More minor refactorings, added some comments

9 files changed, 71 insertions, 54 deletions

diff --git a/res/mult3.plu b/res/mult3.plu
new file mode 100644
index 0000000..3cfb9d4
--- /dev/null
+++ b/res/mult3.plu
@@ -0,0 +1,6 @@
+.i 6

+.o 6

+.p 2

+0 4294901760 4278255360 4042322160 3435973836 2863311530   0 3221225472 955252736 3033329664 1722469376 2852170240 

+4294967295 4294901760 4278255360 4042322160 3435973836 2863311530   3770712064 2553835760 1421110476 510024362 1722469376 2852170240 

+.e
\ No newline at end of file
diff --git a/res/mult4.plu b/res/mult4.plu
new file mode 100644
index 0000000..c984944
--- /dev/null
+++ b/res/mult4.plu
@@ -0,0 +1,12 @@
+.i 8

+.o 8

+.p 8

+0 0 0 4294901760 4278255360 4042322160 3435973836 2863311530   0 0 0 0 4278190080 4042260480 3435921408 2863267840 

+0 0 4294967295 4294901760 4278255360 4042322160 3435973836 2863311530   0 0 4160749568 130088704 3342397680 3031747788 1718004394 2863267840 

+0 4294967295 0 4294901760 4278255360 4042322160 3435973836 2863311530   0 3758096384 528547584 477163760 2473381068 1515891370 3435921408 2863267840 

+0 4294967295 4294967295 4294901760 4278255360 4042322160 3435973836 2863311530   0 4227921920 3286239168 865650488 2874455220 505308774 1718004394 2863267840 

+4294967295 0 0 4294901760 4278255360 4042322160 3435973836 2863311530   2147483648 2130771712 2029056240 1724697804 1437248170 4042260480 3435921408 2863267840 

+4294967295 0 4294967295 4294901760 4278255360 4042322160 3435973836 2863311530   4026589184 264249216 2386041968 1227133804 1838307930 3031747788 1718004394 2863267840 

+4294967295 4294967295 0 4294901760 4278255360 4042322160 3435973836 2863311530   4227921920 2212497344 1662568248 1385477300 969303654 1515891370 3435921408 2863267840 

+4294967295 4294967295 4294967295 4294901760 4278255360 4042322160 3435973836 2863311530   4261477376 3789603808 2576888728 1431612244 33431070 505308774 1718004394 2863267840 

+.e
\ No newline at end of file
diff --git a/src/jcgp/gui/population/GUIGene.java b/src/jcgp/gui/population/GUIGene.java
index 3d9cffb..9980d53 100644
--- a/src/jcgp/gui/population/GUIGene.java
+++ b/src/jcgp/gui/population/GUIGene.java
@@ -26,9 +26,9 @@ public abstract class GUIGene extends Group {
 		ACTIVE_HOVER,
 		LOCKED_HOVER,
 		SOURCE,
-		TARGET,
+		VALID_TARGET,
 		NO_CHANGE_TARGET,
-		FORBIDDEN_TARGET
+		INVALID_TARGET
 	}
 	
 	protected Text text = new Text();
@@ -67,7 +67,7 @@ public abstract class GUIGene extends Group {
 		return locked;
 	}
 	
-	abstract void setLocked(boolean value);
+	protected abstract void setLocked(boolean value);
 	
 	public abstract void addLocks(int value);
 	
@@ -79,7 +79,7 @@ public abstract class GUIGene extends Group {
 	
 	public abstract Connection getChangingConnection();
 
-	public abstract void setConnections(GUIGeneState newState);
+	public abstract void setConnectionStates(GUIGeneState newState);
 
 	public abstract void resetState();
 	
