public Graph orient() {
Graph skeleton = GraphUtils.undirectedGraph(getPattern());
Graph graph = new EdgeListGraph(skeleton.getNodes());
List<Node> nodes = skeleton.getNodes();
// Collections.shuffle(nodes);
if (isR1Done()) {
ruleR1(skeleton, graph, nodes);
}
for (Edge edge : skeleton.getEdges()) {
if (!graph.isAdjacentTo(edge.getNode1(), edge.getNode2())) {
graph.addUndirectedEdge(edge.getNode1(), edge.getNode2());
}
}
if (isR2Done()) {
ruleR2(skeleton, graph);
}
if (isMeekDone()) {
new MeekRules().orientImplied(graph);
}
return graph;
}
/** Get a graph and direct only the unshielded colliders. */
public static void basicPattern(Graph graph) {
Set<Edge> undirectedEdges = new HashSet<Edge>();
NEXT_EDGE:
for (Edge edge : graph.getEdges()) {
Node head = null, tail = null;
if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.TAIL) {
head = edge.getNode1();
tail = edge.getNode2();
} else if (edge.getEndpoint2() == Endpoint.ARROW && edge.getEndpoint1() == Endpoint.TAIL) {
head = edge.getNode2();
tail = edge.getNode1();
}
if (head != null) {
for (Node node : graph.getParents(head)) {
if (node != tail && !graph.isAdjacentTo(tail, node)) {
continue NEXT_EDGE;
}
}
undirectedEdges.add(edge);
}
}
for (Edge nextUndirected : undirectedEdges) {
Node node1 = nextUndirected.getNode1(), node2 = nextUndirected.getNode2();
graph.removeEdge(nextUndirected);
graph.addUndirectedEdge(node1, node2);
}
}
private void resolveOneEdgeMax(Graph graph, Node x, Node y, boolean strong, Graph oldGraph) {
if (RandomUtil.getInstance().nextDouble() > 0.5) {
Node temp = x;
x = y;
y = temp;
}
TetradLogger.getInstance().log("info", "\nEDGE " + x + " --- " + y);
SortedMap<Double, String> scoreReports = new TreeMap<Double, String>();
List<Node> neighborsx = graph.getAdjacentNodes(x);
neighborsx.remove(y);
double max = Double.NEGATIVE_INFINITY;
boolean left = false;
boolean right = false;
DepthChoiceGenerator genx = new DepthChoiceGenerator(neighborsx.size(), neighborsx.size());
int[] choicex;
while ((choicex = genx.next()) != null) {
List<Node> condxMinus = GraphUtils.asList(choicex, neighborsx);
List<Node> condxPlus = new ArrayList<Node>(condxMinus);
condxPlus.add(y);
double xPlus = score(x, condxPlus);
double xMinus = score(x, condxMinus);
List<Node> neighborsy = graph.getAdjacentNodes(y);
neighborsy.remove(x);
DepthChoiceGenerator geny = new DepthChoiceGenerator(neighborsy.size(), neighborsy.size());
int[] choicey;
while ((choicey = geny.next()) != null) {
List<Node> condyMinus = GraphUtils.asList(choicey, neighborsy);
// List<Node> parentsY = oldGraph.getParents(y);
// parentsY.remove(x);
// if (!condyMinus.containsAll(parentsY)) {
// continue;
// }
List<Node> condyPlus = new ArrayList<Node>(condyMinus);
condyPlus.add(x);
double yPlus = score(y, condyPlus);
double yMinus = score(y, condyMinus);
// Checking them all at once is expensive but avoids lexical ordering problems in the
// algorithm.
if (normal(y, condyPlus)
|| normal(x, condxMinus)
|| normal(x, condxPlus)
|| normal(y, condyMinus)) {
continue;
}
double delta = 0.0;
if (strong) {
if (yPlus <= xPlus + delta && xMinus <= yMinus + delta) {
double score = combinedScore(xPlus, yMinus);
if (yPlus <= yMinus + delta && xMinus <= xPlus + delta) {
StringBuilder builder = new StringBuilder();
builder.append("\nStrong " + y + "->" + x + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
if (score > max) {
max = score;
left = true;
right = false;
}
} else {
StringBuilder builder = new StringBuilder();
builder.append("\nNo directed edge " + x + "--" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
}
} else if (xPlus <= yPlus + delta && yMinus <= xMinus + delta) {
double score = combinedScore(yPlus, xMinus);
if (yMinus <= yPlus + delta && xPlus <= xMinus + delta) {
StringBuilder builder = new StringBuilder();
builder.append("\nStrong " + x + "->" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
if (score > max) {
max = score;
left = false;
right = true;
}
} else {
StringBuilder builder = new StringBuilder();
builder.append("\nNo directed edge " + x + "--" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
}
} else if (yPlus <= xPlus + delta && yMinus <= xMinus + delta) {
double score = combinedScore(yPlus, xMinus);
StringBuilder builder = new StringBuilder();
builder.append("\nNo directed edge " + x + "--" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
} else if (xPlus <= yPlus + delta && xMinus <= yMinus + delta) {
double score = combinedScore(yPlus, xMinus);
StringBuilder builder = new StringBuilder();
builder.append("\nNo directed edge " + x + "--" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
}
} else {
if (yPlus <= xPlus + delta && xMinus <= yMinus + delta) {
double score = combinedScore(xPlus, yMinus);
StringBuilder builder = new StringBuilder();
builder.append("\nWeak " + y + "->" + x + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
if (score > max) {
max = score;
left = true;
right = false;
}
} else if (xPlus <= yPlus + delta && yMinus <= xMinus + delta) {
double score = combinedScore(yPlus, xMinus);
StringBuilder builder = new StringBuilder();
builder.append("\nWeak " + x + "->" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
if (score > max) {
max = score;
left = false;
right = true;
}
} else if (yPlus <= xPlus + delta && yMinus <= xMinus + delta) {
double score = combinedScore(yPlus, xMinus);
StringBuilder builder = new StringBuilder();
builder.append("\nNo directed edge " + x + "--" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
} else if (xPlus <= yPlus + delta && xMinus <= yMinus + delta) {
double score = combinedScore(yPlus, xMinus);
StringBuilder builder = new StringBuilder();
builder.append("\nNo directed edge " + x + "--" + y + " " + score);
builder.append("\n Parents(" + x + ") = " + condxMinus);
builder.append("\n Parents(" + y + ") = " + condyMinus);
scoreReports.put(-score, builder.toString());
}
}
}
}
for (double score : scoreReports.keySet()) {
TetradLogger.getInstance().log("info", scoreReports.get(score));
}
graph.removeEdges(x, y);
if (left) {
graph.addDirectedEdge(y, x);
}
if (right) {
graph.addDirectedEdge(x, y);
}
if (!graph.isAdjacentTo(x, y)) {
graph.addUndirectedEdge(x, y);
}
}