Grrrr Trigonometry

I did Trigonometry while I was in high school, and I actually did pretty well at it. But its been such a long time since I've used it that I cannot remember anything! I've been trying to get a vector to follow the mouse around the screen, and just keep hitting a brick wall. I've talked to Pete over the past week and he's been trying to help me with the problem providing a few equations and what not, but everything I try just doesn't seem to be working right.

I've tried these equations that Pete gave me:

tanӨ = o / a
Ө = artan( o / a)
Ө = artan( Y2 - Y1 / X2 - X1)

These equations are telling me what the angle is, but I'm not sure if that's exactly what I am trying to achieve here. I keep getting the vector pointing in the wrong direction, when I would move the mouse to different corners of the screen (for example, if i put it in the top right corner the vector would point 90 degrees to the right, and top left corner would result in the vector point 90 degrees to the north). This is getting frustrating now, because I've spent a while trying to solve this problem that is probably really really easy.

The whole point of getting the vector to follow mouse, is so that we can make a start on making our first game (Missile Command), which requires a missle/bullet to move to were the player is pointing.

Now the reason I think I've been getting skewed results is because of the mouse coordinates that Java has been giving me in comparison to the actual coordinate system in OpenGL. I did a test to find out if the coordinate system was actually working as intended (0, 0 at the bottom left), to determine this I set the vector to start at 0,0 and point out at a 45 degree angle towards the center, this proved that coordinates are setup right. Since OpenGL is working as expected, I did a mouse test to determine what sort of values it was giving in relation to how it should be setup. I am confident it is the mouse coordinates that are causing the problem because when I move the mouse to the bottom of the screen it gives me a Y value of 500, which means its reversed. Hmmmmmmmm I should be able to reverse it so it works with the OGL coordinates by using this simple equation.

Y = 500 - mouseY

oo