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);
}
ComplexSequence * init_cDNADB(cDNADB * cdnadb,int * return_status)
{
ComplexSequence * cs;
Sequence * seq;
if( cdnadb->is_single_seq == TRUE) {
*return_status = DB_RETURN_OK;
cdnadb->done_forward = TRUE;
return hard_link_ComplexSequence(cdnadb->forw);
}
/* is a seq db */
seq = init_SequenceDB(cdnadb->sdb,return_status);
if( seq == NULL || *return_status == DB_RETURN_ERROR || *return_status == DB_RETURN_END ) {
return NULL; /** error already reported **/
}
if( force_to_dna_Sequence(seq,cdnadb->error_tol,NULL) == FALSE ) {
warn("first sequence below error level, have to fail at the moment. Ooops...");
free_Sequence(seq);
*return_status = DB_RETURN_ERROR;
return NULL;
}
cdnadb->current = seq;
cdnadb->done_forward = TRUE;
cs = new_ComplexSequence(seq,cdnadb->cses);
if( cs == NULL ) {
warn("Cannot make initial ComplexSequence. Unable to error catch this. Failing!");
*return_status = DB_RETURN_ERROR;
return NULL;
}
return cs;
}
ComplexSequence * init_GenomicDB(GenomicDB * gendb,int * return_status)
{
ComplexSequence * cs;
Sequence * seq;
if( gendb->is_single_seq == TRUE) {
*return_status = DB_RETURN_OK;
gendb->done_forward = TRUE;
return hard_link_ComplexSequence(gendb->forw);
}
/* is a seq db */
seq = init_SequenceDB(gendb->sdb,return_status);
if( seq == NULL || *return_status == DB_RETURN_ERROR || *return_status == DB_RETURN_END ) {
return NULL; /** error already reported **/
}
/* 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",seq->name);
}
force_to_dna_Sequence(seq,1.0,NULL);
/* map to Genomic on length of N buiness */
gendb->current = Genomic_from_Sequence_Nheuristic(seq,gendb->length_of_N);
gendb->done_forward = TRUE;
cs = evaluate_ComplexSequence_Genomic(gendb->current,gendb->cses,0,gendb->repeat_in_cds_score);
if( cs == NULL ) {
warn("Cannot make initial ComplexSequence. Unable to error catch this. Failing!");
*return_status = DB_RETURN_ERROR;
return NULL;
}
return cs;
}
ComplexSequence * reload_cDNADB(ComplexSequence * last,cDNADB * cdnadb,int * return_status)
{
ComplexSequence * cs;
Sequence * seq,*temp;
/** free Complex Sequence **/
if ( last != NULL ) {
free_ComplexSequence(last);
}
if( cdnadb->forward_only == TRUE) {
temp = reload_SequenceDB(NULL,cdnadb->sdb,return_status);
if ( *return_status != DB_RETURN_OK ) {
return NULL;
}
cs = new_ComplexSequence(temp,cdnadb->cses);
return cs;
}
if( cdnadb->is_single_seq == TRUE ) {
if( cdnadb->done_forward == TRUE ) {
*return_status = DB_RETURN_OK;
cdnadb->done_forward = FALSE;
return hard_link_ComplexSequence(cdnadb->rev);
} else {
*return_status = DB_RETURN_END;
return NULL;
}
}
/** standard database **/
if( cdnadb->done_forward == TRUE ) {
if( cdnadb->current == NULL ) {
warn("A bad internal cDNA db error - unable to find current sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
temp = reverse_complement_Sequence(cdnadb->current);
if( temp == NULL ) {
warn("A bad internal cDNA db error - unable to reverse complements current");
*return_status = DB_RETURN_ERROR;
return NULL;
}
cs = new_ComplexSequence(temp,cdnadb->cses);
if( cs == NULL ) {
warn("A bad internal cDNA db error - unable to make complex sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
free_Sequence(temp);
cdnadb->done_forward = FALSE;
return cs;
}
/* otherwise we have to get a new sequence */
seq = reload_SequenceDB(NULL,cdnadb->sdb,return_status);
if( seq == NULL || *return_status == DB_RETURN_ERROR || *return_status == DB_RETURN_END ) {
