// Helper method for updateM( boolean, Node, Node )
// Calculates M for Node n, given that M for the two children
// of n has been calculated.
// (Last modified: 10/02/01)
private void calculateMforNode(Node n) {
if (!n.isExternal()) {
boolean was_duplication = n.isDuplication();
Node a = n.getChild1().getLink(), b = n.getChild2().getLink();
while (a != b) {
if (a.getID() > b.getID()) {
a = a.getParent();
} else {
b = b.getParent();
}
}
n.setLink(a);
if (a == n.getChild1().getLink() || a == n.getChild2().getLink()) {
n.setDuplication(true);
if (!was_duplication) {
increaseDuplications();
}
} else {
n.setDuplication(false);
if (was_duplication) {
decreaseDuplications();
}
}
}
} // calculateMforNode( Node )
/**
* Traverses the subtree of Node g in postorder, calculating the mapping function M, and
* determines which nodes represent speciation events and which ones duplication events.
*
* <p>Preconditions: Mapping M for external nodes must have been calculated and the species tree
* must be labelled in preorder.
*
* <p>(Last modified: 01/11/01)
*
* @param g starting node of a gene tree - normally the root
*/
void geneTreePostOrderTraversal(Node g) {
Node a, b;
if (!g.isExternal()) {
geneTreePostOrderTraversal(g.getChild1());
geneTreePostOrderTraversal(g.getChild2());
a = g.getChild1().getLink();
b = g.getChild2().getLink();
while (a != b) {
if (a.getID() > b.getID()) {
a = a.getParent();
} else {
b = b.getParent();
}
}
g.setLink(a);
// Determines whether dup. or spec.
g.setDuplicationOrSpecAssigned(true);
if (a == g.getChild1().getLink() || a == g.getChild2().getLink()) {
g.setDuplication(true);
increaseDuplications();
} else {
g.setDuplication(false);
}
}
} // geneTreePostOrderTraversal( Node )
/**
* Updates the mapping function M after the root of the gene tree has been moved by one branch. It
* calculates M for the root of the gene tree and one of its two children.
*
* <p>To be used ONLY by method "SDIunrooted.fastInfer(Tree,Tree)".
*
* <p>(Last modfied: 10/02/01)
*
* @param prev_root_was_dup true if the previous root was a duplication, false otherwise
* @param prev_root_c1 child 1 of the previous root
* @param prev_root_c2 child 2 of the previous root
* @return number of duplications which have been assigned in gene tree
*/
int updateM(boolean prev_root_was_dup, Node prev_root_c1, Node prev_root_c2) {
Node root = getGeneTree().getRoot();
if (root.getChild1() == prev_root_c1 || root.getChild2() == prev_root_c1) {
calculateMforNode(prev_root_c1);
} else {
calculateMforNode(prev_root_c2);
}
root.setDuplication(prev_root_was_dup);
calculateMforNode(root);
return getDuplications();
} // updateM( boolean, Node, Node )