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/* codata.c - CODATA sequence functions */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdio.h>
#ifdef STDC_HEADERS
# include <string.h>
#endif
#include "sequence.h"
#include "sequence/codata.h"
#include "sequence/protein.h"
/* Functions prototypes */
extern sequence_t *codatay_parse(FILE *);
extern int codatay_check(FILE *);
unsigned int codata_checksum(char *);
/* Parse CODATA sequence */
sequence_t *codata_parse(FILE *f) {
sequence_t *seq;
seq = codatay_parse(f);
return seq; }
/* Checks CODATA sequence */
int codata_check(FILE *f) {
int i;
i = codatay_check(f);
return i; }
/* Print CODATA sequence */
void codata_print(FILE *f, sequence_t *seq) {
char *p, *q, **x;
const char *r, *s;
float w;
int i, max;
long l;
size_t len, sep;
unsigned int c;
if (seq == NULL) { return; }
/* Inits */
max = 80;
/* Name */
r = (seq->nam != NULL) ? seq->nam : "UNKNWN" ; s = "complete";
(void)fprintf(f, "ENTRY %.6s #type %s\n", r, s);
/* Description */
p = seq->dsc; i = 1;
while (p && *p) {
while (*p && *p == ' ') { p++; }
if (i == 1) {
(void)fprintf(f, "TITLE "); i = 0; }
else {
(void)fprintf(f, " "); }
q = p;
while (*q && q - p < max - 16) { q++; }
while (*q && *q != ' ') { q--; }
while (*p && q - p > 0) {
(void)fputc(*p, f); p++; }
(void)fputc('\n', f);
p = q; }
/* Accession */
x = seq->acc; l = 0;
while (x && *x) {
switch (l) {
case 0: s = "ACCESSIONS "; break;
case 16: s = ""; break;
default: s = "; "; break; }
len = strlen(*x); sep = strlen(s);
if (l + sep + len + 2 > max - 5) {
l = 0; (void)fprintf(f, ";\n"); continue; }
(void)fprintf(f, "%s%s", s, *x);
l += sep + len; x++; }
if (l != 0) { (void)fputc('\n', f); }
/* Sequence Header */
w = protein_weight(seq->str); c = codata_checksum(seq->str);
(void)fprintf(f, "SUMMARY #length %lu", seq->strlen);
(void)fprintf(f, " #molecular-weight %u ", (unsigned int)w);
(void)fprintf(f, " #checksum %u", c);
(void)fputc('\n', f);
/* Sequence */
(void)fprintf(f, "SEQUENCE\n");
(void)fprintf(f, " ");
for (i = 5; i <= 30; i += 5) {
(void)fprintf(f, "%10i", i); }
(void)fputc('\n', f);
p = seq->str;
while (*p) {
l = p - seq->str;
if (l % 30 == 0 && l > 0) {
(void)fputc('\n', f); }
if (l % 30 == 0) {
(void)fprintf(f, "%8li", l+1); }
if (*p == '*') { p++; continue; }
(void)fputc(' ', f);
(void)fputc(*p, f);
p++; }
(void)fputc('\n', f);
/* End */
(void)fprintf(f, "///\n");
return; }
/* Codata sequence checksum */
unsigned int codata_checksum(char *seq) {
char *p;
unsigned int nb, lsum, cksum;
p = seq; cksum = nb = 0;
while (*p) {
nb++;
cksum += nb * (*p);
if (nb == 57) { nb = 0; }
p++; }
lsum = cksum / 10000;
cksum -= lsum * 10000;
return cksum; }
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