When I set the outpanel into a BoxLayout then the panel disappears. However the scrollbar shows that indicates my panel in ArrayList are in the right position. I am totally new to Java so I'll appreciate any comments.
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.util.*;
import javax.swing.*;
public class gui extends JFrame{
    int ctr=0, top=5;
    public List<JPanel> o_panels = new ArrayList<JPanel>(); //Your List    
    public gui(){
        super("MCC");
        setLayout(null);
        //Output panel for the results
        JPanel outpanel = new JPanel();
        outpanel.setBackground(Color.blue); 
        outpanel.setVisible(true);
        outpanel.setLayout(new BoxLayout(outpanel, BoxLayout.PAGE_AXIS));           
        //Scroll pane
        JScrollPane scrollPane = new JScrollPane(outpanel,
                JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
                JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);            
        scrollPane.setBounds(0,0,780,400);
        add(scrollPane);            
        //result panel
        //creating and adding panels in to the array list
        while(ctr<=4){
            JPanel label1 = new JPanel();
            label1.setPreferredSize(new Dimension(600,100));
            o_panels.add(label1);
            outpanel.add(o_panels.get(ctr));        
        ctr++;
        }
    }
    public void runGui(){
        this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        this.setSize(800,600);
        this.setVisible(true);
        this.setResizable(false);
        //i call this on the other class
    }
}
 
     
    
 
    