Cleanup: Remove the composite features from the phenotypes

* Reduce the Phenotypes to remove unused features.
* Remove the DebugUtils (not used anymore).
* Remove the getPhenotypeType method that became obsolete after
  migrating the DSE to Guice.

Issue-Ref: 3557
Issue-Url: https://af3-developer.fortiss.org/issues/3557


Signed-off-by: Alexander Diewald <diewald@fortiss.org>

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/comm/.ratings

-MessageEncoding.java 6a4bb9c487db5055ea263253e3e3247177476065 YELLOW
+MessageEncoding.java 3c04ebae651542778e45c7d47352fdc47e2439ee YELLOW

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/comm/MessageEncoding.java

@@ -21,7 +21,6 @@ import java.util.Collection;
 
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.TaskMappingEncoding;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.TaskMappingEntry;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.PhenotypeBase;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.IExecutionUnitAdapter;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.ISignalAdapter;
@@ -56,10 +55,4 @@ public class MessageEncoding<S extends TaskMappingEntry<ITaskAdapter<?>, IExecut
 		return filterSet(messages,
 				m -> m.getSignalAdapter().getSignalType() == ISignalAdapter.SignalType.PERIODIC);
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return MessageEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/partitionmapping/.ratings

 Partition.java 89cfb87a73d3ae080a9dbe5594b48ad552f7a9f1 RED
-PartitionMappingEncoding.java 95bf57d5cdeb40c37fdcfdd6a02e2ac96a6d9959 RED
+PartitionMappingEncoding.java 2d1af8dac3fa1e9cf4d94aae01bdd76057d22057 RED
 PartitionMappingEntry.java 3f413a060aad18e6ffb088b1a035ffb536e591cf YELLOW

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/partitionmapping/PartitionMappingEncoding.java

@@ -21,7 +21,6 @@ import java.util.List;
 import java.util.Map;
 
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.MappingEncoding;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.operator.copy.Copyable;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.IExecutionUnitAdapter;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.IResourceAdapter;
@@ -130,12 +129,6 @@ public class PartitionMappingEncoding extends
 		return new PartitionMappingEncoding();
 	}
 
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return getClass();
-	}
-
 	/** {@inheritDoc} */
 	@Override
 	public PartitionMappingEncoding copy() {

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/platform/.ratings

-PlatformCommunicationGraphEncoding.java c49bd0227357686cf929b782c7a714f1aab4c196 RED
+PlatformCommunicationGraphEncoding.java accc939c90f2d32c2507da2f4e8d20b0d7c5c158 YELLOW

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/platform/PlatformCommunicationGraphEncoding.java

@@ -16,7 +16,6 @@
 package org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.platform;
 
 import org.eclipse.draw2d.graph.DirectedGraph;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.PhenotypeBase;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.operator.copy.Copyable;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.IResourceAdapter;
@@ -78,12 +77,6 @@ public class PlatformCommunicationGraphEncoding extends PhenotypeBase
 		return new PlatformCommunicationGraphEncoding(platformGraph);
 	}
 
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return PlatformCommunicationGraphEncoding.class;
-	}
-
 	/** {@inheritDoc} */
 	@Override
 	public PlatformCommunicationGraphEncoding copy() {

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/safetyfunctionarch/.ratings

-SafetyFunctionArchEncoding.java 4a229eb97cf0a9aa22fb1f54b4a24190613aa6c3 YELLOW
+SafetyFunctionArchEncoding.java 007ad2ec378e37abef9865c9b7aa22f9d06fc168 YELLOW
 SafetyFunctionArchEntry.java 83b2819b2d749611aed25170e60eee11fc0edd2b RED

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/safetyfunctionarch/SafetyFunctionArchEncoding.java

@@ -26,7 +26,6 @@ import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.PhenotypeBase;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.operator.copy.Copyable;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.ISafetyFunctionAdapter;
@@ -168,10 +167,4 @@ public class SafetyFunctionArchEncoding extends PhenotypeBase
 	public String toString() {
 		return getAllEntries().toString();
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return SafetyFunctionArchEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskgraph/.ratings

-AbstractTaskGraphEncoding.java 70dcfb88d40b3e4e4aa19e2de470db705de0337e RED
-InstantiatedAcyclicTaskGraphEncoding.java 6c26aa4cca73a33c031c5cea6eab0d3efb197078 RED
-InstantiatedTaskGraphEncoding.java bfbad1a4bb3f984432688f281c7354b36fda607a RED
-SafeTaskGraphEncoding.java 31c8db24f2d41118b9d1341ceed7e7d931c0927a RED
+AbstractTaskGraphEncoding.java 4122c068748a41d609035d9a578df4e6b79bb148 RED
+InstantiatedAcyclicTaskGraphEncoding.java a82e3bd19abf5908c92d0524b02fd3d82c466889 YELLOW
+InstantiatedTaskGraphEncoding.java 820e6fe50893fcbd82e862ddfbfb11f8d6da95aa YELLOW
+SafeTaskGraphEncoding.java 1f0aff0d964d1c183dbe327dc7a1fe411c84314a YELLOW
 TaskGraphEncoding.java 80043ff18bfb4c196b040c533ce0c328977d4e1f RED

