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Find out used classes and methods from Java source code

For Java source files, I would like to find out:
Which classes use which other classes (fully qualified names)?
Which methods call which other methods (fully qualified names)?
What would be a reasonable way to achieve that?
EDIT:
To clarify: I want a list of source code files as input. The output should be (as specified above) which class uses which other class and which method calls which other method. I do not want to inspect other loaded classes at runtime, like when using reflection.

You need to use static analysis tool as STAN standalone mode:
The standalone application is targeted to architects and project managers who are typically not using the IDE.
Or JArchitect (available also using command line)
JArchitect is a powerful tool for static code analysis. It can provide a lot of insight into complex code bases. Using custom code queries you are able to build your own rule sets in a very comfortable way.
In the Class Browser right-click menu, JArchitect proposes to explore the graph of dependencies between members (methods + fields) of a type.
Another option is SourceTrail
The graph visualization provides a quick overview of any class, method, field, etc., of interest and all its relations. The graph is fully interactive. Use it to move through the codebase by focusing on related nodes and edges.
(source: sourcetrail.com)

Unfortunately, reflection doesn't give you all the information you need to do this.
I've done it with ASM (https://asm.ow2.io/).
It provides the ability to walk the byte code of all of your classes using the visitor pattern, including the actual method implementations, from which you can extract the references to other classes.
I'm sorry that I cannot provide the implementation, because it's proprietary.
Note that this works from your .jar files, not your sources. If you really need to work from sources, then have a look at https://github.com/javaparser . Really, though, it's better to use the byte code, since the java language changes frequently, while the byte code specification does not.

I am not sure how to get a listing, but for identifying refactoring opportunities, you might try IntelliJ IDEA. It will dull out the signature line of any methods that are not accessed in the project. It will also detect code segments that are repeated elsewhere in the project, so you can extract common code.

Migrating C++ project to Java, protecting implementation details

I have a quite complex project to migrate from C++ (Linux) to Java
Currently, the C++ version is being distributed as a shared library (.so) followed by top-level interface header class. The implementation details are fully hidden from the final user.
This question is not about porting the C++ code to Java, but rather about creating similar distribution package.
Let's assume I have a very simple 'public' class in C++, topapi.h:
class TopApi
{
public:
void do( const string& v );
}
The actual implementation is hidden from the API user. The actual project may contain another 100 files/classes do() will call.
The distribution will contain 2 files: topapi.so and topapi.h
Users will #include "topapi.h" in their code, and link their applications with topapi.so.
The questions are:
1. How can I achieve a similar effect in Java (hide the IP related code)
2. How do I show public methods to the user ( not related to code protection, just a java version of the header file above )

Check out proguard. It will at least obfuscate the jar file, which otherwise is basically human readable. It's not absolutely safe from reverse engineering, but I guess neither is an so file.
I'm not an expert with Java, but this is what we have done to protect implementations in the past.
I don't know exactly what the motivations are for a Java port, but if it is just to support a Java end user, you could consider a JNI wrapper. I guess this probably isn't the case, but I thought I would mention it.
As far as exposing interface code to the user, you could write a Java interface class (like a pure virtual abstract c++ class) and simply not proguard that class.

To answer the question of how to show public methods to the user. This is usually done through a combination of declaring the internal classes without an access modifier, which makes them only accessible from within the same package, and not documenting them. Don't depend on the former though, it's easily circumventable, but it sends the message to the user that those classes are internal.
Java 9 adds modules which allow you to encapsulate entire packages, but it's not here yet, and you would still be able to circumvent the encapsulation.
One side effect of ahead of time compilation (usually the case with C++) is that the distributed code is already optimized, and contains no metadata, so it's harder to reverse engineer. Java is distributed in an intermediate language, but the actual machine code is generated at runtime (JIT compilation). The intermediate language is practically un-optimized, so it's easier to reverse engineer. Java also merges the idea of header files and source files where a .class file will contain all the metadata you need to use it.

partial classes/partial class file

In C# .net there is a provision to have two different class files and make them a single class using the keyword partial keyword.this helps it to keep [for ex]UI and logic seperate.
of course we can have two classes to achieve this one for UI and other for logic.
Can this be achieved in java some how?

On source file splitting
No. Java source codes can not be split across multiple files.
From the Wikipedia article Comparison of Java and C Sharp
The Sun Microsystems Java compiler requires that a source file name must match the only public class inside it, while C# allows multiple public classes in the same file, and puts no restrictions on the file name. C# 2.0 and later allows a class definition to be split into several files, by using the partial keyword in the source code. In Java, a public class will always be in its own source file. In C#, source code files and logical units separation are not tightly related.
On separating logic and UI into their own classes
The two classes approach is a much better solution than the one-class-two-source approach in this case, because the separation is enforced in the design, not just physical separation in the source codes.
See also
Separation of logic and UI
oo question - mixing controller logic and business logic
Why is good UI design so hard for some Developers?

