Thread: [cilib-devel] [PATCH 1/3] Refactor Algorithm to interface.

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The need to have an interface for Algorithm is very high. It promotes
better unit testing as it can be mocked out successfully.

Signed-off-by: Gary Pampara <gpa...@gm...>
---
 .../{Algorithm.java => AbstractAlgorithm.java}     |   13 +-
 .../net/sourceforge/cilib/algorithm/Algorithm.java |  350 +-------------------
 .../algorithm/MultistartOptimisationAlgorithm.java |   10 +-
 .../cilib/algorithm/SingularAlgorithm.java         |    2 +-
 .../population/PopulationBasedAlgorithm.java       |    4 +-
 .../rnaprediction/RNAAccuracyMeasurement.java      |    3 +-
 .../sequencealignment/AlignmentVisualizer.java     |    2 +-
 .../DesiredMaximizationFitness.java                |    5 +-
 .../net/sourceforge/cilib/boa/bee/OnlookerBee.java |    4 +-
 .../net/sourceforge/cilib/boa/bee/WorkerBee.java   |    4 +-
 .../cilib/clustering/kmeans/KMeans.java            |    3 +-
 .../ExponentiallyDecreasingControlParameter.java   |    3 +-
 .../ExponentiallyIncreasingControlParameter.java   |    3 +-
 .../LinearDecreasingControlParameter.java          |    3 +-
 .../LinearIncreasingControlParameter.java          |    3 +-
 .../splitstrategies/ImperfectSplitStrategy.java    |    7 +-
 .../splitstrategies/IndexedSplitStrategy.java      |    5 +-
 .../splitstrategies/PerfectSplitStrategy.java      |    3 +-
 .../continuous/dynamic/moo/fda1/FDA1_g.java        |    4 +-
 .../continuous/dynamic/moo/fda2/FDA2_h.java        |    4 +-
 .../discrete/LongestCommonSubsequence.java         |    8 +-
 .../games/random/FixedListSeedingStrategy.java     |    4 +-
 .../games/random/RandomListSeedingStrategy.java    |    4 +-
 .../cilib/measurement/generic/Iterations.java      |    3 +-
 .../measurement/generic/PercentageComplete.java    |    4 +-
 .../measurement/multiple/MultipleFitness.java      |    3 +-
 .../measurement/multiple/MultipleSolutions.java    |    3 +-
 .../measurement/single/ConvergedDimensions.java    |    1 -
 .../measurement/single/FitnessEvaluations.java     |    1 +
 .../AverageDiversityAroundAllEntities.java         |    5 +-
 .../GBestCenterInitialisationStrategy.java         |    4 +-
 .../SpatialCenterInitialisationStrategy.java       |    4 +-
 .../normalisation/TopologyBasedNormalisation.java  |    5 +-
 .../ArchivingIterationStrategy.java                |    3 +-
 .../foundation/EvaluationMediator.java             |    4 +-
 .../foundation/measurements/NNOutput.java          |    3 +-
 .../postSimulation/PostMeasurementSuite.java       |    4 +-
 .../FFNNEvaluationMediator.java                    |    3 +-
 .../SAILAEvaluationMediator.java                   |    3 +-
 .../IterationBasedChangeStrategy.java              |    4 +-
 ...CoevolutionGameLearningOptimizationProblem.java |    5 +-
 .../pso/dynamic/ChargedVelocityUpdateStrategy.java |    4 +-
 .../ArchiveReevaluationResponseStrategy.java       |    4 +-
 ...lutionParticleReevaluationResponseStrategy.java |    4 +-
 .../VEPSOGuideSelectionStrategy.java               |    4 +-
 .../DominantGuideUpdateStrategy.java               |    3 +-
 .../cilib/pso/particle/MultiObjectiveParticle.java |    4 +-
 .../DEPositionUpdateStrategy.java                  |    4 +-
 .../BareBonesDEVelocityUpdate.java                 |    4 +-
 .../CoherenceVelocityUpdate.java                   |    4 +-
 .../FDRVelocityUpdateStrategy.java                 |    6 +-
 .../FIPSVelocityUpdate.java                        |    4 +-
 .../GCVelocityUpdateStrategy.java                  |    6 +-
 .../sourceforge/cilib/simulator/Simulation.java    |    5 +-
 .../net/sourceforge/cilib/simulator/Simulator.java |    5 +-
 .../cilib/stoppingcondition/MinimumDiversity.java  |    3 +-
 .../sourceforge/cilib/util/ClusteringUtils.java    |    3 +-
 .../calculator/EntityBasedFitnessCalculator.java   |    3 +-
 .../calculator/PropertyBasedFitnessCalculator.java |    3 +-
 .../StructuredTypeFitnessCalculator.java           |    3 +-
 .../recipes/RingBasedPopulationSelection.java      |    4 +-
 .../cilib/algorithm/GenericAlgorithmTest.java      |   10 +-
 62 files changed, 146 insertions(+), 457 deletions(-)
 copy src/main/java/net/sourceforge/cilib/algorithm/{Algorithm.java => AbstractAlgorithm.java} (97%)

diff --git a/src/main/java/net/sourceforge/cilib/algorithm/Algorithm.java b/src/main/java/net/sourceforge/cilib/algorithm/AbstractAlgorithm.java
similarity index 97%
copy from src/main/java/net/sourceforge/cilib/algorithm/Algorithm.java
copy to src/main/java/net/sourceforge/cilib/algorithm/AbstractAlgorithm.java
index dd307f4..80d0784 100644
--- a/src/main/java/net/sourceforge/cilib/algorithm/Algorithm.java
+++ b/src/main/java/net/sourceforge/cilib/algorithm/AbstractAlgorithm.java
@@ -27,7 +27,6 @@ import java.util.List;
 import net.sourceforge.cilib.problem.OptimisationProblem;
 import net.sourceforge.cilib.problem.OptimisationSolution;
 import net.sourceforge.cilib.stoppingcondition.StoppingCondition;
-import net.sourceforge.cilib.util.Cloneable;
 
 /**
  * <p>
@@ -40,7 +39,7 @@ import net.sourceforge.cilib.util.Cloneable;
  * </p>
  * @author Edwin Peer
  */
-public abstract class Algorithm implements Cloneable, Runnable {
+public abstract class AbstractAlgorithm implements Algorithm, Runnable {
     private static final long serialVersionUID = 7197544770653732632L;
     private List<StoppingCondition> stoppingConditions;
     private List<AlgorithmListener> algorithmListeners;
@@ -68,7 +67,7 @@ public abstract class Algorithm implements Cloneable, Runnable {
      * for the instance and initialises the needed containers needed for the different
      * {@linkplain AlgorithmEvent}s that are generated.
      */
-    protected Algorithm() {
+    protected AbstractAlgorithm() {
         stoppingConditions = new ArrayList<StoppingCondition>();
         algorithmListeners = new ArrayList<AlgorithmListener>();
 
