/**
* @brief Finds the Gibbs free energy for a stacking structure element.
*
* <PRE>
* 5') [i] [i+1] ...
* | |
* 3') [j] [j-1] ...
* </PRE>
*
*
* @param arg_pair Pair containing nucleotides i and j indicating their positions in the sequence, where i < j.
*
* @todo 3 is hardcoded? << should be used from thermodynamics?
*/
float GibbsFreeEnergy::get_stacking_pair_element(Pair &arg_pair)
{
Nucleotide n1 = this->sequence[arg_pair.first];
Nucleotide n2 = this->sequence[arg_pair.second];
Pairing p = Pairing(n1, n2);
float energy;
if(((arg_pair.second - arg_pair.first - 1) < 3) || !p.is_canonical())///@todo figure out why 3 is not implemented as a constant ? shoudl be this->settings->min_hairpin_length?
{
energy = N_INFINITY;
}
else
{
Nucleotide n1p = this->sequence[arg_pair.first + 1];
Nucleotide n2p = this->sequence[arg_pair.second - 1];
Pairing p2 = Pairing(n1p, n2p);
energy = this->get_stack(p, p2);///@todo figure out why in the original code this penalty was extended with eparam[0] which seemed to be a stack specific penalty of 0
}
return energy;
}
/**
* @brief Energy function for Bulge Loop
*
* @section DESCRIPTION
* This function returns the amount of energy for a bulge loop element. The
* parameters must be: i<ip<jp<j where in particular:
*
* (ip-i == 1) || (j-jp == 1)
*
* There are two types of bulge loops:
*
* - Casus "5 prime bulge":
* <PRE>
* 5': ... i , ... , ip ...
* 3': ... j , jp ...
* </PRE>
*
* - Casus "3 prime bulge":
* <PRE>
* 5': ... i , ip ...
* 3': ... j , ... , jp ...
* </PRE>
*
* The corresponding energy is found in additional tables.
*
*
* @param i Nucleotide position of the sequence, paired to j, where i < i' (ip) < j' (jp) < j
* @param j Nucleotide position of the sequence, paired to i, where i < i' (ip) < j' (jp) < j
* @param ip (i') Nucleotide position of the sequence, paired to j', where i < i' (ip) < j' (jp) < j
* @param jp (j') Nucleotide position of the sequence, paired to i', where i < i' (ip) < j' (jp) < j
*
* @return Amount of corresponding Gibbs free energy if there is an bulge loop betweein (i,j) and (i',j'); infinity otherwise.
*
* @todo check: why check the size of only one size? -> does the algorithm ensure one side is always == 0?
*/
float GibbsFreeEnergy::get_bulge_loop_element(Region &r)
{
float energy;
unsigned int n_unpaired_left = r.pair2.first - r.pair1.first;
unsigned n_unpaired_right = r.pair1.second - r.pair2.second;
unsigned int n_unpaired = std::max(n_unpaired_left, n_unpaired_right) - 1;
if(r.pair2.second - r.pair2.first - 1 <= this->thermodynamics.minimal_hairpin_length)
{
energy = N_INFINITY;
}
#if DEBUG
else if(n_unpaired < 1)
{
throw std::invalid_argument("GibbsFreeEnergy::get_bulge_loop_element({" + std::to_string(r.pair1.first) + "," + std::to_string(r.pair1.second) + "},{" + std::to_string(r.pair2.first) + "," + std::to_string(r.pair2.second) + "}): unnecessary invocation because of loop size");
energy = N_INFINITY;
}
#endif // DEBUG
else
{
energy = this->get_loop_bulge(n_unpaired);
Nucleotide n11 = this->sequence[r.pair1.first];
Nucleotide n12 = this->sequence[r.pair1.second];
Nucleotide n21 = this->sequence[r.pair2.first];
Nucleotide n22 = this->sequence[r.pair2.second];
Pairing pairing1 = Pairing(n11, n12);///@todo don't you get this penalty already when you calculate the hairpin?
Pairing pairing2 = Pairing(n21, n22);
if(n_unpaired == 1)
{
energy += this->get_stack(pairing1, pairing2);///@todo should the v matrix not be filled with the stack instead...? : return N_infinity?
