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[cilib-devel] [PATCH 1/3] Refactor Algorithm to interface.
|
From: Gary P. <gpa...@gm...> - 2009-08-24 08:51:10
|
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<OptimisationSolution></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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