TreeTemplate<Node>* TreeTools::thresholdConsensus(const vector<Tree*>& vecTr, double threshold, bool checkNames) throw (Exception)
{
vector<size_t> bipScore;
vector<string> tr0leaves;
BipartitionList* bipL;
double score;
if (vecTr.size() == 0)
throw Exception("TreeTools::thresholdConsensus. Empty vector passed");
/* check names */
if (checkNames)
{
tr0leaves = vecTr[0]->getLeavesNames();
for (size_t i = 1; i < vecTr.size(); i++)
{
if (!VectorTools::haveSameElements(vecTr[i]->getLeavesNames(), tr0leaves))
throw Exception("TreeTools::thresholdConsensus. Distinct leaf sets between trees");
}
}
bipL = bipartitionOccurrences(vecTr, bipScore);
for (size_t i = bipL->getNumberOfBipartitions(); i > 0; i--)
{
if (bipL->getPartitionSize(i - 1) == 1)
continue;
score = static_cast<int>(bipScore[i - 1]) / static_cast<double>(vecTr.size());
if (score <= threshold && score != 1.)
{
bipL->deleteBipartition(i - 1);
continue;
}
if (score > 0.5)
continue;
for (size_t j = bipL->getNumberOfBipartitions(); j > i; j--)
{
if (!bipL->areCompatible(i - 1, j - 1))
{
bipL->deleteBipartition(i - 1);
break;
}
}
}
TreeTemplate<Node>* tr = bipL->toTree();
delete bipL;
return tr;
}
BipartitionList* TreeTools::bipartitionOccurrences(const vector<Tree*>& vecTr, vector<size_t>& bipScore)
{
vector<BipartitionList*> vecBipL;
BipartitionList* mergedBipL;
vector<size_t> bipSize;
size_t nbBip;
/* build and merge bipartitions */
for (size_t i = 0; i < vecTr.size(); i++)
{
vecBipL.push_back(new BipartitionList(*vecTr[i]));
}
mergedBipL = BipartitionTools::mergeBipartitionLists(vecBipL);
for (size_t i = 0; i < vecTr.size(); i++)
{
delete vecBipL[i];
}
mergedBipL->removeTrivialBipartitions();
nbBip = mergedBipL->getNumberOfBipartitions();
bipScore.clear();
for (size_t i = 0; i < nbBip; i++)
{
bipSize.push_back(mergedBipL->getPartitionSize(i));
bipScore.push_back(1);
}
/* compare bipartitions */
for (size_t i = nbBip; i > 0; i--)
{
if (bipScore[i - 1] == 0)
continue;
for (size_t j = i - 1; j > 0; j--)
{
if (bipScore[j - 1] && bipSize[i - 1] == bipSize[j - 1] && mergedBipL->areIdentical(i - 1, j - 1))
{
bipScore[i - 1]++;
bipScore[j - 1] = 0;
}
}
}
/* keep only distinct bipartitions */
for (size_t i = nbBip; i > 0; i--)
{
if (bipScore[i - 1] == 0)
{
bipScore.erase(bipScore.begin() + static_cast<ptrdiff_t>(i - 1));
mergedBipL->deleteBipartition(i - 1);
}
}
/* add terminal branches */
mergedBipL->addTrivialBipartitions(false);
for (size_t i = 0; i < mergedBipL->getNumberOfElements(); i++)
{
bipScore.push_back(vecTr.size());
}
return mergedBipL;
}