File: use_mase_files.c

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seaview 0.0-4
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#include "seaview.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <time.h>

/* included functions */
int read_mase_seqs_header(const char *masefname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs, 
		char **err_message);
int read_fasta_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs, 
		char **err_message);
int read_phylip_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs,
		char **err_message);
int read_clustal_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs,
		char **err_message);
int read_msf_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs,
		char **err_message);
int is_a_protein_seq(char *seq);
int save_fasta_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used,
	int *sel_seqs, int tot_sel_seqs);
int save_phylip_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used, 
	int *sel_seqs, int tot_sel_seqs);
static int output_next_res_from_region(char *seq, int lenseq, 
	list_segments **segment, int *current, FILE *out, int total, 
	int use_dots);
void save_regions(list_regions *regions, FILE *out);
int save_mase_file(const char *fname, char **seq, char **comments,
	char *header, char **seqname, int totseqs, int *eachlength,
	list_regions *regions, region *region_used, int numb_species_sets,
	int **list_species_sets, char **name_species_sets,
	int *sel_seqs, int tot_sel_seqs, int tot_comment_lines, 
	char **comment_name, char **comment_line);
int save_clustal_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used,
	int *sel_seqs, int tot_sel_seqs);
int calc_gcg_check(list_segments *psegment, char *seq);
int save_msf_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used,
	int protein, int *sel_seqs, int tot_sel_seqs);
char *save_alignment_or_region(const char *fname, char **seq, char **comments,
	char *header, char **seqname, int totseqs, int *eachlength,
	list_regions *regions, region *region_used, known_format format,
	int numb_species_sets, int **list_species_sets, 
	char **name_species_sets, int *sel_seqs, int tot_sel_seqs, int protein,
	int tot_comment_lines, char **comment_name, char **comment_line);
int prepare_printout(const char *filename, char **seq, int totseqs,  
	char **seqname,
	int *eachlength, int char_per_line,
	int block_size, int lines_per_page, char *align_name, int ref0);
FILE *open_path(char *fname);
int check_path(char *fname);
static void save_species_sets(int numb_species_sets, int **list_species_sets, 
	char **name_species_sets, int totseqs, FILE *out);
void save_comment_lines(int tot_comment_lines, char **names, char **lines, 
	FILE *out);


int read_mase_seqs_header(const char *masefname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs, 
		char **err_message)
{
#define MAXLENSEQ 10000 /* unite d'allocation de memoire */
#define lline  2000
FILE *masef;
char line[lline], *i, *base, *header = NULL, *provseq = NULL, *p;
int  l, lenseqs, lpre, lseq, l2, totseqs= -1, want_header, curr_max_header;
static char ret_message[200];
*ret_message = 0;
*err_message = ret_message;
if( (masef=fopen(masefname,"r")) == NULL) {
	sprintf(ret_message,"File not found:%s",masefname);
	return 0;
	}
want_header = (pheader != NULL);

if(fgets(line, lline, masef)==NULL)goto fini;
if(strncmp(line,";;",2)==0) {
	if(want_header) {
		if( (header=(char *)malloc(MAXLENCOM+1)) ==
							 NULL)goto nomem;
		curr_max_header = MAXLENCOM;
		strcpy(header,line);
		lpre=strlen(line);
		}
	do	{
		if( fgets(line,lline,masef)==NULL ) goto fini;
		if(strncmp(line,";;",2)!=0) break;
		if(header != NULL) {
			lseq=strlen(line);
			if(lpre+lseq > curr_max_header) {
				curr_max_header += MAXLENCOM;
				if( (p=(char *)malloc(curr_max_header+1)) 
					== NULL ) goto nomem;
				memcpy(p, header, lpre);
				free(header);
				header = p;
				}
			memcpy(header+lpre,line, lseq);
			lpre += lseq;
			}
		}
	while (1);
	if( want_header ) {
		header[lpre] = 0;
		header=(char *)realloc(header,lpre+1);
		}
	}
if(*line != ';' ) {
	strcpy(ret_message,"Not a mase file!");
	goto fini;
	}

lenseqs=MAXLENSEQ;
if( (provseq=(char *)malloc(lenseqs+1)) ==NULL)goto nomem;

