renamed mutation files (which had the same filename) to different class names and adapted remaining files

changed maven's groupId to com.github.jcfgonc
corrected older swi-prolog's solution counter code to be compatible with the official source (instead of using custom code by us)
added RangeSlider library code from https://github.com/ernieyu/Swing-range-slider

Author: João Gonçalves

.classpath

@@ -6,7 +6,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry combineaccessrules="false" kind="src" path="/Libraries"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
 			<attribute name="module" value="true"/>

pom.xml

@@ -1,6 +1,6 @@
 <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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
-  <groupId>jcfgonc.phd</groupId>
+  <groupId>com.github.jcfgonc</groupId>
   <artifactId>pattern-miner</artifactId>
   <version>0.0.1-SNAPSHOT</version>
   <build>
@@ -22,7 +22,7 @@
   		<version>0.0.1-SNAPSHOT</version>
   	</dependency>
   	<dependency>
-  		<groupId>jcfgonc.phd</groupId>
+  		<groupId>com.github.jcfgonc</groupId>
   		<artifactId>unolibrary</artifactId>
   		<version>0.0.1-SNAPSHOT</version>
   	</dependency>
@@ -46,5 +46,10 @@
   		<artifactId>gs-ui</artifactId>
   		<version>1.3</version>
   	</dependency>
+  	<dependency>
+  		<groupId>jpl</groupId>
+  		<artifactId>jpl</artifactId>
+  		<version>7.4.0</version>
+  	</dependency>
   </dependencies>
 </project>

src/jcfgonc/patternminer/PatternChromosome.java

@@ -11,6 +11,7 @@
 
 import graph.StringGraph;
 import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;
+import jcfgonc.patternminer.moea.MutationCode;
 import structures.ListOfSet;
 
 public class PatternChromosome implements Variable {
@@ -94,7 +95,7 @@ public String toString() {
 	}
 
 	public void mutate() {
-		PatternMutation.mutation(kbGraph, random, pattern, false); // do the mutation IN-PLACE
+		MutationCode.mutation(kbGraph, random, pattern, false); // do the mutation IN-PLACE
 		PatternFinderUtils.removeAdditionalComponents(this, null); // check for components (old repairing operator)
 	}
 

src/jcfgonc/patternminer/PatternFinderSwiProlog.java

@@ -12,10 +12,10 @@
 
 import graph.StringEdge;
 import graph.StringGraph;
+import jcfgonc.patternminer.moea.MutationCode;
 import structures.ObjectIndex;
 import structures.Ticker;
 
-@Deprecated
 public class PatternFinderSwiProlog {
 
 	/**
@@ -34,7 +34,7 @@ public static void findPatterns(final StringGraph graph) {
 		// generate a graph pattern
 		// do {
 		for (int i = 0; i < 3; i++) {
-			PatternMutation.mutation(graph, random, pattern, true);
+			MutationCode.mutation(graph, random, pattern, true);
 		}
 		// match the pattern in the graph
 		long count = countPatternMatches(pattern, 200000000);
@@ -47,8 +47,7 @@ public static void findPatterns(final StringGraph graph) {
 	/**
 	 * 
 	 * @param graph
-	 * @param concepts
-	 *            if null concepts are stored as text, else stored as unique integers
+	 * @param concepts if null concepts are stored as text, else stored as unique integers
 	 */
 	public static void createKnowledgeBase(final StringGraph graph, final ObjectIndex<String> concepts) {
 		JPL.init();
@@ -70,7 +69,8 @@ public static void createKnowledgeBase(final StringGraph graph, final ObjectInde
 
 			Compound factCompound = new Compound("assertz", new Term[] { relationCompound });
 			Query fact = new Query(factCompound);
-			fact.putQuery_jcfgonc();
+			fact.oneSolution();
+//			fact.putQuery_jcfgonc(); //this was a custom jpl7 function which added the query regardless of return values
 		}
 		System.out.println("SWI KB creation took " + t.getTimeDeltaLastCall() + " s");
 	}
@@ -140,10 +140,21 @@ public static long countPatternMatches(final StringGraph pattern, final int solu
 		Query q = new Query(rootCompound);
 		// Query qtest = new Query("isa(X3,X0),isa(X3,X1),isa(X2,X1)."); //test query
 		Ticker t = new Ticker();
-		long matches = q.countSolutions_jcfgonc(solutionLimit);
+
+		// this code is commented to be compatible with the original jpl7 source
+		// this was a custom jpl7 function in which the C side call asked the engine for next
+		// solutions until a limit is reached (and returned the count). Hence it minimized the java-C hasMoreSolutions/nextSolution call overhead
+		// long matches = q.countSolutions_jcfgonc(solutionLimit); 
+
+		long matches = 0;
+		while (q.hasMoreSolutions()) {
+			q.nextSolution();
+			matches++;
+		}
 		double time = t.getElapsedTime();
-		System.out.println("pattern edges\t" + patternWithVars.numberOfEdges() + "\tpattern vars\t" + patternWithVars.numberOfVertices() + "\ttime\t" + time + "\tmatches\t"
-				+ matches + "\tsolutions/s\t" + (matches / time) + "\tpattern\t" + patternWithVars.toString(64, Integer.MAX_VALUE));
+		System.out.println("pattern edges\t" + patternWithVars.numberOfEdges() + "\tpattern vars\t" + patternWithVars.numberOfVertices() + "\ttime\t"
+				+ time + "\tmatches\t" + matches + "\tsolutions/s\t" + (matches / time) + "\tpattern\t"
+				+ patternWithVars.toString(64, Integer.MAX_VALUE));
 		return matches;
 	}
 }

