int main() {
//Boltzmann constant Units of [eV/K]
static const double kB = 8.6173324E-5;
//Planck constant Units of [eV s]
static const double hbar = 6.58211928E-16;
//printf("Value of fracSeed %e.\n",fracSeed);
int attempts = 15;
int rv;
double SiteDistance = 1; //units of [nm]
double AttemptToHop = 1E-13;
double gamma = 2; //Units of [1/nm]
int XElecOn = 1;
int YElecOn = 0;
int ZElecOn = 0;
double reOrgEnergy = 1;
double KT = 1;
double MarcusJ0 = pow( AttemptToHop*hbar*pow(4*reOrgEnergy*kB*300/M_PI,1/2),1/2);
//Calculating full Marcus Coefficient;
double MarcusCoeff = pow(MarcusJ0,2)/hbar * pow(M_PI/(4*reOrgEnergy*KT),1/2)*exp(2*gamma*SiteDistance);
/////////////////////////////////////////////////////////////////////////////////////////////////
//There should be no clusters
//Case Study one clusters in the center Periodic
int OrderLT;
int OrderHT;
int MidPtsTotalT;
int PeriodicXT = 1;
int PeriodicYT = 1;
int PeriodicZT = 1;
int XElecOnT = 1;
int YElecOnT = 0;
int ZElecOnT = 0;
SNarray snAT = newSNarray( 3,4,3);
//Create an artificial trap in snAT which in increment length is
//length 0-2 width 0-3 and height 0-2
SiteNode snT = getSN(snAT,1,1,1);
//printSNarray(snAT);
rv = setEnergy(snT, -3);
assert(rv==0);
snT = getSN(snAT,1,2,1);
rv = setEnergy(snT, -3);
assert(rv==0);
//printSNarray(snAT);
//Testing Periodic x,y and z 0 biasX 0 biasY 0 biasZ KT=1 and reOrgEnergy=1
printf("\nCase Study T Periodic Conditions\n");
matrix mtxT = CalculateAllHops(snAT, 0,0,0, 1,1, SiteDistance,AttemptToHop,gamma,PeriodicXT, PeriodicYT, PeriodicZT);
//printMatrix(mtxT);
//Sorts all the data into midpoints
ArbArray mpAT = MPsort( &OrderLT, &OrderHT, &MidPtsTotalT, mtxT, snAT, PeriodicXT, PeriodicYT, PeriodicZT);
//Sorts midpoints into Nodes in link lists. Each element of mpAT is composed of a
//link list all of the same order of magnitude
//printf("Order Low %d Order High %d\n",OrderLT, OrderHT);
//printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
//printArbArray(mpAT);
//printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbT2 = SortOrderMag( OrderHT-OrderLT+1, OrderLT, mpAT);
assert(ArbT2!=NULL);
int TotalOrdersT = OrderHT-OrderLT+1;
//Sorts nodes into clusters
//printf("********************************************\n");
//printArbArray(ArbT2, OrderLT);
//printf("********************************************\n");
ArbArray ArbT = ClusterSort( TotalOrdersT, OrderLT, ArbT2);
//printf("TotalOrdersT %d OrderLowT %d Elements used by ArbT2 %d\n",TotalOrdersT, OrderLT, getElementsUsed(ArbT2));
assert(ArbT!=NULL);
//Filtering Cluster
rv = FilterCluster( TotalOrdersT, OrderLT, mtxT, &ArbT, snAT, PeriodicXT, PeriodicYT, PeriodicZT, XElecOnT, YElecOnT, ZElecOnT);
assert(rv==0);
//printf("****************CHECK***********************\n");
rv = PrintCheck( TotalOrdersT, OrderLT, ArbT, snAT, mtxT);
//Because the cluster is smaller energy than the rest of the nodes the rest
//of the nodes are not considered to be a cluster
deleteArbArray(&ArbT2);
/*
////////////////////////////////////////////////////////////////////////////////////////
//Case Study no clusters Periodic
int OrderLU;
int OrderHU;
int MidPtsTotalU;
int PeriodicXU = 1;
int PeriodicYU = 1;
int PeriodicZU = 1;
int XElecOnU = 1;
int YElecOnU = 0;
int ZElecOnU = 0;
SNarray snAU = newSNarray( 3,4,3);
//Create an artificial trap in snAT which in increment length is
//length 0-2 width 0-3 and height 0-2
printSNarray(snAU);
//Testing Periodic x,y and z 0 biasX 0 biasY 0 biasZ KT=1 and reOrgEnergy=1
matrix mtxU = CalculateAllHops(snAU, 0,0,0, 1,1, SiteDistance,AttemptToHop,gamma,PeriodicXU, PeriodicYU, PeriodicZU);
printMatrix(mtxU);
//Sorts all the data into midpoints
ArbArray mpAU = MPsort( &OrderLU, &OrderHU, &MidPtsTotalU, mtxU, snAU, PeriodicXU, PeriodicYU, PeriodicZU);
//Sorts midpoints into Nodes in link lists. Each element of mpAT is composed of a
//link list all of the same order of magnitude
printf("Order Low %d Order High %d\n",OrderLU, OrderHU);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAU);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbU2 = SortOrderMag( OrderHU-OrderLU+1, OrderLU, mpAU);
assert(ArbU2!=NULL);
int TotalOrdersU = OrderHU-OrderLU+1;
//Sorts nodes into clusters
printf("********************************************\n");
printArbArray(ArbU2, OrderLU);
printf("********************************************\n");
ArbArray ArbU = ClusterSort( TotalOrdersU, OrderLU, ArbU2);
printf("TotalOrdersT %d OrderLowT %d Elements used by ArbT2 %d\n",TotalOrdersU, OrderLU, getElementsUsed(ArbU2));
printf("****************STARTING FILTER****************************\n");
assert(ArbU!=NULL);
//Filtering Cluster