diff --git a/src/jcgp/gui/population/GUIInput.java b/src/jcgp/gui/population/GUIInput.java
index fd66ab4..a48be51 100644
--- a/src/jcgp/gui/population/GUIInput.java
+++ b/src/jcgp/gui/population/GUIInput.java
@@ -43,7 +43,7 @@ public class GUIInput extends GUIGene {
 				if (input == source) {
 					setState(GUIGeneState.NO_CHANGE_TARGET);
 				} else {
-					setState(GUIGeneState.TARGET);
+					setState(GUIGeneState.VALID_TARGET);
 				}
 			}
 		});
@@ -59,7 +59,7 @@ public class GUIInput extends GUIGene {
 						setState(GUIGeneState.INDIRECT_HOVER);
 					} else {
 						setState(GUIGeneState.NEUTRAL);
-						((GUIGene) event.getGestureSource()).setConnections(GUIGeneState.INDIRECT_HOVER);
+						((GUIGene) event.getGestureSource()).setConnectionStates(GUIGeneState.INDIRECT_HOVER);
 					}
 				}
 			}
@@ -73,10 +73,10 @@ public class GUIInput extends GUIGene {
 				// set states to reflect the new situation
 				if (source.isLocked()) {
 					source.setState(GUIGeneState.HOVER);
-					source.setConnections(GUIGeneState.HOVER);
+					source.setConnectionStates(GUIGeneState.HOVER);
 				} else {
 					source.setState(GUIGeneState.NEUTRAL);
-					source.setConnections(GUIGeneState.NEUTRAL);
+					source.setConnectionStates(GUIGeneState.NEUTRAL);
 				}
 				
 				// the user released the drag gesture on this node, react appropriately
@@ -111,7 +111,7 @@ public class GUIInput extends GUIGene {
 				// cursor has left this node without dragging, or it is dragging and this is the source
 				if (getState() == GUIGeneState.HOVER) {
 					setState(GUIGeneState.NEUTRAL);
-					setConnections(GUIGeneState.NEUTRAL);
+					setConnectionStates(GUIGeneState.NEUTRAL);
 				}
 			}
 		});
@@ -129,7 +129,7 @@ public class GUIInput extends GUIGene {
 				mainCircle.setFill(Paint.valueOf(GUI.SOFT_HIGHLIGHT_COLOUR));
 			}
 			break;
-		case FORBIDDEN_TARGET:
+		case INVALID_TARGET:
 			mainCircle.setFill(Paint.valueOf(GUI.BAD_SELECTION_COLOUR));
 			break;
 		case LOCKED_HOVER:
@@ -155,7 +155,7 @@ public class GUIInput extends GUIGene {
 		case SOURCE:
 			mainCircle.setFill(Paint.valueOf(GUI.MEDIUM_HIGHLIGHT_COLOUR));
 			break;
-		case TARGET:
+		case VALID_TARGET:
 			parent.setTarget(true);
 			mainCircle.setFill(Paint.valueOf(GUI.GOOD_SELECTION_COLOUR));
 			break;
@@ -171,7 +171,7 @@ public class GUIInput extends GUIGene {
 	 * @param newState the state to set connections to.
 	 */
 	@Override
-	public void setConnections(GUIGeneState newState) {
+	public void setConnectionStates(GUIGeneState newState) {
 		// nothing
 	}
 
@@ -181,7 +181,7 @@ public class GUIInput extends GUIGene {
 	}
 
 	@Override
-	void setLocked(boolean value) {
+	protected void setLocked(boolean value) {
 		locked += value ? 1 : -1;
 		setState(locked > 0 ? GUIGeneState.HOVER : GUIGeneState.ACTIVE_HOVER);
 	}
diff --git a/src/jcgp/gui/population/GUINode.java b/src/jcgp/gui/population/GUINode.java
index 3fadbdd..142d650 100644
--- a/src/jcgp/gui/population/GUINode.java
+++ b/src/jcgp/gui/population/GUINode.java
@@ -148,10 +148,10 @@ public class GUINode extends GUIGene {
 					if (node == source) {
 						setState(GUIGeneState.NO_CHANGE_TARGET);
 					} else {
-						setState(GUIGeneState.TARGET);
+						setState(GUIGeneState.VALID_TARGET);
 					}
 				} else {
-					setState(GUIGeneState.FORBIDDEN_TARGET);
+					setState(GUIGeneState.INVALID_TARGET);
 				}
 			}
 		});
@@ -170,7 +170,7 @@ public class GUINode extends GUIGene {
 							setState(GUIGeneState.INDIRECT_HOVER);
 						} else {
 							setState(GUIGeneState.NEUTRAL);
-							((GUIGene) event.getGestureSource()).setConnections(GUIGeneState.INDIRECT_HOVER);
+							((GUIGene) event.getGestureSource()).setConnectionStates(GUIGeneState.INDIRECT_HOVER);
 						}
 					}
 				}
@@ -184,10 +184,10 @@ public class GUINode extends GUIGene {
 				// set states to reflect the new situation
 				if (source.isLocked()) {
 					source.setState(GUIGeneState.HOVER);
-					source.setConnections(GUIGeneState.HOVER);
+					source.setConnectionStates(GUIGeneState.HOVER);
 				} else {
 					source.setState(GUIGeneState.NEUTRAL);
-					source.setConnections(GUIGeneState.NEUTRAL);
+					source.setConnectionStates(GUIGeneState.NEUTRAL);
 				}
 
