Feature: Implement constrained k-mer generation and clique search

This commit introduces core functionality for oligonucleotide family tagging, constrained k-mer generation, and clique finding. It also includes updates to the Go language version and refactors the logic for k-mer dissimilarity metrics.

pkg/obigraph/clique_test.go

@@ -0,0 +1,143 @@
+package obigraph
+
+import (
+	"context"
+	"math/bits"
+	"math/rand"
+	"testing"
+	"time"
+)
+
+// adjacency matrix filter for small graphs
+func matrixFilter(adj [][]bool) NeighborFilter {
+	return func(v int32, candidates, out []int32) []int32 {
+		for _, c := range candidates {
+			if adj[v][c] {
+				out = append(out, c)
+			}
+		}
+		return out
+	}
+}
+
+func randomGraph(rng *rand.Rand, n int, p float64) [][]bool {
+	adj := make([][]bool, n)
+	for i := range adj {
+		adj[i] = make([]bool, n)
+	}
+	for i := 0; i < n; i++ {
+		for j := i + 1; j < n; j++ {
+			if rng.Float64() < p {
+				adj[i][j], adj[j][i] = true, true
+			}
+		}
+	}
+	return adj
+}
+
+// maximum clique size by brute force over all the subsets (n <= 20)
+func bruteMaxClique(adj [][]bool) int {
+	n := len(adj)
+	best := 0
+	for mask := 1; mask < 1<<n; mask++ {
+		size := bits.OnesCount(uint(mask))
+		if size <= best {
+			continue
+		}
+		ok := true
+		for i := 0; i < n && ok; i++ {
+			if mask>>i&1 == 0 {
+				continue
+			}
+			for j := i + 1; j < n; j++ {
+				if mask>>j&1 == 1 && !adj[i][j] {
+					ok = false
+					break
+				}
+			}
+		}
+		if ok {
+			best = size
+		}
+	}
+	return best
+}
+
+func isClique(adj [][]bool, c []int32) bool {
+	seen := map[int32]bool{}
+	for i, a := range c {
+		if seen[a] {
+			return false
+		}
+		seen[a] = true
+		for _, b := range c[i+1:] {
+			if !adj[a][b] {
+				return false
+			}
+		}
+	}
+	return true
+}
+
+func TestFindCliqueAgainstBruteForce(t *testing.T) {
+	rng := rand.New(rand.NewSource(1))
+	for trial := 0; trial < 40; trial++ {
+		n := 8 + rng.Intn(10)
+		adj := randomGraph(rng, n, 0.3+0.5*rng.Float64())
+		maxSize := bruteMaxClique(adj)
+		filter := matrixFilter(adj)
+
+		for _, workers := range []int{1, 3} {
+			r := FindClique(context.Background(), n, filter, maxSize, CliqueOptions{Workers: workers})
+			if !r.Reached || len(r.Clique) < maxSize || !isClique(adj, r.Clique) {
+				t.Fatalf("trial %d: target %d not reached: %+v", trial, maxSize, r)
+			}
+
+			r = FindClique(context.Background(), n, filter, maxSize+1, CliqueOptions{Workers: workers})
+			if r.Reached || !r.Exhausted {
+				t.Fatalf("trial %d: size %d cannot exist, got %+v", trial, maxSize+1, r)
+			}
+			// best effort: a valid clique, not necessarily a maximum one
+			if len(r.Clique) < 1 || len(r.Clique) > maxSize || !isClique(adj, r.Clique) {
+				t.Fatalf("trial %d: invalid best clique %v (maximum is %d)", trial, r.Clique, maxSize)
+			}
+		}
+	}
+}
+
+func TestFindCliqueTrivialTargets(t *testing.T) {
+	adj := randomGraph(rand.New(rand.NewSource(2)), 5, 0.5)
+	if r := FindClique(context.Background(), 5, matrixFilter(adj), 0, CliqueOptions{}); !r.Reached {
+		t.Fatal("target 0 is always reached")
+	}
+	if r := FindClique(context.Background(), 0, matrixFilter(adj), 1, CliqueOptions{}); r.Reached {
+		t.Fatal("no clique in an empty graph")
+	}
+	if r := FindClique(context.Background(), 5, matrixFilter(adj), 1, CliqueOptions{}); !r.Reached || len(r.Clique) != 1 {
+		t.Fatalf("a single vertex is a clique: %+v", r)
+	}
+}
+
+// A hopeless search must stop with the deadline and return a valid clique.
+// (When the target is far above the clique number of a sparse graph, pruning
+// proves the absence at once: see TestFindCliqueAgainstBruteForce.)
+func TestFindCliqueTimeout(t *testing.T) {
+	// dense graph: its largest clique is far below the target, but pruning only
+	// bites after many levels, so the search cannot finish within the deadline
+	const n = 300
+	adj := randomGraph(rand.New(rand.NewSource(3)), n, 0.9)
+	ctx, cancel := context.WithTimeout(context.Background(), 300*time.Millisecond)
+	defer cancel()
+
+	start := time.Now()
+	r := FindClique(ctx, n, matrixFilter(adj), 150, CliqueOptions{Workers: 2})
+	if elapsed := time.Since(start); elapsed > 3*time.Second {
+		t.Fatalf("deadline not honoured: %v", elapsed)
+	}
+	if r.Reached || r.Exhausted {
+		t.Fatalf("size 150 cannot be reached nor proven absent in time: %+v", r)
+	}
+	if len(r.Clique) < 2 || !isClique(adj, r.Clique) {
+		t.Fatalf("invalid best clique %v", r.Clique)
+	}
+}