s->nchars = 1;
zInit(&a);
//printf("starting hex 2 dec conversion\n");
zHex2Dec(n,&a);
sza = abs(a.size);
if (s->alloc < DEC_DIGIT_PER_WORD*sza + 2)
{
s->s = (char *)realloc(s->s,(DEC_DIGIT_PER_WORD*sza + 10)*sizeof(char));
s->alloc = (DEC_DIGIT_PER_WORD*sza + 10);
}
tmp = (char *)malloc(30);
//print negative sign, if necessary
if (n->size < 0)
{
sprintf(s->s,"-");
s->nchars++;
}
//print first word
#if BITS_PER_DIGIT == 32
sprintf(s->s,"%s%u",s->s,(uint32)a.val[sza - 1]);
s->nchars += ndigits_1(a.val[sza-1]) - 1;
//print the rest
for (i=sza - 2; i>=0; i--)
{
//sprintf(s->s,"%s%09u",s->s,a.val[i]);
//s->nchars += 9;
sprintf(tmp,"%09u",(uint32)a.val[i]);
memcpy(s->s + s->nchars, tmp, 9);
s->nchars += 9;
}
#else
sprintf(s->s,"%s%" PRIu64,s->s,a.val[sza - 1]);
s->nchars += ndigits_1(a.val[sza-1]) - 1;
//print the rest
for (i=sza - 2; i>=0; i--)
{
//sprintf(s->s,"%s%09u",s->s,a.val[i]);
//s->nchars += 9;
sprintf(tmp,"%019" PRIu64,a.val[i]);
memcpy(s->s + s->nchars, tmp, 19);
s->nchars += 19;
}
#endif
s->s[s->nchars] = '\0';
s->nchars++;
zFree(&a);
free(tmp);
return s->s;
}
void monty_mul_interleaved(z *a, z *b, z *c, z *n)
{
fp_digit nhat = montyconst.nhat.val[0], u;
int i,j,t=n->size;
int szb = abs(b->size);
fp_digit k;
z *t1,*t2;
z s1,s2;
zInit(&s1);
zInit(&s2);
t1 = &s1;
t2 = &s2;
zClear(t1);
zClear(t2);
for (i=0;i<t;i++)
{
u = (t1->val[0] + a->val[i] * b->val[0]) * nhat; //truncation will provide mod b
/****** short mul of b with ai, simultaneous with addition of A (in t1) ********/
for (j=t1->size;j<szb;j++)
t1->val[j] = 0; //zero any unused words up to size of b, so we can add
//mul and add up to size of b
k=0;
for (j=0;j<szb ;j++)
spMulAdd(b->val[j],a->val[i],t1->val[j],k,t2->val + j,&k);
//continue with add if A has more words
for (;j<t1->size;j++)
spAdd(t1->val[j],k,t2->val+j,&k);
//adjust size
if (t1->size > szb)
t2->size = t1->size;
else
t2->size = szb;
//account for carry
if (k)
{
t2->val[t2->size]=k;
t2->size++;
j++;
}
/****** short mul of b with ai, simultaneous with addition of A (in t1) ********/
/****** short mul of n with u, simultaneous with add. of prev step (in t2)
and with right shift of one word ********/
for (;j<t;j++)
t2->val[j] = 0; //zero any unused words up to size of n, so we can add
//mul and add up to size of n, store into one word previous
k=0;
//needs first mul to get k set right, answer gets shifted to oblivion
spMulAdd(n->val[0],u,t2->val[0],k,t1->val,&k);
for (j=1;j<t;j++)
spMulAdd(n->val[j],u,t2->val[j],k,t1->val + j - 1,&k);
//continue if t2 is bigger than n
for (;j<t2->size;j++)
spAdd(t2->val[j],k,t1->val+j-1,&k);
//adjust size
if (t2->size > t)
t1->size = t2->size - 1;
else
t1->size = t - 1;
//account for carry
if (k)
{
t1->val[t1->size]=k;
t1->size++;
}
/****** short mul of n with u, simultaneous with add. of prev step (in t2)
and with right shift of one word ********/
}
//almost done
if (zCompare(t1,n) >= 0)
zSub(t1,n,c);
else
zCopy(t1,c);
zFree(&s1);
zFree(&s2);
return;
}
int zReadHMM_State (FILE *stream, zHMM_State *state, int iso_groups) {
/*
This function reads a line of the parameter file that
describes a state in the HMM and fills in a zHMM_State
object with information from the line. It also associates
external states with feature factory initilization functions
and converts intitial probabilities to scores.