rv = FilterCluster( TotalOrdersU, OrderLU, mtxU, &ArbU, snAU, PeriodicXU, PeriodicYU, PeriodicZU, XElecOnU, YElecOnU, ZElecOnU);
assert(rv==0);
printf("****************CHECK***********************\n");
rv = PrintCheck( TotalOrdersU, OrderLU, ArbU, snAU, mtxU);
deleteArbArray(&ArbU2);
deleteArbArray(&ArbU);
deleteMatrix(mtxU);
deleteSNarray(snAU);
deleteAllMidPointArray(&mpAU);
//Case Study two clusters in middle non periodic
int OrderLS;
int OrderHS;
int MidPtsTotalS;
int PeriodicXS = 0;
int PeriodicYS = 0;
int PeriodicZS = 0;
int XElecOnS = 1;
int YElecOnS = 0;
int ZElecOnS = 0;
SNarray snAS = newSNarray( 4, 3, 3);
//Create Trap Sites
SiteNode snS = getSN(snAS,2,1,1);
printSNarray(snAS);
rv = setEnergy(snS, -4);
assert(rv==0);
snS = getSN(snAS, 1,1,1);
rv = setEnergy(snS, -4);
assert(rv==0);
printSNarray(snAS);
//Testing non-periodic x, y and z 0 biasX 0 biasY 0 biasZ KT=0.024, and reOrgEnergy =1
matrix mtxS = CalculateAllHops(snAS, 0,0,0, 1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXS, PeriodicYS, PeriodicZS);
printMatrix(mtxS);
ArbArray mpAS = MPsort( &OrderLS, &OrderHS, &MidPtsTotalS, mtxS, snAS, PeriodicXS, PeriodicYS, PeriodicZS);
printf("Order Low %d Order High %d\n",OrderLS, OrderHS);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAS);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbS2 = SortOrderMag( OrderHS-OrderLS+1, OrderLS, mpAS);
assert(ArbS2!=NULL);
int TotalOrdersS = OrderHS-OrderLS+1;
printf("********************************************\n");
printArbArray(ArbS2, OrderLS);
printf("********************************************\n");
ArbArray ArbS = ClusterSort( TotalOrdersS, OrderLS, ArbS2);
printf("TotalOrdersS %d OrderLowS %d Elements used by ArbS2 %d\n",TotalOrdersS, OrderLS, getElementsUsed(ArbS2));
assert(ArbS!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbS, OrderLS);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersS, OrderLS, mtxS, &ArbS, snAS, PeriodicXS, PeriodicYS, PeriodicZS, XElecOnS, YElecOnS, ZElecOnS);
assert(rv==0);
printf("****************CHECK***********************\n");
rv = PrintCheck( TotalOrdersS, OrderLS, ArbS, snAS, mtxS);
deleteMatrix(mtxS);
deleteSNarray(snAS);
deleteArbArray(&ArbS);
deleteAllMidPointArray(&mpAS);
deleteArbArray(&ArbS2);
//Case Study two cluster on oposite edges non periodic
int OrderLR;
int OrderHR;
int MidPtsTotalR;
int PeriodicXR = 0;
int PeriodicYR = 0;
int PeriodicZR = 0;
int XElecOnR = 1;
int YElecOnR = 0;
int ZElecOnR = 0;
SNarray snAR = newSNarray( 4, 3, 3);
//Create Trap Sites one at the left electrode
//One at the right electrode should not consider
//any clusters in the sample
SiteNode snR = getSN(snAR,0,1,1);
printSNarray(snAR);
rv = setEnergy(snR, -4);
assert(rv==0);
snS = getSN(snAR, 3,1,1);
rv = setEnergy(snR, -4);
assert(rv==0);
printSNarray(snAR);
//Testing non-periodic x, y and z 0 biasX 0 biasY 0 biasZ KT=0.024, and reOrgEnergy =1
matrix mtxR = CalculateAllHops(snAR, 0,0,0, 1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXR, PeriodicYR, PeriodicZR);
printMatrix(mtxR);
ArbArray mpAR = MPsort( &OrderLR, &OrderHR, &MidPtsTotalR, mtxR, snAR, PeriodicXR, PeriodicYR, PeriodicZR);
printf("Order Low %d Order High %d\n",OrderLR, OrderHR);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAR);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbR2 = SortOrderMag( OrderHR-OrderLR+1, OrderLR, mpAR);
assert(ArbR2!=NULL);
int TotalOrdersR = OrderHR-OrderLR+1;
printf("********************************************\n");
printArbArray(ArbR2, OrderLR);
printf("********************************************\n");
ArbArray ArbR = ClusterSort( TotalOrdersR, OrderLR, ArbR2);
printf("TotalOrdersR %d OrderLowR %d Elements used by ArbR2 %d\n",TotalOrdersR, OrderLR, getElementsUsed(ArbR2));
assert(ArbR!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbR, OrderLR);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersR, OrderLR, mtxR, &ArbR, snAR, PeriodicXR, PeriodicYR, PeriodicZR, XElecOnR, YElecOnR, ZElecOnR);
assert(rv==0);
printf("****************CHECK***********************\n");
rv = PrintCheck( TotalOrdersR, OrderLR, ArbR, snAR, mtxR);
deleteMatrix(mtxR);
deleteSNarray(snAR);
deleteAllMidPointArray(&mpAR);
deleteArbArray(&ArbR2);
deleteArbArray(&ArbR);
//Case Study two cluster on oposite edges periodic in x
int OrderLP;
int OrderHP;
int MidPtsTotalP;
int PeriodicXP = 1;
int PeriodicYP = 0;
int PeriodicZP = 0;
int XElecOnP = 1;
int YElecOnP = 0;
int ZElecOnP = 0;
SNarray snAP = newSNarray( 4, 3, 3);
//Create Trap Sites one at the left electrode
//One at the right electrode should not consider
//any clusters in the sample
SiteNode snP = getSN(snAP,0,1,1);
printSNarray(snAP);