i=line;
while(i!=NULL){
	if(totseqs>=maxnseqs-1) {
		sprintf(ret_message,
			"too many sequences in mase file (max=%d)",maxnseqs);
		totseqs = -1; 
		goto fini;
		}
	totseqs++;
	if(comments!=NULL) {
		if( (comments[totseqs]=(char *)malloc(MAXLENCOM+1)) ==
							 NULL)goto nomem;
		strcpy(comments[totseqs],line);
		lpre=strlen(line); l=MAXLENCOM;
		while(*fgets(line,lline,masef)==';') {
			lseq=strlen(line);
			if(lpre+lseq <= l) {
				strcpy(comments[totseqs]+lpre,line);
				lpre += lseq;
				}
			else l=lpre-1;
			}
		if(lpre<MAXLENCOM)
		   comments[totseqs]=(char *)realloc(comments[totseqs],lpre+1);
		}
	else	while(*fgets(line,lline,masef)==';');
	l = strlen(line);
	while((line[l-1] == ' ' || line[l-1] == '\n') && l>0 ) l--; line[l] = 0;
	if( (seqname[totseqs]=(char *)malloc(l+1)) == NULL)goto nomem;
	strcpy(seqname[totseqs],line);
	lseq = 0; /* what is already put in provseq */
	while( (i=fgets(line,lline,masef))!= NULL && *i != ';' ) {
	    	l2 = strlen(line);
		if( line[l2 - 1] == '\n' ) l2--;
	   	while(l2>0 && line[l2-1]==' ')l2--;
		if(lseq + l2 > lenseqs) {
			char *temp;
			lenseqs += MAXLENSEQ;
			temp = (char *)malloc(lenseqs+1);
			if(temp == NULL) goto nomem;
			memcpy(temp, provseq, lseq);
			free(provseq);
			provseq = temp;
			}
	   	memcpy(provseq+lseq, line, l2);
		lseq += l2;
		}
	provseq[lseq]='\0';
	seq[totseqs] = (char *)malloc(lseq+1);
	if(seq[totseqs] == NULL) goto nomem;
/* convert all to upper case, ignore non letter characters (e.g. digits)*/
	base=provseq - 1; p = seq[totseqs] - 1;
	while ( *(++base) != 0) {
/*
		if( *base == '-' )
			*(++p) = '-';
		else if( isalpha(*base) ) {
			if(islower(*base)) *base=toupper(*base);
			*(++p) = *base;
			}
*/
		if(isprint(*base) && ! isspace(*base) ) {
			*(++p) = toupper(*base);
			}
		}
	*(++p) = 0;
	}
fini:
fclose(masef);
if(want_header) *pheader = header;
if(provseq != NULL) free(provseq);
return totseqs+1;
nomem:
sprintf(ret_message,"Error: Not enough memory!");
totseqs = -1;
goto fini;
}


int read_fasta_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs, 
		char **err_message)
{
FILE *in;
int totseqs, lseq, l2, l, lenseqs;
char line[100], *p, *i, *provseq = NULL;
static char ret_message[200];
*ret_message = 0;
*err_message = ret_message;
if( (in=fopen(fname,"r")) == NULL) {
	sprintf(ret_message,"File not found:%s", fname);
	return 0;
	}
lenseqs = MAXLENSEQ;
totseqs = -1;
i = fgets(line, sizeof(line), in);
if(line[0] != '>') {
	strcpy(ret_message,"File not in Fasta format!");
	totseqs = -1; goto fini;
	}
while( i != NULL ){
	if(totseqs>=maxnseqs-1) {
		sprintf(ret_message,
			"too many sequences in Fasta file (max=%d)",maxnseqs);
		totseqs = -1; 
		goto fini;
		}
	totseqs++;
	comments[totseqs] = NULL;
	p = line + 1; while(*p != ' ' && *p != '\n') p++;
	l = p - line - 1;
	if( (seqname[totseqs] = (char *)malloc(l+1)) == NULL)goto nomem;
	memcpy(seqname[totseqs], line + 1, l); seqname[totseqs][l] = 0;
	seq[totseqs] = (char *)malloc(lenseqs+1);
	if(seq[totseqs] == NULL) goto nomem;
	lseq = 0;
	while( (i=fgets(line, sizeof(line), in))!= NULL && *i != '>' ) {
	    	l2 = strlen(line);
		if( line[l2 - 1] == '\n' ) l2--;
	   	while(l2>0 && line[l2-1]==' ')l2--;
		if(lseq + l2 > lenseqs) {
			char *temp;
			lenseqs += MAXLENSEQ;
			temp = (char *)malloc(lenseqs+1);
			if(temp == NULL) goto nomem;
			memcpy(temp, seq[totseqs], lseq);
			free(seq[totseqs]);
			seq[totseqs] = temp;
			}
	   	memcpy(seq[totseqs]+lseq, line, l2);
		lseq += l2;
		}
	seq[totseqs][lseq]='\0';
/* convert all to upper case */
	p = seq[totseqs] - 1; while( *(++p) != 0 ) *p = toupper(*p);
	}
fini:
fclose(in);
if(provseq != NULL) free(provseq);
*pheader = NULL;
return totseqs+1;
nomem:
sprintf(ret_message,"Error: Not enough memory!");
totseqs = -1;
goto fini;
}


int read_phylip_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs,
		char **err_message)
{
FILE *in;
char *p, *q, line[PHYNAME + 200];
int totseqs, lenseqs, i, l;
static char ret_message[200];
*ret_message = 0;
*err_message = ret_message;
in=fopen(fname,"r");
if(in==NULL) {
	sprintf(ret_message,"File not found:%s",fname);
	return 0;
	}
fgets(line,sizeof(line),in);
if( sscanf(line,"%d%d",&totseqs, &lenseqs) != 2) {
		sprintf(ret_message,"Not a PHYLIP file");
		totseqs = 0;
		goto fini;
		}
if(totseqs > maxnseqs) {
		sprintf(ret_message,
		"too many sequences in phylip file (max=%d)",maxnseqs);
		totseqs = 0; 
		goto fini;
		}
for(i=0; i<totseqs; i++) {
	if( (seq[i] = (char *)malloc(lenseqs+1) ) == NULL ) goto nomem;
	if( (seqname[i] = (char *)malloc(PHYNAME+1) ) == NULL ) goto nomem;
	comments[i] = NULL;
	}
for(i=0; i<totseqs; i++) {
	fgets(line,sizeof(line),in);
	memcpy(seqname[i],line,PHYNAME); seqname[i][PHYNAME] = 0;
	p = line+PHYNAME; q = seq[i];
	while(*p != '\n') {
		if(*p != ' ') *(q++) = *p;
		p++;
		}
	}
l = q - seq[totseqs - 1];
while( l < lenseqs) {
	fgets(line,sizeof(line),in);
	for(i=0; i<totseqs; i++) {
		fgets(line,sizeof(line),in);
		p = line; q = seq[i] + l;
		while(*p != '\n') {
			if(*p != ' ') *(q++) = *p;
			p++;
			}
		}
	l = q - seq[totseqs - 1];
	}
for(i=0; i<totseqs; i++) seq[i][l] = 0;
fini:
*pheader = NULL;
fclose(in);
return totseqs;
nomem:
sprintf(ret_message,"Error: Not enough memory!");
totseqs = 0;
goto fini;
}


