cDNADB * new_cDNADB(SequenceDB * seqdb)
{
cDNADB * out;
ComplexSequenceEvalSet * cses;
if( seqdb == NULL ) {
warn("No sequencedb - can't make a cDNADB!");
return NULL;
}
/** should check sequence database **/
cses = default_cDNA_ComplexSequenceEvalSet();
if( cses->type != SEQUENCE_CDNA ) {
warn("You can't make a cDNA database with a non SEQUENCE_cDNA cses type [%d]",cses->type);
return NULL;
}
out = cDNADB_alloc();
out->is_single_seq = FALSE;
out->sdb = hard_link_SequenceDB(seqdb);
out->cses = hard_link_ComplexSequenceEvalSet(cses);
free_ComplexSequenceEvalSet(cses);
return out;
}
/* Function: free_GenomicDB(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 [GenomicDB *]
*
* Return [UNKN ] Undocumented return value [GenomicDB *]
*
*/
GenomicDB * free_GenomicDB(GenomicDB * obj)
{
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a GenomicDB obj. Should be trappable");
return NULL;
}
if( obj->dynamite_hard_link > 1) {
obj->dynamite_hard_link--;
return NULL;
}
if( obj->forw != NULL)
free_ComplexSequence(obj->forw);
if( obj->rev != NULL)
free_ComplexSequence(obj->rev);
if( obj->sdb != NULL)
free_SequenceDB(obj->sdb);
if( obj->current != NULL)
free_Genomic(obj->current);
if( obj->cses != NULL)
free_ComplexSequenceEvalSet(obj->cses);
if( obj->single != NULL)
free_Genomic(obj->single);
if( obj->revsingle != NULL)
free_Genomic(obj->revsingle);
ckfree(obj);
return NULL;
}
AlnBlock * Align_Sequences_ProteinBlockAligner(Sequence * one,Sequence * two,CompMat * comp,int bentry,int bexit,int b1exit,int b_self,int b_on,DPRunImpl * dpri)
{
ComplexSequence * cone=NULL;
ComplexSequence * ctwo=NULL;
AlnBlock * alb= NULL;
PackAln * pal=NULL;
ComplexSequenceEvalSet * evalfunc = NULL;
if( one == NULL || two == NULL || comp == NULL ) {
warn("Passed in NULL objects into Align_Sequences_ProteinSmithWaterman!");
return NULL;
}
if( one->type != SEQUENCE_PROTEIN ) {
warn("Sequence %s is not typed as protein... ignoring!\n",one->name);
}
if( two->type != SEQUENCE_PROTEIN ) {
warn("Sequence %s is not typed as protein... ignoring!\n",two->name);
}
evalfunc = default_aminoacid_ComplexSequenceEvalSet();
cone = new_ComplexSequence(one,evalfunc);
if( cone == NULL )
goto cleanup;
ctwo = new_ComplexSequence(two,evalfunc);
if( ctwo == NULL )
goto cleanup;
pal = PackAln_bestmemory_ProteinBlockAligner(cone,ctwo,comp,bentry,b1exit,b_on,b_self,bexit,NULL,dpri);
if( pal == NULL )
goto cleanup;
alb = convert_PackAln_to_AlnBlock_ProteinSW(pal);
goto cleanup;
cleanup :
if( cone != NULL )
free_ComplexSequence(cone);
if( ctwo != NULL )
free_ComplexSequence(ctwo);
if( pal != NULL )
free_PackAln(pal);
if( evalfunc != NULL )
free_ComplexSequenceEvalSet(evalfunc);
return alb;
}
cDNADB * new_cDNADB_from_single_seq(cDNA * seq)
{
ComplexSequence * cs,*cs_rev;
Sequence * temp;
ComplexSequenceEvalSet * cses;
cses = default_cDNA_ComplexSequenceEvalSet();
cs = new_ComplexSequence(seq->baseseq,cses);
temp = reverse_complement_Sequence(seq->baseseq);
cs_rev = new_ComplexSequence(temp,cses);
free_Sequence(temp);
free_ComplexSequenceEvalSet(cses);
return new_cDNADB_from_forrev_cseq(cs,cs_rev);
}
/* Function: free_cDNADB(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 [cDNADB *]
*
* Return [UNKN ] Undocumented return value [cDNADB *]
*
*/
cDNADB * free_cDNADB(cDNADB * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a cDNADB 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->forw != NULL)
free_ComplexSequence(obj->forw);
if( obj->rev != NULL)
free_ComplexSequence(obj->rev);
if( obj->sdb != NULL)
free_SequenceDB(obj->sdb);
if( obj->current != NULL)
free_Sequence(obj->current);
if( obj->cses != NULL)
free_ComplexSequenceEvalSet(obj->cses);
ckfree(obj);
return NULL;
}
AlnBlock * Align_Sequences_ProteinSmithWaterman(Sequence * one,Sequence * two,CompMat * comp,int gap,int ext,DPRunImpl * dpri)
{
AlnBlock * out = NULL;
ComplexSequenceEvalSet * evalfunc = NULL;
ComplexSequence * query_cs = NULL;
ComplexSequence * target_cs = NULL;
PackAln * pal = NULL;
if( one == NULL || two == NULL || comp == NULL ) {
warn("Passed in NULL objects into Align_Sequences_ProteinSmithWaterman!");
return NULL;
}
if( one->type != SEQUENCE_PROTEIN ) {
warn("Sequence %s is not typed as protein... ignoring!\n",one->name);
}
if( two->type != SEQUENCE_PROTEIN ) {
warn("Sequence %s is not typed as protein... ignoring!\n",two->name);
}
if( gap > 0 || ext > 0 ) {
warn("Gap penalties %d,%d only make sense if they are negative",gap,ext);
return NULL;
}
evalfunc = default_aminoacid_ComplexSequenceEvalSet();
query_cs = new_ComplexSequence(one,evalfunc);
if( query_cs == NULL )
goto cleanup;
target_cs = new_ComplexSequence(two,evalfunc);
if( target_cs == NULL )
goto cleanup;
pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp,gap,ext,NULL,dpri);
if( pal == NULL )
goto cleanup;
out = convert_PackAln_to_AlnBlock_ProteinSW(pal);
goto cleanup;
cleanup :
if( query_cs != NULL )
free_ComplexSequence(query_cs);
if( target_cs != NULL )
free_ComplexSequence(target_cs);
if( pal != NULL )
free_PackAln(pal);
if( evalfunc != NULL )
free_ComplexSequenceEvalSet(evalfunc);
return out;
}