Change Set to LinkedHashSet, remove unused methods

5 files changed, 31 insertions, 66 deletions

diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/DesignSpaceExplorationBuilder.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/DesignSpaceExplorationBuilder.java
index 0ec6f599..58eac681 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/DesignSpaceExplorationBuilder.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/DesignSpaceExplorationBuilder.java
@@ -10,15 +10,6 @@ import java.util.Collection;
 import java.util.List;
 
 public interface DesignSpaceExplorationBuilder extends ModelAdapterBuilder {
-        default DesignSpaceExplorationBuilder stopConditions(AnyQuery... stopConditions) {
-                return stopConditions(List.of(stopConditions));
-        }
-
-        default DesignSpaceExplorationBuilder stopConditions(Collection<? extends AnyQuery> stopConditions) {
-                stopConditions.forEach(this::stopCondition);
-                return this;
-        }
-
         default DesignSpaceExplorationBuilder transformations(TransformationRule... transformationRules) {
                 return transformations(List.of(transformationRules));
         }
@@ -46,8 +37,6 @@ public interface DesignSpaceExplorationBuilder extends ModelAdapterBuilder {
                 return this;
         }
 
-        DesignSpaceExplorationBuilder stopCondition(AnyQuery stopCondition);
-
         DesignSpaceExplorationBuilder transformation(TransformationRule transformationRule);
         DesignSpaceExplorationBuilder globalConstraint(RelationalQuery globalConstraint);
         DesignSpaceExplorationBuilder objective(Objective objective);
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationAdapterImpl.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationAdapterImpl.java
index 0fcc719d..35f94dce 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationAdapterImpl.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationAdapterImpl.java
@@ -24,20 +24,19 @@ public class DesignSpaceExplorationAdapterImpl implements DesignSpaceExploration
         private final Model model;
         private final ModelQueryAdapter queryEngine;
         private final DesignSpaceExplorationStoreAdapterImpl storeAdapter;
-        private final Set<TransformationRule> transformationRules;
-        private final Set<RelationalQuery> globalConstraints;
+        private final LinkedHashSet<TransformationRule> transformationRules;
+        private final LinkedHashSet<RelationalQuery> globalConstraints;
         private final List<Objective> objectives;
-        private final Set<ResultSet<Boolean>> globalConstraintResultSets = new HashSet<>();
+        private final LinkedHashSet<ResultSet<Boolean>> globalConstraintResultSets = new LinkedHashSet<>();
         private final Interpretation<Integer> sizeInterpretation;
         private final Strategy strategy;
 
         private ObjectiveComparatorHelper objectiveComparatorHelper;
         private List<Long> trajectory = new LinkedList<>();
         private Fitness lastFitness;
-        private final Set<Long> solutions = new HashSet<>();
-//      private Map<Long, Collection<Activation>> statesAndActivations;
-        private Map<Long, Collection<Activation>> statesAndUntraversedActivations;
-        private Map<Long, Collection<Activation>> statesAndTraversedActivations;
+        private final LinkedHashSet<Long> solutions = new LinkedHashSet<>();
+        private Map<Long, LinkedHashSet<Activation>> statesAndUntraversedActivations;
+        private Map<Long, LinkedHashSet<Activation>> statesAndTraversedActivations;
         private Random random = new Random();
         private Objective[][] leveledObjectives;
         private boolean isNewState = false;
@@ -85,11 +84,11 @@ public class DesignSpaceExplorationAdapterImpl implements DesignSpaceExploration
         }
 
         @Override
-        public Collection<Long> explore() {
+        public LinkedHashSet<Long> explore() {
                 var state = model.commit();
                 trajectory.add(state);
                 statesAndUntraversedActivations.put(state, getAllActivations());
-                statesAndTraversedActivations.put(state, new HashSet<>());
+                statesAndTraversedActivations.put(state, new LinkedHashSet<>());
                 strategy.initStrategy(this);
                 strategy.explore();
                 return solutions;
@@ -196,9 +195,9 @@ public class DesignSpaceExplorationAdapterImpl implements DesignSpaceExploration
                 return trajectory.size() - 1;
         }
 
