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how to visualize a rectangle

I have two rectangles in Libgdx but they seem not to overlap right. Is there a way so I see where the rectangles are?
I have this:
Body2.setSize(72, 72);
Body2.setPosition(20, squiddyY);
Body.setHeight(Assets.sprite_body.getHeight());
Body.setPosition(pipe1X, Assets.sprite_body.getY()+Assets.sprite_body.getHeight());
if(Body2.overlaps(Body)){
squiddyY=1000;
}
but it looks like body is half size of sprite_body(or the Y is just too low?) and is a bit behind it (the X location of sprite_body is pipe1X). Maybe i'm putting it at the wrong place so visualizing it will really help.

You can draw shapes with ShapeRenderer
http://libgdx.badlogicgames.com/nightlies/docs/api/com/badlogic/gdx/graphics/glutils/ShapeRenderer.html
The link includes examples.

Rendering a triangular face in 3d space

Let's say I have a triangular face in 3d space, and I have the 3d coordinates of each vertex of this triangle, and would also have other information about the triangle(angles, lengths of sides, etc.). In Java, if I have the viewing screen and its information, how can I draw that plane, without using libraries like LWJGL, to that image, assuming I can properly project, accounting for perspective, any 3d point to that 2d image.
Would the best course of action just be to run a loop that draws each point on the plain to a point on the image(i.e. setting the corresponding pixel), which will most likely set the same pixel multiple times? If I'd do this, what would be the best way to identify each point in an oblique triangle, or a triangle that doesn't line up nicely with the axes?
tl;dr: I have a triangular face in 3d space, a "camera" looking at the face, and an image in which I can set each pixel. Using no GL libraries, what's the best way to project and draw that face onto the image?

Projection :
won't detail as you seems to know it
Drawing a line
you can look at Bresenham algorithm if you wanna start with the basics
(hardwared in recent graphics card)
Filling
you can fill between left and right borders of the triangle while you use Bresenham on both (you could use a floodfill algorithm starting ... i don't know, maybe at the projection of the center of the triangle)

Your best bet is to check out the g.fillPolygon() function for Java. It allows you to draw polygons with as many sides as possible and theres also g.drawPolygon() if you don't want it solid. Then you can just do some simple maths for the points. Such as each point is basically it's x and y except if the polygon is further away the points move closer to the center of the polygon and if the polygon is closer they move further away from the center of the polygon.
A second idea could be using some sort of array to store pixels and then researching line drawing algorithms and drawing lines then putting all the line data in another array and using some sort of flood-fill. Then whilst it's in that array you could try and do some weird stuff to the pixels if you wanted textures or something.

Jpanel / Jframe / buffering graphics etc game structure direction

I'd like some advice regarding structure of a game I'm working on. Specifically where to place painting methods.
Currently there is a applet wrapper class for a Jpanel which runs the game loop.
The game itself is meant to simulate a very large area. objects will have x&y values which themselves will part of a larger x&y grid.
i.e. object1 position is 150000x30000 in grid block 1,5.
objects will need to be able to move into neighbouring grids, however I'd rather not run each grid block until needed as 99% of them will be empty.
Currently the UI is a Jpanel with a few buttons + listeners, a large drawing pane is needed to display the objects.
my question is:
what class should this internal drawing pane be based on? I'd like to have control to zoom and pan around the grid. it only needs to draw what is visible, but object movements will continue in the game loop.
what painting strategy would be applicable for simple (icons really when zoomed out) moving around vast areas, I'm guessing relying on the EDT to repaint isn't going to be good enough?
I'm not really after specific code, I want to learn myself how to do this, I just need pointing in the right direction, as most things I read don't seam to quite cover what I'm after, or don't make use of JRE6+ features.
Many Thanks

Rather than paint each grid cell in your drawing pane, why don't you have each object repaint itself onto the grid?

Using a canvas much larger than the screen

I'm trying to draw a 2D contour plot of some data on Android and I'm wondering what the best approach would be to draw those. The whole datasets can be relatively large (2k * 2k points) and zooming and moving inside the plot should be very fast. Most of the time only a small part of the data will be drawn as the user has zoomed in on the data.
My idea now would be to draw the whole plot onto a large canvas, but clip it to the portion visible on the screen, so that only that part would be really drawn in the end. I find the 2D drawing API of Android somewhat confusing and I'm not sure if this is really a feasible approach and how I would then go about executing it.
So my questions are:
Is it a good idea to draw onto a canvas much larger than the screen and use clipping to display only the relevant part?
How would I create a larger canvas and how would I select which parts should be drawn?

You should start the other way around. Instead of creating a huge canvas you should detect what part of your plot you need to draw and draw only that.
So basically you need some navigation/scrolling and you need to keep the offset from the starting point in memory to calculate where you are. Using the offset you can easily zoom in and out because you just need to scale the plot to the screen.

Is it a good idea to draw onto a
canvas much larger than the screen and
use clipping to display only the
relevant part?
A better question might be, do you have any other options. Some might argue that this is a bad idea since your going to keep memory in use when it isn't relevant to whats happening on the UI. However, from my experiences with the Canvas, I think you'll find this should work out just fine. Now, if you are trying to keep "5 square miles" of canvas in memory your definitely going to have to find a better way to manage it.
How would I create a larger canvas and
how would I select which parts should
be drawn?
I would expect that you will be creating your own "scrolling" method when the user touches the screen via overriding the onTouchEvent method. Basically your going to need to keep track of a starting point X and Y and just track that value as you move the Canvas on screen. In order to move the Canvas there are a number of built in's like translate and scale that you can use to both move the Canvas in X and Y as well as scale it when the user zooms in or out.

I don't think that is a good idea to draw your 2D contour plot on a big bitmap because you need a vector type graphics to zoom in and out in order to keep it sharp. Only pictures are good to scale down but graphs will lose thin lines or come out deformed when scaled down in bitmaps.
The proper way is to do it all mathematically and to calculate which part of the graph should be drawn for required position and zoom. Using anti_alias paint for lines and text, the graph would always come out sharp and good...
When the user zooms out, some items should not be drawn as they could not fit into the screen or would clutter it. So the graph would be always optimised for the zoom level...

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?