}
else
{
energy += this->get_AU_penalty(pairing1);///@todo don't you get this penalty already when you calculate the hairpin?
energy += this->get_AU_penalty(pairing2);
///http://unafold.math.rpi.edu/lectures/old_RNAfold/node2.html
// "Because free energies are assigned to loops, and not to helices, there is no a priori way of knowing whether or not a stacked pair will be terminal or not. For this reason, the terminal AU penalty is built into the TSTACKH and TSTACKI tables. For bulge, multi-branch and exterior loops, the penalty is applied explicitly. In all of these cases, the penalty is formally assigned to the adjacent loop, although it really belongs to the helix"
}
}
return energy;
}
static EpidStatus DoPrecomputation(VerifierCtx* ctx) {
EpidStatus result = kEpidErr;
FfElement* e12 = NULL;
FfElement* e22 = NULL;
FfElement* e2w = NULL;
FfElement* eg12 = NULL;
Epid2Params_* params = NULL;
GroupPubKey_* pub_key = NULL;
PairingState* ps_ctx = NULL;
if (!ctx) {
return kEpidBadArgErr;
}
if (!ctx->epid2_params || !ctx->epid2_params->GT ||
!ctx->epid2_params->pairing_state || !ctx->pub_key || !ctx->e12 ||
!ctx->e22 || !ctx->e2w || !ctx->eg12) {
return kEpidBadArgErr;
}
pub_key = ctx->pub_key;
params = ctx->epid2_params;
e12 = ctx->e12;
e22 = ctx->e22;
e2w = ctx->e2w;
eg12 = ctx->eg12;
ps_ctx = params->pairing_state;
// do precomputation
// 1. The verifier computes e12 = pairing(h1, g2).
result = Pairing(ps_ctx, e12, pub_key->h1, params->g2);
if (kEpidNoErr != result) {
return result;
}
// 2. The verifier computes e22 = pairing(h2, g2).
result = Pairing(ps_ctx, e22, pub_key->h2, params->g2);
if (kEpidNoErr != result) {
return result;
}
// 3. The verifier computes e2w = pairing(h2, w).
result = Pairing(ps_ctx, e2w, pub_key->h2, pub_key->w);
if (kEpidNoErr != result) {
return result;
}
// 4. The verifier computes eg12 = pairing(g1, g2).
result = Pairing(ps_ctx, eg12, params->g1, params->g2);
if (kEpidNoErr != result) {
return result;
}
return kEpidNoErr;
}
/**
* @brief Finds the Gibbs free energy for a hairpin loop structure element.
*
* @section DESCRIPTION
* The hairpinloops Gibbs free energy levels are from a fixed table upto
* a length of 30 unpaired nucleotides. Extrapoliation is applied for a
* number of unpaired nucleotides which >= 30.
*
* <PRE>
* 5') [i] [i+1] ...
* 3') [j] [j-1] ...
* </PRE>
*
*
* @param arg_pair Pair containing nucleotides i and j indicating their positions in the sequence, where i < j.
*
* @return Amount of Gibbs free energy if (i,j) enclose a hairpin loop.
*/
float GibbsFreeEnergy::get_hairpin_loop_element(Pair &arg_pair)
{
unsigned int n_unpaired = arg_pair.second - arg_pair.first - 1; // The number of unpaired nucleotides between i and j: if i = j+1, unPaired = 0
float energy;
if(n_unpaired < this->thermodynamics.minimal_hairpin_length) // Too small loop
{
energy = N_INFINITY;///@todo this should never happen and should be taken care of in the loops
}
else
{
// Loop size + Terminal mismatch(i',j')
//energy = this->get_loop_hairpin(n_unpaired);
Nucleotide i = this->sequence[arg_pair.first];
Nucleotide j = this->sequence[arg_pair.second];
Pairing pairing = Pairing(i, j);
energy = this->get_loop_hairpin(n_unpaired) +
this->get_tstackh(pairing.type, this->sequence[arg_pair.first + 1], this->sequence[arg_pair.second - 1]);
// Loop-sequence specific penalty
switch(n_unpaired)
{
case 3:
{
Sequence sub_sequence = this->sequence.subseq(arg_pair.first, arg_pair.second);
///@todo AU penalty?