src/jcfgonc/patternminer/PatternFinderUtils.java

@@ -20,6 +20,7 @@
 import graph.StringEdge;
 import graph.StringGraph;
 import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;
+import jcfgonc.patternminer.moea.MutationCode;
 import structures.ListOfSet;
 import structures.Ticker;
 import structures.UnorderedPair;
@@ -303,7 +304,7 @@ public static void calculateRelationHistogram(PatternChromosome patternChromosom
 	public static StringGraph initializePattern(StringGraph kbGraph, StringGraph pattern, RandomGenerator random) {
 		// randomly add edges to an empty graph
 		for (int i = 0; i < 3; i++) { // add N edges
-			PatternMutation.mutation(kbGraph, random, pattern, true);
+			MutationCode.mutation(kbGraph, random, pattern, true);
 		}
 		return pattern;
 	}

src/jcfgonc/patternminer/PatternMutation.java renamed to src/jcfgonc/patternminer/moea/MutationCode.java

@@ -1,4 +1,4 @@
-package jcfgonc.patternminer;
+package jcfgonc.patternminer.moea;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -10,9 +10,11 @@
 import graph.StringEdge;
 import graph.StringGraph;
 import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;
+import jcfgonc.patternminer.PatternFinderUtils;
+import jcfgonc.patternminer.PatternMinerConfig;
 import utils.VariousUtils;
 
-public class PatternMutation {
+public class MutationCode {
 
 	/**
 	 * mutates the pattern IN-PLACE

src/jcfgonc/patternminer/moea/PatternMutation.java renamed to src/jcfgonc/patternminer/moea/MutationOperator.java

@@ -5,7 +5,7 @@
 
 import jcfgonc.patternminer.PatternChromosome;
 
-public class PatternMutation implements Variation {
+public class MutationOperator implements Variation {
 
 	/**
 	 * The probability of mutating each variable in a solution.
@@ -17,7 +17,7 @@ public class PatternMutation implements Variation {
 	 * 
 	 * @param probability the probability of occurring the mutation
 	 */
-	public PatternMutation(double probability) {
+	public MutationOperator(double probability) {
 		super();
 		this.probability = probability;
 	}

src/jcfgonc/patternminer/moea/PatternMinerLauncher.java

@@ -84,7 +84,7 @@ public Variation getVariation(String name, Properties properties, Problem proble
 
 				if (name.equalsIgnoreCase("PatternMutation")) {
 					double probability = typedProperties.getDouble("PatternMutation.Rate", 1.0);
-					PatternMutation pm = new PatternMutation(probability);
+					MutationOperator pm = new MutationOperator(probability);
 					return pm;
 				}
 

src/slider/RangeSlider.java

@@ -0,0 +1,98 @@
+package slider;
+
+import javax.swing.JSlider;
+
+/**
+ * An extension of JSlider to select a range of values using two thumb controls.
+ * The thumb controls are used to select the lower and upper value of a range
+ * with predetermined minimum and maximum values.
+ * 
+ * <p>Note that RangeSlider makes use of the default BoundedRangeModel, which 
+ * supports an inner range defined by a value and an extent.  The upper value
+ * returned by RangeSlider is simply the lower value plus the extent.</p>
+ */
+public class RangeSlider extends JSlider {
+
+    /**
+     * Constructs a RangeSlider with default minimum and maximum values of 0
+     * and 100.
+     */
+    public RangeSlider() {
+        initSlider();
+    }
+
+    /**
+     * Constructs a RangeSlider with the specified default minimum and maximum 
+     * values.
+     */
+    public RangeSlider(int min, int max) {
+        super(min, max);
+        initSlider();
+    }
+
+    /**
+     * Initializes the slider by setting default properties.
+     */
+    private void initSlider() {
+        setOrientation(HORIZONTAL);
+    }
+
+    /**
+     * Overrides the superclass method to install the UI delegate to draw two
+     * thumbs.
+     */
+    @Override
+    public void updateUI() {
+        setUI(new RangeSliderUI(this));
+        // Update UI for slider labels.  This must be called after updating the
+        // UI of the slider.  Refer to JSlider.updateUI().
+        updateLabelUIs();
+    }
+
+    /**
+     * Returns the lower value in the range.
+     */
+    @Override
+    public int getValue() {
+        return super.getValue();
+    }
+
+    /**
+     * Sets the lower value in the range.
+     */
+    @Override
+    public void setValue(int value) {
+        int oldValue = getValue();
+        if (oldValue == value) {
+            return;
+        }
+
+        // Compute new value and extent to maintain upper value.
+        int oldExtent = getExtent();
+        int newValue = Math.min(Math.max(getMinimum(), value), oldValue + oldExtent);
+        int newExtent = oldExtent + oldValue - newValue;
+
+        // Set new value and extent, and fire a single change event.
+        getModel().setRangeProperties(newValue, newExtent, getMinimum(), 
+            getMaximum(), getValueIsAdjusting());
+    }
+
+    /**
+     * Returns the upper value in the range.
+     */
+    public int getUpperValue() {
+        return getValue() + getExtent();
+    }
+
+    /**
+     * Sets the upper value in the range.
+     */
+    public void setUpperValue(int value) {
+        // Compute new extent.
+        int lowerValue = getValue();
+        int newExtent = Math.min(Math.max(0, value - lowerValue), getMaximum() - lowerValue);
+        
+        // Set extent to set upper value.
+        setExtent(newExtent);
+    }
+}