@@ -80,7 +79,7 @@ public abstract class Algorithm implements Cloneable, Runnable {
      * Copy constructor. Create a deep copy of the provided instance and return it.
      * @param copy The instance to copy.
      */
-    protected Algorithm(Algorithm copy) {
+    protected AbstractAlgorithm(AbstractAlgorithm copy) {
         stoppingConditions = new ArrayList<StoppingCondition>();
         for (StoppingCondition stoppingCondition : copy.stoppingConditions) {
             StoppingCondition clone = stoppingCondition.getClone();
@@ -104,7 +103,7 @@ public abstract class Algorithm implements Cloneable, Runnable {
      * {@inheritDoc}
      */
     @Override
-    public abstract Algorithm getClone();
+    public abstract AbstractAlgorithm getClone();
 
 
     /**
@@ -280,8 +279,8 @@ public abstract class Algorithm implements Cloneable, Runnable {
      * Accessor for the top-level currently executing algorithm running in the current thread.
      * @return the instance of the algorithm that is running in the current thread.
      */
-    public static Algorithm get() {
-        return currentAlgorithmStack.get().peek();
+    public static AbstractAlgorithm get() {
+        return (AbstractAlgorithm) currentAlgorithmStack.get().peek();
     }
 
     /**
diff --git a/src/main/java/net/sourceforge/cilib/algorithm/Algorithm.java b/src/main/java/net/sourceforge/cilib/algorithm/Algorithm.java
index dd307f4..d49e5d2 100644
--- a/src/main/java/net/sourceforge/cilib/algorithm/Algorithm.java
+++ b/src/main/java/net/sourceforge/cilib/algorithm/Algorithm.java
@@ -21,358 +21,40 @@
  */
 package net.sourceforge.cilib.algorithm;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import net.sourceforge.cilib.problem.OptimisationProblem;
 import net.sourceforge.cilib.problem.OptimisationSolution;
-import net.sourceforge.cilib.stoppingcondition.StoppingCondition;
 import net.sourceforge.cilib.util.Cloneable;
 
 /**
- * <p>
- * All algorithms in CIlib should be subclasses of <code>Algorithm</code>. This class handles
- * stopping criteria, events, threading and measurements. Subclasses of <code>Algorithm</code>
- * must provide an implementation for <code>protected abstract void performIteration()</code>. If
- * a subclass overrides {@link #initialise()} then it must call <code>super.initialise()</code>.
- * Failure to do so will cause an {@linkplain InitialisationException} to be thrown when {@link #run()}
- * is called.
- * </p>
- * @author Edwin Peer
+ *
  */
-public abstract class Algorithm implements Cloneable, Runnable {
-    private static final long serialVersionUID = 7197544770653732632L;
-    private List<StoppingCondition> stoppingConditions;
-    private List<AlgorithmListener> algorithmListeners;
-    private int iterations;
-    private volatile boolean running;
-    private boolean initialised;
-
-    protected OptimisationProblem optimisationProblem;
-
-    /**
-     * This {@linkplain ThreadLocal} variable maintains the stack of the currently
-     * executing algorithm. It is defined as a static member and as a result is not
-     * required to be marked as transient as static members are not allowed to be
-     * serializable according to the Java Specification.
-     */
-    private static ThreadLocal<AlgorithmStack> currentAlgorithmStack = new ThreadLocal<AlgorithmStack>() {
-        @Override
-        protected AlgorithmStack initialValue() {
-            return new AlgorithmStack();
-        }
-    };
-
-    /**
-     * Default constructor for {@linkplain Algorithm} classes. Sets up the correct state
-     * for the instance and initialises the needed containers needed for the different
-     * {@linkplain AlgorithmEvent}s that are generated.
-     */
-    protected Algorithm() {
-        stoppingConditions = new ArrayList<StoppingCondition>();
-        algorithmListeners = new ArrayList<AlgorithmListener>();
-
-        running = false;
-        initialised = false;
-    }
-
-    /**
-     * Copy constructor. Create a deep copy of the provided instance and return it.
-     * @param copy The instance to copy.
-     */
-    protected Algorithm(Algorithm copy) {
-        stoppingConditions = new ArrayList<StoppingCondition>();
-        for (StoppingCondition stoppingCondition : copy.stoppingConditions) {
-            StoppingCondition clone = stoppingCondition.getClone();
-            clone.setAlgorithm(this);
-            stoppingConditions.add(clone);
-        }
-
-        algorithmListeners = new ArrayList<AlgorithmListener>();
-        for (AlgorithmListener listen : copy.algorithmListeners) {
-            algorithmListeners.add(listen.getClone());
-        }
-
-        running = false;
-        initialised = false;
-
-        if (copy.optimisationProblem != null)
-            optimisationProblem = copy.optimisationProblem.getClone();
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    @Override
-    public abstract Algorithm getClone();
-
-
-    /**
-     * Reset the {@linkplain Algorithm} internals if needed.
-     */
-    public void reset() {
-         throw new UnsupportedOperationException("'reset()' method not implemented for '" + this.getClass().getName() + "'");
-    }
-
-    /**
-     * Initialises the algorithm. Must be called before {@link #run()} is called.
-     */
-    public final void initialise() {
-        iterations = 0;
-        running = true;
-        initialised = true;
-
-        if (stoppingConditions.isEmpty())
-            throw new InitialisationException("No stopping conditions specified");
-
-        for (StoppingCondition stoppingCondition : stoppingConditions)
-            stoppingCondition.setAlgorithm(this);
-
-        currentAlgorithmStack.get().push(this);
-        performInitialisation();
-        currentAlgorithmStack.get().pop();
-    }
-
-    /**
-     * Perform the actions of the current {@linkplain Algorithm} for a single iteration. This
-     * method calls {@linkplain Algorithm#algorithmIteration()} after it performs some
-     * internal tasks by maintaining the stack of the currently executing algorithm instances.
-     */
-    public final void performIteration() {
-        currentAlgorithmStack.get().push(this);
-        algorithmIteration();
-        iterations++;
-        currentAlgorithmStack.get().pop();
-    }
-
-    /**
-     * The actual operations that the current {@linkplain Algorithm} performs within a single
-     * iteration.
-     */
-    protected abstract void algorithmIteration();
-
-    /**
-     * Perform the needed initialisation required before the execution of the algorithm
-     * starts.
-     */
-    public void performInitialisation() {
-        // subclasses can override the behaviour for this method
-    }
-
-    /**
-     * Perform the needed unintialisation steps after the algorithm completes it's
-     * execution.
-     */
-    public void performUninitialisation() {
-        // subclasses can override the behaviour for this method
-    }
-
-    /**
-     * Executes the algorithm.
-     * @exception InitialisationException algorithm was not properly initialised.
-     */
-    @Override
-    public void run() {
-        if (!initialised) {
-            throw new InitialisationException("Algorithm not initialised");
-        }
-
-        fireAlgorithmStarted();
-
-        currentAlgorithmStack.get().push(this);
-
-        while (running && (!isFinished())) {
-            performIteration();
-            fireIterationCompleted();
-        }
+public interface Algorithm extends Cloneable {
 
