void deleteSimpleLoop()
{
unsigned int index;
int loop1=0,loop2=0;
for(index=1; index<=num_ed; index++)
{
ARC * arc1 = getArcBetween(index,index);
if(arc1)
{
arc1->multiplicity=0;
arc1->bal_arc->multiplicity=0;
loop1++;
}
ARC * arc = edge_array[index].arcs;
while(arc)
{
unsigned int to_ed = arc->to_ed;
ARC * arc2 = getArcBetween(to_ed,index);
if(arc2)
{
arc2->multiplicity=0;
arc2->bal_arc->multiplicity=0;
arc->multiplicity=0;
arc->bal_arc->multiplicity=0;
loop2++;
}
arc=arc->next;
}
}
printf("%d loops removed in Graph\n",loop1+loop2);
removeArc();
}
void Magnusson::removeSwapArcs()
{
for(Arc* a : swapArcs_)
{
removeArc(a);
delete a;
}
swapArcs_.clear();
}
void Magnusson::removeSwapArc(Arc* arc)
{
assert(arc->getType() == Arc::Swap);
removeArc(arc);
std::vector<Arc*>::iterator it = std::find(swapArcs_.begin(), swapArcs_.end(), arc);
if(it != swapArcs_.end())
swapArcs_.erase(it);
else
throw std::runtime_error("Did not find arc to remove!");
}
void deleteUnlikeArc()
{
unsigned int index;
ARC * arc ,*arc_temp;
unsigned short source_multi,target_multi,max_multi;
for(index=1; index<=num_ed; index++)
{
arc=edge_array[index].arcs;
source_multi=edge_array[index].cvg;
while(arc)
{
target_multi=edge_array[arc->to_ed].cvg;
max_multi=source_multi>target_multi?source_multi:target_multi;
// printf("test:\t%4.1f",arc->multiplicity/max_multi);
if(arc->multiplicity < (double)max_multi/25 ||arc->multiplicity<3 )
{
arc->multiplicity=0;
}
arc=arc->next;
}
}
/*
for(index=1;index<=num_ed;index++)
{
arc=edge_array[index].arcs;
while(arc)
{
arc_temp=arc;
arc=arc->next;
if(arc_temp->multiplicity == 0)
{
if(arc_temp->prev)
{
arc_temp->prev->next=arc_temp->next;
}
else
{
edge_array[index].arcs=arc_temp->next;
}
if(arc_temp->next)
{
arc_temp->next->prev = arc_temp->prev;
}
dismissArc (arc_temp);
total_changed++;
}
}
}*/
int total_changed = removeArc();
printf("delete unlike arc :%d\n",total_changed);
}
RegionDesc::BlockVec::iterator
RegionDesc::deleteBlock(RegionDesc::BlockVec::iterator it) {
const auto bid = (*it)->id();
for (auto pid : preds(bid)) removeArc(pid, bid);
for (auto sid : succs(bid)) removeArc(bid, sid);
if (auto nextR = nextRetrans(bid)) {
auto prevR = prevRetrans(bid);
clearPrevRetrans(nextR.value());
if (prevR) {
clearNextRetrans(prevR.value());
setNextRetrans(prevR.value(), nextR.value());
} else {
clearPrevRetrans(nextR.value());
}
} else if (auto prevR = prevRetrans(bid)) {
clearNextRetrans(prevR.value());
}
m_data.erase(bid);
return m_blocks.erase(it);
}
void deleteShortContig(int cutLength)
{
unsigned int index;
if(pool== NULL)
pool= (int*)ckalloc (sizeof(int)*(num_ed+1));
int * poolid_length=(int*)ckalloc(sizeof(int)*(num_ed+1));
for(index=0; index<=num_ed; index++)
{
pool[index]=0;
poolid_length[index]=0;
}
int poolid_index=1;
COV_LIST * cov = (COV_LIST * ) ckalloc (sizeof(COV_LIST)*(num_ed+1));
for(index=1; index<=num_ed; index++)
{