energy += this->get_triloop(sub_sequence);
break;
}
case 4:
{
Sequence sub_sequence = this->sequence.subseq(arg_pair.first, arg_pair.second);
energy += this->get_tloop(sub_sequence);
break;
}
}
energy += this->get_poly_C_loop_penalty(arg_pair, n_unpaired);
energy += this->get_GGG_U_loop_penalty(arg_pair);
}
return energy;
}
EpidStatus EpidSignBasic(MemberCtx const* ctx, void const* msg, size_t msg_len,
void const* basename, size_t basename_len,
BasicSignature* sig, BigNumStr* rnd_bsn) {
EpidStatus sts = kEpidErr;
EcPoint* B = NULL;
EcPoint* t = NULL; // temp value in G1
EcPoint* k = NULL;
EcPoint* e = NULL;
FfElement* R2 = NULL;
FfElement* p2y = NULL;
FfElement* t1 = NULL;
FfElement* t2 = NULL;
FfElement* a = NULL;
FfElement* b = NULL;
FfElement* rx = NULL;
FfElement* ra = NULL;
FfElement* rb = NULL;
struct p2x_t {
uint32_t i;
uint8_t bsn[1];
}* p2x = NULL;
FfElement* t3 = NULL; // temporary for multiplication
FfElement* c = NULL;
uint8_t* digest = NULL;
PreComputedSignature curr_presig = {0};
if (!ctx || !sig) {
return kEpidBadArgErr;
}
if (!msg && (0 != msg_len)) {
// if message is non-empty it must have both length and content
return kEpidBadArgErr;
}
if (!basename && (0 != basename_len)) {
// if basename is non-empty it must have both length and content
return kEpidBadArgErr;
}
if (!ctx->epid2_params) {
return kEpidBadArgErr;
}
do {
FiniteField* Fp = ctx->epid2_params->Fp;
SignCommitOutput commit_out = {0};
FpElemStr c_str = {0};
EcGroup* G1 = ctx->epid2_params->G1;
FiniteField* GT = ctx->epid2_params->GT;
FiniteField* Fq = ctx->epid2_params->Fq;
PairingState* ps_ctx = ctx->epid2_params->pairing_state;
const BigNumStr kOne = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1};
BigNumStr t1_str = {0};
BigNumStr t2_str = {0};
size_t digest_size = 0;
uint16_t* rf_ctr = (uint16_t*)&ctx->rf_ctr;
FfElement const* x = ctx->x;
if (basename) {
if (!IsBasenameAllowed(ctx->allowed_basenames, basename, basename_len)) {
sts = kEpidBadArgErr;
BREAK_ON_EPID_ERROR(sts);
}
}
sts = NewEcPoint(G1, &B);
BREAK_ON_EPID_ERROR(sts);
sts = NewEcPoint(G1, &k);
BREAK_ON_EPID_ERROR(sts);
sts = NewEcPoint(G1, &t);
BREAK_ON_EPID_ERROR(sts);
sts = NewEcPoint(G1, &e);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(GT, &R2);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fq, &p2y);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fp, &t1);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fp, &t2);
BREAK_ON_EPID_ERROR(sts);
p2x = (struct p2x_t*)SAFE_ALLOC(sizeof(struct p2x_t) + basename_len - 1);
if (!p2x) {
sts = kEpidMemAllocErr;
break;
}
sts = NewFfElement(Fp, &a);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fp, &b);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fp, &rx);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fp, &ra);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fp, &rb);
BREAK_ON_EPID_ERROR(sts);
sts = MemberGetPreSig((MemberCtx*)ctx, &curr_presig);
BREAK_ON_EPID_ERROR(sts);
// 3. If the pre-computed signature pre-sigma exists, the member
// loads (B, K, T, a, b, rx, rf, ra, rb, R1, R2) from
// pre-sigma. Refer to Section 4.4 for the computation of
// these values.
sts = ReadFfElement(Fp, &curr_presig.a, sizeof(curr_presig.a), a);
BREAK_ON_EPID_ERROR(sts);
sts = ReadFfElement(Fp, &curr_presig.b, sizeof(curr_presig.b), b);
BREAK_ON_EPID_ERROR(sts);
sts = ReadFfElement(Fp, &curr_presig.rx, sizeof(curr_presig.rx), rx);
BREAK_ON_EPID_ERROR(sts);
sts = ReadFfElement(Fp, &curr_presig.ra, sizeof(curr_presig.ra), ra);
BREAK_ON_EPID_ERROR(sts);
sts = ReadFfElement(Fp, &curr_presig.rb, sizeof(curr_presig.rb), rb);
BREAK_ON_EPID_ERROR(sts);
// If the basename is provided, use it, otherwise use presig B
if (basename) {
// 3.a. The member computes (B, i2, y2) = G1.tpmHash(bsn).
