VecDoub PressureTable::DensityFromP(VecDoub_I vec) {
double Press = vec[0]*P_scale;
double rho;
VecDoub vec_out(1, 0.0);
int nPress = GetDimension1();
double P_min = GetCoordinate1(0);
double P_max = GetCoordinate1(nPress-1);
if (Press <= P_max) {
if (Press >= P_min) {
rho = Lookup(Press,Z_newton,Zv_newton,C_newton,"rho0");
} else {
double rho_min = Lookup(P_min,Z_newton,Zv_newton,C_newton,"rho0");
rho = rho_min*Press/P_min;
}
} else {
double rho_max = Lookup(P_max,Z_newton,Zv_newton,C_newton,"rho0");
rho = rho_max*Press/P_max;
}
vec_out[0] = rho-rho_newton;
if (verbose_newton) {
cout << "( " << Press << " ) => ( "
<< rho << " vs " << rho_newton << " )"
<< endl;
}
return vec_out;
}
VecDoub PressureTable::YcAndDensityFromCPT(VecDoub_I vec) {
double eps = 1.0e-4;
double C = vec[0];
double Press = vec[1]*P_scale;
double Yc;
double rho;
VecDoub vec_out(2, 0.0);
double Yc_eq = Lookup(Press,Z_newton,Zv_newton,1.0,"PROG");
Yc = C*Yc_eq;
// Define Yc to find the solution C=0 when Yc_eq = 0 (necessary for Z=0 or 1, Sz = 1)
if (Yc_eq == 0.0) {
Yc = Yc_newton + C;
} else if (Yc_eq < eps) {
// or when Yc_eq < eps
Yc = Yc_newton*C;
}
double RoM = Lookup(Press, Z_newton,Zv_newton,C, "RoM");
rho = Press/(RoM*T_newton);
vec_out[0] = Yc-Yc_newton;
vec_out[1] = rho-rho_newton;
if (verbose_newton) {
cout << "( " << C << " , " << Press << " ) => ( "
<< vec_out[0] << " , " << vec_out[1] << " )"
<< endl;
cout << "Yc : " << Yc << " vs " << Yc_newton << endl;
cout << "rho : " << rho << " vs " << rho_newton << endl;
}
return vec_out;
}
VecDoub PressureTable::DensityFromPT(VecDoub_I vec) {
double Press = vec[0]*P_scale;
double rho;
VecDoub vec_out(1, 0.0);
double RoM = Lookup(Press, Z_newton,Zv_newton,C_newton, "RoM");
rho = Press/(RoM*T_newton);
vec_out[0] = rho-rho_newton;
if (verbose_newton) {
cout << "( " << Press << " ) => ( "
<< rho << " vs " << rho_newton << " )"
<< endl;
}
return vec_out;
}
VecDoub PressureTable::YcAndDensityFromCP(VecDoub_I vec) {
double eps = 1.0e-4;
double C = vec[0];
double Press = vec[1]*P_scale;
double Yc;
double rho;
VecDoub vec_out(2, 0.0);
double Yc_eq = Lookup(Press,Z_newton,Zv_newton,1.0,"PROG");
Yc = C*Yc_eq;
// Define Yc to find the solution C=0 when Yc_eq = 0 (necessary for Z=0 or 1, Sz = 1)
if (Yc_eq == 0.0) {
Yc = Yc_newton + C;
} else if (Yc_eq < eps) {
// or when Yc_eq < eps
Yc = Yc_newton*C;
}
int nPress = GetDimension1();
double P_min = GetCoordinate1(0);
double P_max = GetCoordinate1(nPress-1);
if (Press <= P_max) {
if (Press >= P_min) {
rho = Lookup(Press,Z_newton,Zv_newton,C,"rho0");
} else {
double rho_min = Lookup(P_min,Z_newton,Zv_newton,C,"rho0");
rho = rho_min*Press/P_min;
}
} else {
double rho_max = Lookup(P_max,Z_newton,Zv_newton,C,"rho0");
rho = rho_max*Press/P_max;
}
vec_out[0] = Yc-Yc_newton;
vec_out[1] = rho-rho_newton;
if (verbose_newton) {
cout << "( " << C << " , " << Press << " ) => ( "
<< vec_out[0] << " , " << vec_out[1] << " )"