int read_clustal_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs,
		char **err_message)
{
FILE *in;
char line[200], *p;
int i, l, curr_spec, first=TRUE, curr_len, next_len, tot_spec, curr_max_len,
	carac, wid_name;
static char ret_message[200];
*ret_message = 0;
*err_message = ret_message;
in=fopen(fname,"r");
if(in==NULL) {
	sprintf(ret_message,"File not found:%s",fname);
	return 0;
	}
fgets(line,sizeof(line),in);
if(strncmp(line,"CLUSTAL",7) != 0) { /* skip 1st line with CLUSTAL in it */
	strcpy(ret_message,"File not in CLUSTAL format!");
	tot_spec = -1; goto fini;
	}
/* skip next empty lines */
do	{
	carac = getc(in);
	if(carac == ' ') {
		fgets(line,sizeof(line),in);
		carac = getc(in);
		}
	}
while(carac == '\n');
ungetc(carac, in); /* back to start of 1st non-empty line */
tot_spec = curr_spec = -1; curr_len = next_len = 0;
while( fgets(line, sizeof(line), in) != NULL ) {
	if(*line == '\n' || *line == ' ') {
		curr_spec = -1;
		curr_len = next_len;
		first = FALSE;
		continue;
		}
	else 	{
		curr_spec++;
		if(curr_spec >= maxnseqs) { 
			sprintf(ret_message,
			   "too many sequences in clustal file (max=%d)",
					maxnseqs);
			tot_spec = -1;
			goto fini; 
			}
		}
	if(first && curr_spec == 0) {
/* calcul long partie nom: enlever tout ce qui n'est pas espace en fin */
		p = line + strlen(line) - 2; while(*p == ' ') p--; 
		while (*p != ' ') p--;
		wid_name = p - line + 1;
		}
	if(first) {
		seqname[curr_spec] = (char *)malloc(wid_name+1);
		if(seqname[curr_spec]==NULL) {
			goto nomem;
			}
		memcpy(seqname[curr_spec], line, wid_name);
		p = seqname[curr_spec] + wid_name - 1;
		while(*p==' ') p--; *(p+1)=0;
		if(curr_spec > tot_spec) tot_spec = curr_spec;
		seq[curr_spec] = (char *)malloc(CLU_BLOCK_LEN+1);
		curr_max_len = CLU_BLOCK_LEN;
		if(seq[curr_spec]==NULL) {
			goto nomem;
			}
		comments[curr_spec] = NULL;
		}
	if(curr_spec == 0) {
		l = strlen(line) - 1;
		p = line + l - 1; while(*p == ' ') { p--; l--; }
		l -= wid_name;
		if(curr_len + l > curr_max_len) {
			curr_max_len += CLU_BLOCK_LEN;
			for(i=0; i<=tot_spec; i++) {
				p = (char *)malloc(curr_max_len+1);
				if(p == NULL) goto nomem;
				memcpy(p, seq[i], curr_len);
				free(seq[i]);
				seq[i] = p;
				}
			
			}
		next_len = curr_len + l;
		}
	memcpy(seq[curr_spec]+curr_len, line + wid_name, l);
	}
for(i=0; i<=tot_spec; i++) seq[i][next_len] = 0;
fini:
*pheader = NULL;
fclose(in);
return tot_spec + 1;
nomem:
sprintf(ret_message,"Error: Not enough memory!");
tot_spec = -1;
goto fini;
}


int read_msf_align(const char *fname, char **seq, char **seqname, 
		char ** comments, char **pheader, int maxnseqs,
		char **err_message)
{
FILE *in;
char line[100], *p, *q;
int l, curr_spec, maxwidname=0, curr_len, tot_spec;
static char ret_message[200];
*ret_message = 0;
*err_message = ret_message;
in=fopen(fname,"r");
if(in==NULL) {
	sprintf(ret_message,"File not found:%s",fname);
	return 0;
	}
p = NULL;
while( fgets(line,sizeof(line),in) != NULL) {
	if( (p = strstr(line, "MSF: ")) != NULL) break;
	}
if(p == NULL) {
	strcpy(ret_message,"File not in MSF format!");
	tot_spec = -1; goto fini;
	}
tot_spec = -1;
do	{
	fgets(line,sizeof(line),in);
	if( (p = strstr(line, "Name:") ) == NULL) continue;
	tot_spec++;
	if(tot_spec >= maxnseqs) { 
		sprintf(ret_message,
		   "too many sequences in MSF file (max=%d)", maxnseqs);
		tot_spec = -1;
		goto fini; 
		}
	q = strstr(p, " Len: "); 
	sscanf(q + 5, "%d", &l);
	seq[tot_spec] = (char *)malloc(l + 1);
	if(seq[tot_spec]==NULL) goto nomem;
	p += 5; while(*p == ' ') p++;
	q = p; while(*q != ' ') q++;
	l = q - p;
	seqname[tot_spec] = (char *)malloc(l + 1);
	if(seqname[tot_spec]==NULL) goto nomem;
	memcpy(seqname[tot_spec], p, l); seqname[tot_spec][l] = 0;
	if(l > maxwidname) maxwidname = l;
	comments[tot_spec] = NULL;
	}
while(strncmp(line, "//", 2) != 0);
curr_spec = 0; curr_len = 0;
while( fgets(line, sizeof(line), in) != NULL ) {
	p = line; while(*p == ' ') p++;
	l = strlen(seqname[curr_spec]);
	if(strncmp(p, seqname[curr_spec], l) != 0) continue;
	p += l; while(*p == ' ') p++; p--;
	q = seq[curr_spec] + curr_len;
	while( *(++p) != '\n') {
		if( *p == ' ') continue;
		if(*p == '.') *p = '-';
		*(q++) = *p;
		}
	*q = 0;
	if(curr_spec == tot_spec) {
		curr_len += 50;
		curr_spec = 0;
		}
	else	curr_spec++;
	}
fini:
*pheader = NULL;
fclose(in);
return tot_spec + 1;
nomem:
sprintf(ret_message,"Error: Not enough memory!");
tot_spec = -1;
goto fini;
}