sts = EcHash(G1, basename, basename_len, ctx->hash_alg, B, &p2x->i);
BREAK_ON_EPID_ERROR(sts);
p2x->i = htonl(p2x->i);
sts = WriteEcPoint(G1, B, &commit_out.B, sizeof(commit_out.B));
BREAK_ON_EPID_ERROR(sts);
sts = ReadFfElement(Fq, &commit_out.B.y, sizeof(commit_out.B.y), p2y);
BREAK_ON_EPID_ERROR(sts);
// b.i. (KTPM, LTPM, ETPM, counterTPM) = TPM2_Commit(P1=h1,(s2, y2) = (i2
// || bsn, y2)).
// b.ii.K = KTPM.
if (0 !=
memcpy_S((void*)p2x->bsn, basename_len, basename, basename_len)) {
sts = kEpidBadArgErr;
break;
}
sts =
Tpm2Commit(ctx->tpm2_ctx, ctx->h1, p2x, sizeof(p2x->i) + basename_len,
p2y, k, t, e, (uint16_t*)&ctx->rf_ctr);
BREAK_ON_EPID_ERROR(sts);
sts = WriteEcPoint(G1, k, &commit_out.K, sizeof(commit_out.K));
BREAK_ON_EPID_ERROR(sts);
// c.i. The member computes R1 = LTPM.
sts = WriteEcPoint(G1, t, &commit_out.R1, sizeof(commit_out.R1));
BREAK_ON_EPID_ERROR(sts);
// c.ii. e12rf = pairing(ETPM, g2)
sts = Pairing(ps_ctx, e, ctx->epid2_params->g2, R2);
BREAK_ON_EPID_ERROR(sts);
// c.iii. R2 = GT.sscmMultiExp(ea2, t1, e12rf, 1, e22, t2, e2w,ra).
// 4.i. The member computes t1 = (- rx) mod p.
sts = FfNeg(Fp, rx, t1);
BREAK_ON_EPID_ERROR(sts);
// 4.j. The member computes t2 = (rb - a * rx) mod p.
sts = FfMul(Fp, a, rx, t2);
BREAK_ON_EPID_ERROR(sts);
sts = FfNeg(Fp, t2, t2);
BREAK_ON_EPID_ERROR(sts);
sts = FfAdd(Fp, rb, t2, t2);
BREAK_ON_EPID_ERROR(sts);
sts = WriteFfElement(Fp, t1, &t1_str, sizeof(t1_str));
BREAK_ON_EPID_ERROR(sts);
sts = WriteFfElement(Fp, t2, &t2_str, sizeof(t2_str));
BREAK_ON_EPID_ERROR(sts);
{
FfElement const* points[4];
BigNumStr const* exponents[4];
points[0] = ctx->ea2;
points[1] = R2;
points[2] = ctx->e22;
points[3] = ctx->e2w;
exponents[0] = &t1_str;
exponents[1] = &kOne;
exponents[2] = &t2_str;
exponents[3] = (BigNumStr*)&curr_presig.ra;
sts = FfMultiExp(GT, points, exponents, COUNT_OF(points), R2);
BREAK_ON_EPID_ERROR(sts);
}
sts = WriteFfElement(GT, R2, &commit_out.R2, sizeof(commit_out.R2));
BREAK_ON_EPID_ERROR(sts);
// d. The member over-writes the counterTPM, B, K, R1 and R2 values.
