[Bugfix] Refactored Configurations:

-Configuration refactor
  -stages are toggled individually
  -removed set-up-to-stage method
-MotorInstance refactor: multiple Lists -> one map<MotorId,MotorInstance>
    moved most of the fields to MotorInstance.java

core/src/net/sf/openrocket/aerodynamics/BarrowmanCalculator.java

@@ -74,11 +74,16 @@ public class BarrowmanCalculator extends AbstractAerodynamicCalculator {
 				new LinkedHashMap<RocketComponent, AerodynamicForces>();
 		
 		// Add all components to the map
-		for (RocketComponent c : configuration) {
+		for (RocketComponent component : configuration.getActiveComponents()) {
-			f = new AerodynamicForces();
-			f.setComponent(c);
 			
-			map.put(c, f);
+			// Skip non-aerodynamic components
+			if (!component.isAerodynamic())
+				continue;
+			
+			f = new AerodynamicForces();
+			f.setComponent(component);
+			
+			map.put(component, f);
 		}
 		
 		
@@ -172,7 +177,7 @@ public class BarrowmanCalculator extends AbstractAerodynamicCalculator {
 		if (calcMap == null)
 			buildCalcMap(configuration);
 		
-		for (RocketComponent component : configuration) {
+		for (RocketComponent component : configuration.getActiveComponents()) {
 			
 			// Skip non-aerodynamic components
 			if (!component.isAerodynamic())
@@ -367,7 +372,7 @@ public class BarrowmanCalculator extends AbstractAerodynamicCalculator {
 		double[] roughnessLimited = new double[Finish.values().length];
 		Arrays.fill(roughnessLimited, Double.NaN);
 		
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			
 			// Consider only SymmetricComponents and FinSets:
 			if (!(c instanceof SymmetricComponent) &&
@@ -469,7 +474,7 @@ public class BarrowmanCalculator extends AbstractAerodynamicCalculator {
 		base = calculateBaseCD(conditions.getMach());
 		
 		total = 0;
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (!c.isAerodynamic())
 				continue;
 			
@@ -517,7 +522,7 @@ public class BarrowmanCalculator extends AbstractAerodynamicCalculator {
 		base = calculateBaseCD(conditions.getMach());
 		total = 0;
 		
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (!(c instanceof SymmetricComponent))
 				continue;
 			
@@ -646,7 +651,7 @@ public class BarrowmanCalculator extends AbstractAerodynamicCalculator {
 			cacheLength = 0;
 			cacheDiameter = 0;
 			
-			for (RocketComponent c : configuration) {
+			for (RocketComponent c : configuration.getActiveComponents()) {
 				if (c instanceof SymmetricComponent) {
 					SymmetricComponent s = (SymmetricComponent) c;
 					area += s.getComponentPlanformArea();
@@ -665,7 +670,7 @@ public class BarrowmanCalculator extends AbstractAerodynamicCalculator {
 		
 		// Fins
 		// TODO: LOW: This could be optimized a lot...
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (c instanceof FinSet) {
 				FinSet f = (FinSet) c;
 				mul += 0.6 * Math.min(f.getFinCount(), 4) * f.getFinArea() *

core/src/net/sf/openrocket/document/Simulation.java

@@ -2,7 +2,6 @@ package net.sf.openrocket.document;
 
 import java.util.EventListener;
 import java.util.EventObject;
-import java.util.Iterator;
 import java.util.List;
 
 import net.sf.openrocket.aerodynamics.AerodynamicCalculator;
@@ -10,14 +9,9 @@ import net.sf.openrocket.aerodynamics.BarrowmanCalculator;
 import net.sf.openrocket.aerodynamics.WarningSet;
 import net.sf.openrocket.formatting.RocketDescriptor;
 import net.sf.openrocket.masscalc.MassCalculator;
-import net.sf.openrocket.motor.Motor;
 import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.Configuration;
-import net.sf.openrocket.rocketcomponent.IgnitionConfiguration;
-import net.sf.openrocket.rocketcomponent.MotorConfiguration;
-import net.sf.openrocket.rocketcomponent.MotorMount;
 import net.sf.openrocket.rocketcomponent.Rocket;
-import net.sf.openrocket.rocketcomponent.RocketComponent;
 import net.sf.openrocket.simulation.BasicEventSimulationEngine;
 import net.sf.openrocket.simulation.DefaultSimulationOptionFactory;
 import net.sf.openrocket.simulation.FlightData;
@@ -266,28 +260,14 @@ public class Simulation implements ChangeSource, Cloneable {
 			}
 		}
 		
+		Configuration c = new Configuration(this.getRocket());
+		MotorInstanceConfiguration motors = new MotorInstanceConfiguration(c);
+		c.setFlightConfigurationID(options.getMotorConfigurationID());
 		
 		//Make sure this simulation has motors.
-		Configuration c = new Configuration(this.getRocket());
+		if (0 == motors.getMotorCount()) {
-		MotorInstanceConfiguration motors = new MotorInstanceConfiguration();
-		c.setFlightConfigurationID(options.getMotorConfigurationID());
-		final String flightConfigId = c.getFlightConfigurationID();
-		
-		Iterator<MotorMount> iterator = c.motorIterator();
-		boolean no_motors = true;
-		
-		while (iterator.hasNext()) {
-			MotorMount mount = iterator.next();
-			RocketComponent component = (RocketComponent) mount;
-			MotorConfiguration motorConfig = mount.getMotorConfiguration().get(flightConfigId);
-			IgnitionConfiguration ignitionConfig = mount.getIgnitionConfiguration().get(flightConfigId);
-			Motor motor = motorConfig.getMotor();
-			if (motor != null)
-				no_motors = false;
-		}
-		
-		if (no_motors)
 			status = Status.CANT_RUN;
+		}
 		
 		return status;
 	}

core/src/net/sf/openrocket/masscalc/MassCalculator.java

@@ -4,16 +4,13 @@ import static net.sf.openrocket.util.MathUtil.pow2;
 
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Iterator;
 import java.util.Map;
 
 import net.sf.openrocket.motor.Motor;
-import net.sf.openrocket.motor.MotorId;
 import net.sf.openrocket.motor.MotorInstance;
 import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.AxialStage;
 import net.sf.openrocket.rocketcomponent.Configuration;
-import net.sf.openrocket.rocketcomponent.MotorMount;
 import net.sf.openrocket.rocketcomponent.RocketComponent;
 import net.sf.openrocket.simulation.MassData;
 import net.sf.openrocket.util.Coordinate;
@@ -80,35 +77,21 @@ public class MassCalculator implements Monitorable {
 		checkCache(configuration);
 		calculateStageCache(configuration);
 		
-		Coordinate totalCG = null;
+		Coordinate dryCG = null;
 		
 		// Stage contribution
-		for (int stage : configuration.getActiveStages()) {
+		for (AxialStage stage : configuration.getActiveStages()) {
-			totalCG = cgCache[stage].average(totalCG);
+			int stageNumber = stage.getStageNumber();
+			dryCG = cgCache[stageNumber].average(dryCG);
 		}
 		
-		if (totalCG == null)
+		if (dryCG == null)
-			totalCG = Coordinate.NUL;
+			dryCG = Coordinate.NUL;
 		
-		// Add motor CGs
+		MotorInstanceConfiguration motorConfig = new MotorInstanceConfiguration(configuration);
-		String motorId = configuration.getFlightConfigurationID();
+		Coordinate motorCG = getMotorCG(configuration, motorConfig, MassCalcType.LAUNCH_MASS);
-		if (type != MassCalcType.NO_MOTORS && motorId != null) {
-			Iterator<MotorMount> iterator = configuration.motorIterator();
-			while (iterator.hasNext()) {
-				MotorMount mount = iterator.next();
-				RocketComponent comp = (RocketComponent) mount;
-				Motor motor = mount.getMotorConfiguration().get(motorId).getMotor();
-				if (motor == null)
-					continue;
-				
-				Coordinate motorCG = type.getCG(motor).add(mount.getMotorPosition(motorId));
-				Coordinate[] cgs = comp.toAbsolute(motorCG);
-				for (Coordinate cg : cgs) {
-					totalCG = totalCG.average(cg);
-				}
-			}
-		}
 		
+		Coordinate totalCG = dryCG.average(motorCG);
 		return totalCG;
 	}
 	
@@ -123,23 +106,27 @@ public class MassCalculator implements Monitorable {
 		checkCache(configuration);
 		calculateStageCache(configuration);
 		
-		Coordinate totalCG = getCG(configuration, MassCalcType.NO_MOTORS);
+		Coordinate dryCG = getCG(configuration, MassCalcType.NO_MOTORS);
+		Coordinate motorCG = getMotorCG(configuration, motors, MassCalcType.LAUNCH_MASS);
 		
+		Coordinate totalCG = dryCG.average(motorCG);
+		return totalCG;
+	}
+	
+	public Coordinate getMotorCG(Configuration config, MotorInstanceConfiguration motors, MassCalcType type) {
+		Coordinate motorCG = Coordinate.ZERO;
 		// Add motor CGs
 		if (motors != null) {
-			for (MotorId id : motors.getMotorIDs()) {
+			for (MotorInstance inst : config.getActiveMotors(motors)) {
-				int stage = ((RocketComponent) motors.getMotorMount(id)).getStageNumber();
+				int stage = ((RocketComponent) inst.getMount()).getStageNumber();
-				if (configuration.isStageActive(stage)) {
+				if (config.isStageActive(stage)) {
-					
+					Coordinate position = inst.getPosition();
-					MotorInstance motor = motors.getMotorInstance(id);
+					Coordinate curCG = type.getCG(inst.getMotor()).add(position);
-					Coordinate position = motors.getMotorPosition(id);
+					motorCG = motorCG.average(curCG);
-					Coordinate cg = motor.getCG().add(position);
-					totalCG = totalCG.average(cg);
-					
 				}
 			}
 		}
-		return totalCG;
+		return motorCG;
 	}
 	
 	/**
@@ -158,21 +145,21 @@ public class MassCalculator implements Monitorable {
 		double totalInertia = 0;
 		
 		// Stages
-		for (int stage : configuration.getActiveStages()) {
+		for (AxialStage stage : configuration.getActiveStages()) {
-			Coordinate stageCG = cgCache[stage];
+			int stageNumber = stage.getStageNumber();
+			Coordinate stageCG = cgCache[stageNumber];
 			
-			totalInertia += (longitudinalInertiaCache[stage] +
+			totalInertia += (longitudinalInertiaCache[stageNumber] +
 					stageCG.weight * MathUtil.pow2(stageCG.x - totalCG.x));
 		}
 		
 		
 		// Motors
 		if (motors != null) {
-			for (MotorId id : motors.getMotorIDs()) {
+			for (MotorInstance motor : configuration.getActiveMotors(motors)) {
-				int stage = ((RocketComponent) motors.getMotorMount(id)).getStageNumber();
+				int stage = ((RocketComponent) motor.getMount()).getStageNumber();
 				if (configuration.isStageActive(stage)) {
-					MotorInstance motor = motors.getMotorInstance(id);
+					Coordinate position = motor.getPosition();
-					Coordinate position = motors.getMotorPosition(id);
 					Coordinate cg = motor.getCG().add(position);
 					
 					double inertia = motor.getLongitudinalInertia();
@@ -200,10 +187,11 @@ public class MassCalculator implements Monitorable {
 		double totalInertia = 0;
 		
 		// Stages
-		for (int stage : configuration.getActiveStages()) {
+		for (AxialStage stage : configuration.getActiveStages()) {
-			Coordinate stageCG = cgCache[stage];
+			int stageNumber = stage.getStageNumber();
+			Coordinate stageCG = cgCache[stageNumber];
 			
-			totalInertia += (rotationalInertiaCache[stage] +
+			totalInertia += (rotationalInertiaCache[stageNumber] +
 					stageCG.weight * (MathUtil.pow2(stageCG.y - totalCG.y) +
 							MathUtil.pow2(stageCG.z - totalCG.z)));
 		}
@@ -211,11 +199,10 @@ public class MassCalculator implements Monitorable {
 		
 		// Motors
 		if (motors != null) {
-			for (MotorId id : motors.getMotorIDs()) {
+			for (MotorInstance motor : configuration.getActiveMotors(motors)) {
-				int stage = ((RocketComponent) motors.getMotorMount(id)).getStageNumber();
+				int stage = ((RocketComponent) motor.getMount()).getStageNumber();
 				if (configuration.isStageActive(stage)) {
-					MotorInstance motor = motors.getMotorInstance(id);
+					Coordinate position = motor.getPosition();
-					Coordinate position = motors.getMotorPosition(id);
 					Coordinate cg = motor.getCG().add(position);
 					
 					double inertia = motor.getRotationalInertia();
@@ -241,9 +228,8 @@ public class MassCalculator implements Monitorable {
 		
 		// add up the masses of all motors in the rocket
 		if (motors != null) {
-			for (MotorId id : motors.getMotorIDs()) {
+			for (MotorInstance motor : configuration.getActiveMotors(motors)) {
-				MotorInstance motor = motors.getMotorInstance(id);
+				mass = mass + motor.getCG().weight - motor.getMotor().getEmptyCG().weight;
-				mass = mass + motor.getCG().weight - motor.getParentMotor().getEmptyCG().weight;
 			}
 		}
 		return mass;
@@ -266,13 +252,13 @@ public class MassCalculator implements Monitorable {
 		
