private void computeDependencies(List<GraphNode<T>> nodes) {
List<GraphNode<T>> nextNodesToDisplay = null;
for (GraphNode<T> node : nodes) {
if (!isAlreadyEvaluated(node)) {
List<GraphNode<T>> comingInNodes = node.getComingInNodes();
if (areAlreadyEvaluated(comingInNodes)) {
listener.evaluating(node.value);
evaluatedNodes.add(node);
List<GraphNode<T>> goingOutNodes = node.getGoingOutNodes();
if (goingOutNodes != null) {
if (nextNodesToDisplay == null) nextNodesToDisplay = new ArrayList<GraphNode<T>>();
// add these too, so they get a chance to be displayed
// as well
nextNodesToDisplay.addAll(goingOutNodes);
}
} else {
if (nextNodesToDisplay == null) nextNodesToDisplay = new ArrayList<GraphNode<T>>();
// the checked node should be carried
nextNodesToDisplay.add(node);
}
}
}
if (nextNodesToDisplay != null) {
computeDependencies(nextNodesToDisplay);
}
// here the recursive call ends
}
/**
* Given a set of SCC nodes make this the lead member of the SCC and reroute all incoming and
* outgoing links accordingly. This eager rewrite is based on the assumption that there are few
* cycles so it is better to rewrite once and keep the graph easy to traverse.
*/
public void makeLeadNodeFor(Set<GraphNode> members) {
// Accumulate all successors
Set<GraphNode> newSucc = new HashSet<>();
Set<GraphNode> newSuccClosed = new HashSet<>();
for (GraphNode n : members) {
newSucc.addAll(n.succ);
newSuccClosed.addAll(n.succClosed);
}
newSucc.removeAll(members);
newSuccClosed.removeAll(members);
succ = newSucc;
succClosed = newSuccClosed;
// Rewrite all direct successors to have us as predecessor
for (GraphNode n : succ) {
n.pred.removeAll(members);
n.pred.add(this);
}
// Find all predecessor nodes and relink link them to point to us
Set<GraphNode> done = new HashSet<>();
Set<GraphNode> newAliases = new HashSet<>();
for (GraphNode member : members) {
addSiblings(newAliases, member);
}
becomeLeaderOf(newAliases);
for (GraphNode n : members) {
if (n != this) {
pred.addAll(n.pred);
n.relocateAllRefTo(this, done);
n.becomeSubordinateOf(this);
}
}
pred.removeAll(members);
}
/**
* Recursive DFS algorthm
*
* @param matrix Map of lists representing adj matrix
* @param info Map of nodes representing node info
* @param v Node source
* @param n int number of nodes in graph
* @param: print boolean if to print node during traversal
* @return List of nodes in order visited
*/
public ArrayList<String> dfs_rec(
Map<Integer, List<Integer>> matrix,
Map<Integer, GraphNode> info,
GraphNode v,
Integer n,
boolean print,
ArrayList<String> ops) {
v.setVisited(true);
if (print) System.out.println(v);
ops.add(v.toString());
// if(checkStoppingCondition(v, getN())) {
// return;
// }
List<Integer> edgeTarget = matrix.get(v.getID());
for (int i = 0; i < edgeTarget.size(); ++i) {
if (edgeTarget.get(i) == 1) {
GraphNode node = info.get(i + 1);
if (!node.getVisited()) {
return dfs_rec(matrix, info, node, n, print, ops);
}
}
}
return ops;
}
private double getPMulticluster(List<List<Integer>> clusters, int numRestarts) {
if (false) {
Graph g = new EdgeListGraph();
List<Node> latents = new ArrayList<Node>();
for (int i = 0; i < clusters.size(); i++) {
GraphNode latent = new GraphNode("L" + i);
latent.setNodeType(NodeType.LATENT);
latents.add(latent);
g.addNode(latent);
List<Node> cluster = variablesForIndices(clusters.get(i));