-        public Collection<Activation> getUntraversedActivations() {
+        public LinkedHashSet<Activation> getUntraversedActivations() {
 //              return statesAndUntraversedActivations.get(model.getState());
-                List<Activation> untraversedActivations = new ArrayList<>();
+                LinkedHashSet<Activation> untraversedActivations = new LinkedHashSet<>();
                 for (Activation activation : getAllActivations()) {
                         if (!statesAndTraversedActivations.get(model.getState()).contains(activation)) {
                                 untraversedActivations.add(activation);
@@ -227,7 +226,7 @@ public class DesignSpaceExplorationAdapterImpl implements DesignSpaceExploration
                 trajectory.add(newState);
                 isNewState = !statesAndUntraversedActivations.containsKey(newState);
                 statesAndUntraversedActivations.put(newState, getAllActivations());
-                statesAndTraversedActivations.put(newState, new HashSet<>());
+                statesAndTraversedActivations.put(newState, new LinkedHashSet<>());
                 if (isVisualizationEnabled) {
                         modelVisualizerAdapter.addTransition(trajectory.get(trajectory.size() - 2),
                                         trajectory.get(trajectory.size() - 1), activation.transformationRule().getName(),
@@ -257,8 +256,8 @@ public class DesignSpaceExplorationAdapterImpl implements DesignSpaceExploration
                 return trajectory.contains(model.getState());
         }
 
-        public Collection<Activation> getAllActivations() {
-                Collection<Activation> result = new HashSet<>();
+        public LinkedHashSet<Activation> getAllActivations() {
+                LinkedHashSet<Activation> result = new LinkedHashSet<>();
                 for (var rule : transformationRules) {
                         result.addAll(rule.getAllActivations());
                 }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationBuilderImpl.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationBuilderImpl.java
index 79864de0..638ec641 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationBuilderImpl.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationBuilderImpl.java
@@ -3,7 +3,6 @@ package tools.refinery.store.query.dse.internal;
 import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.query.dnf.AnyQuery;
 import tools.refinery.store.query.dnf.RelationalQuery;
 import tools.refinery.store.query.dse.DesignSpaceExplorationBuilder;
 import tools.refinery.store.query.dse.Strategy;
@@ -12,29 +11,19 @@ import tools.refinery.store.query.dse.objectives.Objective;
 import java.util.LinkedHashSet;
 import java.util.LinkedList;
 import java.util.List;
-import java.util.Set;
 
 public class DesignSpaceExplorationBuilderImpl
                 extends AbstractModelAdapterBuilder<DesignSpaceExplorationStoreAdapterImpl>
                 implements DesignSpaceExplorationBuilder {
-
-        private final Set<AnyQuery> stopConditionSpecifications = new LinkedHashSet<>();
-        private final Set<TransformationRule> transformationSpecifications = new LinkedHashSet<>();
-        private final Set<RelationalQuery> globalConstraints = new LinkedHashSet<>();
+        private final LinkedHashSet<TransformationRule> transformationSpecifications = new LinkedHashSet<>();
+        private final LinkedHashSet<RelationalQuery> globalConstraints = new LinkedHashSet<>();
         private final List<Objective> objectives = new LinkedList<>();
         private Strategy strategy;
 
         @Override
         protected DesignSpaceExplorationStoreAdapterImpl doBuild(ModelStore store) {
-                return new DesignSpaceExplorationStoreAdapterImpl(store, stopConditionSpecifications,
-                                transformationSpecifications, globalConstraints, objectives, strategy);
-        }
-
-        @Override
-        public DesignSpaceExplorationBuilder stopCondition(AnyQuery stopCondition) {
-                checkNotConfigured();
-                stopConditionSpecifications.add(stopCondition);
-                return this;
+                return new DesignSpaceExplorationStoreAdapterImpl(store, transformationSpecifications, globalConstraints,
+                                objectives, strategy);
         }
 
         @Override
@@ -65,10 +54,6 @@ public class DesignSpaceExplorationBuilderImpl
                 return this;
         }
 