rv = setEnergy(snP, -4);
assert(rv==0);
snP = getSN(snAP, 3,1,1);
rv = setEnergy(snP, -4);
assert(rv==0);
printSNarray(snAP);
//Testing non-periodic x, y and z 0 biasX 0 biasY 0 biasZ KT=0.024, and reOrgEnergy =1
matrix mtxP = CalculateAllHops(snAP, 0,0,0, 1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXP, PeriodicYP, PeriodicZP);
printMatrix(mtxP);
ArbArray mpAP = MPsort( &OrderLP, &OrderHP, &MidPtsTotalP, mtxP, snAP, PeriodicXP, PeriodicYP, PeriodicZP);
printf("Order Low %d Order High %d\n",OrderLP, OrderHP);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAP);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbP2 = SortOrderMag( OrderHP-OrderLP+1, OrderLP, mpAP);
assert(ArbP2!=NULL);
int TotalOrdersP = OrderHP-OrderLP+1;
printf("********************************************\n");
printArbArray(ArbP2, OrderLP);
printf("********************************************\n");
ArbArray ArbP = ClusterSort( TotalOrdersP, OrderLP, ArbP2);
printf("TotalOrdersR %d OrderLowR %d Elements used by ArbR2 %d\n",TotalOrdersP, OrderLP, getElementsUsed(ArbP2));
assert(ArbP!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbP, OrderLP);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersP, OrderLP, mtxP, &ArbP, snAP, PeriodicXP, PeriodicYP, PeriodicZP, XElecOnP, YElecOnP, ZElecOnP);
assert(rv==0);
printf("****************CHECK***********************\n");
rv = PrintCheck( TotalOrdersP, OrderLP, ArbP, snAP, mtxP);
deleteArbArray(&ArbP2);
//Case Study two cluster on oposite edges periodic in y
int OrderLO;
int OrderHO;
int MidPtsTotalO;
int PeriodicXO = 0;
int PeriodicYO = 1;
int PeriodicZO = 0;
int XElecOnO = 1;
int YElecOnO = 0;
int ZElecOnO = 0;
SNarray snAO = newSNarray( 4, 3, 3);
//Create Trap Sites one at the left electrode
//One at the right electrode should not consider
//any clusters in the sample
SiteNode snO = getSN(snAO,1,0,1);
printSNarray(snAO);
rv = setEnergy(snO, -4);
assert(rv==0);
snO = getSN(snAO, 1,2,1);
rv = setEnergy(snO, -4);
assert(rv==0);
printSNarray(snAO);
//Testing non-periodic x, y and z 0 biasX 0 biasY 0 biasZ KT=0.024, and reOrgEnergy =1
matrix mtxO = CalculateAllHops(snAO, 0,0,0, 1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXO, PeriodicYO, PeriodicZO);
printMatrix(mtxO);
ArbArray mpAO = MPsort( &OrderLO, &OrderHO, &MidPtsTotalO, mtxO, snAO, PeriodicXO, PeriodicYO, PeriodicZO);
printf("Order Low %d Order High %d\n",OrderLO, OrderHO);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAO);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbO2 = SortOrderMag( OrderHO-OrderLO+1, OrderLO, mpAO);
assert(ArbO2!=NULL);
int TotalOrdersO = OrderHO-OrderLO+1;
printf("********************************************\n");
printArbArray(ArbO2, OrderLO);
printf("********************************************\n");
ArbArray ArbO = ClusterSort( TotalOrdersO, OrderLO, ArbO2);
printf("TotalOrdersR %d OrderLowR %d Elements used by ArbR2 %d\n",TotalOrdersP, OrderLO, getElementsUsed(ArbO2));
assert(ArbO!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbO, OrderLO);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersP, OrderLO, mtxO, &ArbO, snAO, PeriodicXO, PeriodicYO, PeriodicZO, XElecOnO, YElecOnO, ZElecOnO);
assert(rv==0);
printf("****************CHECK***********************\n");
rv = PrintCheck( TotalOrdersO, OrderLO, ArbO, snAO, mtxO);
deleteArbArray(&ArbO2);
//Case Study two cluster on oposite edges non-periodic in y
int OrderLM;
int OrderHM;
int MidPtsTotalM;
int PeriodicXM = 0;
int PeriodicYM = 0;
int PeriodicZM = 0;
int XElecOnM = 1;
int YElecOnM = 0;
int ZElecOnM = 0;
SNarray snAM = newSNarray( 4, 3, 3);
//Create Trap Sites one at the left electrode
//One at the right electrode should not consider
//any clusters in the sample
SiteNode snM = getSN(snAM,1,0,1);
printSNarray(snAM);
rv = setEnergy(snM, -4);
assert(rv==0);
snM = getSN(snAM, 1,2,1);
rv = setEnergy(snM, -4);
assert(rv==0);
printSNarray(snAM);
//Testing non-periodic x, y and z 0 biasX 0 biasY 0 biasZ, KT=0.024, and reOrgEnergy =1
matrix mtxM = CalculateAllHops(snAM, 0,0,0, 1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXM, PeriodicYM, PeriodicZM);
printMatrix(mtxM);
ArbArray mpAM = MPsort( &OrderLM, &OrderHM, &MidPtsTotalM, mtxM, snAM, PeriodicXM, PeriodicYM, PeriodicZM);
printf("Order Low %d Order High %d\n",OrderLM, OrderHM);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAM);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbM2 = SortOrderMag( OrderHM-OrderLM+1, OrderLM, mpAM);
assert(ArbM2!=NULL);
int TotalOrdersM = OrderHM-OrderLM+1;
printf("********************************************\n");
printArbArray(ArbM2, OrderLM);
printf("********************************************\n");
