Merge pull request #1443 from cmu-phil/final_7_1_3_merge

Final merge for 7.1.3

docs/manual/index.html

@@ -7392,7 +7392,7 @@ <h3 class="parameter_description" id="ebicGamma">ebicGamma</h3>
                 class="parameter_description_list">
             <li>Short Description: <span
                     id="percentResampleSize_short_desc">The percentage of resample size
-        (min = 0.1)</span></li>
+        (min = 10%)</span></li>
             <li>Long Description: <span
                     id="percentResampleSize_long_desc"> This parameter specifies the
         percentage of records in the bootstrap (as a percentage of the total
@@ -7401,9 +7401,9 @@ <h3 class="parameter_description" id="ebicGamma">ebicGamma</h3>
                     id="percentResampleSize_default_value">90</span></li>
             <li>Lower
                 Bound: <span
-                        id="percentResampleSize_lower_bound">-2147483648</span></li>
+                        id="percentResampleSize_lower_bound">10</span></li>
             <li>Upper Bound: <span
-                    id="percentResampleSize_upper_bound">2147483647</span></li>
+                    id="percentResampleSize_upper_bound">100</span></li>
             <li>Value
                 Type: <span id="percentResampleSize_value_type">Integer</span></li>
         </ul>

tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphFileMenu.java

@@ -45,6 +45,7 @@ public GraphFileMenu(GraphEditable editable, JComponent comp, boolean saveOnly)
             load.add(new LoadGraph(editable, "XML..."));
             load.add(new LoadGraphTxt(editable, "Text..."));
             load.add(new LoadGraphJson(editable, "Json..."));
+            load.add(new LoadGraphPcalg(editable, "PCALG..."));
         }
 
         JMenu save = new JMenu("Save...");
@@ -55,6 +56,7 @@ public GraphFileMenu(GraphEditable editable, JComponent comp, boolean saveOnly)
         save.add(new SaveGraph(editable, "Json...", SaveGraph.Type.json));
         save.add(new SaveGraph(editable, "R...", SaveGraph.Type.r));
         save.add(new SaveGraph(editable, "Dot...", SaveGraph.Type.dot));
+        save.add(new SaveGraph(editable, "PCALG...", SaveGraph.Type.pcalg));
 
         addSeparator();
         add(new SaveComponentImage(comp, "Save Graph Image..."));

tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphPcalg.java

@@ -0,0 +1,87 @@
+///////////////////////////////////////////////////////////////////////////////
+// For information as to what this class does, see the Javadoc, below.       //
+// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
+// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard        //
+// Scheines, Joseph Ramsey, and Clark Glymour.                               //
+//                                                                           //
+// This program is free software; you can redistribute it and/or modify      //
+// it under the terms of the GNU General Public License as published by      //
+// the Free Software Foundation; either version 2 of the License, or         //
+// (at your option) any later version.                                       //
+//                                                                           //
+// This program is distributed in the hope that it will be useful,           //
+// but WITHOUT ANY WARRANTY; without even the implied warranty of            //
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             //
+// GNU General Public License for more details.                              //
+//                                                                           //
+// You should have received a copy of the GNU General Public License         //
+// along with this program; if not, write to the Free Software               //
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA //
+///////////////////////////////////////////////////////////////////////////////
+
+package edu.cmu.tetradapp.editor;
+
+import edu.cmu.tetrad.graph.Graph;
+import edu.cmu.tetrad.graph.GraphUtils;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.util.prefs.Preferences;
+
+/**
+ * @author Joseph Ramsey [email protected]
+ */
+class LoadGraphPcalg extends AbstractAction {
+
+    /**
+     * The component whose image is to be saved.
+     */
+    private final GraphEditable graphEditable;
+
+    public LoadGraphPcalg(GraphEditable graphEditable, String title) {
+        super(title);
+
+        if (graphEditable == null) {
+            throw new NullPointerException("Component must not be null.");
+        }
+
+        this.graphEditable = graphEditable;
+    }
+
+    /**
+     * Performs the action of loading a session from a file.
+     */
+    public void actionPerformed(ActionEvent e) {
+        JFileChooser chooser = LoadGraphPcalg.getJFileChooser();
+        chooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
+        chooser.showOpenDialog((Component) this.graphEditable);
+
+        File file = chooser.getSelectedFile();
+
+        if (file == null) {
+            System.out.println("File was null.");
+            return;
+        }
+
+        Preferences.userRoot().put("fileSaveLocation", file.getParent());
+
+        Graph graph = GraphUtils.loadGraphPcalg(file);
+        GraphUtils.circleLayout(graph, 200, 200, 150);
+        this.graphEditable.setGraph(graph);
+    }
+
+    private static JFileChooser getJFileChooser() {
+        JFileChooser chooser = new JFileChooser();
+        String sessionSaveLocation =
+                Preferences.userRoot().get("fileSaveLocation", "");
+        chooser.setCurrentDirectory(new File(sessionSaveLocation));
+        chooser.resetChoosableFileFilters();
+        chooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
+        return chooser;
+    }
+}
+
+
+

tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/SaveGraph.java

@@ -57,7 +57,7 @@ public class SaveGraph extends AbstractAction {
      */
     private final Type type;
 
