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JFileChooser from a command line program and popping up Underneath all windows
System.out.println("Please select the file");
JFileChooser fc = new JFileChooser();
int retValue = fc.showOpenDialog(new JPanel());
if(retValue == JFileChooser.APPROVE_OPTION){
    g.inputFile = fc.getSelectedFile();
}else {
    System.out.println("Next time select a file.");
    System.exit(1);
}

int retValue = fc.showOpenDialog(new JPanel());

public class ChooseFile {
    private JFrame frame;
    public ChooseFile() {
        frame = new JFrame();

        frame.setVisible(true);
        BringToFront();
    }
    public File getFile() {
        JFileChooser fc = new JFileChooser();
        if(JFileChooser.APPROVE_OPTION == fc.showOpenDialog(null)){
            frame.setVisible(false);
            return fc.getSelectedFile();
        }else {
            System.out.println("Next time select a file.");
            System.exit(1);
        }
        return null;
    }

    private void BringToFront() {
                    frame.setExtendedState(JFrame.ICONIFIED);
            frame.setExtendedState(JFrame.NORMAL);

    }

}

System.out.println("Please select the file");
g.inputFile = g.new ChooseFile().getFile();