Package org.cytoscape.ClusterViz.internal.algorithm

Examples of org.cytoscape.ClusterViz.internal.algorithm.Algorithm$NodeInfo


        }*/
        //notice, here we set the selected nodes

        currentParamsCopy.setSelectedNodes(selectedNodesRGI);

        Algorithm alg1 = null;
        boolean newNet=isDirty(network);//judge new network
       
        

       

        ParameterSet savedParamsCopy;
        if (this.clusterUtil.containsNetworkAlgorithm(network.getSUID().longValue())) {
//          alg1 = this.clusterUtil.getNetworkAlgorithm(network.getSUID().longValue());

         
         
          savedParamsCopy = this.clusterUtil.getCurrentParameters().getParamsCopy(network.getSUID());
         
          analyze=checkParams(currentParamsCopy, newNet);
         
         
        } else {
          //clusterUtil.getNetworkAlgorithm(network.getSUID().longValue())
         
         
         
          savedParamsCopy = this.clusterUtil.getCurrentParameters().getParamsCopy(null);
        
                 
          this.analyze = 0;
        }
       

       
       

       
        if (analyze == INTERRUPTED || analyze == EXISTS)
          JOptionPane.showMessageDialog(AnalyzeAction.this.swingApplication.getJFrame(),
                interruptedMessage, "Interrupted", JOptionPane.WARNING_MESSAGE);
        else
        final int resultId = this.clusterUtil.getCurrentResultId();

        if ((this.analyze == 0) || (isDirty(network)) || (!currentParamsCopy.getAlgorithm().equals(savedParamsCopy.getAlgorithm())) ||
          (currentParamsCopy.isIncludeLoops() != savedParamsCopy.isIncludeLoops()) ||
          (currentParamsCopy.getDegreeCutoff() != savedParamsCopy.getDegreeCutoff())) {
          this.analyze = 1;
//         logger.debug("Analysis: score network, find clusters");
          this.clusterUtil.getCurrentParameters().setParams(currentParamsCopy, resultId, network.getSUID());
        } else if (!checkEqual(savedParamsCopy, currentParamsCopy)) {
          this.analyze = 2;
  //        logger.debug("Analysis: find clusters");
          this.clusterUtil.getCurrentParameters().setParams(currentParamsCopy, resultId, network.getSUID());
        } else {
          this.analyze = 3;
          interruptedMessage = "The parameters you specified have not changed.";
          this.clusterUtil.getCurrentParameters().setParams(currentParamsCopy, resultId, network.getSUID());
        }

        if(currentParamsCopy.getAlgorithm().equals(ParameterSet.MCODE ))
            alg1 = new MCODE(network.getSUID(), this.clusterUtil);
        if(currentParamsCopy.getAlgorithm().equals(ParameterSet.EAGLE ))
            alg1 = new EAGLE(network.getSUID(), this.clusterUtil);
        if(currentParamsCopy.getAlgorithm().equals(ParameterSet.FAGEC ))
            alg1 = new FAGEC(network.getSUID(), this.clusterUtil);
        this.clusterUtil.addNetworkAlgorithm(network.getSUID().longValue(), alg1);
       
/*      
        //if (!networkManager.containsKey(network.getIdentifier())){
          newNet=true;
      alg = curParams.getAlg();
            //alg = new Algorithm(null);
            networkManager.put(network.getSUID(), alg);
        //}
        //else alg = (Algorithm) networkManager.get(network.getIdentifier());
        //check the validation the input parameters
        analyze=checkParams(curParams, newNet);
       
       
        resultId = this.clusterUtil.getCurrentResultId();
       
        if (analyze == INTERRUPTED || analyze == EXISTS)
            JOptionPane.showMessageDialog(nullCytoscape.getDesktop(),
                interruptedMessage, "Interrupted", JOptionPane.WARNING_MESSAGE);
        else{           
            //update the parameter set with this result title
          clusterUtil.getCurrentParameters().setParams(curParams,  (resultCounter + 1),
                network.getSUID());*/
         

        if ((currentParamsCopy.getScope().equals(ParameterSet.SELECTION)) &&
          (currentParamsCopy.getSelectedNodes().length < 1)) {
          this.analyze = 3;
          interruptedMessage = "You must select ONE OR MORE NODES\nfor this scope.";
        }

        if (this.analyze == 3) {
          JOptionPane.showMessageDialog(this.swingApplication.getJFrame(),
            interruptedMessage,
            "Analysis Interrupted",
            2);
        }
        else {
         
            
         final  Algorithm alg2=alg1;
          AnalysisCompletedListener listener = new AnalysisCompletedListener()
            {
              public void handleEvent(AnalysisCompletedEvent e)
              {
                ResultPanel resultsPanel = null;
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