-        if (running) {
-            fireAlgorithmFinished();
-        }
-        else {
-            fireAlgorithmTerminated();
-        }
+    public OptimisationSolution getBestSolution();
 
-        performUninitialisation();
+    public void performIteration();
 
-        currentAlgorithmStack.remove();
-    }
-
-    /**
-     * Adds a stopping condition.
-     * @param stoppingCondition A {@link net.sourceforge.cilib.stoppingcondition.StoppingCondition}
-     *        to be added.
-     */
-    public final void addStoppingCondition(StoppingCondition stoppingCondition) {
-        stoppingConditions.add(stoppingCondition);
-    }
-
-    /**
-     * Removes a stopping condition.
-     * @param stoppingCondition The {@link net.sourceforge.cilib.stoppingcondition.StoppingCondition}
-     *        to be removed.
-     */
-    public final void removeStoppingCondition(StoppingCondition stoppingCondition) {
-        stoppingConditions.remove(stoppingCondition);
-    }
-
-    /**
-     * Adds an algorithm event listener. Event listeners are notified at various stages during the
-     * execution of an algorithm.
-     * @param listener An {@link AlgorithmListener} to be added.
-     */
-    public final void addAlgorithmListener(AlgorithmListener listener) {
-        algorithmListeners.add(listener);
-    }
-
-    /**
-     * Removes an algorithm event listener.
-     * @param listener The {@link AlgorithmListener} to be removed.
-     */
-    public final void removeAlgorithmListener(AlgorithmListener listener) {
-        algorithmListeners.remove(listener);
-    }
-
-    /**
-     * Returns the number of iterations that have been performed by the algorihtm.
-     * @return The number of iterations.
-     */
-    public final int getIterations() {
-        return iterations;
-    }
-
-    /**
-     * Returns the percentage the algorithm is from completed (as a fraction). The percentage
-     * complete is calculated based on the stopping condition that is closest to finished.
-     * @return The percentage complete as a fraction.
+     /**
+     * Not Needed>??>????????????
      */
-    public final double getPercentageComplete() {
-        double percentageComplete = 0;
-        for (StoppingCondition condition : stoppingConditions) {
-            if (condition.getPercentageCompleted() > percentageComplete) {
-                percentageComplete = condition.getPercentageCompleted();
-            }
-        }
-        return percentageComplete;
-    }
+    public void performInitialisation();
 
-    /**
-     * Returns true if the algorithm has finished executing.
-     * @return true if the algorithm is finished
+     /**
+     * Not Needed>??>????????????
      */
-    public final boolean isFinished() {
-        for (StoppingCondition condition : stoppingConditions) {
-            if (condition.isCompleted()) {
-                return true;
-            }
-        }
-        return false;
-    }
+    public void performUninitialisation();
 
-    /**
-     * Terminates the algorithm.
-     */
-    public final void terminate() {
-        running = false;
-    }
+    public Iterable<OptimisationSolution> getSolutions();
 
-    /**
-     * Accessor for the top-level currently executing algorithm running in the current thread.
-     * @return the instance of the algorithm that is running in the current thread.
-     */
-    public static Algorithm get() {
-        return currentAlgorithmStack.get().peek();
-    }
+    public OptimisationProblem getOptimisationProblem();
 
     /**
-     * Static accessor to allow the current level of algorithm composition to be returned.
-     * @see AlgorithmStack#asList()
-     * @return An unmodifiable list of algorithms.
+     * ???? Not needed?
      */
-    public static List<Algorithm> getAlgorithmList() {
-        return currentAlgorithmStack.get().asList();
-    }
+    public void reset();
 
     /**
-     * Get the current list of {@linkplain StoppingCondition} instances that are
-     * associated with the current {@linkplain Algorithm}.
-     * @return The list of {@linkplain StoppingCondition} instances associated with
-     *         the current {@linkplain Algorithm}.
+     * Not Needed>??>????????????
      */
-    public List<StoppingCondition> getStoppingConditions() {
-        return this.stoppingConditions;
-    }
-
-    /**
-     * Fire the {@linkplain AlgorithmEvent} to indicate that the {@linkplain Algorithm}
-     * has started execution.
-     */
-    private void fireAlgorithmStarted() {
-        for (AlgorithmListener listener : algorithmListeners) {
-            listener.algorithmStarted(new AlgorithmEvent(this));
-        }
-    }
-
-    /**
-     * Fire the {@linkplain AlgorithmEvent} to indicate that the {@linkplain Algorithm}
-     * has finished execution.
-     */
-    private void fireAlgorithmFinished() {
-        for (AlgorithmListener listener : algorithmListeners) {
-            listener.algorithmFinished(new AlgorithmEvent(this));
-        }
-    }
-
-    /**
-     * Fire the {@linkplain AlgorithmEvent} to indicate that the {@linkplain Algorithm}
-     * has been terminated.
-     */
-    private void fireAlgorithmTerminated() {
-        for (AlgorithmListener listener : algorithmListeners) {
-            listener.algorithmTerminated(new AlgorithmEvent(this));
-        }
-    }
-
-    /**
-     * Fire the {@linkplain AlgorithmEvent} to indicate that the {@linkplain Algorithm}
-     * has completed an iteration.
-     */
-    private void fireIterationCompleted() {
-        for (AlgorithmListener listener : algorithmListeners) {
-            listener.iterationCompleted(new AlgorithmEvent(this));
-        }
-    }
-
-    /**
-     * Set the optimisation problem to be solved. By default, the problem is <code>null</code>.
-     * That is, it is necessary to set the optimisation problem before calling {@link #initialise()}.
-     * @param problem An implementation of the
-     *        {@link net.sourceforge.cilib.problem.OptimisationProblemAdapter} interface.
-     */
-    public void setOptimisationProblem(OptimisationProblem problem) {
-        this.optimisationProblem = problem;
-    }
-
-    /**
-     * Get the specified {@linkplain OptimisationProblem}.
-     * @return The specified {@linkplain OptimisationProblem}.
-     */
-    public OptimisationProblem getOptimisationProblem() {
-        return this.optimisationProblem;
-    }
-
-    /**
-     * Get the best current solution. This best solution is determined from the personal bests of the
-     * particles.
-     * @return The <code>OptimisationSolution</code> representing the best solution.
-     */
-    public abstract OptimisationSolution getBestSolution();
-
-    /**
-     * Get the collection of best solutions. This result does not actually make sense in the normal
-     * PSO algorithm, but rather in a MultiObjective optimization.
-     * @return The <code>Collection&lt;OptimisationSolution&gt;</code> containing the solutions.
-     */
-    public abstract List<OptimisationSolution> getSolutions();
-
+     public int getIterations();
 }
diff --git a/src/main/java/net/sourceforge/cilib/algorithm/MultistartOptimisationAlgorithm.java b/src/main/java/net/sourceforge/cilib/algorithm/MultistartOptimisationAlgorithm.java
index 8ef8f51..e875eb6 100644
--- a/src/main/java/net/sourceforge/cilib/algorithm/MultistartOptimisationAlgorithm.java
+++ b/src/main/java/net/sourceforge/cilib/algorithm/MultistartOptimisationAlgorithm.java
@@ -51,7 +51,7 @@ import net.sourceforge.cilib.type.types.Type;
  *
  * @author  Edwin Peer
  */
-public class MultistartOptimisationAlgorithm extends Algorithm implements ParticipatingAlgorithm {
+public class MultistartOptimisationAlgorithm extends AbstractAlgorithm implements ParticipatingAlgorithm {
     private static final long serialVersionUID = 1493525363256406120L;
 
