//------------------------------------------------------------------------------
// Fill in weight, degree, etc.
void Tree::buildtraverse (NodePtr p)
{
if (p)
{
p->SetWeight (0);
/*p->SetModelCategory(vector<double>(1,1.0)); //added by BCO
p->SetStateOrder(vector<int>(1,0)); //Added by BCO
p->SetStateTimes(vector<double>(1,0.0)); //Added by BCO*/
p->SetDegree (0);
buildtraverse (p->GetChild ());
buildtraverse (p->GetSibling ());
if (p->IsLeaf())
{
Leaves++;
p->SetWeight (1);
/*p->SetModelCategory(vector<double>(1,1.0)); //Added by BCO
p->SetStateOrder(vector<int>(1,0)); //Added by BCO
p->SetStateTimes(vector<double>(1,0.0)); //Added by BCO*/
}
else
{
Internals++;
}
if (p != Root)
{
p->GetAnc()->AddWeight (p->GetWeight());
p->GetAnc()->IncrementDegree();
}
}
}
//------------------------------------------------------------------------------
// Add Node below Below. Doesn't update any clusters, weights, etc.
void Tree::AddNodeBelow (NodePtr Node, NodePtr Below)
{
NodePtr Ancestor = NewNode ();
Ancestor->SetChild (Node);
Node->SetAnc (Ancestor);
NodePtr q = Below->GetAnc ();
Internals++;
if (Node->IsLeaf())
Leaves++;
if (q == NULL || Below == q->GetChild())
{
Node->SetSibling (Below);
Ancestor->SetAnc (q);
Ancestor->SetSibling (Below->GetSibling());
Below->SetSibling (NULL);
Below->SetAnc (Ancestor);
if (q == NULL)
Root = Ancestor;
else
q->SetChild (Ancestor);
}
else
{
// Get left sibling of Below
NodePtr r = Below->LeftSiblingOf();
while (Below != r->GetSibling())
r = r->GetSibling();
Node->SetSibling (Below);
Ancestor->SetAnc (q);
Ancestor->SetSibling (Below->GetSibling());
Below->SetSibling (NULL);
Below->SetAnc (Ancestor);
r->SetSibling (Ancestor);
}
}
//------------------------------------------------------------------------------
void Tree::makeNodeList (NodePtr p)
{
if (p)
{
makeNodeList (p->GetChild ());
makeNodeList (p->GetSibling ());
if (p->IsLeaf())
{
int leafnumberposition=p->GetLeafNumber()-1;//modified by BCO
string plabel=p->GetLabel(); //modified by BCO
LeafList[plabel] = leafnumberposition; //modified by BCO
assert((Leaves+Internals)>leafnumberposition);
Nodes[leafnumberposition] = p; //modified by BCO
p->SetIndex (leafnumberposition); //modified by BCO
}
else
{
Nodes[count] = p;
p->SetIndex (count);
count++;
}
if (p != Root)
{
}
}
}
//------------------------------------------------------------------------------
void Tree::drawAsTextTraverse (NodePtr p)
{
if (p)
{
drawAsTextTraverse (p->GetChild ());
if (p->IsLeaf ())
drawPendantEdge (p);
if (p->GetSibling ())
drawInteriorEdge (p);
drawAsTextTraverse (p->GetSibling ());
}
}
//Added by BCO
//------------------------------------------------------------------------------
void Tree::traversenoquote (NodePtr p)
{
if (p)
{
if (p->IsLeaf())
{
for (int i=0; i<(NEXUSString (p->GetLabel())).length(); i++) {
if ((NEXUSString (p->GetLabel()))[i]!= '\'') {
*treeStream <<(NEXUSString (p->GetLabel()))[i];
}
}
//*treeStream<<NEXUSString (p->GetLabel());
if (EdgeLengths)
{
*treeStream << ':' << p->GetEdgeLength ();
}
}
else
{
*treeStream << "(";
}
traversenoquote (p->GetChild());
if (p->GetSibling())
{
*treeStream << ",";
}
else
{
if (p != Root)
{
*treeStream << ")";
// 29/3/96
if ((p->GetAnc()->GetLabel() != "") && InternalLabels)
{
*treeStream << NEXUSString (p->GetAnc()->GetLabel ()) ; //here's the change from traverse
}
if (EdgeLengths && (p->GetAnc () != Root))
{
*treeStream << ':' << p->GetAnc()->GetEdgeLength ();
}
}
}
traversenoquote (p->GetSibling());
}
}
void Tree::drawLine (NodePtr p, bool isChild)
{
*treeStream << Line.c_str();
if (p->IsLeaf())
{
* treeStream<< " " << p->GetLabel () <<endl;
}
else
{
// Draw internal label, if present
string s = p->GetLabel();
if (s != "" && isChild)
*treeStream << p->GetLabel();
*treeStream << endl;
}
}
//------------------------------------------------------------------------------
void Tree::traverse (NodePtr p)
{
if (p)
{
if (p->IsLeaf())
{
*treeStream << NEXUSString (p->GetLabel());
if (EdgeLengths)
{
*treeStream << ':' << p->GetEdgeLength ();
}
}
else
{
*treeStream << "(";
}
traverse (p->GetChild());
if (p->GetSibling())
{
*treeStream << ",";
}
else
{
if (p != Root)
{
*treeStream << ")";
// 29/3/96
if ((p->GetAnc()->GetLabel() != "") && InternalLabels)
{
*treeStream << '\'' << NEXUSString (p->GetAnc()->GetLabel ()) << '\'';
}
if (EdgeLengths && (p->GetAnc () != Root))
{
*treeStream << ':' << p->GetAnc()->GetEdgeLength ();
}
}
}
traverse (p->GetSibling());
}
}
NodePtr Tree::RemoveNode (NodePtr Node)
{
NodePtr result = NULL;
if (Node == Root)
{
if (Leaves == 1)
{
Root = NULL;
Node->SetAnc (NULL);
Leaves = Internals = 0;
}
return result;
}
NodePtr p;
NodePtr Ancestor = Node->GetAnc();
if (Ancestor->GetDegree() == 2)
{
// ancestor is binary, so remove node and its ancestor
if (Node->IsTheChild ())
p = Node->GetSibling();
else
p = Ancestor->GetChild();
NodePtr q = Ancestor->GetAnc();
p->SetAnc (q);
if (q != NULL)
{
if (Ancestor->IsTheChild())
q->SetChild (p);
else
{
NodePtr r = Ancestor->LeftSiblingOf ();
r->SetSibling (p);
}
p->SetSibling (Ancestor->GetSibling());
result = p;
}
else
{
// Ancestor is the root
Root = p;
p->SetSibling (NULL);
result = p;
}
delete Ancestor;
Internals--;
if (Node->IsLeaf())
Leaves--;
Node->SetAnc (NULL);
Node->SetSibling (NULL);
}
else
{
// polytomy, just remove node
NodePtr q;
if (Node->IsTheChild())
{
Ancestor->SetChild (Node->GetSibling());
q = Node->GetSibling ();
}
else
{
q = Node->LeftSiblingOf ();
q->SetSibling (Node->GetSibling ());
}
Node->SetSibling (NULL);
Node->SetAnc (NULL);
if (Node->IsLeaf())
Leaves--;
Ancestor->SetDegree (Ancestor->GetDegree() - 1);
result = q;
}
}
