refactor: Atom -> Literal naming convention

20 files changed, 115 insertions, 141 deletions

diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/DNFAnd.java b/subprojects/store/src/main/java/tools/refinery/store/query/DNFAnd.java
deleted file mode 100644
index 8c3bf05d..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/DNFAnd.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.query.atom.DNFAtom;
-
-import java.util.List;
-import java.util.Set;
-
-public record DNFAnd(Set<Variable> quantifiedVariables, List<DNFAtom> constraints) {
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/DNF.java b/subprojects/store/src/main/java/tools/refinery/store/query/Dnf.java
index 95c5d787..f7b27b81 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/DNF.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/Dnf.java
@@ -1,10 +1,10 @@
 package tools.refinery.store.query;
 
-import tools.refinery.store.query.atom.DNFAtom;
+import tools.refinery.store.query.literal.Literal;
 
 import java.util.*;
 
-public final class DNF implements RelationLike {
+public final class Dnf implements RelationLike {
         private final String name;
 
         private final String uniqueName;
@@ -13,13 +13,13 @@ public final class DNF implements RelationLike {
 
         private final List<FunctionalDependency<Variable>> functionalDependencies;
 
-        private final List<DNFAnd> clauses;
+        private final List<DnfClause> clauses;
 
-        private DNF(String name, List<Variable> parameters, List<FunctionalDependency<Variable>> functionalDependencies,
-                                List<DNFAnd> clauses) {
+        private Dnf(String name, List<Variable> parameters, List<FunctionalDependency<Variable>> functionalDependencies,
+                                List<DnfClause> clauses) {
                 validateFunctionalDependencies(parameters, functionalDependencies);
                 this.name = name;
-                this.uniqueName = DNFUtils.generateUniqueName(name);
+                this.uniqueName = DnfUtils.generateUniqueName(name);
                 this.parameters = parameters;
                 this.functionalDependencies = functionalDependencies;
                 this.clauses = clauses;
@@ -68,7 +68,7 @@ public final class DNF implements RelationLike {
                 return parameters.size();
         }
 
-        public List<DNFAnd> getClauses() {
+        public List<DnfClause> getClauses() {
                 return clauses;
         }
 
@@ -88,7 +88,7 @@ public final class DNF implements RelationLike {
 
                 private final List<FunctionalDependency<Variable>> functionalDependencies = new ArrayList<>();
 
-                private final List<List<DNFAtom>> clauses = new ArrayList<>();
+                private final List<List<Literal>> clauses = new ArrayList<>();
 
                 private Builder(String name) {
                         this.name = name;
@@ -122,46 +122,46 @@ public final class DNF implements RelationLike {
                         return functionalDependency(new FunctionalDependency<>(forEach, unique));
                 }
 
-                public Builder clause(DNFAtom... atoms) {
+                public Builder clause(Literal... atoms) {
                         clauses.add(List.of(atoms));
                         return this;
                 }
 
-                public Builder clause(Collection<DNFAtom> atoms) {
+                public Builder clause(Collection<Literal> atoms) {
                         clauses.add(List.copyOf(atoms));
                         return this;
                 }
 
-                public Builder clause(DNFAnd clause) {
-                        return clause(clause.constraints());
+                public Builder clause(DnfClause clause) {
+                        return clause(clause.literals());
                 }
 
-                public Builder clauses(DNFAnd... clauses) {
+                public Builder clauses(DnfClause... clauses) {
                         for (var clause : clauses) {
                                 this.clause(clause);
                         }
                         return this;
                 }
 
-                public Builder clauses(Collection<DNFAnd> clauses) {
+                public Builder clauses(Collection<DnfClause> clauses) {
                         for (var clause : clauses) {
                                 this.clause(clause);
                         }
                         return this;
                 }
 