     /** Creates a new instance of MultistartOptimisationAlgorithm. */
@@ -83,8 +83,8 @@ public class MultistartOptimisationAlgorithm extends Algorithm implements Partic
      * @param algorithm Any {@link OptimisationAlgorithm} that extends {@link Algorithm}.
      */
     public void setTargetAlgorithm(Algorithm algorithm) {
-        optimisationAlgorithm = algorithm;
-        this.algorithm = (Algorithm) algorithm;
+        optimisationAlgorithm = (AbstractAlgorithm) algorithm;
+        this.algorithm = (AbstractAlgorithm) algorithm;
         this.algorithm.addStoppingCondition(singleIteration);
     }
 
@@ -215,8 +215,8 @@ public class MultistartOptimisationAlgorithm extends Algorithm implements Partic
         return solutions;
     }
 
-    private Algorithm algorithm;
-    private Algorithm optimisationAlgorithm;
+    private AbstractAlgorithm algorithm;
+    private AbstractAlgorithm optimisationAlgorithm;
     private int restarts;
     private SingleIteration singleIteration;
     private MultistartProblemAdapter problem;
diff --git a/src/main/java/net/sourceforge/cilib/algorithm/SingularAlgorithm.java b/src/main/java/net/sourceforge/cilib/algorithm/SingularAlgorithm.java
index 195179e..166a1c9 100644
--- a/src/main/java/net/sourceforge/cilib/algorithm/SingularAlgorithm.java
+++ b/src/main/java/net/sourceforge/cilib/algorithm/SingularAlgorithm.java
@@ -28,7 +28,7 @@ package net.sourceforge.cilib.algorithm;
  * Examples of such algorithms will include <tt>KMeans</tt>, <tt>Gradient Decent</tt> etc.
  *
  */
-public abstract class SingularAlgorithm extends Algorithm {
+public abstract class SingularAlgorithm extends AbstractAlgorithm {
     private static final long serialVersionUID = 8524134633474124524L;
 
     /**
diff --git a/src/main/java/net/sourceforge/cilib/algorithm/population/PopulationBasedAlgorithm.java b/src/main/java/net/sourceforge/cilib/algorithm/population/PopulationBasedAlgorithm.java
index bb81271..e8f54c8 100644
--- a/src/main/java/net/sourceforge/cilib/algorithm/population/PopulationBasedAlgorithm.java
+++ b/src/main/java/net/sourceforge/cilib/algorithm/population/PopulationBasedAlgorithm.java
@@ -22,7 +22,7 @@
 package net.sourceforge.cilib.algorithm.population;
 
 import java.util.List;
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.initialisation.PopulationInitialisationStrategy;
 import net.sourceforge.cilib.entity.Entity;
 import net.sourceforge.cilib.entity.Topology;
@@ -33,7 +33,7 @@ import net.sourceforge.cilib.problem.OptimisationSolution;
  * Base class for all algorithms that manage a collection of
  * {@linkplain Entity entities} in some manner.
  */
-public abstract class PopulationBasedAlgorithm extends Algorithm {
+public abstract class PopulationBasedAlgorithm extends AbstractAlgorithm {
 
     protected PopulationBasedAlgorithm() {
     }
diff --git a/src/main/java/net/sourceforge/cilib/bioinf/rnaprediction/RNAAccuracyMeasurement.java b/src/main/java/net/sourceforge/cilib/bioinf/rnaprediction/RNAAccuracyMeasurement.java
index 8fe8fcf..05a701c 100644
--- a/src/main/java/net/sourceforge/cilib/bioinf/rnaprediction/RNAAccuracyMeasurement.java
+++ b/src/main/java/net/sourceforge/cilib/bioinf/rnaprediction/RNAAccuracyMeasurement.java
@@ -21,7 +21,6 @@
  */
 package net.sourceforge.cilib.bioinf.rnaprediction;
 
-import java.util.Collection;
 
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.measurement.Measurement;
@@ -47,7 +46,7 @@ public class RNAAccuracyMeasurement implements Measurement {
     }
 
     public Type getValue(Algorithm algorithm) {
-        Collection<OptimisationSolution> solutions = algorithm.getSolutions();
+        Iterable<OptimisationSolution> solutions = algorithm.getSolutions();
         StringBuilder sb = new StringBuilder();
         //Iterator i = solutions.iterator();
         for (OptimisationSolution solution : solutions) {
diff --git a/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/AlignmentVisualizer.java b/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/AlignmentVisualizer.java
index 364b91a..a449bd7 100644
--- a/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/AlignmentVisualizer.java
+++ b/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/AlignmentVisualizer.java
@@ -47,7 +47,7 @@ public class AlignmentVisualizer implements Measurement {
         String lineOfStars="";
         fullyMatchedColumnCounter = 0;
 
-        ArrayList<String> as = new ArrayList<String>(((AlignmentCreator) ((MSAProblem) algorithm.getOptimisationProblem()).getAlignmentCreator()).getAlignment());
+        ArrayList<String> as = new ArrayList<String>((((MSAProblem) algorithm.getOptimisationProblem()).getAlignmentCreator()).getAlignment());
 
         //checks for fully matched columns
         if (fullColumns) {
diff --git a/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/DesiredMaximizationFitness.java b/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/DesiredMaximizationFitness.java
index 11aa0c1..2e91123 100644
--- a/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/DesiredMaximizationFitness.java
+++ b/src/main/java/net/sourceforge/cilib/bioinf/sequencealignment/DesiredMaximizationFitness.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.bioinf.sequencealignment;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.stoppingcondition.StoppingCondition;
 
@@ -33,7 +34,7 @@ import net.sourceforge.cilib.stoppingcondition.StoppingCondition;
  */
 public class DesiredMaximizationFitness implements StoppingCondition {
     private static final long serialVersionUID = 6494553632698710933L;
-    private Algorithm algorithm;
+    private AbstractAlgorithm algorithm;
     private double desiredFitness;
     private int quitAnywayAfterIterations;
 
