AdjacencyList

gistfile1.java

public class AdjacencyList implements Graph {

    private final int[][] vertexes;
    private final IAtom[] atoms;

    private final int n;

    public AdjacencyList(final IAtomContainer container) {

        this.n = container.getAtomCount();
        this.vertexes = new int[n][16];
        this.edges = new Edge[n][16];
        this.atoms = new IAtom[n];

        // keep the neighbour count to trim at the end
        int[] neighbours = new int[n];

        for (IBond bond : container.bonds()) {

            IAtom a1 = bond.getAtom(0);
            IAtom a2 = bond.getAtom(1);

            int i = container.getAtomNumber(a1);
            int j = container.getAtomNumber(a2);

            int in = neighbours[i];
            int jn = neighbours[j];

            vertexes[i][in] = j;
            vertexes[j][jn] = i;

            neighbours[i]++;
            neighbours[j]++;

        }

        // trim the adjacency list to size
        for (int i = 0; i < n; i++) {
            this.atoms[i] = container.getAtom(i);
            vertexes[i] = Arrays.copyOf(vertexes[i], neighbours[i]);
        }

    }
    
    public int[] neighbours(int i) {
        return vertexes[i];
    }

    public IAtom getVertexValue(int i){
        return atoms[i]; 
    }

}