 		Map<RocketComponent, Coordinate> map = new HashMap<RocketComponent, Coordinate>();
 		
-		for (RocketComponent c : configuration) {
+		for (RocketComponent comp : configuration.getActiveComponents()) {
-			Coordinate[] cgs = c.toAbsolute(c.getCG());
+			Coordinate[] cgs = comp.toAbsolute(comp.getCG());
 			Coordinate totalCG = Coordinate.NUL;
 			for (Coordinate cg : cgs) {
 				totalCG = totalCG.average(cg);
 			}
-			map.put(c, totalCG);
+			map.put(comp, totalCG);
 		}
 		
 		map.put(configuration.getRocket(), getCG(configuration, type));
@@ -284,7 +270,8 @@ public class MassCalculator implements Monitorable {
 	
 	private void calculateStageCache(Configuration config) {
 		if (cgCache == null) {
-			ArrayList<AxialStage> stageList = config.getRocket().getStageList();
+			ArrayList<AxialStage> stageList = new ArrayList<AxialStage>();
+			stageList.addAll(config.getRocket().getStageList());
 			int stageCount = stageList.size();
 			
 			cgCache = new Coordinate[stageCount];

core/src/net/sf/openrocket/motor/MotorId.java

@@ -12,6 +12,14 @@ public final class MotorId {
 	private final String componentId;
 	private final int number;
 	
+	private final String COMPONENT_ERROR_ID = "Error Motor Instance";
+	private final int ERROR_NUMBER = -1;
+	public final static MotorId ERROR_ID = new MotorId();
+	
+	public MotorId() {
+		this.componentId = COMPONENT_ERROR_ID;
+		this.number = ERROR_NUMBER;
+	}
 	
 	/**
 	 * Sole constructor.
@@ -20,7 +28,6 @@ public final class MotorId {
 	 * @param number		a positive motor doun5 number
 	 */
 	public MotorId(String componentId, int number) {
-		super();
 		
 		if (componentId == null) {
 			throw new IllegalArgumentException("Component ID was null");

core/src/net/sf/openrocket/motor/MotorInstance.java

@@ -1,10 +1,123 @@
 package net.sf.openrocket.motor;
 
 import net.sf.openrocket.models.atmosphere.AtmosphericConditions;
+import net.sf.openrocket.rocketcomponent.IgnitionConfiguration;
+import net.sf.openrocket.rocketcomponent.IgnitionConfiguration.IgnitionEvent;
+import net.sf.openrocket.rocketcomponent.MotorMount;
 import net.sf.openrocket.util.Coordinate;
 import net.sf.openrocket.util.Monitorable;
 
-public interface MotorInstance extends Cloneable, Monitorable {
+public abstract class MotorInstance implements Cloneable, Monitorable {
+	
+	protected MotorId id = null;
+	protected Motor parentMotor = null;
+	protected MotorMount mount = null;
+	protected IgnitionConfiguration.IgnitionEvent ignitionEvent = null;
+	protected double ejectionDelay = 0.0;
+	protected double ignitionDelay = 0.0;
+	protected Coordinate position = null;
+	protected double ignitionTime = 0.0;
+	
+	protected int modID = 0;
+	
+	public MotorInstance() {
+		
+		modID++;
+	}
+	
+	/**
+	 * Add a motor instance to this configuration.  The motor is placed at
+	 * the specified position and with an infinite ignition time (never ignited).
+	 * 
+	 * @param id			the ID of this motor instance.
+	 * @param motor			the motor instance.
+	 * @param mount			the motor mount containing this motor
+	 * @param ignitionEvent	the ignition event for the motor
+	 * @param ignitionDelay	the ignition delay for the motor
+	 * @param position		the position of the motor in absolute coordinates.
+	 * @throws IllegalArgumentException	if a motor with the specified ID already exists.
+	 */
+	public MotorInstance(MotorId _id, Motor _motor, MotorMount _mount, double _ejectionDelay,
+			IgnitionEvent _ignitionEvent, double _ignitionDelay, Coordinate _position) {
+		
+		this.id = _id;
+		this.parentMotor = _motor;
+		this.mount = _mount;
+		this.ejectionDelay = _ejectionDelay;
+		this.ignitionEvent = _ignitionEvent;
+		this.ignitionDelay = _ignitionDelay;
+		this.position = _position;
+		this.ignitionTime = Double.POSITIVE_INFINITY;
+		
+		modID++;
+	}
+	
+	public MotorId getID() {
+		return this.id;
+	}
+	
+	public void setID(final MotorId _id) {
+		this.id = _id;
+	}
+	
+	public double getEjectionDelay() {
+		return this.ejectionDelay;
+	}
+	
+	public void setEjectionDelay(final double newDelay) {
+		this.ejectionDelay = newDelay;
+	}
+	
+	@Override
+	public int getModID() {
+		return this.modID;
+	}
+	
+	public Motor getMotor() {
+		return this.parentMotor;
+	}
+	
+	public MotorMount getMount() {
+		return this.mount;
+	}
+	
+	public void setMount(final MotorMount _mount) {
+		this.mount = _mount;
+	}
+	
+	public Coordinate getPosition() {
+		return this.position;
+	}
+	
+	public void setPosition(Coordinate _position) {
+		this.position = _position;
+		modID++;
+	}
+	
+	public double getIgnitionTime() {
+		return this.ignitionTime;
+	}
+	
+	public void setIgnitionTime(double _time) {
+		this.ignitionTime = _time;
+		modID++;
+	}
+	
+	public double getIgnitionDelay() {
+		return ignitionDelay;
+	}
+	
+	public void setIgnitionDelay(final double _delay) {
+		this.ignitionDelay = _delay;
+	}
+	
+	public IgnitionEvent getIgnitionEvent() {
+		return ignitionEvent;
+	}
+	
+	public void setIgnitionEvent(final IgnitionEvent _event) {
+		this.ignitionEvent = _event;
+	}
 	
 	/**
 	 * Step the motor instance forward in time.
@@ -13,51 +126,49 @@ public interface MotorInstance extends Cloneable, Monitorable {
 	 * @param acceleration	the average acceleration during the step.
 	 * @param cond			the average atmospheric conditions during the step.
 	 */
-	public void step(double time, double acceleration, AtmosphericConditions cond);
+	public abstract void step(double time, double acceleration, AtmosphericConditions cond);
 	
 	
 	/**
 	 * Return the time to which this motor has been stepped.
 	 * @return	the current step time.
 	 */
-	public double getTime();
+	public abstract double getTime();
 	
 	/**
 	 * Return the average thrust during the last step.
 	 */
-	public double getThrust();
+	public abstract double getThrust();
 	
 	/**
 	 * Return the average CG location during the last step.
 	 */
-	public Coordinate getCG();
+	public abstract Coordinate getCG();
 	
 	/**
 	 * Return the average longitudinal moment of inertia during the last step.
 	 * This is the actual inertia, not the unit inertia!
 	 */
-	public double getLongitudinalInertia();
+	public abstract double getLongitudinalInertia();
 	
 	/**
 	 * Return the average rotational moment of inertia during the last step.
 	 * This is the actual inertia, not the unit inertia!
 	 */
-	public double getRotationalInertia();
+	public abstract double getRotationalInertia();
 	
 	/**
 	 * Return whether this motor still produces thrust.  If this method returns false
 	 * the motor has burnt out, and will not produce any significant thrust anymore.
 	 */
-	public boolean isActive();
+	public abstract boolean isActive();
 	
 	
 	/**
 	 * Create a new instance of this motor instance.  The state of the motor is
 	 * identical to this instance and can be used independently from this one.
 	 */
-	public MotorInstance clone();
+	@Override
-
+	public abstract MotorInstance clone();
-
-	public Motor getParentMotor();
 	
 }

core/src/net/sf/openrocket/motor/MotorInstanceConfiguration.java

@@ -1,13 +1,16 @@
 package net.sf.openrocket.motor;
 
-import java.util.ArrayList;
+import java.util.Collection;
-import java.util.Collections;
+import java.util.HashMap;
-import java.util.List;
+import java.util.Iterator;
+import java.util.Set;
 
 import net.sf.openrocket.models.atmosphere.AtmosphericConditions;
+import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.rocketcomponent.IgnitionConfiguration;
-import net.sf.openrocket.rocketcomponent.IgnitionConfiguration.IgnitionEvent;
+import net.sf.openrocket.rocketcomponent.MotorConfiguration;
 import net.sf.openrocket.rocketcomponent.MotorMount;
+import net.sf.openrocket.rocketcomponent.RocketComponent;
 import net.sf.openrocket.util.Coordinate;
 import net.sf.openrocket.util.Monitorable;
 
@@ -17,21 +20,55 @@ import net.sf.openrocket.util.Monitorable;
  * 
  * @author Sampo Niskanen <sampo.niskanen@iki.fi>
  */
-public final class MotorInstanceConfiguration implements Monitorable, Cloneable {
+public class MotorInstanceConfiguration implements Cloneable, Iterable<MotorInstance>, Monitorable {
-	
+	protected final HashMap<MotorId, MotorInstance> motors = new HashMap<MotorId, MotorInstance>();
-	private final List<MotorId> ids = new ArrayList<MotorId>();
-	private final List<MotorId> unmodifiableIds = Collections.unmodifiableList(ids);
-	private final List<MotorInstance> motors = new ArrayList<MotorInstance>();
-	private final List<Double> ejectionDelays = new ArrayList<Double>();
-	private final List<MotorMount> mounts = new ArrayList<MotorMount>();
-	private final List<IgnitionConfiguration.IgnitionEvent> ignitionEvents = new ArrayList<IgnitionConfiguration.IgnitionEvent>();
-	private final List<Double> ignitionDelays = new ArrayList<Double>();
-	private final List<Coordinate> positions = new ArrayList<Coordinate>();
-	private final List<Double> ignitionTimes = new ArrayList<Double>();
-	
 	
 	private int modID = 0;
 	
+	private MotorInstanceConfiguration() {
+	}
+	
+	/**
+	 * Create a new motor instance configuration for the rocket configuration.
+	 *
+	 * @param configuration		the rocket configuration.
+	 */
+	public MotorInstanceConfiguration(Configuration configuration) {
+		// motors == this
+		final String flightConfigId = configuration.getFlightConfigurationID();
+		
+		Iterator<RocketComponent> iterator = configuration.getRocket().iterator(false);
+		while (iterator.hasNext()) {
+			RocketComponent component = iterator.next();
+			if (component instanceof MotorMount) {
+				MotorMount mount = (MotorMount) component;
+				
+				MotorConfiguration motorConfig = mount.getMotorConfiguration().get(flightConfigId);
+				IgnitionConfiguration ignitionConfig = mount.getIgnitionConfiguration().get(flightConfigId);
+				Motor motor = motorConfig.getMotor();
+				
+				if (motor != null) {
+					int count = mount.getMotorConfiguration().size();
+					Coordinate[] positions = component.toAbsolute(mount.getMotorPosition(flightConfigId));
+					for (int i = 0; i < positions.length; i++) {
+						Coordinate position = positions[i];
+						MotorId id = new MotorId(component.getID(), i + 1);
+						MotorInstance inst = motor.getInstance();
+						inst.setID(id);
+						inst.setEjectionDelay(motorConfig.getEjectionDelay());
+						inst.setMount(mount);
+						inst.setIgnitionDelay(ignitionConfig.getIgnitionDelay());
+						inst.setIgnitionEvent(ignitionConfig.getIgnitionEvent());
+						inst.setPosition(position);
+						
+						motors.put(id, inst);
+					}
+				}
+			}
+		}
+		
+		
+	}
 	
 	/**
 	 * Add a motor instance to this configuration.  The motor is placed at
@@ -45,89 +82,70 @@ public final class MotorInstanceConfiguration implements Monitorable, Cloneable
 	 * @param position		the position of the motor in absolute coordinates.
 	 * @throws IllegalArgumentException	if a motor with the specified ID already exists.
 	 */
-	public void addMotor(MotorId id, MotorInstance motor, double ejectionDelay, MotorMount mount,
+	//	public void addMotor(MotorId _id, Motor _motor, double _ejectionDelay, MotorMount _mount,
-			IgnitionEvent ignitionEvent, double ignitionDelay, Coordinate position) {
+	//			IgnitionEvent _ignitionEvent, double _ignitionDelay, Coordinate _position) {
-		if (this.ids.contains(id)) {
+	//		
+	//		MotorInstance instanceToAdd = new MotorInstance(_id, _motor, _mount, _ejectionDelay,
+	//				_ignitionEvent, _ignitionDelay, _position);
+	//		
+	//		
+	//		//		this.ids.add(id);
+	//		//		this.motors.add(motor);
+	//		//		this.ejectionDelays.add(ejectionDelay);
+	//		//		this.mounts.add(mount);
+	//		//		this.ignitionEvents.add(ignitionEvent);
+	//		//		this.ignitionDelays.add(ignitionDelay);
+	//		//		this.positions.add(position);
+	//		//		this.ignitionTimes.add(Double.POSITIVE_INFINITY);
+	//	}
+	
+	
+	/**
+	 * Add a motor instance to this configuration.  
+	 * 
+	 * @param motor			the motor instance.
+	 * @throws IllegalArgumentException	if a motor with the specified ID already exists.
+	 */
+	public void addMotor(MotorInstance motor) {
+		MotorId id = motor.getID();
+		if (this.motors.containsKey(id)) {
 			throw new IllegalArgumentException("MotorInstanceConfiguration already " +
 					"contains a motor with id " + id);
 		}
-		this.ids.add(id);
+		this.motors.put(id, motor);
-		this.motors.add(motor);
+		
-		this.ejectionDelays.add(ejectionDelay);
-		this.mounts.add(mount);
-		this.ignitionEvents.add(ignitionEvent);
-		this.ignitionDelays.add(ignitionDelay);
-		this.positions.add(position);
-		this.ignitionTimes.add(Double.POSITIVE_INFINITY);
 		modID++;
 	}
 	