<< endl;
cout << "Yc : " << Yc << " vs " << Yc_newton << endl;
cout << "rho : " << rho << " vs " << rho_newton << endl;
}
return vec_out;
}
VecDoub PressureTable::YcAndDensityFromCP_new(VecDoub_I vec) {
double eps = 1.0e-4;
double C = vec[0];
double Press = vec[1]*P_scale;
double Yc;
double rho;
VecDoub vec_out(2, 0.0);
double Yc_eq = Lookup(Press,Z_newton,Zv_newton,1.0,"PROG");
Yc = C*Yc_eq;
// Define Yc to find the solution C=0 when Yc_eq = 0 (necessary for Z=0 or 1, Sz = 1)
if (Yc_eq == 0.0) {
Yc = Yc_newton + C;
} else if (Yc_eq < eps) {
// or when Yc_eq < eps
Yc = Yc_newton*C;
}
double RoM, T0, E0, GAMMA0, AGAMMA;
LookupSelectedCoeff(RoM, T0, E0, GAMMA0, AGAMMA, Press, Z_newton,Zv_newton,C);
double Temp;
if (AGAMMA == 0.0)
Temp = T0 + (GAMMA0 - 1.0) / RoM * (E_newton - E0);
else
Temp = T0 + (GAMMA0 - 1.0) / AGAMMA * (exp(AGAMMA * (E_newton - E0) / RoM) - 1.0);
rho = Press/(RoM*Temp);
vec_out[0] = Yc-Yc_newton;
vec_out[1] = rho-rho_newton;
if (verbose_newton) {
cout << "( " << C << " , " << Press << " ) => ( "
<< vec_out[0] << " , " << vec_out[1] << " )"
<< endl;
cout << "Yc : " << Yc << " vs " << Yc_newton << endl;
cout << "rho : " << rho << " vs " << rho_newton << endl;
}
return vec_out;
}
VecDoub PressureTable::DensityFromP_new(VecDoub_I vec) {
double Press = vec[0]*P_scale;
double rho;
VecDoub vec_out(1, 0.0);
double RoM, T0, E0, GAMMA0, AGAMMA;
LookupSelectedCoeff(RoM, T0, E0, GAMMA0, AGAMMA, Press, Z_newton,Zv_newton,C_newton);
double Temp;
if (AGAMMA == 0.0)
Temp = T0 + (GAMMA0 - 1.0) / RoM * (E_newton - E0);
else
Temp = T0 + (GAMMA0 - 1.0) / AGAMMA * (exp(AGAMMA * (E_newton - E0) / RoM) - 1.0);
rho = Press/(RoM*Temp);
vec_out[0] = rho-rho_newton;
if (verbose_newton) {
cout << "( " << Press << " ) => ( "
<< rho << " vs " << rho_newton << " )"
<< endl;
}
return vec_out;
}
// moving average on vector nPoints a,(b,(c)) of given sensor, thread safe
// container: unique class object
// xma: average type
// pv: use xma to smooth position or velocity
// nPoints: window length, longer window equals smoother results, but slower end-point convergence
// estimate: nPoints = freq * w_time; [s = 1/s * s]
// initEndEff: user set start point
void moving_average(DataContainer* container, int sensor_in)
{
// xma average type
int xma = container->getInt(1);
int pv = container->getInt(2);
int nPoints = container->getInt(3);
// tell container in getVec which flag to strike
int accessor;
// to smooth vector entries
int a = 0;
int b = 0;
int c = 0;
// interactive marker menu 1:notchecked 2:checked
double ui_validjumps = 1;
// iteration counter
int count = 1;
// invalid iteration counter
int invalidCount = 0;
// time between last saved window-entry
double t_delta = 0.;
// smoothed entries
double x = 0.;
double y = 0.;
double z = 0.;
// velocity is calculated by the last two smoothed entries divided by their t_delta
// Suffix _delta indicates incremental steps.