cov[index].contig=index;
cov[index].cov=edge_array[index].cvg;
}
qsort(&cov[1], num_ed, sizeof(COV_LIST), cmp_cov);
for(index=1; index<=num_ed; index++)
{
poolid_length[poolid_index]=extern_contig(cov[index].contig,poolid_index);
if(poolid_length[poolid_index]!=0)
poolid_index++;
}
int num_delelte=0;
for(index=1; index<=num_ed; index++)
{
if(poolid_length[pool[index]]<cutLength)
{
delete1contig(index);
num_delelte++;
}
if(!EdSameAsTwin(index))
index++;
}
free(poolid_length);
free(pool);
free(cov);
printf("%d short contig(<%d) removed \n",num_delelte,cutLength);
removeArc();
}
void deleteWeakEdge(unsigned short cutoff)
{
if(cutoff > 30)
cutoff=30;
printf("Start to remove the low coverage edge < %d\n",cutoff/10);
unsigned int index;
int total=0;
for(index=1; index<=num_ed; index++)
{
if(edge_array[index].cvg < cutoff)
{
delete1contig(index);
total++;
}
if(!EdSameAsTwin(index))
index++;
}
printf("%d edges removed\n\n",total);
removeArc();
}
int deleteLightArc()
{
printf("Start to remove light arc using the rate %f and %f\n",(double)da/100,(double)dA/100);
unsigned int changed = deleteLightOutArc((double)da/100);
unsigned int flow_changed = deleteLightFlowArc((double)dA/100);
/*
unsigned int index,total_changed=0;
ARC * arc ,*arc_temp;
for(index=1;index<=num_ed;index++)
{
arc=edge_array[index].arcs;
while(arc)
{
arc_temp=arc;
arc=arc->next;
if(arc_temp->multiplicity == 0)
{
if(arc_temp->prev)
{
arc_temp->prev->next=arc_temp->next;
}
else
{
edge_array[index].arcs=arc_temp->next;
}
if(arc_temp->next)
{
arc_temp->next->prev = arc_temp->prev;
}
dismissArc (arc_temp);
total_changed++;
}
}
}*/
int total_changed = removeArc();
printf("delete light arc :%d/%d\n",total_changed/2,changed+flow_changed);
return (changed+flow_changed)>0 ? 1 : 0;
}
void NavMesh::removeArc(Arc* arc)
{
removeArc( arc->from, arc->to );
}
int deleteLightContig()
{
double prev_cov,next_cov,max,min,curr_cov;
unsigned int index;
int change=0;
ARC * arc,*arc_temp;
for(index=1; index<=num_ed; index++)
{
if(EdSameAsTwin(index))
continue;
computeNextCov(index,&next_cov);
computeNextCov(getTwinEdge(index),&prev_cov);
if(next_cov ==0 || prev_cov ==0)
continue;
if(next_cov > prev_cov)
{
max=next_cov;
min=prev_cov;
}
else
{
max=prev_cov;
min=next_cov;
}
curr_cov = (double)edge_array[index].cvg;
printf("contig_cov:\t%0.1f\t%0.1f\t%0.1f\n",curr_cov,max,min);
if(min / max <0.1)
{
if(curr_cov /min < 0.5)
{
delete1contig(index);
}
}
else
{
if(curr_cov / max <0.05)
{
delete1contig(index);
}
}
index++;
}
/*
for(index=1;index<=num_ed;index++)
{
arc=edge_array[index].arcs;
while(arc)
{
arc_temp=arc;
arc=arc->next;
if(arc_temp->multiplicity == 0)
{
if(arc_temp->prev)
{
arc_temp->prev->next=arc_temp->next;
}
else
{
edge_array[index].arcs=arc_temp->next;
}
if(arc_temp->next)
{
arc_temp->next->prev = arc_temp->prev;
}
dismissArc (arc_temp);
change++;
}
}
}*/
change = removeArc();
return change>0?1:0;;
}