@@ -69,7 +70,7 @@ public class DesiredMaximizationFitness implements StoppingCondition {
     }
 
     public void setAlgorithm(Algorithm algorithm) {
-        this.algorithm = algorithm;
+        this.algorithm = (AbstractAlgorithm) algorithm;
     }
 
     public int getQuitAnywayAfterIterations() {
diff --git a/src/main/java/net/sourceforge/cilib/boa/bee/OnlookerBee.java b/src/main/java/net/sourceforge/cilib/boa/bee/OnlookerBee.java
index 15e3d02..56f614d 100644
--- a/src/main/java/net/sourceforge/cilib/boa/bee/OnlookerBee.java
+++ b/src/main/java/net/sourceforge/cilib/boa/bee/OnlookerBee.java
@@ -21,7 +21,7 @@
  */
 package net.sourceforge.cilib.boa.bee;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.boa.ABC;
 
 
@@ -68,7 +68,7 @@ public class OnlookerBee extends AbstractBee implements HoneyBee {
      */
     @Override
     public void updatePosition() {
-        ABC algorithm = (ABC) Algorithm.get();
+        ABC algorithm = (ABC) AbstractAlgorithm.get();
         HoneyBee target = targetSelectionStrategy.select(algorithm.getWorkerBees());
 
         while (target == this) {
diff --git a/src/main/java/net/sourceforge/cilib/boa/bee/WorkerBee.java b/src/main/java/net/sourceforge/cilib/boa/bee/WorkerBee.java
index 33339d8..479201f 100644
--- a/src/main/java/net/sourceforge/cilib/boa/bee/WorkerBee.java
+++ b/src/main/java/net/sourceforge/cilib/boa/bee/WorkerBee.java
@@ -21,7 +21,7 @@
  */
 package net.sourceforge.cilib.boa.bee;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.boa.ABC;
 import net.sourceforge.cilib.controlparameter.ConstantControlParameter;
 import net.sourceforge.cilib.controlparameter.ControlParameter;
@@ -67,7 +67,7 @@ public class WorkerBee extends AbstractBee implements HoneyBee {
      */
     @Override
     public void updatePosition() {
-        ABC algorithm = (ABC) Algorithm.get();
+        ABC algorithm = (ABC) AbstractAlgorithm.get();
         HoneyBee target = targetSelectionStrategy.select(algorithm.getWorkerBees());
 
         while (target == this) {
diff --git a/src/main/java/net/sourceforge/cilib/clustering/kmeans/KMeans.java b/src/main/java/net/sourceforge/cilib/clustering/kmeans/KMeans.java
index 8f85a73..7be5f1d 100644
--- a/src/main/java/net/sourceforge/cilib/clustering/kmeans/KMeans.java
+++ b/src/main/java/net/sourceforge/cilib/clustering/kmeans/KMeans.java
@@ -26,7 +26,6 @@ import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.algorithm.SingularAlgorithm;
 import net.sourceforge.cilib.math.Stats;
 import net.sourceforge.cilib.problem.OptimisationSolution;
@@ -85,7 +84,7 @@ public class KMeans extends SingularAlgorithm {
      * {@inheritDoc}
      */
     @Override
-    public Algorithm getClone() {
+    public KMeans getClone() {
         return new KMeans(this);
     }
 
diff --git a/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyDecreasingControlParameter.java b/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyDecreasingControlParameter.java
index 47db47c..1693b1e 100644
--- a/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyDecreasingControlParameter.java
+++ b/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyDecreasingControlParameter.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.controlparameter;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 
 /**
@@ -60,7 +61,7 @@ public class ExponentiallyDecreasingControlParameter extends BoundedControlParam
      */
     @Override
     public void update() {
-        double result = Math.exp((-1) * Algorithm.get().getPercentageComplete());
+        double result = Math.exp((-1) * AbstractAlgorithm.get().getPercentageComplete());
         this.parameter.setReal(result);
     }
 
diff --git a/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyIncreasingControlParameter.java b/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyIncreasingControlParameter.java
index d5a7dd1..43c15b7 100644
--- a/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyIncreasingControlParameter.java
+++ b/src/main/java/net/sourceforge/cilib/controlparameter/ExponentiallyIncreasingControlParameter.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.controlparameter;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 
 /**
@@ -60,7 +61,7 @@ public class ExponentiallyIncreasingControlParameter extends BoundedControlParam
      */
     @Override
     public void update() {
-        double result = Math.exp(Algorithm.get().getPercentageComplete() - 1);
+        double result = Math.exp(AbstractAlgorithm.get().getPercentageComplete() - 1);
         this.parameter.setReal(result);
     }
 
diff --git a/src/main/java/net/sourceforge/cilib/controlparameter/LinearDecreasingControlParameter.java b/src/main/java/net/sourceforge/cilib/controlparameter/LinearDecreasingControlParameter.java
index 84fc6d5..190ca5c 100644
--- a/src/main/java/net/sourceforge/cilib/controlparameter/LinearDecreasingControlParameter.java
+++ b/src/main/java/net/sourceforge/cilib/controlparameter/LinearDecreasingControlParameter.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.controlparameter;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 
 /**
@@ -60,7 +61,7 @@ public class LinearDecreasingControlParameter extends BoundedControlParameter {
      * {@inheritDoc}
      */
     public void update() {
-        double result = getUpperBound() - (getUpperBound() - getLowerBound()) * Algorithm.get().getPercentageComplete();
+        double result = getUpperBound() - (getUpperBound() - getLowerBound()) * AbstractAlgorithm.get().getPercentageComplete();
         parameter.setReal(result);
     }
 
diff --git a/src/main/java/net/sourceforge/cilib/controlparameter/LinearIncreasingControlParameter.java b/src/main/java/net/sourceforge/cilib/controlparameter/LinearIncreasingControlParameter.java
index cf18d0b..3f3fb5e 100644
--- a/src/main/java/net/sourceforge/cilib/controlparameter/LinearIncreasingControlParameter.java
+++ b/src/main/java/net/sourceforge/cilib/controlparameter/LinearIncreasingControlParameter.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.controlparameter;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 
 /**
@@ -62,7 +63,7 @@ public class LinearIncreasingControlParameter extends BoundedControlParameter {
      * The update is done in an increasing manner.
      */
     public void update() {
-        double result = getLowerBound() + (getUpperBound() - getLowerBound()) * Algorithm.get().getPercentageComplete();
+        double result = getLowerBound() + (getUpperBound() - getLowerBound()) * AbstractAlgorithm.get().getPercentageComplete();
         parameter.setReal(result);
     }
 
diff --git a/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/ImperfectSplitStrategy.java b/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/ImperfectSplitStrategy.java
index 48a2b17..c27b197 100644
--- a/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/ImperfectSplitStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/ImperfectSplitStrategy.java
@@ -23,7 +23,6 @@ package net.sourceforge.cilib.cooperative.splitstrategies;
 
 import java.util.List;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.algorithm.InitialisationException;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
 import net.sourceforge.cilib.cooperative.CooperativeEntity;
@@ -54,7 +53,7 @@ public class ImperfectSplitStrategy extends IndexedSplitStrategy {
         int offset = 0;
 
