boolean show_output(void)
{
int i;
cDNA * cdna;
Protein * trans;
GenomicOverlapResults * gor;
AlnColumn * alt;
if( show_pretty == TRUE ) {
show_pretty_aln();
}
if( show_match_sum == TRUE ) {
show_MatchSummary_genewise_header(ofp);
show_MatchSummarySet_genewise(mss,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_pretty_gene == TRUE ) {
show_pretty_GenomicRegion(gr,0,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_supp_gene == TRUE ) {
show_pretty_GenomicRegion(gr,1,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_embl == TRUE ) {
write_Embl_FT_GenomicRegion(gr,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_diana == TRUE ) {
write_Diana_FT_GenomicRegion(gr,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_overlap == TRUE ) {
gor = Genomic_overlap(gr,embl);
show_GenomicOverlapResults(gor,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_trans == TRUE ) {
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(ofp,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,ofp);
}
}
fprintf(ofp,"%s\n",divide_str);
}
if( show_pep == TRUE ) {
alt = alb->start;
for(;alt != NULL;) {
trans = Protein_from_GeneWise_AlnColumn(gen->baseseq,alt,1,&alt,ct,is_random_AlnColumn_genewise);
if ( trans == NULL )
break;
write_fasta_Sequence(trans->baseseq,ofp);
free_Protein(trans);
}
fprintf(ofp,"%s\n",divide_str);
}
if( show_cdna == TRUE ) {
for(i=0;i<gr->len;i++) {
cdna = get_cDNA_from_Transcript(gr->gene[i]->transcript[0]);
write_fasta_Sequence(cdna->baseseq,ofp);
}
fprintf(ofp,"%s\n",divide_str);
}
if( show_ace == TRUE ) {
show_ace_GenomicRegion(gr,gen->baseseq->name,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_gff == TRUE ) {
show_GFF_GenomicRegion(gr,gen->baseseq->name,"GeneWise",ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_gene_plain == TRUE ) {
show_GenomicRegion(gr,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_AlnBlock == TRUE ) {
mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_cumlative_PackAln == TRUE ) {
show_bits_and_cumlative_PackAln(pal,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_PackAln == TRUE ) {
show_simple_PackAln(pal,ofp);
fprintf(ofp,"%s\n",divide_str);
}
return TRUE;
}
boolean show_output(void)
{
int i,k;
ThreeStateModel * temptsm;
AlnBlock * alb;
PackAln * pal;
MatchSummarySet * mss;
Protein * ps;
cDNA * cdna;
double bits;
boolean fitted_res = FALSE;
AlnBlockList * alist;
AlnBlock * anchored;
SequenceSet * set;
AlnColumn * alt;
Protein * trans;
/* sort by bit score first */
sort_Hscore_by_score(hs);
if( search_mode == PC_SEARCH_S2DB ) {
if( hs->his == NULL || hs->his->total < 1000 ) {
info("Cannot fit histogram to a db smaller than 1,000");
fprintf(ofp,"[Warning: Can't fit histogram to a db smaller than 1,000]\n\n");
show_histogram = FALSE;
} else {
fitted_res = TRUE;
fit_Hscore_to_EVD(hs,20);
}
}
/* deal with initialising anchored alignment.
* Could be done for either single HMMs or single proteins,
* but we will only do it for HMMs at the moment
*/
if( make_anchored_aln == TRUE ) {
if( tsm == NULL ) {
warn("Attempting to make an achored alignment without a HMM. impossible!");
make_anchored_aln = FALSE;
} else {
anchored = single_unit_AlnBlock(tsm->len,"MATCH_STATE");
set = SequenceSet_alloc_std();
}
}
/* dofus catcher */
if( aln_alg != alg ) {
fprintf(ofp,"\n#\n#WARNING!\n#\n# Your alignment algorithm is different from your search algorithm.\n# This is probably quite sensible but will lead to differing scores.\n# Use the search score as an indicator of the significance of the match\n# Read the docs for more information\n#\n");
}
fprintf(ofp,"\n\n#High Score list\n");
fprintf(ofp,"#Protein ID DNA Str ID Bits Evalue\n");
fprintf(ofp,"--------------------------------------------------------------------------\n");
for(i=0;i<hs->len;i++) {
bits = Score2Bits(hs->ds[i]->score);
if( bits < search_cutoff ) {
break;
}
if( fitted_res == TRUE && evalue_search_str != NULL ) {
if( hs->ds[i]->evalue > evalue_search_cutoff )
break;
}
if( fitted_res == TRUE)
