Fixing JavaDocs

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/CodebaseGraphDTO.java

@@ -12,6 +12,11 @@
 import org.jgrapht.Graph;
 import org.jgrapht.graph.DefaultWeightedEdge;
 
+/**
+ * Data transfer object containing the complete codebase graph analysis results.
+ * Includes class and package reference graphs, class-to-package relationships,
+ * source file mappings, and detected disharmonies (antipatterns).
+ */
 @Getter
 @EqualsAndHashCode
 @ToString
@@ -26,6 +31,16 @@ public class CodebaseGraphDTO {
     private final List<ClassDisharmony> classDisharmonies;
     private final List<MethodDisharmony> methodDisharmonies;
 
+    /**
+     * Creates a new CodebaseGraphDTO.
+     *
+     * @param classReferencesGraph                    the class reference graph
+     * @param packageReferencesGraph                  the package reference graph
+     * @param classRelationshipsInPackageRelationship the class-to-package relationships
+     * @param classToSourceFilePathMapping            the class to source file path mapping
+     * @param classDisharmonies                       the list of class disharmonies
+     * @param methodDisharmonies                      the list of method disharmonies
+     */
     public CodebaseGraphDTO(
             Graph<String, DefaultWeightedEdge> classReferencesGraph,
             Graph<String, DefaultWeightedEdge> packageReferencesGraph,
@@ -41,12 +56,24 @@ public CodebaseGraphDTO(
         this.methodDisharmonies = methodDisharmonies;
     }
 
+    /**
+     * Returns class disharmonies filtered by type.
+     *
+     * @param disharmonyType the disharmony type to filter by
+     * @return list of matching class disharmonies
+     */
     public List<ClassDisharmony> getClassDisharmoniesOfType(String disharmonyType) {
         return classDisharmonies.stream()
                 .filter(d -> disharmonyType.equals(d.getDisharmonyType()))
                 .collect(Collectors.toList());
     }
 
+    /**
+     * Returns method disharmonies filtered by type.
+     *
+     * @param disharmonyType the disharmony type to filter by
+     * @return list of matching method disharmonies
+     */
     public List<MethodDisharmony> getMethodDisharmoniesOfType(String disharmonyType) {
         return methodDisharmonies.stream()
                 .filter(d -> disharmonyType.equals(d.getDisharmonyType()))

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/CompositeGraphBuilder.java

@@ -26,14 +26,14 @@
 public class CompositeGraphBuilder {
 
     /**
-     * Build a unified {@link CodebaseGraphDTO} from a directory that may contain
-     * both Java and Kotlin source files.
+     * Builds a unified graph for Java and Kotlin source files in a repository.
      *
-     * @param repositoryPath     path to the source directory
-     * @param excludeTests      whether to exclude test files
+     * @param repositoryPath      path to the source directory
+     * @param excludeTests        whether to exclude test files
      * @param testSourceDirectory test source directory pattern
-     * @return a merged CodebaseGraphDTO
-     * @throws IOException if parsing fails
+     * @return the combined Java and Kotlin codebase graph
+     * @throws IllegalArgumentException if {@code repositoryPath} is null or empty
+     * @throws IOException if source analysis fails
      */
     public CodebaseGraphDTO getCodebaseGraphDTO(String repositoryPath, boolean excludeTests, String testSourceDirectory)
             throws IOException {
@@ -49,6 +49,15 @@ public CodebaseGraphDTO getCodebaseGraphDTO(String repositoryPath, boolean exclu
         return getCodebaseGraphDTO(repositoryPath, config);
     }
 
+    /**
+     * Build a unified {@link CodebaseGraphDTO} from a directory that may contain
+     * both Java and Kotlin source files.
+     *
+     * @param repositoryPath path to the source directory
+     * @param config         graph-builder configuration
+     * @return a merged CodebaseGraphDTO
+     * @throws IOException if parsing fails
+     */
     public CodebaseGraphDTO getCodebaseGraphDTO(String repositoryPath, GraphBuilderConfig config) throws IOException {
         String repositoryRoot = config.getRepositoryRoot() != null ? config.getRepositoryRoot() : "";
         return getCodebaseGraphDTO(repositoryPath, repositoryRoot, config);

