Method apply has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    @Override
    public ClusteringAlgorithm<V> apply(Graph<V, E> graph) {
        switch (algorithm) {
            case EMPTY:
                return EmptyClustering.<V, E>builder().apply(graph);

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Method write has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    public static <V> void write(BufferedWriter writer, List<NodeEmbedding<V>> embeddings, SpaceStrategy spaceStrategy) throws IOException {
        if (embeddings.isEmpty()) {
            throw new IllegalArgumentException("embeddings should not be empty");
        }

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Method extractClusters has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

        protected Map<V, Set<V>> extractClusters() {
            final var leaves = new HashSet<>(graph.vertexSet().size());
            final var clusters = new HashMap<V, Set<V>>();

            for (final var u : digraph.vertexSet()) {

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Method evaluate has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    public PrecisionRecall evaluate(Set<Pair<V, V>> clusterPairs, Set<Pair<V, V>> classPairs) {
        final var union = new HashSet<>(clusterPairs);
        union.addAll(classPairs);

        final var preds = new boolean[union.size()];

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Method apply has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    @Override
    public ClusteringAlgorithm<V> apply(Graph<V, E> graph) {
        switch (algorithm) {
            case EMPTY:
                return EmptyClustering.<V, E>builder().apply(graph);

Method main has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    public static void main(String[] args) {
        var graph = SimpleWeightedGraph.<String, DefaultWeightedEdge>createBuilder(DefaultWeightedEdge.class).
                addVertices("a", "b", "c", "d", "e").
                addEdge("a", "b").
                addEdge("a", "c").

Method compute has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

        public Clustering<V> compute() {
            if (graph.vertexSet().isEmpty()) {
                return new ClusteringImpl<>(Collections.emptyList());
            }

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Method getContexts has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

        @Override
        public Map<Sense<V>, Map<Sense<V>, Number>> getContexts() {
            if (isNull(contexts)) {
                contexts = new HashMap<>(senseGraph.vertexSet().size());

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Method run has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    @Override
    public void run() {
        final var clusters = transform(getClusters());
        final var classes = transform(getClasses());

Method process has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        protected void process() throws IOException {
            output = File.createTempFile("mcl", "output");
            output.deleteOnExit();

            final var input = writeInputFile();

Method write has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    public static <V> void write(BufferedWriter writer, List<NodeEmbedding<V>> embeddings, SpaceStrategy spaceStrategy) throws IOException {
        if (embeddings.isEmpty()) {
            throw new IllegalArgumentException("embeddings should not be empty");
        }

Avoid deeply nested control flow statements.

Open

                            if (digraph.containsVertex(v)) queue.addAll(Graphs.successorListOf(digraph, v));

Method argrandmax has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    public static <V, S extends Comparable<S>> Optional<V> argrandmax(Iterable<V> iterable, Function<V, S> scorer, Random random) {
        final var results = new ArrayList<V>();
        S score = null;

        for (final var current : iterable) {

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Method run has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    @Override
    public void run() {
        final var clusters = transform(getClusters());
        final var classes = transform(getClasses());

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Method computeWeights has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

        private void computeWeights() {
            for (final var edge : graph.edgeSet()) {
                final var u = graph.getEdgeSource(edge);
                final var v = graph.getEdgeTarget(edge);
                final var weight = graph.getEdgeWeight(edge);

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Method write has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    public static void write(BufferedWriter writer, ClusteringAlgorithm.Clustering<String> clustering) throws IOException {
        final Iterable<Set<String>> clusters = () -> clustering.getClusters().stream().
                sorted((smaller, larger) -> Integer.compare(larger.size(), smaller.size())).
                iterator();

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Avoid too many return statements within this method.

Open

                return mclOfficial.apply(graph);

Method argmax has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    public static <V, S extends Comparable<S>> Optional<V> argmax(Iterable<V> iterable, Predicate<V> checker, Function<V, S> scorer) {
        V result = null;
        S score = null;

        for (final var current : iterable) {

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