void zoom_bookmark_jump_to(const ZoomBookmark* mark, GDisplay *gdisp)
{
zoom_bookmark_check_init();
change_scale(gdisp, mark->zoom);
scroll_display(gdisp, mark->image_offset_x - gdisp->offset_x,
mark->image_offset_y - gdisp->offset_y);
}
/**
* \brief The fonction called when a corrupting_bonus is updated.
* \param value The new number of corrupting_bonus.
*/
void ptb::corrupting_bonus_component::on_corrupting_bonus_updated
(unsigned int value)
{
if ( value < m_last_corrupting_bonus_count )
change_scale();
else
create_floating_corrupting_bonus();
move();
} // corrupting_bonus_component::on_corrupting_bonus_updated()
void output_repeat_legend(FILE *fp, int *startpos, int **breaks, int *numsegment, int **colorindex, char **chrname, int num)
{
int i, j, k, l, m, n;
int base[50], point[4][2];
char c, name[100], temp[100];
char **str;
double label[3];
str = (char **) ckalloc(10 * sizeof(char *));
for(i = 0; i < 10; i ++) {
str[i] = (char *) ckalloc(100 * sizeof(char));
}
sprintf(str[0], "Repeat ID");
sprintf(str[1], "Length");
sprintf(str[2], "Chromosome");
sprintf(str[3], "From-to");
sprintf(str[4], "Subrepeats");
sprintf(str[5], "From-to");
base[0] = 50;
base[1] = 800;
outputline(fp, str, 6, base, 90, 10);
base[1] -= 20;
for(i = 0; i < num; i ++) {
for(j = 0; j < numsegment[i]; j ++) {
if(j == 0) {
sprintf(str[0], "R%d", i + 1);
sprintf(str[1], "%d", breaks[i][numsegment[i]]);
sprintf(str[2], "%s", chrname[i]);
sprintf(str[3], "%d-%d", startpos[i], startpos[i] + breaks[i][numsegment[i]] - 1);
} else {
str[0][0] = str[1][0] = str[2][0] = str[3][0] = '\0';
}
m = (colorindex[i][j] - 1) % total_color;
sprintf(str[4], "s%d", colorindex[i][j]);
sprintf(str[5], "%d-%d", startpos[i] + breaks[i][j], startpos[i] + breaks[i][j + 1] - 1);
base[0] = 50;
base[1] -= 10;
outputline(fp, str, 6, base, 90, 8);
if(base[1] <= 50) {
base[0] = 50;
base[1] = 800;
showpage(fp);
fprintf(fp, "%%%%Page: P%d\n", npages);
npages ++;
change_scale(fp, scale);
}
}
}
for(i = 0; i < 10; i ++) {
free((void *) str[i]);
}
free((void *) str);
}
int key_hook(int keycode, t_all *all)
{
if (keycode == 65453)
change_scale(all, 1);
if (keycode == 65451)
change_scale(all, 2);
if (keycode == 65364)
change_scale(all, 3);
if (keycode == 65362)
change_scale(all, 4);
if (keycode == 65363)
change_scale(all, 5);
if (keycode == 65361)
change_scale(all, 6);
if (keycode == 65307)
exit (0);
return (0);
}
main(int argc, char **argv)
{
int i, j, k, l, m, n, len_seq[100], reallen[100];
char **chrname;
int *dir, **breaks, **colorindex, base[2];
char **brchrname;
int *multip, *multip2, *repeat_length, num_repeat, *startpos, *numsegment;
int num_ins, *insertpos, *insertlen;
int global_scale;
SEGMENT *segment, segment0;
long int START_POS;
int num_segment;
int **repeats;
int range[2];
int num_chro;
char name[1000], temp[1000], c;
char pt;
FILE *fp, *fp1;
if(argc < 4) {
printf("Usage: makefig intv_file output_file(ps format) chrolistfile\n");
exit(-1);
}
chrname = alloc_name(100, 100);
fp = ckopen(argv[3], "r");
num_chro = readchrolist(len_seq, chrname, reallen, fp);
fclose(fp);
segment = (SEGMENT *) ckalloc(20000 * sizeof(SEGMENT));
fp = ckopen(argv[1], "r");
num_segment = input_segment(segment, chrname, num_chro, fp);
fclose(fp);
/* Sort the segments */
qsort((void *) segment, num_segment, sizeof(SEGMENT), (void *) segcompar);
/*
for(i = 0; i < num_segment; i ++) {
printf("aftersort segment %d %d %d\n", segment[i].pos[0], segment[i].pos[1], segment[i].eq_pos[1]);
}
getchar();
*/
/* Compute multiplicity of each sub-repeat */
repeat_length = (int *) ckalloc(20000 * sizeof(int));
multip = (int *) ckalloc(20000 * sizeof(int));
num_repeat = 0;
k = 0;
for(i = 0; i < num_segment; i ++) {
repeat_length[segment[i].eq_pos[0] - 1] = segment[i].length;
multip[segment[i].eq_pos[0] - 1] ++;
if(segment[i].eq_pos[0] > num_repeat) {
num_repeat = segment[i].eq_pos[0];
}
}
printf("num_repeat %d\n", num_repeat);
global_scale = 25;
multip2 = (int *) ckalloc(num_repeat * sizeof(int));
repeats = (int **) ckalloc(num_repeat * sizeof(int *));
for(i = 0; i < num_repeat; i ++) {
repeats[i] = (int *) ckalloc((1 + multip[i]) * sizeof(int));
}
startpos = (int *) ckalloc(num_segment * sizeof(int));
numsegment = (int *) ckalloc(num_segment * sizeof(int));