-    public enum Type {text, xml, json, r, dot}
+    public enum Type {text, xml, json, r, dot, pcalg}
 
     public SaveGraph(GraphEditable graphEditable, String title, Type type) {
         super(title);
@@ -130,6 +130,23 @@ public void actionPerformed(ActionEvent e) {
             try {
                 String text = GraphUtils.graphToDot(graph);
 
+                PrintWriter out = new PrintWriter(file);
+                out.println(text);
+                Preferences.userRoot().put("fileSaveLocation", file.getParent());
+                out.close();
+            } catch (FileNotFoundException e1) {
+                e1.printStackTrace();
+                throw new RuntimeException("Not a directed graph.", e1);
+            } catch (IllegalArgumentException e1) {
+
+                // Probably not a directed graph.
+                JOptionPane.showMessageDialog(getGraphEditable().getWorkbench(), e1.getMessage());
+            }
+        }else if (this.type == Type.pcalg) {
+            File file = EditorUtils.getSaveFile("graph", "pcalg.csv", parent, false, this.title);
+            try {
+                String text = GraphUtils.graphToPcalg(graph);
+
                 PrintWriter out = new PrintWriter(file);
                 out.println(text);
                 Preferences.userRoot().put("fileSaveLocation", file.getParent());

tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/TabularComparisonEditor.java

@@ -93,7 +93,7 @@ private Box getTableDisplay() {
 
     private TextTable getTextTable(DataSet dataSet, NumberFormat nf) {
         TextTable table = new TextTable(dataSet.getNumRows() + 2, dataSet.getNumColumns() + 1);
-        table.setTabDelimited(true);
+        table.setDelimiter(TextTable.Delimiter.TAB);
         table.setToken(0, 0, "Run");
 
         for (int j = 0; j < dataSet.getNumColumns(); j++) {

tetrad-gui/src/main/java/edu/cmu/tetradapp/util/ParameterComponents.java

@@ -129,6 +129,35 @@ public static IntTextField getIntTextField(String parameter, Parameters paramete
         return field;
     }
 
+    public static LongTextField getLongTextField(String parameter, Parameters parameters,
+                                               long defaultValue, double lowerBound, double upperBound) {
+        LongTextField field = new LongTextField(parameters.getLong(parameter, defaultValue), 10);
+
+        field.setFilter((value, oldValue) -> {
+            if (value == field.getValue()) {
+                return oldValue;
+            }
+
+            if (value < lowerBound) {
+                return oldValue;
+            }
+
+            if (value > upperBound) {
+                return oldValue;
+            }
+
+            try {
+                parameters.set(parameter, value);
+            } catch (Exception e) {
+                // Ignore.
+            }
+
+            return value;
+        });
+
+        return field;
+    }
+
     public static Box getBooleanSelectionBox(String parameter, Parameters parameters, boolean defaultValue) {
         Box selectionBox = Box.createHorizontalBox();
 
@@ -203,6 +232,10 @@ private static Box createParameterComponent(String parameter, Parameters paramet
             int lowerBoundInt = paramDesc.getLowerBoundInt();
             int upperBoundInt = paramDesc.getUpperBoundInt();
             component = ParameterComponents.getIntTextField(parameter, parameters, (Integer) defaultValue, lowerBoundInt, upperBoundInt);
+        } else if (defaultValue instanceof Long) {
+            int lowerBoundInt = paramDesc.getLowerBoundInt();
+            int upperBoundInt = paramDesc.getUpperBoundInt();
+            component = ParameterComponents.getLongTextField(parameter, parameters, (Long) defaultValue, lowerBoundInt, upperBoundInt);
         } else if (defaultValue instanceof Boolean) {
             component = ParameterComponents.getBooleanSelectionBox(parameter, parameters, (Boolean) defaultValue);
         } else if (defaultValue instanceof String) {

tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/AbstractWorkbench.java

@@ -1792,6 +1792,10 @@ private void edgeClicked(Object source, MouseEvent e) {
                 graphEdge.setSelected(true);
             }
         }
+
+        if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+            GraphUtils.addPagColoring(new EdgeListGraph(graph));
+        }
     }
 
     private void nodeClicked(Object source, MouseEvent e) {
@@ -1814,6 +1818,10 @@ private void nodeClicked(Object source, MouseEvent e) {
             selectConnectingEdges();
             fireNodeSelection();
         }
+
+        if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+            GraphUtils.addPagColoring(new EdgeListGraph(graph));
+        }
     }
 
     private void reorientEdge(Object source, MouseEvent e) {
@@ -1828,7 +1836,7 @@ private void reorientEdge(Object source, MouseEvent e) {
         if (e.isShiftDown()) {
             if (AbstractWorkbench.distance(point, pointA) < endpointRadius) {
                 toggleEndpoint(graphEdge, 1);
-                firePropertyChange("modelChanged", null, null);
+                fireModelChanged();
             } else if (AbstractWorkbench.distance(point, pointB) < endpointRadius) {
                 toggleEndpoint(graphEdge, 2);
                 firePropertyChange("modelChanged", null, null);
@@ -1842,6 +1850,14 @@ private void reorientEdge(Object source, MouseEvent e) {
                 firePropertyChange("modelChanged", null, null);
             }
         }
+
+        if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+            GraphUtils.addPagColoring(new EdgeListGraph(graph));
+        }
+    }
+
+    private void fireModelChanged() {
+        firePropertyChange("modelChanged", null, null);
     }
 