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/DependencyCollector.java

@@ -2,6 +2,11 @@
 
 import org.jgrapht.graph.DefaultWeightedEdge;
 
+/**
+ * Interface for collecting dependencies between classes and packages during
+ * source file analysis. Implementations build the class and package reference
+ * graphs used by the graph builder.
+ */
 // TODO: Revisit - I don't think this is really needed
 public interface DependencyCollector {
 
@@ -18,6 +23,7 @@ public interface DependencyCollector {
      *
      * @param fromPackageName The package that depends on another
      * @param toPackageName The package being depended upon
+     * @return the package dependency edge, or {@code null} when no package edge is created
      */
     DefaultWeightedEdge addPackageDependency(String fromPackageName, String toPackageName);
 

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/graphbuilder/KotlinSourceFileGraphBuilder.java

@@ -27,7 +27,7 @@
 
 /**
  * Kotlin-language source-file graph builder. Invoked unconditionally by
- * {@link CompositeGraphBuilder} (Kotlin analysis is always on). This
+ * {@link org.hjug.graphbuilder.CompositeGraphBuilder} (Kotlin analysis is always on). This
  * module declares a compile dependency on
  * {@code org.openrewrite:rewrite-kotlin}, so the Kotlin parser is always
  * on the classpath of any consumer of this builder.

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/metrics/ClassMetrics.java

@@ -369,8 +369,10 @@ public void addMethod(MethodMetrics methodMetrics) {
     /**
      * Aggregated class-level count of Kotlin/Java callable references
      * ({@code Klass::method}) across all declared methods. Returns the sum
-     * of {@link MethodMetrics#getNumberOfCallableReferences()} across every
+     * of {@code MethodMetrics#getNumberOfCallableReferences()} across every
      * method on this class.
+     *
+     * @return the total number of callable references
      */
     public int getNumberOfCallableReferences() {
         return methods.values().stream()

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/metrics/ComplexityCalculator.java

@@ -4,16 +4,31 @@
 import org.openrewrite.java.JavaIsoVisitor;
 import org.openrewrite.java.tree.J;
 
+/**
+ * Calculates cyclomatic complexity and maximum nesting depth for a method
+ * by visiting its AST nodes. Extends {@link JavaIsoVisitor} to traverse
+ * the OpenRewrite Java AST.
+ */
 public class ComplexityCalculator extends JavaIsoVisitor<ExecutionContext> {
 
     private int cyclomaticComplexity = 1;
     private int nestingLevel = 0;
     private int maxNestingDepth = 0;
 
+    /**
+     * Provides the calculated cyclomatic complexity.
+     *
+     * @return the cyclomatic complexity
+     */
     public int getCyclomaticComplexity() {
         return cyclomaticComplexity;
     }
 
+    /**
+     * Returns the calculated maximum nesting depth.
+     *
+     * @return the maximum nesting depth
+     */
     public int getMaxNestingDepth() {
         return maxNestingDepth;
     }

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/metrics/DisharmonyDetector.java

@@ -4,6 +4,18 @@
 import lombok.Data;
 import org.hjug.graphbuilder.metrics.DisharmonyMetric.Direction;
 
+/**
+ * Detects disharmonies (code smells / antipatterns) in the collected class and
+ * method metrics. Based on the HIDOOP / DECOR / Lanza-Marinescu catalog.
+ *
+ * <p>This class is a pure function of the {@link ClassMetrics} and {@link
+ * MethodMetrics} populations produced by {@link GraphMetricsCollector}. It has
+ * no side effects and no external dependencies.
+ *
+ * <p>Threshold constants (FEW, HALF, ONE_THIRD, etc.) are defined at the top
+ * of the class and tuned to the literature values cited in the Lanza-Marinescu
+ * book. They can be adjusted for specific codebase characteristics if needed.
+ */
 public class DisharmonyDetector {
 
     // Linguistic quantifiers (Lanza & Marinescu, Table 2.4)
@@ -371,8 +383,10 @@ public boolean isBrainMethod(MethodMetrics metrics) {
     }
 