breaks = (int **) ckalloc(num_segment * sizeof(int *));
brchrname = (char **) ckalloc(num_segment * sizeof(char *));
colorindex = (int **) ckalloc(num_segment * sizeof(int *));
for(i = 0; i < num_segment; i ++) {
breaks[i] = (int *) ckalloc(num_segment * sizeof(int));
brchrname[i] = (char *) ckalloc(100 * sizeof(char));
colorindex[i] = (int *) ckalloc(num_segment * sizeof(int));
}
dir = (int *) ckalloc(num_segment * sizeof(int));
k = m = 0;
fp = ckopen(argv[2], "w");
prt_Header(fp, "Tang Hai-xu", "OUTPUT", "2-21-2004", 0);
prt_Macro(fp);
scale[0] = 0.7;
scale[1] = 0.8;
change_scale(fp, scale);
base[0] = 50;
base[1] = 850;
for(i = 0; i < num_segment; i ++) {
if(i == num_segment - 1 || segment[i + 1].pos[0] > segment[i].pos[1] + min_length ||
segment[i + 1].chro != segment[i].chro) {
for(j = k; j <= i; j ++) {
breaks[m][j - k + 1] += segment[j].pos[1] - segment[k].pos[0] + 1;
colorindex[m][j - k] = segment[j].eq_pos[0];
dir[j - k] = segment[j].eq_pos[1];
repeats[segment[j].eq_pos[0] - 1][multip2[segment[j].eq_pos[0] - 1] ++] = m;
}
startpos[m] = range[0] = segment[k].pos[0];
numsegment[m] = i - k + 1;
strcpy(brchrname[m], chrname[segment[i].chro]);
range[1] = segment[i].pos[1];
sprintf(name, "R%d", m + 1);
l = output_region(fp, base, name, chrname[segment[k].chro], range,
global_scale, breaks[m], i - k + 2, colorindex[m], dir);
m ++;
base[0] = 50;
base[1] -= 25;
if(base[1] < 150) {
showpage(fp);
fprintf(fp, "%%%%Page: P%d\n", npages);
npages ++;
change_scale(fp, scale);
base[0] = 50;
base[1] = 850;
}
k = i + 1;
}
}
showpage(fp);
fprintf(fp, "%%%%Page: P%d\n", npages);
npages ++;
change_scale(fp, scale);
fflush(fp);
for(i = 0; i < num_repeat; i ++) {
if(multip[i] != multip2[i]) {
printf("i %d multip %d %d\n", i, multip[i], multip2[i]);
exit(0);
}
}
output_length_legend(fp);
output_legend(fp, repeat_length, multip, num_repeat, repeats);
showpage(fp);
fprintf(fp, "%%%%Page: P%d\n", npages);
npages ++;
change_scale(fp, scale);
output_repeat_legend(fp, startpos, breaks, numsegment, colorindex, brchrname, m);
showpage(fp);
page_trailer(fp);
restore_scale(fp);
prt_Trailer(fp, k + 1);
fclose(fp);
printf("%d regions output.\n", m);
chrname = free_name(chrname, 100);
for(i = 0; i < num_repeat; i ++) {
free((void *) repeats[i]);
}
free((void **) repeats);
free((void *) repeat_length);
for(i = 0; i < num_segment; i ++) {
free((void *) brchrname[i]);
free((void *) breaks[i]);
free((void *) colorindex[i]);
}
free((void *) multip);
free((void *) multip2);
free((void **) brchrname);
free((void **) breaks);
free((void **) colorindex);
free((void *) startpos);
free((void *) numsegment);
free((void *) dir);
free((void *) segment);
}
void output_legend(FILE *fp, int *repeat_length, int *multip, int num_repeat, int **repeats)
{
int i, j, k, l, m, n;
int base[50], point[4][2];
char c, name[100], temp[100];
char **str;
double label[3];
str = (char **) ckalloc(10 * sizeof(char *));
for(i = 0; i < 10; i ++) {
str[i] = (char *) ckalloc(100 * sizeof(char));
}
sprintf(str[0], "Subrepeat ID");
sprintf(str[1], "Length");
sprintf(str[2], "Multiplicity");
sprintf(str[3], "Repeats");
sprintf(str[4], "Color coding");
base[0] = 50;
base[1] = 680;
outputline(fp, str, 5, base, 60, 10);
for(i = 0; i < num_repeat; i ++) {
if(multip[i] == 0) continue;
sprintf(name, "s%d", i + 1);
strcpy(str[0], name);
sprintf(str[1], "%d", repeat_length[i]);
sprintf(str[2], "%d", multip[i]);
str[3][0] = '\0';
for(j = 0; j < min(multip[i], MIN_NUM); j ++) {
sprintf(temp, "R%d ", repeats[i][j] + 1);
strcat(str[3], temp);
}
base[0] = 50;
base[1] -= 10;
outputline(fp, str, 4, base, 60, 8);
point[0][0] = 370;
point[0][1] = base[1];
point[1][0] = 370 + length_intv(repeat_length[i]);
point[1][1] = base[1];
point[2][0] = 370 + length_intv(repeat_length[i]);
point[2][1] = base[1] + 5;
point[3][0] = 370;
point[3][1] = base[1] + 5;
m = i % total_color;
for(j = 0; j < 3; j ++) {
label[j] = color_box[m][j];
}
prt_box(fp, point, label, 0, 0, 0);
base[0] = 370 + length_intv(repeat_length[i]) / 2;
base[1] += 2;
prt_Text(fp, name, base, 8, 0);
if(base[1] <= 50 && i < num_repeat - 1) {
base[0] = 50;
base[1] = 800;
showpage(fp);
fprintf(fp, "%%%%Page: P%d\n", npages);
npages ++;
change_scale(fp, scale);
}
}
for(i = 0; i < 10; i ++) {
free((void *) str[i]);
}
free((void *) str);
}