return NULL; /** error already reported **/
}
uppercase_Sequence(seq);
if( force_to_dna_Sequence(seq,cdnadb->error_tol,NULL) == FALSE ) {
if( cdnadb->error_handling == CDNADB_READ_THROUGH ) {
warn("Unable to map %s sequence to a cDNA sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_cDNADB(NULL,cdnadb,return_status);
} else {
warn("Unable to map %s sequence to a cDNA sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
cs = new_ComplexSequence(seq,cdnadb->cses);
if( cs == NULL ) {
if( cdnadb->error_handling == CDNADB_READ_THROUGH ) {
warn("Unable to map %s sequence to a cDNA sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_cDNADB(NULL,cdnadb,return_status);
} else {
warn("Unable to map %s sequence to a cDNA sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
cdnadb->current = free_Sequence(cdnadb->current);
cdnadb->current = seq;
cdnadb->done_forward= TRUE;
return cs;
}
ComplexSequence * reload_GenomicDB(ComplexSequence * last,GenomicDB * gendb,int * return_status)
{
ComplexSequence * cs;
Sequence * seq;
Genomic *temp;
Genomic * gen;
/** NB - notice that we don't do silly things with free's. Maybe we should **/
if( gendb->is_single_seq == TRUE ) {
if( gendb->done_forward == TRUE ) {
*return_status = DB_RETURN_OK;
gendb->done_forward = FALSE;
return hard_link_ComplexSequence(gendb->rev);
} else {
*return_status = DB_RETURN_END;
return NULL;
}
}
/** standard database **/
/** free Complex Sequence **/
if ( last != NULL ) {
free_ComplexSequence(last);
}
if( gendb->done_forward == TRUE ) {
if( gendb->current == NULL ) {
warn("A bad internal genomic db error - unable to find current sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
temp = reverse_complement_Genomic(gendb->current);
if( temp == NULL ) {
warn("A bad internal genomic db error - unable to reverse complements current");
*return_status = DB_RETURN_ERROR;
return NULL;
}
cs = evaluate_ComplexSequence_Genomic(temp,gendb->cses,0,gendb->repeat_in_cds_score);
if( cs == NULL ) {
warn("A bad internal genomic db error - unable to make complex sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
free_Genomic(temp);
gendb->done_forward = FALSE;
return cs;
}
/* otherwise we have to get a new sequence */
seq = reload_SequenceDB(NULL,gendb->sdb,return_status);
if( seq == NULL || *return_status == DB_RETURN_ERROR || *return_status == DB_RETURN_END ) {
return NULL; /** error already reported **/
}
uppercase_Sequence(seq);
/* 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",seq->name);
}
force_to_dna_Sequence(seq,1.0,NULL);
if( force_to_dna_Sequence(seq,0.1,NULL) == FALSE ) {
if( gendb->error_handling == GENDB_READ_THROUGH ) {
warn("Unable to map %s sequence to a genomic sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_GenomicDB(NULL,gendb,return_status);
} else {
warn("Unable to map %s sequence to a genomic sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
gen = Genomic_from_Sequence_Nheuristic(seq,gendb->length_of_N);
cs = evaluate_ComplexSequence_Genomic(gen,gendb->cses,0,gendb->repeat_in_cds_score);
if( cs == NULL ) {
if( gendb->error_handling == GENDB_READ_THROUGH ) {
warn("Unable to map %s sequence to a genomic sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_GenomicDB(NULL,gendb,return_status);
} else {
warn("Unable to map %s sequence to a genomic sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
gendb->current = free_Genomic(gendb->current);
gendb->current = gen;
gendb->done_forward= TRUE;
return cs;
}