int is_a_protein_seq(char *seq)
/* returns TRUE if seq looks like a protein sequence (less than 80% ACGTU) */
{
static char dna[]="ACGTU";
int total=0, length=0;
while(*seq != 0) {
	if(*seq != '-') {
		if( strchr(dna, toupper(*seq)) != NULL ) total++;
		length++; 
		}
	seq++;
	}
return ( (float)(total) / length ) <= 0.8 ;
}


int save_phylip_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used, 
	int *sel_seqs, int tot_sel_seqs)
/* sauver des sequences ou des regions au format phylip
region_used pointe vers la region a sauver
si region_used == NULL, toutes les sequences sont sauvees
rend 0 si ok, 
	1 si erreur d'ecriture dans le fichier
	2 si tentative de depasser la longueur d'une sequence
*/
{
const int widphylin = 50;
FILE *out;
int lenseqs, i, j, retval = 1, current, save_current, err, vtotseqs;
list_segments *psegment, all_sequence, *curr_segment;
region maregion;

if(totseqs == 0) return 0;
if( (out = fopen(fname,"w")) == NULL) return 1;
if(region_used == NULL) { /* on veut tout sauver */
	tot_sel_seqs = 0;
	all_sequence.debut = 1;
	all_sequence.fin = eachlength[0];
	for(i = 1; i < totseqs; i++)
		if( eachlength[i] < all_sequence.fin )  
			 all_sequence.fin = eachlength[i];
	all_sequence.next = NULL;
	maregion.list = &all_sequence;
	region_used = &maregion;
	}
/* calcul longueur des regions */
lenseqs = 0;
psegment = region_used->list;
while(psegment != NULL) {
	lenseqs += psegment->fin - psegment->debut + 1;
	psegment = psegment->next;
	}
vtotseqs = 0;
for(i=0; i < totseqs; i++) 
	if(tot_sel_seqs == 0 || sel_seqs[i]) ++vtotseqs;
fprintf(out,"%d   %d\n", vtotseqs, lenseqs);
for(i=0; i < totseqs; i++) {
	if(tot_sel_seqs != 0 && ! sel_seqs[i]) continue;
	psegment = region_used->list; current = 0;
	for(j = 0; j < PHYNAME; j++) {
		if(seqname[i][j] == 0) break;
		putc(seqname[i][j],out);
		}
	while(j < PHYNAME) { putc( ' ', out ); j++; }
	err = output_next_res_from_region(seq[i], eachlength[i], &psegment, 
		&current, out, widphylin, FALSE);
	putc('\n', out);
	if(err == -1) { retval = 2; goto fin; }
	if(ferror(out)) goto fin;
	}
while( psegment != NULL ) {
	putc('\n',out);
	curr_segment = psegment; save_current = current;
	for(i=0; i < totseqs; i++) {
		if(tot_sel_seqs != 0 && ! sel_seqs[i]) continue;
		psegment = curr_segment; current = save_current;
		err = output_next_res_from_region(seq[i], eachlength[i], 
			&psegment, &current, out, widphylin, FALSE);
		putc('\n', out);
		if(err == -1) { retval = 2; goto fin; }
		if(ferror(out)) goto fin;
		}
	}
retval = 0;
fin:
fclose(out);
return retval;
}


static int output_next_res_from_region(char *seq, int lenseq, 
	list_segments **segment, int *current, FILE *out, int total, 
	int use_dots)
/* ecrire dans le fichier out les total residus a partir de la position courante
dans une liste de regions. lenseq est la longueur de la sequence seq.
La position courante est determinee par le segment courant (*segment, qui peut
etre modifie par la fonction) et par la position (from 0) dans celui-ci (*current
qui est modifie par la fonction pour etre pret pour l'appel suivant)
Rend le nombre de residus effectivement ecrits, ou -1 si depassement longueur de seq.
Doit etre appelle la premiere fois avec *current = 0
*/
{
int debut, fin, vfin, ecrit = 0, nombre;
char *p;
static char line[500];
if( *segment == NULL) 
	return 0;
do	{
	debut = (*segment)->debut; fin = (*segment)->fin; 
	vfin = fin; if(fin > lenseq) vfin = lenseq;
	nombre = total;
	if( nombre - 1 + *current + debut > vfin)
		nombre = vfin + 1 - *current - debut;
	memcpy(line, seq + *current + debut - 1, nombre); line[nombre] = 0;
	if(use_dots) {
		p = line;
		while( (p = strchr(p, '-')) != NULL) *p = '.';
		}
	fwrite(line, 1, nombre, out);
	ecrit += nombre; total -= nombre; (*current) += nombre;
	if( fin > lenseq && total > 0 ) return -1;
	if( *current + debut > fin) {
		*segment = (*segment)->next;
		if(*segment == NULL) return ecrit;
		*current = 0;
		}
	}
while(total > 0);
return ecrit;
}