     /**
-     * Feature Envy (Fig. 5.4): method accesses more foreign data than local data.
-     * ATFD &gt; FEW AND LAA &lt; ONE_THIRD AND FDP &lt;= FEW
+     * Identifies methods that access substantially more foreign data than local data.
+     *
+     * @param metrics the method metrics to evaluate
+     * @return {@code true} if the method has feature envy, {@code false} otherwise
      */
     public boolean hasFeatureEnvy(MethodMetrics metrics) {
         return metrics.getAccessToForeignData() > FEW

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/metrics/GraphMetricsCollector.java

@@ -153,8 +153,8 @@ public void recordMethodMetric(String className, String methodSignature, String
 
     /**
      * Returns {@code true} iff at least one collected {@link ClassMetrics}
-     * carries a Kotlin-specific signal — i.e. {@link ClassMetrics#isDataClass()},
-     * {@link ClassMetrics#isSealed()}, {@link ClassMetrics#getNumberOfExtensionFunctions()}
+     * carries a Kotlin-specific signal — i.e. {@code ClassMetrics#isDataClass()},
+     * {@code ClassMetrics#isSealed()}, {@code ClassMetrics#getNumberOfExtensionFunctions()}
      * > 0, a non-empty {@link ClassMetrics#getExtensionReceiverTypes()}, or a
      * non-empty {@link ClassMetrics#getSealedHierarchyAncestors()}.
      *
@@ -174,7 +174,7 @@ public void recordMethodMetric(String className, String methodSignature, String
      * only after {@link #finalizeMetrics()} has run (detection always runs
      * post-finalization); before finalization the cached value is still
      * computed on demand but may not reflect {@link #computeKotlinDerivedMetrics()}
-     * derived flags such as {@link ClassMetrics#isHasExplicitLogic()}.
+     * derived flags such as {@code ClassMetrics#isHasExplicitLogic()}.
      *
      * @return {@code true} if any class carries a Kotlin-specific metric signal,
      *         {@code false} for an empty or Java-only collector
@@ -199,11 +199,9 @@ public boolean hasKotlinMetrics() {
     }
 
     /**
-     * Read-only lookup of a class's metrics. Returns {@code null} when the
-     * class has never been registered with this collector. Prefer
-     * {@link #getOrCreateClassMetrics(String)} from visitor logic that
-     * intends to mutate the returned instance and have the mutation
-     * reflected by {@link #getAllClassMetrics()}.
+     * Looks up the metrics recorded for a class.
+     *
+     * @return the class metrics, or {@code null} if no metrics are recorded
      */
     public ClassMetrics getClassMetrics(String className) {
         return classMetrics.get(className);
@@ -315,20 +313,10 @@ private int computeSealedDepth(ClassMetrics metrics) {
     }
 
     /**
-     * Canonical get-or-create entry point used by {@link MetricsVisitorLogic}
-     * and the metrics-collecting visitors. Returns the existing
-     * {@link ClassMetrics} for {@code className} if present, otherwise
-     * creates one, stores it in {@link #getAllClassMetrics()}, and returns
-     * it.
-     * <p>The returned instance is the <em>same object</em> later returned by
-     * {@link #getAllClassMetrics()}. This is the invariant the historical
-     * {@code instanceof GraphMetricsCollector} branch in
-     * {@link MetricsVisitorLogic#enterClass} emulated: the
-     * {@link ClassMetrics} the visitor mutates during the walk is the
-     * instance the downstream disharmony detectors read from
-     * {@link #getAllClassMetrics()}. Any get-or-create path that builds an
-     * instance without storing it would silently discard every class's
-     * metrics.
+     * Retrieves or creates metrics for a class.
+     *
+     * @param className the class name
+     * @return the existing or newly created class metrics
      */
     public ClassMetrics getOrCreateClassMetrics(String className) {
         return classMetrics.computeIfAbsent(className, ClassMetrics::new);

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/visitor/AbstractDependencyVisitor.java

@@ -30,6 +30,13 @@ public abstract class AbstractDependencyVisitor<P> extends JavaIsoVisitor<P> {
     @Getter
     private final DependencyVisitorState state;
 
