From 96aae74146bed192cedd41deffb4772af0960233 Mon Sep 17 00:00:00 2001
From: Joseph Ramsey <jdramsey@andrew.cmu.edu>
Date: Fri, 17 Jun 2016 17:10:27 -0400
Subject: [PATCH] Fixed knowledge for FGS.

---
 causal-cmd/causal-cmd.iml                               | 1 -
 tetrad-lib/src/main/java/edu/cmu/tetrad/search/Fgs.java | 7 +++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/causal-cmd/causal-cmd.iml b/causal-cmd/causal-cmd.iml
index 810a18e556..9361361897 100644
--- a/causal-cmd/causal-cmd.iml
+++ b/causal-cmd/causal-cmd.iml
@@ -16,7 +16,6 @@
       <excludeFolder url="file://$MODULE_DIR$/target/maven-archiver" />
       <excludeFolder url="file://$MODULE_DIR$/target/maven-status" />
       <excludeFolder url="file://$MODULE_DIR$/target/site" />
-      <excludeFolder url="file://$MODULE_DIR$/target/surefire" />
       <excludeFolder url="file://$MODULE_DIR$/target/surefire-reports" />
     </content>
     <orderEntry type="inheritedJdk" />
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Fgs.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Fgs.java
index 3793a6f588..d9e86af705 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Fgs.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Fgs.java
@@ -1315,6 +1315,7 @@ private boolean insert(Node x, Node y, Set<Node> T, double bump) {
         }
 
         if (boundGraph != null && !boundGraph.isAdjacentTo(x, y)) return false;
+        if (knowledge != null && knowledge.isForbidden(x.getName(), y.getName())) return false;
 
         graph.addDirectedEdge(x, y);
 
@@ -1339,6 +1340,7 @@ private boolean insert(Node x, Node y, Set<Node> T, double bump) {
         for (Node _t : T) {
             graph.removeEdge(_t, y);
             if (boundGraph != null && !boundGraph.isAdjacentTo(_t, y)) continue;
+            if (knowledge != null && knowledge.isForbidden(y.getName(), _t.getName())) continue;
 
             graph.addDirectedEdge(_t, y);
 
@@ -1468,6 +1470,7 @@ private void addRequiredEdges(Graph graph) {
             Node nodeB = graph.getNode(next.getTo());
 
             if (!graph.isAncestorOf(nodeB, nodeA)) {
+                if (knowledge != null && knowledge.isForbidden(nodeA.getName(), nodeB.getName()));
                 graph.removeEdges(nodeA, nodeB);
                 graph.addDirectedEdge(nodeA, nodeB);
                 TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeA, nodeB));
@@ -1484,6 +1487,7 @@ private void addRequiredEdges(Graph graph) {
 
                 if (graph.isAdjacentTo(nodeA, nodeB) && !graph.isChildOf(nodeA, nodeB)) {
                     if (!graph.isAncestorOf(nodeA, nodeB)) {
+                        if (knowledge != null && knowledge.isForbidden(nodeB.getName(), nodeA.getName()));
                         graph.removeEdges(nodeA, nodeB);
                         graph.addDirectedEdge(nodeB, nodeA);
                         TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
@@ -1492,6 +1496,7 @@ private void addRequiredEdges(Graph graph) {
 
                 if (!graph.isChildOf(nodeA, nodeB) && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
                     if (!graph.isAncestorOf(nodeA, nodeB)) {
+                        if (knowledge != null && knowledge.isForbidden(nodeB.getName(), nodeA.getName()));
                         graph.removeEdges(nodeA, nodeB);
                         graph.addDirectedEdge(nodeB, nodeA);
                         TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
@@ -1504,6 +1509,7 @@ private void addRequiredEdges(Graph graph) {
 
                 if (graph.isAdjacentTo(nodeA, nodeB) && !graph.isChildOf(nodeA, nodeB)) {
                     if (!graph.isAncestorOf(nodeA, nodeB)) {
+                        if (knowledge != null && knowledge.isForbidden(nodeB.getName(), nodeA.getName()));
                         graph.removeEdges(nodeA, nodeB);
                         graph.addDirectedEdge(nodeB, nodeA);
                         TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
@@ -1511,6 +1517,7 @@ private void addRequiredEdges(Graph graph) {
                 }
                 if (!graph.isChildOf(nodeA, nodeB) && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
                     if (!graph.isAncestorOf(nodeA, nodeB)) {
+                        if (knowledge != null && knowledge.isForbidden(nodeA.getName(), nodeB.getName()));
                         graph.removeEdges(nodeA, nodeB);
                         graph.addDirectedEdge(nodeB, nodeA);
                         TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));