RCaller，线程处理和Java GUI

Question

I am making a Java GUI to go with my colleague's custom made R package, IntramiRExploreR, which includes a function made to create an interactive graphic via igraph and IntramiRExploreR's Visualisation function, using the following parameters:

    Visualisation(miR,mRNA_type=c('GeneSymbol'),method,thresh,platform=Platform,visualisation = 'igraph',layout = 'interactive')

where miR is a vector made via selected JCheckboxes, and method, thresh, and platform are populated from JRadioButtons. I've no doubt the function itself and how the variables are filled in is correct, as I have run the function in R and run the function using a text output format and both run correctly.

The code first fills out a JTable correctly with the results from

    Visualisation(miR,mRNA_type=c('GeneSymbol'),method,thresh,platform=Platform)

which outputs text accessible using

    caller.getParser().getAsStringArray(//one of seven parameters)

then provides a JButton to use the same parameters and objects to call the aforementioned igraph function in R. However, when the JButton is clicked, the igraph is created but then its frame is disposed as soon as the graphic is fully made. The second time the button is clicked, calling the function again, the provided error is:

    Exception in thread "AWT-EventQueue-0" com.github.rcaller.exception.ExecutionException: Can not run C:\Program Files\R\R-3.3.0\bin\x64\Rscript.exe. Reason: java.lang.IllegalThreadStateException

Should I create new thread to handle the igraph visualisation, or is there some method in RCaller I am missing that can handle this? Is Java emptying its memory of my objects after I call a second RCaller and RCode block?

Here's what of my code I can show without violating my agreement to confidentiality:

    public void actionPerformed(ActionEvent e){//if goButton is clicked
                if(e.getSource() == goButton){
                    JFrame resultFrame = new JFrame("Results: For full readout, use export button below.");//creates entire resultFrame
                    resultFrame.setLayout(new BorderLayout());
                    resultFrame.setSize(new Dimension(950,750));
                    JPanel resultBack = new JPanel();
                    resultBack.setLayout(new BorderLayout());//creates the resultBack to be placed into JScrollPane

                //RESULTS (from user query; calls R commands to fill out JTable)
                    //create int checkCnt to keep track of how much info is needed
                        int checkCnt = 0;
                        for(int t = 0;t<155;t++){
                            if(selected[0][t]==true){//if targets for one miR with index t is queried
                                checkCnt++;
                            }}

                //create JTable 
                        //create column names
                        String[] colNames = {"miRNA", "tar_GS", "tar_FB", "tar_CG", "Score", "Function", "Experiment", "Method"};

                        //determine threshold
                            int threshold=0;
                            if(checkCnt==1){threshold=100;}
                            if(checkCnt==2){threshold=50;}
                            if(checkCnt==3){threshold=33;}
                            if(checkCnt==4){threshold=25;}
                            if(checkCnt>=5){threshold=20;}

                            /*create RCaller and wire query to buttons; 
                            code handles table filling,
                            ///code1 handles graphic display*/
                             RCaller caller = RCaller.create();
                             RCaller caller1 = RCaller.create();
                             RCode code = RCode.create();
                             RCode code1 = RCode.create();
                             code.R_require("IntramiRExploreR");
                             code.R_require("futile.logger");
                             code.R_require("devtools");
                             code.R_require("Runiversal");
                             code1.R_require("IntramiRExploreR");
                             code1.R_require("futile.logger");
                             code1.R_require("devtools");

                             //create array of selected miRs to input to R code
                             String[] chosen = new String[checkCnt];
                             for(int kk=0;kk<checkCnt;kk++){
                                 chosen[kk] = litmiR(selected)[kk];
                             }
                             code.addStringArray("miR", chosen);
                             code.addInt("thresh", threshold);
                             code1.addStringArray("miR", chosen);
                             code1.addInt("thresh", threshold);
                             String method =new String();

                             if(Pears.isSelected()){
                                 method="Pearson";
                                 code.addString("method", method);
                                 code1.addString("method", method);
                                }
                             else if(Dist.isSelected()){
                                 method="Distance";
                                 code.addString("method", method);
                                 code1.addString("method", method);
                                }
                             else{
                                 method="Both";
                                 code.addString("method", method);
                                 code1.addString("method", method);
                             }
                             if(Affy1.isSelected()){
                                 String Platform="Affy1";
                                 code.addString("Platform", Platform);
                                 code1.addString("Platform", Platform);
                             }
                             else{
                                 String Platform="Affy2";
                                 code.addString("Platform", Platform);
                                 code1.addString("Platform", Platform);
                             }


