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PaintComponent disrupting grid drawing

I'm new to Java as well as user interfaces, and I have a problem with Java Graphics. What I'm trying to achieve is drawing a grid on a JPanel, and then paint custom components into the grid.
Here is the class I want to draw the grid on (its base extends JPanel).
public class RectGridPanel extends GridPanel
{
List<Rectangle> rects;
public RectGridPanel(Simulator sim)
{
super(sim);
this.rects = new ArrayList<Rectangle>();
this.setLayout(new GridLayout(20,20));
for(int x = 1; x < 801; x += 40)
{
for(int y = 2; y < 801; y += 40)
{
Cell newCell = new RectCell(x, y, sim);
this.add(newCell);
}
}
}
#Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g;
g2.setPaint(Color.BLACK);
for(int x = 1; x < 801; x += 40)
{
for(int y = 2; y < 801; y += 40)
{
Rectangle rect = new Rectangle(x, y, 40, 40);
g2.draw(rect);
rects.add(rect);
}
}
}
}
Here are the cells I want to draw inside the grid:
public class RectCell extends Cell
{
Rectangle shape;
public RectCell(int x, int y, Simulator sim)
{
super(x, y, sim);
shape = new Rectangle(x, y, CELL_SIZE, CELL_SIZE);
}
#Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g;
g2.setPaint(Color.BLACK);
g2.fill(shape);
}
}
So the grid on its own draws out fine, but as soon as I try to create cells inside it it gets disrupted like that:

public class RectCell extends Cell
{
Rectangle shape;
public RectCell(int x, int y, Simulator sim)
{
super(x, y, sim);
shape = new Rectangle(x, y, CELL_SIZE, CELL_SIZE);
}
#Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g;
g2.setPaint(Color.BLACK);
g2.fill(shape);
}
}
The Graphics object that is passed to this paintComponent() function defines the screen space where the current RectCell can draw. The coordinate sysetem is relative to the upper left corner of the RectCell, so drawing the background should always start at x = 0 and y = 0 or some other meaningful value. The coordinates here are not relative to the parent component as you seem to assume.
Better yet, set the background color and let Swing take care of painting it rather than painting a rectangle yourself.

It is not clear what you try to achive.
What is the reason for RectCell? Why not paint the shapes direct in the RectGridPanel?
The nested loop in the paintComponent it not a good idea. Be aware that the paintComponent is called very often and every time you in crease the rects list with new objects. The former painted rectangles get lost (qraphicaly) and new rectangles with the same parameters are blowing the list.

How to remove original object after rotation in java graphics2D?

Specifically, I am trying to display only the rotated object. I have a drawn rectangle and I rotate it.
How to I display only the rotated rectangle and dispose of the old one?
EDITED:
The following is the code to rotate my rectangle:
private void rotateRectangle(Graphics g, Rectangle rect, Color c){
Graphics2D g2d = (Graphics2D) g.create();
x = rect.x;
y = rect.y;
g2d.setColor(c);
g2d.rotate(Math.PI/6, PANEL_WIDTH/2,PANEL_HEIGHT/2);
g2d.drawRect(PANEL_WIDTH/2-x/2, PANEL_HEIGHT/2-y/2, x, y);
}
And this is the paintComponent where I call it from:
#Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2d = (Graphics2D) g.create();
g2d.setStroke(new BasicStroke(3));
//these are declared before
rect.x = x;
rect.y = y;
if(rotateClicked){
rotateRectangle(g2d,rect,squareColor);
rotateClicked = false;
}
drawRectangle(g2d, rect, squareColor);
getArea(x,y);
}

If custom rendering shapes with a Graphics object by overwriting paintComponent(Graphics g), ensure you use super.paintComponent(g) as the first line to clear the drawing area
From there draw your Rectangle/rotated Rectangle
Without using super.paintComponent(g), your previous drawings (the unrotated Rectangle) will remain visible
EDIT
With the update of source code: you are drawing both the new and the old rectangle because your if statement does not have an else clause
Try inserting an else clause so that it will draw one rectangle or the other, currently it maybe draws a rotated rectangle and then draws the unrotated rectangle
if(rotateClicked)
{
rotateRectangle(g2d,rect,squareColor);
rotateClicked = false;
}
else
drawRectangle(g2d, rect, squareColor);
You may or may not want a rotateClicked = true in the else so it will flip back and forth between rotated and unrotated