} else {
if (!rnd_bsn) {
sts = kEpidBadArgErr;
break;
}
sts = ReadEcPoint(G1, &curr_presig.B, sizeof(curr_presig.B), B);
BREAK_ON_EPID_ERROR(sts);
commit_out.B = curr_presig.B;
commit_out.K = curr_presig.K;
commit_out.R1 = curr_presig.R1;
((MemberCtx*)ctx)->rf_ctr = curr_presig.rf_ctr;
commit_out.R2 = curr_presig.R2;
*rnd_bsn = curr_presig.rnd_bsn;
}
commit_out.T = curr_presig.T;
sts = HashSignCommitment(Fp, ctx->hash_alg, &ctx->pub_key, &commit_out, msg,
msg_len, &c_str);
BREAK_ON_EPID_ERROR(sts);
digest_size = EpidGetHashSize(ctx->hash_alg);
digest = (uint8_t*)SAFE_ALLOC(digest_size);
if (!digest) {
sts = kEpidNoMemErr;
break;
}
memcpy_S(digest + digest_size - sizeof(c_str), sizeof(c_str), &c_str,
sizeof(c_str));
sts = NewFfElement(Fp, &t3);
BREAK_ON_EPID_ERROR(sts);
sts = NewFfElement(Fp, &c);
BREAK_ON_EPID_ERROR(sts);
sts = ReadFfElement(Fp, &c_str, sizeof(c_str), c);
BREAK_ON_EPID_ERROR(sts);
// 7. The member computes sx = (rx + c * x) mod p.
sts = FfMul(Fp, c, x, t3);
BREAK_ON_EPID_ERROR(sts);
sts = FfAdd(Fp, rx, t3, t3);
BREAK_ON_EPID_ERROR(sts);
sts = WriteFfElement(Fp, t3, &sig->sx, sizeof(sig->sx));
BREAK_ON_EPID_ERROR(sts);
// 8. The member computes sf = (rf + c * f) mod p.
sts = Tpm2Sign(ctx->tpm2_ctx, digest, digest_size, *rf_ctr, NULL, t3);
BREAK_ON_EPID_ERROR(sts);
sts = WriteFfElement(Fp, t3, &sig->sf, sizeof(sig->sf));
BREAK_ON_EPID_ERROR(sts);
// 9. The member computes sa = (ra + c * a) mod p.
sts = FfMul(Fp, c, a, t3);
BREAK_ON_EPID_ERROR(sts);
sts = FfAdd(Fp, ra, t3, t3);
BREAK_ON_EPID_ERROR(sts);
sts = WriteFfElement(Fp, t3, &sig->sa, sizeof(sig->sa));
BREAK_ON_EPID_ERROR(sts);
// 10. The member computes sb = (rb + c * b) mod p.
sts = FfMul(Fp, c, b, t3);
BREAK_ON_EPID_ERROR(sts);
sts = FfAdd(Fp, rb, t3, t3);
BREAK_ON_EPID_ERROR(sts);
sts = WriteFfElement(Fp, t3, &sig->sb, sizeof(sig->sb));
BREAK_ON_EPID_ERROR(sts);
sig->B = commit_out.B;
sig->K = commit_out.K;
sig->T = commit_out.T;
sig->c = c_str;
sts = kEpidNoErr;
} while (0);
if (sts != kEpidNoErr) {
(void)Tpm2ReleaseCounter(ctx->tpm2_ctx, (uint16_t)ctx->rf_ctr);
(void)Tpm2ReleaseCounter(ctx->tpm2_ctx, curr_presig.rf_ctr);
} else if (basename) {
(void)Tpm2ReleaseCounter(ctx->tpm2_ctx, curr_presig.rf_ctr);
}
EpidZeroMemory(&curr_presig, sizeof(curr_presig));
DeleteEcPoint(&B);
DeleteEcPoint(&k);
DeleteEcPoint(&t);
DeleteEcPoint(&e);
DeleteFfElement(&R2);
DeleteFfElement(&p2y);
DeleteFfElement(&t1);
DeleteFfElement(&t2);
DeleteFfElement(&a);
DeleteFfElement(&b);
DeleteFfElement(&rx);
DeleteFfElement(&ra);
DeleteFfElement(&rb);
SAFE_FREE(p2x);
DeleteFfElement(&t3);
DeleteFfElement(&c);
SAFE_FREE(digest);
return sts;
}
// implements section 3.2.2 "Validation of Private Key" from
// Intel(R) EPID 2.0 Spec
bool EpidIsPrivKeyInGroup(GroupPubKey const* pub_key, PrivKey const* priv_key) {
bool result;
// Intel(R) EPID Parameters
Epid2Params_* params = NULL;
PairingState* ps = NULL;
// private key
EcPoint* a_pt = NULL; // an element in G1
FfElement* x_el = NULL; // an integer between [1, p-1]
FfElement* f_el = NULL; // an integer between [1, p-1]
// public key
EcPoint* h1_pt = NULL; // an element in G1
EcPoint* h2_pt = NULL; // an element in G1
EcPoint* w_pt = NULL; // an element in G2
// local variables
EcPoint* t1_pt = NULL; // an element in G2
EcPoint* t2_pt = NULL; // an element in G1
FfElement* t3_el = NULL; // an element in GT
FfElement* t4_el = NULL; // an element in GT
if (!pub_key || !priv_key) {
return false;
}
do {
EpidStatus sts;
EcGroup* G1 = NULL;
EcGroup* G2 = NULL;
FiniteField* GT = NULL;
FiniteField* Fp = NULL;
BigNumStr t_str = {0};
sts = CreateEpid2Params(¶ms);
if (kEpidNoErr != sts) {
result = false;
break;
}
G1 = params->G1;
G2 = params->G2;
GT = params->GT;
