refactor(store): NeighborhoodCalculator API

* Use US English spelling consistently
* Avoid Eclipse Collections types on API

11 files changed, 84 insertions, 32 deletions

diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateCodeCalculatorFactory.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateCodeCalculatorFactory.java
index 809205e4..5e2a94b3 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateCodeCalculatorFactory.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateCodeCalculatorFactory.java
@@ -5,12 +5,13 @@
  */
 package tools.refinery.store.statecoding;
 
-import org.eclipse.collections.api.set.primitive.IntSet;
 import tools.refinery.store.model.Interpretation;
 import tools.refinery.store.model.Model;
+import tools.refinery.store.statecoding.neighborhood.IndividualsSet;
 
 import java.util.List;
 
 public interface StateCodeCalculatorFactory {
-        StateCodeCalculator create(Model model, List<? extends Interpretation<?>> interpretations, IntSet individuals);
+        StateCodeCalculator create(Model model, List<? extends Interpretation<?>> interpretations,
+                               IndividualsSet individuals);
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateEquivalenceChecker.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateEquivalenceChecker.java
index 0f0023ed..ae599dff 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateEquivalenceChecker.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/StateEquivalenceChecker.java
@@ -5,8 +5,8 @@
  */
 package tools.refinery.store.statecoding;
 
-import org.eclipse.collections.api.set.primitive.IntSet;
 import tools.refinery.store.model.AnyInterpretation;
+import tools.refinery.store.statecoding.neighborhood.IndividualsSet;
 
 import java.util.List;
 
@@ -16,6 +16,6 @@ public interface StateEquivalenceChecker {
         }
 
         EquivalenceResult constructMorphism(
-                        IntSet individuals, List<? extends AnyInterpretation> interpretations1, ObjectCode code1,
+                        IndividualsSet individuals, List<? extends AnyInterpretation> interpretations1, ObjectCode code1,
                         List<? extends AnyInterpretation> interpretations2, ObjectCode code2);
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderBuilderImpl.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderBuilderImpl.java
index 36d7d4c7..7fec59c4 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderBuilderImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderBuilderImpl.java
@@ -15,7 +15,7 @@ import tools.refinery.store.statecoding.StateCodeCalculatorFactory;
 import tools.refinery.store.statecoding.StateCoderBuilder;
 import tools.refinery.store.statecoding.StateCoderStoreAdapter;
 import tools.refinery.store.statecoding.StateEquivalenceChecker;
-import tools.refinery.store.statecoding.neighbourhood.NeighbourhoodCalculator;
+import tools.refinery.store.statecoding.neighborhood.NeighborhoodCalculator;
 import tools.refinery.store.statecoding.stateequivalence.StateEquivalenceCheckerImpl;
 import tools.refinery.store.tuple.Tuple1;
 
@@ -27,7 +27,7 @@ public class StateCoderBuilderImpl extends AbstractModelAdapterBuilder<StateCode
                 implements StateCoderBuilder {
         private final Set<AnySymbol> excluded = new HashSet<>();
         private final MutableIntSet individuals = IntSets.mutable.empty();
-        private StateCodeCalculatorFactory calculator = NeighbourhoodCalculator.factory();
+        private StateCodeCalculatorFactory calculator = NeighborhoodCalculator.factory();
         private StateEquivalenceChecker checker = new StateEquivalenceCheckerImpl();
 