         if (remainder == 0) {
-            for (Algorithm population : populations) {
+            for (PopulationBasedAlgorithm population : populations) {
                 population.setOptimisationProblem(new CooperativeOptimisationProblemAdapter(problem, context, splitSize, offset));
                 offset += splitSize;
             }
@@ -75,7 +74,7 @@ public class ImperfectSplitStrategy extends IndexedSplitStrategy {
             }
 
             for (int i = 0; i < populations.size(); ++i) {
-                Algorithm population = (Algorithm) populations.get(i);
+                PopulationBasedAlgorithm population = populations.get(i);
                 offset = indices.get(i);
                 int dimension;
                 if ((i + 1) < indices.size())
@@ -83,7 +82,7 @@ public class ImperfectSplitStrategy extends IndexedSplitStrategy {
                 else
                     dimension = problem.getDomain().getDimension() - indices.get(i);
                 // TODO check whether this cast is safe
-                ((Algorithm) population).setOptimisationProblem(new CooperativeOptimisationProblemAdapter(problem, context, dimension, offset));
+                population.setOptimisationProblem(new CooperativeOptimisationProblemAdapter(problem, context, dimension, offset));
             }
         }
     }
diff --git a/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/IndexedSplitStrategy.java b/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/IndexedSplitStrategy.java
index 228d402..a5ab93c 100644
--- a/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/IndexedSplitStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/IndexedSplitStrategy.java
@@ -24,7 +24,6 @@ package net.sourceforge.cilib.cooperative.splitstrategies;
 import java.util.ArrayList;
 import java.util.List;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.algorithm.InitialisationException;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
 import net.sourceforge.cilib.cooperative.CooperativeEntity;
@@ -67,7 +66,7 @@ public class IndexedSplitStrategy implements SplitStrategy {
             throw new InitialisationException("Problem dimensionality should be equal to or greater than the number of cooperating populations.");
 
         for (int i = 0; i < populations.size(); ++i) {
-            Algorithm population = (Algorithm) populations.get(i);
+            PopulationBasedAlgorithm population = populations.get(i);
             int offset = indices.get(i);
             int dimension;
             if ((i + 1) < indices.size())
@@ -75,7 +74,7 @@ public class IndexedSplitStrategy implements SplitStrategy {
             else
                 dimension = problem.getDomain().getDimension() - indices.get(i);
             // TODO check whether this cast is safe
-            ((Algorithm) population).setOptimisationProblem(new CooperativeOptimisationProblemAdapter(problem, context, dimension, offset));
+            population.setOptimisationProblem(new CooperativeOptimisationProblemAdapter(problem, context, dimension, offset));
         }
     }
 }
diff --git a/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/PerfectSplitStrategy.java b/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/PerfectSplitStrategy.java
index 3e053a5..28c17c9 100644
--- a/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/PerfectSplitStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/cooperative/splitstrategies/PerfectSplitStrategy.java
@@ -23,7 +23,6 @@ package net.sourceforge.cilib.cooperative.splitstrategies;
 
 import java.util.List;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.algorithm.InitialisationException;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
 import net.sourceforge.cilib.cooperative.CooperativeEntity;
@@ -43,7 +42,7 @@ public class PerfectSplitStrategy implements SplitStrategy {
             throw new InitialisationException("A Problem with dimension " + problem.getDomain().getDimension() + " cannot be split into parts of equal size when using " + populations.size() + " populations");
         int dimension = problem.getDomain().getDimension() / populations.size();
         int offset = 0;
-        for (Algorithm population : populations) {
+        for (PopulationBasedAlgorithm population : populations) {
             // TODO check whether this cast is safe
             population.setOptimisationProblem(new CooperativeOptimisationProblemAdapter(problem, context, dimension, offset));
             offset += dimension;
diff --git a/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda1/FDA1_g.java b/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda1/FDA1_g.java
index b753f71..5e0ed80 100755
--- a/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda1/FDA1_g.java
+++ b/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda1/FDA1_g.java
@@ -21,7 +21,7 @@
  */
 package net.sourceforge.cilib.functions.continuous.dynamic.moo.fda1;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.functions.ContinuousFunction;
 import net.sourceforge.cilib.type.types.container.Vector;
 
@@ -130,7 +130,7 @@ public class FDA1_g extends ContinuousFunction {
      */
     @Override
     public Double evaluate(Vector input) {
-        this.tau = Algorithm.get().getIterations();
+        this.tau = AbstractAlgorithm.get().getIterations();
 
         double t = (1.0/(double)n_t)*Math.floor((double)this.tau/(double)this.tau_t);
         double G = Math.sin(0.5*Math.PI*t);
diff --git a/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda2/FDA2_h.java b/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda2/FDA2_h.java
index d949cb3..ba6f4e7 100755
--- a/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda2/FDA2_h.java
+++ b/src/main/java/net/sourceforge/cilib/functions/continuous/dynamic/moo/fda2/FDA2_h.java
@@ -21,7 +21,7 @@
  */
 package net.sourceforge.cilib.functions.continuous.dynamic.moo.fda2;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.functions.ContinuousFunction;
 import net.sourceforge.cilib.type.types.container.Vector;
 import net.sourceforge.cilib.problem.FunctionMinimisationProblem;
@@ -209,7 +209,7 @@ public class FDA2_h extends ContinuousFunction {
      */
     @Override
     public Double evaluate(Vector input) {
-        this.tau = Algorithm.get().getIterations();
+        this.tau = AbstractAlgorithm.get().getIterations();
 
         double t = (1.0/(double)n_t)*Math.floor((double)this.tau/(double)this.tau_t);
         double H = 0.75 + 0.7*(Math.sin(0.5*Math.PI*t));
diff --git a/src/main/java/net/sourceforge/cilib/functions/discrete/LongestCommonSubsequence.java b/src/main/java/net/sourceforge/cilib/functions/discrete/LongestCommonSubsequence.java
index 7e9b33a..3707e7e 100644
--- a/src/main/java/net/sourceforge/cilib/functions/discrete/LongestCommonSubsequence.java
+++ b/src/main/java/net/sourceforge/cilib/functions/discrete/LongestCommonSubsequence.java
@@ -22,7 +22,7 @@
 package net.sourceforge.cilib.functions.discrete;
 
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
 import net.sourceforge.cilib.functions.DiscreteFunction;
 import net.sourceforge.cilib.problem.OptimisationProblem;
@@ -76,7 +76,7 @@ public class LongestCommonSubsequence extends DiscreteFunction {
      * @return The shortest length
      */
     private String getShortestString() {
-        PopulationBasedAlgorithm popAlgorithm = (PopulationBasedAlgorithm) Algorithm.get();
+        PopulationBasedAlgorithm popAlgorithm = (PopulationBasedAlgorithm) AbstractAlgorithm.get();
         OptimisationProblem problem = popAlgorithm.getOptimisationProblem();
         TextDataSetBuilder dataSetBuilder = (TextDataSetBuilder) problem.getDataSetBuilder();
 
