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hybrid-ss-min.cpp
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#include "hybrid-ss-min.h"
#include "util.h"
#include "CtEnergy.h"
#include "HybridMin.h"
double interiorLoopEnergies[30] = {999999,5,3.2,3.6,4,4.4,4.6,4.8,4.9,4.9,4.9,5,5.1,5.2,5.2,5.3,5.3,5.4,5.5,5.5,5.6,5.6,5.7,5.7,5.7,5.8,5.8,5.9,5.9,5.9};
double bulgeLoopEnergies[30] = {4,2.9,3.1,3.2,3.3,3.5,3.7,3.8,3.9,4,4.1,4.2,4.2,4.3,4.3,4.4,4.4,4.5,4.6,4.6,4.7,4.7,4.8,4.8,4.9,4.9,5,5.1,5.1,5.2};
double hairpinLoopEnergies[30] = {999999,999999,3.5,3.5,3.3,4,4.3,4.3,4.3,4.3,4.4,4.5,4.6,4.6,4.7,4.8,4.9,5,5,5.1,5.2,5.3,5.4,5.6,5.7,5.8,5.9,6,6.1,6.2};
double interiorLoopEnthalpies[30] = {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};
double bulgeLoopEnthalpies[30] = {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};
double hairpinLoopEnthalpies[30] = {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};
double multiEnergies[3]={4.5,0.2,0.2};
double multiEnthalpies[3]={0,0,0};
double miscEnergies[13]={0.4,0.3,0.2,0.1,3.0,1.96,0.05,0.0,0.0,0.0,0.0,0.0,1.07857764};
double miscEnthalpies[13]={0.0,0.0,0.0,0.0,0.0,0.2,2.2,0.0,0.0,0.0,0.0,0.0,0.0};
/**
* @brief Read all the stuff we need and get that done with!
*/
HybridSSMin::HybridSSMin(double SelfHybT, double HybTemperature)
{
//Initialize ctEn computer
enComputer = new CtEnergy();
hybridComputer = new HybridMin(HybTemperature);
selfHybTemp = SelfHybT;
char gotSeq;
int count, i, j;
double t, tRatio;
char *buffer;
time_t now;
int NA, polymer, constraints;
//double tMin, tInc, tMax;
double naConc, mgConc;
double saltCorrection;
q = qprime = qm = q5 = q3 = NULL;
#if ENABLE_FORCE
g_ssok = NULL;
#endif
//DNA!!!!!!!! NOT :) RNA
NA = 1;
gotSeq = 0;
g_allPairs = 0;
g_maxLoop = 30;
g_nodangle = 0;
g_simple = 0;
g_prefix = NULL;
naConc = 1.0;
mgConc = 0.0;
polymer = 0;
g_prefilter1 = g_prefilter2 = 2;
prohibitList = forceList = NULL;
g_mfoldP = 0;
g_mfoldW = 0;
g_maxBP = 0;
g_circular = 0;
g_quiet = 1;
g_verbose = 0;
/* initializations below are unnecessary but prevent compiler warnings */
g_string = NULL;
// g_oneTemp = (tMin + tInc > tMax) ? 1 : 0;
if (g_maxLoop < 0)
g_maxLoop = 999999999;
if (g_maxBP <= 0)
g_maxBP = 999999999;
saltCorrection = ion(NA, polymer, naConc, mgConc);
/* read free energies and entropies */
loadStack(stackEnergies, stackEnthalpies, NA, saltCorrection);
symmetryCheckStack(stackEnergies, (char*)"energy");
/* symmetryCheckStack(stackEnthalpies, "enthalpy"); */
if (!g_nodangle)
loadDangle(dangleEnergies3, dangleEnthalpies3, dangleEnergies5, dangleEnthalpies5, NA, saltCorrection);
loadLoop(hairpinLoopEnergies, interiorLoopEnergies, bulgeLoopEnergies, hairpinLoopEnthalpies, interiorLoopEnthalpies, bulgeLoopEnthalpies, NA, saltCorrection);
loadSint2(sint2Energies, sint2Enthalpies, NA, saltCorrection);
symmetryCheckSint2(sint2Energies, (char*)"energy");
/* symmetryCheckSint2(sint2Enthalpies, "enthalpy"); */
loadAsint1x2(asint1x2Energies, asint1x2Enthalpies, NA, saltCorrection);
loadSint4(sint4Energies, sint4Enthalpies, NA, saltCorrection);
symmetryCheckSint4(sint4Energies, (char*)"energy");
/* symmetryCheckSint4(sint4Enthalpies, "enthalpy"); */
loadTstackh(tstackhEnergies, tstackhEnthalpies, NA);
loadTstacki(tstackiEnergies, tstackiEnthalpies, NA);
loadTstacki23(tstacki23Energies, tstacki23Enthalpies, NA);
if (!g_nodangle)
{
loadTstackm(tstackmEnergies, tstackmEnthalpies, NA, saltCorrection);
loadTstacke(tstackeEnergies, tstackeEnthalpies, NA, saltCorrection);
}
loadTriloop(&triloopEnergies, &triloopEnthalpies, &numTriloops, NA);
g_triloop = (struct triloop*) xcalloc(numTriloops, sizeof(struct triloop));
loadTloop(&tloopEnergies, &tloopEnthalpies, &numTloops, NA);
g_tloop = (struct tloop*) xcalloc(numTloops, sizeof(struct tloop));
loadHexaloop(&hexaloopEnergies, &hexaloopEnthalpies, &numHexaloops, NA);
g_hexaloop = (struct hexaloop*) xcalloc(numHexaloops, sizeof(struct hexaloop));
//Never mind this one, we have them already!