ArbArray ArbM = ClusterSort( TotalOrdersM, OrderLM, ArbM2);
printf("TotalOrdersR %d OrderLowR %d Elements used by ArbR2 %d\n",TotalOrdersM, OrderLM, getElementsUsed(ArbM2));
assert(ArbM!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbM, OrderLM);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersM, OrderLM, mtxM, &ArbM, snAM, PeriodicXM, PeriodicYM, PeriodicZM, XElecOnM, YElecOnM, ZElecOnM);
assert(rv==0);
printf("****************CHECK M***********************\n");
rv = PrintCheck( TotalOrdersM, OrderLM, ArbM, snAM, mtxM);
deleteArbArray(&ArbM2);
//Case Study two cluster on oposite edges periodic in z
int OrderLN;
int OrderHN;
int MidPtsTotalN;
int PeriodicXN = 0;
int PeriodicYN = 0;
int PeriodicZN = 0;
int XElecOnN = 1;
int YElecOnN = 0;
int ZElecOnN = 0;
SNarray snAN = newSNarray( 4, 3, 3);
//Create Trap Sites one at the left electrode
//One at the right electrode should not consider
//any clusters in the sample
SiteNode snN = getSN(snAN,1,1,0);
printSNarray(snAN);
rv = setEnergy(snN, -4);
assert(rv==0);
snN = getSN(snAN, 1,1,2);
rv = setEnergy(snN, -4);
assert(rv==0);
printSNarray(snAN);
//Testing non-periodic x, y and z 0 biasX, 0 biasY, 0 biasZ KT=0.024, and reOrgEnergy =1
matrix mtxN = CalculateAllHops(snAN, 0,0,0, 1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXN, PeriodicYN, PeriodicZN);
printMatrix(mtxN);
ArbArray mpAN = MPsort( &OrderLN, &OrderHN, &MidPtsTotalN, mtxN, snAN, PeriodicXN, PeriodicYN, PeriodicZN);
printf("Order Low %d Order High %d\n",OrderLN, OrderHN);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAN);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbN2 = SortOrderMag( OrderHN-OrderLN+1, OrderLN, mpAN);
assert(ArbN2!=NULL);
int TotalOrdersN = OrderHN-OrderLN+1;
printf("********************************************\n");
printArbArray(ArbN2, OrderLN);
printf("********************************************\n");
ArbArray ArbN = ClusterSort( TotalOrdersN, OrderLN, ArbN2);
printf("TotalOrdersR %d OrderLowR %d Elements used by ArbR2 %d\n",TotalOrdersN, OrderLN, getElementsUsed(ArbN2));
assert(ArbN!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbN, OrderLN);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersN, OrderLN, mtxN, &ArbN, snAN, PeriodicXN, PeriodicYN, PeriodicZN, XElecOnN, YElecOnN, ZElecOnN);
assert(rv==0);
printf("****************CHECK N***********************\n");
rv = PrintCheck( TotalOrdersN, OrderLN, ArbN, snAN, mtxN);
deleteArbArray(&ArbN2);
//Case Study two cluster on oposite edges periodic in z
int OrderLK;
int OrderHK;
int MidPtsTotalK;
int PeriodicXK = 0;
int PeriodicYK = 0;
int PeriodicZK = 1;
int XElecOnK = 1;
int YElecOnK = 0;
int ZElecOnK = 0;
SNarray snAK = newSNarray( 4, 3, 3);
//Create Trap Sites one at the left electrode
//One at the right electrode should not consider
//any clusters in the sample
SiteNode snK = getSN(snAK,1,1,0);
printSNarray(snAK);
rv = setEnergy(snK, -4);
assert(rv==0);
snK = getSN(snAK, 1,1,2);
rv = setEnergy(snK, -4);
assert(rv==0);
printSNarray(snAK);
//Testing non-periodic x, y and z 0 biasX 0 biasY 0 biasZ KT=0.024, and reOrgEnergy =1
matrix mtxK = CalculateAllHops(snAK, 0,0,0, 1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXK, PeriodicYK, PeriodicZK);
printMatrix(mtxK);
ArbArray mpAK = MPsort( &OrderLK, &OrderHK, &MidPtsTotalK, mtxK, snAK, PeriodicXK, PeriodicYK, PeriodicZK);
printf("Order Low %d Order High %d\n",OrderLK, OrderHK);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAK);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbK2 = SortOrderMag( OrderHK-OrderLK+1, OrderLK, mpAK);
assert(ArbK2!=NULL);
int TotalOrdersK = OrderHK-OrderLK+1;
printf("********************************************\n");
printArbArray(ArbK2, OrderLK);
printf("********************************************\n");
ArbArray ArbK = ClusterSort( TotalOrdersK, OrderLK, ArbK2);
printf("TotalOrdersR %d OrderLowR %d Elements used by ArbR2 %d\n",TotalOrdersK, OrderLK, getElementsUsed(ArbK2));
assert(ArbK!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbK, OrderLK);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersK, OrderLK, mtxK, &ArbK, snAK, PeriodicXK, PeriodicYK, PeriodicZK, XElecOnK, YElecOnK, ZElecOnK);
assert(rv==0);
printf("****************CHECK K***********************\n");
rv = PrintCheck( TotalOrdersK, OrderLK, ArbK, snAK, mtxK);
deleteArbArray(&ArbK2);
//Case Study periodic conditions percolation pathway across sample
int OrderLJ;
int OrderHJ;
int MidPtsTotalJ;
int PeriodicXJ = 1;
int PeriodicYJ = 1;
int PeriodicZJ = 1;
int XElecOnJ = 1;
int YElecOnJ = 0;
int ZElecOnJ = 0;
SNarray snAJ = newSNarray( 4, 3, 3);
//Create Trap Sites that cross the sample