*/
char state_name[33];
char state_type[33];
char strand[2];
char dur[33];
char model[33];
char phase[5];
float temp;
score_t *init;
int i;
init = zCalloc((size_t) iso_groups, (size_t) sizeof(score_t), "zReadHMM_State ISO");
state->init = zCalloc((size_t)iso_groups, (size_t) sizeof(score_t), "zReadHMM_State ISO");
/* get state information and initial prob of first isochore */
if (fscanf(stream, "%32s %32s %1s %4s %32s %32s %f",
state_name, state_type, strand, phase, dur, model, &temp) != 7) {
zWarn("zReadHMM_State header");
zFree(init);
return 0;
}
init[0] = temp;
/* read in initial probs of other isochores */
for (i = 1; i < iso_groups; i++){
if(fscanf(stream, "%f", &temp) != 1){
zWarn("zReadHMM_State header ISO");
zFree(init);
return 0;
}
init[i] = temp;
}
/* convert strings read in from paramter file to internal representations and store them */
state->type = zGetStateType(state_type);
if (zStrIdxExists(state_name)) {
zWarn("duplicate state name: %s", state_name);
return 0;
}
state->name = zChar2StrIdx(state_name);
state->strand = zText2Strand(strand);
state->phase = zText2Phase(phase);
state->duration = zChar2StrIdx(dur);
state->model = zChar2StrIdx(model);
/* Associate feature factory initilization function with each external state */
state->ffactory = zGetFactory(model);
/* external states must have a feature factory initilization function defined to compute their scores */
if (state->ffactory == NULL && state->type == EXTERNAL) {
zWarn("Cannot find a factory for state \"%s\" using model \"%s\"",
state_name, model);
}
/* convert initial probabilities to scores */
for (i = 0; i < iso_groups; i++) {
if (init[i] > 0) {
state->init[i] = zFloat2Score((double)init[i]);
} else {
state->init[i] = MIN_SCORE;
}
}
zFree(init);
return 1;
}
void zREDC(z *T, z *n)
{
/* from handbook of applied cryptography, ch. 14
INPUT: integers m = (mn-1 . . .m1m0)b with gcd(m; b) = 1, R = b^n,m' = -m^-1 mod
b, and T = (t2n-1 . . . t1t0)b <mR.
OUTPUT: TR^-1 mod m, the reduction of T mod m in montgomery representation...
1. A=T . (Notation: A = (a2n-1 . . . a1a0)b.)
2. For i from 0 to (n - 1) do the following:
2.1 ui=ai*m' mod b.
2.2 A=A + ui*m*b^i.
3. A=A/b^n.
4. If A > m then A=A-m.
5. Return(A).
*/
int i,j,ix,su;
fp_digit nhat = montyconst.nhat.val[0], ui,k;
z mtmp3;
if (TFM_MONTY == 1)
{
fp_montgomery_reduce(T,n,montyconst.nhat.val[0]);
return;
}
//printf("shouldn't get to here\n");
zInit(&mtmp3);
if (mtmp3.alloc < n->size * 2)
zGrow(&mtmp3,n->size * 2);
//T needs to have allocated montyconst.n.size + T.size
if (T->alloc < n->size + T->size)
zGrow(T,n->size + T->size + 1);
for (i=0;i<n->size;i++)
{
//the mod b happens automatically because only the
//lower 32 bits of the product is returned.
