Examples of CyRootNetwork

org.cytoscape.model.subnetwork.CyRootNetwork

Examples of org.cytoscape.model.subnetwork.CyRootNetwork

    if (clusters != null) {
      for (Cluster c : clusters)
        clusterNetworks.put(c.getNetwork(), Boolean.TRUE);
    }
    
    final CyRootNetwork rootNet = rootNetworkMgr.getRootNetwork(network);
    final Set<CySubNetwork> snSet = createdSubNetworks.get(rootNet);
    
    if (snSet != null) {
      final Set<CySubNetwork> disposedSet = new HashSet<CySubNetwork>();

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Examples of org.cytoscape.model.subnetwork.CyRootNetwork

    }
  }


  public void destroy(final CySubNetwork net) {
    if (net != null) {
      final CyRootNetwork rootNet = rootNetworkMgr.getRootNetwork(net);
      
      if (rootNet.containsNetwork(net)) {
        rootNet.removeSubNetwork(net);
        net.dispose();
      }
    }
  }

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Examples of org.cytoscape.model.subnetwork.CyRootNetwork

    
    return image;
  }


  public ClusterGraph createGraph(final CyNetwork net, final Collection<CyNode> nodes) {
    final CyRootNetwork root = rootNetworkMgr.getRootNetwork(net);
    final Set<CyEdge> edges = new HashSet<CyEdge>();


    for (final CyNode n : nodes) {
      final Set<CyEdge> adjacentEdges = new HashSet<CyEdge>(net.getAdjacentEdgeList(n, CyEdge.Type.ANY));

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Examples of org.cytoscape.model.subnetwork.CyRootNetwork


    return graph;
  }
  
  public CySubNetwork createSubNetwork(final CyNetwork net, final Collection<CyNode> nodes, final SavePolicy policy) {
    final CyRootNetwork root = rootNetworkMgr.getRootNetwork(net);
    final Set<CyEdge> edges = new HashSet<CyEdge>();


    for (CyNode n : nodes) {
      Set<CyEdge> adjacentEdges = new HashSet<CyEdge>(net.getAdjacentEdgeList(n, CyEdge.Type.ANY));


      // Get only the edges that connect nodes that belong to the subnetwork:
      for (CyEdge e : adjacentEdges) {
        if (nodes.contains(e.getSource()) && nodes.contains(e.getTarget())) {
          edges.add(e);
        }
      }
    }
    
    final CySubNetwork subNet = root.addSubNetwork(nodes, edges, policy);
    
    // Save it for later disposal
    Set<CySubNetwork> snSet = createdSubNetworks.get(root);
    
    if (snSet == null) {

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