void rsf_out(FILE *rsfout, sint fres, sint len, ALN mult_aln, ALNOUT_OPT alnout_opt)
{
char *seq, residue;
char val;
sint n;
sint i,ii,nseqs;
sint j,k,slen,cstart,cend;
sint start,query_start,query_end;
sint line_length=60;
sint max_aln_length,max_names;
sint color;
char shape[20];
char type[20];
sint nrep,*reptype;
nseqs=0;
max_aln_length=max_names=0;
for(i=0; i<mult_aln.nseqs; i++) {
if (mult_aln.seqs[i].output_index>=0) {
if(mult_aln.seqs[i].len>max_aln_length) max_aln_length=mult_aln.seqs[i].len;
if(strlen(mult_aln.seqs[i].name)>max_names) max_names=strlen(mult_aln.seqs[i].name);
nseqs++;
}
}
seq = (char *)ckalloc((max_aln_length+1) * sizeof(char));
fprintf(rsfout,"!!RICH_SEQUENCE 1.0\n..\n");
/* set n to the number of sequence groups */
n=0;
for(i=0; i<nseqs; i++)
if(mult_aln.seqs[i].simgroup>n) n=mult_aln.seqs[i].simgroup;
n++;
for(ii=0; ii<nseqs; ii++) {
i = get_seq_with_index(mult_aln.seqs,mult_aln.nseqs,ii);
if(i<0) continue;
fprintf(rsfout, "{\nname ");
if(alnout_opt.output_names==1)
fprintf(rsfout, "%s\n", mult_aln.seqs[i].nid);
else if(alnout_opt.output_names==2)
fprintf(rsfout, "%s\n", mult_aln.seqs[i].access);
else
fprintf(rsfout, "%s\n", mult_aln.seqs[i].name);
fprintf(rsfout, "descrip %s\n", mult_aln.seqs[i].title);
fprintf(rsfout, "creator %s %s\n", mult_aln.seqs[i].org,mult_aln.seqs[i].lifedomain);
fprintf(rsfout, "type ");
fprintf(rsfout, mult_aln.dnaflag ? "DNA" : "PROTEIN");
fprintf(rsfout, "\n");
if(mult_aln.seqs[i].simgroup>0)
fprintf(rsfout, "group %d\n",mult_aln.seqs[i].simgroup);
else {
fprintf(rsfout, "group %d\n",n);
}
if(mult_aln.seqs[i].sense!=0)
fprintf(rsfout, "strand %d\n",mult_aln.seqs[i].sense);
for(j=0;j<MAXFTTYPE;j++) {
for(k=0;k<mult_aln.ft[i].nentries[j];k++) {
if(mult_aln.ft[i].data[j][k].start<0) continue;
pos2col(mult_aln.seqs[i].data,mult_aln.ft[i].data[j][k].start,mult_aln.ft[i].data[j][k].end,&cstart,&cend);
color=mult_aln.ft[i].data[j][k].color;
if(color>=0) {
if(color>12) color=12;
fprintf(rsfout, "feature %d %d %d %s %s %s\n",cstart+1,cend+1,
color,
"square",
"solid",
mult_aln.ft[i].data[j][k].type);
fprintf(rsfout," FT %-10s%5d %5d %s\n",
mult_aln.ft[i].data[j][k].type,
mult_aln.ft[i].data[j][k].start+1,
mult_aln.ft[i].data[j][k].end+1,
mult_aln.ft[i].data[j][k].name);
}
}
}
slen = 0;
for(j=fres; j<fres+len; j++) {
val = mult_aln.seqs[i].data[j];
if(val==EOS)
break;
else if(!isalpha(val))
residue = '.';
else {
residue = val;
}
seq[j-fres] = (char)toupper((int)residue);
slen++;
}
fprintf(rsfout,"sequence\n ");
for(j=0; j<slen; j++) {
fprintf(rsfout,"%c",seq[j]);
if( (j == slen-1))
fprintf(rsfout,"\n");
else if(( j!=0 && (j+1) % line_length == 0))
fprintf(rsfout,"\n ");
}
fprintf(rsfout,"}\n");
}
seq=ckfree((void *)seq);
}
void add_ft_entry(ALNPTR mult_aln,sint seq,sint first,sint last,sint type,sint code,float score,char *ctype,char *iname,sint is,sint ie)
{
sint n,color;
sint fr,lr;
sint fc,lc;
char name[100];
if(mult_aln->ft[seq].nentries[type]>MAXFT) {
fprintf(stdout,"WARNING: too many features in %s %d (%d)\n",mult_aln->seqs[seq].name,mult_aln->ft[seq].nentries[type],type);
return;
}
if(last<is || first>ie) return;
if(first<is) first=is;
if(last>ie) last=ie;
n=mult_aln->ft[seq].nentries[type];
alloc_ft_entry(&mult_aln->ft[seq].data[type][n]);
strcpy(mult_aln->ft[seq].data[type][n].type,ctype);
col2pos(mult_aln->seqs[seq].data,first,last,&fr,&lr);
pos2col(mult_aln->seqs[seq].data,fr,lr,&fc,&lc);
if(fc==first)
mult_aln->ft[seq].data[type][n].start=fr;
else
mult_aln->ft[seq].data[type][n].start=fr+1;
if(lc==last)
mult_aln->ft[seq].data[type][n].end=lr;
else
mult_aln->ft[seq].data[type][n].end=lr-1;
strcpy(name,iname);
