TreeTemplate<Node>* TreeTemplateTools::parenthesisToTree(const string& description, bool bootstrap, const string& propertyName, bool withId, bool verbose) throw (Exception)
{
string::size_type semi = description.rfind(';');
if (semi == string::npos)
throw Exception("TreeTemplateTools::parenthesisToTree(). Bad format: no semi-colon found.");
string content = description.substr(0, semi);
unsigned int nodeCounter = 0;
Node* node = parenthesisToNode(content, nodeCounter, bootstrap, propertyName, withId, verbose);
TreeTemplate<Node>* tree = new TreeTemplate<Node>();
tree->setRootNode(node);
if (!withId)
{
tree->resetNodesId();
}
if (verbose) {
(*ApplicationTools::message) << " nodes loaded.";
ApplicationTools::message->endLine();
}
return tree;
}
TreeTemplate<Node>* TreeTemplateTools::getRandomTree(vector<string>& leavesNames, bool rooted)
{
if (leavesNames.size() == 0)
return 0; // No taxa.
// This vector will contain all nodes.
// Start with all leaves, and then group nodes randomly 2 by 2.
// Att the end, contains only the root node of the tree.
vector<Node*> nodes(leavesNames.size());
// Create all leaves nodes:
for (size_t i = 0; i < leavesNames.size(); ++i)
{
nodes[i] = new Node(leavesNames[i]);
}
// Now group all nodes:
while (nodes.size() > (rooted ? 2 : 3))
{
// Select random nodes:
size_t pos1 = RandomTools::giveIntRandomNumberBetweenZeroAndEntry<size_t>(nodes.size());
Node* node1 = nodes[pos1];
nodes.erase(nodes.begin() + static_cast<ptrdiff_t>(pos1));
size_t pos2 = RandomTools::giveIntRandomNumberBetweenZeroAndEntry<size_t>(nodes.size());
Node* node2 = nodes[pos2];
nodes.erase(nodes.begin() + static_cast<ptrdiff_t>(pos2));
// Add new node:
Node* parent = new Node();
parent->addSon(node1);
parent->addSon(node2);
nodes.push_back(parent);
}
// Return tree with last node as root node:
Node* root = new Node();
for (size_t i = 0; i < nodes.size(); ++i)
{
root->addSon(nodes[i]);
}
TreeTemplate<Node>* tree = new TreeTemplate<Node>(root);
tree->resetNodesId();
return tree;
}
TreeTemplate<Node>* BipartitionList::toTree() const throw (Exception)
{
BipartitionList* sortedBipL;
vector<int*> sortedBitBipL;
int* bip;
vector<Node*> vecNd, sonNd;
vector<bool> alive;
size_t lword, nbword, nbint, ii;
/* check, copy and prepare bipartition list */
if (!BipartitionList::areAllCompatible())
throw Exception("Trying to build a tree from incompatible bipartitions");
sortedBipL = dynamic_cast<BipartitionList*>(clone());
for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
{
if (sortedBipL->getPartitionSize(i) > sortedBipL->getNumberOfElements() / 2)
sortedBipL->flip(i);
}
sortedBipL->sortByPartitionSize();
sortedBipL->removeRedundantBipartitions();
sortedBitBipL = sortedBipL->getBitBipartitionList();
for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
{
alive.push_back(true);
}
vecNd.resize(sortedBipL->getNumberOfBipartitions() + 1);
lword = static_cast<size_t>(BipartitionTools::LWORD);
nbword = (elements_.size() + lword - 1) / lword;
nbint = nbword * lword / (CHAR_BIT * sizeof(int));
bip = new int[1]; bip[0] = 0;
/* main loop: create one node per bipartition */
for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
{
if (sortedBipL->getPartitionSize(i) == 1)
{ // terminal
for (size_t j = 0; j < sortedBipL->getNumberOfElements(); j++)
{
if (BipartitionTools::testBit(sortedBitBipL[i], static_cast<int>(j)))
{
vecNd[i] = new Node(elements_[j]);
break;
}
}
}
else
{ // internal
sonNd.clear();
for (size_t j = 0; j < i; j++)
{
if (alive[j])
{
for (ii = 0; ii < nbint; ii++)
{
BipartitionTools::bitOr(bip, sortedBitBipL[j] + ii, sortedBitBipL[i] + ii, 1);
if (bip[0] != sortedBitBipL[i][ii])
break;
}
if (ii == nbint)
{
sonNd.push_back(vecNd[j]);
alive[j] = false;
}
}
}
vecNd[i] = new Node();
for (size_t k = 0; k < sonNd.size(); k++)
{
vecNd[i]->addSon(sonNd[k]);
}
}
}
/* create last node, which joins alive bipartitions = fatherless nodes */
Node* rootNd = new Node();
for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
{
if (alive[i])
rootNd->addSon(vecNd[i]);
}
/* construct tree and return */
TreeTemplate<Node>* tr = new TreeTemplate<Node>(rootNd);
tr->resetNodesId();
delete sortedBipL;
return tr;
}