void initialize_grid(struct grid *g, struct parList *par)
{
int nq = g->nq;
int ng11 = g->ng11;
int ng21 = g->ng21;
int nx1_int = g->nx1_int;
int nx2_int = g->nx2_int;
int d1 = g->d1;
int d2 = g->d2;
int i, j;
for(i=ng11; i < ng11+nx1_int; i++)
for(j=ng21; j < ng21+nx2_int; j++)
{
double xm[2] = {g->x1[i], g->x2[j]};
double xp[2] = {g->x1[i+1], g->x2[j+1]};
double x[2];
geom_CM(xm, xp, x);
initial_value(&(g->prim[d1*i+d2*j]), x, nq, par);
}
bc_1L(g, par);
bc_1R(g, par);
bc_2L(g, par);
bc_2R(g, par);
calc_cons(g, par);
}
static void benchmark(GapIO *io, contig_t **c) {
int i;
char cons[10000];
srandom(0);
fprintf(stderr, "=== Benchmarking ===\n");
for (i = 0; i < 1000; i++) {
int xpos = random() % 2000000;
int size = random() % 1000;
int nr;
rangec_t *r;
r = contig_seqs_in_range(io, c, xpos, xpos+size, 0, &nr);
calc_cons(io, r, nr, xpos, size, cons);
printf("%.*s\n", size, cons);
fputc('.', stderr);
fflush(stderr);
free(r);
}
gio_close(io);
exit(0);
}
void substep(struct grid *g, double rkfac1, double rkfac2, double dt,
struct parList *pars)
{
//Calculate gradients of grid quantities
calc_grad(g, pars);
//Solve Riemann problems.
add_fluxes(g, dt, pars);
//Add Sources.
add_sources(g, dt, pars);
//Update prims.
calc_prim(g, pars);
//Boundary Conditions.
bc_1L(g, pars);
bc_1R(g, pars);
bc_2L(g, pars);
bc_2R(g, pars);
//Re-update cons.
calc_cons(g, pars);
}
static void display_gap(GapIO *io, contig_t **c, int xpos, int ypos,
int nlines, int wid, int mode, int qual_cutoff,
int in_curses) {
rangec_t *r;
int i, nr, lno, y;
char line[1024], *lp;
char cons[1024];
int attr;
static int lookup_1conf[256];
static int lookup_4conf[256];
static int lookup_init = 0;
if (!lookup_init) {
for (i = 0; i < 256; i++)
lookup_1conf[i] = lookup_4conf[0] = 0;
lookup_4conf['a'] = lookup_4conf['A'] = 0;
lookup_4conf['c'] = lookup_4conf['C'] = 1;
lookup_4conf['g'] = lookup_4conf['G'] = 2;
lookup_4conf['t'] = lookup_4conf['T'] = 3;
}
wid -= MAX_NAME_LEN+2;
//if (xpos < wid/2 + (*c)->start)
// xpos = wid/2 + (*c)->start;
xpos -= wid/2;
/* Query visible objects */
r = contig_seqs_in_range(io, c, xpos, xpos+wid-1, CSIR_SORT_BY_X, &nr);
/* Consensus */
calc_cons(io, r, nr, xpos, wid, cons);
if (in_curses) {
clear();
mvaddnstr(0, 1, contig_get_name(c), strlen(contig_get_name(c)));
mvaddnstr(0, MAX_NAME_LEN+2, cons, wid);
} else {
printf(" %-*s %.*s\n", MAX_NAME_LEN, contig_get_name(c), wid, cons);
}
/* Position */
for (lp = line, i = xpos; i < xpos+wid+19; i++) {
if (i % 10 == 0) {
sprintf(lp, "%10d", i-10);
lp += 10;
}
}
if (in_curses) {
int m = (xpos-1)%10;
if (m < 0) m += 10;
mvaddnstr(1, MAX_NAME_LEN+2, line+10+m, wid);
} else {
printf("%*s%.*s\n", MAX_NAME_LEN+2, "", wid,
line+9+((xpos-1)%10));
}
/* Sequences */
for (i = y = 0; i < nr && y < ypos; i++, y++);
for (lno = 2; i < nr && lno < nlines; i++, lno++) {
seq_t *s = get_seq(io, r[i].rec);
seq_t *sorig = s;