         @Override
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderStoreAdapterImpl.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderStoreAdapterImpl.java
index 2cb6f3c1..70beedae 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderStoreAdapterImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/internal/StateCoderStoreAdapterImpl.java
@@ -14,6 +14,8 @@ import tools.refinery.store.statecoding.StateCodeCalculatorFactory;
 import tools.refinery.store.statecoding.StateCoderAdapter;
 import tools.refinery.store.statecoding.StateCoderStoreAdapter;
 import tools.refinery.store.statecoding.StateEquivalenceChecker;
+import tools.refinery.store.statecoding.neighborhood.IndividualsSet;
+import tools.refinery.store.statecoding.neighborhood.IndividualsArray;
 
 import java.util.Collection;
 import java.util.Objects;
@@ -21,7 +23,7 @@ import java.util.Objects;
 public class StateCoderStoreAdapterImpl implements StateCoderStoreAdapter {
         final ModelStore store;
         final Collection<Symbol<?>> symbols;
-        final IntSet individuals;
+        final IndividualsSet individuals;
 
         final StateEquivalenceChecker equivalenceChecker;
         final StateCodeCalculatorFactory codeCalculatorFactory;
@@ -36,7 +38,7 @@ public class StateCoderStoreAdapterImpl implements StateCoderStoreAdapter {
                 this.equivalenceChecker = equivalenceChecker;
                 this.store = store;
                 this.symbols = symbols;
-                this.individuals = individuals;
+                this.individuals = new IndividualsArray(individuals.toSortedArray());
         }
 
         @Override
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/AbstractNeighbourhoodCalculator.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/AbstractNeighborhoodCalculator.java
index a4060e74..fcc1c72d 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/AbstractNeighbourhoodCalculator.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/AbstractNeighborhoodCalculator.java
@@ -3,11 +3,10 @@
  *
  * SPDX-License-Identifier: EPL-2.0
  */
-package tools.refinery.store.statecoding.neighbourhood;
+package tools.refinery.store.statecoding.neighborhood;
 
 import org.eclipse.collections.api.factory.primitive.IntLongMaps;
 import org.eclipse.collections.api.map.primitive.MutableIntLongMap;
-import org.eclipse.collections.api.set.primitive.IntSet;
 import tools.refinery.store.map.Cursor;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.statecoding.ObjectCode;
@@ -17,9 +16,9 @@ import tools.refinery.store.tuple.Tuple;
 
 import java.util.*;
 
-public abstract class AbstractNeighbourhoodCalculator<T> implements StateCodeCalculator {
+public abstract class AbstractNeighborhoodCalculator<T> implements StateCodeCalculator {
         private final Model model;
-        private final IntSet individuals;
+        private final IndividualsSet individuals;
         private final int depth;
         private List<T> nullImpactValues;
         private LinkedHashMap<T, long[]> impactValues;
@@ -29,7 +28,7 @@ public abstract class AbstractNeighbourhoodCalculator<T> implements StateCodeCal
 
         protected static final long PRIME = 31;
 
-        protected AbstractNeighbourhoodCalculator(Model model, IntSet individuals, int depth) {
+        protected AbstractNeighborhoodCalculator(Model model, IndividualsSet individuals, int depth) {
                 this.model = model;
                 this.individuals = individuals;
                 this.depth = depth;
@@ -84,10 +83,7 @@ public abstract class AbstractNeighbourhoodCalculator<T> implements StateCodeCal
                 @SuppressWarnings("squid:S2245")
                 Random random = new Random(1);
 
-                var individualsInOrder = individuals.toSortedList(Integer::compare);
-                for (int i = 0; i < individualsInOrder.size(); i++) {
-                        individualHashValues.put(individualsInOrder.get(i), random.nextLong());
-                }
+                individuals.stream().forEach(o -> individualHashValues.put(o, random.nextLong()));
 