SiteNode snJ = getSN(snAJ,0,1,1);
printSNarray(snAJ);
rv = setEnergy(snJ, -4);
assert(rv==0);
snJ = getSN(snAJ, 1,1,1);
rv = setEnergy(snJ, -4);
assert(rv==0);
snJ = getSN(snAJ, 2,1,1);
rv = setEnergy(snJ, -4);
assert(rv==0);
snJ = getSN(snAJ, 3, 1, 1);
rv = setEnergy(snJ, -4);
assert(rv==0);
printSNarray(snAJ);
//Testing non-periodic x, y and z 0 biasX 0 biasY 0 biasZ KT=0.024, and reOrgEnergy =1
matrix mtxJ = CalculateAllHops(snAJ, 0, 0,0,1, 1, SiteDistance,AttemptToHop,gamma,PeriodicXJ, PeriodicYJ, PeriodicZJ);
printMatrix(mtxJ);
ArbArray mpAJ = MPsort( &OrderLJ, &OrderHJ, &MidPtsTotalJ, mtxJ, snAJ, PeriodicXJ, PeriodicYJ, PeriodicZJ);
printf("Order Low %d Order High %d\n",OrderLJ, OrderHJ);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
printArbArray(mpAJ);
printf("oooooooooooooooooooooooooooooooooooooooooooo\n");
ArbArray ArbJ2 = SortOrderMag( OrderHJ-OrderLJ+1, OrderLJ, mpAJ);
assert(ArbJ2!=NULL);
int TotalOrdersJ = OrderHJ-OrderLJ+1;
printf("********************************************\n");
printArbArray(ArbJ2, OrderLJ);
printf("********************************************\n");
ArbArray ArbJ = ClusterSort( TotalOrdersJ, OrderLJ, ArbJ2);
printf("TotalOrdersR %d OrderLowR %d Elements used by ArbR2 %d\n",TotalOrdersJ, OrderLJ, getElementsUsed(ArbJ2));
assert(ArbJ!=NULL);
printf("--------------------------------------------\n");
printArbArray(ArbJ, OrderLJ);
printf("--------------------------------------------\n");
rv = FilterCluster( TotalOrdersJ, OrderLJ, mtxJ, &ArbJ, snAJ, PeriodicXJ, PeriodicYJ, PeriodicZJ, XElecOnJ, YElecOnJ, ZElecOnJ);
assert(rv==0);
printf("****************CHECJ***********************\n");
rv = PrintCheck( TotalOrdersJ, OrderLJ, ArbJ, snAJ, mtxJ);
printf("****************CHECK J NeighNodes*********************\n");
rv = CalculateNeighNodes(TotalOrdersJ, OrderLJ, &ArbJ, snAJ, PeriodicXJ, PeriodicYJ, PeriodicZJ);
assert(rv==0);
rv = PrintCheck( TotalOrdersJ, OrderLJ, ArbJ, snAJ, mtxJ);
deleteArbArray(&ArbJ2);
printf("****************CHECK K NeighNodes*********************\n");
//SNarray snAK = newSNarray( 4, 3, 3);
//int PeriodicXK = 0;
//int PeriodicYK = 0;
//int PeriodicZK = 1;
//SiteNode snK = getSN(snAK,1,1,0);
//snK = getSN(snAK, 1,1,2);
rv = PrintCheck( TotalOrdersK, OrderLK, ArbK, snAK, mtxK);
rv = CalculateNeighNodes(TotalOrdersK, OrderLK, &ArbK, snAK, PeriodicXK, PeriodicYK, PeriodicZK);
assert(rv==0);
rv = PrintCheck( TotalOrdersK, OrderLK, ArbK, snAK, mtxK);
deleteAllMidPointArray(&mpAK);
deleteMatrix(mtxK);
deleteSNarray(snAK);
deleteArbArray(&ArbK);
printf("****************CHECK M NeighNodes*********************\n");
//int PeriodicXM = 0;
//int PeriodicYM = 0;
//int PeriodicZM = 0;
//SNarray snAM = newSNarray( 4, 3, 3);
//SiteNode snM = getSN(snAM,1,0,1);
//snM = getSN(snAM, 1,2,1);
rv = PrintCheck( TotalOrdersM, OrderLM, ArbM, snAM, mtxM);
rv = CalculateNeighNodes(TotalOrdersM, OrderLM, &ArbM, snAM, PeriodicXM, PeriodicYM, PeriodicZM);
assert(rv==0);
rv = PrintCheck( TotalOrdersM, OrderLM, ArbM, snAM, mtxM);
printf("****************CHECK N NeighNodes*********************\n");
//int PeriodicXN = 0;
//int PeriodicYN = 0;
//int PeriodicZN = 0;
//SNarray snAN = newSNarray( 4, 3, 3);
//SiteNode snN = getSN(snAN,1,1,0);
//snN = getSN(snAN, 1,1,2);
rv = PrintCheck( TotalOrdersN, OrderLN, ArbN, snAN, mtxN);
rv = CalculateNeighNodes(TotalOrdersN, OrderLN, &ArbN, snAN, PeriodicXN, PeriodicYN, PeriodicZN);
assert(rv==0);
rv = PrintCheck( TotalOrdersN, OrderLN, ArbN, snAN, mtxN);
printf("****************CHECK O NeighNodes*********************\n");
//int PeriodicXO = 0;
//int PeriodicYO = 1;
//int PeriodicZO = 0;
//SNarray snAO = newSNarray( 4, 3, 3);
//SiteNode snO = getSN(snAO,1,0,1);
//snO = getSN(snAO, 1,2,1);
rv = PrintCheck( TotalOrdersO, OrderLO, ArbO, snAO, mtxO);
rv = CalculateNeighNodes(TotalOrdersO, OrderLO, &ArbO, snAO, PeriodicXO, PeriodicYO, PeriodicZO);
assert(rv==0);
rv = PrintCheck( TotalOrdersO, OrderLO, ArbO, snAO, mtxO);
printf("****************CHECK P NeighNodes*********************\n");
//int PeriodicXP = 1;
//int PeriodicYP = 0;
//int PeriodicZP = 0;
//SNarray snAP = newSNarray( 4, 3, 3);
//SiteNode snP = getSN(snAP,1,1,1);
//snP = getSN(snAP, 1,2,1);
rv = PrintCheck( TotalOrdersP, OrderLP, ArbP, snAP, mtxP);
rv = CalculateNeighNodes(TotalOrdersP, OrderLP, &ArbP, snAP, PeriodicXP, PeriodicYP, PeriodicZP);
assert(rv==0);
rv = PrintCheck( TotalOrdersP, OrderLP, ArbP, snAP, mtxP);
printf("****************CHECK T NeighNodes*********************\n");
//int PeriodicXT = 1;
//int PeriodicYT = 1;
//int PeriodicZT = 1;
//SNarray snAP = newSNarray( 3, 4, 3);
//SiteNode snP = getSN(snAP,0,1,1);