//TODO: Print out that this doesn't work for RNA!!!!!!!!!!!
//loadMulti(multiEnergies, multiEnthalpies, NA);
//loadMisc(miscEnergies, miscEnthalpies, NA);
t=selfHybTemp;
tRatio = (t + 273.15) / 310.15;
RT = R * (t + 273.15);
combineStack(stackEnergies, stackEnthalpies, tRatio, g_stack);
if (!g_nodangle)
combineDangle(dangleEnergies3, dangleEnergies5, dangleEnthalpies3, dangleEnthalpies5, tRatio, g_dangle3, g_dangle5);
else
calculateInfDangle(g_dangle3, g_dangle5);
combineLoop(hairpinLoopEnergies, interiorLoopEnergies, bulgeLoopEnergies, hairpinLoopEnthalpies, interiorLoopEnthalpies, bulgeLoopEnthalpies, tRatio, g_hairpinLoop, g_interiorLoop, g_bulgeLoop);
combineSint2(sint2Energies, sint2Enthalpies, tRatio, g_sint2);
combineAsint1x2(asint1x2Energies, asint1x2Enthalpies, tRatio, g_asint1x2);
combineSint4(sint4Energies, sint4Enthalpies, tRatio, g_sint4);
combineTstack(tstackiEnergies, tstackiEnthalpies, tRatio, g_tstacki);
combineTstack(tstacki23Energies, tstacki23Enthalpies, tRatio, g_tstacki23);
combineTstack(tstackhEnergies, tstackhEnthalpies, tRatio, g_tstackh);
if (g_nodangle)
{
calculateInfStack2(g_tstackm);
calculateInfStack2(g_tstacke);
}
else
{
combineTstack2(tstackmEnergies, tstackmEnthalpies, tRatio, g_tstackm);
combineTstack2(tstackeEnergies, tstackeEnthalpies, tRatio, g_tstacke);
}
combineMulti(multiEnergies, multiEnthalpies, tRatio, g_multi);
combineMisc(miscEnergies, miscEnthalpies, tRatio, g_misc);
combineTriloop(triloopEnergies, triloopEnthalpies, tRatio, g_triloop, numTriloops);
combineTloop(tloopEnergies, tloopEnthalpies, tRatio, g_tloop, numTloops);
combineHexaloop(hexaloopEnergies, hexaloopEnthalpies, tRatio, g_hexaloop, numHexaloops);
}
void HybridSSMin::computeTwoProbeHybridization(double& dG, double& dH, const char* seq1, const char* seq2)
{
hybridComputer->compute(dG,dH,seq1,seq2);
}
double HybridSSMin::computeGibsonFreeEnergy(double& gE, double& ctE, const char* sequence)
{
int i,skipTraceback;
skipTraceback=0;
double t,tRatio;
double tInc=1.0;
//Get sequence!!!!
g_string = sequence;
g_len = strlen(g_string);
g_seq = NULL;
/* convert sequence to numbers for speed */
g_seq = (unsigned char*) xrealloc(g_seq, g_circular ? 2 * g_len + 2 : g_len + 2);
for (i = 1; i <= g_len; ++i)
g_seq[i] = util::toNum(g_string[i - 1]);
if (g_circular)
{
for (i = 1; i <= g_len; ++i)
g_seq[g_len + i] = util::toNum(g_string[i - 1]);
g_seq[0] = g_seq[2 * g_len + 1] = 5;
}
else
g_seq[0] = g_seq[g_len + 1] = 5;
if (g_circular)
g_len *= 2;
q = recalloc2(q, g_len);
qprime = recalloc2(qprime, g_len);
qm = recalloc2(qm, g_len);
q5 = (double*) xrealloc(q5, (g_len + 1) * sizeof(ENERGY));
q3 = (double*) xrealloc(q3, (g_len + 1) * sizeof(ENERGY));
#if ENABLE_FORCE
g_ssok = xrealloc(g_ssok, (g_len + 2) * (g_len + 2));
#endif
int *bp, *upst, *dnst;
t = selfHybTemp;
int bestI, bestJ;
ENERGY mfe;
tRatio = (t + 273.15) / 310.15;
RT = R * (t + 273.15);
makeAUPenalty(g_misc, g_aup, 0);
if (g_simple)
g_multi[1] = g_multi[2] = 0;
bestI = bestJ = 0;
initializeMatrices();
fillMatrices1();
computeQ53();
if (fabs(Q5(g_len) - Q3(1)) > 1e-12)
fprintf(stderr, "Warning: Q5(n) = %g but Q3(1) = %g.\n", (double) Q5(g_len) / PRECISION, (double) Q3(1) / PRECISION);
mfe = Q5(g_len);
int k;
bp = new int[g_len];
upst = new int[g_len];
dnst = new int[g_len];
for (k = 0; k < g_len; ++k)
bp[k] = upst[k] = dnst[k] = 0;
if (g_noisolate && isFinite(Q5(g_len)))
traceback_noI(0, 0, 0, bp, upst, dnst);
else if (isFinite(Q5(g_len)))
traceback(0, 0, 0, bp, upst, dnst);
