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#include <string.h>
#include "tkSeqed.h"
#include "genetic_code.h"
#include "dna_utils.h"
#include "seqed_restriction_enzymes.h"
#include "seqed_translate.h"
#include "xalloc.h"
#include "seqed_write.h"
/*
* all the write functions eg write the function to disk
*/
void seqed_write_sequence(char *sequence,
int pos,
int line_length,
char *line)
{
if (line_length <= 0)
return;
/* strncpy(line, &sequence[pos], line_length); */
strncpy(line, sequence, line_length);
line[line_length] = '\0';
}
void seqed_write_ruler(int pos,
int line_length,
char *line)
{
char *k;
char *tmp;
int j, lower, times;
if (line_length <= 0)
return;
lower = (pos - pos%10);
times = line_length/10 + 3;
if (NULL == (tmp = (char *)xmalloc((line_length + 31) * sizeof(char))))
return;
for (j = 0, k = tmp; j < times; j++, k+=10, lower+=10)
sprintf(k,"%10d",lower);
strncpy(line, &tmp[9+pos%10], line_length);
line[line_length] = '\0';
xfree(tmp);
}
void seqed_write_complement(char *sequence,
int pos,
int line_length,
char *line)
{
if (line_length <= 0)
return;
strncpy(line, sequence, line_length);
line[line_length] = '\0';
complement_dna(line, line_length);
}
int seqed_init_write_renzyme(int line_length,
char ***lines,
int max_renz_lines)
{
char **alines;
int i;
if (NULL == (alines = (char **)xmalloc(max_renz_lines * sizeof(char *))))
return -1;
for (i = 0; i < max_renz_lines; i++) {
if (NULL == (alines[i] = (char *)xmalloc((line_length+1) *
sizeof(char))))
return -1;
memset(alines[i], ' ', line_length);
alines[i][line_length] = '\0';
}
*lines = alines;
return 0;
}
int seqed_write(tkSeqed *se,
FILE *fp,
int from,
int to,
int line_length)
{
int i, j, k;
char *line;
char **lines = NULL;
int num_renz_lines;
int width;
int max_renz_lines = 10;
int overlap = 0;
if (line_length <= 0)
return -1;
if (NULL == (line = (char *)xmalloc((line_length+4) * sizeof(char))))
return -1;
if (se->renzDisplayed) {
overlap = seqed_get_max_name_length()+1;
seqed_init_write_renzyme(line_length+overlap, &lines, max_renz_lines);
}
for (j = from; j < to; j += line_length) {
if (to - j + 1 < line_length) {
width = to - j + 1;
} else {
width = line_length;
}
/* restriction enzymes */
if (se->renzDisplayed) {
seqed_write_renzyme(se->sequence, se->sequence_type, se->r_enzyme,
se->num_enzymes, j, width,
overlap, &lines, &max_renz_lines,
&num_renz_lines);
for (k = num_renz_lines-1; k >= 0; k--) {
#ifdef DEBUG
printf(" %s\n",lines[k]);
#endif
fprintf(fp, " %s\n",lines[k]);
}
}
/* forward translations */
if (se->translationDisplayed) {
for (k = 0; k < se->trans_lines; k++) {
line[0] = ' ';
if (se->trans[k] < 4) {
seqed_write_translation(&se->sequence[j-1], se->trans[k],
se->trans_mode, j,
width, 1, &line[1]);
#ifdef DEBUG
printf("%s\n", line);
#endif
fprintf(fp, "%s\n",line);
}
}
}
/* HACK leave for now */
if (se->autoDisplayed) {
}
/* forward sequence */
line[0] = ' ';
seqed_write_sequence(&se->sequence[j+1], j+1, width, &line[1]);
#ifdef DEBUG
printf("%s\n", line);
#endif
fprintf(fp, "%s\n",line);
/* position numbers */
if (se->rulerDisplayed) {
seqed_write_ruler(j, width, &line[1]);
#ifdef DEBUG
printf("%s\n", line);
#endif
fprintf(fp, "%s\n",line);
}
/* complemented sequence */
if (se->complementDisplayed) {
seqed_write_complement(&se->sequence[j+1], j+1, width, &line[1]);
#ifdef DEBUG
printf("%s\n", line);
#endif
fprintf(fp, "%s\n",line);
}
/* complemented translations */
if (se->translationDisplayed) {
for (k = 0; k < se->trans_lines; k++) {
line[0] = ' ';
if (se->trans[k] > 3) {
seqed_write_translation(&se->sequence[j-1], se->trans[k],
se->trans_mode, j,
width, 1, &line[1]);
#ifdef DEBUG
printf("%s\n", line);
#endif
fprintf(fp, "%s\n",line);
}
}
}
#ifdef DEBUG
printf("\n");
#endif
fprintf(fp, "\n");
}
if (se->renzDisplayed) {
for (i = 0; i < max_renz_lines; i++) {
xfree(lines[i]);
}
xfree(lines);
}
xfree(line);
return 0;
}
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