-        public Set<AnyQuery> getStopConditionSpecifications() {
-                return stopConditionSpecifications;
-        }
-
         @Override
         protected void doConfigure(ModelStoreBuilder storeBuilder) {
                 storeBuilder.symbols(DesignSpaceExplorationAdapterImpl.NODE_COUNT_SYMBOL);
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationStoreAdapterImpl.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationStoreAdapterImpl.java
index 9c2fa4d6..f58715b7 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationStoreAdapterImpl.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/DesignSpaceExplorationStoreAdapterImpl.java
@@ -1,31 +1,28 @@
 package tools.refinery.store.query.dse.internal;
 
 import tools.refinery.store.adapter.ModelAdapter;
-import tools.refinery.store.query.dnf.AnyQuery;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import tools.refinery.store.query.dse.DesignSpaceExplorationStoreAdapter;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.dnf.RelationalQuery;
+import tools.refinery.store.query.dse.DesignSpaceExplorationStoreAdapter;
 import tools.refinery.store.query.dse.Strategy;
 import tools.refinery.store.query.dse.objectives.Objective;
 
+import java.util.LinkedHashSet;
 import java.util.List;
-import java.util.Set;
 
 public class DesignSpaceExplorationStoreAdapterImpl implements DesignSpaceExplorationStoreAdapter {
         private final ModelStore store;
-        private final Set<AnyQuery> stopConditionSpecifications;
-        private final Set<TransformationRule> transformationSpecifications;
-        private final Set<RelationalQuery> globalConstraints;
+        private final LinkedHashSet<TransformationRule> transformationSpecifications;
+        private final LinkedHashSet<RelationalQuery> globalConstraints;
         private final List<Objective> objectives;
         private final Strategy strategy;
 
-        public DesignSpaceExplorationStoreAdapterImpl(ModelStore store, Set<AnyQuery> stopConditionSpecifications,
-                                                                                                  Set<TransformationRule> transformationSpecifications,
-                                                                                                  Set<RelationalQuery> globalConstraints, List<Objective> objectives,
-                                Strategy strategy) {
+        public DesignSpaceExplorationStoreAdapterImpl(ModelStore store,
+                                                                                                  LinkedHashSet<TransformationRule> transformationSpecifications,
+                                                                                                  LinkedHashSet<RelationalQuery> globalConstraints,
+                                                                                                  List<Objective> objectives, Strategy strategy) {
                         this.store = store;
-                        this.stopConditionSpecifications = stopConditionSpecifications;
                         this.transformationSpecifications = transformationSpecifications;
                         this.globalConstraints = globalConstraints;
                         this.objectives = objectives;
@@ -42,15 +39,11 @@ public class DesignSpaceExplorationStoreAdapterImpl implements DesignSpaceExplor
                 return new DesignSpaceExplorationAdapterImpl(model, this);
         }
 
-        public Set<AnyQuery> getStopConditionSpecifications() {
-                return stopConditionSpecifications;
-        }
-
-        public Set<TransformationRule> getTransformationSpecifications() {
+        public LinkedHashSet<TransformationRule> getTransformationSpecifications() {
                 return transformationSpecifications;
         }
 
-        public Set<RelationalQuery> getGlobalConstraints() {
+        public LinkedHashSet<RelationalQuery> getGlobalConstraints() {
                 return globalConstraints;
         }
 
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/TransformationRule.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/TransformationRule.java
index c46ff712..950ca930 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/TransformationRule.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/dse/internal/TransformationRule.java
@@ -9,9 +9,8 @@ import tools.refinery.store.query.resultset.OrderedResultSet;
 import tools.refinery.store.query.resultset.ResultSet;
 import tools.refinery.store.tuple.Tuple;
 
-import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.Random;
-import java.util.Set;
 
 public class TransformationRule {
 
@@ -66,8 +65,8 @@ public class TransformationRule {
                 return activations;
         }
 
-        public Set<Activation> getAllActivations() {
-                var result = new HashSet<Activation>();
+        public LinkedHashSet<Activation> getAllActivations() {
+                var result = new LinkedHashSet<Activation>();
                 var cursor = activations.getAll();
                 while (cursor.move()) {
                         result.add(new Activation(this, cursor.getKey()));