//snP = getSN(snAP, 3,1,1);
rv = PrintCheck( TotalOrdersT, OrderLT, ArbT, snAT, mtxT);
rv = CalculateNeighNodes(TotalOrdersT, OrderLT, &ArbT, snAT, PeriodicXT, PeriodicYT, PeriodicZT);
assert(rv==0);
rv = PrintCheck( TotalOrdersT, OrderLT, ArbT, snAT, mtxT);
printf("****************Calculate Pval J*********************\n");
rv = PrintCheck( TotalOrdersJ, OrderLJ, ArbJ, snAJ, mtxJ);
rv = CalculateSumAndP(TotalOrdersJ, snAJ, &ArbJ, mtxJ, attempts, PeriodicXJ, PeriodicYJ, PeriodicZJ);
printf("\n** After Run **\n");
rv = PrintCheck( TotalOrdersJ, OrderLJ, ArbJ, snAJ, mtxJ);
printf("****************Calculate Pval M*********************\n");
//int PeriodicXM = 0;
//int PeriodicYM = 0;
//int PeriodicZM = 0;
//SNarray snAM = newSNarray( 4, 3, 3);
//SiteNode snM = getSN(snAM,1,0,1);
//snM = getSN(snAM, 1,2,1);
rv = PrintCheck( TotalOrdersM, OrderLM, ArbM, snAM, mtxM);
printMatrix(mtxM);
rv = CalculateSumAndP(TotalOrdersM, snAM, &ArbM, mtxM, attempts, PeriodicXM, PeriodicYM, PeriodicZM);
printf("\n** After Run **\n");
rv = PrintCheck( TotalOrdersM, OrderLM, ArbM, snAM, mtxM);
deleteAllMidPointArray(&mpAM);
deleteMatrix(mtxM);
deleteSNarray(snAM);
deleteArbArray(&ArbM);
printf("****************Calculate Pval N*********************\n");
//int PeriodicXN = 0;
//int PeriodicYN = 0;
//int PeriodicZN = 0;
//SNarray snAN = newSNarray( 4, 3, 3);
//SiteNode snN = getSN(snAN,1,1,0);
//snN = getSN(snAN, 1,1,2);
rv = PrintCheck( TotalOrdersN, OrderLN, ArbN, snAN, mtxN);
printMatrix(mtxN);
rv = CalculateSumAndP(TotalOrdersN, snAN, &ArbN, mtxN, attempts, PeriodicXN, PeriodicYN, PeriodicZN);
printf("\n** After Run **\n");
rv = PrintCheck( TotalOrdersN, OrderLN, ArbN, snAN, mtxN);
deleteAllMidPointArray(&mpAN);
deleteMatrix(mtxN);
deleteSNarray(snAN);
deleteArbArray(&ArbN);
printf("****************Calculate Pval O*********************\n");
//int PeriodicXO = 0;
//int PeriodicYO = 1;
//int PeriodicZO = 0;
//SNarray snAO = newSNarray( 4, 3, 3);
//SiteNode snO = getSN(snAO,1,0,1);
//snO = getSN(snAO, 1,2,1);
rv = PrintCheck( TotalOrdersO, OrderLO, ArbO, snAO, mtxO);
printMatrix(mtxO);
rv = CalculateSumAndP(TotalOrdersO, snAO, &ArbO, mtxO, attempts, PeriodicXO, PeriodicYO, PeriodicZO);
printf("\n** After Run **\n");
rv = PrintCheck( TotalOrdersO, OrderLO, ArbO, snAO, mtxO);
printf("\nPrintArb Array\n");
printArbArray(ArbO,OrderLO);
printf("****************Calculate Pval P*********************\n");
//int PeriodicXP = 1;
//int PeriodicYP = 0;
//int PeriodicZP = 0;
//SNarray snAP = newSNarray( 4, 3, 3);
//SiteNode snP = getSN(snAP,0,1,1);
//snP = getSN(snAP, 3,1,1);
//Periodic in the X
rv = PrintCheck( TotalOrdersP, OrderLP, ArbP, snAP, mtxP);
printMatrix(mtxP);
rv = CalculateSumAndP(TotalOrdersP, snAP, &ArbP, mtxP, attempts, PeriodicXP, PeriodicYP, PeriodicZP);
printf("\n** After Run **\n");
rv = PrintCheck( TotalOrdersP, OrderLP, ArbP, snAP, mtxP);
printf("****************Calculate Pval T*********************\n");
if(ArbT==NULL){
printf("Arb T is NULL\n");
}else if(snAT==NULL){
printf("snAT is NULL\n");
}else if(mtxT==NULL){
printf("mtxT is NULL\n");
}
printf("Total Orders %d OrderL %d\n",TotalOrdersT, OrderLT);
rv = PrintCheck( TotalOrdersT, OrderLT, ArbT, snAT, mtxT);
printf("Printing Matrix T\n");
printMatrix(mtxT);
rv = CalculateSumAndP(TotalOrdersT, snAT, &ArbT, mtxT, attempts, PeriodicXT, PeriodicYT, PeriodicZT);
printf("\n** After Run **\n");
rv = PrintCheck( TotalOrdersT, OrderLT, ArbT, snAT, mtxT);
printf("PrintArb Array\n");
printArbArray(ArbT,OrderLT);
deleteAllMidPointArray(&mpAT);
deleteMatrix(mtxT);
deleteSNarray(snAT);
deleteArbArray(&ArbT);
printf("***************Connect Cluster J Check*****************\n");
//int PeriodicXJ = 1;
//int PeriodicYJ = 1;
//int PeriodicZJ = 1;
//SNarray snAJ = newSNarray( 4, 3, 3);
//Create Trap Sites that cross the sample
//SiteNode snJ = getSN(snAJ,0,1,1);
//snJ = getSN(snAJ, 1,1,1);
//snJ = getSN(snAJ, 2,1,1);
//snJ = getSN(snAJ, 3, 1, 1);
rv = ConnectClusterSN( TotalOrdersJ, snAJ, ArbJ);
printSNarray(snAJ);
printf("***************Connect Cluster O Check*****************\n");
//int PeriodicXO = 0;
//int PeriodicYO = 1;
//int PeriodicZO = 0;
//SNarray snAO = newSNarray( 4, 3, 3);
//SiteNode snO = getSN(snAO,1,0,1);
//snO = getSN(snAO, 1,2,1);
rv = ConnectClusterSN( TotalOrdersO, snAO, ArbO);
printSNarray(snAO);
deleteAllMidPointArray(&mpAO);
deleteMatrix(mtxO);
deleteSNarray(snAO);
deleteArbArray(&ArbO);
printf("***************FindCluster J Check*****************\n");
//int PeriodicXJ = 1;
//int PeriodicYJ = 1;
//int PeriodicZJ = 1;
//SNarray snAJ = newSNarray( 4, 3, 3);
//Create Trap Sites that cross the sample
//SiteNode snJ = getSN(snAJ,0,1,1);
