void ParsSprProposer::testInsertParsimony(TreeAln &traln, nodeptr insertPos, nodeptr prunedTree, branch2parsScore &result, int curDepth)
{
if(curDepth == 0 )
return;
--curDepth;
nodeptr insertBack = insertPos->back;
traln.clipNode(insertPos, prunedTree->next);
traln.clipNode( insertBack, prunedTree->next->next);
auto b = BranchPlain(insertPos->number, insertBack->number);
if(_computedInsertions.size() > 0 && _computedInsertions.find(b) != _computedInsertions.end())
{
result[b] = _computedInsertions.at(b);
}
else
{
ParsimonyEvaluator::disorientNode(prunedTree);
result[b] = _pEval.evaluate(traln, prunedTree, false );
}
traln.clipNode(insertPos, insertBack);
prunedTree->next->back = prunedTree->next->next->back = NULL;
// recursively descend
if(not traln.isTipNode(insertPos))
{
testInsertParsimony(traln, insertPos->next->back, prunedTree, result, curDepth);
testInsertParsimony(traln, insertPos->next->next->back, prunedTree, result, curDepth);
}
}
ParsSprProposer::branch2parsScore
ParsSprProposer::determineScoresOfInsertions(TreeAln& traln, BranchPlain prunedTree )
{
auto result = branch2parsScore{};
nodeptr
p = traln.findNodePtr(prunedTree),
pn = p->next->back ,
pnn = p->next->next->back ;
// prune the subtree
traln.clipNode( pn, pnn);
p->next->back = p->next->next->back = NULL;
// fetch all parsimony scores
if(not traln.isTipNode(pn))
{
testInsertParsimony(traln, pn->next->back, p, result, _depth);
testInsertParsimony(traln, pn->next->next->back, p, result, _depth);
}
if(not traln.isTipNode(pnn))
{
testInsertParsimony(traln, pnn->next->back,p, result, _depth);
testInsertParsimony(traln, pnn->next->next->back,p, result, _depth);
}
traln.clipNode( p->next, pn );
traln.clipNode( p->next->next, pnn);
return result;
}
static void addTraverseParsimony (tree *tr, nodeptr p, nodeptr q, int mintrav, int maxtrav, boolean doAll, boolean saveBranches)
{
if (doAll || (--mintrav <= 0))
testInsertParsimony(tr, p, q, saveBranches);
if (((q->number > tr->mxtips)) && ((--maxtrav > 0) || doAll))
{
addTraverseParsimony(tr, p, q->next->back, mintrav, maxtrav, doAll, saveBranches);
addTraverseParsimony(tr, p, q->next->next->back, mintrav, maxtrav, doAll, saveBranches);
}
}
