Attempt integrating mce solver

src/main/java/de/uni/bremen/grapa/library/algorithms/NativeMaximumCliqueEnnumerationSolver.java

+package de.uni.bremen.grapa.library.algorithms;
+
+import de.uni.bremen.grapa.library.graphs.api.DirectedEdge;
+import de.uni.bremen.grapa.library.graphs.api.DirectedGraph;
+import de.uni.bremen.grapa.library.graphs.api.Vertex;
+import de.uni.bremen.grapa.library.helper.GetUndirectedGraph;
+import de.uni.bremen.grapa.library.helper.GraphRenaming;
+import de.uni.bremen.grapa.library.helper.GraphRenamingResult;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Scanner;
+import java.util.Set;
+
+/**
+ * Calls a native VC solver on an undirected graph instance.
+ * The solver is expected to be an executable binary called vc_solver in the working directory.
+ */
+public class NativeMaximumCliqueEnnumerationSolver {
+
+    private GetUndirectedGraph getUndirectedGraph = new GetUndirectedGraph();
+
+    /**
+     * Solves the vertex cover problem on a graph.
+     * Requires the directed graph to be in fact undirected.
+     *
+     * @param graph an undirected directed graph
+     * @return a vertex cover solution
+     */
+    public Collection<Set<Vertex>> solveMaximumCliqueEnumeration(final DirectedGraph<Vertex> graph) {
+        final DirectedGraph<Vertex> blueGraph = getUndirectedGraph.getBlueGraph(graph);
+
+
+        File solver = new File("mce_solver");
+
+        if (!solver.exists()) {
+            // Use packaged vc_solver instead
+            try (InputStream solverResource = (getClass().getResourceAsStream("/mce_solver"))) {
+                solver = File.createTempFile("mce_solver", "");
+                assert solverResource != null;
+                Files.copy(solverResource, solver.toPath(), StandardCopyOption.REPLACE_EXISTING);
+
+                // Set executable flag on solver.
+                // Return value may be unused, cause failure to set this will result in appropriate error later
+                solver.setExecutable(true);
+
+                // Clear the temporary file upon JVM shutdown
+                solver.deleteOnExit();
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        }
+
+        final ProcessBuilder processBuilder = new ProcessBuilder(solver.getAbsolutePath(), "--input-file=ignored", "--algorithm=tomita");
+        final GraphRenamingResult rename = new GraphRenaming().rename(blueGraph);
+        final DirectedGraph<Vertex> renamedGraph = rename.renamedGraph();
+        try {
+            final Process process = processBuilder.start();
+            final int offset = renamedGraph.vertexExists(0) ? 1 : 0;
+
+            final Scanner scanner = new Scanner(new BufferedInputStream(process.getInputStream()));
+            writeProblem(process, renamedGraph, offset);
+
+            final List<Set<Vertex>> readResult = readResult(renamedGraph, offset, scanner);
+
+            final Scanner errors = new Scanner(process.getErrorStream());
+            while (errors.hasNext()) {
+                System.err.println(errors.nextLine());
+            }
+
+            return rename.decipher(readResult);
+        } catch (IOException e) {
+            e.printStackTrace();
+            throw new IllegalStateException("MCE Solver not successful");
+        }
+    }
+
+    /**
+     * Reads a result from the peaty solver.
+     *
+     * @param graph input graph
+     * @param offset an offset which needs to be substracted as the input was shifted to avoid exceptions
+     * @return a minimum vertex cover determined by peaty
+     */
+    private List<Set<Vertex>> readResult(final DirectedGraph<Vertex> graph, final int offset, final Scanner scanner) {
+        List<Set<Vertex>> result = new ArrayList<>();
+
+        while (scanner.hasNext()){
+            final String line = scanner.nextLine();
+
+            if (line.startsWith("NOTE") || line.startsWith("Reading")) {
+                continue;
+            }
+            System.out.println(line);
+
+        }
+
+        return result;
+    }
+
+    /**
+     * Writes a problem for the peaty solver in its own process.
+     *
+     * @param process process called
+     * @param graph graph to write
+     * @param offset can be passed to eliminate values smaller than 1, needs to be kept in mind when parsin the result
+     */
+    private void writeProblem(final Process process, final DirectedGraph<Vertex> graph, final int offset) {
+        final PrintWriter writer = new PrintWriter(new OutputStreamWriter(new BufferedOutputStream(process.getOutputStream())));
+
+        writer.println(graph.maxId() + offset);
+        writer.println(graph.edgeCount() / 2);
+
+        for (final DirectedEdge edge : graph.getEdges()) {
+            if (edge.getStartId() < edge.getEndId()) {
+                writer.println((edge.getStartId() + offset) + "," + (edge.getEndId() + offset));
+            }
+        }
+
+        writer.close();
+    }
+
+}