Drawing a shape but keeping the most previous shape on screen in java

I've created a function to where I can click somewhere in a Jpanel and it draws a shape at the position where the mouse clicked. The problem I am having is when I click in a new position, it moves the shape and redraws it. I would like the previous shape to "Burn" into the screen and stay there. It doesn't have to have any data tied to it, I just want the image of the shape to show where it used to be each time. I have tried many different things, but no success. here is what I mean:
public void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g;
g2.setColor(Color.BLUE);
g2.fillRect(n, m, 32, 32); //I want each one of these shapes to be new, not
//moving, but redrawn
////////////////////////////////////////////////
//This is just drawing a grid and doing other things(irrelevant)
g2.fill(new Ellipse2D.Double(x, y, 32, 32));
for (int i = 0; i < 500; i += 32) {
g2.drawRect(i, j, 32, 32);
for (int j = 0; j < 500; j += 32) {
g2.drawRect(i, j, 32, 32);
}
}
if (paintColBlock){
System.out.println("Drawing Block at " + n +"," + m);
paintColBlock = false;
}
/////////////////////////////////////////////////////////////////////
}

Keep an ArrayList of Points like this:
public void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g;
g2.setColor(Color.BLUE);
for(Point p : points)
g2.fillRect(p.x, p.y, 32, 32);
Adding a new Point to the array at each mouse click, and call repaint():
public void mousePressed(MouseEvent evt){
points.add(new Point(evt.getX(),evt.getY());
repaint();
}

Inner-Transparent Selection Window in Java using GlassPane

I am trying to achieve the following
http://www.qksnap.com/i/3hunq/4ld0v/screenshot.png
I am currently able to draw rectangles successfully on a semi-transparent glasspane background using the following code:
protected void paintComponent(Graphics g) {
Graphics2D g2 = (Graphics2D) g;
g.setColor(Color.black); // black background
g.fillRect(0, 0, frame.getWidth(), frame.getHeight());
g2.setColor(Color.GREEN.darker());
if (getRect() != null && isDrawing()) {
g2.draw(getRect()); // draw our rectangle (simple Rectangle class)
}
g2.dispose();
}
Which works great, however, I would love to have the area within the rectangle be completely transparent while the outside was still darken much like the screenshot above.
Any ideas?

..have the area within the rectangle be completely transparent while the outside was still darken much like the screenshot above.
Create a Rectangle (componentRect) that is the size of the component being painted.
Create an Area (componentArea) of that shape (new Area(componentRect)).
Create an Area (selectionArea) of the selectionRectangle.
Call componentArea.subtract(selectionArea) to remove the selected part.
Call Graphics.setClip(componentArea)
Paint the semi-transparent color.
(Clear the clipping area if more paint operations are required).

As Andrew has suggested (just beat me while I was finishing off my example)
protected void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g.create();
g.setColor(Color.black); // black background
Area area = new Area();
// This is the area that will filled...
area.add(new Area(new Rectangle2D.Float(0, 0, getWidth(), getHeight())));
g2.setColor(Color.GREEN.darker());
int width = getWidth() - 1;
int height = getHeight() - 1;
int openWidth = 200;
int openHeight = 200;
int x = (width - openWidth) / 2;
int y = (height - openHeight) / 2;
// This is the area that will be uneffected
area.subtract(new Area(new Rectangle2D.Float(x, y, openWidth, openHeight)));
// Set up a AlphaComposite
g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.5f));
g2.fill(area);
g2.dispose();
}

How to center align background image in JPanel

I wanted to add background image to my JFrame.
Background image means I can later add Components on the JFrame or JPanel
Although I coudn't find how to add background image to a JFrame,
I found out how to add background image to a JPanel from here:
How to set background image in Java?
This solved my problem, but now since my JFrame is resizable I want to keep the image in center.
The code I found uses this method
public void paintComponent(Graphics g) { //Draw the previously loaded image to Component.
g.drawImage(img, 0, 0, null); 　//Draw image
}
Can anyone say how to align the image to center of the JPanel.
As g.drawImage(img, 0, 0, null); provides x=0 and y=0
Also if there is a method to add background image to a JFrame then I would like to know.
Thanks.

Assuming a suitable image, you can center it like this:
#Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2d = (Graphics2D) g;
int x = (this.getWidth() - image.getWidth(null)) / 2;
int y = (this.getHeight() - image.getHeight(null)) / 2;
g2d.drawImage(image, x, y, null);
}
If you want the other components to move with the background, you can alter the graphics context's affine transform to keep the image centered, as shown in this more complete example that includes rotation.
#Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2d = (Graphics2D) g;
g2d.translate(this.getWidth() / 2, this.getHeight() / 2);
g2d.translate(-image.getWidth(null) / 2, -image.getHeight(null) / 2);
g2d.drawImage(image, 0, 0, null);
}