-	/**
+	public Collection<MotorInstance> getAllMotors() {
-	 * Return a list of all motor IDs in this configuration (not only ones in active stages).
+		return motors.values();
-	 */
+	}
-	public List<MotorId> getMotorIDs() {
+	
-		return unmodifiableIds;
+	public int getMotorCount() {
+		return motors.size();
+	}
+	
+	public Set<MotorId> getMotorIDs() {
+		return this.motors.keySet();
 	}
 	
 	public MotorInstance getMotorInstance(MotorId id) {
-		return motors.get(indexOf(id));
+		return motors.get(id);
 	}
 	
-	public double getEjectionDelay(MotorId id) {
+	public boolean hasMotors() {
-		return ejectionDelays.get(indexOf(id));
+		return (0 < motors.size());
 	}
 	
-	public MotorMount getMotorMount(MotorId id) {
-		return mounts.get(indexOf(id));
-	}
-	
-	public Coordinate getMotorPosition(MotorId id) {
-		return positions.get(indexOf(id));
-	}
-	
-	public void setMotorPosition(MotorId id, Coordinate position) {
-		positions.set(indexOf(id), position);
-		modID++;
-	}
-	
-	public double getMotorIgnitionTime(MotorId id) {
-		return ignitionTimes.get(indexOf(id));
-	}
-	
-	public void setMotorIgnitionTime(MotorId id, double time) {
-		this.ignitionTimes.set(indexOf(id), time);
-		modID++;
-	}
-	
-	public double getMotorIgnitionDelay(MotorId id) {
-		return ignitionDelays.get(indexOf(id));
-	}
-	
-	public IgnitionEvent getMotorIgnitionEvent(MotorId id) {
-		return ignitionEvents.get(indexOf(id));
-	}
-	
-	
-	private int indexOf(MotorId id) {
-		int index = ids.indexOf(id);
-		if (index < 0) {
-			throw new IllegalArgumentException("MotorInstanceConfiguration does not " +
-					"contain a motor with id " + id);
-		}
-		return index;
-	}
-	
-	
-	
 	/**
 	 * Step all of the motor instances to the specified time minus their ignition time.
 	 * @param time	the "global" time
 	 */
 	public void step(double time, double acceleration, AtmosphericConditions cond) {
-		for (int i = 0; i < motors.size(); i++) {
+		for (MotorInstance inst : motors.values()) {
-			double t = time - ignitionTimes.get(i);
+			double t = time - inst.getIgnitionTime();
 			if (t >= 0) {
-				motors.get(i).step(t, acceleration, cond);
+				inst.step(t, acceleration, cond);
 			}
 		}
 		modID++;
@@ -136,7 +154,7 @@ public final class MotorInstanceConfiguration implements Monitorable, Cloneable
 	@Override
 	public int getModID() {
 		int id = modID;
-		for (MotorInstance motor : motors) {
+		for (MotorInstance motor : motors.values()) {
 			id += motor.getModID();
 		}
 		return id;
@@ -149,18 +167,17 @@ public final class MotorInstanceConfiguration implements Monitorable, Cloneable
 	@Override
 	public MotorInstanceConfiguration clone() {
 		MotorInstanceConfiguration clone = new MotorInstanceConfiguration();
-		clone.ids.addAll(this.ids);
+		for (MotorInstance motor : this.motors.values()) {
-		clone.mounts.addAll(this.mounts);
+			clone.motors.put(motor.id, motor.clone());
-		clone.positions.addAll(this.positions);
-		clone.ejectionDelays.addAll(this.ejectionDelays);
-		clone.ignitionTimes.addAll(this.ignitionTimes);
-		clone.ignitionEvents.addAll(this.ignitionEvents);
-		clone.ignitionDelays.addAll(this.ignitionDelays);
-		for (MotorInstance motor : this.motors) {
-			clone.motors.add(motor.clone());
 		}
 		clone.modID = this.modID;
 		return clone;
 	}
 	
+	@Override
+	public Iterator<MotorInstance> iterator() {
+		return this.motors.values().iterator();
+	}
+	
+	
 }

core/src/net/sf/openrocket/motor/ThrustCurveMotor.java

@@ -415,9 +415,9 @@ public class ThrustCurveMotor implements Motor, Comparable<ThrustCurveMotor>, Se
 	
 	
 	////////  Motor instance implementation  ////////
-	private class ThrustCurveMotorInstance implements MotorInstance {
+	private class ThrustCurveMotorInstance extends MotorInstance {
 		
-		private int position;
+		private int timeIndex;
 		
 		// Previous time step value
 		private double prevTime;
@@ -434,13 +434,12 @@ public class ThrustCurveMotor implements Motor, Comparable<ThrustCurveMotor>, Se
 		
 		private final double unitRotationalInertia;
 		private final double unitLongitudinalInertia;
-		private final Motor parentMotor;
 		
 		private int modID = 0;
 		
 		public ThrustCurveMotorInstance() {
 			log.debug("ThrustCurveMotor:  Creating motor instance of " + ThrustCurveMotor.this);
-			position = 0;
+			timeIndex = 0;
 			prevTime = 0;
 			instThrust = 0;
 			stepThrust = 0;
@@ -451,11 +450,6 @@ public class ThrustCurveMotor implements Motor, Comparable<ThrustCurveMotor>, Se
 			parentMotor = ThrustCurveMotor.this;
 		}
 		
-		@Override
-		public Motor getParentMotor() {
-			return parentMotor;
-		}
-		
 		@Override
 		public double getTime() {
 			return prevTime;
@@ -500,7 +494,7 @@ public class ThrustCurveMotor implements Motor, Comparable<ThrustCurveMotor>, Se
 			
 			modID++;
 			
-			if (position >= time.length - 1) {
+			if (timeIndex >= time.length - 1) {
 				// Thrust has ended
 				prevTime = nextTime;
 				stepThrust = 0;
@@ -511,33 +505,33 @@ public class ThrustCurveMotor implements Motor, Comparable<ThrustCurveMotor>, Se
 			
 			
 			// Compute average & instantaneous thrust
-			if (nextTime < time[position + 1]) {
+			if (nextTime < time[timeIndex + 1]) {
 				
 				// Time step between time points
-				double nextF = MathUtil.map(nextTime, time[position], time[position + 1],
+				double nextF = MathUtil.map(nextTime, time[timeIndex], time[timeIndex + 1],
-						thrust[position], thrust[position + 1]);
+						thrust[timeIndex], thrust[timeIndex + 1]);
 				stepThrust = (instThrust + nextF) / 2;
 				instThrust = nextF;
 				
 			} else {
 				
 				// Portion of previous step
-				stepThrust = (instThrust + thrust[position + 1]) / 2 * (time[position + 1] - prevTime);
+				stepThrust = (instThrust + thrust[timeIndex + 1]) / 2 * (time[timeIndex + 1] - prevTime);
 				
 				// Whole steps
-				position++;
+				timeIndex++;
-				while ((position < time.length - 1) && (nextTime >= time[position + 1])) {
+				while ((timeIndex < time.length - 1) && (nextTime >= time[timeIndex + 1])) {
-					stepThrust += (thrust[position] + thrust[position + 1]) / 2 *
+					stepThrust += (thrust[timeIndex] + thrust[timeIndex + 1]) / 2 *
-							(time[position + 1] - time[position]);
+							(time[timeIndex + 1] - time[timeIndex]);
-					position++;
+					timeIndex++;
 				}
 				
 				// End step
-				if (position < time.length - 1) {
+				if (timeIndex < time.length - 1) {
-					instThrust = MathUtil.map(nextTime, time[position], time[position + 1],
+					instThrust = MathUtil.map(nextTime, time[timeIndex], time[timeIndex + 1],
-							thrust[position], thrust[position + 1]);
+							thrust[timeIndex], thrust[timeIndex + 1]);
-					stepThrust += (thrust[position] + instThrust) / 2 *
+					stepThrust += (thrust[timeIndex] + instThrust) / 2 *
-							(nextTime - time[position]);
+							(nextTime - time[timeIndex]);
 				} else {
 					// Thrust ended during this step
 					instThrust = 0;
@@ -549,9 +543,9 @@ public class ThrustCurveMotor implements Motor, Comparable<ThrustCurveMotor>, Se
 			
 			// Compute average and instantaneous CG (simple average between points)
 			Coordinate nextCG;
-			if (position < time.length - 1) {
+			if (timeIndex < time.length - 1) {
-				nextCG = MathUtil.map(nextTime, time[position], time[position + 1],
+				nextCG = MathUtil.map(nextTime, time[timeIndex], time[timeIndex + 1],
-						cg[position], cg[position + 1]);
+						cg[timeIndex], cg[timeIndex + 1]);
 			} else {
 				nextCG = cg[cg.length - 1];
 			}
@@ -564,11 +558,12 @@ public class ThrustCurveMotor implements Motor, Comparable<ThrustCurveMotor>, Se
 		
 		@Override
 		public MotorInstance clone() {
-			try {
+			throw new BugException("CloneNotSupportedException");
-				return (MotorInstance) super.clone();
+			//try {
-			} catch (CloneNotSupportedException e) {
+			//	return (MotorInstance) super.clone();
-				throw new BugException("CloneNotSupportedException", e);
+			//} catch (CloneNotSupportedException e) {
-			}
+			//	throw new BugException("CloneNotSupportedException", e);
+			//}
 		}
 		
 		@Override

core/src/net/sf/openrocket/optimization/rocketoptimization/domains/StabilityDomain.java

@@ -91,7 +91,7 @@ public class StabilityDomain implements SimulationDomain {
 		absolute = cpx - cgx;
 		
 		double diameter = 0;
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (c instanceof SymmetricComponent) {
 				double d1 = ((SymmetricComponent) c).getForeRadius() * 2;
 				double d2 = ((SymmetricComponent) c).getAftRadius() * 2;

core/src/net/sf/openrocket/optimization/rocketoptimization/parameters/StabilityParameter.java

@@ -84,7 +84,7 @@ public class StabilityParameter implements OptimizableParameter {
 		
 		if (!absolute) {
 			double diameter = 0;
-			for (RocketComponent c : configuration) {
+			for (RocketComponent c : configuration.getActiveComponents()) {
 				if (c instanceof SymmetricComponent) {
 					double d1 = ((SymmetricComponent) c).getForeRadius() * 2;
 					double d2 = ((SymmetricComponent) c).getAftRadius() * 2;

core/src/net/sf/openrocket/rocketcomponent/AxialStage.java

@@ -15,13 +15,11 @@ public class AxialStage extends ComponentAssembly implements FlightConfigurableC
 	private FlightConfigurationImpl<StageSeparationConfiguration> separationConfigurations;
 	
 	protected int stageNumber;
-	private static int stageCount;
 	
 	public AxialStage() {
 		this.separationConfigurations = new FlightConfigurationImpl<StageSeparationConfiguration>(this, ComponentChangeEvent.EVENT_CHANGE, new StageSeparationConfiguration());
 		this.relativePosition = Position.AFTER;
-		stageNumber = AxialStage.stageCount;
+		this.stageNumber = 0;
-		AxialStage.stageCount++;
 	}
 	
 	@Override
@@ -35,10 +33,6 @@ public class AxialStage extends ComponentAssembly implements FlightConfigurableC
 		return trans.get("Stage.Stage");
 	}
 	
-	public static int getStageCount() {
-		return AxialStage.stageCount;
-	}
-	
 	public FlightConfiguration<StageSeparationConfiguration> getStageSeparationConfiguration() {
 		return separationConfigurations;
 	}
@@ -107,23 +101,21 @@ public class AxialStage extends ComponentAssembly implements FlightConfigurableC
 		if (null == this.parent) {
 			return -1;
 		} else if (this.isCenterline()) {
-			if (0 < this.stageNumber) {
 			return --this.stageNumber;
+		} else {
+			return this.parent.getStageNumber();
 		}
 	}
 	
-		return -1;
-	}
-	
-	public static void resetStageCount() {
-		AxialStage.stageCount = 0;
-	}
-	
 	@Override
 	public int getStageNumber() {
 		return this.stageNumber;
 	}
 	