Fp = params->Fp;
sts = WriteBigNum(params->t, sizeof(t_str), &t_str);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewPairingState(G1, G2, GT, &t_str, params->neg, &ps);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Load private key
sts = NewEcPoint(G1, &a_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = ReadEcPoint(G1, &priv_key->A, sizeof(priv_key->A), a_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewFfElement(Fp, &x_el);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = ReadFfElement(Fp, &priv_key->x, sizeof(priv_key->x), x_el);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewFfElement(Fp, &f_el);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = ReadFfElement(Fp, &priv_key->f, sizeof(priv_key->f), f_el);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Load public key
sts = NewEcPoint(G1, &h1_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = ReadEcPoint(G1, &pub_key->h1, sizeof(pub_key->h1), h1_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewEcPoint(G1, &h2_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = ReadEcPoint(G1, &pub_key->h2, sizeof(pub_key->h2), h2_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewEcPoint(G2, &w_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = ReadEcPoint(G2, &pub_key->w, sizeof(pub_key->w), w_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
// local variables
sts = NewEcPoint(G2, &t1_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewEcPoint(G1, &t2_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewFfElement(GT, &t3_el);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = NewFfElement(GT, &t4_el);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Step 1. The member verifies that the gid in the public key matches the
// gid in the private key.
if (0 != memcmp(&pub_key->gid, &priv_key->gid, sizeof(priv_key->gid))) {
result = false;
break;
}
// Step 2. The member computes t1 = G2.sscmExp(g2, x).
sts = EcSscmExp(G2, params->g2, (BigNumStr const*)&priv_key->x, t1_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Step 3. The member computes t1 = G2.mul(t1, w).
sts = EcMul(G2, t1_pt, w_pt, t1_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Step 4. The member computes t3 = pairing(A, t1).
sts = Pairing(ps, t3_el, a_pt, t1_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Step 5. The member computes t2 = G1.sscmExp(h1, f).
sts = EcSscmExp(G1, h1_pt, (BigNumStr const*)&priv_key->f, t2_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Step 6. The member computes t2 = G1.mul(t2, g1).
sts = EcMul(G1, t2_pt, params->g1, t2_pt);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Step 7. The member computes t4 = pairing(t2, g2).
sts = WriteBigNum(params->t, sizeof(t_str), &t_str);
if (kEpidNoErr != sts) {
result = false;
break;
}
sts = Pairing(ps, t4_el, t2_pt, params->g2);
if (kEpidNoErr != sts) {
result = false;
break;
}
// Step 8. If GT.isEqual(t3, t4) = false, reports bad private key.
sts = FfIsEqual(GT, t3_el, t4_el, &result);
if (kEpidNoErr != sts) {
result = false;
break;
}
} while (0);
// local variables
DeleteFfElement(&t4_el);
DeleteFfElement(&t3_el);
DeleteEcPoint(&t2_pt);
DeleteEcPoint(&t1_pt);
// public key
DeleteEcPoint(&w_pt);
DeleteEcPoint(&h2_pt);
DeleteEcPoint(&h1_pt);
// private key
DeleteFfElement(&f_el);
DeleteFfElement(&x_el);
DeleteEcPoint(&a_pt);
// Intel(R) EPID Parameters
DeletePairingState(&ps);
DeleteEpid2Params(¶ms);
return result;
}
/**
* @brief Energy function for Interior Loop
*
* @section DESCRIPTION
* <PRE>
* 5': i ... i' ... : 3'
* 3': j ... j' ... : 5'
* </PRE>
*
* @todo Check code for:
* - loop contains end or beginning of sequence
* - loop internal loop < min hairpin loop?