 				// the user released the drag gesture on this node, react appropriately
@@ -210,7 +210,6 @@ public class GUINode extends GUIGene {
 			}
 		});
 
-
 		addEventFilter(MouseEvent.MOUSE_ENTERED, new EventHandler<MouseEvent>() {
 			@Override
 			public void handle(MouseEvent event) {
@@ -218,7 +217,7 @@ public class GUINode extends GUIGene {
 				if (getState() == GUIGeneState.NEUTRAL) {
 					setState(GUIGeneState.HOVER);
 				} else if (locked > 0) {
-					setConnections(GUIGeneState.LOCKED_HOVER);
+					setConnectionStates(GUIGeneState.LOCKED_HOVER);
 				}
 			}
 		});
@@ -229,12 +228,12 @@ public class GUINode extends GUIGene {
 				// cursor has left this node without dragging, or it is dragging and this is the source
 				if (getState() == GUIGeneState.HOVER && locked <= 0) {
 					setState(GUIGeneState.NEUTRAL);
-					setConnections(GUIGeneState.NEUTRAL);
+					setConnectionStates(GUIGeneState.NEUTRAL);
 				} else if (locked > 0) {
-					if (getState() == GUIGeneState.SOURCE || getState() == GUIGeneState.FORBIDDEN_TARGET) {
-						setConnections(GUIGeneState.INDIRECT_HOVER);
+					if (getState() == GUIGeneState.SOURCE || getState() == GUIGeneState.INVALID_TARGET) {
+						setConnectionStates(GUIGeneState.INDIRECT_HOVER);
 					} else {
-						setConnections(GUIGeneState.HOVER);
+						setConnectionStates(GUIGeneState.HOVER);
 					}
 					
 				}
@@ -257,21 +256,21 @@ public class GUINode extends GUIGene {
 				mainCircle.setFill(Paint.valueOf(GUI.SOFT_HIGHLIGHT_COLOUR));
 				showLines(true);
 			}
-			setConnections(GUIGeneState.ACTIVE_HOVER);
+			setConnectionStates(GUIGeneState.ACTIVE_HOVER);
 			break;
 		case LOCKED_HOVER:
 			mainCircle.setFill(Paint.valueOf(GUI.SOFT_HIGHLIGHT_COLOUR));
 			break;
-		case FORBIDDEN_TARGET:
+		case INVALID_TARGET:
 			mainCircle.setFill(Paint.valueOf(GUI.BAD_SELECTION_COLOUR));
 			break;
 		case HOVER:
 			mainCircle.setFill(Paint.valueOf(GUI.MEDIUM_HIGHLIGHT_COLOUR));
 			showLines(true);
 			if (locked <= 0) {
-				setConnections(GUIGeneState.INDIRECT_HOVER);
+				setConnectionStates(GUIGeneState.INDIRECT_HOVER);
 			} else {
-				setConnections(GUIGeneState.HOVER);
+				setConnectionStates(GUIGeneState.HOVER);
 			}
 			break;
 		case INDIRECT_HOVER:
@@ -284,7 +283,7 @@ public class GUINode extends GUIGene {
 				mainCircle.setFill(Paint.valueOf(GUI.NEUTRAL_COLOUR));
 				showLines(false);
 				if (getState() == GUIGeneState.ACTIVE_HOVER) {
-					setConnections(GUIGeneState.NEUTRAL);
+					setConnectionStates(GUIGeneState.NEUTRAL);
 				}
 			}
 			break;
@@ -295,7 +294,7 @@ public class GUINode extends GUIGene {
 		case SOURCE:
 			mainCircle.setFill(Paint.valueOf(GUI.HARD_HIGHLIGHT_COLOUR));
 			break;
-		case TARGET:
+		case VALID_TARGET:
 			parent.setTarget(true);
 			mainCircle.setFill(Paint.valueOf(GUI.GOOD_SELECTION_COLOUR));
 			break;
@@ -387,7 +386,7 @@ public class GUINode extends GUIGene {
 	}
 