int sp = r[i].start;
int l = s->len > 0 ? s->len : -s->len;
unsigned char seq_a[MAX_SEQ_LEN], *seq = seq_a;
int j, dir = '+';
int left, right;
char *conf;
int nc = s->format == SEQ_FORMAT_CNF4 ? 4 : 1;
int *L = s->format == SEQ_FORMAT_CNF4 ? lookup_4conf : lookup_1conf;
/* Complement data on-the-fly */
if ((s->len < 0) ^ r[i].comp) {
dir = '-';
s = dup_seq(s);
complement_seq_t(s);
}
left = s->left;
right = s->right;
memcpy(seq, s->seq, l);
conf = s->conf;
if (sp < xpos) {
seq += xpos - sp;
conf += nc * (xpos - sp);
l -= xpos - sp;
left -= xpos - sp;
right -= xpos - sp;
sp = xpos;
}
if (l > wid - (sp-xpos))
l = wid - (sp-xpos);
if (in_curses) {
/* Test of sequence_get_position */
/*
int c, p;
sequence_get_position(io, r[i].rec, &c, &p);
s->name_len = sprintf(s->name, ":%d-%d:", p, p+ABS(s->len)-1);
*/
mvaddch(lno, 0, dir);
addnstr(s->name, MIN(MAX_NAME_LEN, s->name_len));
move(lno, MAX_NAME_LEN+2+sp-xpos);
} else {
printf("%c%.*s%*s",
dir,
MIN(MAX_NAME_LEN, s->name_len), s->name,
MAX_NAME_LEN+1-MIN(MAX_NAME_LEN, s->name_len) +sp-xpos, "");
}
for (j = 0; j < l; j++) {
attr = (mode & DISPLAY_COLOURS) ? COLOR_PAIR(lookup[seq[j]]) : 0;
if (mode & DISPLAY_DIFFS
&& sp-xpos+j < wid && seq[j] == cons[sp-xpos+j])
seq[j] = '.';
if (j < left-1 || j > right-1)
seq[j] = (mode & DISPLAY_CUTOFFS) ? tolower(seq[j]) : ' ';
if (conf[j*nc+L[seq[j]]] >= qual_cutoff && mode & DISPLAY_QUAL) {
attr |= A_BOLD;
}
if (in_curses) {
addch(seq[j] | attr);
} else {
putchar(seq[j]);
}
}
if (!in_curses)
putchar('\n');
if (s != sorig)
free(s);
}
/* Useful debugging code to show bin locations. */
#if 0
free(r);
r = contig_bins_in_range(io, c, xpos, xpos+wid-1, &nr);
/* Bins */
for (i=0; i < nr && lno < nlines; i++, lno++) {
bin_index_t *bin = (bin_index_t *)cache_search(io, GT_Bin, r[i].rec);
unsigned char *seq, *seqm;
int j, dir = "+-"[r[i].comp];
int sp = r[i].start;
int l = ABS(r[i].end - r[i].start + 1);
char name[100];
sprintf(name, "bin-%d", bin->rec);
seqm = seq = malloc(l+1);
memset(seq, '-', l);
if (!(bin->start_used == 0 && bin->end_used == 0)) {
if (r[i].comp) {
memset(&seq[bin->size - bin->end_used - 1], '=',
bin->end_used - bin->start_used + 1);
} else {
memset(&seq[bin->start_used], '=',
bin->end_used - bin->start_used + 1);
}
}
/*
fprintf(stderr, "Bin-%d: %d+%d %d..%d\n",
bin->rec,
bin->pos, bin->size,
bin->start_used, bin->end_used);
*/
if (sp < xpos) {
seq += xpos - sp;
l -= xpos - sp;
sp = xpos;
}
if (l > wid - (sp-xpos))
l = wid - (sp-xpos);
if (in_curses) {
mvaddch(lno, 0, dir);
addnstr(name, strlen(name));
move(lno, MAX_NAME_LEN+2+sp-xpos);
} else {
printf("%c%.*s%*s",
dir,
(int)MIN(MAX_NAME_LEN, strlen(name)),
name,
(int)(MAX_NAME_LEN+1-MIN(MAX_NAME_LEN,
strlen(name)) +sp-xpos),
"");
}
for (j = 0; j < l; j++) {
if (in_curses) {
addch(seq[j]);
} else {
putchar(seq[j]);
}
}
if (!in_curses)
putchar('\n');
free(seqm);
}
#endif
if (in_curses)
refresh();
free(r);
}