double v_x = 0.;
double v_y = 0.;
double v_z = 0.;
double x_delta = 0.;
double y_delta = 0.;
double z_delta = 0.;
double v_x_delta = 0.;
double v_y_delta = 0.;
double v_z_delta = 0.;
// EMA adjusting factor
double alpha;
// XMA weights
std::vector<double> weights;
// temporary for setVec, p:3,4,5 v:6,7,8
std::vector<double> vec_out(9, 0);
// first t_delta will therefore be huge
vec_out[0] = ros::Time::now().toNSec();
// info on how many points were involved
vec_out[2] = nPoints;
// temporary vector for getVec
std::vector<double> tmp(6, 0);
// intital end-effector position
std::vector<double> initEndEff(6, 0);
// window holds past nPoints, w[length-1] is the oldest entry
std::vector<std::vector<double> > w;
// timespan before rechecking Flag
struct timespec req, rem;
req.tv_sec = 0;
req.tv_nsec = 30000000; // 33Hz
if (sensor_in == 15)
{ // 3D point
accessor = 1;
a = 3;
b = 4;
c = 5;
initEndEff[0] = ros::Time::now().toNSec();
initEndEff[1] = sensor_in;
initEndEff[2] = nPoints;
initEndEff[3] = container->getInt(5);
initEndEff[4] = container->getInt(6);
initEndEff[5] = container->getInt(7);
for (int i = 0; i < nPoints; ++i)
{
w.push_back(initEndEff);
}
vec_out[1] = 16;
}
else
{
ROS_ERROR(NNAME": xma for Sensor_in %d not set up.", sensor_in);
return;
}
// calculate weights
weights.resize(nPoints, 1. / nPoints); // SMA
if (xma == 1)
{ // LMA
double sum = 0.;
for (int i = 1; i <= nPoints; ++i)
{
weights[nPoints - i] = 1. / nPoints * i;
sum += 1. / nPoints * i;
}
// normalize, division gets superfluous
for (int i = 0; i < nPoints; ++i)
weights[i] /= sum;
}
else if (xma == 2)
{ // EMA
// choose alpha (0;1), close to 1: aggressive response
// 0: stay on init value
// 1: output the input
alpha = nPoints/100;
}
while (!ros::isShuttingDown() && container->getInt(14) == 0)
{
// do until valid vector
bool valid = false;
while (!valid)
{
if (container->checkVecFlag(accessor, sensor_in) == 1)
{
container->getVec(accessor, sensor_in, tmp);
if (validPoint(container, tmp, w[0]))
{
valid = true;
w.insert(w.begin(), 1, tmp);
w.pop_back();
container->setInt(12, 0);
invalidCount = 0;
}
else if (invalidCount > 90)
{
container->setInt(12, 1);
invalidCount = 0;
}
else
{
invalidCount++;
}
}
else
{
nanosleep(&req, &rem);
if (ros::isShuttingDown()) {
return;
}
}
}
if (xma < 2)
{ // SMA LMA
x = 0.;
y = 0.;
z = 0.;
for (int i = 0; i < nPoints; ++i)
{
x += w[i][a] * weights[i];
y += w[i][b] * weights[i];
z += w[i][c] * weights[i];
}
}
else
{ // EMA
x = alpha * w[0][a] + (1. - alpha) * vec_out[3];
y = alpha * w[0][b] + (1. - alpha) * vec_out[4];
z = alpha * w[0][c] + (1. - alpha) * vec_out[5];
}
// calculate deltas and (velocity @EXPERIMENTAL), change!