fprintf(ofp,"Protein %-20sDNA [%c] %-24s %.2f %.2g\n",hs->ds[i]->query->name,hs->ds[i]->target->is_reversed == TRUE ? '-' : '+',hs->ds[i]->target->name,bits,hs->ds[i]->evalue);
else
fprintf(ofp,"Protein %-20sDNA [%c] %-24s %.2f\n",hs->ds[i]->query->name,hs->ds[i]->target->is_reversed == TRUE ? '-' : '+',hs->ds[i]->target->name,bits);
}
if( search_mode == PC_SEARCH_S2DB && show_histogram == TRUE ) {
fprintf(ofp,"\n\n#Histogram\n");
fprintf(ofp,"-----------------------------------------------------------------------\n");
PrintASCIIHistogram(hs->his,ofp);
}
fprintf(ofp,"\n\n#Alignments\n");
fprintf(ofp,"-----------------------------------------------------------------------\n");
for(i=0;i<hs->len;i++) {
bits = Score2Bits(hs->ds[i]->score);
if( bits < search_cutoff ) {
break;
}
if( i >= aln_number ) {
break;
}
if( fitted_res == TRUE && evalue_search_str != NULL ) {
if( hs->ds[i]->evalue > evalue_search_cutoff )
break;
}
fprintf(ofp,"\n\n>Results for %s vs %s (%s) [%d]\n",hs->ds[i]->query->name,hs->ds[i]->target->name,hs->ds[i]->target->is_reversed == TRUE ? "reverse" : "forward",i+1 );
cdna = get_cDNA_from_cDNADB(cdb,hs->ds[i]->target);
temptsm = indexed_ThreeStateModel_ThreeStateDB(tsmdb,hs->ds[i]->query);
alb = AlnBlock_from_TSM_estwise_wrap(temptsm,cdna,cps,cm,ct,rmd,aln_alg,use_syn,allN,flat_insert,dpri,&pal);
if( alb == NULL ) {
warn("Got a NULL alignment. Exiting now due to presumed problems");
fprintf(ofp,"\n\n*Got a NULL alignment. Exiting now due to presumed problems*\n\n");
return FALSE;
}
if( use_single_pro == FALSE)
mss = MatchSummarySet_from_AlnBlock_genewise(alb,temptsm->name,1,cdna->baseseq);
else
mss = MatchSummarySet_from_AlnBlock_genewise(alb,pro->baseseq->name,pro->baseseq->offset,cdna->baseseq);
if( show_pretty == TRUE ) {
fprintf(ofp,"\n%s output\nScore %4.2f bits over entire alignment.\nThis will be different from per-alignment scores. See manual for details\nFor computer parsable output, try %s -help or read the manual\n",program_name,Score2Bits(pal->score),program_name);
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");
}
ps = pseudo_Protein_from_ThreeStateModel(temptsm);
protcdna_ascii_display(alb,ps->baseseq->seq,ps->baseseq->name,ps->baseseq->offset,cdna,ct,15,main_block,TRUE,ofp);
free_Protein(ps);
fprintf(ofp,"%s\n",divide_str);
}
if( show_match_sum == TRUE ) {
show_MatchSummary_genewise_header(ofp);
show_MatchSummarySet_genewise(mss,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_pep == TRUE ) {
alt = alb->start;
for(;alt != NULL;) {
trans = Protein_from_GeneWise_AlnColumn(cdna->baseseq,alt,1,&alt,ct,is_random_AlnColumn_genewise);
if ( trans == NULL )
break;
write_fasta_Sequence(trans->baseseq,ofp);
free_Protein(trans);
}
fprintf(ofp,"%s\n",divide_str);
}
if( show_AlnBlock == TRUE ) {
mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp);
fprintf(ofp,"%s\n",divide_str);
}
if( show_PackAln == TRUE ) {
show_simple_PackAln(pal,ofp);
fprintf(ofp,"%s\n",divide_str);
}
/*
* This goes at the end because it destroys the alb structure
*/
if( make_anchored_aln == TRUE ) {
/* attach sequence to als in alb, so we have it for later use */
alb->seq[1]->data = (void *) cdna->baseseq;
/* add to SequenceSet so we can destroy the memory */
add_SequenceSet(set,hard_link_Sequence(cdna->baseseq));
alist = split_AlnBlock(alb,is_random_AlnColumn_genewise);
for(k=0;k<alist->len;k++) {
/* actually produce the anchored alignment */
/*mapped_ascii_AlnBlock(alist->alb[k],Score2Bits,stderr);*/
add_to_anchored_AlnBlock(anchored,alist->alb[k]);
/* dump_ascii_AlnBlock(anchored,stderr);*/
}
}
alb = free_AlnBlock(alb);
pal = free_PackAln(pal);
mss = free_MatchSummarySet(mss);
cdna = free_cDNA(cdna);
temptsm = free_ThreeStateModel(temptsm);
}
if( do_complete_analysis == TRUE ) {
fprintf(ofp,"\n\n#Complete Analysis\n");
fprintf(ofp,"-------------------------------------------------------------\n\n");
/* ok - end of loop over relevant hits. If we have an
* anchored alignment, print it out!
*/
if( make_anchored_aln == TRUE ) {
/*dump_ascii_AlnBlock(anchored,stderr);*/
write_mul_estwise_AlnBlock(anchored,ct,ofp);
fprintf(ofp,"%s\n",divide_str);
}
}
return TRUE;
}