 	@Override
-	public void setConnections(GUIGeneState newState) {
+	public void setConnectionStates(GUIGeneState newState) {
 		for (int i = 0; i < lines.length; i++) {
 			parent.getGuiGene(node.getConnection(i)).setState(newState);
 		}
@@ -408,13 +407,13 @@ public class GUINode extends GUIGene {
 			setState(GUIGeneState.HOVER);
 		} else {
 			setState(GUIGeneState.NEUTRAL);
-			setConnections(GUIGeneState.NEUTRAL);
+			setConnectionStates(GUIGeneState.NEUTRAL);
 		}
 
 	}
 
 	@Override
-	void setLocked(boolean value) {
+	protected void setLocked(boolean value) {
 		locked += value ? 1 : -1;
 		setState(locked > 0 ? GUIGeneState.HOVER : GUIGeneState.ACTIVE_HOVER);
 
diff --git a/src/jcgp/gui/population/GUIOutput.java b/src/jcgp/gui/population/GUIOutput.java
index 364458b..a3f5a28 100644
--- a/src/jcgp/gui/population/GUIOutput.java
+++ b/src/jcgp/gui/population/GUIOutput.java
@@ -112,7 +112,7 @@ public class GUIOutput extends GUIGene {
 			@Override
 			public void handle(MouseDragEvent event) {
 				// the drag has entered this node, react appropriately
-				setState(GUIGeneState.FORBIDDEN_TARGET);
+				setState(GUIGeneState.INVALID_TARGET);
 			}
 		});
 
@@ -140,10 +140,10 @@ public class GUIOutput extends GUIGene {
 				
 				if (source.isLocked()) {
 					source.setState(GUIGeneState.HOVER);
-					source.setConnections(GUIGeneState.HOVER);
+					source.setConnectionStates(GUIGeneState.HOVER);
 				} else {
 					source.setState(GUIGeneState.NEUTRAL);
-					source.setConnections(GUIGeneState.NEUTRAL);
+					source.setConnectionStates(GUIGeneState.NEUTRAL);
 				}
 				
 				source.updateLines();
@@ -175,7 +175,7 @@ public class GUIOutput extends GUIGene {
 				// cursor has left this node without dragging, or it is dragging and this is the source
 				if (getState() == GUIGeneState.HOVER && !isLocked()) {
 					setState(GUIGeneState.NEUTRAL);
-					setConnections(GUIGeneState.NEUTRAL);
+					setConnectionStates(GUIGeneState.NEUTRAL);
 				}
 			}
 		});
@@ -192,14 +192,14 @@ public class GUIOutput extends GUIGene {
 		switch (newState) {
 		case ACTIVE_HOVER:
 			break;
-		case FORBIDDEN_TARGET:
+		case INVALID_TARGET:
 			mainCircle.setFill(Paint.valueOf(GUI.BAD_SELECTION_COLOUR));
 			break;
 		case HOVER:
 			mainCircle.setFill(Paint.valueOf(GUI.MEDIUM_HIGHLIGHT_COLOUR));
 			sourceLine.setVisible(true);
 			if (!isLocked()) {
-				setConnections(GUIGeneState.ACTIVE_HOVER);
+				setConnectionStates(GUIGeneState.ACTIVE_HOVER);
 			}
 			break;
 		case INDIRECT_HOVER:
@@ -214,10 +214,10 @@ public class GUIOutput extends GUIGene {
 			break;
 		case SOURCE:
 			mainCircle.setFill(Paint.valueOf(GUI.HARD_HIGHLIGHT_COLOUR));
-			setConnections(GUIGeneState.NEUTRAL);
-			setConnections(GUIGeneState.INDIRECT_HOVER);
+			setConnectionStates(GUIGeneState.NEUTRAL);
+			setConnectionStates(GUIGeneState.INDIRECT_HOVER);
 			break;
-		case TARGET:
+		case VALID_TARGET:
 			mainCircle.setFill(Paint.valueOf(GUI.GOOD_SELECTION_COLOUR));
 			break;
 		default:
@@ -240,7 +240,7 @@ public class GUIOutput extends GUIGene {
 	}
 