if(strcmp(ctype,"BLOCK")==0) {
if (strcmp(name,"SBLOCK")==0)
color=code;
else if (strcmp(name,"LBLOCK")==0)
color=12;
}
else if(strcmp(ctype,"REGION")==0) {
color=10;
}
else if(strcmp(ctype,"SEQERR")==0) {
color=3;
}
else if(strcmp(ctype,"ANCHOR")==0) {
color=code;
}
else if(strcmp(ctype,"REPEAT")==0) {
color=code;
}
else if(strcmp(ctype,"STRUCT")==0) {
if(strncmp(name,"PRED_HELIX",10)==0) color=VLRED;
else if(strncmp(name,"PRED_STRAND",11)==0) color=VLGREEN;
else if(strncmp(name,"PROP_HELIX",10)==0) color=LRED;
else if(strncmp(name,"PROP_STRAND",11)==11) color=LGREEN;
else if(strcmp(name,"HELIX")==0) color=RED;
else if(strcmp(name,"STRAND")==0) color=GREEN;
}
else if(strcmp(ctype,"TRANSMEM")==0) {
if(strncmp(name,"PRED_",5)==0) {
sprintf(name,"%s %.2f",name,score);
color=10;
}
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else color=1;
}
else if(strcmp(ctype,"COIL")==0) {
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else color=6;
}
else if(strcmp(ctype,"LOWCOMP")==0) {
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else color=6;
}
else if(strcmp(ctype,"DOMAIN")==0) {
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else if(strncmp(name,"DNA_BIND",8)==0) color=2;
else if(strncmp(name,"ZN_FING",7)==0) color=3;
else color=1;
}
else if(strcmp(ctype,"PFAM-A")==0) {
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else color=code;
}
else if(strcmp(ctype,"PFAM-B")==0) {
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else color=code;
}
else if(strcmp(ctype,"PROSITE")==0) {
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else color=code;
}
else if(strcmp(ctype,"SIGNAL")==0) {
if(strncmp(name,"PRED_",5)==0) {
sprintf(name,"%s %.2f",name,score);
color=LGRAY;
}
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else if(strncmp(name,"NUCLEAR",7)==0) color=1;
else if(strncmp(name,"CHLOROPLAST",11)==0) color=2;
else if(strncmp(name,"MITOCHONDRION",13)==0) color=3;
else if(strncmp(name,"MICROBODY",9)==0) color=4;
else color=5;
}
else if(strcmp(ctype,"VARSPLIC")==0) {
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else color=5;
}
else if(strcmp(ctype,"MOD_RES")==0) {
color=0;
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else if(strncmp(name,"ACETYLATION",11)==0) color=1;
else if(strncmp(name,"ALKYLATION",10)==0) color=2;
else if(strncmp(name,"HYDROXYLATION",13)==0) color=3;
else if(strncmp(name,"METHYLATION",11)==0) color=4;
else if(strncmp(name,"PHOSPHORYLATION",15)==0) color=5;
else if(strncmp(name,"SULFATION",9)==0) color=6;
else if(strncmp(name,"PYRROLIDONE",11)==0) color=7;
else if(strncmp(name,"MYRISTATE",9)==0) color=8;
else if(strncmp(name,"PALMITATE",9)==0) color=9;
else if(strncmp(name,"FARNESYL",8)==0) color=10;
else if(strncmp(name,"GERANYL",7)==0) color=11;
else if(strncmp(name,"GPI-ANCHOR",3)==0) color=12;
else if(strncmp(name,"N-ACYL",5)==0) color=13;
}
else if(strcmp(ctype,"SITE")==0) {
color=0;
if(strncmp(name,"PRED_",5)==0) color=LGRAY;
else if(strncmp(name,"PROP_",5)==0) color=GRAY;
else if(strncmp(name,"SITE",4)==0) color=0;
else if(strncmp(name,"ACT_SITE",8)==0) color=1;
else if(strncmp(name,"CARBOHYD",8)==0) color=2;
else if(strncmp(name,"DISULFID",8)==0) color=3;
else if(strncmp(name,"BINDING",7)==0) color=4;
else if(strncmp(name,"NP_BIND",7)==0) color=5;
else if(strncmp(name,"CA_BIND",7)==0) color=6;
else if(strncmp(name,"TRANSIT",7)==0) color=7;
else if(strncmp(name,"LIPID",5)==0) color=8;
else if(strncmp(name,"METAL",5)==0) color=9;
}
strcpy(mult_aln->ft[seq].data[type][n].name,name);
mult_aln->ft[seq].data[type][n].score=score;
mult_aln->ft[seq].data[type][n].color=color;
mult_aln->ft[seq].nentries[type]++;
}