ui = T->val[i] * nhat; //ui = a1*nhat mod b
//zShortMul(&montyconst.n,ui,&mtmp3); //t1 = ui * n
//short mul
k=0;
su = n->size;
for (ix=0;ix<su;++ix)
spMulAdd(n->val[ix],ui,0,k,&mtmp3.val[ix],&k);
//if still have a carry, add a digit to w
if (k)
{
mtmp3.val[su]=k;
su++;
}
//check for significant digits. only necessary if v or u = 0?
for (ix = su - 1;ix>=0;--ix)
{
if (mtmp3.val[ix] != 0)
break;
}
mtmp3.size = ix+1;
for (j=mtmp3.size - 1;j>=0;j--) //t1 *= b^i
mtmp3.val[j+i] = mtmp3.val[j];
mtmp3.size += i;
zAdd(T,&mtmp3,T); //A += t1
}
for (j=0; j<T->size; j++) //A /= b^n
T->val[j] = T->val[j+n->size];
T->size -= n->size;
if (zCompare(T,n) > 0) //if A > n, A = A-n
zSub(T,n,T);
if (T->size == 0)
zCopy(n,T);
zFree(&mtmp3);
return;
}
void xGCD(z *a, z *b, z *x, z *y, z *g)
{
//compute the extended GCD of a, b, returning g = GCD(a,b) and x, y
//such that ax + by = GCD(a,b) if a,b are coprime
z t1,t2,t3,u,v,r,R,q,tmp;
// int i;
/*
Step 1:
if a < b then
Set u=0, v=1, and r=b
Set U=1, V=0, and R=a
else
Set u=1, v=0, and r=a
Set U=0, V=1, and R=b
Step 2:
if R = 0 then return r (for the gcd) and no inverses exist.
if R = 1 then return R (for the gcd), V (for the inverse a(mod b)) and U (for the inverse of b(mod a)).
Step 3:
Calculate q = int(r/R)
Calculate t1 = u - U*q
Calculate t2 = v - V*q
Calculate t3 = r - R*q
set u=U, v=V, r=R
set U=t1, V=t2, R=t3
goto Step 2.
*/
zInit(&tmp);
zInit(&t1);
zInit(&t2);
zInit(&t3);
zInit(&q);
zInit(&r);
zInit(&R);
zInit(&u);
zInit(&v);
//need to check for temp allocation
zClear(x);
zClear(y);
if (zCompare(a,b) < 0)
{
u.val[0]=0;
v.val[0]=1;
zCopy(b,&r);
x->val[0]=1;
y->val[0]=0;
zCopy(a,&R);
}
else
{
u.val[0]=1;
v.val[0]=0;
zCopy(a,&r);
x->val[0]=0;
y->val[0]=1;
zCopy(b,&R);
}
while (1)
{
if (zCompare(&zZero,&R) == 0)
{
zCopy(&r,g);
zCopy(&zZero,x);
zCopy(&zZero,y);
break;
}
if (zCompare(&zOne,&R) == 0)
{
zCopy(&R,g);
break;
}
zCopy(&r,&tmp);
zDiv(&tmp,&R,&q,&t3); //q = int(r/R), t3 = r % R
zMul(&q,x,&tmp); //t1 = u - U*q
zSub(&u,&tmp,&t1);
zMul(&q,y,&tmp); //t2 = v - V*q
zSub(&v,&tmp,&t2);
zCopy(x,&u);
zCopy(y,&v);
zCopy(&R,&r);
zCopy(&t1,x);
zCopy(&t2,y);
zCopy(&t3,&R);
}
if (x->size < 0)
{
x->size *= -1;
zSub(b,x,x);
}
if (y->size < 0)
{
y->size *= -1;
zSub(a,y,y);
}
zFree(&tmp);
zFree(&t1);
zFree(&t2);
zFree(&t3);
zFree(&q);
zFree(&r);
zFree(&R);
zFree(&u);
zFree(&v);
x->type = UNKNOWN;
y->type = UNKNOWN;
g->type = UNKNOWN;
return;
}
void zmModExpw(z *a, z *e, z *u, z *n, int k)
{
//computes a^e mod m = u using the sliding window left to right binary method
//see, for instance, the handbook of applied cryptography
//uses monty arith
//a is already in monty rep, b doesn't need to be. k is the window size
/*
INPUT: g, e = (etet-1 . . . e1e0)2 with et = 1, and an integer k >= 1.