-                public DNF build() {
-                        var postProcessedClauses = new ArrayList<DNFAnd>();
+                public Dnf build() {
+                        var postProcessedClauses = new ArrayList<DnfClause>();
                         for (var constraints : clauses) {
                                 var variables = new HashSet<Variable>();
                                 for (var constraint : constraints) {
                                         constraint.collectAllVariables(variables);
                                 }
                                 parameters.forEach(variables::remove);
-                                postProcessedClauses.add(new DNFAnd(Collections.unmodifiableSet(variables),
+                                postProcessedClauses.add(new DnfClause(Collections.unmodifiableSet(variables),
                                                 Collections.unmodifiableList(constraints)));
                         }
-                        return new DNF(name, Collections.unmodifiableList(parameters),
+                        return new Dnf(name, Collections.unmodifiableList(parameters),
                                         Collections.unmodifiableList(functionalDependencies),
                                         Collections.unmodifiableList(postProcessedClauses));
                 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/DnfClause.java b/subprojects/store/src/main/java/tools/refinery/store/query/DnfClause.java
new file mode 100644
index 00000000..2ba6becc
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/DnfClause.java
@@ -0,0 +1,9 @@
+package tools.refinery.store.query;
+
+import tools.refinery.store.query.literal.Literal;
+
+import java.util.List;
+import java.util.Set;
+
+public record DnfClause(Set<Variable> quantifiedVariables, List<Literal> literals) {
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/DNFUtils.java b/subprojects/store/src/main/java/tools/refinery/store/query/DnfUtils.java
index 0ef77d49..c7a2849c 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/DNFUtils.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/DnfUtils.java
@@ -2,8 +2,8 @@ package tools.refinery.store.query;
 
 import java.util.UUID;
 
-public final class DNFUtils {
-        private DNFUtils() {
+public final class DnfUtils {
+        private DnfUtils() {
                 throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
         }
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
index 7449e39b..f7762444 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
@@ -5,7 +5,7 @@ import tools.refinery.store.adapter.ModelAdapter;
 public interface ModelQueryAdapter extends ModelAdapter {
         ModelQueryStoreAdapter getStoreAdapter();
 
-        ResultSet getResultSet(DNF query);
+        ResultSet getResultSet(Dnf query);
 
         boolean hasPendingChanges();
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
index 4364d844..b3cfb4b4 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
@@ -7,16 +7,16 @@ import java.util.Collection;
 import java.util.List;
 
 public interface ModelQueryBuilder extends ModelAdapterBuilder {
-        default ModelQueryBuilder queries(DNF... queries) {
+        default ModelQueryBuilder queries(Dnf... queries) {
                 return queries(List.of(queries));
         }
 
-        default ModelQueryBuilder queries(Collection<DNF> queries) {
+        default ModelQueryBuilder queries(Collection<Dnf> queries) {
                 queries.forEach(this::query);
                 return this;
         }
 
-        ModelQueryBuilder query(DNF query);
+        ModelQueryBuilder query(Dnf query);
 
         @Override
         ModelQueryStoreAdapter createStoreAdapter(ModelStore store);
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
index ef5a4587..3efeacaa 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
@@ -9,7 +9,7 @@ import java.util.Collection;
 public interface ModelQueryStoreAdapter extends ModelStoreAdapter {
         Collection<AnyRelationView> getRelationViews();
 
-        Collection<DNF> getQueries();
+        Collection<Dnf> getQueries();
 
         @Override
         ModelQueryAdapter createModelAdapter(Model model);
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/Variable.java b/subprojects/store/src/main/java/tools/refinery/store/query/Variable.java
index 3632f3c5..6a6831ae 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/Variable.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/Variable.java
@@ -13,7 +13,7 @@ public class Variable {
         public Variable(String name) {
                 super();
                 this.name = name;
-                this.uniqueName = DNFUtils.generateUniqueName(name);
+                this.uniqueName = DnfUtils.generateUniqueName(name);
 
         }
         public String getName() {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFCallAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFCallAtom.java
deleted file mode 100644
index 3b4f5cd1..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFCallAtom.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.DNF;
-import tools.refinery.store.query.Variable;
-
-import java.util.List;
-
-public class DNFCallAtom extends CallAtom<DNF> {
-        public DNFCallAtom(CallPolarity polarity, DNF target, List<Variable> substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public DNFCallAtom(CallPolarity polarity, DNF target, Variable... substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public DNFCallAtom(boolean positive, DNF target, List<Variable> substitution) {
-                super(positive, target, substitution);
-        }
-
-        public DNFCallAtom(boolean positive, DNF target, Variable... substitution) {
-                super(positive, target, substitution);
-        }
-
-        public DNFCallAtom(DNF target, List<Variable> substitution) {
-                super(target, substitution);
-        }
-
-        public DNFCallAtom(DNF target, Variable... substitution) {
-                super(target, substitution);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/RelationViewAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/RelationViewAtom.java
deleted file mode 100644
index a2b176c4..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/RelationViewAtom.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.Variable;
-import tools.refinery.store.query.view.AnyRelationView;
-
-import java.util.List;
-
-public final class RelationViewAtom extends CallAtom<AnyRelationView> {
-        public RelationViewAtom(CallPolarity polarity, AnyRelationView target, List<Variable> substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public RelationViewAtom(CallPolarity polarity, AnyRelationView target, Variable... substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public RelationViewAtom(boolean positive, AnyRelationView target, List<Variable> substitution) {
-                super(positive, target, substitution);
-        }
-
-        public RelationViewAtom(boolean positive, AnyRelationView target, Variable... substitution) {
-                super(positive, target, substitution);
-        }
-
-        public RelationViewAtom(AnyRelationView target, List<Variable> substitution) {
-                super(target, substitution);
-        }
-
-        public RelationViewAtom(AnyRelationView target, Variable... substitution) {
-                super(target, substitution);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
index 47121870..59120434 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallAtom.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
@@ -1,4 +1,4 @@
-package tools.refinery.store.query.atom;
+package tools.refinery.store.query.literal;
 