void save_regions(list_regions *regions, FILE *out)
{
int total, l_line;
list_segments *segment;
char line[80];
do	{
	total = 0;
	segment = regions->element->list;
	while(segment != NULL) {
		total++;
		segment = segment->next;
		}
	if(total == 0) continue;
	fprintf(out,";;# of segments=%d %s\n",total,regions->element->name);
	strcpy(line, ";;"); l_line=2;
	segment = regions->element->list;
	while(segment != NULL) {
		if(l_line + 12 >= sizeof(line)-1) {
			fputs(line,out); putc('\n',out);
			strcpy(line,";;"); l_line=2;
			}
		sprintf(line+l_line," %d,%d", segment->debut, segment->fin);
		l_line += strlen(line+l_line);
		segment= segment->next;
		}
	fputs(line,out); putc('\n',out);
	}
while(	regions = regions->next, regions != NULL );
}


int save_mase_file(const char *fname, char **seq, char **comments,
	char *header, char **seqname, int totseqs, int *eachlength,
	list_regions *regions, region *region_used, int numb_species_sets,
	int **list_species_sets, char **name_species_sets,
	int *sel_seqs, int tot_sel_seqs, int tot_comment_lines, 
	char **comment_name, char **comment_line)
/* sauver un alignement au format mase
regions: l'ensemble des regions a ecrire (si on sauve tout l'alignement)
	NULL si on ne sauve que des regions
region_used: pointeur vers la region a sauver 
	     et on ne sauve que les seqs selectionnees s'il y en a, 
	ou NULL pour sauver tout l'alignement
rend 0 si OK, 
	1 si erreur ecriture du fichier
	2 si depassement de longueur d'une sequence (avec region seulement)
*/
{
FILE *out;
int num, retval = 1, current, ecrit;
time_t heure;
list_segments *psegment, all_sequence;
region maregion;

if(totseqs == 0) return 0;
out=fopen(fname,"w");
if(out == NULL) return 1;

time(&heure);
fprintf(out,";; saved by seaview on %s",ctime(&heure));
if(region_used == NULL) { /* on veut tout sauver */
	all_sequence.debut = 1;
	all_sequence.next = NULL;
	maregion.list = &all_sequence;
	maregion.name = NULL;
	region_used = &maregion;
	tot_sel_seqs = 0;
	}
else
	fprintf(out,";; region choice only: %s\n",region_used->name);
if(ferror(out)) goto fin;
if(header != NULL && *header != 0) {
	fputs(header,out);
	if(ferror(out)) goto fin;
	}
if(regions != NULL) {
	save_regions(regions, out);
	if(ferror(out)) goto fin;
	}
if(tot_comment_lines > 0) {
	save_comment_lines(tot_comment_lines, comment_name, comment_line, out);
	if(ferror(out)) goto fin;
	}
if(numb_species_sets != 0) { /* sauver les species sets */
	save_species_sets(numb_species_sets, list_species_sets, 
		name_species_sets, totseqs, out);
	if(ferror(out)) goto fin;
	}
for(num=0; num<totseqs; num++) {
	if( tot_sel_seqs != 0 && ! sel_seqs[num] ) continue;
	current = 0; psegment = region_used->list;
	all_sequence.fin = eachlength[num];
	if(comments[num] != NULL)
		fputs(comments[num], out);
	else fputs(";no comment\n", out);
	if(ferror(out)) goto fin;
	fprintf(out,"%s\n",seqname[num]);
	if(ferror(out)) goto fin;
	do	{
		ecrit = output_next_res_from_region(seq[num], eachlength[num], 
			&psegment, &current, out, 60, FALSE);
		if( ecrit > 0) putc('\n', out);
		else if(ecrit == -1) {retval = 2; goto fin; }
		}
	while(ecrit != 0);
	if(ferror(out)) goto fin;
	}
retval = 0;
fin:
fclose(out);
return retval;
}


int save_fasta_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used,
	int *sel_seqs, int tot_sel_seqs)
/* sauver des sequences ou des regions au format fasta
region_used pointe vers la liste des regions a sauver
si region_used == NULL, toutes les sequences sont sauvees
rend 0 si ok, 1 si erreur d'ecriture dans le fichier
	2 si tentative de depasser la longueur d'une sequence
*/
{
FILE *out;
int num, retval = 1, current, ecrit;
list_segments *psegment, all_sequence;
region maregion;

if(totseqs == 0) return 0;
if( (out = fopen(fname,"w")) == NULL) return 1;
if(region_used == NULL) { /* on veut tout sauver */
	tot_sel_seqs = 0;
	all_sequence.debut = 1;
	all_sequence.fin = eachlength[0];
	for(num = 1; num < totseqs; num++)
		if( eachlength[num] < all_sequence.fin )  
			 all_sequence.fin = eachlength[num];
	all_sequence.next = NULL;
	maregion.list = &all_sequence;
	region_used = &maregion;
	}
for(num=0; num<totseqs; num++) {
	if( tot_sel_seqs != 0 && ! sel_seqs[num] ) continue;
	current = 0; psegment = region_used->list;
	all_sequence.fin = eachlength[num];
	fprintf(out,">%s\n",seqname[num]);
	if(ferror(out)) goto fin;
	do	{
		ecrit = output_next_res_from_region(seq[num], eachlength[num], 
			&psegment, &current, out, 60, FALSE);
		if( ecrit > 0) putc('\n', out);
		else if(ecrit == -1) {retval = 2; goto fin; }
		}
	while(ecrit != 0);
	if(ferror(out)) goto fin;
	}
retval = 0;
fin:
fclose(out);
return retval;
}