gE = (double) Q5(g_len) / PRECISION;
ctE = enComputer->compute(this,bp,upst,dnst);
delete[] bp;
delete[] upst;
delete[] dnst;
return EXIT_SUCCESS;
}
int HybridSSMin::helixLength(int i, int j, ENERGY* qprime)
{
int k, length;
if (!isFinite(Qprime(i, j)))
return 0;
length = 1;
for (k = 1; i + k < j - k && isFinite(Qprime(i + k, j - k)); ++k);
length += k - 1;
for (k = 1; i > k && j + k <= g_len && isFinite(Qprime(i - k, j + k)); ++k);
length += k - 1;
return length;
}
void HybridSSMin::prefilter()
{
char** in;
int i, j, k, count;
in = (char**) xcalloc(g_len, sizeof(char*));
for (i = 1; i <= g_len; ++i)
in[i - 1] = (char*) xcalloc(g_len, 1);
for (i = 1; i <= g_len - g_prefilter2 + 1; ++i)
for (j = g_len; j >= g_prefilter2 && j >= i; --j)
{
count = 0;
for (k = 0; k < g_prefilter2 && k <= (j - i) / 2; ++k)
if (isFinite(Qprime(i + k, j - k)))
++count;
if (count >= g_prefilter1)
for (k = 0; k < g_prefilter2 && k <= (j - i) / 2; ++k)
++in[i + k - 1][j - k - 1];
}
for (i = 1; i <= g_len; ++i)
{
for (j = g_len; j >= i; --j)
if (!in[i - 1][j - 1])
Qprime(i, j) = INFINITY;
free(in[i - 1]);
}
free(in);
}
void HybridSSMin::initializeMatrices()
{
int i, j, k;
struct constraintListNode* top;
/* Q' is initialized to +infinity iff base pair is illegal; 0 otherwise
Q and QM are always initialized to +infinity */
for (i = 1; i <= g_len; ++i)
for (j = i; j <= g_len; ++j)
if (j - i < TURN + 1 || (basePairIndex(g_seq[i], g_seq[j]) == 6 && !g_allPairs))
Q(i, j) = Qprime(i, j) = QM(i, j) = INFINITY;
else if (j - i > g_maxBP)
Q(i, j) = Qprime(i, j) = QM(i, j) = INFINITY;
else
{
Q(i, j) = QM(i, j) = INFINITY;
Qprime(i, j) = 0;
}
top = prohibitList;
while (top)
{
if (top->i >= 1 && top->i <= g_len && top->j >= 1 && top->j <= g_len &&
top->k >= 1 && top->k <= g_len && top->l >= 1 && top->l <= g_len)
for (i = top->i; i <= top->j; ++i)
for (j = top->k; j <= top->l; ++j)
{
if (i <= j)
Qprime(i, j) = INFINITY;
else
Qprime(j, i) = INFINITY;
}
else if (top->l == 0 && top->i >= 1 && top->i <= g_len && top->j >= 1 && top->j <= g_len)
for (k = 0; k < top->k; ++k)
{
if (top->i + k <= top->j - k)
Qprime(top->i + k, top->j - k) = INFINITY;
else
Qprime(top->j - k, top->i + k) = INFINITY;
}
else if (top->l == 0 && top->i >= 1 && top->i <= g_len && top->j == 0)
for (k = 0; k < top->k; ++k)
{
for (j = 1; j <= top->i + k; ++j)
Qprime(j, top->i + k) = INFINITY;
for (j = top->i + k; j <= g_len; ++j)
Qprime(top->i + k, j) = INFINITY;
}
else if (top->l == 0 && top->j >= 1 && top->j <= g_len && top->i == 0)
for (k = 0; k < top->k; ++k)
{
for (i = 1; i <= top->j + k; ++i)
Qprime(i, top->j + k) = INFINITY;
for (i = top->j + k; i <= g_len; ++i)
Qprime(top->j + k, i) = INFINITY;
}
top = top->next;
}
#if ENABLE_FORCE
for (i = 0; i <= g_len + 1; ++i)
for (j = 0; j <= g_len + 1; ++j)
ssOK(i, j) = 1;
top = forceList;
while (top)
{
if (top->i >= 1 && top->i <= g_len)
for (i = 0; i <= g_len + 1; ++i)
for (j = i; j <= g_len + 1; ++j)
for (k = 0; k < top->k; ++k)
if (i <= top->i + k && top->i + k <= j)
ssOK(i, j) = 0;
if (top->j >= 1 && top->j <= g_len)
{
if (top->i == 0)
{
for (i = 0; i <= g_len + 1; ++i)
for (j = i; j <= g_len + 1; ++j)
for (k = 0; k < top->k; ++k)
if (i <= top->j + k && top->j + k <= j)
ssOK(i, j) = 0;
}
else
{
for (i = 0; i <= g_len + 1; ++i)
for (j = i; j <= g_len + 1; ++j)
for (k = 0; k < top->k; ++k)
if (i <= top->j - k && top->j - k <= j)
ssOK(i, j) = 0;
}
}
if (top->i >= 1 && top->i <= g_len && top->j >= 1 && top->j <= g_len)
{
for (i = 1; i <= g_len; ++i)