if (accessor == 1)
t_delta = (w[0][0] - vec_out[0]); // kinect uses secs
else
t_delta = (w[0][0] - vec_out[0]) * 1e-9; // android nsces to secs
if (pv > 0)
{
x_delta = x - vec_out[3];
y_delta = y - vec_out[4];
z_delta = z - vec_out[5];
if (pv > 1)
{
v_x = x_delta / t_delta;
v_y = y_delta / t_delta;
v_z = z_delta / t_delta;
if (pv > 2 && count > 0)
{
v_x_delta = (v_x - vec_out[6]);
v_y_delta = (v_y - vec_out[7]);
v_z_delta = (v_z - vec_out[8]);
}
}
}
// refresh outgoing vector
vec_out[0] = w[0][0];
if (pv == 0)
{
vec_out[3] = x;
vec_out[4] = y;
vec_out[5] = z;
}
else if (pv == 1)
{
vec_out[3] = x_delta;
vec_out[4] = y_delta;
vec_out[5] = z_delta;
}
else if (pv == 2)
{
vec_out[3] = v_x;
vec_out[4] = v_y;
vec_out[5] = v_z;
}
else if (pv == 3 && count > 0)
{
vec_out[3] = v_x_delta;
vec_out[4] = v_y_delta;
vec_out[5] = v_z_delta;
}
container->setVec(vec_out);
// hold on to data for next loop
if (pv > 0)
{
vec_out[3] = x;
vec_out[4] = y;
vec_out[5] = z;
if (pv > 2)
{
vec_out[6] = v_x;
vec_out[7] = v_y;
vec_out[8] = v_z;
}
}
count++;
}
}
int complement_match (Representation* X_rep, Representation* Y_rep,
Map * map, int map_max,
int * map_ctr, int * map_best, int best_max, int parent_map){
Penalty_parametrization penalty_params; /* for SW */
double **x = X_rep->full;
int * x_type = X_rep->full_type;
int NX = X_rep->N_full;
double **y = Y_rep->full;
int * y_type = Y_rep->full_type;
int NY = Y_rep->N_full;
double F_effective = 0.0;
double F_current;
double q[4] = {0.0}, q_init[4] = {0.0};
double **x_rotated = NULL;
double **tr_x_rotated = NULL;
double **R;
double z_scr = 0.0, *z_best;
double avg, avg_sq, stdev;
double alpha = options.alpha;
double rmsd, best_rmsd[TOP_RMSD];
double **best_quat;
double cutoff_rmsd = 3.0; /* <<<<<<<<<<<<<<<<< hardcoded */
int *x_type_fudg, *y_type_fudg;
int *anchor_x, *anchor_y, no_anchors;
int no_top_rmsd = TOP_RMSD, chunk;
int x_ctr, y_ctr, top_ctr;
int **best_triple_x;
int **best_triple_y;
int x_triple[3], y_triple[3];
int retval, done = 0;
int best_ctr;
int i, j;
int t;
int smaller;
int my_map_ctr;
int stored_new;
int * x2y, map_unstable;
//time_t time_now, time_start;
int cull_by_dna (Representation * X_rep, int *set_of_directions_x,
Representation * Y_rep, int *set_of_directions_y,
int set_size, Map *map, double cutoff_rmsd);
int distance_of_nearest_approach (Representation * X_rep, int *set_of_directions_x,
Representation * Y_rep, int *set_of_directions_y,
int set_size, double * rmsd_ptr);
int same_hand_triple (Representation * X_rep, int *set_of_directions_x,
Representation * Y_rep, int *set_of_directions_y, int set_size);
int find_map (Penalty_parametrization * params, Representation *X_rep, Representation *Y_rep,
double ** R, double alpha, double * F_effective, Map *map,
int *anchor_x, int * anchor_y, int anchor_size );
int find_next_triple (double **X, double **Y,
int *x_type, int *y_type, int NX, int NY,
int *x_triple, int *y_triple);
int gradient_descent (int first_call, double alpha,
double **x, int * x_type, int NX,
double **y, int * y_type, int NY,
double *q_best, double *F_best_ptr) ;
int map_quality_metrics (Representation *X_rep, Representation *Y_rep,
double ** tr_x_rotated, Map * map, int *reasonable_angle_ct);
int monte_carlo (double alpha,