 import tools.refinery.store.query.Variable;
 import tools.refinery.store.query.RelationLike;
@@ -7,12 +7,12 @@ import java.util.List;
 import java.util.Objects;
 import java.util.Set;
 
-public abstract class CallAtom<T extends RelationLike> implements DNFAtom {
+public abstract class CallLiteral<T extends RelationLike> implements Literal {
         private final CallPolarity polarity;
         private final T target;
         private final List<Variable> substitution;
 
-        protected CallAtom(CallPolarity polarity, T target, List<Variable> substitution) {
+        protected CallLiteral(CallPolarity polarity, T target, List<Variable> substitution) {
                 if (substitution.size() != target.arity()) {
                         throw new IllegalArgumentException("%s needs %d arguments, but got %s".formatted(target.name(),
                                         target.arity(), substitution.size()));
@@ -25,26 +25,6 @@ public abstract class CallAtom<T extends RelationLike> implements DNFAtom {
                 this.substitution = substitution;
         }
 
-        protected CallAtom(CallPolarity polarity, T target, Variable... substitution) {
-                this(polarity, target, List.of(substitution));
-        }
-
-        protected CallAtom(boolean positive, T target, List<Variable> substitution) {
-                this(CallPolarity.fromBoolean(positive), target, substitution);
-        }
-
-        protected CallAtom(boolean positive, T target, Variable... substitution) {
-                this(positive, target, List.of(substitution));
-        }
-
-        protected CallAtom(T target, List<Variable> substitution) {
-                this(true, target, substitution);
-        }
-
-        protected CallAtom(T target, Variable... substitution) {
-                this(target, List.of(substitution));
-        }
-
         public CallPolarity getPolarity() {
                 return polarity;
         }
@@ -68,9 +48,9 @@ public abstract class CallAtom<T extends RelationLike> implements DNFAtom {
         public boolean equals(Object o) {
                 if (this == o) return true;
                 if (o == null || getClass() != o.getClass()) return false;
-                CallAtom<?> callAtom = (CallAtom<?>) o;
-                return polarity == callAtom.polarity && Objects.equals(target, callAtom.target) && Objects.equals(substitution
-                                , callAtom.substitution);
+                CallLiteral<?> callAtom = (CallLiteral<?>) o;
+                return polarity == callAtom.polarity && Objects.equals(target, callAtom.target) &&
+                                Objects.equals(substitution, callAtom.substitution);
         }
 
         @Override
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallPolarity.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/CallPolarity.java
index 957e9b7b..ddea0221 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallPolarity.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/CallPolarity.java
@@ -1,4 +1,4 @@
-package tools.refinery.store.query.atom;
+package tools.refinery.store.query.literal;
 
 public enum CallPolarity {
         POSITIVE(true, false),
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/ConstantAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java
index 13dae7d0..41426fdd 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/ConstantAtom.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java
@@ -1,10 +1,10 @@
-package tools.refinery.store.query.atom;
+package tools.refinery.store.query.literal;
 
 import tools.refinery.store.query.Variable;
 
 import java.util.Set;
 
