[Riftwalker]

I'm pretty sure that this is the case, but I'll post the pertinent code for each.

JPanel 1 (the one that works)

Code:

public class displayPanel extends JPanel implements Scrollable
{	
	private mainWindow mainWin;
	private Graphics2D g2;
	private sequenceDisplayPanel sdPanel;
	private int contigNum = 0;
	private Contig[] contigArray;
	private interactiveRectangle[] rectArray;
	private displayPanel displaypanel;
	private Rectangle backbone;
	private String contigName;

	public displayPanel(mainWindow mw, sequenceDisplayPanel sdP)
	{
		mainWin = mw;
		sdPanel = sdP;
		displaypanel = this;
		setPreferredSize(new Dimension(1000,500));
		setBackground(Color.WHITE);
		
		displaypanelMListener clickListener = new displaypanelMListener();
		addMouseListener(clickListener);
	}
	
	public void paintComponent(Graphics g)
	{
		super.paintComponent(g);
		g2 = (Graphics2D)g;
		
		try
		{
			g2.setColor(Color.BLACK);
			g2.drawString(contigName, 40, 35);
			g2.fill(backbone);
			for(int j = 40; j < contigArray[contigNum].getContigLength(); j += 100)
			{
				g2.drawString(String.valueOf(j-40), j , 50);
				g2.drawLine(j, 55, j, 80);
			}
			
			for(int i = 0; i < rectArray.length; i++)
			{
				Rectangle tempRect = rectArray[i];
				g2.setColor(Color.BLUE);
				g2.fill(tempRect);
			}
		}
		catch(NullPointerException nullPointerException){}
	}

JPanel 2 (the one with problems)

Code:

public class sequenceDisplayPanel extends JPanel implements Scrollable
{
	private JFrame mainWin;
	private Graphics2D g2;
	private interactiveRectangle[] rectArray;
	private sequenceDisplayPanel sdPanel;
	private int paintY = 20;
	private int rectNum = 0;
	
	public sequenceDisplayPanel(JFrame mW)
	{
		mainWin = mW;
		sdPanel = this;
		setPreferredSize(new Dimension(1000,100));
		setBackground(Color.WHITE);
	}
	
	public void paintComponent(Graphics g)
	{
		super.paintComponent(g);
		g2 = (Graphics2D)g;
		
		try
		{
			g2.drawString(rectArray[rectNum].getContigName(), 20, paintY);
			paintY += 15;
			String tempString = rectArray[rectNum].getContigSeq();
			int xDistance = 20;
			for(int i = 0; i < tempString.length(); i++)
			{
				if(i < (rectArray[rectNum].getStartOfUsedRegion() -1) || i > (rectArray[rectNum].getEndOfUsedRegion()-1))
					g2.setColor(Color.BLACK);
				else
					g2.setColor(Color.RED);
					
				g2.drawString(String.valueOf(tempString.charAt(i)), xDistance, paintY);
				xDistance += 8;
			}
			
			g2.setColor(Color.BLACK);
			paintY +=20;
			String totalLength = ("The total length is: " + String.valueOf(rectArray[rectNum].getTotalLength()));
			g2.drawString(totalLength, 20, paintY);
			paintY += 20;
		}
		catch(NullPointerException nullPointerException){}		
	}

Now this isn't the complete code for each class but it's the only drawing I have in each, etc.