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);
}
}
}
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 assingPreds(
MyNode v, HashSet<MyNode> preds, HashMap<MyNode, HashSet<MyNode>> nodeToPreds) {
boolean isCritical = false;
Iterator<MyEdge> it = v.getOutEdges();
while (it.hasNext()) {
MyEdge e = it.next();
if (v.getOwner().isSpecial(e)) {
if (!nodeToPreds.containsKey(v)) nodeToPreds.put(v, (HashSet<MyNode>) preds.clone());
else nodeToPreds.get(v).addAll(preds);
isCritical = true;
break;
}
}
if (isCritical) preds.add(v);
it = v.getOutEdges();
while (it.hasNext()) {
MyEdge e = it.next();
assingPreds(e.getTarget(), (HashSet<MyNode>) preds.clone(), nodeToPreds);
}
}
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);
}
}
}
}
public void computeOcurrences() {
int networksFactor = 0;
for (HybridNetwork n : networks) {
Vector<BitSet> hybridClusters = new Vector<BitSet>();
int netFactor = 1;
Iterator<MyNode> it = n.getNodes().iterator();
while (it.hasNext()) {
MyNode v = it.next();
if (v.getInDegree() > 1) {
BitSet cluster = computeReticulationCluster(n, v);
hybridClusters.add(cluster);
netFactor *= v.getInDegree() - 1;
}
}
for (BitSet cluster : hybridClusters) {
if (clusterToNumber.containsKey(cluster)) {
int num = clusterToNumber.get(cluster) + netFactor;
clusterToNumber.remove(cluster);
clusterToNumber.put(cluster, num);
} else clusterToNumber.put(cluster, netFactor);
}
networksFactor += netFactor;
}
for (HybridNetwork n : networks) {
double sumOcc = 0;
Iterator<MyNode> it = n.nodeIterator();
while (it.hasNext()) {
MyNode v = it.next();
if (v.getInDegree() > 1 && !isClusterNode(v)) {
if (getWeight(n, v) != null) {
double w = getWeight(n, v);
double s = networksFactor;
double occProc = (w / s) * 100;
occProc = Math.round(occProc * 100) / 100.;
v.setLabel((int) Math.floor(occProc) + "%");
sumOcc += occProc;
}
}
}
networkToOcc.put(n, sumOcc);
}
// Collections.sort(networks, new NetworkSorter());
}
private boolean isClusterNode(MyNode v) {
MyEdge outEdge = v.getOutEdges().next();
if (((HashSet<Integer>) outEdge.getInfo()).contains(-1)) return true;
return false;
}