* - use switches
*
* @param arg_region as region with Nucleotides i (pair1.first), j (pair1.second), i') and j' as positions of the sequence, where i paired to j, i' to j' and where i < i' < j' < j
*
* @return Amount of corresponding Gibbs free energy if there is an internal/interior loop betweein (i,j) and (i',j'); infinity otherwise.
*/
float GibbsFreeEnergy::get_interior_loop_element(Region &arg_region)
{
unsigned int n_unpaired;
signed int n_asym;
float energy = 0.0;
unsigned int l1 = arg_region.pair2.first - arg_region.pair1.first;
unsigned int l2 = arg_region.pair1.second - arg_region.pair2.second;
//{i}{i'}.. -> l1 = 2 - 1 = 1
//{j}{j'}.. -> l2 = 8 - 9 = 1
//nup = 1 + 1 - 2 = 0 (correct)
n_unpaired = l1 + l2 - 2;// saves one CPU operation
///@todo the following conversion is WEIRD but seems to solve the error
///Only the results should be converted, so max(l1,l2) , min(l1,l2) and make negative if l2 > l1
n_asym = ((signed int) l1 - (signed int) l2); // saves two CPU operations
// 5') [i] ... [...] [i'] ... (3'
// | |
// 3') [j] ... [...] [j'] ... (5'
if(arg_region.pair2.second - arg_region.pair2.first - 1 <= this->thermodynamics.minimal_hairpin_length)///@todo arg_region.pair2.size() + test
{
energy = N_INFINITY;
}
else if(n_unpaired > 4 || abs(n_asym) > 1)
{
Nucleotide ni = this->sequence[arg_region.pair1.first];
Nucleotide nj = this->sequence[arg_region.pair1.second];
Nucleotide nip = this->sequence[arg_region.pair2.first];
Nucleotide njp = this->sequence[arg_region.pair2.second];
Pairing pairing1 = Pairing(ni, nj);
Pairing pairing2 = Pairing(njp, nip); // I and J are switched because 5' and 3' rotate after a hairpin
//@todo this would mean that 2,2 loops get an equal penalty as 1,3 and 3,1 ?
energy += this->get_loop_interior(n_unpaired);
// tstki example:
//
// [x1]{R1}[y2]
// 5') xxxG Axxxh
// | | h
// 3') xxxC Uxxxh
// [x2]{R2}[y1]
//
// {h} and {x} are nucleotides that don't matter of which h represent the hairpin.
