ThreeStateScore * reload_ThreeStateDB(ThreeStateScore * prev,ThreeStateDB * mdb,int * return_status)
{
ThreeStateModel * tsm;
ThreeStateScore * tss;
free_ThreeStateScore(prev);
if( mdb->dbtype == TSMDB_SINGLE ) {
*return_status = DB_RETURN_END;
return NULL;
}
tsm = read_TSM_ThreeStateDB(mdb,return_status);
if( *return_status != DB_RETURN_OK)
return NULL;
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
fold_RandomModel_into_ThreeStateModel(tsm,mdb->rm);
tss = ThreeStateScore_from_ThreeStateModel(tsm);
free_ThreeStateModel(tsm);
*return_status = DB_RETURN_OK;
return tss;
}
void free_objects(void)
{
if( gwdb != NULL )
gwdb = free_GeneWiseDB(gwdb);
if( cdb != NULL )
cdb = free_cDNADB(cdb);
if( sdb != NULL )
sdb = free_SequenceDB(sdb);
if( cdna != NULL )
cdna = free_cDNA(cdna);
if( pro != NULL )
pro = free_Protein(pro);
if( tsm != NULL )
tsm = free_ThreeStateModel(tsm);
if( tsmdb != NULL )
tsmdb = free_ThreeStateDB(tsmdb);
if( gws != NULL )
gws = free_GeneWiseScore(gws);
if( hs != NULL )
hs = free_Hscore(hs);
if( cm != NULL )
cm = free_CodonMapper(cm);
if( cps != NULL )
cps = free_cDNAParser(cps);
}
ThreeStateScore * init_ThreeStateDB(ThreeStateDB * mdb,int * return_status)
{
ThreeStateModel * tsm;
ThreeStateScore * tss;
if( open_ThreeStateDB(mdb) == FALSE) {
warn("Could not open ThreeStateDB, hence could not init it!");
*return_status = DB_RETURN_ERROR;
return NULL;
}
tsm = read_TSM_ThreeStateDB(mdb,return_status);
if( *return_status == DB_RETURN_ERROR)
return NULL;
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
fold_RandomModel_into_ThreeStateModel(tsm,mdb->rm);
tss = ThreeStateScore_from_ThreeStateModel(tsm);
free_ThreeStateModel(tsm);
*return_status = DB_RETURN_OK;
return tss;
}
/* Function: free_PhasedHMM(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [PhasedHMM *]
*
* Return [UNKN ] Undocumented return value [PhasedHMM *]
*
*/
PhasedHMM * free_PhasedHMM(PhasedHMM * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a PhasedHMM obj. Should be trappable");
return NULL;
}
#ifdef PTHREAD
assert(pthread_mutex_lock(&(obj->dynamite_mutex)) == 0);
#endif
if( obj->dynamite_hard_link > 1) {
return_early = 1;
obj->dynamite_hard_link--;
}
#ifdef PTHREAD
assert(pthread_mutex_unlock(&(obj->dynamite_mutex)) == 0);
#endif
if( return_early == 1)
return NULL;
if( obj->tsm != NULL)
free_ThreeStateModel(obj->tsm);
if( obj->list != NULL)
free_ProteinIntronList(obj->list);
ckfree(obj);
return NULL;
}
/* Function: free_ThreeStateDB(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [ThreeStateDB *]
*
* Return [UNKN ] Undocumented return value [ThreeStateDB *]
*
*/
ThreeStateDB * free_ThreeStateDB(ThreeStateDB * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a ThreeStateDB obj. Should be trappable");
return NULL;
}
#ifdef PTHREAD
assert(pthread_mutex_lock(&(obj->dynamite_mutex)) == 0);
#endif
if( obj->dynamite_hard_link > 1) {
return_early = 1;
obj->dynamite_hard_link--;
}
#ifdef PTHREAD
assert(pthread_mutex_unlock(&(obj->dynamite_mutex)) == 0);
#endif
if( return_early == 1)
return NULL;
if( obj->filename != NULL)
ckfree(obj->filename);
/* obj->current_file is linked in */
if( obj->rm != NULL)
free_RandomModel(obj->rm);
if( obj->single != NULL)
free_ThreeStateModel(obj->single);
if( obj->phdb != NULL)
free_PfamHmmer1DB(obj->phdb);
if( obj->sdb != NULL)
free_SequenceDB(obj->sdb);
if( obj->comp != NULL)
free_CompMat(obj->comp);
if( obj->seq_cache != NULL)
free_Sequence(obj->seq_cache);
/* obj->reload_generic is a function pointer */
/* obj->open_generic is a function pointer */
/* obj->close_generic is a function pointer */
/* obj->dataentry_add is a function pointer */
/* obj->open_index_generic is a function pointer */
/* obj->index_generic is a function pointer */
/* obj->close_index_generic is a function pointer */
/* obj->data is linked in */
ckfree(obj);
return NULL;
}
boolean open_ThreeStateDB(ThreeStateDB * mdb)
{
int ret;
int return_status;
ThreeStateModel * temp;
int count;
mdb->current_no = 0;
switch( mdb->dbtype ) {
case TSMDB_SINGLE :
return TRUE; /* should be fine! */
case TSMDB_HMMER1PFAM :
if( mdb->phdb == NULL ) {
warn("No hmmer1 db to open for threestatedb!");
return FALSE;
}
mdb->phdb->cur = 0;
break;
case TSMDB_PROTEIN :
if( mdb->sdb == NULL ) {
warn("Attempting to open a protein tsm with no sequence db!");
return FALSE;
}
mdb->seq_cache = init_SequenceDB(mdb->sdb,&ret);
if( ret == DB_RETURN_ERROR ) {
return FALSE;
}
if( ret == DB_RETURN_END ) {
warn("Due to some bad coding, can't cope with single protein databases in tsmdbs. oooops!");
}
break;
case TSMDB_GENERIC :
((*mdb->open_generic)(mdb));
break;
default :
warn("Got an unrecognisable tsm db type in opening tsm %d",mdb->dbtype);
return FALSE;
}
if( mdb->hmm_model_start != -1 && mdb->hmm_model_end != -1 ) {
for(count=0;count<mdb->hmm_model_start;count++) {
temp = read_TSM_ThreeStateDB(mdb,&return_status);
free_ThreeStateModel(temp);
}
}
return TRUE;
}
boolean free_io_objects(void)
{
if( use_tsm == TRUE) {
free_ThreeStateModel(tsm);
} else {
free_Protein(pro);
}
free_CodonTable(ct);
if( gf != NULL ) {
free_GeneFrequency21(gf);
}
free_RandomModelDNA(rmd);
if( is_embl ) {
free_GenomicRegion(embl);
}
free_Genomic(gen);
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;
}