double **x, int * x_type, int NX,
double **y, int * y_type, int NY,
double *q_best, double *F_best_ptr);
int opt_quat (double ** x, int NX, int *set_of_directions_x,
double ** y, int NY, int *set_of_directions_y,
int set_size, double * q, double * rmsd);
int qmap (double *x0, double *x1, double *y0, double *y1, double * quat);
int store_sorted (Map * map, int NX, int NY, int *map_best, int map_max,
double * z_best, int best_ctr,
double z_scr, int my_map_ctr, int *stored);
map_best[0] = -1; /* it is the end-of-array flag */
if ( *map_ctr >= map_max ) {
fprintf (stderr, "Map array undersized.\n");
exit (1);
}
smaller = (NX <= NY) ? NX : NY;
/***********************/
/* memory allocation */
/***********************/
if ( ! (R=dmatrix(3,3) ) ) return 1; /* compiler is bugging me otherwise */
if ( ! (x_rotated = dmatrix (NX,3)) ) return 1;
if ( ! (tr_x_rotated = dmatrix (NX,3)) ) return 1;
if ( ! (best_quat = dmatrix (no_top_rmsd,4)) ) return 1;
if ( ! (best_triple_x = intmatrix (no_top_rmsd,3)) ) return 1;
if ( ! (best_triple_y = intmatrix (no_top_rmsd,3)) ) return 1;
if ( ! (z_best = emalloc(NX*NY*sizeof(double) )) ) return 1;
if ( ! (x_type_fudg = emalloc(NX*sizeof(int) )) ) return 1;
if ( ! (y_type_fudg = emalloc(NY*sizeof(int) )) ) return 1;
if ( ! (anchor_x = emalloc(NX*sizeof(int) )) ) return 1;
if ( ! (anchor_y = emalloc(NY*sizeof(int) )) ) return 1;
penalty_params.custom_gap_penalty_x = NULL;
penalty_params.custom_gap_penalty_y = NULL;
//if ( ! (penalty_params.custom_gap_penalty_x = emalloc(NX*sizeof(double) )) ) return 1;
//if ( ! (penalty_params.custom_gap_penalty_y = emalloc(NY*sizeof(double) )) ) return 1;
/***********************/
/***********************/
/* expected quantities */
/***********************/
avg = avg_sq = stdev = 0.0;
//if (options.postprocess) {
if (0) {
if (F_moments (x, x_type, NX, y, y_type, NY, alpha, &avg, &avg_sq, &stdev)) return 1;
}
/***********************/
/***********************/
/* initialization */
/***********************/
best_ctr = 0;
penalty_params.gap_opening = options.gap_open;
penalty_params.gap_extension = options.gap_extend;
penalty_params.endgap = options.endgap;
penalty_params.endgap_special_treatment = options.use_endgap;
/***********************/
/***************************************/
/* find reasonble triples of SSEs */
/* that correspond in type */
/* and can be mapped onto each other */
/***************************************/
for (top_ctr=0; top_ctr<no_top_rmsd; top_ctr++) {
best_rmsd[top_ctr] = BAD_RMSD+1;
best_triple_x[top_ctr][0] = -1;
}
for (x_ctr=0; x_ctr < NX-2 && !done; x_ctr++) {
for (y_ctr=0; y_ctr < NY-2 && !done; y_ctr++) {
if ( y_type[y_ctr] != x_type[x_ctr] ) continue;
x_triple[0] = x_ctr;
y_triple[0] = y_ctr;
if (find_next_triple (x, y, x_type, y_type,
NX, NY, x_triple, y_triple) ){
continue;
}
if ( x_triple[1] < 0 || x_triple[2] < 0 ) continue;
if ( y_triple[1] < 0 || y_triple[2] < 0 ) continue;
/* do these three have kind-of similar layout in space?*/
/* is handedness the same? */
if ( ! same_hand_triple ( X_rep, x_triple, Y_rep, y_triple, 3)) continue;
/* are distances comparab;e? */
if (distance_of_nearest_approach ( X_rep, x_triple,
Y_rep, y_triple, 3, &rmsd)) continue;