int save_clustal_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used,
	int *sel_seqs, int tot_sel_seqs)
/* sauver des sequences ou des regions au format clustal
region_used pointe vers la liste des regions a sauver
si region_used == NULL, toutes les sequences sont sauvees
rend 0 si ok, 1 si erreur d'ecriture dans le fichier
	2 si tentative de depasser la longueur d'une sequence
*/
{
const int widcluslin = 60;
FILE *out;
int i, j, retval = 1, current, save_current, err;
list_segments *psegment, all_sequence, *curr_segment;
region maregion;

if(totseqs == 0) return 0;
if( (out = fopen(fname,"w")) == NULL) return 1;
if(region_used == NULL) { /* on veut tout sauver */
	tot_sel_seqs = 0;
	all_sequence.debut = 1;
	all_sequence.fin = eachlength[0];
	for(i = 1; i < totseqs; i++)
		if( eachlength[i] < all_sequence.fin )  
			 all_sequence.fin = eachlength[i];
	all_sequence.next = NULL;
	maregion.list = &all_sequence;
	region_used = &maregion;
	}
fprintf(out,"CLUSTAL W multiple sequence alignment\n\n\n");
current = 0; psegment = region_used->list;
while( psegment != NULL ) {
	curr_segment = psegment; save_current = current;
	for(i=0; i < totseqs; i++) {
		if( tot_sel_seqs != 0 && ! sel_seqs[i] ) continue;
		psegment = curr_segment; current = save_current;
/* tronquer les noms a 14 et remplacer espaces internes par _ */
		for(j = 0; j < 14; j++) {
			if(seqname[i][j] == 0) break;
			putc( (seqname[i][j] == ' ' ? '_' : seqname[i][j] ), 
				out);
			}
		while( j < CLU_WID_NAME) {
			putc(' ', out); j++;
			}
		err= output_next_res_from_region(seq[i], eachlength[i], 
			&psegment, &current, out, widcluslin, FALSE);
		putc('\n', out);
		if(err == -1) {retval = 2; goto fin; }
		if(ferror(out)) goto fin;
		}
	fprintf(out, "\n\n");
	}
retval = 0;
fin:
fclose(out);
return retval;
}


int calc_gcg_check(list_segments *psegment, char *seq)
{
int  i, debut, fin, residue, pos = 0;
long check = 0;
while(psegment != NULL) {
	debut = psegment->debut; fin = psegment->fin;
        for( i=debut; i<= fin; i++) {
		residue = toupper(seq[i - 1]);
		if(residue == '-') residue = '.';
                check += (( (pos++) % 57)+1) * residue;
		}
	psegment = psegment->next;
	}
return (check % 10000);
}


int save_msf_file(const char *fname, char **seq,
	char **seqname, int totseqs, int *eachlength, region *region_used,
	int protein, int *sel_seqs, int tot_sel_seqs)
/* sauver des sequences ou des regions au format MSF
region_used pointe vers la liste des regions a sauver
si region_used == NULL, toutes les sequences sont sauvees
rend 0 si ok, 1 si erreur d'ecriture dans le fichier
	2 si tentative de depasser la longueur d'une sequence
*/
{
FILE *out;
int i, j, k, retval = 1, current, save_current, err, lenseqs, gen_check,
	*check_val, curr_len, toprint, save_complete, fromseq;
list_segments *psegment, all_sequence, *curr_segment;
region maregion;

if(totseqs == 0) return 0;
if( (out = fopen(fname,"w")) == NULL) return 1;
save_complete = (region_used == NULL);
if(save_complete) { /* on veut tout sauver */
	tot_sel_seqs = 0;
	all_sequence.debut = 1;
	all_sequence.fin = 0;
	for(i = 0; i < totseqs; i++) {
		if( eachlength[i] > all_sequence.fin )  
			 all_sequence.fin = eachlength[i];
		}
	lenseqs = all_sequence.fin;
	all_sequence.next = NULL;
	maregion.list = &all_sequence;
	region_used = &maregion;
	}
else	{
	/* calcul longueur des regions */
	lenseqs = 0;
	psegment = region_used->list;
	while(psegment != NULL) {
		lenseqs += psegment->fin - psegment->debut + 1;
		psegment = psegment->next;
		}
	}
for(i = 0, k = 0; i < totseqs; i++) /* nbre de seqs editees */
	if( tot_sel_seqs == 0 || sel_seqs[i] ) k++;
check_val = (int *)malloc( k * sizeof(int) );
if(check_val == NULL) {
	fclose(out);
	return 1; /* pas tres precis */
	}
gen_check = 0;
for(i = 0, j = 0; i < totseqs; i++, j++) {
	if( tot_sel_seqs != 0 && ! sel_seqs[i] ) continue;
	check_val[j] = calc_gcg_check(region_used->list, seq[i]);
	gen_check += check_val[j];
	}
gen_check = gen_check % 10000;
fprintf(out,"PileUp\n\n\n\n   MSF:%5d  Type: %c    Check:%6d   .. \n\n",
	lenseqs, (protein ? 'P' : 'N'), gen_check);
for(i = 0 , j = 0; i < totseqs; i++, j++) {
	if( tot_sel_seqs != 0 && ! sel_seqs[i] ) continue;
	fprintf(out, " Name: %-15.15s oo  Len:%5d  Check:%6d  Weight:  1.00\n",
		seqname[i], lenseqs, check_val[j]);
	}
fprintf(out,"\n//\n\n\n");
current = 0; psegment = region_used->list; curr_len = 0;
while( psegment != NULL && curr_len < lenseqs) {
	curr_segment = psegment; save_current = current;
	fprintf(out, "\n");
	for(i=0; i < totseqs; i++) {
		if( tot_sel_seqs != 0 && ! sel_seqs[i] ) continue;
		psegment = curr_segment; current = save_current;
		for(j = 0; j < MSF_WID_NAME; j++) {
			if(seqname[i][j] == 0) break;
			putc(seqname[i][j],out);
			}
		while( j < MSF_WID_NAME + 1) {
			putc(' ', out); j++;
			}
		for(k = curr_len; k < curr_len + 50 && k < lenseqs; k += 10) {
			toprint = 10;
			if(k + toprint > lenseqs) toprint = lenseqs - k;
			fromseq = toprint;
			if(save_complete && k + fromseq > eachlength[i])
					fromseq = eachlength[i] - k;
			if(fromseq < 0) fromseq = 0;
			if(fromseq > 0) {
				err= output_next_res_from_region(
					seq[i], eachlength[i], &psegment, 
					&current, out, fromseq, TRUE);
				if(err == -1) {retval = 2; goto fin; }
				}
			while(fromseq < toprint) {
				putc('.', out); fromseq++;
				}
			putc(' ', out);
			}
		putc('\n', out);
		if(ferror(out)) goto fin;
		}
	curr_len += 50;
	fprintf(out, "\n");
	}
retval = 0;
fin:
fclose(out);
free(check_val);
return retval;
}