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskgraph/AbstractTaskGraphEncoding.java

@@ -17,7 +17,6 @@ package org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskgraph;
 
 import java.util.Set;
 
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.taskgraph.TaskGraph;
 
 import com.google.inject.Inject;
@@ -42,10 +41,4 @@ public class AbstractTaskGraphEncoding extends TaskGraphEncoding<TaskGraph> {
 	public AbstractTaskGraphEncoding(AbstractTaskGraphEncoding encoding) {
 		super(encoding);
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return AbstractTaskGraphEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskgraph/InstantiatedAcyclicTaskGraphEncoding.java

@@ -18,7 +18,6 @@ package org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskgraph;
 import java.util.Collection;
 
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.instantiatedmapping.InstantiatedTaskMappingEntry;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.taskgraph.AcyclicTaskGraph;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.taskgraph.TaskGraph;
 
@@ -42,10 +41,4 @@ public class InstantiatedAcyclicTaskGraphEncoding<T extends InstantiatedTaskMapp
 	public InstantiatedAcyclicTaskGraphEncoding(InstantiatedAcyclicTaskGraphEncoding<T> encoding) {
 		super(encoding);
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return InstantiatedAcyclicTaskGraphEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskgraph/InstantiatedTaskGraphEncoding.java

@@ -18,7 +18,6 @@ package org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskgraph;
 import java.util.Collection;
 
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.instantiatedmapping.InstantiatedTaskMappingEntry;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.taskgraph.TaskGraph;
 
 /**
@@ -37,10 +36,4 @@ public class InstantiatedTaskGraphEncoding<T extends InstantiatedTaskMappingEntr
 	public InstantiatedTaskGraphEncoding(InstantiatedTaskGraphEncoding<T> encoding) {
 		super(encoding);
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return InstantiatedTaskGraphEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskgraph/SafeTaskGraphEncoding.java

@@ -19,7 +19,6 @@ import java.util.Collection;
 import java.util.Set;
 
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.safetyfunctionarch.SafetyFunctionArchEncoding;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.ITaskAdapter;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.taskgraph.TaskGraph;
 
@@ -56,10 +55,4 @@ public class SafeTaskGraphEncoding extends AbstractTaskGraphEncoding {
 		}
 		return null;
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return SafeTaskGraphEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskmapping/abstractmapping/.ratings

-AbstractTaskMappingEncoding.java 006baeeb60eecb28a20cdd5b2d894dae44fdf758 YELLOW
+AbstractTaskMappingEncoding.java e7b9f51e9839e87488f845b33784fceeb8d56722 YELLOW
 AbstractTaskMappingEntry.java b1beede941a2bcd43ff514fbd1347f6f7fefd2b1 YELLOW

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskmapping/abstractmapping/AbstractTaskMappingEncoding.java

@@ -24,7 +24,6 @@ import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskgraph.Safe
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskgraph.TaskGraphEncoding;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.TaskMappingEncoding;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.TaskMappingEntry;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.IExecutionUnitAdapter;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.ITaskAdapter;
 import org.fortiss.af3.exploration.alg.exception.ExplorationException;
@@ -135,10 +134,4 @@ public class AbstractTaskMappingEncoding
 		clonedEncoding.getRequesters().forEach(c -> c.updateInstatiationData());
 		return clonedEncoding;
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return AbstractTaskMappingEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskmapping/instantiatedmapping/.ratings

@@ -2,5 +2,5 @@ FailSilentTaskMappingEncoding.java a35383d317862a9876baf4296ad2371c75c36e88 RED
 FailSilentTaskMappingEntry.java 93c2deb62b39860893e94729b85844fe38e90e17 RED
 FaultDetectionVotingTaskMappingEncoding.java 118ff5f99f6a2f734ddd2b3f1ac44d013c6167be RED
 FaultDetectionVotingTaskMappingEntry.java 932d37aa71e912be4e6b29e44911ebc48f6fe697 RED
-InstantiatedTaskMappingEncoding.java 1dcb81896275bec4b5d1d7d12b063cf4cbc8bbc8 RED
+InstantiatedTaskMappingEncoding.java e1c037b489d9b7357b59e267a634bb43eb33335b RED
 InstantiatedTaskMappingEntry.java 101b9eefe449e73c6fff89cb76574ca14c93d33f RED

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/encoding/taskmapping/instantiatedmapping/InstantiatedTaskMappingEncoding.java

@@ -22,7 +22,6 @@ import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskgraph.Task
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.TaskMappingEncoding;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.abstractmapping.AbstractTaskMappingEncoding;
 import org.fortiss.af3.exploration.alg.dse.backend.opt4j.encoding.taskmapping.abstractmapping.AbstractTaskMappingEntry;
-import org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype.Phenotype;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.IExecutionUnitAdapter;
 import org.fortiss.af3.exploration.alg.dse.sysmodel.arch.ITaskAdapter;
 import org.fortiss.af3.exploration.alg.exception.ExplorationException;
@@ -102,10 +101,4 @@ public abstract class InstantiatedTaskMappingEncoding<T extends InstantiatedTask
 		}
 		return super.getDisAllowedAllocations(deployableComponent);
 	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		return InstantiatedTaskMappingEncoding.class;
-	}
 }