-public record ConstantAtom(Variable variable, int nodeId) implements DNFAtom {
+public record ConstantLiteral(Variable variable, int nodeId) implements Literal {
         @Override
         public void collectAllVariables(Set<Variable> variables) {
                 variables.add(variable);
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/literal/DnfCallLiteral.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/DnfCallLiteral.java
new file mode 100644
index 00000000..e3410c21
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/DnfCallLiteral.java
@@ -0,0 +1,32 @@
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.Dnf;
+import tools.refinery.store.query.Variable;
+
+import java.util.List;
+
+public final class DnfCallLiteral extends CallLiteral<Dnf> {
+        public DnfCallLiteral(CallPolarity polarity, Dnf target, List<Variable> substitution) {
+                super(polarity, target, substitution);
+        }
+
+        public DnfCallLiteral(CallPolarity polarity, Dnf target, Variable... substitution) {
+                this(polarity, target, List.of(substitution));
+        }
+
+        public DnfCallLiteral(boolean positive, Dnf target, List<Variable> substitution) {
+                this(CallPolarity.fromBoolean(positive), target, substitution);
+        }
+
+        public DnfCallLiteral(boolean positive, Dnf target, Variable... substitution) {
+                this(positive, target, List.of(substitution));
+        }
+
+        public DnfCallLiteral(Dnf target, List<Variable> substitution) {
+                this(CallPolarity.POSITIVE, target, substitution);
+        }
+
+        public DnfCallLiteral(Dnf target, Variable... substitution) {
+                this(target, List.of(substitution));
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/EquivalenceAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java
index b1b3a6f7..a1ec2c41 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/EquivalenceAtom.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java
@@ -1,11 +1,11 @@
-package tools.refinery.store.query.atom;
+package tools.refinery.store.query.literal;
 
 import tools.refinery.store.query.Variable;
 
 import java.util.Set;
 
-public record EquivalenceAtom(boolean positive, Variable left, Variable right) implements DNFAtom {
-        public EquivalenceAtom(Variable left, Variable right) {
+public record EquivalenceLiteral(boolean positive, Variable left, Variable right) implements Literal {
+        public EquivalenceLiteral(Variable left, Variable right) {
                 this(true, left, right);
         }
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/Literal.java
index ebf71236..676ac7fd 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFAtom.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/Literal.java
@@ -1,9 +1,9 @@
-package tools.refinery.store.query.atom;
+package tools.refinery.store.query.literal;
 
 import tools.refinery.store.query.Variable;
 
 import java.util.Set;
 
-public interface DNFAtom {
+public interface Literal {
         void collectAllVariables(Set<Variable> variables);
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/Modality.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/Modality.java
index e389f563..93826161 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/Modality.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/Modality.java
@@ -1,4 +1,4 @@
-package tools.refinery.store.query.atom;
+package tools.refinery.store.query.literal;
 
 import java.util.Locale;
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/literal/RelationViewLiteral.java b/subprojects/store/src/main/java/tools/refinery/store/query/literal/RelationViewLiteral.java
new file mode 100644
index 00000000..e2106ba9
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/query/literal/RelationViewLiteral.java
@@ -0,0 +1,32 @@
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.Variable;
+import tools.refinery.store.query.view.AnyRelationView;
+
+import java.util.List;
+
+public final class RelationViewLiteral extends CallLiteral<AnyRelationView> {
+        public RelationViewLiteral(CallPolarity polarity, AnyRelationView target, List<Variable> substitution) {
+                super(polarity, target, substitution);
+        }
+
+        public RelationViewLiteral(CallPolarity polarity, AnyRelationView target, Variable... substitution) {
+                this(polarity, target, List.of(substitution));
+        }
+
+        public RelationViewLiteral(boolean positive, AnyRelationView target, List<Variable> substitution) {
+                this(CallPolarity.fromBoolean(positive), target, substitution);
+        }
+
+        public RelationViewLiteral(boolean positive, AnyRelationView target, Variable... substitution) {
+                this(positive, target, List.of(substitution));
+        }
+
+        public RelationViewLiteral(AnyRelationView target, List<Variable> substitution) {
+                this(CallPolarity.POSITIVE, target, substitution);
+        }
+
+        public RelationViewLiteral(AnyRelationView target, Variable... substitution) {
+                this(target, List.of(substitution));
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java b/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java
index 85ea15f4..30b1c03f 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java
@@ -1,12 +1,6 @@
 package tools.refinery.store.representation;
 
-import java.util.Objects;
-
 public record Symbol<T>(String name, int arity, Class<T> valueType, T defaultValue) implements AnySymbol {
-        public boolean isDefaultValue(T value) {
-                return Objects.equals(defaultValue, value);
-        }
-
         @Override
         public boolean equals(Object o) {
                 return this == o;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java b/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java
index 371b5e47..9536a444 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java
@@ -49,7 +49,7 @@ class ModelTest {
 
                 assertEquals(3, ageInterpretation.get(Tuple.of(0)));
                 assertEquals(1, ageInterpretation.get(Tuple.of(1)));
-                assertNull(ageInterpretation.get( Tuple.of(2)));
+                assertNull(ageInterpretation.get(Tuple.of(2)));
 
                 assertTrue(friendInterpretation.get(Tuple.of(0, 1)));
                 assertFalse(friendInterpretation.get(Tuple.of(0, 5)));