char *save_alignment_or_region(const char *fname, char **seq, char **comments,
	char *header, char **seqname, int totseqs, int *eachlength,
	list_regions *regions, region *region_used, known_format format,
	int numb_species_sets, int **list_species_sets, 
	char **name_species_sets, int *sel_seqs, int tot_sel_seqs, int protein,
	int tot_comment_lines, char **comment_name, char **comment_line)
/* sauver des sequences ou des regions au format de fichier format
region_used pointe vers la liste des regions a sauver
si region_used == NULL, toutes les sequences entieres sont sauvees
rend NULL si ok
	un message d'erreur sinon.
*/
{
int err;
static char err_message[200];

if(format == MASE_FORMAT) 
	err = save_mase_file(fname, seq, comments,
		header, seqname, totseqs, eachlength,
		regions, region_used, numb_species_sets, list_species_sets,
		name_species_sets, sel_seqs, tot_sel_seqs,
		tot_comment_lines, comment_name, comment_line);
else if(format == PHYLIP_FORMAT) 
	err = save_phylip_file(fname, seq,
		seqname, totseqs, eachlength, region_used, 
		sel_seqs, tot_sel_seqs);
else if(format == CLUSTAL_FORMAT) 
	err = save_clustal_file(fname, seq,
		seqname, totseqs, eachlength, region_used, 
		sel_seqs, tot_sel_seqs);
else if(format == MSF_FORMAT) 
	err = save_msf_file(fname, seq,
		seqname, totseqs, eachlength, region_used, protein,
		sel_seqs, tot_sel_seqs);
else if(format == FASTA_FORMAT) 
	err = save_fasta_file(fname, seq,
		seqname, totseqs, eachlength, region_used,
		sel_seqs, tot_sel_seqs);
if(err == 0)
	return NULL;
else if(err == 1) 
	sprintf(err_message,"Error while writing to file %s",fname);
else if(err == 2) 
	strcpy(err_message,
		"Error: region goes beyond the end of one sequence");
return err_message;
}


int prepare_printout(const char *filename, char **seq, int totseqs,  
	char **seqname,
	int *eachlength, int char_per_line,
	int block_size, int lines_per_page, char *align_name, int ref0)
{
FILE *out;
int num, i, j, current, max_seq_length, fin, curr_lines, widnames, res_per_line;
int retval = TRUE;
time_t heure;
static char unnamed[] = "<unnamed>";
static char num_line[200];
int lettre;