//
// G-C is the first pair (5' -> 3')
// U-A is the second pair (5' -> 3')
//
// For this example you want to find the stacking panalties for forward: [G-C][x1][x2]
// And the 'reverse' stack: [U-A][y1][y2]
//
// This is done in the following two lines:
energy += this->get_tstacki(pairing1, this->sequence[arg_region.pair1.first + 1], this->sequence[arg_region.pair1.second - 1]);
energy += this->get_tstacki(pairing2, this->sequence[arg_region.pair2.second + 1], this->sequence[arg_region.pair2.first - 1]); // watch out for 5' <-> 3' rotation: (jp + 1) and (ip - 1)
// Asymetrical penalty
energy += std::min(
this->get_miscloop(MISCLOOP_ASYMETRIC_INTENRAL_LOOP),
(
(float) abs(n_asym) * this->get_poppen(
std::min(
(unsigned int) this->thermodynamics.poppen_p.size(),
std::min(
l1,
l2
)
) - 1
)
)
);
}
else
{
///@todo SWITCH(n_unpaired)
// 5') [i] [i+1] [i']
// | |
// 3') [j] [j-1] [j']
if(n_unpaired == 2 && n_asym == 0)
{
Nucleotide ni = this->sequence[arg_region.pair1.first];
Nucleotide nj = this->sequence[arg_region.pair1.second];
Nucleotide nip = this->sequence[arg_region.pair2.first];
Nucleotide njp = this->sequence[arg_region.pair2.second];
Pairing pairing1 = Pairing(ni, nj);
Pairing pairing2 = Pairing(nip, njp); ///@todo double check this order in the .dat file
#if DEBUG
if(pairing2.type == PairingType::None)
{
fprintf(stderr, "GibbsFreeEnergy::get_interior_loop_element - Requesting energy for interior loop enclosing with non canonical pairing [%i,%i].\n", arg_region.pair2.first, arg_region.pair2.second);
energy += N_INFINITY;
}
else
{
energy += this->get_int11(pairing1.type, pairing2.type, this->sequence[arg_region.pair1.first + 1], this->sequence[arg_region.pair1.second - 1]);
}
#else
energy += this->get_int11(pairing1.type, pairing2.type, this->sequence[arg_region.pair1.first + 1], this->sequence[arg_region.pair1.second - 1]);
#endif //DEBUG
}
// 5') [i] [i+1] [i']
// | |
// 3') [j] [j-1] [j-2] [j']
else if(n_unpaired == 3 && n_asym == -1)
{
Nucleotide ni = this->sequence[arg_region.pair1.first];
Nucleotide nj = this->sequence[arg_region.pair1.second];
Nucleotide nip = this->sequence[arg_region.pair2.first];
Nucleotide njp = this->sequence[arg_region.pair2.second];
Pairing pairing1 = Pairing(ni, nj);
Pairing pairing2 = Pairing(nip, njp);
energy += this->get_int21(
pairing1.type,
pairing2.type,
this->sequence[arg_region.pair1.first + 1],
this->sequence[arg_region.pair1.second - 1],
this->sequence[arg_region.pair1.second - 2]); // checked : correct
}
// The situation we encounter is:
// 5') [i] [i+1] [i+2] [i'] ... (3'
// | |
// 3') [j] [j-1] [j'] ... (5'
//
// If we rotate it 180 degrees, we get:
//
// 5') [j'] [j-1] [j] (3'
// | |
// 3') [i'] [i+2] [i+1] [i] (5'
//
// And we can make use of the same energy vector
else if(n_unpaired == 3 && n_asym == 1)
{
Nucleotide ni = this->sequence[arg_region.pair1.first];
Nucleotide nj = this->sequence[arg_region.pair1.second];
Nucleotide nip = this->sequence[arg_region.pair2.first];
Nucleotide njp = this->sequence[arg_region.pair2.second];
Pairing pairing1 = Pairing(njp, nip); // Rotated
Pairing pairing2 = Pairing(nj, ni); // Rotated
energy += this->thermodynamics.int21
[pairing1.type]
[pairing2.type]
[this->sequence[arg_region.pair2.second + 1]]
[this->sequence[arg_region.pair2.first - 1]]
[this->sequence[arg_region.pair2.first - 2]];
}
// 5') [i] [i+1] [i+2] [i'] (3'
// | |
// 3') [j] [j-1] [j-2] [j'] (5'
else if(n_unpaired == 4 && n_asym == 0)//@todo figure out whether n_asym must be checked - if it would be 2, it would be a bulge loop and shouldn't reach this point. Also, the first if statement contains "|| abs(n_asym) > 1" which is always true if n_unpaired == 4 and n_asym != 0
{
Nucleotide ni = this->sequence[arg_region.pair1.first];
Nucleotide nj = this->sequence[arg_region.pair1.second];
Nucleotide nip = this->sequence[arg_region.pair2.first];
Nucleotide njp = this->sequence[arg_region.pair2.second];
Pairing pairing1 = Pairing(ni, nj);
Pairing pairing2 = Pairing(nip, njp);
energy += this->thermodynamics.int22
[pairing1.type]
[pairing2.type]
[this->sequence[arg_region.pair1.first + 1]]
[this->sequence[arg_region.pair1.second - 1]]
[this->sequence[arg_region.pair1.first + 2]]
[this->sequence[arg_region.pair1.second - 2]];
}
else//@todo figure out when this should happen - probably never << probably when very small loops are requested
{
energy = N_INFINITY;
}
}
return energy;
}