private void cmpTrivialInteractions(MyPhyloTree n, HashMap<MyNode, HashSet<MyNode>> nodeToPreds) {
HashSet<MyNode> retNodes = new HashSet<MyNode>();
for (MyNode v : n.getNodes()) {
if (v.getInDegree() > 1) {
retNodes.add(v);
}
}
HashSet<MyEdge> toResolve = new HashSet<MyEdge>();
for (MyNode v : retNodes) {
Vector<MyNode> parentNodes = new Vector<MyNode>();
Vector<MyEdge> parentEdges = new Vector<MyEdge>();
Iterator<MyEdge> it = v.getInEdges();
while (it.hasNext()) {
MyEdge e = it.next();
parentNodes.add(e.getSource());
parentEdges.add(e);
}
for (MyNode p1 : parentNodes) {
for (MyNode p2 : parentNodes) {
if (nodeToPreds.get(p1).contains(p2)) {
if (ancestorCheck(p1, p2)) toResolve.add(parentEdges.get(parentNodes.indexOf(p2)));
}
}
}
}
for (MyEdge e : toResolve) trivialEdges.add(e);
}
public int run(MyPhyloTree net, int border, boolean storeNetworkInfo, boolean smartMode) {
int result = 0;
for (MyPhyloTree n : new GetNetworkCluster().run(net)) {
trivialEdges = new HashSet<MyEdge>();
if (smartMode) {
HashMap<MyNode, HashSet<MyNode>> nodeToPreds = new HashMap<MyNode, HashSet<MyNode>>();
assingPreds(n.getRoot(), new HashSet<MyNode>(), nodeToPreds);
cmpTrivialInteractions(n, nodeToPreds);
}
Vector<MyEdge> retEdges = new Vector<MyEdge>();
for (MyNode v : n.getNodes()) {
if (v.getInDegree() > 1) {
Iterator<MyEdge> it = v.getInEdges();
while (it.hasNext()) {
MyEdge e = it.next();
if (!trivialEdges.contains(e)) retEdges.add(e);
}
}
}
int addTaxaDegree = -1;
for (int k = trivialEdges.size(); k <= border; k++) {
HashSet<Vector<MyEdge>> allSubsets = new HashSet<Vector<MyEdge>>();
getAllSubsets(0, retEdges, k - trivialEdges.size(), new Vector<MyEdge>(), allSubsets);
for (Vector<MyEdge> subset : allSubsets) {
clearEdges(n);
setEdges(subset);
if (checkTree(n)) {
if (storeNetworkInfo) {
n.setAddTaxaDegree(k);
setEdges(subset);
} else clearEdges(n);
addTaxaDegree = k;
break;
}
}
if (addTaxaDegree != -1) break;
}
if (addTaxaDegree == -1) return -1;
else {
result += addTaxaDegree;
border -= addTaxaDegree;
}
}
if (result != -1) net.setAddTaxaDegree(result);
return result;
}
private void cmpImplicitAncestorsRec(boolean b, MyNode v, Vector<MyNode> implicitAncestors) {
if (v.getInDegree() > 1 || b) {
Iterator<MyEdge> it = v.getInEdges();
while (it.hasNext()) {
MyEdge e = it.next();
MyNode a = e.getSource();
implicitAncestors.add(a);
cmpImplicitAncestorsRec(v.getInDegree() != 1, a, implicitAncestors);
}
}
}