/*
* ----------------------------------------------------------------------
* Remove Pad Columns. Sometimes we don't want to realign data, we just
* want to remove (aligned) columns of pads.
* ----------------------------------------------------------------------
*/
int remove_pad_columns(GapIO *io, int ncontigs, contig_list_t *contigs,
int percent_pad, int quiet) {
int i;
consensus_t *cons = NULL;
size_t max_alloc = 0;
for (i = 0; i < ncontigs; i++) {
tg_rec cnum = contigs[i].contig;
size_t len, j;
int ndel = 0;
contig_t *c;
if (!quiet) {
vmessage("Processing contig %d of %d (#%"PRIrec")\n",
i+1, ncontigs, cnum);
UpdateTextOutput();
}
c = cache_search(io, GT_Contig, cnum);
if (!c)
return -1;
cache_incr(io, c);
len = contigs[i].end - contigs[i].start + 1;
if (max_alloc < len) {
max_alloc = len;
cons = realloc(cons, max_alloc * sizeof(*cons));
}
if (0 != calculate_consensus(io, cnum,
contigs[i].start, contigs[i].end,
cons)) {
free(cons);
cache_decr(io, c);
return -1;
}
for (j = 0; j < len; j++) {
if (cons[j].call != 4)
continue;
if (100 * cons[j].counts[4] / cons[j].depth < percent_pad)
continue;
if (!quiet)
vmessage(" Removing column %d %d%% pad (%d of %d), conf. %f)\n",
(int)j+contigs[i].start,
100 * cons[j].counts[4] / cons[j].depth,
cons[j].counts[4], cons[j].depth,
cons[j].scores[cons[j].call]);
contig_delete_base(io, &c, contigs[i].start + j - ndel);
ndel++;
}
cache_decr(io, c);
}
if (cons)
free(cons);
return 0;
}
void curses_loop(GapIO *io, contig_t **cp, int xpos, int mode) {
int ypos = 0;
int maxy, maxx;
int qual_cutoff = 29;
#ifdef NCURSES_VERSION
getmaxyx(stdscr, maxy, maxx);
#else
maxx = 80;
maxy = 40;
#endif
if (xpos < (maxx-MAX_NAME_LEN+2)/2)
xpos = (maxx-MAX_NAME_LEN+2)/2;
display_gap(io, cp, xpos, ypos, maxy, maxx, mode, qual_cutoff, 1);
for(;;) {
switch (getch()) {
case '!':
edit_contig_name(io, cp);
break;
case '"': /* control-x */
save(io);
break;
case 'd':
mode ^= DISPLAY_DIFFS;
break;
case 'c':
mode ^= DISPLAY_CUTOFFS;
break;
case 'C':
mode ^= DISPLAY_COLOURS;
break;
case 'q':
mode ^= DISPLAY_QUAL;
break;
case 'g':
xpos = wgotonum(xpos, gotowin);
break;
case 'G': {
char *seq = wgotoseq(gotowin);
tg_rec n;
if (seq) {
if ((n = sequence_index_query(io, seq)) < 0) {
putchar('\a');
fflush(stdout);
} else {
tg_rec c;
int x;
sequence_get_position(io, n, &c, &x, NULL, NULL);
/* FIXME: check c and *cp are same contig */
xpos = x;
}
}
break;
}
case '?':
whelp(helpwin);
break;
case '-':
qual_cutoff--;
break;
case '+':
qual_cutoff++;
break;
case 'n':
next_contig(io, cp);
xpos = ypos = 0;
break;
case 'p':
prev_contig(io, cp);
xpos = ypos = 0;
break;
/* Orthoganol movements */
case KEY_RIGHT:
case 'l':
xpos++;
break;
case KEY_SRIGHT:
case 'L':
xpos+=20;
break;
case '\014':
xpos+=1000;
break;
case KEY_LEFT:
case 'h':
xpos--;
break;
case KEY_SLEFT:
case 'H':
xpos-=20;
break;
case KEY_BACKSPACE:
case '\010':
xpos-=1000;
break;
case KEY_DOWN:
case 'j':
ypos++;
break;
case 'J':
ypos+=20;
break;
case KEY_UP:
case 'k':
ypos--;
break;
case 'K':
ypos-=20;
break;
case 'x':
return;
case '<':
xpos = (*cp)->start;
break;
case '>':
xpos = (*cp)->end;
break;
case 'f':
complement_bin(io, contig_get_bin(cp));
break;
case 'i':
contig_insert_base(io, cp, xpos, '-', 20);
break;
case 'o':
contig_delete_base(io, cp, xpos);
break;
#ifdef KEY_RESIZE
case KEY_RESIZE:
getmaxyx(stdscr, maxy, maxx);
break;
#endif
default:
continue;
}
if (xpos < (*cp)->start) xpos = (*cp)->start;
if (xpos > (*cp)->end) xpos = (*cp)->end;
if (ypos < 0) ypos = 0;
display_gap(io, cp, xpos, ypos, maxy, maxx, mode, qual_cutoff, 1);
}
}