                 for (var interpretation : getInterpretations()) {
                         int arity = getArity(interpretation);
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/IndividualsArray.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/IndividualsArray.java
new file mode 100644
index 00000000..107a01b8
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/IndividualsArray.java
@@ -0,0 +1,27 @@
+/*
+ * SPDX-FileCopyrightText: 2024 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.statecoding.neighborhood;
+
+import java.util.Arrays;
+import java.util.stream.IntStream;
+
+public class IndividualsArray implements IndividualsSet {
+        private final int[] sortedArray;
+
+        public IndividualsArray(int[] sortedArray) {
+                this.sortedArray = sortedArray;
+        }
+
+        @Override
+        public boolean isIndividual(int nodeId) {
+                return Arrays.binarySearch(sortedArray, nodeId) >= 0;
+        }
+
+        @Override
+        public IntStream stream() {
+                return Arrays.stream(sortedArray);
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/IndividualsSet.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/IndividualsSet.java
new file mode 100644
index 00000000..059dad41
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/IndividualsSet.java
@@ -0,0 +1,26 @@
+/*
+ * SPDX-FileCopyrightText: 2024 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.statecoding.neighborhood;
+
+import java.util.stream.IntStream;
+
+public interface IndividualsSet {
+        IndividualsSet EMPTY = new IndividualsSet() {
+                @Override
+                public boolean isIndividual(int nodeId) {
+                        return false;
+                }
+
+                @Override
+                public IntStream stream() {
+                        return IntStream.empty();
+                }
+        };
+
+        boolean isIndividual(int nodeId);
+
+        IntStream stream();
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/NeighbourhoodCalculator.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/NeighborhoodCalculator.java
index 5859ccc2..83ad133d 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/NeighbourhoodCalculator.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/NeighborhoodCalculator.java
@@ -3,9 +3,8 @@
  *
  * SPDX-License-Identifier: EPL-2.0
  */
-package tools.refinery.store.statecoding.neighbourhood;
+package tools.refinery.store.statecoding.neighborhood;
 
-import org.eclipse.collections.api.set.primitive.IntSet;
 import tools.refinery.store.map.Cursor;
 import tools.refinery.store.model.Interpretation;
 import tools.refinery.store.model.Model;
@@ -14,13 +13,13 @@ import tools.refinery.store.tuple.Tuple;
 
 import java.util.List;
 
-public class NeighbourhoodCalculator extends AbstractNeighbourhoodCalculator<Interpretation<?>> {
+public class NeighborhoodCalculator extends AbstractNeighborhoodCalculator<Interpretation<?>> {
         public static final int DEFAULT_DEPTH = 7;
 
         private final List<Interpretation<?>> interpretations;
 
-        protected NeighbourhoodCalculator(Model model, List<? extends Interpretation<?>> interpretations,
-                                                                          IntSet individuals, int depth) {
+        protected NeighborhoodCalculator(Model model, List<? extends Interpretation<?>> interpretations,
+                                                                         IndividualsSet individuals, int depth) {
                 super(model, individuals, depth);
                 this.interpretations = List.copyOf(interpretations);
         }
@@ -46,7 +45,7 @@ public class NeighbourhoodCalculator extends AbstractNeighbourhoodCalculator<Int
         }
 
         public static StateCodeCalculatorFactory factory(int depth) {
-                return (model, interpretations, individuals) -> new NeighbourhoodCalculator(model, interpretations,
+                return (model, interpretations, individuals) -> new NeighborhoodCalculator(model, interpretations,
                                 individuals, depth);
         }
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/ObjectCodeImpl.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/ObjectCodeImpl.java
index 422e1d73..d6ef2e89 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/ObjectCodeImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighborhood/ObjectCodeImpl.java
@@ -3,7 +3,7 @@
  *
  * SPDX-License-Identifier: EPL-2.0
  */
-package tools.refinery.store.statecoding.neighbourhood;
+package tools.refinery.store.statecoding.neighborhood;
 