+	public void setStageNumber(final int newStageNumber) {
+		this.stageNumber = newStageNumber;
+	}
+	
 	@Override
 	public Coordinate[] shiftCoordinates(Coordinate[] c) {
 		checkState();

core/src/net/sf/openrocket/rocketcomponent/BoosterSet.java

@@ -130,32 +130,6 @@ public class BoosterSet extends AxialStage implements FlightConfigurableComponen
 		return this.getAxialOffset();
 	}
 	
-	/** 
-	 * Stages may be positioned relative to other stages. In that case, this will set the stage number 
-	 * against which this stage is positioned.
-	 * 
-	 * @return the stage number which this stage is positioned relative to
-	 */
-	@Override
-	public int getRelativeToStage() {
-		if (null == this.parent) {
-			return -1;
-		} else if (this.parent instanceof BoosterSet) {
-			return this.parent.parent.getChildPosition(this.parent);
-		} else if (this.isCenterline()) {
-			if (0 < this.stageNumber) {
-				return --this.stageNumber;
-			}
-		}
-		
-		return -1;
-	}
-	
-	@Override
-	public int getStageNumber() {
-		return this.stageNumber;
-	}
-	
 	@Override
 	public Coordinate[] shiftCoordinates(Coordinate[] c) {
 		checkState();

core/src/net/sf/openrocket/rocketcomponent/Configuration.java

@@ -1,13 +1,13 @@
 package net.sf.openrocket.rocketcomponent;
 
-import java.util.BitSet;
 import java.util.Collection;
 import java.util.EventListener;
 import java.util.EventObject;
-import java.util.Iterator;
+import java.util.HashMap;
 import java.util.List;
-import java.util.NoSuchElementException;
 
+import net.sf.openrocket.motor.MotorInstance;
+import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.util.ArrayList;
 import net.sf.openrocket.util.BugException;
 import net.sf.openrocket.util.ChangeSource;
@@ -16,26 +16,38 @@ import net.sf.openrocket.util.MathUtil;
 import net.sf.openrocket.util.Monitorable;
 import net.sf.openrocket.util.StateChangeListener;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 
 /**
- * A class defining a rocket configuration, including motors and which stages are active.
+ * A class defining a rocket configuration, including which stages are active.
  * 
- * TODO: HIGH: Remove motor ignition times from this class.
  * 
  * @author Sampo Niskanen <sampo.niskanen@iki.fi>
  */
-public class Configuration implements Cloneable, ChangeSource, ComponentChangeListener,
+public class Configuration implements Cloneable, ChangeSource, ComponentChangeListener, Monitorable {
-		Iterable<RocketComponent>, Monitorable {
+	private static final Logger log = LoggerFactory.getLogger(Configuration.class);
-	
-	private Rocket rocket;
-	private BitSet stagesActive = new BitSet();
-	
-	private String flightConfigurationId = null;
 	
+	protected Rocket rocket;
+	protected String flightConfigurationId = null;
 	private List<EventListener> listenerList = new ArrayList<EventListener>();
 	
+	protected class StageFlags {
+		public boolean active = true;
+		public int prev = -1;
+		public AxialStage stage = null;
+		
+		public StageFlags(AxialStage _stage, int _prev, boolean _active) {
+			this.stage = _stage;
+			this.prev = _prev;
+			this.active = _active;
+		}
+	}
 	
 	/* Cached data */
+	protected HashMap<Integer, StageFlags> stageMap = new HashMap<Integer, StageFlags>();
+	
 	private int boundsModID = -1;
 	private ArrayList<Coordinate> cachedBounds = new ArrayList<Coordinate>();
 	private double cachedLength = -1;
@@ -43,7 +55,6 @@ public class Configuration implements Cloneable, ChangeSource, ComponentChangeLi
 	private int refLengthModID = -1;
 	private double cachedRefLength = -1;
 	
-	
 	private int modID = 0;
 	
 	
@@ -55,98 +66,156 @@ public class Configuration implements Cloneable, ChangeSource, ComponentChangeLi
 	 */
 	public Configuration(Rocket rocket) {
 		this.rocket = rocket;
-		setAllStages();
+		updateStageMap();
 		rocket.addComponentChangeListener(this);
 	}
 	
-	
-	
 	public Rocket getRocket() {
 		return rocket;
 	}
 	
 	
+	public void clearAllStages() {
+		this.setAllStages(false);
+	}
+	
 	public void setAllStages() {
-		stagesActive.clear();
+		this.setAllStages(true);
-		stagesActive.set(0, AxialStage.getStageCount());
-		fireChangeEvent();
 	}
 	
-	
+	public void setAllStages(final boolean _value) {
-	/**
+		for (StageFlags cur : stageMap.values()) {
-	 * Set all stages up to and including the given stage number.  For example,
+			cur.active = _value;
-	 * <code>setToStage(0)</code> will set only the first stage active.
-	 * 
-	 * @param stage		the stage number.
-	 */
-	public void setToStage(int stage) {
-		stagesActive.clear();
-		stagesActive.set(0, stage + 1, true);
-		//		stages.set(stage+1, rocket.getStageCount(), false);
-		fireChangeEvent();
 		}
-	
-	public void setOnlyStage(int stage) {
-		stagesActive.clear();
-		stagesActive.set(stage, stage + 1, true);
 		fireChangeEvent();
 	}
 	
 	/** 
-	 * Check whether the up-most stage of the rocket is in this configuration.
+	 * This method flags a stage inactive.  Other stages are unaffected.
 	 * 
-	 * @return	<code>true</code> if the first stage is active in this configuration.
+	 * @param stageNumber  stage number to inactivate
 	 */
-	public boolean isHead() {
+	public void clearOnlyStage(final int stageNumber) {
-		return isStageActive(0);
+		setStage(stageNumber, false);
+	}
+	
+	/** 
+	 * This method flags a stage active.  Other stages are unaffected.
+	 * 
+	 * @param stageNumber  stage number to activate
+	 */
+	public void setOnlyStage(final int stageNumber) {
+		setStage(stageNumber, true);
+	}
+	
+	/** 
+	 * This method flags the specified stage as requested.  Other stages are unaffected.
+	 * 
+	 * @param stageNumber   stage number to flag
+	 * @param _active       inactive (<code>false</code>) or active (<code>true</code>)
+	 */
+	public void setStage(final int stageNumber, final boolean _active) {
+		if ((0 <= stageNumber) && (stageMap.containsKey(stageNumber))) {
+			log.error("debug: setting stage " + stageNumber + " to " + _active);
+			stageMap.get(stageNumber).active = _active;
+			fireChangeEvent();
+			return;
+		}
+		log.error("error: attempt to retrieve via a bad stage number: " + stageNumber);
 	}
 	
 	
+	public void toggleStage(final int stageNumber) {
+		if ((0 <= stageNumber) && (stageMap.containsKey(stageNumber))) {
+			
+			StageFlags flags = stageMap.get(stageNumber);
+			log.error("debug: toggling stage " + stageNumber + " to " + !flags.active);
+			flags.active = !flags.active;
+			fireChangeEvent();
+			return;
+		}
+		log.error("error: attempt to retrieve via a bad stage number: " + stageNumber);
+	}
+	
+	/**
+	 * Check whether the stage is active.
+	 */
+	public boolean isStageActive(final AxialStage stage) {
+		return this.isStageActive(stage.getStageNumber());
+	}
 	
 	/**
 	 * Check whether the stage specified by the index is active.
 	 */
-	public boolean isStageActive(int stage) {
+	public boolean isStageActive(int stageNumber) {
-		if (stage >= AxialStage.getStageCount())
+		if (stageNumber >= this.rocket.getStageCount()) {
 			return false;
-		return stagesActive.get(stage);
+		}
+		return stageMap.get(stageNumber).active;
 	}
 	
-	public int getStageCount() {
+	public List<RocketComponent> getActiveComponents() {
-		return AxialStage.getStageCount();
+		ArrayList<RocketComponent> toReturn = new ArrayList<RocketComponent>();
+		for (StageFlags curFlags : this.stageMap.values()) {
+			if (curFlags.active) {
+				toReturn.add(curFlags.stage);
+			}
+		}
+		
+		return toReturn;
+	}
+	
+	public List<MotorInstance> getActiveMotors(final MotorInstanceConfiguration mic) {
+		ArrayList<MotorInstance> toReturn = new ArrayList<MotorInstance>();
+		for (MotorInstance inst : mic.getAllMotors()) {
+			MotorMount mount = inst.getMount();
+			if (mount instanceof RocketComponent) {
+				RocketComponent comp = (RocketComponent) mount;
+				if (this.isStageActive(comp.getStage().getStageNumber())) {
+					toReturn.add(inst);
+				}
+			}
+		}
+		
+		return toReturn;
+	}
+	
+	public List<AxialStage> getActiveStages() {
+		List<AxialStage> activeStages = new ArrayList<AxialStage>();
+		
+		for (StageFlags flags : this.stageMap.values()) {
+			activeStages.add(flags.stage);
+		}
+		
+		return activeStages;
 	}
 	
 	public int getActiveStageCount() {
-		int count = 0;
+		int activeCount = 0;
-		int s = AxialStage.getStageCount();
+		for (StageFlags cur : this.stageMap.values()) {
-		
+			if (cur.active) {
-		for (int i = 0; i < s; i++) {
+				activeCount++;
-			if (stagesActive.get(i))
-				count++;
-		}
-		return count;
-	}
-	
-	public int[] getActiveStages() {
-		// temporary hack fix 
-		//int stageCount = Stage.getStageCount();
-		
-		int stageCount = getRocket().getChildCount();
-		List<Integer> active = new ArrayList<Integer>();
-		int[] ret;
-		
-		for (int i = 0; i < stageCount; i++) {
-			if (stagesActive.get(i)) {
-				active.add(i);
 			}
 		}
-		
+		return activeCount;
-		ret = new int[active.size()];
-		for (int i = 0; i < ret.length; i++) {
-			ret[i] = active.get(i);
 	}
 	
-		return ret;
+	/** 
+	 * Retrieve the bottom-most active stage.
+	 * @return 
+	 */
+	public AxialStage getBottomStage() {
+		AxialStage bottomStage = null;
+		for (StageFlags curFlags : this.stageMap.values()) {
+			if (curFlags.active) {
+				bottomStage = curFlags.stage;
+			}
+		}
+		return bottomStage;
+	}
+	
+	public int getStageCount() {
+		return stageMap.size();
 	}
 	
 	
@@ -221,8 +290,38 @@ public class Configuration implements Cloneable, ChangeSource, ComponentChangeLi
 				((StateChangeListener) l).stateChanged(e);
 			}
 		}
+		
+		updateStageMap();
 	}
 	
+	private void updateStageMap() {
+		if (this.rocket.getStageCount() == this.stageMap.size()) {
+			// no changes needed
+			return;
+		}
+		
+		this.stageMap.clear();
+		for (AxialStage curStage : this.rocket.getStageList()) {
+			int prevStageNum = curStage.getStageNumber() - 1;
+			if (curStage.getParent() instanceof AxialStage) {
+				prevStageNum = curStage.getParent().getStageNumber();
+			}
+			StageFlags flagsToAdd = new StageFlags(curStage, prevStageNum, true);
+			this.stageMap.put(curStage.getStageNumber(), flagsToAdd);
+		}
+	}
+	
+	// DEBUG / DEVEL
+	public String toDebug() {
+		StringBuilder buf = new StringBuilder();
+		buf.append(String.format("\nDumping stage config: \n"));
+		for (StageFlags flags : this.stageMap.values()) {
+			AxialStage curStage = flags.stage;
+			buf.append(String.format("    [%d]: %24s: %b\n", curStage.getStageNumber(), curStage.getName(), flags.active));
+		}
+		buf.append("\n\n");
+		return buf.toString();
+	}
 	
 	@Override
 	public void componentChanged(ComponentChangeEvent e) {
@@ -232,26 +331,6 @@ public class Configuration implements Cloneable, ChangeSource, ComponentChangeLi
 	
 	///////////////  Helper methods  ///////////////
 	
-	/**
-	 * Return whether this configuration has any motors defined to it.
-	 * 
-	 * @return  true if this configuration has active motor mounts with motors defined to them.
-	 */
-	public boolean hasMotors() {
-		for (RocketComponent c : this) {
-			if (c instanceof MotorMount) {
-				MotorMount mount = (MotorMount) c;
-				if (!mount.isMotorMount())
-					continue;
-				if (mount.getMotor(this.flightConfigurationId) != null) {
-					return true;
-				}
-			}
-		}
-		return false;
-	}
-	
-	
 	/**
 	 * Return whether a component is in the currently active stages.
 	 */
@@ -272,7 +351,7 @@ public class Configuration implements Cloneable, ChangeSource, ComponentChangeLi
 			cachedBounds.clear();
 			
 			double minX = Double.POSITIVE_INFINITY, maxX = Double.NEGATIVE_INFINITY;
-			for (RocketComponent component : this) {
+			for (RocketComponent component : this.getActiveComponents()) {
 				for (Coordinate coord : component.getComponentBounds()) {
 					cachedBounds.add(coord);
 					if (coord.x < minX)
@@ -308,57 +387,17 @@ public class Configuration implements Cloneable, ChangeSource, ComponentChangeLi
 	
 	
 	
