Merge pull request #453 from cmu-phil/fang

fang
cmu-phil · Jun 13, 2017 · c10a64d · c10a64d
2 parents 68660d8 + f6be1be
commit c10a64d
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Showing 7 changed files with 41 additions and 21 deletions.
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/StandardizedSemImEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/StandardizedSemImEditor.java
@@ -107,14 +107,14 @@ public StandardizedSemImEditor(final StandardizedSemImWrapper wrapper) {
         boolean shown = wrapper.isShowErrors();
         graph.setShowErrorTerms(shown);
 
-        errorTerms = new JMenuItem();
-
-        if (shown) {
-            errorTerms.setText("Hide Error Terms");
-        }
-        else {
-            errorTerms.setText("Show Error Terms");
-        }
+//        errorTerms = new JMenuItem();
+//
+//        if (shown) {
+//            errorTerms.setText("Hide Error Terms");
+//        }
+//        else {
+//            errorTerms.setText("Show Error Terms");
+//        }
 
         errorTerms.addActionListener(new ActionListener() {
             public void actionPerformed(ActionEvent e) {
@@ -142,7 +142,7 @@ else if ("Show Error Terms".equals(menuItem.getText())) {
 //        } else {
 //            errorTerms.setText("Show Error Terms");
 //        }
-//
+
 //        errorTerms.addActionListener(new ActionListener() {
 //            public void actionPerformed(ActionEvent e) {
 //                JMenuItem menuItem = (JMenuItem) e.getSource();
@@ -159,12 +159,12 @@ else if ("Show Error Terms".equals(menuItem.getText())) {
 //            }
 //        });
 
-        JMenu params = new JMenu("Parameters");
-        params.add(errorTerms);
+//        JMenu params = new JMenu("Parameters");
+//        params.add(errorTerms);
 //        params.addSeparator();
 //        params.addSeparator();
 
-        menuBar.add(params);
+//        menuBar.add(params);
         menuBar.add(new LayoutMenu(this));
 
         add(menuBar, BorderLayout.NORTH);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/StandardizedSemImGraphicalEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/StandardizedSemImGraphicalEditor.java
@@ -293,6 +293,10 @@ private void beginEdgeEdit(final Edge edge) {
     }
 
     private void setEditorToEdge(Edge edge) {
+        if (edge.getNode1().getNodeType() == NodeType.ERROR || edge.getNode2().getNodeType() == NodeType.ERROR) {
+            return;
+        }
+
         if (editingEdge != null) {
             try {
                 double value = Double.parseDouble(valueField.getText());

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/knowledge_editor/KnowledgeBoxEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/knowledge_editor/KnowledgeBoxEditor.java
@@ -65,6 +65,8 @@ public class KnowledgeBoxEditor extends JPanel {
     private boolean showRequiredByGroups = true;
     private boolean showForbiddenByGroups = true;
     private JTextArea textArea;
+
+    // Unused, moved to KnowledgeBoxModel. Keeping for serialization. Can delete after a while. 2017.06.17
     private int numTiers = 2;
     private final KnowledgeBoxModel knowledgeBoxModel;
     private JTabbedPane tabbedPane = null;
@@ -229,11 +231,11 @@ public void stateChanged(ChangeEvent e) {
     // }
 
     private Box tierDisplay() {
-        if (numTiers < 0) {
+        if (getNumTiers() < 0) {
             int numTiers = getKnowledge().getNumTiers();
             int _default = (int) (Math.pow(varNames.size(), 0.5) + 1);
             numTiers = numTiers < _default ? _default : numTiers;
-            this.numTiers = numTiers;
+            setNumDisplayTiers(numTiers);
         }
 
