boolean show_pretty_aln(void)
{
Protein * ps;
fprintf(ofp,"\n%s output\nScore %4.2f bits over entire alignment\n",program_name,Score2Bits(pal->score));
if( alg == GWWRAP_2193L || alg == GWWRAP_2193) {
fprintf(ofp,"Entrie alignment score contains unseen 'random' score segments\nYou should only use the per-alignments score printed below\nfor the bits score of the alignment\n\n");
}
if( use_syn == FALSE ) {
fprintf(ofp,"Scores as bits over a flat simple random model\n\n");
} else {
fprintf(ofp,"Scores as bits over a synchronous coding model\n\n");
}
if( use_tsm == FALSE ) {
fprintf(ofp,"Warning: The bits scores is not probablistically correct for single seqs\nSee WWW help for more info\n\n");
protgene_ascii_display(alb,pro->baseseq->seq,pro->baseseq->name,pro->baseseq->offset,gen,ct,15,main_block,(alg == GWWRAP_623L || alg == GWWRAP_2193L || alg == GWWRAP_2193) ? TRUE : FALSE, ofp);
} else {
ps = pseudo_Protein_from_ThreeStateModel(tsm);
protgene_ascii_display(alb,ps->baseseq->seq,ps->baseseq->name,ps->baseseq->offset,gen,ct,15,main_block,(alg == GWWRAP_623L || alg == GWWRAP_2193L || alg == GWWRAP_2193) ? TRUE : FALSE,ofp);
free_Protein(ps);
}
fprintf(ofp,"%s\n",divide_str);
return TRUE;
}
boolean protein2genomic_ascii_display(AlnBlock * alb,Protein * p,Genomic * gen,CodonTable * ct,int name,int main,FILE * ofp)
{
return protgene_ascii_display(alb,p->baseseq->seq,p->baseseq->name,p->baseseq->offset,gen,ct,name,main,FALSE,ofp);
}