for (k = 0; k < top->k; ++k)
if (i != top->i + k && i <= top->j - k)
/* Qprime(i, top->j - k) = Qprime(top->j - k, i) = INFINITY; */
Qprime(i, top->j - k) = INFINITY;
for (j = 1; j <= g_len; ++j)
for (k = 0; k < top->k; ++k)
if (j != top->j - k && top->i + k <= j)
/* Qprime(top->i + k, j) = Qprime(j, top->i + k) = INFINITY; */
Qprime(top->i + k, j) = INFINITY;
}
top = top->next;
}
#endif
if (g_prefilter1 > 1 && !g_allPairs)
prefilter();
/* for (i = 1; i <= g_len; ++i)
for (j = i; j <= g_len; ++j)
if (helixLength(i, j, qprime) <= g_prefilter)
Qprime(i, j) = INFINITY; */
}
void HybridSSMin::fillMatrices1()
{
int i, j, k;
/* start at top left, fill each column bottom->top
when Q' is +infinity, don't consider it */
for (j = 2; j <= g_len; ++j)
for (i = j - TURN - 1; i >= (g_circular && j > g_len / 2 ? j - g_len / 2: 1); --i)
{
ENERGY au;
au = auPenalty(i, j);
if (g_circular)
{
if (j - i > g_len / 2)
continue;
if (i > g_len / 2)
{
Q(i, j) = Q(i - g_len / 2, j - g_len / 2);
Qprime(i, j) = Qprime(i - g_len / 2, j - g_len / 2);
QM(i, j) = QM(i - g_len / 2, j - g_len / 2);
continue;
}
}
if (isFinite(Qprime(i, j)))
{
Qprime(i, j) = min4(Eh(i, j),
Es(i, j) + Qprime(i + 1, j - 1),
QBI(i, j),
g_multi[0] + g_multi[2] + au + QM(i + 1, j - 1));
if (!g_nodangle)
{
if (j > 2)
Qprime(i, j) = min2(Qprime(i, j), g_multi[0] + g_multi[1] + g_multi[2] + au + Ed5(i, j) + QM(i + 1, j - 2));
if (i < g_len - 1)
Qprime(i, j) = min2(Qprime(i, j), g_multi[0] + g_multi[1] + g_multi[2] + au + Ed3(i, j) + QM(i + 2, j - 1));
if (j > 2 && i < g_len - 1)
Qprime(i, j) = min2(Qprime(i, j), g_multi[0] + 2.0 * g_multi[1] + g_multi[2] + au + Etstackm(i, j) + QM(i + 2, j - 2));
}
}
QM(i, j) = INFINITY;
for (k = i + TURN + 1; k <= j - TURN - 2; ++k)
QM(i, j) = min2(QM(i, j), Q(i, k) + Q(k + 1, j));
if (g_noisolate)
Q(i, j) = min4(ssOK(i, i) ? g_multi[1] + Q(i + 1, j) : INFINITY,
ssOK(j, j) ? g_multi[1] + Q(i, j - 1) : INFINITY,
i <= j - 2 ? g_multi[2] + au + Es(i, j) + Qprime(i + 1, j - 1) : INFINITY,
QM(i, j));
else
Q(i, j) = min4(ssOK(i, i) ? g_multi[1] + Q(i + 1, j) : INFINITY,
ssOK(j, j) ? g_multi[1] + Q(i, j - 1) : INFINITY,
g_multi[2] + au + Qprime(i, j),
QM(i, j));
if (!g_nodangle)
{
if (g_noisolate)
{
if (i < j - TURN - 3)
{
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i + 1, j) + Ed5(j, i + 1) + Es(i + 1, j) + Qprime(i + 2, j - 1));
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i, j - 1) + Ed3(j - 1, i) + Es(i, j - 1) + Qprime(i + 1, j - 2));
}
if (i < j - TURN - 4)
Q(i, j) = min2(Q(i, j), 2.0 * g_multi[1] + g_multi[2] + auPenalty(i + 1, j - 1) + Etstackm(j - 1, i + 1) + Es(i + 1, j - 1) + Qprime(i + 2, j - 2));
}
else
{
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i + 1, j) + Ed5(j, i + 1) + Qprime(i + 1, j));
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i, j - 1) + Ed3(j - 1, i) + Qprime(i, j - 1));
if (i < j - TURN - 2)
Q(i, j) = min2(Q(i, j), 2.0 * g_multi[1] + g_multi[2] + auPenalty(i + 1, j - 1) + Etstackm(j - 1, i + 1) + Qprime(i + 1, j - 1));
}
}
}
}
void HybridSSMin::fillMatrices2()
{
int i, j, k;
FILE* file;
for (j = g_len + 1; j < 2 * g_len; ++j)
for (i = g_len; i > j - g_len; --i)
{
ENERGY au;
au = auPenalty(i, j - g_len);
if (isFinite(Qprime(i, j)))
{
Qprime(i, j) = min4(i < g_len ? Es(i, j) + Qprime(i + 1, j - 1) : INFINITY,
QBI2(i, j),
i < g_len ? g_multi[0] + g_multi[2] + au + QM(i + 1, j - 1) : INFINITY,
au + min2(Q5(j - 1 - g_len), ssOK(1, j - 1 - g_len) ? 0.0 : INFINITY) + min2(Q3(i + 1), ssOK(i + 1, g_len) ? 0.0 : INFINITY));
