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 computeClusterRec(MyPhyloTree n, MyNode v, BitSet cluster, int treeIndex) {
if (v.getOutDegree() == 0) cluster.set(taxaOrdering.indexOf(n.getLabel(v)));
else {
Iterator<MyEdge> it = n.getOutEdges(v);
while (it.hasNext()) {
MyEdge e = it.next();
HashSet<Integer> indices = (HashSet<Integer>) e.getInfo();
if (indices.contains(treeIndex)) {
MyNode c = e.getTarget();
computeClusterRec(n, c, cluster, treeIndex);
}
}
}
}
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);
}
private boolean checkTree(MyPhyloTree net) {
MyPhyloTree n = new MyPhyloTree(net);
n.setTimeDegree(null);
HashSet<MyEdge> criticalEdges = new HashSet<MyEdge>();
for (MyEdge e : n.getEdges()) {
if (e.isCritical()) criticalEdges.add(e);
}
for (MyEdge e : criticalEdges) {
MyNode s = e.getSource();
MyNode t = e.getTarget();
s.removeOutEdge(e);
MyNode x = n.newNode();
n.newEdge(s, x);
n.newEdge(x, t);
}
CheckTimeConsistency checker = new CheckTimeConsistency();
int k = checker.run(n, 0, false, true, -1);
if (k != 0) return false;
return true;
}
private void clearEdges(MyPhyloTree n) {
for (MyEdge e : n.getEdges()) {
e.setCritical(false);
}
}