-	/**
-	 * Return an iterator that iterates over the currently active components.
-	 * The <code>Rocket</code> and <code>Stage</code> components are not returned,
-	 * but instead all components that are within currently active stages.
-	 */
-	@Override
-	public Iterator<RocketComponent> iterator() {
-		List<RocketComponent> accumulator = new ArrayList<RocketComponent>();
-		
-		accumulator = this.getActiveComponents(accumulator, rocket.getChildren());
-		
-		return accumulator.iterator();
-	}
-	
-	private List<RocketComponent> getActiveComponents(List<RocketComponent> accumulator, final List<RocketComponent> toScan) {
-		for (RocketComponent rc : toScan) {
-			if (rc instanceof AxialStage) {
-				if (!isStageActive(rc.getStageNumber())) {
-					continue;
-				}
-			} else {
-				accumulator.add(rc);
-			}
-			// recurse to children
-			getActiveComponents(accumulator, rc.getChildren());
-		}
-		return accumulator;
-	}
-	
-	
-	/**
-	 * Return an iterator that iterates over all <code>MotorMount</code>s within the
-	 * current configuration that have an active motor.
-	 * 
-	 * @return  an iterator over active motor mounts.
-	 */
-	public Iterator<MotorMount> motorIterator() {
-		return new MotorIterator();
-	}
-	
-	
 	/**
 	 * Perform a deep-clone.  The object references are also cloned and no
 	 * listeners are listening on the cloned object.  The rocket instance remains the same.
 	 */
+	@SuppressWarnings("unchecked")
 	@Override
 	public Configuration clone() {
 		try {
 			Configuration config = (Configuration) super.clone();
 			config.listenerList = new ArrayList<EventListener>();
-			config.stagesActive = (BitSet) this.stagesActive.clone();
+			config.stageMap = (HashMap<Integer, StageFlags>) this.stageMap.clone();
 			config.cachedBounds = new ArrayList<Coordinate>();
 			config.boundsModID = -1;
 			config.refLengthModID = -1;
@@ -375,51 +414,5 @@ public class Configuration implements Cloneable, ChangeSource, ComponentChangeLi
 		return modID + rocket.getModID();
 	}
 	
-	private class MotorIterator implements Iterator<MotorMount> {
-		private final Iterator<RocketComponent> iterator;
-		private MotorMount next = null;
-		
-		public MotorIterator() {
-			this.iterator = iterator();
-		}
-		
-		@Override
-		public boolean hasNext() {
-			getNext();
-			return (next != null);
-		}
-		
-		@Override
-		public MotorMount next() {
-			getNext();
-			if (next == null) {
-				throw new NoSuchElementException("iterator called for too long");
-			}
-			
-			MotorMount ret = next;
-			next = null;
-			return ret;
-		}
-		
-		@Override
-		public void remove() {
-			throw new UnsupportedOperationException("remove unsupported");
-		}
-		
-		private void getNext() {
-			if (next != null)
-				return;
-			while (iterator.hasNext()) {
-				RocketComponent c = iterator.next();
-				if (c instanceof MotorMount) {
-					MotorMount mount = (MotorMount) c;
-					if (mount.isMotorMount() && mount.getMotor(flightConfigurationId) != null) {
-						next = mount;
-						return;
-					}
-				}
-			}
-		}
-	}
 	
 }

core/src/net/sf/openrocket/rocketcomponent/ReferenceType.java

@@ -8,7 +8,7 @@ public enum ReferenceType {
 	NOSECONE {
 		@Override
 		public double getReferenceLength(Configuration config) {
-			for (RocketComponent c: config) {
+			for (RocketComponent c : config.getActiveComponents()) {
 				if (c instanceof SymmetricComponent) {
 					SymmetricComponent s = (SymmetricComponent) c;
 					if (s.getForeRadius() >= 0.0005)
@@ -25,7 +25,7 @@ public enum ReferenceType {
 		@Override
 		public double getReferenceLength(Configuration config) {
 			double r = 0;
-			for (RocketComponent c: config) {
+			for (RocketComponent c : config.getActiveComponents()) {
 				if (c instanceof SymmetricComponent) {
 					SymmetricComponent s = (SymmetricComponent) c;
 					r = Math.max(r, s.getForeRadius());

core/src/net/sf/openrocket/rocketcomponent/Rocket.java

@@ -80,7 +80,7 @@ public class Rocket extends RocketComponent {
 	// Does the rocket have a perfect finish (a notable amount of laminar flow)
 	private boolean perfectFinish = false;
 	
-	
+	private final HashMap<Integer, AxialStage> stageMap = new HashMap<Integer, AxialStage>();
 	
 	/////////////  Constructor  /////////////
 	
@@ -93,7 +93,6 @@ public class Rocket extends RocketComponent {
 		functionalModID = modID;
 		defaultConfiguration = new Configuration(this);
 		
-		AxialStage.resetStageCount();
 	}
 	
 	
@@ -130,7 +129,7 @@ public class Rocket extends RocketComponent {
 	 */
 	public int getStageCount() {
 		checkState();
-		return AxialStage.getStageCount();
+		return this.stageMap.size();
 	}
 	
 	/**
@@ -195,29 +194,34 @@ public class Rocket extends RocketComponent {
 		return functionalModID;
 	}
 	
-	public ArrayList<AxialStage> getStageList() {
+	public Collection<AxialStage> getStageList() {
-		ArrayList<AxialStage> toReturn = new ArrayList<AxialStage>();
+		return this.stageMap.values();
-		
-		toReturn = Rocket.getStages(toReturn, this);
-		
-		return toReturn;
 	}
 	
-	private static ArrayList<AxialStage> getStages(ArrayList<AxialStage> accumulator, final RocketComponent parent) {
+	private int getNewStageNumber() {
-		if ((null == accumulator) || (null == parent)) {
+		int guess = 0;
-			return new ArrayList<AxialStage>();
+		while (stageMap.containsKey(guess)) {
+			guess++;
+		}
+		return guess;
 	}
 	
-		for (RocketComponent curChild : parent.getChildren()) {
+	public void trackStage(final AxialStage newStage) {
-			if (curChild instanceof AxialStage) {
+		int stageNumber = newStage.getStageNumber();
-				AxialStage curStage = (AxialStage) curChild;
+		AxialStage value = stageMap.get(stageNumber);
-				accumulator.add(curStage);
+		
+		if (newStage.equals(value)) {
+			// stage is already added. skip.
+		} else {
+			stageNumber = getNewStageNumber();
+			newStage.setStageNumber(stageNumber);
+			this.stageMap.put(stageNumber, newStage);
 		}
-			getStages(accumulator, curChild);
-		}
-		return accumulator;
 	}
 	
+	public void forgetStage(final AxialStage oldStage) {
+		this.stageMap.remove(oldStage.getStageNumber());
+	}
 	
 	public ReferenceType getReferenceType() {
 		checkState();

core/src/net/sf/openrocket/rocketcomponent/RocketComponent.java

@@ -29,6 +29,7 @@ import org.slf4j.LoggerFactory;
 
 
 public abstract class RocketComponent implements ChangeSource, Cloneable, Iterable<RocketComponent> {
+	@SuppressWarnings("unused")
 	private static final Logger log = LoggerFactory.getLogger(RocketComponent.class);
 	
 	// Because of changes to Java 1.7.0-45's mechanism to construct DataFlavor objects (used in Drag and Drop)
@@ -985,8 +986,7 @@ public abstract class RocketComponent implements ChangeSource, Cloneable, Iterab
 	 * it should override this with a public method that simply calls this
 	 * supermethod AND fire a suitable ComponentChangeEvent.
 	 * 
-	 * @deprecated name is ambiguous in three-dimensional space: value may refer to any of the three dimensions.  Please use 'setPositionX' instead.
+	 * @deprecated name is ambiguous in three-dimensional space: value may refer to any of the three dimensions.  Please use 'setAxialOffset' instead.
-	 * 
 	 * @param value		the position value of the component.
 	 */
 	public void setPositionValue(double value) {
@@ -1346,6 +1346,11 @@ public abstract class RocketComponent implements ChangeSource, Cloneable, Iterab
 		children.add(index, component);
 		component.parent = this;
 		
+		if (component instanceof AxialStage) {
+			AxialStage nStage = (AxialStage) component;
+			this.getRocket().trackStage(nStage);
+		}
+		
 		this.checkComponentStructure();
 		component.checkComponentStructure();
 		
@@ -1363,6 +1368,11 @@ public abstract class RocketComponent implements ChangeSource, Cloneable, Iterab
 		RocketComponent component = children.remove(n);
 		component.parent = null;
 		
+		if (component instanceof AxialStage) {
+			AxialStage nStage = (AxialStage) component;
+			this.getRocket().forgetStage(nStage);
+		}
+		
 		this.checkComponentStructure();
 		component.checkComponentStructure();
 		

core/src/net/sf/openrocket/simulation/AbstractSimulationStepper.java

@@ -1,12 +1,12 @@
 package net.sf.openrocket.simulation;
 
+import java.util.List;
+
 import net.sf.openrocket.masscalc.MassCalculator;
 import net.sf.openrocket.models.atmosphere.AtmosphericConditions;
-import net.sf.openrocket.motor.MotorId;
 import net.sf.openrocket.motor.MotorInstance;
 import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.Configuration;
-import net.sf.openrocket.rocketcomponent.RocketComponent;
 import net.sf.openrocket.simulation.exception.SimulationException;
 import net.sf.openrocket.simulation.listeners.SimulationListenerHelper;
 import net.sf.openrocket.util.BugException;
@@ -171,19 +171,18 @@ public abstract class AbstractSimulationStepper implements SimulationStepper {
 		}
 		
 		Configuration configuration = status.getConfiguration();
+		MotorInstanceConfiguration mic = status.getMotorConfiguration();
 		
 		// Iterate over the motors and calculate combined thrust
-		MotorInstanceConfiguration mic = status.getMotorConfiguration();
 		if (!stepMotors) {
 			mic = mic.clone();
 		}
 		mic.step(status.getSimulationTime() + timestep, acceleration, atmosphericConditions);
 		thrust = 0;
-		for (MotorId id : mic.getMotorIDs()) {
+		
-			if (configuration.isComponentActive((RocketComponent) mic.getMotorMount(id))) {
+		List<MotorInstance> activeMotors = configuration.getActiveMotors(mic);
-				MotorInstance motor = mic.getMotorInstance(id);
+		for (MotorInstance currentMotorInstance : activeMotors) {
-				thrust += motor.getThrust();
+			thrust += currentMotorInstance.getThrust();
-			}
 		}
 		
 		// Post-listeners

core/src/net/sf/openrocket/simulation/BasicEventSimulationEngine.java

@@ -1,6 +1,6 @@
 package net.sf.openrocket.simulation;
 
-import java.util.Iterator;
+import java.util.List;
 
 import net.sf.openrocket.aerodynamics.Warning;
 import net.sf.openrocket.l10n.Translator;
@@ -8,14 +8,13 @@ import net.sf.openrocket.motor.Motor;
 import net.sf.openrocket.motor.MotorId;
 import net.sf.openrocket.motor.MotorInstance;
 import net.sf.openrocket.motor.MotorInstanceConfiguration;
+import net.sf.openrocket.rocketcomponent.AxialStage;
 import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.rocketcomponent.DeploymentConfiguration;
 import net.sf.openrocket.rocketcomponent.IgnitionConfiguration;
-import net.sf.openrocket.rocketcomponent.MotorConfiguration;
 import net.sf.openrocket.rocketcomponent.MotorMount;
 import net.sf.openrocket.rocketcomponent.RecoveryDevice;
 import net.sf.openrocket.rocketcomponent.RocketComponent;
-import net.sf.openrocket.rocketcomponent.AxialStage;
 import net.sf.openrocket.rocketcomponent.StageSeparationConfiguration;
 import net.sf.openrocket.simulation.exception.MotorIgnitionException;
 import net.sf.openrocket.simulation.exception.SimulationException;
@@ -68,7 +67,7 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 		// Set up rocket configuration
 		Configuration configuration = setupConfiguration(simulationConditions);
 		flightConfigurationId = configuration.getFlightConfigurationID();
-		MotorInstanceConfiguration motorConfiguration = setupMotorConfiguration(configuration);
+		MotorInstanceConfiguration motorConfiguration = new MotorInstanceConfiguration(configuration);
 		if (motorConfiguration.getMotorIDs().isEmpty()) {
 			throw new MotorIgnitionException(trans.get("BasicEventSimulationEngine.error.noMotorsDefined"));
 		}
@@ -199,7 +198,7 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 					MotorInstance motor = status.getMotorConfiguration().getMotorInstance(motorId);
 					if (!motor.isActive() && status.addBurntOutMotor(motorId)) {
 						addEvent(new FlightEvent(FlightEvent.Type.BURNOUT, status.getSimulationTime(),
-								(RocketComponent) status.getMotorConfiguration().getMotorMount(motorId), motorId));
+								(RocketComponent) status.getMotorConfiguration().getMotorInstance(motorId).getMount(), motorId));
 					}
 				}
 				
@@ -221,7 +220,7 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 					
 					if (wantToTumble) {
 						final boolean tooMuchThrust = t > THRUST_TUMBLE_CONDITION;
-						final boolean isSustainer = status.getConfiguration().isStageActive(0);
+						//final boolean isSustainer = status.getConfiguration().isStageActive(0);
 						final boolean isApogee = status.isApogeeReached();
 						if (tooMuchThrust) {
 							status.getWarnings().add(Warning.TUMBLE_UNDER_THRUST);
@@ -261,37 +260,6 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 	
 	
