public SemiTagTree clone() {
SemiTagTree newtree = new SemiTagTree();
Hashtable<SemiTagNode, SemiTagNode> dup = new Hashtable<SemiTagNode, SemiTagNode>();
for (SemiTagNode hn : allnodes) dup.put(hn, new SemiTagNode());
for (SemiTagNode hn : allnodes) {
SemiTagNode shadow = dup.get(hn);
for (SemiTagEdge p : hn.inegdes)
shadow.inegdes.add(new SemiTagEdge(dup.get(p.source), dup.get(p.target), p.methodsig));
for (SemiTagEdge s : hn.outegdes)
shadow.outegdes.add(new SemiTagEdge(dup.get(s.source), dup.get(s.target), s.methodsig));
shadow.Value = hn.Value.clone();
shadow.status = hn.status;
shadow.gene = hn.gene;
shadow.sigs = hn.sigs;
}
for (SemiTagNode hn : heads) newtree.heads.add(dup.get(hn));
for (SemiTagNode hn : tails) newtree.tails.add(dup.get(hn));
for (SemiTagNode hn : allnodes) newtree.allnodes.add(dup.get(hn));
return newtree;
}
public void mark(String s) {
for (SemiTagNode n : allnodes) {
n.sigs = new HashSet<String>();
n.sigs.add(s);
}
}