if (!g_nodangle)
{
if (i < g_len && j > g_len + 2)
Qprime(i, j) = min2(Qprime(i, j), g_multi[0] + g_multi[1] + g_multi[2] + au + Ed5(i, j - g_len) + QM(i + 1, j - 2));
if (i < g_len - 1)
Qprime(i, j) = min2(Qprime(i, j), g_multi[0] + g_multi[1] + g_multi[2] + au + Ed3(i, j - g_len) + QM(i + 2, j - 1));
if (j > g_len + 2 && i < g_len - 1)
Qprime(i, j) = min2(Qprime(i, j), g_multi[0] + 2.0 * g_multi[1] + g_multi[2] + au + Etstackm(i, j - g_len) + QM(i + 2, j - 2));
if (j > g_len + 1)
Qprime(i, j) = min2(Qprime(i, j), au + Ed5(i, j - g_len) + min2(Q5(j - 2 - g_len), ssOK(1, j - 2 - g_len) ? 0.0 : INFINITY) + min2(Q3(i + 1), ssOK(i + 1, g_len) ? 0.0 : INFINITY));
if (i < g_len)
Qprime(i, j) = min2(Qprime(i, j), au + Ed3(i, j - g_len) + min2(Q5(j - 1 - g_len), ssOK(1, j - 1 - g_len) ? 0.0 : INFINITY) + min2(Q3(i + 2), ssOK(i + 2, g_len) ? 0.0 : INFINITY));
if (j > g_len + 1 && i < g_len)
Qprime(i, j) = min2(Qprime(i, j), au + Etstacke(i, j - g_len) + min2(Q5(j - 2 - g_len), ssOK(1, j - 2 - g_len) ? 0.0 : INFINITY) + min2(Q3(i + 2), ssOK(i + 2, g_len) ? 0.0 : INFINITY));
}
}
QM(i, j) = INFINITY;
for (k = i + TURN + 1; k <= g_len - 1; ++k)
QM(i, j) = min2(QM(i, j), Q(i, k) + Q(k + 1, j));
for (k = g_len + 1; k <= j - TURN - 2; ++k)
QM(i, j) = min2(QM(i, j), Q(i, k) + Q(k + 1 - g_len, j - g_len));
if (g_noisolate)
Q(i, j) = min4(ssOK(i, i) && i < g_len ? g_multi[1] + Q(i + 1, j) : INFINITY,
ssOK(j - g_len, j - g_len) && j > g_len + 1 ? g_multi[1] + Q(i, j - 1) : INFINITY,
i < g_len && j > g_len + 1 ? g_multi[2] + au + Es(i, j) + Qprime(i + 1, j - 1) : INFINITY,
QM(i, j));
else
Q(i, j) = min4(ssOK(i, i) && i < g_len ? g_multi[1] + Q(i + 1, j) : INFINITY,
ssOK(j - g_len, j - g_len) && j > g_len + 1 ? g_multi[1] + Q(i, j - 1) : INFINITY,
g_multi[2] + au + Qprime(i, j),
QM(i, j));
if (!g_nodangle)
{
if (g_noisolate)
{
if (i < g_len - 1 && j > g_len + 1)
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i + 1, j - g_len) + Ed5(j - g_len, i + 1) + Es(i + 1, j) + Qprime(i + 2, j - 1));
if (i < g_len && j > g_len + 2)
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i, j - 1 - g_len) + Ed3(j - 1 - g_len, i) + Es(i, j - 1) + Qprime(i + 1, j - 2));
if (i < g_len - 1 && j > g_len + 2)
Q(i, j) = min2(Q(i, j), 2.0 * g_multi[1] + g_multi[2] + auPenalty(i + 1, j - 1 - g_len) + Etstackm(j - 1 - g_len, i + 1) + Es(i + 1, j - 1) + Qprime(i + 2, j - 2));
}
else
{
if (i < g_len)
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i + 1, j - g_len) + Ed5(j - g_len, i + 1) + Qprime(i + 1, j));
if (j > g_len + 1)
Q(i, j) = min2(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i, j - 1 - g_len) + Ed3(j - 1 - g_len, i) + Qprime(i, j - 1));
if (i < g_len && j > g_len + 1)
Q(i, j) = min2(Q(i, j), 2.0 * g_multi[1] + g_multi[2] + auPenalty(i + 1, j - 1 - g_len) + Etstackm(j - 1 - g_len, i + 1) + Qprime(i + 1, j - 1));
}
}
}
if (g_debug)
{
file = fopen("Qprime-E", "wt");
for (i = 1; i <= g_len; ++i)
{
for (j = g_len + 1; j <= 2 * g_len; ++j)
fprintf(file, "%f\t", (double) Qprime(i, j) / PRECISION);
fputs("\n", file);
}
fclose(file);
file = fopen("Q-E", "wt");
for (i = 1; i <= g_len; ++i)
{
for (j = g_len + 1; j <= 2 * g_len; ++j)
fprintf(file, "%f\t", (double) Q(i, j) / PRECISION);
fputs("\n", file);
}
fclose(file);
file = fopen("QM-E", "wt");
for (i = 1; i <= g_len; ++i)
{
for (j = g_len + 1; j <= 2 * g_len; ++j)
fprintf(file, "%f\t", (double) QM(i, j) / PRECISION);
fputs("\n", file);
}
fclose(file);
}
}