 	
-	/**
-	 * Create a new motor instance configuration for the rocket configuration.
-	 *
-	 * @param configuration		the rocket configuration.
-	 * @return					a new motor instance configuration with all motors in place.
-	 */
-	private MotorInstanceConfiguration setupMotorConfiguration(Configuration configuration) {
-		MotorInstanceConfiguration motors = new MotorInstanceConfiguration();
-		final String flightConfigId = configuration.getFlightConfigurationID();
-		
-		Iterator<MotorMount> iterator = configuration.motorIterator();
-		while (iterator.hasNext()) {
-			MotorMount mount = iterator.next();
-			RocketComponent component = (RocketComponent) mount;
-			MotorConfiguration motorConfig = mount.getMotorConfiguration().get(flightConfigId);
-			IgnitionConfiguration ignitionConfig = mount.getIgnitionConfiguration().get(flightConfigId);
-			Motor motor = motorConfig.getMotor();
-			
-			if (motor != null) {
-				Coordinate[] positions = component.toAbsolute(mount.getMotorPosition(flightConfigId));
-				for (int i = 0; i < positions.length; i++) {
-					Coordinate position = positions[i];
-					MotorId id = new MotorId(component.getID(), i + 1);
-					motors.addMotor(id, motor.getInstance(), motorConfig.getEjectionDelay(), mount,
-							ignitionConfig.getIgnitionEvent(), ignitionConfig.getIgnitionDelay(), position);
-				}
-			}
-		}
-		return motors;
-	}
-	
 	/**
 	 * Handles events occurring during the flight from the event queue.
 	 * Each event that has occurred before or at the current simulation time is
@@ -340,12 +308,13 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 			
 			// Check for motor ignition events, add ignition events to queue
 			for (MotorId id : status.getMotorConfiguration().getMotorIDs()) {
-				IgnitionConfiguration.IgnitionEvent ignitionEvent = status.getMotorConfiguration().getMotorIgnitionEvent(id);
+				MotorInstance inst = status.getMotorConfiguration().getMotorInstance(id);
-				MotorMount mount = status.getMotorConfiguration().getMotorMount(id);
+				IgnitionConfiguration.IgnitionEvent ignitionEvent = inst.getIgnitionEvent();
+				MotorMount mount = inst.getMount();
 				RocketComponent component = (RocketComponent) mount;
 				
 				if (ignitionEvent.isActivationEvent(event, component)) {
-					double ignitionDelay = status.getMotorConfiguration().getMotorIgnitionDelay(id);
+					double ignitionDelay = inst.getIgnitionDelay();
 					addEvent(new FlightEvent(FlightEvent.Type.IGNITION,
 							status.getSimulationTime() + ignitionDelay,
 							component, id));
@@ -354,11 +323,12 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 			
 			
 			// Check for stage separation event
-			for (int stageNo : status.getConfiguration().getActiveStages()) {
+			
+			for (AxialStage stage : status.getConfiguration().getActiveStages()) {
+				int stageNo = stage.getStageNumber();
 				if (stageNo == 0)
 					continue;
 				
-				AxialStage stage = (AxialStage) status.getConfiguration().getRocket().getChild(stageNo);
 				StageSeparationConfiguration separationConfig = stage.getStageSeparationConfiguration().get(flightConfigurationId);
 				if (separationConfig.getSeparationEvent().isSeparationEvent(event, stage)) {
 					addEvent(new FlightEvent(FlightEvent.Type.STAGE_SEPARATION,
@@ -368,9 +338,7 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 			
 			
 			// Check for recovery device deployment, add events to queue
-			Iterator<RocketComponent> rci = status.getConfiguration().iterator();
+			for (RocketComponent c : status.getConfiguration().getActiveComponents()) {
-			while (rci.hasNext()) {
-				RocketComponent c = rci.next();
 				if (!(c instanceof RecoveryDevice))
 					continue;
 				DeploymentConfiguration deployConfig = ((RecoveryDevice) c).getDeploymentConfiguration().get(flightConfigurationId);
@@ -393,8 +361,10 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 			case IGNITION: {
 				// Ignite the motor
 				MotorId motorId = (MotorId) event.getData();
-				MotorInstanceConfiguration config = status.getMotorConfiguration();
+				MotorInstanceConfiguration motorConfig = status.getMotorConfiguration();
-				config.setMotorIgnitionTime(motorId, event.getTime());
+				MotorInstance inst = motorConfig.getMotorInstance(motorId);
+				inst.setIgnitionTime(event.getTime());
+				
 				status.setMotorIgnited(true);
 				status.getFlightData().addEvent(event);
 				
@@ -422,7 +392,7 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 				}
 				// Add ejection charge event
 				MotorId motorId = (MotorId) event.getData();
-				double delay = status.getMotorConfiguration().getEjectionDelay(motorId);
+				double delay = status.getMotorConfiguration().getMotorInstance(motorId).getEjectionDelay();
 				if (delay != Motor.PLUGGED) {
 					addEvent(new FlightEvent(FlightEvent.Type.EJECTION_CHARGE, status.getSimulationTime() + delay,
 							event.getSource(), event.getData()));
@@ -450,7 +420,7 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 				stages.add(boosterStatus);
 				
 				// Mark the status as having dropped the booster
-				status.getConfiguration().setToStage(n - 1);
+				status.getConfiguration().clearOnlyStage(n);
 				
 				// Mark the booster status as only having the booster.
 				boosterStatus.getConfiguration().setOnlyStage(n);
@@ -476,12 +446,14 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 					// TODO: HIGH: Check stage activeness for other events as well?
 					
 					// Check whether any motor in the active stages is active anymore
-					for (MotorId motorId : status.getMotorConfiguration().getMotorIDs()) {
+					List<MotorInstance> activeMotors = status.getConfiguration().getActiveMotors(status.getMotorConfiguration());
-						int stage = ((RocketComponent) status.getMotorConfiguration().
+					for (MotorInstance curInstance : activeMotors) {
-								getMotorMount(motorId)).getStageNumber();
+						MotorId curID = curInstance.getID();
+						RocketComponent comp = ((RocketComponent) curInstance.getMount());
+						int stage = comp.getStageNumber();
 						if (!status.getConfiguration().isStageActive(stage))
 							continue;
-						if (!status.getMotorConfiguration().getMotorInstance(motorId).isActive())
+						if (!status.getMotorConfiguration().getMotorInstance(curID).isActive())
 							continue;
 						status.getWarnings().add(Warning.RECOVERY_DEPLOYMENT_WHILE_BURNING);
 					}

core/src/net/sf/openrocket/simulation/SimulationStatus.java

@@ -119,7 +119,7 @@ public class SimulationStatus implements Monitorable {
 		 */
 		double length = this.simulationConditions.getLaunchRodLength();
 		double lugPosition = Double.NaN;
-		for (RocketComponent c : this.configuration) {
+		for (RocketComponent c : this.configuration.getActiveComponents()) {
 			if (c instanceof LaunchLug) {
 				double pos = c.toAbsolute(new Coordinate(c.getLength()))[0].x;
 				if (Double.isNaN(lugPosition) || pos > lugPosition) {

core/src/net/sf/openrocket/simulation/listeners/example/DampingMoment.java

@@ -6,8 +6,9 @@ import java.util.Map;
 import net.sf.openrocket.aerodynamics.AerodynamicCalculator;
 import net.sf.openrocket.aerodynamics.AerodynamicForces;
 import net.sf.openrocket.aerodynamics.FlightConditions;
-import net.sf.openrocket.motor.MotorId;
+import net.sf.openrocket.motor.MotorInstance;
 import net.sf.openrocket.motor.MotorInstanceConfiguration;
+import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.rocketcomponent.RocketComponent;
 import net.sf.openrocket.simulation.FlightDataBranch;
 import net.sf.openrocket.simulation.FlightDataType;
@@ -20,7 +21,9 @@ import net.sf.openrocket.util.Coordinate;
 public class DampingMoment extends AbstractSimulationListener {
 	
 	private static final FlightDataType type = FlightDataType.getType("Damping moment coefficient", "Cdm", UnitGroup.UNITS_COEFFICIENT);
-	private static final FlightDataType[] typeList = { type };
+	
+	// unused
+	//private static final FlightDataType[] typeList = { type };
 	
 	@Override
 	public FlightConditions postFlightConditions(SimulationStatus status, FlightConditions flightConditions) throws SimulationException {
@@ -66,11 +69,12 @@ public class DampingMoment extends AbstractSimulationListener {
 		
 		// find the maximum distance from nose to nozzle. 
 		double nozzleDistance = 0;
-		for (MotorId id : status.getMotorConfiguration().getMotorIDs()) {
+		Configuration config = status.getConfiguration();
-			MotorInstanceConfiguration config = status.getMotorConfiguration();
+		MotorInstanceConfiguration motorConfig = status.getMotorConfiguration();
-			Coordinate position = config.getMotorPosition(id);
+		for (MotorInstance inst : config.getActiveMotors(motorConfig)) {
+			Coordinate position = inst.getPosition();
 			
-			double x = position.x + config.getMotorInstance(id).getParentMotor().getLength();
+			double x = position.x + inst.getMotor().getLength();
 			if (x > nozzleDistance) {
 				nozzleDistance = x;
 			}

core/src/net/sf/openrocket/simulation/listeners/example/RollControlListener.java

@@ -78,7 +78,7 @@ public class RollControlListener extends AbstractSimulationListener {
 		
 		// Find the fin set named CONTROL
 		FinSet finset = null;
-		for (RocketComponent c : status.getConfiguration()) {
+		for (RocketComponent c : status.getConfiguration().getActiveComponents()) {
 			if ((c instanceof FinSet) && (c.getName().equals(CONTROL_FIN_NAME))) {
 				finset = (FinSet) c;
 				break;

core/src/net/sf/openrocket/unit/CaliberUnit.java

@@ -98,7 +98,7 @@ public class CaliberUnit extends GeneralUnit {
 	 * @return			the caliber of the rocket, or the default caliber.
 	 */
 	public static double calculateCaliber(Configuration config) {
-		return calculateCaliber(config.iterator());
+		return calculateCaliber(config.getActiveComponents().iterator());
 	}
 	
 	/**

core/test/net/sf/openrocket/rocketcomponent/BoosterSetTest.java

@@ -647,7 +647,6 @@ public class BoosterSetTest extends BaseTestCase {
 		assertEquals(" init order error: " + treeDump + " Booster B: resultant positions: ", expectedOffset, resultantOffsetB, EPSILON);
 	}
 	
-	
 	@Test
 	public void testStageNumbering() {
 		Rocket rocket = createTestRocket();
@@ -679,8 +678,29 @@ public class BoosterSetTest extends BaseTestCase {
 		actualStageNumber = boosterB.getStageNumber();
 		assertEquals(" init order error: Booster B: resultant positions: ", expectedStageNumber, actualStageNumber);
 		
-	}
+		//rocket.getDefaultConfiguration().dumpConfig();
 		
+		core.removeChild(2);
+		
+		String treedump = rocket.toDebugTree();
+		int expectedStageCount = 3;
+		int actualStageCount = rocket.getStageCount();
+		
+		assertEquals(" Stage tracking error:  removed booster A, but count not updated: " + treedump, expectedStageCount, actualStageCount);
+		actualStageCount = rocket.getDefaultConfiguration().getStageCount();
+		assertEquals(" Stage tracking error:  removed booster A, but configuration not updated: " + treedump, expectedStageCount, actualStageCount);
+		
+		BoosterSet boosterC = createBooster();
+		boosterC.setName("Booster C Stage");
+		core.addChild(boosterC);
+		boosterC.setAxialOffset(Position.BOTTOM, 0);
+		
+		expectedStageNumber = 2;
+		actualStageNumber = boosterC.getStageNumber();
+		assertEquals(" init order error: Booster B: resultant positions: ", expectedStageNumber, actualStageNumber);
+		
+		//rocket.getDefaultConfiguration().dumpConfig();
+	}
 	
 	@Test
 	public void testToAbsolute() {

core/test/net/sf/openrocket/rocketcomponent/ConfigurationTest.java

@@ -1,11 +1,12 @@
 package net.sf.openrocket.rocketcomponent;
 
+import static org.hamcrest.CoreMatchers.equalTo;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 
 import java.util.BitSet;
 import java.util.EventObject;
-import java.util.Iterator;
 
 import net.sf.openrocket.rocketcomponent.RocketComponent.Position;
 import net.sf.openrocket.util.StateChangeListener;
@@ -72,20 +73,9 @@ public class ConfigurationTest extends BaseTestCase {
 		Configuration config = r1.getDefaultConfiguration();
 		
 		/* Test */
-		
 		// Test rocket component iterator
-		// TODO: validate iterator iterates correctly
+		// the component iterator is no longer a custom iterator.... 
-		for (Iterator<RocketComponent> i = config.iterator(); i.hasNext();) {
+		// use the standard iterator over the Collection<> returned by config.getActiveComponents()  
-			i.next();
-		}
-		
-		// Rocket component iterator remove method is unsupported, should throw exception
-		try {
-			Iterator<RocketComponent> configIterator = config.iterator();
-			configIterator.remove();
-		} catch (UnsupportedOperationException e) {
-			assertTrue(e.getMessage().equals("remove unsupported"));
-		}
 		
