/* Function: free_GeneStats(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 [GeneStats *]
*
* Return [UNKN ] Undocumented return value [GeneStats *]
*
*/
GeneStats * free_GeneStats(GeneStats * obj)
{
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a GeneStats obj. Should be trappable");
return NULL;
}
if( obj->dynamite_hard_link > 1) {
obj->dynamite_hard_link--;
return NULL;
}
if( obj->splice5 != NULL)
free_SeqAlign(obj->splice5);
if( obj->splice3 != NULL)
free_SeqAlign(obj->splice3);
if( obj->intron != NULL)
free_RandomModelDNA(obj->intron);
if( obj->polyp != NULL)
free_RandomModelDNA(obj->polyp);
if( obj->rnd != NULL)
free_RandomModelDNA(obj->rnd);
ckfree(obj);
return NULL;
}
/* Function: free_GeneStats(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 [GeneStats *]
*
* Return [UNKN ] Undocumented return value [GeneStats *]
*
*/
GeneStats * free_GeneStats(GeneStats * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a GeneStats 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->splice5 != NULL)
free_SeqAlign(obj->splice5);
if( obj->splice3 != NULL)
free_SeqAlign(obj->splice3);
if( obj->intron != NULL)
free_RandomModelDNA(obj->intron);
if( obj->polyp != NULL)
free_RandomModelDNA(obj->polyp);
if( obj->rnd != NULL)
free_RandomModelDNA(obj->rnd);
ckfree(obj);
return NULL;
}
/* Function: free_DnaHmmProb(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 [DnaHmmProb *]
*
* Return [UNKN ] Undocumented return value [DnaHmmProb *]
*
*/
DnaHmmProb * free_DnaHmmProb(DnaHmmProb * obj)
{
int return_early = 0;
int i;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a DnaHmmProb 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->unit != NULL) {
for(i=0;i<obj->len;i++) {
if( obj->unit[i] != NULL)
free_DnaHmmProbUnit(obj->unit[i]);
}
ckfree(obj->unit);
}
if( obj->ref_align != NULL)
free_SeqAlign(obj->ref_align);
if( obj->consensus != NULL)
ckfree(obj->consensus);
ckfree(obj);
return NULL;
}
DnaProfileSet * DnaProfileSet_from_leaf_leaf(Sequence * one,Sequence * two,DnaProfileEnginePara * dpep)
{
DnaProfileSet * out;
DnaMatrix * dm;
DnaProbMatrix * dmp;
PairwiseShortDna * psd;
LocalCisHitSet * set;
Sequence * two_rev;
DnaProfile * dp;
SeqAlign * sa;
Sequence * temp1;
Sequence * temp2;
char * temp_seq1;
char * temp_seq2;
int unmatched;
int seq1_i,seq2_i;
AlnColumn * alc;
int i;
two_rev = reverse_complement_Sequence(two);
dmp = DnaProbMatrix_from_match(0.65,NMaskType_BANNED);
assert(dmp);
flat_null_DnaProbMatrix(dmp);
dm = DnaMatrix_from_DnaProbMatrix(dmp);
show_DnaMatrix(dm,stderr);
psd = query_to_reverse_target(one,two,dm,0,one->len,0,two->len);
set = make_LocalCisHitSet(one,two,two_rev,psd->forward,psd->reverse,dpep->setpara,dpep->lchs,NULL,NULL,NULL,NULL,0,dpep->dpri);
temp_seq1 = calloc(one->len > two->len ? one->len : two->len,sizeof(char));
temp_seq2 = calloc(one->len > two->len ? one->len : two->len,sizeof(char));
out = DnaProfileSet_alloc_std();
for(i=0; i<set->len; i++) {
unmatched = 1;
sa = NULL;
/*
* Main loop over DBA style alignment. We need to make one
* DnaProfile per matching block, which are separated by unmatched
* blocks. Could potentially be no blocks.
*
* Extra annoyance provided by the "wrong" convention being used in
* DBA alignments, meaning that "inserts" label the "sequence" containing
* strand, not the non-sequence containing strand. Stupid, but dbadisplay
* uses this convention, so if we changed, would have to fix lots of exisiting
* code. Not ideal.
*
*/
for(alc=set->lch[i]->alb->start; alc != NULL; alc=alc->next) {
/* hitting an unmatched block */
if( unmatched == 0 && (strcmp(alc->alu[0]->text_label,"UM") == 0 ||
strcmp(alc->alu[0]->text_label,"UI") == 0 || strcmp(alc->alu[0]->text_label,"END") == 0) ) {
/* if we have an alignment, put it away now */
if( sa != NULL ) {
temp_seq1[seq1_i] = '\0';
temp_seq2[seq2_i] = '\0';
temp1 = Sequence_from_static_memory(one->name,temp_seq1);
temp2 = Sequence_from_static_memory(two->name,temp_seq2);
add_SeqAlign(sa,temp1);
add_SeqAlign(sa,temp2);
dp = naive_DnaProfile_from_SeqAlign(sa,0.15,0.1,0.1,0.8,0.8);
fold_RandomModel_DnaProfile(dp,dpep->rm);
add_DnaProfileSet(out,dp);
free_SeqAlign(sa); /* hard linked inside DP */
sa = NULL;
}
continue;
} else if( unmatched == 1 && (strstartcmp(alc->alu[0]->text_label,"MM") == 0 ||
strstartcmp(alc->alu[0]->text_label,"MI") == 0 ) ) {
unmatched = 0;
sa = SeqAlign_alloc_len(2);
seq1_i = 0;
seq2_i = 0;
}
/* only if we are in a matched block */
if( unmatched == 0 ) {
/* Bloody twisted DBA convention - Niclas has alot to answer for.
Evil stuff -- MI is on the wrong strand! */
if( strstartcmp(alc->alu[0]->text_label,"MI") == 0 ) {
/* means 0 has sequence, other has gap */
temp_seq1[seq1_i++] = one->seq[alc->alu[0]->end];
temp_seq2[seq2_i++] = '-';
} else if ( strstartcmp(alc->alu[1]->text_label,"MI") == 0 ) {
temp_seq1[seq1_i++] = '-';
temp_seq2[seq2_i++] = two->seq[alc->alu[1]->end];
} else if ( strstartcmp(alc->alu[0]->text_label,"MM") == 0 &&
strstartcmp(alc->alu[1]->text_label,"MM") == 0 ) {
temp_seq1[seq1_i++] = one->seq[alc->alu[0]->end];
temp_seq2[seq2_i++] = two->seq[alc->alu[1]->end];
} else {
warn("Impossible label pair reached in matched block local cis hit stuff, %s,%s",alc->alu[0]->text_label,alc->alu[1]->text_label);
}
}
}
}
free(temp_seq1);
free(temp_seq2);
free_PairwiseShortDna(psd);
free_LocalCisHitSet(set);
free_DnaMatrix(dm);
free_DnaProbMatrix(dmp);
return out;
}