@@ -84,7 +84,7 @@ public class LongestCommonSubsequence extends DiscreteFunction {
     }
 
     private int getDataSetSize() {
-        PopulationBasedAlgorithm popAlgorithm = (PopulationBasedAlgorithm) Algorithm.get();
+        PopulationBasedAlgorithm popAlgorithm = (PopulationBasedAlgorithm) AbstractAlgorithm.get();
         OptimisationProblem problem = popAlgorithm.getOptimisationProblem();
         TextDataSetBuilder dataSetBuilder = (TextDataSetBuilder) problem.getDataSetBuilder();
 
@@ -110,7 +110,7 @@ public class LongestCommonSubsequence extends DiscreteFunction {
 
 
     private int matches(Vector x) {
-        PopulationBasedAlgorithm popAlgorithm = (PopulationBasedAlgorithm) Algorithm.get();
+        PopulationBasedAlgorithm popAlgorithm = (PopulationBasedAlgorithm) AbstractAlgorithm.get();
         OptimisationProblem problem = popAlgorithm.getOptimisationProblem();
         TextDataSetBuilder dataSetBuilder = (TextDataSetBuilder) problem.getDataSetBuilder();
 
diff --git a/src/main/java/net/sourceforge/cilib/games/random/FixedListSeedingStrategy.java b/src/main/java/net/sourceforge/cilib/games/random/FixedListSeedingStrategy.java
index fba7f5e..f85d7b3 100644
--- a/src/main/java/net/sourceforge/cilib/games/random/FixedListSeedingStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/games/random/FixedListSeedingStrategy.java
@@ -21,7 +21,7 @@
  */
 package net.sourceforge.cilib.games.random;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 
 /**
  * This class is similar to the {@linkplain ListSeedingStrategy} but differs in the following way.
@@ -79,7 +79,7 @@ public class FixedListSeedingStrategy extends RandomListSeedingStrategy {
         if(index >= maxIndex)
             index = minIndex;
         //index changes with algorithm iterations
-        int currentIteration = Algorithm.get().getIterations();
+        int currentIteration = AbstractAlgorithm.get().getIterations();
         if (currentIteration != changeIteration && currentIteration  % iterationModulus == 0) {
             changeIteration = currentIteration;
             minIndex += useCount;
diff --git a/src/main/java/net/sourceforge/cilib/games/random/RandomListSeedingStrategy.java b/src/main/java/net/sourceforge/cilib/games/random/RandomListSeedingStrategy.java
index a55c9bc..ff767bf 100644
--- a/src/main/java/net/sourceforge/cilib/games/random/RandomListSeedingStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/games/random/RandomListSeedingStrategy.java
@@ -23,7 +23,7 @@ package net.sourceforge.cilib.games.random;
 
 import java.util.ArrayList;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.math.random.generator.Seeder;
 
 /**
@@ -66,7 +66,7 @@ public class RandomListSeedingStrategy extends ListSeedingStrategy {
      * Check if the seed list needs to be randomised. If so, generate a new list of seeds
      */
     protected void updateSeed(){
-        int currentIteration = Algorithm.get().getIterations();
+        int currentIteration = AbstractAlgorithm.get().getIterations();
         if(currentIteration != changeIteration && currentIteration  % iterationModulus == 0){
             changeIteration = currentIteration;
             randomizeSeeds(seeds.size());
diff --git a/src/main/java/net/sourceforge/cilib/measurement/generic/Iterations.java b/src/main/java/net/sourceforge/cilib/measurement/generic/Iterations.java
index cb3d91c..e9eac18 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/generic/Iterations.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/generic/Iterations.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.measurement.generic;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.measurement.Measurement;
 import net.sourceforge.cilib.type.types.Int;
@@ -63,7 +64,7 @@ public class Iterations implements Measurement {
      */
     public Type getValue(Algorithm algorithm) {
         Int i = new Int();
-        i.setInt(algorithm.getIterations());
+        i.setInt(((AbstractAlgorithm)algorithm).getIterations());
 
         return i;
     }
diff --git a/src/main/java/net/sourceforge/cilib/measurement/generic/PercentageComplete.java b/src/main/java/net/sourceforge/cilib/measurement/generic/PercentageComplete.java
index 6871341..2d40451 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/generic/PercentageComplete.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/generic/PercentageComplete.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.measurement.generic;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.measurement.Measurement;
 import net.sourceforge.cilib.type.types.Real;
@@ -49,7 +50,8 @@ public class PercentageComplete implements Measurement {
     }
 
     public Type getValue(Algorithm algorithm) {
-        return new Real(algorithm.getPercentageComplete());
+        AbstractAlgorithm alg = (AbstractAlgorithm) algorithm;
+        return new Real(alg.getPercentageComplete());
     }
 
 }
diff --git a/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleFitness.java b/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleFitness.java
index ee03830..82dc010 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleFitness.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleFitness.java
@@ -21,7 +21,6 @@
  */
 package net.sourceforge.cilib.measurement.multiple;
 
-import java.util.Collection;
 
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.measurement.Measurement;
@@ -89,7 +88,7 @@ public class MultipleFitness implements Measurement {
         return fitnessValues.toArray();*/
 
         Vector fitnessValues = new Vector();
-        Collection<OptimisationSolution> solutions = algorithm.getSolutions();
+        Iterable<OptimisationSolution> solutions = algorithm.getSolutions();
 
         for (OptimisationSolution solution : solutions) {
             Double fitness = solution.getFitness().getValue();
diff --git a/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleSolutions.java b/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleSolutions.java
index 7eb41f7..f4de0ed 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleSolutions.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/multiple/MultipleSolutions.java
@@ -21,7 +21,6 @@
  */
 package net.sourceforge.cilib.measurement.multiple;
 
-import java.util.List;
 
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.measurement.Measurement;
@@ -56,7 +55,7 @@ public class MultipleSolutions implements Measurement {
 
     public Type getValue(Algorithm algorithm) {
         Vector v = new Vector();
-        List<OptimisationSolution> solutions = algorithm.getSolutions();
+        Iterable<OptimisationSolution> solutions = algorithm.getSolutions();
 
         for (OptimisationSolution solution : solutions) {
             v.append((Vector) solution.getPosition());
diff --git a/src/main/java/net/sourceforge/cilib/measurement/single/ConvergedDimensions.java b/src/main/java/net/sourceforge/cilib/measurement/single/ConvergedDimensions.java
index 1d56a41..80065fb 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/single/ConvergedDimensions.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/single/ConvergedDimensions.java
@@ -100,7 +100,6 @@ public class ConvergedDimensions implements Measurement {
      * @throws ParseException if the provided {@code String} cannot be parsed.
      */
     public void setTargetSolution(String stringRepresentation) throws ParseException {
-        System.out.println("Setting the target solition to: " + stringRepresentation);
         this.targetSolution = (Vector) DomainParser.parse(stringRepresentation);
     }
 