void HybridSSMin::computeQ53()
{
int i, j;
Q5(0) = Q5(1) = INFINITY;
Q3(g_len + 1) = Q3(g_len) = INFINITY;
if (g_nodangle)
{
for (i = 2; i <= g_len; ++i)
Q5(i) = min2(ssOK(i, i) ? Q5(i - 1) : INFINITY, Q5_1(i));
for (j = g_len - 1; j >= 1; --j)
Q3(j) = min2(ssOK(j, j) ? Q3(j + 1) : INFINITY, Q3_1(j));
}
else
{
for (i = 2; i <= g_len; ++i)
Q5(i) = min5(ssOK(i, i) ? Q5(i - 1) : INFINITY, Q5_1(i), Q5_2(i), Q5_3(i), Q5_4(i));
for (j = g_len - 1; j >= 1; --j)
Q3(j) = min5(ssOK(j, j) ? Q3(j + 1) : INFINITY, Q3_1(j), Q3_2(j), Q3_3(j), Q3_4(j));
}
}
void HybridSSMin::traceback(int i, int j, int force, int* bp, int* upst, int* dnst)
{
int k, ii, jj;
struct stackNode *top, *stack = NULL;
/* find best folding from i to j; force i-j pair iff force
if i=j=0, best folding including Q5 and Q3 is found */
if (i == 0 && j == 0)
push(&stack, g_len, 0, 3);
else
{
if (force)
push(&stack, i, j, j > g_len ? 5 : 0);
else
push(&stack, i, j, 2);
}
while (stack)
{
top = stack;
stack = stack->next;
i = top->i;
j = top->j;
if (top->matrix == 1) /* QM */
{
for (k = i + TURN + 1; k < j - TURN - 1; ++k)
if (equal(QM(i, j), Q(i, k) + Q(k + 1, j)))
{
push(&stack, i, k, 2);
push(&stack, k + 1, j, 2);
break;
}
}
else if (top->matrix == 2) /* Q */
{
while ((ssOK(i, i) && equal(Q(i, j), g_multi[1] + Q(i + 1, j))) ||
(ssOK(j, j) && equal(Q(i, j), g_multi[1] + Q(i, j - 1))))
{
if (ssOK(i, i) && equal(Q(i, j), g_multi[1] + Q(i + 1, j)))
++i;
else if (ssOK(j, j) && equal(Q(i, j), g_multi[1] + Q(i, j - 1)))
--j;
}
if (equal(Q(i, j), g_multi[2] + auPenalty(i, j) + Qprime(i, j)))
push(&stack, i, j, 0);
else if (equal(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i + 1, j) + Ed5(j, i + 1) + Qprime(i + 1, j)))
{
setDangle5(i + 1, upst, dnst);
push(&stack, i + 1, j, 0);
}
else if (equal(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i, j - 1) + Ed3(j - 1, i) + Qprime(i, j - 1)))
{
setDangle3(j - 1, upst, dnst);
push(&stack, i, j - 1, 0);
}
else if (equal(Q(i, j), 2.0 * g_multi[1] + g_multi[2] + auPenalty(i + 1, j - 1) + Etstackm(j - 1, i + 1) + Qprime(i + 1, j - 1)))
{
setDangle5(i + 1, upst, dnst);
setDangle3(j - 1, upst, dnst);
push(&stack, i + 1, j - 1, 0);
}
else
{
for (k = i + TURN + 1; k <= j - TURN - 2; ++k)
if (equal(Q(i, j), Q(i, k) + Q(k + 1, j)))
{
push(&stack, i, k, 2);
push(&stack, k + 1, j, 2);
break;
}
}
}
else if (top->matrix == 0) /* Q' */
{
bp[i - 1] = j;
bp[j - 1] = i;
if (equal(Qprime(i, j), Es(i, j) + Qprime(i + 1, j - 1)))
{
setStack(i, j, upst, dnst);
push(&stack, i + 1, j - 1, 0);
}
else if (equal(Qprime(i, j), Eh(i, j)))
;
else if (equal(Qprime(i, j), QBI(i, j)))
{
int d, done;
for (done = 0, d = j - i - 3; d >= TURN + 1 && d >= j - i - 2 - g_maxLoop && !done; --d)
for (ii = i + 1; ii < j - d; ++ii)
{
jj = d + ii;
if (equal(Qprime(i, j), Ebi(i, j, ii, jj) + Qprime(ii, jj)))
{
setBI(i, j, ii, jj, upst, dnst);
push(&stack, ii, jj, 0);
++done;
break;
}
}
}
else if (i <= j - 2 && equal(Qprime(i, j), g_multi[0] + g_multi[2] + auPenalty(i, j) + QM(i + 1, j - 1)))
push(&stack, i + 1, j - 1, 1);
else if (i <= j - 3 && equal(Qprime(i, j), g_multi[0] + g_multi[1] + g_multi[2] + auPenalty(i, j) + Ed5(i, j) + QM(i + 1, j - 2)))
{
setDangle5(j, upst, dnst);
push(&stack, i + 1, j - 2, 1);
}
else if (i <= j - 3 && equal(Qprime(i, j), g_multi[0] + g_multi[1] + g_multi[2] + auPenalty(i, j) + Ed3(i, j) + QM(i + 2, j - 1)))
{
setDangle3(i, upst, dnst);
push(&stack, i + 2, j - 1, 1);
}
else
#ifdef DEBUG