if ( rmsd > cutoff_rmsd) continue;
/* find q_init that maps the two triples as well as possible*/
if ( opt_quat ( x, NX, x_triple, y, NY, y_triple, 3, q_init, &rmsd)) continue;
for (top_ctr=0; top_ctr<no_top_rmsd; top_ctr++) {
if ( rmsd <= best_rmsd[top_ctr] ) {
chunk = no_top_rmsd - top_ctr -1;
if (chunk) {
memmove (best_rmsd+top_ctr+1, best_rmsd+top_ctr, chunk*sizeof(double));
memmove (best_quat[top_ctr+1],
best_quat[top_ctr], chunk*4*sizeof(double));
memmove (best_triple_x[top_ctr+1],
best_triple_x[top_ctr], chunk*3*sizeof(int));
memmove (best_triple_y[top_ctr+1],
best_triple_y[top_ctr], chunk*3*sizeof(int));
}
best_rmsd[top_ctr] = rmsd;
memcpy (best_quat[top_ctr], q_init, 4*sizeof(double));
memcpy (best_triple_x[top_ctr], x_triple, 3*sizeof(int));
memcpy (best_triple_y[top_ctr], y_triple, 3*sizeof(int));
break;
}
}
}
}
# if 0
for (top_ctr=0; top_ctr<no_top_rmsd; top_ctr++) {
if ( best_rmsd[top_ctr] > BAD_RMSD ) break;
printf (" %3d %8.3lf ", top_ctr, best_rmsd[top_ctr]);
vec_out ( best_quat[top_ctr], 4, "quat: ");
for (t=0; t<3; t++ ) {
printf ("\t %3d %3d \n", best_triple_x[top_ctr][t]+1, best_triple_y[top_ctr][t]+1 );
}
}
exit (1);
# endif
/*********************************************/
/* main loop */
/*********************************************/
for (top_ctr=0; top_ctr<no_top_rmsd; top_ctr++) {
if ( best_rmsd[top_ctr] > BAD_RMSD ) break;
quat_to_R (best_quat[top_ctr], R);
rotate (x_rotated, NX, R, x);
F_current = F( y, y_type, NY, x_rotated, x_type, NX, alpha);
# if 0
printf ("\n***********************************\n");
printf (" %3d %8.3lf %8.3lf ", top_ctr, best_rmsd[top_ctr], F_current);
vec_out ( best_quat[top_ctr], 4, "quat: ");
for (t=0; t<3; t++ ) {
printf ("\t %3d %3d \n", best_triple_x[top_ctr][t]+1, best_triple_y[top_ctr][t]+1 );
}
# endif
/* find map which uses the 2 triples as anchors */
no_anchors = 3;
find_map (&penalty_params, X_rep, Y_rep, R, alpha, &F_effective, map + (*map_ctr),
best_triple_x[top_ctr], best_triple_y[top_ctr], no_anchors);
x2y = ( map + (*map_ctr) ) ->x2y;
map_unstable = 0;
for (t=0; t<3; t++ ) {
if ( x2y[best_triple_x[top_ctr][t]] != best_triple_y[top_ctr][t] ) {
map_unstable = 1;
}
}
if ( map_unstable) continue;
/* dna here is not DNA but "distance of nearest approach" */
cull_by_dna ( X_rep, best_triple_x[top_ctr],
Y_rep, best_triple_y[top_ctr], 3, map + (*map_ctr), cutoff_rmsd );
//printf ("map after culling by dna:\n");
//print_map (stdout, map+ (*map_ctr), NULL, NULL, NULL, NULL, 1);
/* monte that optimizes the aligned vectors only */
for (i=0; i<NX; i++) {
x_type_fudg[i] = JACKFRUIT;
}
for (j=0; j<NY; j++) {
y_type_fudg[j] = JACKFRUIT*2;
}
no_anchors = 0;
for (i=0; i<NX; i++) {
j = (map+(*map_ctr))->x2y[i];
if (j < 0 ) continue;
x_type_fudg[i] = x_type[i];
y_type_fudg[j] = y_type[j];
anchor_x[no_anchors] = i;
anchor_y[no_anchors] = j;
no_anchors ++;
}
if ( opt_quat ( x, NX, anchor_x, y, NY, anchor_y, no_anchors, q, &rmsd)) continue;
retval = monte_carlo ( alpha, x, x_type_fudg, NX,
y, y_type_fudg, NY, q, &F_current);
if (retval) return retval;
if (options.postprocess) {
z_scr = stdev ? (F_current - avg)/stdev : 0.0;
} else {
z_scr = 0.0;
}
quat_to_R (q, R);
/* store_image() is waste of time, but perhaps not critical */