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/extensions/compositegene/phenotype/.ratings

-FlatPhenotypeMap.java f29317abac6af034248a1b24dd95a0a330e202ec RED
-Phenotype.java f23b94b0ee54fbf3a685ebeebccad4abd6c12b91 RED
-PhenotypeBase.java f0357666cdda6cfbe0877fdc5b397366f8e504c4 RED
+Phenotype.java f05a45ea3b3577079b4f894aa97af1ab3620c5e7 YELLOW
+PhenotypeBase.java 73397a01276ccf72c1569bfa577e9fd3f5874324 YELLOW
 ProvidingPhenotype.java b18a8385e97c98f83219daa508d156ac57ba365b RED

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/extensions/compositegene/phenotype/Phenotype.java

@@ -15,12 +15,6 @@
 +--------------------------------------------------------------------------*/
 package org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype;
 
-import java.util.List;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.fortiss.af3.exploration.alg.service.IExplorationEncoding;
-import org.opt4j.core.Genotype;
 import org.opt4j.core.genotype.CompositeGenotype;
 
 /**
@@ -29,33 +23,7 @@ import org.opt4j.core.genotype.CompositeGenotype;
  * 
  * @author diewald
  */
-public interface Phenotype
-		extends IExplorationEncoding, Iterable<Entry<Class<? extends Phenotype>, Phenotype>> {
-
-	/**
-	 * Returns the type which shall be used to register the {@link Phenotype} at its
-	 * containing {@link Phenotype}.
-	 */
-	Class<? extends Phenotype> getPTypeToRegister();
-
-	/**
-	 * Returns the {@link Phenotype} that corresponds to the given {@link Phenotype} class.
-	 */
-	<CP extends Phenotype> CP getSubPhenotype(Class<CP> subPhenotype);
-
-	/**
-	 * Defines a correspondence between a {@link Genotype} class and its {@link Phenotype}
-	 * .
-	 */
-	<CP extends Phenotype> void putSubPhenotype(Class<CP> subGenotype, CP curPhenotype);
-
-	/**
-	 * Returns the collection of {@link Phenotype}s that make up this {@link Genotype}.
-	 */
-	List<Phenotype> getSubPhenotypes();
-
-	/** Returns the Class -> {@link Phenotype} entries of the enclosed map. */
-	Set<Class<? extends Phenotype>> keySet();
+public interface Phenotype {
 
 	/** Marks a phenotype as being processed by sub-decoders. */
 	void setSubDecoding(boolean isSubDecoding);

org.fortiss.af3.exploration.alg/src/org/fortiss/af3/exploration/alg/dse/backend/opt4j/extensions/compositegene/phenotype/PhenotypeBase.java

@@ -15,14 +15,6 @@
 +--------------------------------------------------------------------------*/
 package org.fortiss.af3.exploration.alg.dse.backend.opt4j.extensions.compositegene.phenotype;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
 /**
  * Base class for {@link Phenotype}s which consists of {@link Phenotype}s.
  * 
@@ -30,55 +22,9 @@ import java.util.Set;
  */
 public class PhenotypeBase implements Phenotype {
 
-	/**
-	 * Map which correlates the {@link Phenotype} classes with their corresponding {@link Phenotype}
-	 * s, out of which this {@link Phenotype} consists.
-	 */
-	protected Map<Class<? extends Phenotype>, Phenotype> subPhenotypes = new HashMap<>();
-
 	/** Flag to mark a phenotype as being processed by sub-Decoders. */
 	private boolean isSubDecoding;
 
-	/** {@inheritDoc} */
-	@Override
-	public <CP extends Phenotype> CP getSubPhenotype(Class<CP> subGenotypeClass) {
-		return (CP)subPhenotypes.get(subGenotypeClass);
-	}
-
-	/** {@inheritDoc} */
-	@Override
-	public <CP extends Phenotype> void putSubPhenotype(Class<CP> subGenotypeClass,
-			CP subPhenotype) {
-		subPhenotypes.put(subGenotypeClass, subPhenotype);
-	}
-
-	/** {@inheritDoc} */
-	@Override
-	public List<Phenotype> getSubPhenotypes() {
-		ArrayList<Phenotype> retList = new ArrayList<>();
-		subPhenotypes.values().stream().forEachOrdered(p -> retList.add(p));
-		return retList;
-	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Iterator<Entry<Class<? extends Phenotype>, Phenotype>> iterator() {
-		return subPhenotypes.entrySet().iterator();
-	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Set<Class<? extends Phenotype>> keySet() {
-		return subPhenotypes.keySet();
-	}
-
-	/** {@inheritDoc} */
-	@Override
-	public Class<? extends Phenotype> getPTypeToRegister() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
 	/** {@inheritDoc} */
 	@Override
 	public void setSubDecoding(boolean isSubDecoding) {