for (int j = 0; j < cluster.size(); j++) {
g.addNode(cluster.get(j));
g.addDirectedEdge(latent, cluster.get(j));
}
}
SemPm pm = new SemPm(g);
// pm.fixOneLoadingPerLatent();
SemOptimizerPowell semOptimizer = new SemOptimizerPowell();
semOptimizer.setNumRestarts(numRestarts);
SemEstimator est = new SemEstimator(cov, pm, semOptimizer);
est.setScoreType(SemIm.ScoreType.Fgls);
est.estimate();
return est.getEstimatedSem().getPValue();
} else {
double max = Double.NEGATIVE_INFINITY;
for (int i = 0; i < numRestarts; i++) {
Mimbuild2 mimbuild = new Mimbuild2();
List<List<Node>> _clusters = new ArrayList<List<Node>>();
for (List<Integer> _cluster : clusters) {
_clusters.add(variablesForIndices(_cluster));
}
List<String> names = new ArrayList<String>();
for (int j = 0; j < clusters.size(); j++) {
names.add("L" + j);
}
mimbuild.search(_clusters, names, cov);
double c = mimbuild.getpValue();
if (c > max) max = c;
}
return max;
}
}
private List<GraphNode<T>> getOrphanNodes() {
List<GraphNode<T>> orphanNodes = null;
Set<T> keys = nodes.keySet();
for (T key : keys) {
GraphNode<T> node = nodes.get(key);
if (node.getComingInNodes() == null) {
if (orphanNodes == null) orphanNodes = new ArrayList<GraphNode<T>>();
orphanNodes.add(node);
}
}
return orphanNodes;
}
public void computeDependencies() {
List<GraphNode<T>> orphanNodes = getOrphanNodes();
List<GraphNode<T>> nextNodesToDisplay = new ArrayList<GraphNode<T>>();
if (orphanNodes != null) {
for (GraphNode<T> node : orphanNodes) {
listener.evaluating(node.value);
evaluatedNodes.add(node);
nextNodesToDisplay.addAll(node.getGoingOutNodes());
}
computeDependencies(nextNodesToDisplay);
}
}
/** Dump a set to a string for debug. */
private static String dumpSet(Set<GraphNode> s) {
StringBuffer sb = new StringBuffer();
sb.append("{");
boolean started = false;
for (GraphNode value : s) {
if (started) {
sb.append(", ");
} else {
started = true;
}
sb.append(value.toString());
}
sb.append("}");
return sb.toString();
}
/**
* BFS algorith
*
* @param: print boolean if to print node during traversal
* @return List of nodes in order visited
*/
public ArrayList<String> bfs(boolean print) {
ArrayList<String> ops = new ArrayList<>();
GraphNode v = source;
ArrayList<GraphNode> Q = new ArrayList<>();
Q.add(v);
v.setVisited(true);
while (Q.size() != 0) {
v = Q.remove(0);
if (print) System.out.println(v);
ops.add(v.toString());
// if(checkStoppingCondition(v, getN())) {
// return;
// }
List<Integer> edgeTarget = matrix.get(v.getID());
for (int i = 0; i < edgeTarget.size(); ++i) {
if (edgeTarget.get(i) == 1) {
GraphNode w = info.get(i + 1);
if (!w.getVisited()) {
Q.add(w);
w.setVisited(true);
}
}
}
}
return ops;
}
public void add(T evalFirstValue, T evalAfterValue) {
GraphNode<T> firstNode = null;
GraphNode<T> afterNode = null;
if (nodes.containsKey(evalFirstValue)) {
firstNode = nodes.get(evalFirstValue);
} else {
firstNode = createNode(evalFirstValue);
nodes.put(evalFirstValue, firstNode);
}
if (nodes.containsKey(evalAfterValue)) {
afterNode = nodes.get(evalAfterValue);
} else {
afterNode = createNode(evalAfterValue);
nodes.put(evalAfterValue, afterNode);
}
firstNode.addGoingOutNode(afterNode);
afterNode.addComingInNode(firstNode);
}
/** Visit each predecessor of this node applying the given visitor. Breadth first. */
private <Alpha, Beta> void doVisitPredecessors(