 import tools.refinery.store.statecoding.ObjectCode;
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/stateequivalence/StateEquivalenceCheckerImpl.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/stateequivalence/StateEquivalenceCheckerImpl.java
index 5a62d8a0..54d6efdc 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/stateequivalence/StateEquivalenceCheckerImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/stateequivalence/StateEquivalenceCheckerImpl.java
@@ -11,13 +11,13 @@ import org.eclipse.collections.api.factory.primitive.LongObjectMaps;
 import org.eclipse.collections.api.map.primitive.IntIntMap;
 import org.eclipse.collections.api.map.primitive.MutableIntIntMap;
 import org.eclipse.collections.api.map.primitive.MutableLongObjectMap;
-import org.eclipse.collections.api.set.primitive.IntSet;
 import org.eclipse.collections.api.set.primitive.MutableIntSet;
 import tools.refinery.store.model.AnyInterpretation;
 import tools.refinery.store.model.Interpretation;
 import tools.refinery.store.statecoding.Morphism;
 import tools.refinery.store.statecoding.ObjectCode;
 import tools.refinery.store.statecoding.StateEquivalenceChecker;
+import tools.refinery.store.statecoding.neighborhood.IndividualsSet;
 import tools.refinery.store.tuple.Tuple;
 
 import java.util.ArrayList;
@@ -28,7 +28,7 @@ public class StateEquivalenceCheckerImpl implements StateEquivalenceChecker {
         public static final int LIMIT = 1000;
 
         @Override
-        public EquivalenceResult constructMorphism(IntSet individuals,
+        public EquivalenceResult constructMorphism(IndividualsSet individuals,
                                                                                            List<? extends AnyInterpretation> interpretations1,
                                                                                            ObjectCode code1,
                                                                                            List<? extends AnyInterpretation> interpretations2,
@@ -67,10 +67,10 @@ public class StateEquivalenceCheckerImpl implements StateEquivalenceChecker {
                 }
         }
 
-        private MutableLongObjectMap<MutableIntSet> indexByHash(ObjectCode code, IntSet individuals) {
+        private MutableLongObjectMap<MutableIntSet> indexByHash(ObjectCode code, IndividualsSet individuals) {
                 MutableLongObjectMap<MutableIntSet> result = LongObjectMaps.mutable.empty();
                 for (int o = 0; o < code.getSize(); o++) {
-                        if (!individuals.contains(o)) {
+                        if (!individuals.isIndividual(o)) {
                                 long hash = code.get(o);
                                 if (hash != 0) {
                                         var equivalenceClass = result.get(hash);
@@ -86,8 +86,9 @@ public class StateEquivalenceCheckerImpl implements StateEquivalenceChecker {
         }
 
         private EquivalenceResult constructPermutationNavigation(
-                        IntSet individuals, MutableLongObjectMap<MutableIntSet> map1, MutableLongObjectMap<MutableIntSet> map2,
-                        MutableIntIntMap object2OptionIndex, List<List<IntIntMap>> listOfOptions) {
+                        IndividualsSet individuals, MutableLongObjectMap<MutableIntSet> map1,
+            MutableLongObjectMap<MutableIntSet> map2, MutableIntIntMap object2OptionIndex,
+                        List<List<IntIntMap>> listOfOptions) {
                 if (map1.size() != map2.size()) {
                         return EquivalenceResult.DIFFERENT;
                 }
@@ -116,7 +117,7 @@ public class StateEquivalenceCheckerImpl implements StateEquivalenceChecker {
                         listOfOptions.add(pairing.permutations());
                 }
 
-                individuals.forEach(o -> listOfOptions.add(o, List.of(IntIntMaps.immutable.of(o, o))));
+                individuals.stream().forEach(o -> listOfOptions.add(o, List.of(IntIntMaps.immutable.of(o, o))));
 
                 if (allComplete) {
                         return EquivalenceResult.ISOMORPHIC;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/statecoding/EquivalenceTest.java b/subprojects/store/src/test/java/tools/refinery/store/statecoding/EquivalenceTest.java
index f2d2f7b5..31726133 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/statecoding/EquivalenceTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/statecoding/EquivalenceTest.java
@@ -10,7 +10,7 @@ import tools.refinery.store.map.Version;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.representation.Symbol;
-import tools.refinery.store.statecoding.neighbourhood.ObjectCodeImpl;
+import tools.refinery.store.statecoding.neighborhood.ObjectCodeImpl;
 import tools.refinery.store.tuple.Tuple;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;