if (i <= j - 4 && equal(Qprime(i, j), g_multi[0] + 2.0 * g_multi[1] + g_multi[2] + auPenalty(i, j) + Etstackm(i, j) + QM(i + 2, j - 2)))
#endif
{
setDangle5(j, upst, dnst);
setDangle3(i, upst, dnst);
push(&stack, i + 2, j - 2, 1);
}
#ifdef DEBUG
else
fprintf(stderr, "Error in traceback: Q'(%d, %d)\n", i, j);
#endif
}
else if (top->matrix == 3) /* Q5 */
{
while (ssOK(i, i) && equal(Q5(i), Q5(i - 1)))
--i;
if (i == 0)
continue;
if (equal(Q5(i), Q5_1(i)))
{
for (k = 0; k <= i - TURN - 2; ++k)
if (ssOK(1, k) && equal(Q5(i), auPenalty(k + 1, i) + Qprime(k + 1, i)))
{
push(&stack, k + 1, i, 0);
break;
}
else if (equal(Q5(i), Q5(k) + auPenalty(k + 1, i) + Qprime(k + 1, i)))
{
push(&stack, k + 1, i, 0);
push(&stack, k, 0, 3);
break;
}
}
else if (equal(Q5(i), Q5_2(i)))
{
for (k = 0; k <= i - TURN - 3; ++k)
if (ssOK(1, k) && equal(Q5(i), auPenalty(k + 2, i) + Ed5(i, k + 2) + Qprime(k + 2, i)))
{
setDangle5(k + 2, upst, dnst);
push(&stack, k + 2, i, 0);
break;
}
else if (equal(Q5(i), Q5(k) + auPenalty(k + 2, i) + Ed5(i, k + 2) + Qprime(k + 2, i)))
{
setDangle5(k + 2, upst, dnst);
push(&stack, k + 2, i, 0);
push(&stack, k, 0, 3);
break;
}
}
else if (equal(Q5(i), Q5_3(i)))
{
for (k = 0; k <= i - TURN - 3; ++k)
if (ssOK(1, k) && equal(Q5(i), auPenalty(k + 1, i - 1) + Ed3(i - 1, k + 1) + Qprime(k + 1, i - 1)))
{
setDangle3(i - 1, upst, dnst);
push(&stack, k + 1, i - 1, 0);
break;
}
else if (equal(Q5(i), Q5(k) + auPenalty(k + 1, i - 1) + Ed3(i - 1, k + 1) + Qprime(k + 1, i - 1)))
{
setDangle3(i - 1, upst, dnst);
push(&stack, k + 1, i - 1, 0);
push(&stack, k, 0, 3);
break;
}
}
else
#ifdef DEBUG
if (equal(Q5(i), Q5_4(i)))
#endif
{
for (k = 0; k <= i - TURN - 4; ++k)
if (ssOK(1, k) && equal(Q5(i), auPenalty(k + 2, i - 1) + Etstacke(i - 1, k + 2) + Qprime(k + 2, i - 1)))
{
setDangle5(k + 2, upst, dnst);
setDangle3(i - 1, upst, dnst);
push(&stack, k + 2, i - 1, 0);
break;
}
else if (equal(Q5(i), Q5(k) + auPenalty(k + 2, i - 1) + Etstacke(i - 1, k + 2) + Qprime(k + 2, i - 1)))
{
setDangle5(k + 2, upst, dnst);
setDangle3(i - 1, upst, dnst);
push(&stack, k + 2, i - 1, 0);
push(&stack, k, 0, 3);
break;
}
}
#ifdef DEBUG
else
fprintf(stderr, "Error in traceback: Q5(%d)\n", i);
#endif
}
else if (top->matrix == 4) /* Q3 */
{
while (ssOK(j, j) && equal(Q3(j), Q3(j + 1)))
++j;
if (j == g_len + 1)
continue;
if (equal(Q3(j), Q3_1(j)))
{
for (k = j + TURN + 2; k <= g_len + 1; ++k)
if (ssOK(k, g_len) && equal(Q3(j), auPenalty(j, k - 1) + Qprime(j, k - 1)))
{
push(&stack, j, k - 1, 0);
break;
}
else if (equal(Q3(j), auPenalty(j, k - 1) + Qprime(j, k - 1) + Q3(k)))
{
push(&stack, j, k - 1, 0);
push(&stack, 0, k, 4);
break;
}
}
else if (equal(Q3(j), Q3_2(j)))
{
for (k = j + TURN + 3; k <= g_len + 1; ++k)
if (ssOK(k, g_len) && equal(Q3(j), auPenalty(j, k - 2) + Ed3(k - 2, j) + Qprime(j, k - 2)))
{
setDangle3(k - 2, upst, dnst);
push(&stack, j, k - 2, 0);
break;
}
else if (equal(Q3(j), auPenalty(j, k - 2) + Ed3(k - 2, j) + Qprime(j, k - 2) + Q3(k)))
{
setDangle3(k - 2, upst, dnst);
push(&stack, j, k - 2, 0);
push(&stack, 0, k, 4);
break;
}
}
else if (equal(Q3(j), Q3_3(j)))
{
for (k = j + TURN + 3; k <= g_len + 1; ++k)
if (ssOK(k, g_len) && equal(Q3(j), auPenalty(j + 1, k - 1) + Ed5(k - 1, j + 1) + Qprime(j + 1, k - 1)))
{
setDangle5(j + 1, upst, dnst);
push(&stack, j + 1, k - 1, 0);
break;
}
else if (equal(Q3(j), auPenalty(j + 1, k - 1) + Ed5(k - 1, j + 1) + Qprime(j + 1, k - 1) + Q3(k)))
{
setDangle5(j + 1, upst, dnst);
push(&stack, j + 1, k - 1, 0);
push(&stack, 0, k, 4);
break;
}
}
else
#ifdef DEBUG
if (equal(Q3(j), Q3_4(j)))
