void ReactantList::removeMappingSet(unsigned int mappingSetId)
{
//Make sure this mappingSet is not empty
if(n_mappingSets==0) {
printDetails();
cout.flush();
cerr<<"Trying to remove from an empty ReactantList!!"<<endl;
exit(1);
}
//First, get the position of the mappingSet we need to remove
int pos = msPositionMap[mappingSetId];
//Make sure the position is valid (not out of bounds of the List)
if(pos+1>(n_mappingSets)) {
cout<<"Error in ReactantList: you can't remove a mappingSet that has been cleared! (trying to remove: "<< mappingSetId << " in pos " << pos <<" but size is: "<<size()<<endl;
printDetails();
return;
}
//If the array has only one element, or we just happened to select the last element,
//then just remove the last element without a swap
if( pos+1 == (n_mappingSets) ) {
popLastMappingSet();
return;
}
//Otherwise, we have to swap with the last element in the list
MappingSet *tempMappingSet = mappingSets[pos];
mappingSets[pos] = mappingSets[n_mappingSets-1];
mappingSets[n_mappingSets-1] = tempMappingSet;
//Careful here! We have to swap values in the msPositionMap
//so that msPositionMap[mappingId] points correctly to where
//that MappingSet now lives. Notice that this is a different
//swap than above in the MappingSets array!
msPositionMap[mappingSetId] = n_mappingSets-1;
msPositionMap[mappingSets[pos]->getId()] = pos;
//Remember to remove
n_mappingSets--;
//Make sure we clear what we don't need
unsigned int clone = tempMappingSet->getClonedMapping();
tempMappingSet->clear();
//Now, IF this mapping set had a clone, we have to remove it as well
if(clone!=MappingSet::NO_CLONE) {
this->removeMappingSet(clone);
}
}
bool TransformationSet::transform(MappingSet **mappingSets)
{
if(!finalized) { cerr<<"TransformationSet cannot apply a transform if it is not finalized!"<<endl; exit(1); }
//cout<<"transforming!"<<endl;
//list <Molecule *> deleteList;
for(unsigned int r=0; r<n_reactants; r++) {
MappingSet *ms = mappingSets[r];
for(unsigned int t=0; t<transformations[r].size(); t++)
{
if(transformations[r].at(t)->getType()==(int)TransformationFactory::REMOVE) {
Mapping *m1 = ms->get(t);
if(transformations[r].at(t)->getRemovalType()==TransformationFactory::COMPLETE_SPECIES_REMOVAL) {
m1->getMolecule()->traverseBondedNeighborhood(deleteList,ReactionClass::NO_LIMIT);
} else if (transformations[r].at(t)->getRemovalType()==TransformationFactory::DELETE_MOLECULES) {
deleteList.push_back(m1->getMolecule());
}
} else {
//cout<<"applying!"<<endl;
//cout<<transformations[r].at(t)->getType()<<endl;
transformations[r].at(t)->apply(ms->get(t),mappingSets);
}
}
}
if(deleteList.size()>0) {
list <Molecule *>::iterator it;
//Each molecule that is on the list must be dealt with
for(it = deleteList.begin(); it!=deleteList.end(); it++) {
(*it)->getMoleculeType()->removeMoleculeFromRunningSystem((*it));
}
deleteList.clear();
}
int size = addMoleculeTransformations.size();
if(size>0) {
for(int i=0; i<size; i++) {
addMoleculeTransformations.at(i)->apply(NULL,NULL);
}
}
return true;
}
void ReactantTree::removeMappingSet(unsigned int mappingSetId)
{
if(n_mappingSets==0) {
cerr<<"Trying to remove from an empty ReactantTree!!"<<endl;
exit(1);
}
//first get the position of this mappingSet in the tree
int msTreeArrayPosition = msTreePositionMap[mappingSetId];
//If we have already confirmed this push on the tree, we must take it out of
//the tree. IF we didn't find this on the tree, then perhaps it just wasn't
//pushed on yet.
if(msTreeArrayPosition>=0) {
removeFromTreeOnly(msTreeArrayPosition,mappingSetId);
}
//At this point, the tree is up to date, but we still have to get rid of the empty mappingSet
//by swapping it with the end of the list... This will allow us to reuse the mappingSet without
//destroying it and creating it again later...
//So first, get the position of the mappingSet we need to remove
int pos = msPositionMap[mappingSetId];
//Make sure the position is valid (not out of bounds of the List)
if(pos+1>(n_mappingSets)) {
cout<<"Error in ReactantTree: you can't remove a mappingSet that has been cleared! (trying to remove: ";
cout<< mappingSetId << " in pos " << pos <<" but size is: "<<size()<<endl;
exit(1);
}
//If the array has only one element, or we just happened to select the last element,
//then just remove the last element without a swap - we can do this by popping the
//last mapping set. This will work, because we already cleared the tree at this location
if( pos+1 == (n_mappingSets) ) {
popLastMappingSet();
return;
}
//Otherwise, we have to swap with the last element in the list
MappingSet *tempMappingSet = mappingSets[pos];
mappingSets[pos] = mappingSets[n_mappingSets-1];
mappingSets[n_mappingSets-1] = tempMappingSet;
//Careful here! We have to swap values in the msPositionMap
//so that msPositionMap[mappingId] points correctly to where
//that MappingSet now lives.
msPositionMap[mappingSetId] = n_mappingSets-1;
msPositionMap[mappingSets[pos]->getId()] = pos;
//Make sure we clear what we don't need
unsigned int clone = mappingSets[n_mappingSets-1]->getClonedMapping();
tempMappingSet->clear();
//Remember to mark the removal on our counter...
n_mappingSets--;
//Remove all the clones as well
if(clone!=MappingSet::NO_CLONE) {
this->removeMappingSet(clone);
}
}