Visitor<Alpha, Beta> visitor, Alpha arg1, Beta arg2, Set<GraphNode> seen) {
if (seen.add(this)) {
Collection<GraphNode> allKill = null;
for (Iterator<GraphNode> i = pred.iterator(); i.hasNext(); ) {
GraphNode pred = i.next();
List<GraphNode> kill = visitor.visit(pred, this, arg1, arg2);
if (kill != null) {
if (allKill == null) allKill = new ArrayList<GraphNode>();
allKill.addAll(kill);
}
}
if (allKill != null) pred.removeAll(allKill);
for (Iterator<GraphNode> i = pred.iterator(); i.hasNext(); ) {
GraphNode pred = i.next();
pred.doVisitPredecessors(visitor, arg1, arg2, seen);
}
}
}
/**
* @param fname String file name to read info from
* @return Map indexed by node id of Node classes
*/
public Map<Integer, GraphNode> getNodeInfo(String fname) {
try {
BufferedReader br = new BufferedReader(new FileReader(fname));
String line;
boolean firstLine = true;
Map<Integer, GraphNode> nodes = new HashMap<>();
while ((line = br.readLine()) != null) {
if (firstLine) {
firstLine = false;
continue;
}
List<String> words = Arrays.asList(line.split("\\s"));
ArrayList<String> realWords = new ArrayList<>();
for (String w : words) {
if (w.equals("")) continue;
else {
realWords.add(w);
}
}
if (realWords.size() != 4) {
continue;
}
GraphNode node =
new GraphNode(
Integer.parseInt(realWords.get(0)),
realWords.get(1),
realWords.get(2),
realWords.get(3));
nodes.put(node.getID(), node);
}
br.close();
return nodes;
} catch (FileNotFoundException e) {
e.printStackTrace();
return null;
} catch (IOException e) {
e.printStackTrace();
return null;
}
}
/**
* Iterative DFS algorithm
*
* @return List of nodes in order visited
*/
public ArrayList<String> dfs_iter(boolean print) {
ArrayList<String> ops = new ArrayList<>();
GraphNode v = source;
List<GraphNode> stack = new ArrayList<>();
stack.add(v);
while (stack.size() != 0) {
v = stack.remove(stack.size() - 1);
if (v.getVisited() == false) {
if (print) System.out.println(v);
ops.add(v.toString());
v.setVisited(true);
List<Integer> edgeTarget = matrix.get(v.getID());
for (int i = 0; i < edgeTarget.size(); ++i) {
if (edgeTarget.get(i) == 1) {
GraphNode w = info.get(i + 1);
stack.add(w);
}
}
}
}
return ops;
}
@Override
GraphNode leadNode(GraphNode unlessSpecified) {
return leader.leadNode();
}
public void resetNodes() {
for (GraphNode node : info.values()) {
node.setVisited(false);
}
}
/**
* Check if we have found our node
*
* @param v Node we are analyzing
* @param n int size of graph
* @return True if v is our searched node
*/
public boolean checkStoppingCondition(GraphNode v, Integer n) {
if (n == 6) {
if (Integer.parseInt(v.getPopulation()) > 500000
&& 150 <= Float.parseFloat(v.getElevation())
&& Float.parseFloat(v.getElevation()) <= 200) {
return true;
}
} else if (n == 100) {
if (v.getCity().equals("SouthAva")
&& Integer.parseInt(v.getPopulation()) == 2042542
&& Float.parseFloat(v.getElevation()) <= 1074.0) {
return true;
}
} else if (n == 1000) {
if (v.getCity().equals("NewMarlene")
&& Integer.parseInt(v.getPopulation()) == 47182047
&& Float.parseFloat(v.getElevation()) >= 8.0) {
return true;
}
} else if (n == 10000) {
if (v.getCity().equals("Careyland")
&& Integer.parseInt(v.getPopulation()) <= 5086547
&& Float.parseFloat(v.getElevation()) >= 1645.0) {
return true;
}
}
return false;
}
private GraphNode<T> createNode(T value) {
GraphNode<T> node = new GraphNode<T>();
node.value = value;
return node;
}