ForceDirectedGraph.java

import java.util.List;

public class ForceDirectedGraph<Atom, Spring> extends Graph {

        List<Applicator> applicatorList;
        ForceDirectedGraph(List<Atom> vertexList, List<Spring> edgeList,
                           List<Applicator> applicatorList) {
                super(vertexList, edgeList);
                this.applicatorList = applicatorList;
        }

        public void update() {
                Integer nodeListLength = vertexList.size();
                Integer edgeListLength = edgeList.size();

                for (Applicator app : applicatorList) {
                        for (int i = 0; i < nodeListLength; i++) {
                                Node a = (Node)vertexList.get(i);
                                if (app instanceof SecondOrderApplicator) {
                                        for (int j = i + 1; j < nodeListLength; j++) {
                                                if (i != j) {
                                                        Node b = (Node)vertexList.get(j);
                                                        if (a.getClass().equals(app.getAppliedClassByIndex(0)) &&
                                                            b.getClass().equals(app.getAppliedClassByIndex(1))) {
                                                                app.apply(a, b);
                                                        }
                                                }
                                        }
                                }
                                if (app instanceof FirstOrderApplicator) {
                                        if (a.getClass().equals(app.getAppliedClassByIndex(0)) || 
                                           (app.getAppliedClassByIndex(0).isInstance(a))) {
                                                app.apply(a);
                                        }
                                }
                        }

                        for (int i = 0; i < edgeListLength; i++) {
                                Edge e = (Edge)edgeList.get(i);
                                /* UNTESTED AS OF 12/2/15 */
                                if (app instanceof SecondOrderApplicator) {
                                        for (int j = i + 1; j < edgeListLength; j++) {
                                                if (i != j) {
                                                        Edge f = (Edge)edgeList.get(j);
                                                        if (e.getClass().equals(app.getAppliedClassByIndex(0)) &&
                                                            f.getClass().equals(app.getAppliedClassByIndex(1))) {
                                                                app.apply(e, f);
                                                        }
                                                }
                                        }
                                }
                                if (app instanceof FirstOrderApplicator) {
                                        if (e.getClass().equals(app.getAppliedClassByIndex(0)) ||
                                           (app.getAppliedClassByIndex(0).isInstance(e))) {
                                                app.apply(e);
                                        }
                                }
                        }
                }
                super.update();
        }

        public Double getKineticEnergy() {
                Double sum = 0.0d;
                Integer nodeListLength = vertexList.size();
                for (int i = 0; i < nodeListLength; i++) {
                        Node node = (Node)vertexList.get(i);
                        sum += node.getKineticEnergy();
                }
                return sum;
        }

}