store_image (X_rep, Y_rep, R, alpha, map + (*map_ctr));
map_assigned_score ( X_rep, map + (*map_ctr));
//printf ("map %2d assigned score: %8.3lf z_score: %8.3lf \n\n",
// *map_ctr+1, (map + (*map_ctr)) -> assigned_score, z_scr);
/* store the map that passed all the filters down to here*/
my_map_ctr = *map_ctr;
map[my_map_ctr].F = F_current;
map[my_map_ctr].avg = avg;
map[my_map_ctr].avg_sq = avg_sq;
map[my_map_ctr].z_score = z_scr;
memcpy ( map[my_map_ctr].q, q, 4*sizeof(double) );
/* recalculate the assigned score*/
//if (top_ctr==24) exit (1);
/************************/
/* store sorted */
/************************/
/* find the place for the new z-score */
store_sorted (map, NX, NY, map_best, map_max,
z_best, best_ctr, -map[my_map_ctr].assigned_score, my_map_ctr, &stored_new);
if ( stored_new ) { /* we want to keep this map */
(*map_ctr) ++;
best_ctr++;
} /* otherwise this map space is reusable */
/* is this pretty much as good as it can get ? */
if ( fabs (map[my_map_ctr].assigned_score - smaller)
< options.tol ) done = 1;
}
map_best[best_ctr] = -1;
/******************************************************/
/* look for the sub-map of a couple of best hits */
/******************************************************/
/* initialization:*/
map_consistence ( NX, NY, NULL, NULL, NULL, NULL, NULL);
best_ctr = 0;
while ( map_best[best_ctr] > -1 ) {
best_ctr ++;
}
//exit (1);
if (best_ctr) {
int nr_maps = (best_ctr<options.number_maps_cpl)?
best_ctr : options.number_maps_cpl;
int best_i;
int consistent;
double z;
double total_assigned_score, score, best_score = -100;
double gap_score;
for (i=0; i<nr_maps; i++) { /* look for the complement */
best_i = map_best[i];
/*intialize the (list of) submatch map(s) */
if ( !map[best_i].submatch_best) {
/* for now look for a single map only */
/* TODO - would it be worth any to look at more maps?*/
int map_max = 1;
map[best_i].submatch_best = emalloc (map_max*sizeof(int) );
if (! map[best_i].submatch_best) return 1;
}
map[best_i].submatch_best[0] = -1;
map[best_i].score_with_children = 0;
map[best_i].compl_z_score = 0;
for (j=0; j<best_ctr; j++) {
if (i==j) continue;
map_complementarity ( map+best_i, map + map_best[j], &z);
map_consistence ( NX, NY, map+best_i, map + map_best[j],
&total_assigned_score, &gap_score, NULL);
consistent = ( (map+best_i)->assigned_score < total_assigned_score
&& (map + map_best[j])->assigned_score
< total_assigned_score);
if ( consistent ) {
score = total_assigned_score;
if ( score > best_score ) {
best_score = score;
map[best_i].submatch_best[0] = map_best[j];
map[best_i].score_with_children = total_assigned_score;
map[best_i].compl_z_score = z;
}
}
}
}
}
/**********************/
/* garbage collection */
gradient_descent (1, 0.0, NULL, NULL, 0,
NULL, NULL, 0, NULL, NULL);
free_dmatrix (R);
free_dmatrix (x_rotated);
free_dmatrix (tr_x_rotated);
free_dmatrix (best_quat);
free_imatrix (best_triple_x);
free_imatrix (best_triple_y);
free (z_best);
free (x_type_fudg);
free (y_type_fudg);
free (anchor_x);
free (anchor_y);
if (penalty_params.custom_gap_penalty_x) free (penalty_params.custom_gap_penalty_x);
if (penalty_params.custom_gap_penalty_y) free (penalty_params.custom_gap_penalty_y);
/*********************/
return 0;
}
