void Graph::insertMutEvents(nat genC, AddrArrayBackwardIter<Node,true> &mutBackIter, Node** nodeBufferNowGen, Chromosome &chrom, Randomness &rng)
{
bool canGoBack = NOT mutBackIter.empty();
nat chromId = chrom.getId();
while(canGoBack && mutBackIter()->originGen == genC)
{
Node *node = mutBackIter();
nat indiNr = node->indiNr;
node->ancId1 = nodeBufferNowGen[indiNr] ? nodeBufferNowGen[indiNr]->id : NO_NODE ;
// determine the base
// :TODO: this currently does not allow for a double mutation occuring in one line
node->base = chrom.mutateSite(rng, node->loc);
#ifdef DEBUG_HOOKUP
cout << "MUT: [" << *node << "]" << "\t===>" << (nodeBufferNowGen[indiNr] ? nodeBufferNowGen[indiNr]->id : 0) << endl;
#endif
nodeBufferNowGen[indiNr] = node;
canGoBack = mutBackIter.back();
}
}
/** Algorithm:
* * two buffers, nodes are propagated according to survivor information
* * when recombinations are introduced, the "directions" of these nodes have to alternate
* * laying the mutations on top of the recombinations should not be a problem
*/
void Graph::hookup(const Survivors &survivors, const Ancestry &ancestry, const PopulationManager &popMan, Chromosome &chrom, Randomness &rng, nat startGen, nat endOfSection)
{
nat chromId = chrom.getId();
// set up both buffers
Node **nodeBufferPrevGen = (Node**) malloc(previousState.size() * sizeof(Node*)),
**nodeBufferNowGen = (Node**) malloc(popMan.getTotalNumHaploByGen(startGen) * sizeof(Node*));
nat i = 0;
for(Node *node : previousState)
nodeBufferPrevGen[i++] = node;
AddrArrayBackwardIter<Node,true> mutBackIter;
mutNodes.getEnd(mutBackIter);
AddrArrayBackwardIter<Node,true> recBackIter;
recNodes.getEnd(recBackIter);
for(nat genC = startGen; genC < endOfSection; ++genC)
{
#ifdef DEBUG_HOOKUP
cout << "======== hooking up generation " << genC << endl;
#endif
// resize buffer
nodeBufferNowGen = (Node**) myRealloc(nodeBufferNowGen, popMan.getTotalNumHaploByGen(genC) * sizeof(Node*));
memset(nodeBufferNowGen,0, popMan.getTotalNumHaploByGen(genC) * sizeof(Node*));
propagateSurvivorNodes(genC, chromId, nodeBufferNowGen, nodeBufferPrevGen, ancestry, survivors);
insertRecEvents(genC, chromId, recBackIter, nodeBufferNowGen, nodeBufferPrevGen, ancestry);
insertMutEvents(genC, mutBackIter, nodeBufferNowGen, chrom, rng);
std::swap(nodeBufferPrevGen, nodeBufferNowGen);
}
// we swapped once too much
std::swap(nodeBufferNowGen, nodeBufferPrevGen);
nat lastSize = popMan.getTotalNumHaploByGen(endOfSection-1);
previousState.resize(lastSize);
for(nat i = 0; i < lastSize; ++i)
previousState[i] = nodeBufferNowGen[i];
free(nodeBufferPrevGen);
free(nodeBufferNowGen);
#ifdef DEBUG_HOOKUP
cout << "================> hookup finished"<< endl;
#endif
}
