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How to make a JFrame one colour?

I'm trying to add some polish to a small game I made and, every time a round finishes, I'd like the whole JFrame to flash white and quickly lose opacity until you can see the game again. How would I do this?
Note: I'm thinking about hiding all the components and adding a JPanel on top that loses opacity quickly but this doesn't seem right (and I'd like to be able to see the components behind the white flash as it goes from opaque to transparent).

You could probably use the JLayer class. Take a look at the section from the Swing tutorial on How to Decorate Components with the JLayer Class.
The tutorial has examples that:
paint translucent layers
do animation
Put the examples together and you should have a solution.

You can use fading out image to achieve the same. AlphaComposite is used for fading effect.
Graphics2D g2d = (Graphics2D) g;
g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, alpha));
Refer Fade Out Image to access the sample code.

Fading a portion of Graphics in Java Swing

I am trying to implement the fade in/fade out animation in swing.
I am using a JPanel which does not have any components in it. It is completely drawn by paintComponent() method.
Now in one of the portion of this JPanel, I want to implement the fade in/fade-out animation. When I tried using AlphaComposite, the animation is being triggered for whole JPanel.
Can I limit this animation in a small clipped region in that panel?
Graphics2D g2d = (Graphics2D) g;
g2d.setComposite(AlphaComposite.getInstance(
AlphaComposite.XOR, alpha));

Have you tried using an Graphics object (like rectangle, circle etc..) for your fade in/out? That way it won't be triggered for the complete panel.
Good luck!

Perhaps, but that may be more difficult to achieve than what it's worth. Create a JComponent of the size you want to animate (or fade), add it to your JPanel, and have repaint() called on your smaller component during animation instead of the larger JPanel.

You can use setClip() before painting to restrict the fading area.
Suppose you want a small fading rectangle. Using Area class create 2 Shapes. Intersection of original clip and fading rect and subtraction (subtract the fading rectangle from the original clip).
Call super.paintComponent() twice with 2 different clips. For the second paint you can set your alpha filter.

Clear JFrame background on transparent window

i have a transparent JFrame AWTUtilities.setWindowOpaque(this, false);
I have a problem when resizing the window. I need something that could clear the background of the window before drawing on it,I need to make it all the background empty and transparent. Now the painting is draw over the old background and looks ugly.
I tried to draw a transparent image over the background but i have same issues.

If you have an opaque component you're completely responsible for drawing its content. The windowing system or AWT does NOTHING to set the background to some defined state.
So at least you should do something like the basic Canvas code
g.clearRect(0, 0, width, height);
What exactly do you mean with "transparent". Do you want to look through to the desktop? Do you want to see panel behind your component (then at least it should not be "opaque").

can we zoom in zoom out the drawing we draw on the Canvas?

We have an old (more than 10yrs old) Java Swing applicatin which draws lots of circles and connections (lines) between those circles on a JCanvas (a subclass of JComponent) based on lab data.
Because the data becames bigger and bigger, we cannot display the entire drawing now. We have put the JCavans into a JScrollPane but it is not convenience to scroll the drawing.
Can we add zoom in zoom out for it? if yes, how? I know we can zoom image but the drawing on Canvas is an image?
thanks,
EDIT:
we draw those circles and line with Graphics within paintComponent(Graphics g) method.

You could apply a scaling Transform to the Graphics2D object passed to the paintComponent method. You can learn how to use it in the Java 2D programming trail.

Without knowing anything about your application it's hard to provide useful advice (adding a code snippet or better yet a cutdown example app would be helpful to show how things are being drawn), but I'll give it a shot:
Why don't you multiply the x,y and width,height values by a scaling factor before you draw each circle/line? I assume that somewhere your canvas is using a Graphics object to draw each shape?

java changing attributes of shapes programmatically

I want to create a number of straight lines connecting small circle shapes. then I want to change the color and width of the lines from within my program. I was thinking of using Canvas to do this but there does not seem to be a way to access individual shapes drawn on canvas to change their attributes after they are drawn. What would be an easy way to implement this?

First of all, what version of Java and which UI toolkit? AWT's Canvas is very dumb, it will not even "remember" what you have painted; when you minimize and restore the window, it will send a paint() event because it wants to be repainted.
The easiest way (if you are using AWT and stuck to Canvas) is to have a List of your shapes (either one list for all or one for circles and one for lines, or whatever you like) and make your paint method draw all of them. Then update the objects in your list. When you are done updating, call repaint() on your canvas and it will call paint() for you again.

You don't paint shapes onto a Canvas if you're using Graphics and Graphics2D functions like drawRect, drawPolygon, drawOval, etc. Once they're drawn, they don't exist as shapes anymore. You just have an image with filled-in pixels.
As mihi said, you may have to keep track of the shapes you're trying to draw, then regenerate your image if it changes. Perhaps you could also "unpaint" a shape you're trying to change by painting over it in the background color and repainting the changed shape.