diff --git a/src/main/java/net/sourceforge/cilib/measurement/single/FitnessEvaluations.java b/src/main/java/net/sourceforge/cilib/measurement/single/FitnessEvaluations.java
index 336d09c..a2b0a2d 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/single/FitnessEvaluations.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/single/FitnessEvaluations.java
@@ -21,6 +21,7 @@
  */
 package net.sourceforge.cilib.measurement.single;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.measurement.Measurement;
 import net.sourceforge.cilib.type.types.Int;
diff --git a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/AverageDiversityAroundAllEntities.java b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/AverageDiversityAroundAllEntities.java
index 169c567..7c52288 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/AverageDiversityAroundAllEntities.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/AverageDiversityAroundAllEntities.java
@@ -23,7 +23,7 @@ package net.sourceforge.cilib.measurement.single.diversity;
 
 import java.util.Iterator;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
 import net.sourceforge.cilib.entity.Entity;
 import net.sourceforge.cilib.type.types.Real;
@@ -45,8 +45,7 @@ public class AverageDiversityAroundAllEntities extends Diversity {
      * {@inheritDoc}
      */
     public Type getValue() {
-
-        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) Algorithm.get();
+        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) AbstractAlgorithm.get();
         int numberOfEntities = algorithm.getTopology().size();
 
         Iterator<? extends Entity> populationCenterIterator = algorithm.getTopology().iterator();
diff --git a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/GBestCenterInitialisationStrategy.java b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/GBestCenterInitialisationStrategy.java
index 6e7cbf0..a4cb746 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/GBestCenterInitialisationStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/GBestCenterInitialisationStrategy.java
@@ -21,7 +21,7 @@
  */
 package net.sourceforge.cilib.measurement.single.diversity.centerinitialisationstrategies;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
 import net.sourceforge.cilib.type.types.container.Vector;
 
@@ -32,7 +32,7 @@ public class GBestCenterInitialisationStrategy extends CenterInitialisationStrat
 
     @Override
     public Vector getCenter() {
-        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) Algorithm.get();
+        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) AbstractAlgorithm.get();
 
         return (Vector) algorithm.getTopology().getBestEntity().getCandidateSolution();
     }
diff --git a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/SpatialCenterInitialisationStrategy.java b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/SpatialCenterInitialisationStrategy.java
index 8e92169..10074e8 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/SpatialCenterInitialisationStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/centerinitialisationstrategies/SpatialCenterInitialisationStrategy.java
@@ -23,7 +23,7 @@ package net.sourceforge.cilib.measurement.single.diversity.centerinitialisations
 
 import java.util.Iterator;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
 import net.sourceforge.cilib.entity.Entity;
 import net.sourceforge.cilib.type.types.container.Vector;
@@ -35,7 +35,7 @@ public class SpatialCenterInitialisationStrategy extends CenterInitialisationStr
 
     @Override
     public Vector getCenter() {
-        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) Algorithm.get();
+        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) AbstractAlgorithm.get();
         int numberOfEntities = algorithm.getTopology().size();//getPopulationSize();
 
         Iterator<? extends Entity> averageIterator = algorithm.getTopology().iterator();
diff --git a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/normalisation/TopologyBasedNormalisation.java b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/normalisation/TopologyBasedNormalisation.java
index 04981d0..5ebb10c 100644
--- a/src/main/java/net/sourceforge/cilib/measurement/single/diversity/normalisation/TopologyBasedNormalisation.java
+++ b/src/main/java/net/sourceforge/cilib/measurement/single/diversity/normalisation/TopologyBasedNormalisation.java
@@ -21,8 +21,9 @@
  */
 package net.sourceforge.cilib.measurement.single.diversity.normalisation;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
+import net.sourceforge.cilib.entity.Topology;
 import net.sourceforge.cilib.entity.visitor.DiameterVisitor;
 import net.sourceforge.cilib.entity.visitor.TopologyVisitor;
 
@@ -46,7 +47,7 @@ public class TopologyBasedNormalisation extends NormalisationParameter {
      */
     @Override
     public double getValue() {
-        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) Algorithm.get();
+        PopulationBasedAlgorithm algorithm = (PopulationBasedAlgorithm) AbstractAlgorithm.get();
         visitor.setDistanceMeasure(distanceMeasure);
         algorithm.accept(visitor);
         this.normalisationParameter = (Double) visitor.getResult();
diff --git a/src/main/java/net/sourceforge/cilib/moo/iterationstrategies/ArchivingIterationStrategy.java b/src/main/java/net/sourceforge/cilib/moo/iterationstrategies/ArchivingIterationStrategy.java
index 124747d..768b16c 100644
--- a/src/main/java/net/sourceforge/cilib/moo/iterationstrategies/ArchivingIterationStrategy.java
+++ b/src/main/java/net/sourceforge/cilib/moo/iterationstrategies/ArchivingIterationStrategy.java
@@ -24,6 +24,7 @@ package net.sourceforge.cilib.moo.iterationstrategies;
 import java.util.ArrayList;
 import java.util.List;
 
+import net.sourceforge.cilib.algorithm.AbstractAlgorithm;
 import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.algorithm.population.IterationStrategy;
 import net.sourceforge.cilib.algorithm.population.PopulationBasedAlgorithm;
@@ -72,7 +73,7 @@ public class ArchivingIterationStrategy<E extends PopulationBasedAlgorithm> impl
     }
 
     protected void updateArchive(Topology<? extends Entity> population) {
-        Algorithm topLevelAlgorithm = Algorithm.getAlgorithmList().get(0);
+        Algorithm topLevelAlgorithm = AbstractAlgorithm.getAlgorithmList().get(0);
         List<OptimisationSolution> optimisationSolutions = new ArrayList<OptimisationSolution>();
         for (Entity entity : population) {
             Type solution = entity.getCandidateSolution().getClone();
diff --git a/src/main/java/net/sourceforge/cilib/neuralnetwork/foundation/EvaluationMediator.java b/src/main/java/net/sourceforge/cilib/neuralnetwork/foundation/EvaluationMediator.java
index 6173f89..0ed61b1 100644
--- a/src/main/java/net/sourceforge/cilib/neuralnetwork/foundation/EvaluationMediator.java
+++ b/src/main/java/net/sourceforge/cilib/neuralnetwork/foundation/EvaluationMediator.java
@@ -24,13 +24,11 @@ package net.sourceforge.cilib.neuralnetwork.foundation;
 
 import java.util.List;
 
-import net.sourceforge.cilib.algorithm.Algorithm;
 import net.sourceforge.cilib.algorithm.SingularAlgorithm;
 import net.sourceforge.cilib.neuralnetwork.foundation.epochstrategy.EmptyEpochStrategy;
 import net.sourceforge.cilib.neuralnetwork.foundation.epochstrategy.EpochStrategy;
 import net.sourceforge.cilib.problem.OptimisationSolution;
 import net.sourceforge.cilib.type.types.container.TypeList;
-import net.sourceforge.cilib.type.types.container.Vector;
 
 
 
@@ -258,7 +256,7 @@ public class EvaluationMediator extends SingularAlgorithm {
     }
 
     @Override
-    public Al...
 
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