src/LRMCseedsTUD_streamsafe.java

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.*;
import java.util.function.Consumer;

/**
 * LRMCseedsTUD_streamsafe.java
 *
 * Streaming LRMC seeder for graph-classification datasets (e.g., TUDataset:
 * ENZYMES, PROTEINS, COLLAB, D&D). Accepts either a single canonical
 * 0-indexed undirected edgelist file (u v with u < v), or a directory of such
 * files, and produces seeds JSON using the streaming reconstruction entry point
 * in clique2_ablations_parallel2.
 *
 * Usage:
 *   Single file:
 *     java -Xmx4g LRMCseedsTUD_streamsafe input_graph.txt output_seeds.json [DIAM|INV_SQRT_LAMBDA2] [epsilon]
 *
 *   Directory of files:
 *     java -Xmx4g LRMCseedsTUD_streamsafe input_dir output_dir [DIAM|INV_SQRT_LAMBDA2] [epsilon]
 *
 * Input edgelists are expected 0-indexed, undirected, no self-loops, one line
 * per edge with u < v. Output JSON mirrors LRMCseedsReddit_streamsafe format.
 */
public class LRMCseedsTUD_streamsafe {

    public static void main(String[] args) throws Exception {
        if (args.length < 2) {
            System.err.println("Usage: java LRMCseedsTUD_streamsafe <input_file_or_dir> <output_file_or_dir> [alpha_kind] [epsilon]");
            return;
        }

        final Path inPath = Paths.get(args[0]);
        final Path outPath = Paths.get(args[1]);
        final AlphaKind alphaKind = (args.length >= 3 ? parseAlpha(args[2]) : AlphaKind.DIAM);
        final double eps = (args.length >= 4 ? Double.parseDouble(args[3]) : 1e-6);

        if (Files.isDirectory(inPath)) {
            Files.createDirectories(outPath);
            try (java.util.stream.Stream<Path> stream = Files.list(inPath)) {
                stream.filter(Files::isRegularFile)
                      .filter(p -> {
                          String s = p.getFileName().toString().toLowerCase(Locale.ROOT);
                          return s.endsWith(".txt") || s.endsWith(".csv");
                      })
                      .forEach(p -> {
                          try {
                              GraphData Gi = loadEdgeList0Based(p);
                              String base = p.getFileName().toString().replaceFirst("\\.(txt|csv)$", "");
                              Path outFile = outPath.resolve(base + ".json");
                              runOnce(Gi, outFile, alphaKind, eps);
                          } catch (Exception e) {
                              throw new RuntimeException("Failed on " + p, e);
                          }
                      });
            }
        } else {
            GraphData G = loadEdgeList0Based(inPath);
            System.out.printf(Locale.US, "# Loaded edge list: n=%d, m=%d%n", G.n, G.m);
            runOnce(G, outPath, alphaKind, eps);
        }
    }

    static void runOnce(GraphData G, Path outSeeds, AlphaKind alphaKind, double eps) throws Exception {
        PeakTracker tracker = new PeakTracker(G, eps, alphaKind);
        // Streaming entry point (required by current pipeline)
        clique2_ablations_parallel2.runLaplacianRMCStreaming(G.adj1Based, tracker);
        tracker.writeJson(outSeeds);
        System.out.println("# Done. wrote " + outSeeds.toAbsolutePath());
    }

    // Streaming peak tracker (same output schema as Reddit seeder)
    static final class PeakTracker implements Consumer<clique2_ablations_parallel2.SnapshotDTO> {
        final GraphData G;
        final double epsilon;
        final AlphaKind alphaKind;

        final boolean[] inC;
        final Map<Integer, Integer> bestIdxByComp = new LinkedHashMap<>();
        final Map<Integer, Double> bestScoreByComp = new HashMap<>();
        final List<Rec> arrivals = new ArrayList<>();
        int idx = 0;

        static final class Rec {
            final int compId;
            final int sid;
            final double score;
            final int[] nodes;
            Rec(int compId, int sid, double score, int[] nodes) {
                this.compId = compId; this.sid = sid; this.score = score; this.nodes = nodes;
            }
        }

        PeakTracker(GraphData G, double epsilon, AlphaKind alphaKind) {
            this.G = G; this.epsilon = epsilon; this.alphaKind = alphaKind;
            this.inC = new boolean[G.n];
        }

        @Override
        public void accept(clique2_ablations_parallel2.SnapshotDTO s) {
            final int[] nodes = s.nodes;
            final int k = nodes.length;
            if (k == 0) return;
            for (int u : nodes) inC[u] = true;

            final double Q = s.Q;
            final double sc = k / (Q + epsilon);
            final int compId = s.componentId;
            final int sid = idx++;

            if (!bestIdxByComp.containsKey(compId) || sc > bestScoreByComp.get(compId)) {
                bestIdxByComp.put(compId, sid);
                bestScoreByComp.put(compId, sc);
            }
            arrivals.add(new Rec(compId, sid, sc, Arrays.copyOf(nodes, nodes.length)));

            for (int u : nodes) inC[u] = false;
        }

        void writeJson(Path outJson) throws IOException {
            final int n = G.n;
            boolean[] covered = new boolean[n];