                             code.addRCode("yy <-Visualisation(miR,mRNA_type=c('GeneSymbol'),method,thresh,platform=Platform)"); 
                              String [] aa= caller.getParser().getAsStringArray("miRNA"); 
                              String [] aa1= caller.getParser().getAsStringArray("Target_GeneSymbol"); 
                              String [] aa2= caller.getParser().getAsStringArray("Targets_FBID"); 
                              String [] aa3= caller.getParser().getAsStringArray("Targets_CGID"); 
                              double [] aa4= caller.getParser().getAsDoubleArray("Score"); 
                              //convert double array to string array
                              String [] sa4= new String[aa4.length];
                              for(int ss=0;ss<aa4.length;ss++){
                                  sa4[ss]= Double.toString(aa4[ss]);
                              }
                              String [] aa5 = caller.getParser().getAsStringArray("GeneFunction");
                              String [] aa6 = caller.getParser().getAsStringArray("Experiments");


                        //create JTable objects
                            String[][] results = new String[checkCnt*threshold][8];
                            int w = 0;
                            int x = 0;
                            for(int n=0;n<checkCnt;n++){
                                for(int jj=0;jj<threshold;jj++){//first miR
                                    results[jj+w][0]=aa[jj+x*threshold];//the first miR, then the next one after n loops once
                                    results[jj+w][1]=aa1[jj+x*threshold];//tar_GS
                                    results[jj+w][2]=aa2[jj+x*threshold];//tar_FB
                                    results[jj+w][3]=aa3[jj+x*threshold];//tar_CG
                                    results[jj+w][4]= sa4[jj+x*threshold];//Score
                                    results[jj+w][5]=aa5[jj+x*threshold];//Function
                                    results[jj+w][6]=aa6[jj+x*threshold];//Experiment

                                }
                                w=w+threshold;
                                x++;
                            }
                            System.out.println(checkCnt);

                        //make JTable
                            JTable resultTable = new JTable(results, colNames); 

                    //create scroll pane to embed results JTable in; allow for vertical scrolling
                        JScrollPane scrollTable = new JScrollPane(resultTable);
                        resultTable.setFillsViewportHeight(true);
                        scrollTable.setPreferredSize(new Dimension(resultBack.getWidth(),(resultFrame.getHeight()-150)));
                        scrollTable.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
                        scrollTable.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
                        scrollTable.getVerticalScrollBar().setUnitIncrement(12);

                    //create bottom buttonPanel to allow for visualization, exportation, and ontological research
                        JPanel buttonPanel = new JPanel();
                        buttonPanel.setPreferredSize(new Dimension(200, 150));
                        buttonPanel.setBackground(Color.LIGHT_GRAY);
                        buttonPanel.setLayout(null);


                        //create buttons
                            JButton gOnt = new JButton("Gene Ontology");
                            gOnt.setFont(new Font("Arial", Font.PLAIN, 18));
                            gOnt.setBorder(BorderFactory.createLineBorder(Color.BLACK));
                            gOnt.setBounds(50,50,250,100);
                            buttonPanel.add(gOnt);
                            JButton vis = new JButton("Visualization");
                            vis.setFont(new Font("Arial", Font.PLAIN, 18));
                            vis.setBorder(BorderFactory.createLineBorder(Color.BLACK));
                            vis.setBounds(650,50,250,100);
                            buttonPanel.add(vis);
                            vis.addActionListener(new ActionListener(){
                                **public void actionPerformed(ActionEvent v){
                                    if(v.getSource() == vis){

                                        code1.addRCode("yy1<-Visualisation(miR,mRNA_type=c('GeneSymbol'),method,thresh,platform=Platform,visualisation = 'igraph',layout = 'interactive')");
                                        caller1.setRCode(code1);
                                        caller1.runAndReturnResult("yy1");
                                    }
                                }
                            });**
                            JButton exp = new JButton("Export as .txt file");
                            exp.setFont(new Font("Arial", Font.PLAIN, 18));
                            exp.setBorder(BorderFactory.createLineBorder(Color.BLACK));
                            exp.setBounds(350, 50, 250, 100);
                            buttonPanel.add(exp);


                    resultFrame.setLocation(470,150);//add in the panels and display the resultFrame
                    resultFrame.add(buttonPanel, BorderLayout.PAGE_END);
                    resultFrame.add(scrollTable, BorderLayout.PAGE_START);
                    resultFrame.setVisible(true);
                    }}});

The area of concern is the ActionListener for my JButton vis. I am absolutely certain that all else is well, but the igraph is unresponsive at first after populating and then a second call provides the IllegalThreadException error.

Answer 1

This is what I would check first:

The GUI can NOT be modified from a NON gui thread.

Make sure you have a background thread that passes the info to the GUI. Otherwise the GUI will become unresponsive until it finishes the processing (this is in the scenario of no background thread)

You can always put a gui runnable around the actionPerformed code.

In your case

SwingUtilities.invokeLater(new Runnable() {...});