 		// Test motor iterator
 		/* TODO: no motors in model Iterator<MotorMount> motorIterator() 
@@ -95,14 +85,14 @@ public class ConfigurationTest extends BaseTestCase {
 		}
 		*/
 		
-		// Motor iterator remove method is unsupported, should throw exception
+		//		// Motor iterator remove method is unsupported, should throw exception
-		try {
+		//		try {
-			Iterator<MotorMount> motorIterator = config.motorIterator();
+		//			Iterator<MotorMount> motorIterator = config.motorIterator();
-			motorIterator.remove();
+		//			motorIterator.remove();
-		} catch (UnsupportedOperationException e) {
+		//		} catch (UnsupportedOperationException e) {
-			assertTrue(e.getMessage().equals("remove unsupported"));
+		//			assertTrue(e.getMessage().equals("remove unsupported"));
-		}
+		//		}
-		
+		//		
 		/* Cleanup */
 		config.release();
 		
@@ -119,7 +109,7 @@ public class ConfigurationTest extends BaseTestCase {
 		
 		Configuration configClone = config.clone(); // TODO validate clone worked
 		assertFalse(config.getRocket() == null);
-		assertFalse(config.hasMotors());
+		//		assertFalse(config.hasMotors());
 		
 		config.release();
 	}
@@ -211,31 +201,34 @@ public class ConfigurationTest extends BaseTestCase {
 		Rocket r1 = makeSingleStageTestRocket();
 		Configuration config = r1.getDefaultConfiguration();
 		
-		BitSet activeStageFlags = new BitSet();
-		activeStageFlags.set(0, false); // first stage
-		
 		/* Test */
 		
 		// test cloning of single stage rocket
 		Configuration configClone = config.clone(); // TODO validate clone worked
+		configClone.release();
 		
 		// test explicitly setting only first stage active
+		config.clearAllStages();
 		config.setOnlyStage(0);
-		activeStageFlags.clear();
+		
-		activeStageFlags.set(0, true);
+		
-		validateStages(config, 1, activeStageFlags);
+		//config.dumpConfig();
+		//System.err.println("treedump: \n" + treedump);
+		
+		// test that getStageCount() returns correct value
+		int expectedStageCount = 1;
+		int stageCount = config.getStageCount();
+		assertTrue("stage count doesn't match", stageCount == expectedStageCount);
+		
+		expectedStageCount = 1;
+		stageCount = config.getActiveStageCount();
+		assertThat("active stage count doesn't match", stageCount, equalTo(expectedStageCount));
 		
 		// test explicitly setting all stages up to first stage active
-		config.setToStage(0);
+		config.setOnlyStage(0);
-		activeStageFlags.clear();
-		activeStageFlags.set(0, true);
-		validateStages(config, 1, activeStageFlags);
 		
 		// test explicitly setting all stages active
 		config.setAllStages();
-		activeStageFlags.clear();
-		activeStageFlags.set(0, true);
-		validateStages(config, 1, activeStageFlags);
 		
 		// Cleanup
 		config.release();
@@ -252,43 +245,57 @@ public class ConfigurationTest extends BaseTestCase {
 		Rocket r1 = makeTwoStageTestRocket();
 		Configuration config = r1.getDefaultConfiguration();
 		
-		BitSet activeStageFlags = new BitSet();
-		activeStageFlags.set(0, false); // booster (first) stage
-		activeStageFlags.set(1, false); // sustainer (second) stage
-		
-		/* Test */
-		
 		// test cloning of two stage rocket
 		Configuration configClone = config.clone(); // TODO validate clone worked
+		configClone.release();
+		
+		int expectedStageCount;
+		int stageCount;
+		
+		expectedStageCount = 2;
+		stageCount = config.getStageCount();
+		assertThat("stage count doesn't match", stageCount, equalTo(expectedStageCount));
+		
+		config.clearAllStages();
+		assertThat(" clear all stages: check #0: ", config.isStageActive(0), equalTo(false));
+		assertThat(" clear all stages: check #1: ", config.isStageActive(1), equalTo(false));
 		
 		// test explicitly setting only first stage active
 		config.setOnlyStage(0);
-		activeStageFlags.clear();
-		activeStageFlags.set(0, true);
-		validateStages(config, 2, activeStageFlags);
 		
-		// test explicitly setting all stages up to first stage active
+		expectedStageCount = 1;
-		config.setToStage(0);
+		stageCount = config.getActiveStageCount();
-		activeStageFlags.clear();
+		assertThat("active stage count doesn't match", stageCount, equalTo(expectedStageCount));
-		activeStageFlags.set(0, true);
+		
-		validateStages(config, 2, activeStageFlags);
+		assertThat(" setting single stage active: ", config.isStageActive(0), equalTo(true));
 		
 		// test explicitly setting all stages up to second stage active
-		config.setToStage(1);
+		config.setOnlyStage(1);
-		activeStageFlags.clear();
+		assertThat(config.toDebug() + "Setting single stage active: ", config.isStageActive(1), equalTo(true));
-		activeStageFlags.set(0, 2, true);
+		
-		validateStages(config, 2, activeStageFlags);
+		config.clearOnlyStage(0);
+		assertThat(" deactivate stage #0: ", config.isStageActive(0), equalTo(false));
+		assertThat(" deactive stage #0: ", config.isStageActive(1), equalTo(true));
 		
 		// test explicitly setting all two stages active
 		config.setAllStages();
-		activeStageFlags.clear();
+		assertThat(" activate all stages: check #0: ", config.isStageActive(0), equalTo(true));
-		activeStageFlags.set(0, 2, true);
+		assertThat(" activate all stages: check #1: ", config.isStageActive(1), equalTo(true));
-		validateStages(config, 2, activeStageFlags);
+		
+		// test toggling single stage
+		config.setAllStages();
+		config.toggleStage(0);
+		assertThat(" toggle stage #0: ", config.isStageActive(0), equalTo(false));
+		
+		config.toggleStage(0);
+		assertThat(" toggle stage #0: ", config.isStageActive(0), equalTo(true));
+		
+		config.toggleStage(0);
+		assertThat(" toggle stage #0: ", config.isStageActive(0), equalTo(false));
 		
 		// Cleanup
 		config.release();
 		
-		
 	}
 	
 	///////////////////// Helper Methods ////////////////////////////
@@ -307,43 +314,45 @@ public class ConfigurationTest extends BaseTestCase {
 			}
 		}
 		assertTrue(config.getActiveStageCount() == expectedActiveStageCount);
-		int[] stages = config.getActiveStages();
-		assertTrue(stages.length == expectedActiveStageCount);
 		
-		// test if isHead() detects first stage being active or inactive
+		assertTrue("this test is not yet written.", false);
-		if (activeStageFlags.get(0)) {
+		//		int[] stages = config.getActiveStages();
-			assertTrue(config.isHead());
+		//		
-		} else {
+		//		assertTrue(stages.length == expectedActiveStageCount);
-			assertFalse(config.isHead());
+		//		
-		}
+		//		// test if isHead() detects first stage being active or inactive
-		
+		//		if (activeStageFlags.get(0)) {
-		// test if isStageActive() detects stage x being active or inactive
+		//			assertTrue(config.isHead());
-		for (int i = 0; i < expectedStageCount; i++) {
+		//		} else {
-			if (activeStageFlags.get(i)) {
+		//			assertFalse(config.isHead());
-				assertTrue(config.isStageActive(i));
+		//		}
-			} else {
+		//		
-				assertFalse(config.isStageActive(i));
+		//		// test if isStageActive() detects stage x being active or inactive
-			}
+		//		for (int i = 0; i < expectedStageCount; i++) {
-		}
+		//			if (activeStageFlags.get(i)) {
-		
+		//				assertTrue(config.isStageActive(i));
-		// test boundary conditions 
+		//			} else {
-		
+		//				assertFalse(config.isStageActive(i));
-		// stage -1 should not exist, and isStageActive() should throw exception
+		//			}
-		boolean IndexOutOfBoundsExceptionFlag = false;
+		//		}
-		try {
+		//		
-			assertFalse(config.isStageActive(-1));
+		//		// test boundary conditions 
-		} catch (IndexOutOfBoundsException e) {
+		//		
-			IndexOutOfBoundsExceptionFlag = true;
+		//		// stage -1 should not exist, and isStageActive() should throw exception
-		}
+		//		boolean IndexOutOfBoundsExceptionFlag = false;
-		assertTrue(IndexOutOfBoundsExceptionFlag);
+		//		try {
-		
+		//			assertFalse(config.isStageActive(-1));
-		// n+1 stage should not exist, isStageActive() should return false
+		//		} catch (IndexOutOfBoundsException e) {
-		// TODO: isStageActive(stageCount + 1) really should throw IndexOutOfBoundsException
+		//			IndexOutOfBoundsExceptionFlag = true;
-		assertFalse(config.isStageActive(stageCount + 1));
+		//		}
+		//		assertTrue(IndexOutOfBoundsExceptionFlag);
+		//		
+		//		// n+1 stage should not exist, isStageActive() should return false
+		//		// TODO: isStageActive(stageCount + 1) really should throw IndexOutOfBoundsException
+		//		assertFalse(config.isStageActive(stageCount + 1));
 		
 	}
 	
-	
 	//////////////////// Test Rocket Creation Methods /////////////////////////
 	
 	public static Rocket makeEmptyRocket() {

swing/src/net/sf/openrocket/gui/components/StageSelector.java

@@ -11,12 +11,15 @@ import javax.swing.JToggleButton;
 
 import net.miginfocom.swing.MigLayout;
 import net.sf.openrocket.l10n.Translator;
+import net.sf.openrocket.rocketcomponent.AxialStage;
 import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.startup.Application;
 import net.sf.openrocket.util.StateChangeListener;
 
 
 public class StageSelector extends JPanel implements StateChangeListener {
+	private static final long serialVersionUID = -2898763402479628711L;
+
 	private static final Translator trans = Application.getTranslator();
 	
 	private final Configuration configuration;
@@ -40,13 +43,11 @@ public class StageSelector extends JPanel implements StateChangeListener {
 		if (buttons.size() == stages)
 			return;
 		
-		while (buttons.size() > stages) {
+		buttons.clear();
-			JToggleButton button = buttons.remove(buttons.size() - 1);
+		this.removeAll();
-			this.remove(button);
+		for(AxialStage stage : configuration.getRocket().getStageList()){
-		}
+			int stageNum = stage.getStageNumber(); 
-		
+			JToggleButton button = new JToggleButton(new StageAction(stageNum));
-		while (buttons.size() < stages) {
-			JToggleButton button = new JToggleButton(new StageAction(buttons.size()));
 			this.add(button);
 			buttons.add(button);
 		}
@@ -55,8 +56,6 @@ public class StageSelector extends JPanel implements StateChangeListener {
 	}
 	
 	
-
-
 	@Override
 	public void stateChanged(EventObject e) {
 		updateButtons();
@@ -64,10 +63,11 @@ public class StageSelector extends JPanel implements StateChangeListener {
 	
 	
 	private class StageAction extends AbstractAction implements StateChangeListener {
-		private final int stage;
+		private static final long serialVersionUID = 7433006728984943763L;
+		private final int stageNumber;
 		
 		public StageAction(final int stage) {
-			this.stage = stage;
+			this.stageNumber = stage;
 			configuration.addChangeListener(this);
 			stateChanged(null);
 		}
@@ -75,37 +75,20 @@ public class StageSelector extends JPanel implements StateChangeListener {
 		@Override
 		public Object getValue(String key) {
 			if (key.equals(NAME)) {
-				//// Stage
+				// Stage
-				return trans.get("StageAction.Stage") + " " + (stage + 1);
+				return trans.get("StageAction.Stage") + " " + (stageNumber );
 			}
 			return super.getValue(key);
 		}
 		
 		@Override
 		public void actionPerformed(ActionEvent e) {
-			configuration.setToStage(stage);
+			configuration.toggleStage(stageNumber);
-			
-			//			boolean state = (Boolean)getValue(SELECTED_KEY);
-			//			if (state == true) {
-			//				// Was disabled, now enabled
-			//				configuration.setToStage(stage);
-			//			} else {
-			//				// Was enabled, check what to do
-			//				if (configuration.isStageActive(stage + 1)) {
-			//					configuration.setToStage(stage);
-			//				} else {
-			//					if (stage == 0)
-			//						configuration.setAllStages();
-			//					else 
-			//						configuration.setToStage(stage-1);
-			//				}
-			//			}
-			//			stateChanged(null);
 		}
 		