src/slider/RangeSliderDemo.java

@@ -0,0 +1,105 @@
+package slider;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+
+import javax.swing.BorderFactory;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.UIManager;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+/**
+ * Demo application panel to display a range slider.
+ */
+public class RangeSliderDemo extends JPanel {
+
+    private JLabel rangeSliderLabel1 = new JLabel();
+    private JLabel rangeSliderValue1 = new JLabel();
+    private JLabel rangeSliderLabel2 = new JLabel();
+    private JLabel rangeSliderValue2 = new JLabel();
+    private RangeSlider rangeSlider = new RangeSlider();
+
+    public RangeSliderDemo() {
+        setBorder(BorderFactory.createEmptyBorder(6, 6, 6, 6));
+        setLayout(new GridBagLayout());
+        
+        rangeSliderLabel1.setText("Lower value:");
+        rangeSliderLabel2.setText("Upper value:");
+        rangeSliderValue1.setHorizontalAlignment(JLabel.LEFT);
+        rangeSliderValue2.setHorizontalAlignment(JLabel.LEFT);
+        
+        rangeSlider.setPreferredSize(new Dimension(240, rangeSlider.getPreferredSize().height));
+        rangeSlider.setMinimum(0);
+        rangeSlider.setMaximum(10);
+        
+        // Add listener to update display.
+        rangeSlider.addChangeListener(new ChangeListener() {
+            public void stateChanged(ChangeEvent e) {
+                RangeSlider slider = (RangeSlider) e.getSource();
+                rangeSliderValue1.setText(String.valueOf(slider.getValue()));
+                rangeSliderValue2.setText(String.valueOf(slider.getUpperValue()));
+            }
+        });
+
+        add(rangeSliderLabel1, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
+            GridBagConstraints.NORTHWEST, GridBagConstraints.NONE, new Insets(0, 0, 3, 3), 0, 0));
+        add(rangeSliderValue1, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
+            GridBagConstraints.NORTHWEST, GridBagConstraints.NONE, new Insets(0, 0, 3, 0), 0, 0));
+        add(rangeSliderLabel2, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
+            GridBagConstraints.NORTHWEST, GridBagConstraints.NONE, new Insets(0, 0, 3, 3), 0, 0));
+        add(rangeSliderValue2, new GridBagConstraints(1, 1, 1, 1, 0.0, 0.0,
+            GridBagConstraints.NORTHWEST, GridBagConstraints.NONE, new Insets(0, 0, 6, 0), 0, 0));
+        add(rangeSlider      , new GridBagConstraints(0, 2, 2, 1, 0.0, 0.0,
+            GridBagConstraints.NORTHWEST, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
+    }
+    
+    public void display() {
+        // Initialize values.
+        rangeSlider.setValue(3);
+        rangeSlider.setUpperValue(7);
+        
+        // Initialize value display.
+        rangeSliderValue1.setText(String.valueOf(rangeSlider.getValue()));
+        rangeSliderValue2.setText(String.valueOf(rangeSlider.getUpperValue()));
+        
+        // Create window frame.
+        JFrame frame = new JFrame();
+        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+        frame.setResizable(false);
+        frame.setTitle("Range Slider Demo");
+        
+        // Set window content and validate.
+        frame.getContentPane().setLayout(new BorderLayout());
+        frame.getContentPane().add(this, BorderLayout.CENTER);
+        frame.pack();
+        
+        // Set window location and display.
+        frame.setLocationRelativeTo(null);
+        frame.setVisible(true);
+    }
+    
+    /**
+     * Main application method.
+     * @param args String[]
+     */
+    public static void main(String[] args) {
+        try {
+            UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
+
+        SwingUtilities.invokeLater(new Runnable() {
+            public void run() {
+                new RangeSliderDemo().display();
+            }
+        });
+    }
+}