     private void handleMousePressed(MouseEvent e) {
@@ -1894,6 +1910,10 @@ private void handleMousePressed(MouseEvent e) {
 
                 break;
         }
+
+        if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+            GraphUtils.addPagColoring(new EdgeListGraph(graph));
+        }
     }
 
     private void launchPopup(MouseEvent e) {
@@ -1935,6 +1955,10 @@ private void handleMouseReleased(MouseEvent e) {
                 finishEdge();
                 break;
         }
+
+        if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+            GraphUtils.addPagColoring(new EdgeListGraph(graph));
+        }
     }
 
     private void handleMouseDragged(MouseEvent e) {
@@ -1960,6 +1984,10 @@ private void handleMouseDragged(MouseEvent e) {
                 dragNewEdge(source, newPoint);
                 break;
         }
+
+        if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+            GraphUtils.addPagColoring(new EdgeListGraph(graph));
+        }
     }
 
     private void handleMouseEntered(MouseEvent e) {
@@ -2245,17 +2273,28 @@ private void directEdge(IDisplayEdge graphEdge, int endpoint) {
 
         try {
             boolean added = getGraph().addEdge(newEdge);
+
             if (!added) {
                 getGraph().addEdge(edge);
                 JOptionPane.showMessageDialog(JOptionUtils.centeringComp(),
                         "Reorienting that edge would violate graph constraints.");
             }
+
+            if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+                GraphUtils.addPagColoring(new EdgeListGraph(graph));
+            }
         } catch (IllegalArgumentException e) {
             getGraph().addEdge(edge);
+
+            if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+                GraphUtils.addPagColoring(new EdgeListGraph(graph));
+            }
+
             JOptionPane.showMessageDialog(JOptionUtils.centeringComp(),
                     "Reorienting that edge would violate graph constraints.");
         }
 
+        revalidate();
         repaint();
     }
 
@@ -2299,13 +2338,23 @@ private void toggleEndpoint(IDisplayEdge graphEdge, int endpointNumber) {
             boolean added = getGraph().addEdge(newEdge);
             if (!added) {
                 getGraph().addEdge(edge);
+
+                if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+                    GraphUtils.addPagColoring(new EdgeListGraph(graph));
+                }
+
                 return;
             }
         } catch (IllegalArgumentException e) {
             getGraph().addEdge(edge);
             return;
         }
 
+        if (graph.getGraphType() == EdgeListGraph.GraphType.PAG) {
+            GraphUtils.addPagColoring(new EdgeListGraph(graph));
+        }
+
+        revalidate();
         repaint();
     }
 

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/Comparison.java

@@ -65,7 +65,7 @@
  */
 public class Comparison {
 
-    private boolean parallelized = true;
+    private boolean parallelized = false;
 
     public void setParallelized(boolean parallelized) {
         this.parallelized = parallelized;
@@ -1467,7 +1467,7 @@ private void printStats(double[][][] statTables, Statistics statistics, Mode mod
                     + (isShowUtilities() ? 1 : 0);
 
             TextTable table = new TextTable(rows, cols);
-            table.setTabDelimited(isTabDelimitedTables());
+            table.setDelimiter(isTabDelimitedTables() ? TextTable.Delimiter.TAB : TextTable.Delimiter.JUSTIFIED);
 
             int initialColumn = 0;
 

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/TimeoutComparison.java

@@ -1370,7 +1370,7 @@ private void printStats(double[][][] statTables, Statistics statistics, Mode mod
                     + (isShowUtilities() ? 1 : 0);
 
             TextTable table = new TextTable(rows, cols);
-            table.setTabDelimited(isTabDelimitedTables());
+            table.setDelimiter(isTabDelimitedTables() ? TextTable.Delimiter.TAB : TextTable.Delimiter.JUSTIFIED);
 
             int initialColumn = 0;
 

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/CciScore.java

@@ -16,14 +16,14 @@
 import java.util.ArrayList;
 import java.util.List;
 
-/**
- * Wrapper for CCI Score.
- *
- * @author jdramsey
- */
-@edu.cmu.tetrad.annotation.Score(name = "CCI-Score (Conditional Correlation Independence Score)", command = "cci-score", dataType = DataType.Continuous)
-@General
-@Experimental
+///**
+// * Wrapper for CCI Score.
+// *
+// * @author jdramsey
+// */
+//@edu.cmu.tetrad.annotation.Score(name = "CCI-Score (Conditional Correlation Independence Score)", command = "cci-score", dataType = DataType.Continuous)
+//@General
+//@Experimental
 public class CciScore implements ScoreWrapper {
 
     static final long serialVersionUID = 23L;