OUTPUT: g^e.
1. Precomputation.
1.1 g1 = g, g2 = g^2.
1.2 For i from 1 to (2^(k-1) - 1) do: g_{2i+1} = g_{2i-1} * g2.
2. A = 1, i = t.
3. While i >= 0 do the following:
3.1 If ei = 0 then do: A = A^2, i = i - 1.
3.2 Otherwise (ei != 0), find the longest bitstring eiei-1 . . . el such that i-l+1 <= k
and el = 1, and do the following:
A = A^{2^{i-l+1}} * g_{eiei-1...el}2 , i = l - 1.
4. Return(A).
test -> 11749. 3 multiplications at i=7,4,0
*/
//need to allocate (2^(k-1) + 1) g's for precomputation.
z *g, g2, ztmp;
int numg, i, j, l, t, tmp1, tmp2;
fp_digit utmp1;
uint8 *bitarray;
//overflow possibilities:
//t ranges to 2x input 'a'
//u needs at least as much space as modulus
numg = (int)((1<<(k-1))+1);
g = (z *)malloc(numg*sizeof(z));
for (i=0;i<numg;i++)
zInit(&g[i]);
zInit(&g2);
zInit(&ztmp);
//precomputation
zCopy(a,&g[0]); //g[0] = a
monty_sqr(a,&g2,n); //g2 = a^2
for (i=1;i<numg;i++)
monty_mul(&g[i-1],&g2,&g[i],n); //g[i] = g[i-1] * g2, where g[i] holds g^{2*i+1}
zCopy(&montyconst.one,u);
t = zBits(e);
bitarray = (uint8 *)malloc(t * sizeof(uint8));
//get e in one array
for (i=0;i< e->size - 1;i++)
{
utmp1 = e->val[i];
j=0;
while (j<BITS_PER_DIGIT)
{
bitarray[BITS_PER_DIGIT*i+j] = (uint8)(utmp1 & 0x1);
utmp1 >>= 1;
j++;
}
}
utmp1 = e->val[i];
j=0;
while (utmp1)
{
bitarray[BITS_PER_DIGIT*i+j] = (uint8)(utmp1 & 0x1);
utmp1 >>= 1;
j++;
}
i=t-1;
while (i >= 0)
{
if (bitarray[i])
{
//find the longest bitstring ei,e1-1,...el such that i-l+1 <= k and el == 1
l=i;
if (i >= (k-1))
{
//protect against accessing bitarray past its boundaries
for (j=k-1;j>0;j--)
{
if (bitarray[i-j])
{
//this is the longest possible string, exit
l=i-j;
break;
}
}
}
//now, bitarray[i] to bitarray[i-j] is the longest bitstring
//figure out the g value to use corresponding to this bitstring
tmp1 = 1;
tmp2 = 0;
for (j=l;j<=i;j++)
{
tmp2 += tmp1 * bitarray[j];
tmp1 <<= 1;
}
tmp2 = (tmp2-1)/2;
//do the operation A = A^{2^{i-l+1}} * g_{eiei-1...el}2
for (j=0;j<(i-l+1);j++)
{
monty_sqr(u,&ztmp,n);
zCopy(&ztmp,u);
}
monty_mul(u,&g[tmp2],&ztmp,n);
zCopy(&ztmp,u);
//decrement bit pointer
i = l-1;
}
else
{
monty_sqr(u,&ztmp,n);
zCopy(&ztmp,u);
i--;
}
}
for (i=0;i<numg;i++)
zFree(&g[i]);
free(g);
zFree(&g2);
zFree(&ztmp);
free(bitarray);
return;
}
void zFreeGTFConvInfo(zGTFConvInfo *conv) {
zFree(conv->strIdx2gtft);
conv->strIdx2gtft = NULL;
}