/**
* override this for proposals,
*
* @return log of Hastings Ratio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
*/
@Override
public double proposal() {
testing = isTestInput.get();
speciesTreeNodes = speciesTree.getNodesAsArray();
nLeafNodes = speciesTree.getLeafNodeCount();
nInternalNodes = speciesTree.getInternalNodeCount();
nSpeciesNodes = speciesTree.getNodeCount();
boolean isNarrow = isNarrowInput.get();
double logHastingsRatio = 0.0;
if (isNarrow) {
// only proceed to rearrange gene trees if the species tree can be changed
// doesn't execute if testing
if (!testing && !pickNarrow()) return Double.NEGATIVE_INFINITY;
int validGP = 0;
for (int i = nLeafNodes; i < nSpeciesNodes; ++i) {
validGP += isg(speciesTree.getNode(i));
}
final int c2 = sisg(yNode) + sisg(cNode);
fillNodes(); // fills in movedNodes and graftNodes
pruneAndRegraft(yNode, cNode, bNode);
final int validGPafter = validGP - c2 + sisg(yNode) + sisg(cNode);
logHastingsRatio += Math.log(validGP) - Math.log(validGPafter);
} else {
// only proceed to rearrange gene trees if the species tree can be changed
// doesn't execute if testing
if (!testing && !pickWide()) return Double.NEGATIVE_INFINITY;
fillNodes(); // fills in movedNodes and graftNodes
pruneAndRegraft(yNode, cNode, bNode);
}
for (final Tree geneTree : geneTreeInput.get())
geneTree.startEditing(null); // hack to stop beast.core.State.Trie memory leak
for (int i = 0; i < czBranchCount; i++) {
final List<SortedMap<Node, Node>> perBranchMovedNodes = movedNodes.get(i);
final SetMultimap<Integer, Node> perBranchGraftNodes = graftNodes.get(i);
final double logForward = rearrangeGeneTrees(perBranchMovedNodes, perBranchGraftNodes, true);
assert logForward != Double.NEGATIVE_INFINITY;
if (logForward == Double.NEGATIVE_INFINITY) return Double.NEGATIVE_INFINITY;
else logHastingsRatio += logForward;
}
// compute reverse move (Hastings ratio denominator)
final Node bNodeTmp = bNode;
final Node cNodeTmp = cNode;
bNode = cNodeTmp;
cNode = bNodeTmp;
fillNodes(); // fills in movedNodes and graftNodes for reverse move
for (int i = 0; i < czBranchCount; i++) {
final List<SortedMap<Node, Node>> perBranchMovedNodes = movedNodes.get(i);
final SetMultimap<Integer, Node> perBranchGraftNodes = graftNodes.get(i);
final double logReverse = rearrangeGeneTrees(perBranchMovedNodes, perBranchGraftNodes, false);
assert logReverse != Double.NEGATIVE_INFINITY;
if (logReverse == Double.NEGATIVE_INFINITY) return Double.NEGATIVE_INFINITY;
else logHastingsRatio -= logReverse;
}
return logHastingsRatio;
}