#endif
{
for (k = j + TURN + 4; k <= g_len + 1; ++k)
if (ssOK(k, g_len) && equal(Q3(j), auPenalty(j + 1, k - 2) + Etstacke(k - 2, j + 1) + Qprime(j + 1, k - 2)))
{
setDangle3(k - 2, upst, dnst);
setDangle5(j + 1, upst, dnst);
push(&stack, j + 1, k - 2, 0);
break;
}
else if (equal(Q3(j), auPenalty(j + 1, k - 2) + Etstacke(k - 2, j + 1) + Qprime(j + 1, k - 2) + Q3(k)))
{
setDangle3(k - 2, upst, dnst);
setDangle5(j + 1, upst, dnst);
push(&stack, j + 1, k - 2, 0);
push(&stack, 0, k, 4);
break;
}
}
#ifdef DEBUG
else
fprintf(stderr, "Error in traceback: Q3(%d)\n", j);
#endif
}
else if (top->matrix == 6) /* QM */
{
for (k = i; k <= j - 1; ++k)
if (k < g_len && equal(QM(i, j), Q(i, k) + Q(k + 1, j)))
{
push(&stack, i, k, 2);
push(&stack, k + 1, j, 7);
break;
}
else if (k > g_len && equal(QM(i, j), Q(i, k) + Q(k + 1 - g_len, j - g_len)))
{
push(&stack, i, k, 7);
push(&stack, k + 1 - g_len, j - g_len, 2);
break;
}
}
else if (top->matrix == 7) /* Q */
{
while ((i < g_len && ssOK(i, i) && equal(Q(i, j), g_multi[1] + Q(i + 1, j))) ||
(j > g_len + 1 && ssOK(j - g_len, j - g_len) && equal(Q(i, j), g_multi[1] + Q(i, j - 1))))
{
if (i < g_len && ssOK(i, i) && equal(Q(i, j), g_multi[1] + Q(i + 1, j)))
++i;
else if (j > g_len + 1 && ssOK(j - g_len, j - g_len) && equal(Q(i, j), g_multi[1] + Q(i, j - 1)))
--j;
}
if (equal(Q(i, j), g_multi[2] + auPenalty(i, j - g_len) + Qprime(i, j)))
push(&stack, i, j, 5);
else if (i < g_len && equal(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i + 1, j - g_len) + Ed5(j - g_len, i + 1) + Qprime(i + 1, j)))
{
setDangle5(i + 1, upst, dnst);
push(&stack, i + 1, j, 5);
}
else if (j > g_len + 1 && equal(Q(i, j), g_multi[1] + g_multi[2] + auPenalty(i, j - 1 - g_len) + Ed3(j - 1 - g_len, i) + Qprime(i, j - 1)))
{
setDangle3(j - 1 - g_len, upst, dnst);
push(&stack, i, j - 1, 5);
}
else if (i < g_len && j > g_len + 1 && equal(Q(i, j), 2.0 * g_multi[1] + g_multi[2] + auPenalty(i + 1, j - 1 - g_len) + Etstackm(j - 1 - g_len, i + 1) + Qprime(i + 1, j - 1)))
{
setDangle5(i + 1, upst, dnst);
setDangle3(j - 1 - g_len, upst, dnst);
push(&stack, i + 1, j - 1, 5);
}
else
{
for (k = i; k <= j - 1; ++k)
if (k < g_len && equal(Q(i, j), Q(i, k) + Q(k + 1, j)))
{
push(&stack, i, k, 2);
push(&stack, k + 1, j, 7);
break;
}
else if (k > g_len && equal(Q(i, j), Q(i, k) + Q(k + 1 - g_len, j - g_len)))
{
push(&stack, i, k, 7);
push(&stack, k + 1 - g_len, j - g_len, 2);
break;
}
}
}
else /* Q' */
#ifdef DEBUG
if (top->matrix == 5)
#endif
{
bp[(i - 1) % g_len] = j - g_len;
bp[j - 1 - g_len] = i > g_len ? i - g_len : i;
if (i < g_len && equal(Qprime(i, j), Es(i, j) + Qprime(i + 1, j - 1)))
{
setStack(i, j - g_len, upst, dnst);
push(&stack, i + 1, j - 1, 5);
}
else if (equal(Qprime(i, j), QBI2(i, j)))
{
int d, done;
for (done = 0, d = j - i - 3; d >= 1 && d >= j - i - 2 - g_maxLoop && !done; --d)
for (ii = MAX(i + 1, g_len + 1 - d); ii < j - d && ii <= g_len; ++ii)
{
jj = d + ii;
if (equal(Qprime(i, j), Ebi(jj - g_len, ii, j - g_len, i) + Qprime(ii, jj)))
{
setBI(i, j - g_len, ii, jj - g_len, upst, dnst);
push(&stack, ii, jj, 5);
++done;
break;
}
}
}
else if (i < g_len && equal(Qprime(i, j), g_multi[0] + g_multi[2] + auPenalty(i, j - g_len) + QM(i + 1, j - 1)))
push(&stack, i + 1, j - 1, 6);
else if (i < g_len && j > g_len + 2 && equal(Qprime(i, j), g_multi[0] + g_multi[1] + g_multi[2] + auPenalty(i, j - g_len) + Ed5(i, j - g_len) + QM(i + 1, j - 2)))
{
setDangle5(j - g_len, upst, dnst);
push(&stack, i + 1, j - 2, 6);
}