//snJ = getSN(snAJ, 1,1,1);
//snJ = getSN(snAJ, 2,1,1);
//snJ = getSN(snAJ, 3, 1, 1);
ParameterFrame PF = newParamFrame();
PFset_AttemptToHop(PF,AttemptToHop);
PFset_gamma(PF,gamma);
PFset_Px(PF,PeriodicXJ);
PFset_Py(PF,PeriodicYJ);
PFset_Pz(PF,PeriodicZJ);
PFset_XElecOn(PF,XElecOnJ);
PFset_YElecOn(PF,YElecOnJ);
PFset_ZElecOn(PF,ZElecOnJ);
PFset_Attempts(PF,15);
PFset_reOrg(PF,1);
PFset_MovieFrames(PF,10);
PFset_SiteDist(PF,SiteDistance);
ArbArray ClArLLJJ;
rv = FindCluster( &OrderLJ, snAJ, 0,0,0, &ClArLLJJ, 1,PF);
printf("\nOld\n");
printArbArray(ArbJ,OrderLJ);
printf("\nNew\n");
printArbArray(ClArLLJJ, OrderLJ);
deleteAllMidPointArray(&mpAJ);
deleteMatrix(mtxJ);
deleteSNarray(snAJ);
deleteArbArray(&ArbJ);
deleteArbArray(&ClArLLJJ);
printf("***************FindCluster P Check*****************\n");
//int PeriodicXP = 1;
//int PeriodicYP = 0;
//int PeriodicZP = 0;
//SNarray snAP = newSNarray( 4, 3, 3);
//SiteNode snP = getSN(snAP,0,1,1);
PFset_Px(PF,PeriodicXJ);
PFset_Py(PF,PeriodicYJ);
PFset_Pz(PF,PeriodicZJ);
PFset_XElecOn(PF,XElecOnJ);
PFset_YElecOn(PF,YElecOnJ);
PFset_ZElecOn(PF,ZElecOnJ);
//snP = getSN(snAP, 3,1,1);
char FileName[] = "Data";
ArbArray ClArLLPP;
rv = FindCluster( &OrderLP, snAP, 0,0,0, &ClArLLPP, 1, PF);
printArbArray(ClArLLPP);
//rv = SaveCluster( FileName,OrderLP, snAP, 0.0,0.0,0.0, ClArLLPP, 1.0, PF);
printf("\nOld\n");
printArbArray(ArbP,OrderLP);
printf("\nNew\n");
printArbArray(ClArLLPP, OrderLP);
deleteAllMidPointArray(&mpAP);
deleteMatrix(mtxP);
deleteSNarray(snAP);
deleteArbArray(&ArbP);
deleteArbArray(&ClArLLPP);
deleteParamFrame(&PF);
double electricEnergyPx;
double electricEnergyPy;
double electricEnergyPz;
double KbT;
LoadCluster( FileName, &OrderLP, &snAP,&electricEnergyPx,&electricEnergyPy,&electricEnergyPz,&ClArLLPP,&KbT,&PF);
printSNarray_Detailed(snAP);
deleteSNarray(snAP);
deleteArbArray(&ClArLLPP);
deleteParamFrame(&PF);
int OrderLB;
int OrderHB;
int MidPtsTotalB;
int PeriodicXB = 1;
int PeriodicYB = 1;
int PeriodicZB = 1;
int XElecOnB = 1;
int YElecOnB = 0;
int ZElecOnB = 0;
SNarray snAB = newSNarray( 3,4,3);
//Create an artificial trap in snAB which in increment length is
//length 0-2 width 0-3 and height 0-2
SiteNode snB = getSN(snAB,1,1,1);
rv = setEnergy(snB, -3);
snB = getSN(snAB,1,2,1);
rv = setEnergy(snB, -3);
//Testing Periodic x,y and z 0 biasX 0 biasY 0 biasZ KT=1 and reOrgEnergy=1
matrix mtxB = CalculateAllHops(snAB, 0,0,0, 1,1,SiteDistance, AttemptToHop, gamma, PeriodicXB, PeriodicYB, PeriodicZB);
//Sorts all the data into midpoints
ArbArray mpAB = MPsort( &OrderLB, &OrderHB, &MidPtsTotalB, mtxB, snAB, PeriodicXB, PeriodicYB, PeriodicZB);
//Sorts midpoints into Nodes in link lists. Each element of mpAT is composed of a
//link list all of the same order of magnitude
int TotalOrdersB = OrderHB-OrderLB+1;
ArbArray ArbB2 = SortOrderMag( TotalOrdersB, OrderLB, mpAB);
//Sorts nodes into clusters
printf("Sorting Nodes into Clusters\n");
ArbArray ArbB = ClusterSort( TotalOrdersB, OrderLB, ArbB2);
//Filtering Cluster
printf("Filtering Clusters\n");
rv = FilterCluster( TotalOrdersB, OrderLB, mtxB, &ArbB, snAB,\
PeriodicXB, PeriodicYB, PeriodicZB,\
XElecOnB, YElecOnB, ZElecOnB);
printf("Calculating NeighNodes\n");
CalculateNeighNodes(TotalOrdersB, OrderLB, &ArbB, snAB, PeriodicXB, PeriodicYB, PeriodicZB);
printf("Calculating P values\n");
CalculateSumAndP( TotalOrdersB, snAB, &ArbB, mtxB, 15, PeriodicXB, PeriodicYB, PeriodicZB);
printf("Connecting nodes to clusters\n");
ConnectClusterSN( TotalOrdersB, snAB, ArbB);
//Deleting Every thing
printf("Deleting Phase\n");
deleteSNarray(snAB);
deleteAllMidPointArray(&mpAB);
deleteMatrix(mtxB);
deleteArbArray(&ArbB2);
deleteArbArray(&ArbB);
//atexit(mem_term);
*/
/*
printf("\nCreating Matrix with data to test cluster functions\n");
SNarray snA=newSNarray(SLength,SWidth,SHeight);
double electricField;
double electricEnergy;
electricField = voltage /(SLength*SiteDistance);
electricEnergy= SiteDistance*electricField;
initSite(electricEnergy, snA);
printf("\nCalling FindCluster Function\n");
ArbArray ClArLL;
ArbArray NeighClArLL;
FindCluster(snA, electricEnergy,0,0, &ClArLL, &NeighClArLL);
*/
return 0;
}
// Checkpoint algorithm.
// O(n^3) time
// O(n^2) space
score_t Phaser::partial_aligner(size_t i_ini,
size_t j_ini,
size_t k_ini,
size_t i_end,
size_t j_end,
size_t k_end,
size_t *i_med,
size_t *j_med,
size_t *k_med) {
assert(j_end >= j_ini || j_end + 1 == j_ini);
assert(i_end >= i_ini || i_end + 1 == i_ini);
assert(k_end >= k_ini);
score_t * prev_face[8];
score_t * curr_face[8];
my_pair * prev_check[8];
my_pair * curr_check[8];
// Obs: we will use local i (resp. j, k) from 0 to I_len (J_len, K_len).