 		@Override
 		public void stateChanged(EventObject e) {
-			this.putValue(SELECTED_KEY, configuration.isStageActive(stage));
+			this.putValue(SELECTED_KEY, configuration.isStageActive(stageNumber));
 		}
 	}
 }

swing/src/net/sf/openrocket/gui/dialogs/ComponentAnalysisDialog.java

@@ -513,7 +513,7 @@ public class ComponentAnalysisDialog extends JDialog implements StateChangeListe
 		cgData.clear();
 		dragData.clear();
 		rollData.clear();
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			forces = aeroData.get(c);
 			Coordinate cg = massData.get(c);
 			

swing/src/net/sf/openrocket/gui/figure3d/RocketRenderer.java

@@ -2,7 +2,6 @@ package net.sf.openrocket.gui.figure3d;
 
 import java.awt.Point;
 import java.nio.ByteBuffer;
-import java.util.Iterator;
 import java.util.Set;
 import java.util.Vector;
 
@@ -62,7 +61,7 @@ public abstract class RocketRenderer {
 		// Store a vector of pickable parts.
 		final Vector<RocketComponent> pickParts = new Vector<RocketComponent>();
 		
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (ignore != null && ignore.contains(c))
 				continue;
 			
@@ -116,7 +115,7 @@ public abstract class RocketRenderer {
 			gl.glMaterialfv(GL.GL_FRONT_AND_BACK, GLLightingFunc.GL_SPECULAR, colorBlack, 0);
 			gl.glLineWidth(5.0f);
 			
-			for (RocketComponent c : configuration) {
+			for (RocketComponent c : configuration.getActiveComponents()) {
 				if (selection.contains(c)) {
 					// Draw as lines, set Z to nearest
 					gl.glPolygonMode(GL.GL_FRONT_AND_BACK, GL2GL3.GL_LINE);
@@ -141,7 +140,7 @@ public abstract class RocketRenderer {
 		gl.glCullFace(GL.GL_BACK);
 		
 		// Draw all inner components
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (isDrawn(c)) {
 				if (!isDrawnTransparent(c)) {
 					renderComponent(gl, c, 1.0f);
@@ -153,7 +152,7 @@ public abstract class RocketRenderer {
 		
 		// Draw T&T front faces blended, without depth test
 		gl.glEnable(GL.GL_BLEND);
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (isDrawn(c)) {
 				if (isDrawnTransparent(c)) {
 					renderComponent(gl, c, 0.2f);
@@ -166,9 +165,11 @@ public abstract class RocketRenderer {
 	
 	private void renderMotors(GL2 gl, Configuration configuration) {
 		String motorID = configuration.getFlightConfigurationID();
-		Iterator<MotorMount> iterator = configuration.motorIterator();
+		
-		while (iterator.hasNext()) {
+		for( RocketComponent comp : configuration.getActiveComponents()){
-			MotorMount mount = iterator.next();
+			if( comp instanceof MotorMount){
+			
+				MotorMount mount = (MotorMount) comp;
 				Motor motor = mount.getMotorConfiguration().get(motorID).getMotor();
 				double length = motor.getLength();
 			
@@ -182,6 +183,7 @@ public abstract class RocketRenderer {
 					gl.glPopMatrix();
 				}
 			}
+		}
 		
 	}
 	

swing/src/net/sf/openrocket/gui/figure3d/photo/PhotoPanel.java

@@ -14,7 +14,6 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
-import javax.media.opengl.DebugGL2;
 import javax.media.opengl.GL;
 import javax.media.opengl.GL2;
 import javax.media.opengl.GLAutoDrawable;
@@ -44,7 +43,6 @@ import net.sf.openrocket.motor.Motor;
 import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.rocketcomponent.MotorMount;
 import net.sf.openrocket.rocketcomponent.RocketComponent;
-import net.sf.openrocket.rocketcomponent.AxialStage;
 import net.sf.openrocket.startup.Application;
 import net.sf.openrocket.startup.Preferences;
 import net.sf.openrocket.util.Color;
@@ -416,22 +414,24 @@ public class PhotoPanel extends JPanel implements GLEventListener {
 		rr.render(drawable, configuration, new HashSet<RocketComponent>());
 		
 		//Figure out the lowest stage shown
-		final int currentStageNumber = configuration.getActiveStages()[configuration.getActiveStages().length-1];
+		final int bottomStageNumber = configuration.getBottomStage().getStageNumber();
-		final AxialStage currentStage = (AxialStage)configuration.getRocket().getChild(currentStageNumber);
+		//final int currentStageNumber = configuration.getActiveStages()[configuration.getActiveStages().length-1];
+		//final AxialStage currentStage = (AxialStage)configuration.getRocket().getChild( bottomStageNumber);
 		
 		final String motorID = configuration.getFlightConfigurationID();
-		final Iterator<MotorMount> iterator = configuration.motorIterator();
+		
-		motor: while (iterator.hasNext()) {
+		
-			final MotorMount mount = iterator.next();
+		final Iterator<RocketComponent> iter = configuration.getActiveComponents().iterator();
+		while( iter.hasNext()){
+			RocketComponent comp = iter.next();
+			if( comp instanceof MotorMount){
+				
+				final MotorMount mount = (MotorMount) comp;
+				int curStageNumber = comp.getStageNumber();
 			
 				//If this mount is not in currentStage continue on to the next one.
-			RocketComponent parent = ((RocketComponent)mount);
+				if( curStageNumber != bottomStageNumber ){
-			while ( null != (parent = parent.getParent()) ){
+					continue;
-				if ( parent instanceof AxialStage ){
-					if ( parent != currentStage )
-						continue motor;
-					break;
-				}
 				}
 				
 				final Motor motor = mount.getMotorConfiguration().get(motorID).getMotor();
@@ -449,6 +449,7 @@ public class PhotoPanel extends JPanel implements GLEventListener {
 					gl.glPopMatrix();
 				}
 			}
+		}
 
 		gl.glDisable(GL.GL_BLEND);
 		gl.glFrontFace(GL.GL_CCW);

swing/src/net/sf/openrocket/gui/figureelements/RocketInfo.java

@@ -13,6 +13,7 @@ import java.awt.geom.Rectangle2D;
 import net.sf.openrocket.aerodynamics.Warning;
 import net.sf.openrocket.aerodynamics.WarningSet;
 import net.sf.openrocket.l10n.Translator;
+import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.simulation.FlightData;
 import net.sf.openrocket.startup.Application;
@@ -47,7 +48,9 @@ public class RocketInfo implements FigureElement {
 	private double cg = 0, cp = 0;
 	private double length = 0, diameter = 0;
 	private double mass = 0;
-	private double aoa = Double.NaN, theta = Double.NaN, mach = Application.getPreferences().getDefaultMach();
+	private double aoa = Double.NaN;
+	private double theta = Double.NaN;
+	private double mach = Application.getPreferences().getDefaultMach();
 	
 	private WarningSet warnings = null;
 	
@@ -151,7 +154,8 @@ public class RocketInfo implements FigureElement {
 				UnitGroup.UNITS_LENGTH.getDefaultUnit().toStringUnit(diameter));
 		
 		String massText;
-		if (configuration.hasMotors())
+		MotorInstanceConfiguration mic = new MotorInstanceConfiguration(configuration);
+		if (mic.hasMotors())
 			//// Mass with motors 
 			massText = trans.get("RocketInfo.massText1") +" ";
 		else

swing/src/net/sf/openrocket/gui/print/DesignReport.java

@@ -16,6 +16,7 @@ import net.sf.openrocket.gui.scalefigure.RocketPanel;
 import net.sf.openrocket.masscalc.MassCalculator;
 import net.sf.openrocket.masscalc.MassCalculator.MassCalcType;
 import net.sf.openrocket.motor.Motor;
+import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.rocketcomponent.MotorMount;
 import net.sf.openrocket.rocketcomponent.Rocket;
@@ -192,7 +193,9 @@ public class DesignReport {
 		canvas.showText("" + rocket.getStageCount());
 		
 		
-		if (configuration.hasMotors()) {
+		
+		MotorInstanceConfiguration mic = new MotorInstanceConfiguration(configuration);
+		if (mic.hasMotors()){
 			if (configuration.getStageCount() > 1) {
 				canvas.newlineShowText(MASS_WITH_MOTORS);
 			} else {
@@ -341,7 +344,8 @@ public class DesignReport {
 		for (RocketComponent c : rocket) {
 			
 			if (c instanceof AxialStage) {
-				config.setToStage(stage);
+				config.clearAllStages();
+				config.setOnlyStage(stage);
 				stage++;
 				stageMass = massCalc.getCG(config, MassCalcType.LAUNCH_MASS).weight;
 				// Calculate total thrust-to-weight from only lowest stage motors

swing/src/net/sf/openrocket/gui/scalefigure/RocketFigure.java

@@ -23,6 +23,8 @@ import net.sf.openrocket.gui.figureelements.FigureElement;
 import net.sf.openrocket.gui.util.ColorConversion;
 import net.sf.openrocket.gui.util.SwingPreferences;
 import net.sf.openrocket.motor.Motor;
+import net.sf.openrocket.motor.MotorInstance;
+import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.ComponentAssembly;
 import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.rocketcomponent.MotorMount;
@@ -339,13 +341,13 @@ public class RocketFigure extends AbstractScaleFigure {
 				RenderingHints.VALUE_STROKE_NORMALIZE);
 	
 		// Draw motors
-		String motorID = configuration.getFlightConfigurationID();
 		Color fillColor = ((SwingPreferences)Application.getPreferences()).getMotorFillColor();
 		Color borderColor = ((SwingPreferences)Application.getPreferences()).getMotorBorderColor();
-		Iterator<MotorMount> iterator = configuration.motorIterator();
+		
-		while (iterator.hasNext()) {
+		MotorInstanceConfiguration mic = new MotorInstanceConfiguration(configuration);
-			MotorMount mount = iterator.next();
+		for( MotorInstance curInstance : configuration.getActiveMotors(mic)){
-			Motor motor = mount.getMotor(motorID);
+			MotorMount mount = curInstance.getMount();
+			Motor motor = curInstance.getMotor();
 			double motorLength = motor.getLength();
 			double motorRadius = motor.getDiameter() / 2;
 		

swing/src/net/sf/openrocket/gui/scalefigure/RocketPanel.java

@@ -56,6 +56,7 @@ import net.sf.openrocket.gui.util.SwingPreferences;
 import net.sf.openrocket.l10n.Translator;
 import net.sf.openrocket.masscalc.MassCalculator;
 import net.sf.openrocket.masscalc.MassCalculator.MassCalcType;
+import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.ComponentChangeEvent;
 import net.sf.openrocket.rocketcomponent.ComponentChangeListener;
 import net.sf.openrocket.rocketcomponent.Configuration;
@@ -640,7 +641,7 @@ public class RocketPanel extends JPanel implements TreeSelectionListener, Change
 			length = maxX - minX;
 		}
 		
-		for (RocketComponent c : configuration) {
+		for (RocketComponent c : configuration.getActiveComponents()) {
 			if (c instanceof SymmetricComponent) {
 				double d1 = ((SymmetricComponent) c).getForeRadius() * 2;
 				double d2 = ((SymmetricComponent) c).getAftRadius() * 2;
@@ -692,8 +693,10 @@ public class RocketPanel extends JPanel implements TreeSelectionListener, Change
 		// Stop previous computation (if any)
 		stopBackgroundSimulation();
 		
+		MotorInstanceConfiguration mic = new MotorInstanceConfiguration( configuration);
+		
 		// Check that configuration has motors
-		if (!configuration.hasMotors()) {
+		if (!mic.hasMotors()){
 			extraText.setFlightData(FlightData.NaN_DATA);
 			extraText.setCalculatingData(false);
 			return;

swing/src/net/sf/openrocket/gui/simulation/SimulationRunDialog.java

@@ -8,6 +8,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.Collection;
 import java.util.Iterator;
 import java.util.List;
 import java.util.concurrent.Executors;
@@ -30,6 +31,8 @@ import net.sf.openrocket.gui.dialogs.DetailDialog;
 import net.sf.openrocket.gui.util.GUIUtil;
 import net.sf.openrocket.gui.util.SwingPreferences;
 import net.sf.openrocket.l10n.Translator;
+import net.sf.openrocket.motor.MotorInstance;
+import net.sf.openrocket.motor.MotorInstanceConfiguration;
 import net.sf.openrocket.rocketcomponent.Configuration;
 import net.sf.openrocket.rocketcomponent.IgnitionConfiguration;
 import net.sf.openrocket.rocketcomponent.MotorMount;
@@ -306,11 +309,13 @@ public class SimulationRunDialog extends JDialog {
 			// Calculate estimate of motor burn time
 			double launchBurn = 0;
 			double otherBurn = 0;
-			Configuration config = simulation.getConfiguration();
 			String id = simulation.getOptions().getMotorConfigurationID();
-			Iterator<MotorMount> iterator = config.motorIterator();
+			
-			while (iterator.hasNext()) {
+			Configuration config = simulation.getConfiguration();
-				MotorMount m = iterator.next();
+			MotorInstanceConfiguration mic = new MotorInstanceConfiguration(config);
+			Collection<MotorInstance> activeMotors = config.getActiveMotors(mic );
+			for( MotorInstance curInstance : activeMotors ){
+				MotorMount m = curInstance.getMount();
 				if (m.getIgnitionConfiguration().getDefault().getIgnitionEvent() == IgnitionConfiguration.IgnitionEvent.LAUNCH)
 					launchBurn = MathUtil.max(launchBurn, m.getMotor(id).getBurnTimeEstimate());
 				else