            try (BufferedWriter w = Files.newBufferedWriter(outJson, StandardCharsets.UTF_8)) {
                w.write("{\n");
                w.write("\"meta\":{");
                w.write("\"epsilon\":" + epsilon);
                w.write(",\"alpha_kind\":\"" + (alphaKind == AlphaKind.DIAM ? "DIAM" : "INV_SQRT_LAMBDA2") + "\"");
                w.write(",\"n\":" + G.n);
                w.write(",\"m\":" + G.m);
                w.write(",\"mode\":\"peaks_per_component+singletons(stream)\"");
                w.write("},\n");
                w.write("\"clusters\":[\n");

                boolean first = true;
                int nextClusterId = 0;

                for (Rec r : arrivals) {
                    Integer best = bestIdxByComp.get(r.compId);
                    if (best != null && best == r.sid) {
                        if (!first) w.write(",\n");
                        first = false;
                        w.write("  {\"cluster_id\":" + (nextClusterId++));
                        w.write(",\"component_id\":" + r.compId);
                        w.write(",\"snapshot_id\":" + r.sid);
                        w.write(",\"score\":" + r.score);
                        w.write(",\"k_seed\":" + r.nodes.length);
                        w.write(",\"members\":" + intArrayToJson(r.nodes));
                        w.write(",\"seed_nodes\":" + intArrayToJson(r.nodes));
                        w.write("}");
                        for (int u : r.nodes) covered[u] = true;
                    }
                }

                for (int u = 0; u < n; u++) {
                    if (!covered[u]) {
                        if (!first) w.write(",\n");
                        first = false;
                        int[] singleton = new int[]{u};
                        w.write("  {\"cluster_id\":" + (nextClusterId++));
                        w.write(",\"component_id\":-1");
                        w.write(",\"snapshot_id\":-1");
                        w.write(",\"score\":0.0");
                        w.write(",\"k_seed\":1");
                        w.write(",\"members\":" + intArrayToJson(singleton));
                        w.write(",\"seed_nodes\":" + intArrayToJson(singleton));
                        w.write(",\"is_singleton\":true");
                        w.write("}");
                    }
                }
                w.write("\n]}");
            }
        }
    }

    // Loader for canonical 0-based undirected edgelists (u < v). Builds 1-based adjacency.
    static GraphData loadEdgeList0Based(Path edgesFile) throws IOException {
        int[] deg = new int[1 << 12];
        int maxNode = -1;
        long mUndir = 0;
        try (BufferedReader br = Files.newBufferedReader(edgesFile, StandardCharsets.UTF_8)) {
            String s;
            while ((s = br.readLine()) != null) {
                s = s.trim();
                if (s.isEmpty() || s.startsWith("#")) continue;
                String[] tok = s.split("\\s+|,");
                if (tok.length < 2) continue;
                int u = Integer.parseInt(tok[0]);
                int v = Integer.parseInt(tok[1]);
                if (u == v) continue;
                int needed = Math.max(u, v) + 1;
                if (needed > deg.length) {
                    int newLen = deg.length;
                    while (newLen < needed) newLen <<= 1;
                    deg = Arrays.copyOf(deg, newLen);
                }
                deg[u]++; deg[v]++;
                if (u < v) mUndir++;
                if (u > maxNode) maxNode = u;
                if (v > maxNode) maxNode = v;
            }
        }
        final int n = maxNode + 1;
        @SuppressWarnings("unchecked")
        List<Integer>[] adj1 = (List<Integer>[]) new List<?>[n + 1];
        for (int i = 1; i <= n; i++) adj1[i] = new ArrayList<>(deg[i - 1]);
        try (BufferedReader br = Files.newBufferedReader(edgesFile, StandardCharsets.UTF_8)) {
            String s;
            while ((s = br.readLine()) != null) {
                s = s.trim();
                if (s.isEmpty() || s.startsWith("#")) continue;
                String[] tok = s.split("\\s+|,");
                if (tok.length < 2) continue;
                int u = Integer.parseInt(tok[0]);
                int v = Integer.parseInt(tok[1]);
                if (u == v) continue;
                adj1[u + 1].add(v + 1);
                adj1[v + 1].add(u + 1);
            }
        }
        GraphData G = new GraphData();
        G.n = n; G.m = mUndir; G.adj1Based = adj1;
        G.labels = new int[n]; Arrays.fill(G.labels, -1);
        G.labelNames = new String[0];
        return G;
    }

    static AlphaKind parseAlpha(String s) {
        String t = s.trim().toUpperCase(Locale.ROOT);
        if (t.startsWith("DIAM")) return AlphaKind.DIAM;
        if (t.contains("LAMBDA")) return AlphaKind.INV_SQRT_LAMBDA2;
        return AlphaKind.DIAM;
    }

    static String intArrayToJson(int[] arr) {
        StringBuilder sb = new StringBuilder();
        sb.append('[');
        for (int i = 0; i < arr.length; i++) {
            if (i > 0) sb.append(',');
            sb.append(arr[i]);
        }
        sb.append(']');
        return sb.toString();
    }

    enum AlphaKind {DIAM, INV_SQRT_LAMBDA2}

    static final class GraphData {
        int n;
        long m;
        List<Integer>[] adj1Based;
        int[] labels;
        String[] labelNames;
    }
}