// characters are stracted from i_ini+i (j, k resp.).
// checkpoint answer is shifted back at the end.
I_len = i_end - i_ini + 1;
J_len = j_end - j_ini + 1;
size_t K_len = k_end - k_ini + 1;
size_t mid_k = K_len/2;
for (size_t m = 0; m < 8; m++) {
prev_face[m] = new score_t[(I_len+1) * (J_len+1)];
prev_check[m] = new my_pair[(I_len+1) * (J_len+1)];
}
// 8 points:
for (bool cf : {false, true}) {
for (bool ff : {false, true}) {
for (bool mf : {false, true}) {
size_t m = m_index(mf, ff, cf);
prev_face[m][IJ(0, 0)] = 0;
prev_check[m][IJ(0, 0)] = my_pair(0, 0);
}
}
}
// 8 lines (j=0):
for (size_t i = 1; i <= I_len; i++) {
for (bool cf : {false, true}) {
for (bool ff : {false, true}) {
for (bool mf : {false, true}) {
size_t m = m_index(mf, ff, cf);
char m_char = mf ? M2[i_ini + i-1] : M1[i_ini + i-1];
prev_face[m][IJ(i, 0)] = std::max(prev_face[m_index(0, ff, cf)][IJ(i-1, 0)] + score(m_char, '-'), // NOLINT
prev_face[m_index(1, ff, cf)][IJ(i-1, 0)] + score(m_char, '-')); // NOLINT
prev_check[m][IJ(i, 0)] = my_pair(i, 0);
}
}
}
}
// 8 faces:
for (size_t j = 1; j <= J_len; j++) {
for (size_t i = 0; i <= I_len; i++) {
for (bool cf : {false, true}) {
for (bool ff : {false, true}) {
for (bool mf : {false, true}) {
size_t m = m_index(mf, ff, cf);
char f_char = ff ? F2[j_ini + j-1] : F1[j_ini + j-1];
prev_face[m][IJ(i, j)] = std::max(prev_face[m_index(mf, 0, cf)][IJ(i, j-1)] + score(f_char, '-'), // NOLINT
prev_face[m_index(mf, 1, cf)][IJ(i, j-1)] + score(f_char, '-')); // NOLINT
prev_check[m][IJ(i, j)] = my_pair(i, j);
}
}
}
}
}
PrintFace(prev_face);
bool malloc_opt = true;
if (malloc_opt) {
for (size_t m = 0; m < 8; m++) {
curr_face[m] = new score_t[(I_len+1) * (J_len+1)];
curr_check[m] = new my_pair[(I_len+1) * (J_len+1)];
}
}
// the rest of the faces:
for (size_t k = 1; k <= K_len; k++) {
if (!malloc_opt) {
for (size_t m = 0; m < 8; m++) {
curr_face[m] = new score_t[(I_len+1) * (J_len+1)];
curr_check[m] = new my_pair[(I_len+1) * (J_len+1)];
}
}
for (size_t j = 0; j <= J_len; j++) {
for (size_t i = 0; i <= I_len; i++) {
for (bool cf : {false, true}) {
for (bool ff : {false, true}) {
for (bool mf : {false, true}) {
// m_char anf f_char should not be used, at least i > 0 (j > 0).
// If that is not the case, we initilize with a non-accepted character that
// will trig an error if used.
char m_char, f_char;
if (i > 0) {
m_char = mf ? M2[i_ini + i-1] : M1[i_ini + i-1];
} else {
m_char = 'J'; // Not in gen alphabet, will trigger an error if used.
}
if (j > 0) {
f_char = ff ? F2[j_ini + j-1] : F1[j_ini + j-1];
} else {
f_char = 'J'; // Not in gen alphabet, will trigger an error if used.
}
char c_1 = cf ? C2[k_ini + k-1] : C1[k_ini + k-1];
char c_2 = cf ? C1[k_ini + k-1] : C2[k_ini + k-1];
UpdateGeneral(curr_face,
prev_face,
curr_check,
prev_check,
i,
j,
k,
mid_k,
mf,
ff,
cf,
m_char,
f_char,
c_1,
c_2);
}
}
}
}
}
for (size_t m = 0; m < 8; m++) {
if (malloc_opt) {
score_t * tmp_face = prev_face[m];
my_pair * tmp_check = prev_check[m];
prev_face[m] = curr_face[m];
prev_check[m] = curr_check[m];
curr_face[m] = tmp_face;
curr_check[m] = tmp_check;
} else { delete[] (prev_face[m]);
delete[] (prev_check[m]);
prev_face[m] = curr_face[m];
prev_check[m] = curr_check[m];
}
}
if (k >= mid_k) {
// verbose = true;
}
PrintFace(prev_face);
PrintCheck(prev_check);
}
// we use char_i = M[i-1]
for (int i = 0; i < 8; i++) {
assert(prev_check[i][IJ(I_len, J_len)].first <= I_len);
assert(prev_check[i][IJ(I_len, J_len)].second <= J_len);
prev_check[i][IJ(I_len, J_len)].first--;
prev_check[i][IJ(I_len, J_len)].second--;
}
mid_k--;
// extract max:
score_t ans;
bool flip_ans;
ExtractMax(prev_face, prev_check, &ans, i_med, j_med, &flip_ans);
*k_med = k_ini + mid_k;
*i_med = i_ini + (*i_med);
*j_med = j_ini + (*j_med);
assert(CorrectIniMedEnd(i_ini, *i_med, i_end));
assert(CorrectIniMedEnd(j_ini, *j_med, j_end));
assert(CorrectIniMedEnd(k_ini, *k_med, k_end));
char phase_char = flip_ans ? '1' : '0';
if (phase_string[k_end] != '?') {
assert(phase_string[k_end] == phase_char);
}
if (phase_string[k_end] == '?') {
phase_string[k_end] = phase_char;
}
for (size_t m = 0; m < 8; m++) {
delete[] (prev_face[m]);
delete[] (prev_check[m]);
if (malloc_opt) {
delete[] (curr_face[m]);
delete[] (curr_check[m]);
}
}
return ans;
}