src/main/java/de/uni/bremen/grapa/library/helper/GetUndirectedGraph.java

+package de.uni.bremen.grapa.library.helper;
+
+import de.uni.bremen.grapa.library.graphs.api.DirectedEdge;
+import de.uni.bremen.grapa.library.graphs.api.DirectedGraph;
+import de.uni.bremen.grapa.library.graphs.api.Vertex;
+
+import java.util.ArrayList;
+import java.util.LinkedList;
+
+/**
+ * Easy access to the undirected graph.
+ */
+public class GetUndirectedGraph {
+
+
+    /**
+     * Strips away red edges.
+     *
+     * @param originalGraph original graph
+     * @return just the blue graph with undirected edges
+     */
+    public DirectedGraph<Vertex> getBlueGraph(DirectedGraph<Vertex> originalGraph) {
+        final DirectedGraph<Vertex> blueGraph = originalGraph.shadowCopy();
+
+        for (final DirectedEdge edge : new ArrayList<>(blueGraph.getEdges())) {
+            if (blueGraph.edgeExists(edge.reverse())) {
+                continue;
+            } else {
+                blueGraph.removeEdge(edge);
+            }
+        }
+
+        for (final Vertex vertex : new ArrayList<>(blueGraph.getVertices())) {
+            if (blueGraph.inDegreeOf(vertex) == 0) {
+                blueGraph.removeVertex(vertex);
+            }
+        }
+
+        return blueGraph;
+    }
+}

src/main/java/de/uni/bremen/grapa/library/helper/GraphRenaming.java

+package de.uni.bremen.grapa.library.helper;
+
+import de.uni.bremen.grapa.library.graphs.api.DirectedGraph;
+import de.uni.bremen.grapa.library.graphs.api.Edge;
+import de.uni.bremen.grapa.library.graphs.api.Vertex;
+import de.uni.bremen.grapa.library.graphs.implementation.directed.BasicDirectedGraph;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Renames graphs to only make use of the lowest vertex ids.
+ */
+public class GraphRenaming {
+
+
+    /**
+     * Renames a graph.
+     *
+     * @param graph graph to be renamed
+     * @return result of renaming and a mapping to the original ids
+     */
+    public GraphRenamingResult rename(DirectedGraph<Vertex> graph) {
+        int[] backMapping = graph.getVertices().stream().mapToInt(Vertex::getId).toArray();
+        Map<Integer, Integer> forwardMapping = new HashMap<>();
+
+        DirectedGraph<Vertex> replacement = new BasicDirectedGraph();
+        for (int i = 0; i < backMapping.length; i++) {
+            forwardMapping.put(backMapping[i], i);
+            replacement.addVertex(new Vertex(i));
+        }
+
+        for (final Edge edge : graph.getEdges()) {
+            replacement.addEdge(forwardMapping.get(edge.getStartId()), forwardMapping.get(edge.getEndId()));
+        }
+
+        return new GraphRenamingResult(backMapping, replacement);
+    }
+
+
+}

src/main/java/de/uni/bremen/grapa/library/helper/GraphRenamingResult.java

+package de.uni.bremen.grapa.library.helper;
+
+import de.uni.bremen.grapa.library.graphs.api.DirectedGraph;
+import de.uni.bremen.grapa.library.graphs.api.Vertex;
+
+import java.util.Collection;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+/**
+ * A mapping and a renamed graph.
+ *
+ * @param mapping the previous value at the respective index
+ * @param renamedGraph the directed graph
+ */
+public record GraphRenamingResult(int[] mapping, DirectedGraph<Vertex> renamedGraph) {
+
+    public Collection<Set<Vertex>> decipher(final Collection<Set<Vertex>> input) {
+        return input.stream().map(this::decipher).toList();
+    }
+
+    public Set<Vertex> decipher(final Set<Vertex> input) {
+        return input.stream()
+                .mapToInt(Vertex::getId)
+                .map(id -> mapping[id])
+                .mapToObj(Vertex::new)
+                .collect(Collectors.toSet());
+    }
+}