Examples of nodesList()

Examples of cytoscape.CyNetwork.nodesList()

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  }
 
  public static void saveLayoutOfViewInFile(CyNetworkView view, File file){
    CyNetwork network = view.getNetwork();
      @SuppressWarnings("unchecked")
    List<CyNode> nodes = network.nodesList();
      List<CySBMLBoundingBox> boxes = new LinkedList<CySBMLBoundingBox>();
      for (CyNode node : nodes){
        NodeView nodeView = view.getNodeView(node);
       
        String nodeId = node.getIdentifier();
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Examples of cytoscape.CyNetwork.nodesList()

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      HashMap<String, CySBMLBoundingBox> boxesMap = XMLInterface.readLayoutFromXML(file);
      if (boxesMap != null){
     
        @SuppressWarnings("unchecked")
      List<CyNode> nodes = network.nodesList();
        for (CyNode node : nodes){
          // if position is stored
          String nodeId = node.getIdentifier();
          if (boxesMap.containsKey(nodeId)){
            CySBMLBoundingBox box = boxesMap.get(nodeId);
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Examples of cytoscape.CyNetwork.nodesList()

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    layout.setId(layoutId);
    layout.setName(layoutId);
   
    CyNetwork network = view.getNetwork();
      @SuppressWarnings("unchecked")
    List<CyNode> nodes = network.nodesList();
      CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
     
      for (CyNode node : nodes){
        NodeView nodeView = view.getNodeView(node);
        // Test if reaction or species node
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