cmu-phil · jdramsey · May 6, 2024 · Apr 13, 2024 · Apr 13, 2024 · Apr 14, 2024
diff --git a/docs/manual/flowchart.html b/docs/manual/flowchart.html
@@ -0,0 +1,13 @@
+<!DOCTYPE html>
+<html>
+<head>
+    <title>Redirecting...</title>
+    <meta content="0;url=https://htmlpreview.github.io/?https:///github.com/cmu-phil/tetrad/blob/development/tetrad-lib/src/main/resources/docs/manual/flowchart.html"
+          http-equiv="refresh">
+</head>
+<body>
+<p>If you are not redirected automatically, follow this <a
+        href="https://htmlpreview.github.io/?https:///github.com/cmu-phil/tetrad/blob/development/tetrad-lib/src/main/resources/docs/manual/flowchart.html">link
+    to the new page</a>.</p>
+</body>
+</html>
diff --git a/tetrad-gui/dependency-reduced-pom.xml b/tetrad-gui/dependency-reduced-pom.xml
@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <parent>
+    <artifactId>tetrad</artifactId>
+    <groupId>io.github.cmu-phil</groupId>
+    <version>7.6.4-SNAPSHOT</version>
+  </parent>
+  <modelVersion>4.0.0</modelVersion>
+  <artifactId>tetrad-gui</artifactId>
+  <build>
+    <extensions>
+      <extension>
+        <groupId>org.apache.maven.wagon</groupId>
+        <artifactId>wagon-ssh</artifactId>
+        <version>2.10</version>
+      </extension>
+    </extensions>
+    <resources>
+      <resource>
+        <filtering>true</filtering>
+        <directory>src/main/resources</directory>
+        <includes>
+          <include>resources/version</include>
+        </includes>
+      </resource>
+      <resource>
+        <directory>src/main/resources</directory>
+        <excludes>
+          <exclude>resources/version</exclude>
+        </excludes>
+      </resource>
+    </resources>
+    <plugins>
+      <plugin>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.11.0</version>
+        <configuration>
+          <source>17</source>
+          <target>17</target>
+        </configuration>
+      </plugin>
+      <plugin>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.5.1</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+            <configuration>
+              <transformers>
+                <transformer>
+                  <manifestEntries>
+                    <Main-Class>edu.cmu.tetradapp.Tetrad</Main-Class>
+                    <Permissions>all-permissions</Permissions>
+                    <Implementation-Title>${project.name}</Implementation-Title>
+                    <Implementation-Version>${project.version}</Implementation-Version>
+                  </manifestEntries>
+                </transformer>
+              </transformers>
+              <shadedArtifactAttached>true</shadedArtifactAttached>
+              <shadedClassifierName>launch</shadedClassifierName>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <properties>
+    <java.version>1.8</java.version>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+</project>
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LaunchFlowchartAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LaunchFlowchartAction.java
@@ -50,8 +50,8 @@ public LaunchFlowchartAction() {
     public void actionPerformed(ActionEvent e) {
         Desktop d = Desktop.getDesktop();
         try {
-            d.browse(new URI("https://htmlpreview.github.io/?https://raw.githubusercontent.com/cmu-phil/tetrad/" +
-                             "development/docs/manual/flowchart.html"));
+            d.browse(new URI("https://htmlpreview.github.io/?https:///github.com/cmu-phil/" +
+                    "tetrad/blob/development/tetrad-lib/src/main/resources/docs/manual/flowchart.html"));
         } catch (IOException | URISyntaxException e2) {
             e2.printStackTrace();
         }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/TetradMenuBar.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/TetradMenuBar.java
@@ -186,7 +186,6 @@ private void buildEditMenu(JMenu editMenu) {
         editMenu.add(cut);
         editMenu.add(copy);
         editMenu.add(paste);
-        editMenu.addSeparator();
     }
 
     /**
@@ -241,13 +240,13 @@ public SuggestionDialog(JComponent parent, String url) {
 
             // Create a clickable link
             JLabel label = new JLabel("<html>" +
-                                      "<p>Please submit any issues you may have,</p>" +
-                                      "<p>whether bug reports, general encouragement,</p>" +
-                                      "<p>or feature requests, to our issues list. We'd</p>" +
-                                      "<p>love to hear from you as we continue to</p>" +
-                                      "<p>improve the Tetrad tools!</p>" +
-                                      "<p><center><a href=\"" + url + "\">" + url + "</a></center>" +
-                                      "</html>");
+                    "<p>Please submit any issues you may have,</p>" +
+                    "<p>whether bug reports, general encouragement,</p>" +
+                    "<p>or feature requests, to our issues list. We'd</p>" +
+                    "<p>love to hear from you as we continue to</p>" +
+                    "<p>improve the Tetrad tools!</p>" +
+                    "<p><center><a href=\"" + url + "\">" + url + "</a></center>" +
+                    "</html>");
             label.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
             label.setFont(label.getFont().deriveFont(Font.PLAIN, 14));
             label.addMouseListener(new MouseAdapter() {

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AlgcomparisonEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AlgcomparisonEditor.java
@@ -757,8 +757,19 @@ public static StringTextField getStringField(String parameter, Parameters parame
      * @throws IllegalAccessException    If the graph or simulation constructor or class is inaccessible.
      */
     @NotNull
-    private static edu.cmu.tetrad.algcomparison.simulation.Simulation getSimulation(Class<? extends edu.cmu.tetrad.algcomparison.graph.RandomGraph> graphClazz, Class<? extends edu.cmu.tetrad.algcomparison.simulation.Simulation> simulationClazz) throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
-        RandomGraph randomGraph = graphClazz.getConstructor().newInstance();
+    private edu.cmu.tetrad.algcomparison.simulation.Simulation getSimulation(Class<? extends edu.cmu.tetrad.algcomparison.graph.RandomGraph> graphClazz, Class<? extends edu.cmu.tetrad.algcomparison.simulation.Simulation> simulationClazz) throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
+        RandomGraph randomGraph;
+
+        if (graphClazz == SingleGraph.class) {
+            if (model.getSuppliedGraph() == null) {
+                throw new IllegalArgumentException("No graph supplied.");
+            }
+
+            randomGraph = new SingleGraph(model.getSuppliedGraph());
+        } else {
+            randomGraph = graphClazz.getConstructor().newInstance();
+        }
+
         return simulationClazz.getConstructor(RandomGraph.class).newInstance(randomGraph);
     }
 
