Develop Reference

Interactive Flow Chart

I have written a few C programs that are pretty extensive. I am looking to draw a flow chart/ER Diagram of how the header files are called and which call to which. While I could use Visio and draw this in a few hours, I am looking to make an interactive diagram. I have started one in Python using Imagine Magick but I am wondering whether Java/JavaFX/JavaGraphics would be the best way to go about this task. Any suggestions for the most efficient way to make a program that will draw a diagram of my large scale project?
NOTE: Python has worked thus far and it has drawn a small scale diagram with arrows to each relation but it is slow.

The use of image processing to extract data from a diagram

I have a data flow diagram (a diagram that looks like a flow chart). It has a set of specific geometrical components like rectangles, circles, ellipses and arrows.
What I'm trying to achieve is to detect these shapes and be able to know which component is connected to which component (through the lines) and finally read the text inside each one to extract data from the diagram and do further processing. It is also notable to mention that the diagram will not be drawn by hand but computer generated so we don't have to worry about angles and ratios being inaccurate.
I'm currently working in Java and I was wondering if this is going to be possible since Java is not the best language when it comes to image processing (correct me if I'm wrong). And if it's possible I'd you guys to point out where I should start looking.

I think Java is fine, and it has many libraries to process images. ImageJ is just one example. Personally, I like to use Python, so I write scripts in this language using Java API of the DMelt platform. Look at the documentation of this projecst, wiki. Here is a link to a few examples.

Doing this in Java wasn't a great idea because mainly the lack of online resources. After a good amount of research, I found that the best and the easiest approach was the use of C# and Emgu CV which is a cross platform .Net wrapper to the OpenCV image processing library.
This example helped me to get started with detecting basic geometrical shapes like Lines, Rectangles and Triangles.

High level API for creating 2D Shapes in Java

I am seeking an API or program which I can use to create Shapes graphically in Java (specifically closed shapes). A tool simalar to paint in windows, but without the colors and such. After the shapes are created, I will be using them as part of a simulation program, so I need to get access to the actual java Shape objects.
I could create my own tool using Java2D, but I am sure I would be wasting my time as there must be some useful tools out there. However, after a long time scowering google, I had no luck. Any tips would be much appreciated.

Here's an article describing how to do it accompanied with source code that you might be able to use.

blackberry - java - 2D geometry and collision package

My current problem is not so much a blackberry issue as it is a java
package issue.
In the application I have a rectangular region. This region is rotated by
about 30%.
I need to accomplish two things:
when a user clicks, is he inside the region?
when a user draws a straight line on the screen,
does any part of that line intersect the region? if so, what is the
length of the line inside the region?
I know that I can write my own functions to accomplish this (after dusting
off some algebra and geometry skills that aren't needed for web forms) but
I was thinking that this is a common issue in game programming. I found
some libraries for c++ and some for c# but nothing for java.
Does anyone have suggestions for good java packages? The packages don't need to have graphical components. In fact it would be best if they just handled the geometry and calculations based on x,y co-ordinates alone.

The usefulness of this answer will depend on exactly what type (SE or ME) and what version (and, for ME, what config and profile) of JVM you are targeting. Since it's a blackberry, you are likely J2ME of some flavor - YMMV.
That said, the functions you want appear to be present in java.awt.Rectangle, java.awt.geom.Rectangle2D and java.awt.geom.Line2D.

What libraries are available to help create 2D Java games for phones?

I want to begin developing 2D Java games for phones (on J2ME) therefore I'd like to know if any libraries or "engines" exist to help out in the various graphical tasks:
Drawing text with pixel fonts?
Drawing bitmaps for sprites with multiple frames like animated GIFs?
Drawing graphics with code, lines, beziers, flood-filling and gradient fills?
Ordering / layering of sprites?
Or maybe a great book exists, that gives you enough code samples to get off the ground quickly?

MIDP (JSR-118) includes the basics (most of the things you listed above) mainly in the javax.microedition.lcdui and javax.microedition.lcdui.game namespaces.

I didn't use it myself, but heard some good reference on here.
And here is even a list of libraries, you might need.

There was a book released quite a few years ago called Developing Games in Java by David Brackeen.
That covers the basics of 2d and 3d development in pure Java as well as how to handle time jumps and update the physical properties of your game characters. It is a good introduction to the topic.