+    /**
+     * Creates a new AbstractDependencyVisitor.
+     *
+     * @param repositoryPath       path to the source directory
+     * @param repositoryRoot       path to the repository root
+     * @param dependencyCollector  the dependency collector to use
+     */
     protected AbstractDependencyVisitor(
             String repositoryPath, String repositoryRoot, DependencyCollector dependencyCollector) {
         BaseTypeProcessor typeProcessor = new BaseTypeProcessor() {
@@ -61,6 +68,8 @@ public Javadoc visitDocComment(Javadoc.DocComment docComment, P p) {
      * Source-file extension used when synthetic source paths are produced for junit-based
      * tests (where the parser's URI is not usable as a repo path). Java returns {@code ".java"},
      * Kotlin returns {@code ".kt"}.
+     *
+     * @return the source file extension
      */
     protected String sourceFileExtension() {
         return ".java";
@@ -189,8 +198,9 @@ public J.MethodDeclaration visitMethodDeclaration(J.MethodDeclaration method, P
     }
 
     /**
-     * Returns the class-to-source-file-path mapping collected during the visit.
-     * Delegates to the internal state.
+     * Provides the source file path associated with each visited class.
+     *
+     * @return the class-to-source-file-path mapping
      */
     public Map<String, String> getClassToSourceFilePathMapping() {
         return state.getClassToSourceFilePathMapping();

codebase-graph-builder/src/main/java/org/hjug/graphbuilder/visitor/BaseTypeProcessor.java

@@ -9,13 +9,29 @@
 import org.openrewrite.java.tree.JavaType;
 import org.openrewrite.java.tree.TypeTree;
 
+/**
+ * Base type processor that provides common type-processing logic for
+ * dependency extraction. Subclasses implement {@link #getDependencyCollector()}
+ * to provide the dependency collector instance.
+ */
 @Slf4j
 public abstract class BaseTypeProcessor {
 
     private final TypeDependencyExtractor typeDependencyExtractor = new TypeDependencyExtractor();
 
+    /**
+     * Returns the dependency collector to use for recording class dependencies.
+     *
+     * @return the dependency collector
+     */
     protected abstract DependencyCollector getDependencyCollector();
 
+    /**
+     * Processes a Java type and extracts class dependencies.
+     *
+     * @param ownerFqn the fully qualified name of the type owner
+     * @param javaType the Java type to process
+     */
     protected void processType(String ownerFqn, JavaType javaType) {
         if (javaType == null || javaType instanceof JavaType.Unknown) {
             return;
@@ -26,6 +42,13 @@ protected void processType(String ownerFqn, JavaType javaType) {
         }
     }
 
+    /**
+     * Processes an annotation and records its class and argument type dependencies.
+     *
+     * @param ownerFqn   the fully qualified name of the owning type
+     * @param annotation the annotation to process
+     * @param cursor     the cursor providing processing context
+     */
     protected void processAnnotation(String ownerFqn, J.Annotation annotation, Cursor cursor) {
         if (annotation.getType() instanceof JavaType.Unknown) {
             return;
@@ -45,6 +68,14 @@ protected void processAnnotation(String ownerFqn, J.Annotation annotation, Curso
         }
     }
 
+    /**
+     * Processes a type parameter and extracts class dependencies from its bounds
+     * and annotations.
+     *
+     * @param ownerFqn      the fully qualified name of the type owner
+     * @param typeParameter the type parameter to process
+     * @param cursor        the cursor for context
+     */
     protected void processTypeParameter(String ownerFqn, J.TypeParameter typeParameter, Cursor cursor) {
         if (null != typeParameter.getBounds()) {
             for (TypeTree bound : typeParameter.getBounds()) {
@@ -59,6 +90,12 @@ protected void processTypeParameter(String ownerFqn, J.TypeParameter typeParamet
         }
     }
 
+    /**
+     * Processes all annotations at the given cursor position.
+     *
+     * @param ownerFqn the fully qualified name of the type owner
+     * @param cursor   the cursor for context
+     */
     protected void processAnnotations(String ownerFqn, Cursor cursor) {
         AnnotationService annotationService = new AnnotationService();
         for (J.Annotation annotation : annotationService.getAllAnnotations(cursor)) {