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I have a project with many packages and classes. It is obvious that it will have many Methods too. Currently, i am using Netbeans7.0 IDE. Is there any program, API or way to track all the possible path/methods/options like tree structure of all the classes? I wish to see all the branches which starts from first Method.
So, basically, what you need is a call graph of your project? Call graphs can be generated either through static code analysis or dynamically as your code is executed. Both approaches are useful and both have their advantages and disadvantages.
Both the Eclipse and the Netbeans profiler are able to do this dynamically, as mentioned here.
For static call graph generation have a look here and here.
EDIT:
The Eclipse IDE also has the capability to generate a tree-like call structure using the Call Hierarchy tab, as mentioned here. NetBeans has something similar since version 6.5.