cDNA * get_cDNA_from_cDNADB(cDNADB * cdnadb,DataEntry * de)
{
Sequence * seq;
Sequence * temp;
if( cdnadb == NULL ) {
warn("Cannot get entry from a null database");
return NULL;
}
if( de == NULL ) {
warn("Cannot get entry with a null dataentry");
return NULL;
}
if( cdnadb->is_single_seq == TRUE ) {
if( de->is_reversed == TRUE )
return cDNA_from_Sequence(hard_link_Sequence(cdnadb->rev->seq));
else
return cDNA_from_Sequence(hard_link_Sequence(cdnadb->forw->seq));
}
/* we need to get out the Sequence from seqdb */
seq = get_Sequence_from_SequenceDB(cdnadb->sdb,de);
if( seq == NULL ) {
warn("Cannot get entry for %s from cDNA db",de->name);
return NULL;
}
if( seq->type != SEQUENCE_DNA) {
warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
}
force_to_dna_Sequence(seq,1.0,NULL);
if( de->is_reversed == TRUE ) {
temp = reverse_complement_Sequence(seq);
free_Sequence(seq);
seq = temp;
}
return cDNA_from_Sequence(seq);
}
Genomic * get_Genomic_from_GenomicDB(GenomicDB * gendb,DataEntry * de)
{
Sequence * seq;
Sequence * temp;
/* we need to get out the Sequence from seqdb */
if( gendb == NULL || de == NULL ) {
warn("Cannot get a genomic sequence from NULL objects. Ugh!");
return NULL;
}
if( gendb->is_single_seq) {
if( de->is_reversed == TRUE )
return hard_link_Genomic(gendb->revsingle);
else
return hard_link_Genomic(gendb->single);
}
seq = get_Sequence_from_SequenceDB(gendb->sdb,de);
if( seq == NULL ) {
warn("Cannot get entry for %s from Genomic db",de->name);
}
/* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
if( seq->type != SEQUENCE_DNA) {
warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
}
force_to_dna_Sequence(seq,1.0,NULL);
if( de->is_reversed == TRUE ) {
temp = reverse_complement_Sequence(seq);
free_Sequence(seq);
seq = temp;
}
return Genomic_from_Sequence_Nheuristic(seq,gendb->length_of_N);
}
ThreeStateModel * indexed_ThreeStateModel_ThreeStateDB(ThreeStateDB * mdb,DataEntry * en)
{
Sequence * seq;
Protein * pro;
ThreeStateModel * tsm;
switch(mdb->dbtype) {
case TSMDB_SINGLE :
return hard_link_ThreeStateModel(mdb->single);
case TSMDB_HMMER1PFAM :
tsm = ThreeStateModel_from_name_PfamHmmer1DB(mdb->phdb,en->name);
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
return tsm;
case TSMDB_PROTEIN :
seq = get_Sequence_from_SequenceDB(mdb->sdb,en);
if( seq == NULL ) {
warn("could not retrieve %s as a sequence from database",en->name);
return NULL;
}
pro = Protein_from_Sequence(seq);
if( pro == NULL ) {
warn("Could not convert sequence to a protein. Exiting!");
return NULL;
}
/* convert protein to threestatemodel */
tsm = ThreeStateModel_from_half_bit_Sequence(pro,mdb->comp,mdb->rm,mdb->gap,mdb->ext);
if( tsm == NULL ) {
warn("Could not convert protein to threestatemode. Exiting!");
free_Protein(pro);
return NULL;
}
free_Protein(pro);
/* DB status already set by seqdb */
return tsm;
case TSMDB_GENERIC :
tsm = ((*mdb->index_generic)(mdb,en));
if( tsm == NULL ) {
return NULL;
}
/* fprintf(stdout,"Setting %d as policy\n",mdb->type); */
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
return tsm;
default :
warn("Unknown threestatedb type");
return NULL;
}
warn("Should never get here - in threestatedb reload!");
return NULL;
}