if(totseqs == 0) return 0;
if( ( out=fopen(filename, "w") ) == NULL) {
	return TRUE;
	}
time(&heure);
if(align_name == NULL) align_name = unnamed;
fprintf(out,"Alignment:  %s\n",
		align_name);
fprintf(out,"printed by seaview [blocks=%d cpl=%d lpp=%d] on %s\n",
		block_size, char_per_line, lines_per_page, ctime(&heure));
max_seq_length = 0; widnames = 0;
for(i=0; i<totseqs; i++) {
	if(eachlength[i] > max_seq_length) max_seq_length = eachlength[i];
	if( ( fin=strlen(seqname[i]) ) > widnames) widnames = fin;
	}
widnames += 2;
/* nombre max de blocks qui tiennent sur une ligne de cpl chars */
fin = (char_per_line - widnames + 1) / (block_size + 1);
if(fin < 1) { /* garde fou */
	fin = 1; block_size = char_per_line - widnames;
	}
res_per_line = fin * block_size;
current = 0; curr_lines = 3;
if( totseqs + 1 > lines_per_page) lines_per_page = 1000000;
while( current < max_seq_length ) {
	if(curr_lines + totseqs + 1 > lines_per_page) {
		for(i = 0; i < lines_per_page - curr_lines; i++)
			putc('\n', out);
		curr_lines = 0;
		}
	sprintf(num_line, "%d", current + 1);
	fin = strlen(num_line);
	memmove(num_line + widnames - fin + 1, num_line, fin+1);
	if(fin <= widnames) memset(num_line, ' ', widnames - fin + 1);
	fputs(num_line, out); putc('\n', out); ++curr_lines;
	for(num=0; num < totseqs; num++) {
		for(j = 0; j < widnames; j++) {
			if(seqname[num][j] == 0) break;
			putc(seqname[num][j],out);
			}
		while( j < widnames) {
			putc(' ', out); j++;
			}
		fin = res_per_line;
		if(current+fin > eachlength[num]) 
			fin = eachlength[num] - current;
		if(ref0 != -1 && num != ref0) {
			/* ecriture par reference a seq ref0 */
			for(i=0; i<fin; i++) {
				lettre = 
( seq[num][current+i] == seq[ref0][current+i] ? '.' : seq[num][current+i] );
				putc(lettre, out);
				if( i < fin-1 && (i+1)%block_size == 0) 
					putc(' ', out);
				}
			}
		else	{ /* ecriture normale de seq */
			for(i=0; i<fin; i++) {
				putc(seq[num][current+i], out);
				if( i < fin-1 && (i+1)%block_size == 0) 
					putc(' ', out);
				}
			}
		putc('\n', out); ++curr_lines;
		if(ferror(out)) goto fin;
		}
	if(curr_lines + 1 <= lines_per_page) {
		fprintf(out, "\n"); ++curr_lines;
		}
	current += res_per_line;
	}
if(ferror(out)) goto fin;
retval = FALSE;
fin:
fclose(out);
return retval;
}


FILE *open_path(char *fname)  /* to open in read-only file fname searching for 
				 it through all path directories */
{
#define Mxdir 200
        char dir[Mxdir+1], *path, *deb, *fin;
        FILE *fich;
        int lf, ltot;
#ifdef __VMS
	static char vmspath[] = "seaview";
	path = vmspath;
#else 
        path=getenv("PATH"); 	/* get the list of path directories, 
					separated by :
    				*/
#endif
        if (path == NULL ) return fopen(fname,"r");
        lf=strlen(fname);
        deb=path;
        do
                {
                fin=strchr(deb,':');
                if(fin!=NULL)
                        { strncpy(dir,deb,fin-deb); ltot=fin-deb; }
                else
                        { strcpy(dir,deb); ltot=strlen(dir); }
                /* now one directory is in string dir */
                if( ltot + lf + 1 <= Mxdir)
                        {
#ifdef __VMS
                        dir[ltot]=':';
#else 
                        dir[ltot]='/';
#endif
                        strcpy(dir+ltot+1,fname); /* now dir is appended with fi
   lename */
                        if( (fich = fopen(dir,"r") ) != NULL) break;
                        }
                else fich = NULL;
                deb=fin+1;
                }
        while (fin != NULL);
	if(fich == NULL) fich=fopen(fname,"r"); /* try also current directory */
        return fich;
#undef Mxdir
}


int check_path(char *fname)  
/* to check for presence of file fname 
searching for it through all path directories 
returns 0 if found, != 0 if not found
*/
{
#ifdef __VMS
	return 0;
#else 
#define Mxdir 200
    extern int stat(char *, void *);
    char dir[Mxdir+1], *path, *deb, *fin;
    int lf, ltot;
    static char stat_struct[250]; /* bigger than necessary */
    path=getenv("PATH"); 	/* get the list of path directories, 
				    separated by :
				*/
    if (path == NULL ) return -1;
    lf=strlen(fname);
    deb=path;
    do
	    {
	    fin=strchr(deb,':');
	    if(fin!=NULL)
		    { strncpy(dir,deb,fin-deb); ltot=fin-deb; }
	    else
		    { strcpy(dir,deb); ltot=strlen(dir); }
	    /* now one directory is in string dir */
	    if( ltot + lf + 1 <= Mxdir)
		    {
		    dir[ltot]='/';
		    strcpy(dir+ltot+1,fname); 
			/* now dir is appended with filename */
		    if( stat(dir, stat_struct)  == 0) return 0;
		    }
	    deb=fin+1;
	    }
    while (fin != NULL);
    return -1;
#undef Mxdir
#endif
}



static void save_species_sets(int numb_species_sets, int **list_species_sets, 
	char **name_species_sets, int totseqs, FILE *out)
{
int num, i, previous, total;
for(num=0; num < numb_species_sets; num++) {
	total = 0;
	for(i=0; i< totseqs; i++) 
		if( list_species_sets[num][i] ) total++;
	if( total == 0 ) continue;
	fprintf(out,";;@ of species = %d %s\n;;", total, 
		name_species_sets[num]);
	for(previous = 0; previous < totseqs; previous++) 
		if( list_species_sets[num][previous] ) break;
	total = 0;
	for(i = previous+1; i < totseqs; i++) {
		if( list_species_sets[num][i] ) {
			fprintf(out," %d,", previous+1);
			previous = i;
			total++;
			if( total >= 15 ) {
				fprintf(out, "\n;;");
				total = 0;
				}
			}
		}
	fprintf(out," %d\n", previous+1);
	}
}


void save_comment_lines(int tot_comment_lines, char **names, char **lines, 
	FILE *out)
{
int num, l, pos;

for(num = 0; num < tot_comment_lines; num++) {
	if( (l = strlen(lines[num]) ) == 0) continue;
	fprintf(out, ";;|%s\n", names[num]);
	for(pos = 0; pos < l; pos += 60)
		fprintf(out, ";;%.60s\n", lines[num]+pos);
	fprintf(out, ";;||\n");
	}
}