         Box b = Box.createVerticalBox();
@@ -800,11 +802,11 @@ private JTextArea getTextArea() {
     }
 
     private int getNumTiers() {
-        return numTiers;
+        return knowledgeBoxModel.getNumTiers();
     }
 
     private void setNumTiers(int numTiers) {
-        this.numTiers = numTiers;
+        knowledgeBoxModel.setNumTiers(numTiers);
     }
 
     private Graph getSourceGraph() {

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/KnowledgeBoxModel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/KnowledgeBoxModel.java
@@ -53,6 +53,8 @@ public class KnowledgeBoxModel implements SessionModel, ParamsResettable, Knowle
     private List<String> variableNames = new ArrayList<>();
     private final Graph sourceGraph = new EdgeListGraph();
     private IKnowledge knowledge = new Knowledge2();
+    private int numTiers = 3;
+
 
     public KnowledgeBoxModel(GeneralAlgorithmRunner runner) {
         this.knowledge = runner.getKnowledge();
@@ -186,6 +188,14 @@ KnowledgeBoxInput getKnowledgeBoxInput() {
     void setKnowledgeBoxInput(KnowledgeBoxInput knowledgeBoxInput) {
         this.knowledgeBoxInput = knowledgeBoxInput;
     }
+
+    public int getNumTiers() {
+        return numTiers;
+    }
+
+    public void setNumTiers(int numTiers) {
+        this.numTiers = numTiers;
+    }
 }
 
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/AbstractWorkbench.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/AbstractWorkbench.java
@@ -1246,12 +1246,14 @@ private void adjustForNewModelNodes() {
             return;
         }
 
-        if (graph.isHighlighted(modelEdge)) displayEdge.setHighlighted(true);
+        if (graph.isHighlighted(modelEdge)) {
+            displayEdge.setHighlighted(true);
+        }
 
         boolean dashed = modelEdge.getProperties().contains(Edge.Property.nl) || modelEdge.isDashed();
 
         Color lineColor = modelEdge.getProperties().contains(Edge.Property.dd) ?
-                Color.green : modelEdge.getLineColor();
+                Color.green : graph.isHighlighted(modelEdge) ? displayEdge.getHighlightedColor() : modelEdge.getLineColor();
 
         displayEdge.setLineColor(lineColor);
         displayEdge.setDashed(dashed);

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/DagInPatternIterator.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/DagInPatternIterator.java
@@ -241,6 +241,7 @@ public DecoratedGraph orient() {
                 graph.removeEdges(edge.getNode1(), edge.getNode2());
 
                 graph.addDirectedEdge(edge.getNode2(), edge.getNode1());
+                graph.setHighlighted(graph.getEdge(edge.getNode2(), edge.getNode1()), true);
 
                 edges.add(graph.getEdge(edge.getNode2(), edge.getNode1()));
                 edges.addAll(new HashSet<>(getChangedEdges().get(this.graph)));
@@ -272,6 +273,7 @@ public DecoratedGraph orient() {
                 Graph graph = new EdgeListGraphSingleConnections(this.graph);
                 graph.removeEdges(edge.getNode1(), edge.getNode2());
                 graph.addDirectedEdge(edge.getNode1(), edge.getNode2());
+                graph.setHighlighted(graph.getEdge(edge.getNode1(), edge.getNode2()), true);
 
                 edges.add(graph.getEdge(edge.getNode1(), edge.getNode2()));
                 edges.addAll(new HashSet<>(getChangedEdges().get(this.graph)));

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/SearchGraphUtils.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/SearchGraphUtils.java
@@ -2237,9 +2237,9 @@ public static Graph chooseDagInPattern(Graph graph) {
 //            }
 //        }
 //
-//        PatternToDag search = new PatternToDag(new Pattern(newGraph));
-//        Graph dag = search.patternToDagMeekRules();
-//        DataGraphUtils.arrangeBySourceGraph(dag, graph);
+//        PatternToDag search = new PatternToDag(new EdgeListGraph(newGraph));
+//        Graph dag = search.patternToDagMeek();
+//        GraphUtils.arrangeBySourceGraph(dag, graph);
 //        return dag;
     }