 	@Override
-	public void setConnections(GUIGeneState newState) {
+	public void setConnectionStates(GUIGeneState newState) {
 		parent.getGuiGene(output.getSource()).setState(newState);
 	}
 
@@ -248,17 +248,17 @@ public class GUIOutput extends GUIGene {
 	public void resetState() {
 		if (locked > 0) {
 			setState(GUIGeneState.HOVER);
-			setConnections(GUIGeneState.HOVER);
+			setConnectionStates(GUIGeneState.HOVER);
 		} else {
 			setState(GUIGeneState.NEUTRAL);
-			setConnections(GUIGeneState.NEUTRAL);
+			setConnectionStates(GUIGeneState.NEUTRAL);
 		}
 	}
 
 	@Override
-	void setLocked(boolean value) {
+	protected void setLocked(boolean value) {
 		locked += value ? 1 : -1;
-		setConnections(value ? GUIGeneState.HOVER : GUIGeneState.ACTIVE_HOVER);
+		setConnectionStates(value ? GUIGeneState.HOVER : GUIGeneState.ACTIVE_HOVER);
 
 		parent.getGuiGene(output.getSource()).setLocked(value);
 
@@ -295,7 +295,7 @@ public class GUIOutput extends GUIGene {
 		if (isLocked()) {
 			setLocked(false);
 			setState(GUIGeneState.NEUTRAL);
-			setConnections(GUIGeneState.NEUTRAL);
+			setConnectionStates(GUIGeneState.NEUTRAL);
 		}
 	}
 
diff --git a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java b/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
index 29f8e1f..a13a52b 100644
--- a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
@@ -22,11 +22,11 @@ public class GUIBooleanParameter extends GUIParameter<Boolean> {
 	private CheckBox checkBox;
 	
 	/**
-	 * This default-visibility constructor is intended for use
+	 * This protected constructor is intended for use
 	 * by the factory method only.
 	 * 
 	 */
-	GUIBooleanParameter(final BooleanParameter parameter, final SettingsPane sp) {
+	protected GUIBooleanParameter(BooleanParameter parameter, SettingsPane sp) {
 		super(parameter, sp);
 	}
 	
diff --git a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
index c3c1f59..9f4ea28 100644
--- a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
@@ -7,7 +7,7 @@ import javafx.beans.value.ObservableValue;
 import javafx.geometry.Pos;
 import javafx.scene.control.Control;
 import javafx.scene.control.TextField;
-import jcgp.backend.parameters.Parameter;
+import jcgp.backend.parameters.DoubleParameter;
 import jcgp.backend.parameters.ParameterStatus;
 import jcgp.gui.settings.SettingsPane;
 
@@ -30,7 +30,7 @@ public class GUIDoubleParameter extends GUIParameter<Number> {
 	 * by the factory method only.
 	 * 
 	 */
-	protected GUIDoubleParameter(Parameter<Number> parameter, SettingsPane sp) {
+	protected GUIDoubleParameter(DoubleParameter parameter, SettingsPane sp) {
 		super(parameter, sp);
 	}
 	
diff --git a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java b/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
index 5bf6d9c..d36c1b3 100644
--- a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
@@ -5,7 +5,7 @@ import javafx.beans.value.ObservableValue;
 import javafx.geometry.Pos;
 import javafx.scene.control.Control;
 import javafx.scene.control.TextField;
-import jcgp.backend.parameters.Parameter;
+import jcgp.backend.parameters.IntegerParameter;
 import jcgp.backend.parameters.ParameterStatus;
 import jcgp.gui.settings.SettingsPane;
 
@@ -27,7 +27,7 @@ public class GUIIntegerParameter extends GUIParameter<Number> {
 	 * by the factory method only.
 	 * 
 	 */
-	protected GUIIntegerParameter(Parameter<Number> parameter, SettingsPane sp) {
+	protected GUIIntegerParameter(IntegerParameter parameter, SettingsPane sp) {
 		super(parameter, sp);
 	}