@@ -821,8 +832,12 @@ public static void scrollToWord(JTextArea textArea, JScrollPane scrollPane, Stri
     }
 
     @NotNull
-    private static Class<? extends RandomGraph> getGraphClazz(String graphString) {
-        List<String> graphTypeStrings = Arrays.asList(ParameterTab.GRAPH_TYPE_ITEMS);
+    private Class<? extends RandomGraph> getGraphClazz(String graphString) {
+        List<String> graphTypeStrings = new ArrayList<>(Arrays.asList(ParameterTab.GRAPH_TYPE_ITEMS));
+
+        if (model.getSuppliedGraph() != null) {
+            graphTypeStrings.add("User Supplied Graph");
+        }
 
         return switch (graphTypeStrings.indexOf(graphString)) {
             case 0:
@@ -831,12 +846,14 @@ private static Class<? extends RandomGraph> getGraphClazz(String graphString) {
                 yield ErdosRenyi.class;
             case 2:
                 yield ScaleFree.class;
-            case 4:
+            case 3:
                 yield Cyclic.class;
-            case 5:
+            case 4:
                 yield RandomSingleFactorMim.class;
-            case 6:
+            case 5:
                 yield RandomTwoFactorMim.class;
+            case 6:
+                yield SingleGraph.class;
             default:
                 throw new IllegalArgumentException("Unexpected value: " + graphString);
         };
@@ -1441,6 +1458,11 @@ private void addAddSimulationListener() {
             JComboBox<String> graphsDropdown = getGraphsDropdown();
 
             Arrays.stream(ParameterTab.GRAPH_TYPE_ITEMS).forEach(graphsDropdown::addItem);
+
+            if (model.getSuppliedGraph() != null) {
+                graphsDropdown.addItem("User Supplied Graph");
+            }
+
             graphsDropdown.setMaximumSize(graphsDropdown.getPreferredSize());
             graphsDropdown.setSelectedItem(model.getLastGraphChoice());
 
@@ -1507,6 +1529,7 @@ private JComboBox<String> getGraphsDropdown() {
                 model.setLastGraphChoice(selectedItem);
             }
         });
+
         return graphsDropdown;
     }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AllPathsAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AllPathsAction.java
@@ -102,7 +102,7 @@ public void watch() {
     }
 
     private void addTreks(Node node1, Node node2, Graph graph, JTextArea textArea) {
-        List<List<Node>> treks = graph.paths().allPathsFromTo(node1, node2, 8);
+        List<List<Node>> treks = graph.paths().allPaths(node1, node2, 8);
 
         if (treks.isEmpty()) {
             return;

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/ApplyFinalFciRules.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/ApplyFinalFciRules.java
@@ -0,0 +1,95 @@
+///////////////////////////////////////////////////////////////////////////////
+// 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.EdgeListGraph;
+import edu.cmu.tetrad.graph.Graph;
+import edu.cmu.tetrad.search.utils.DagSepsets;
+import edu.cmu.tetrad.search.utils.FciOrient;
+import edu.cmu.tetradapp.workbench.GraphWorkbench;
+
+import javax.swing.*;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.ActionEvent;
+
+/**
+ * This class represents an action to run the final FCI (Fast Causal Inference) rules on a graph in a GraphWorkbench.
+ * It extends the AbstractAction class and implements the ClipboardOwner interface.
+ */
+public class ApplyFinalFciRules extends AbstractAction implements ClipboardOwner {
+
+    /**
+     * The desktop containing the target session editor.
+     */
+    private final GraphWorkbench workbench;
+
+    /**
+     * Runs the final FCI (Fast Causal Inference) rules on a graph in a GraphWorkbench.
+     * This action is triggered by clicking a button or selecting a menu option.
+     *
+     * @param workbench the GraphWorkbench instance containing the graph to run final FCI rules on.
+     * @throws NullPointerException if workbench is null.
+     */
+    public ApplyFinalFciRules(GraphWorkbench workbench) {
+        super("Apply Final FCI Rules");
+
+        if (workbench == null) {
+            throw new NullPointerException("Desktop must not be null.");
+        }
+
+        this.workbench = workbench;
+    }
+
+    /**
+     * Performs an action when an event occurs.
+     *
+     * @param e the event that triggered the action.
+     */
+    public void actionPerformed(ActionEvent e) {
+        this.workbench.deselectAll();
+        Graph graph = this.workbench.getGraph();
+
+        if (graph == null) {
+            JOptionPane.showMessageDialog(this.workbench, "No graph to apply final FCI rules to.");
+            return;
+        }
+
+        Graph __g = new EdgeListGraph(graph);
+        FciOrient finalFciRules = new FciOrient(new DagSepsets(__g));
+        finalFciRules.zhangFinalOrientation(__g);
+        workbench.setGraph(__g);
+    }
+
+    /**
+     * Called when ownership of the clipboard contents is lost.
+     *
+     * @param clipboard the clipboard that lost ownership
+     * @param contents the contents that were lost
+     */
+    public void lostOwnership(Clipboard clipboard, Transferable contents) {
+    }
+}
+
+
+