IntelliJ IDEA suggests the following means of analyzing dependencies in your projects:
Analysis of usages, which helps you locate all references to a certain class, variable, method or parameter. This facility includes search and view usages across the project and highlighting usages in a file.
Possibility to view file structure.
Possibility to explore hierarchy of the types, methods, and method calls.
Search for repetitive code fragments.
Exploring complicated dependencies using Dependency Structure Matrix Analysis.