import org.gephi.graph.api.UndirectedGraph; //导入依赖的package包/类
private void rebuildGraph(UndirectedGraph graph, Cluster[] clusters, double[][] annFreq, double K) {
    graph.clearEdges();

    for (int i = 0; i < clusters.length; i++) {
        for (int j = i + 1; j < clusters.length; j++) {
            double cos = MatrixOp.getEuclideanCosine(annFreq[i], annFreq[j]);
            /*double weight = 1; 
             for (double k = cos; k <= 1.0; k+=0.01) {
             weight -= vonMisesFisherDistribution.getProbabilityDensityOverCosAforK(k, 0, annFreq[0].length);
             }
             weight+=Math.max(weight,0)*2;
             */
            double weight = Math.exp(K * cos) / Math.exp(K);

            float dist = (float) (weight * EDGE_SCALING);
            if (dist > 0.05) {
                graph.addEdge(nodes[i], nodes[j]);
                graph.getEdge(nodes[i], nodes[j]).setWeight(dist);
            }
        }
    }
    for (int i = 0; i < 1000 && layout.canAlgo(); i++) {
        layout.goAlgo();
    }
}
 

import org.gephi.graph.api.UndirectedGraph; //导入依赖的package包/类
public Partition<Node> partition(Graph<MultimodalItem, SameClassLink> itemsGraph) {

		UndirectedGraph graph = getGraph(itemsGraph);
		
		System.out.println("Nodes: " + graph.getNodeCount());
		System.out.println("Edges: " + graph.getEdgeCount());

		AttributeModel attributeModel = Lookup.getDefault().lookup(AttributeController.class).getModel();
		
		// Run modularity algorithm - community detection
		Modularity modularity = new Modularity();
		modularity.setUseWeight(true);
		modularity.setResolution(1.);
		modularity.setRandom(true);
		modularity.execute(graphModel, attributeModel);
		
		AttributeColumn modColumn = attributeModel.getNodeTable().getColumn(Modularity.MODULARITY_CLASS);

		@SuppressWarnings("unchecked")
		Partition<Node> p = partitionController.buildPartition(modColumn, graph);
		
		return p;
	}
 

import org.gephi.graph.api.UndirectedGraph; //导入依赖的package包/类
public void setGraph(UndirectedGraph graph) {
    this.graph = graph;
}
 

import org.gephi.graph.api.UndirectedGraph; //导入依赖的package包/类
private UndirectedGraph getGraph(Graph<MultimodalItem, SameClassLink> itemsGraph) {
   	UndirectedGraph graph = graphModel.getUndirectedGraph();
   	
	int v = 0;
   	Collection<MultimodalItem> vertices = itemsGraph.getVertices();
   	for(MultimodalItem vertex : vertices) {
   		if(!nodes.containsKey(vertex.id)) {
   			Node node = factory.newNode(vertex.id);
   			nodes.put(vertex.id, node);
   			graph.addNode(node);
   		}
   		if(++v%10000==0) {
   			System.out.println(v + " nodes inserted into graph");
   		}
   	}
   	
   	int e = 0;
   	long t1 = 0, t2 = 0;
   	Collection<SameClassLink> edges = itemsGraph.getEdges();
   	for(SameClassLink edge : edges) {
   		long t = System.currentTimeMillis();
   		Pair<MultimodalItem> endpoints = itemsGraph.getEndpoints(edge);
   		
   		MultimodalItem item1 = endpoints.getFirst();
   		MultimodalItem item2 = endpoints.getSecond();
   		t1 += (System.currentTimeMillis() - t);
   		
   		
   		Node n1 = nodes.get(item1.id);
   		Node n2 = nodes.get(item2.id);
   		
   		if(edge.weight == 1) {
   			t = System.currentTimeMillis();
   			graph.addEdge(factory.newEdge(n1, n2, edge.weight, false));
   			t2 += (System.currentTimeMillis() - t);
   		}
   		
   		if(++e%100000==0) {
   			System.out.println(e + " edges inserted into graph. Load:" + t1 + ", Insert:" + t2);
   		}
   	}
   	
   	return graph;
}