Why is each public class in a separate file?

I recently started learning Java and found it very strange that every Java public class must be declared in a separate file. I am a C# programmer and C# doesn't enforce any such restriction.
Why does Java do this? Were there any design considerations?
Edit (based on a few answers):
Why is Java not removing this restriction now in the age of IDEs? This will not break any existing code (or will it?).

I have just taken a C# solution and did just this (remove any file that had multiple public classes in them) and broke them out to individual files and this has made life much easier.
If you have multiple public classes in a file you have a few issues:
What do you name the file? One of the public classes? Another name? People have enough issues around poor solution code organization and file naming conventions to have one extra issue.
Also, when you are browsing the file / project explorer its good that things aren't hidden. For example you see one file and drill down and there are 200 classes all mushed together. If you have one file one class, you can organize your tests better and get a feel for the structure and complexity of a solution.
I think Java got this right.

According to the Java Language Specification, Third Edition:
This restriction implies that there must be at most one such type per compilation unit. This restriction makes it easy for a compiler for the Java programming language or an implementation of the Java virtual machine to find a named class within a package; for example, the source code for a public type wet.sprocket.Toad would be found in a file Toad.java in the directory wet/sprocket, and the corresponding object code would be found in the file Toad.class in the same directory.
Emphasis is mine.
It seems like basically they wanted to translate the OS's directory separator into dots for namespaces, and vice versa.
So yes, it was a design consideration of some sort.

From Thinking in Java
:
There can be only one public class per compilation unit (file).
The idea is that each compilation unit has a single public interface represented by that public class. It can have as many supporting “friendly” classes as you want. If you have more than one public class inside a compilation unit, the compiler will give you an error message.
From the specification (7.2.6)
When packages are stored in a file system (?7.2.1), the host system may choose to enforce the restriction that it is a compile-time error if a type is not found in a file under a name composed of the type name plus an extension (such as .java or .jav) if either of the following is true:
The type is referred to by code in other compilation units of the package in which the type is declared.
The type is declared public (and therefore is potentially accessible from code in other packages).
This restriction implies that there must be at most one such type per compilation unit.
This restriction makes it easy for a compiler for the Java programming language or an implementation of the Java virtual machine to find a named class within a package; for example, the source code for a public type wet.sprocket.Toad would be found in a file Toad.java in the directory wet/sprocket, and the corresponding object code would be found in the file Toad.class in the same directory.
In short: it may be about finding classes without having to load everything on your classpath.
Edit: "may choose" seems like it leaves the possibility to not follow that restriction, and the meaning of "may" is probable the one described in RFC 2119 (i.e. "optional")
In practice though, this is enforced in so many platform and relied upon by so many tools and IDE that I do not see any "host system" choosing to not enforce that restriction.
From "Once upon an Oak ..."
It's pretty obvious - like most things are once you know the design reasons - the compiler would have to make an additional pass through all the compilation units (.java files) to figure out what classes were where, and that would make the compilation even slower.
(Note:
the Oak Language Specification for Oak version 0.2 (postcript document): Oak was the original name of what is now commonly known as Java, and this manual is the oldest manual available for Oak (i.e. Java).
For more history on the origins of Java, please have a look at the Green Project and Java(TM) Technology: An Early History
)

It's just to avoid confusion in the sense that Java was created with simplicity in mind from the perspective of the developer. Your "primary" classes are your public classes and they are easy to find (by a human) if they are in a file with the same name and in a directory specified by the class's package.
You must recall that the Java language was developed in the mid-90s, in the days before IDEs made code navigation and searching a breeze.

If a class is only used by one other class, make it a private inner class. This way you have your multiple classes in a file.
If a class is used by multiple other classes, which of these classes would you put into the same file? All three? You would end up having all your classes in a single file...

That's just how the language designers decided to do it. I think the main reason was to optimize the compiler pass-throughs - the compiler does not have to guess or parse through files to locate the public classes. I think it's actually a good thing, it makes the code files much easier to find, and forces you to stay away from putting too much into one file. I also like how Java forces you to put your code files in the same directory structure as the package - that makes it easy to locate any code file.

It is technically legal to have multiple Java top level classes in one file. However this is considered to be bad practice (in most cases), and some Java tools may not work if you do this.
The JLS says this:
When packages are stored in a file
system (§7.2.1), the host system may
choose to enforce the restriction that
it is a compile-time error if a type
is not found in a file under a name
composed of the type name plus an
extension (such as .java or .jav) if
either of the following is true:
The type is referred to by code in other compilation units of the package in which the type is declared.
The type is declared public (and therefore is potentially accessible from code in other packages).
Note the use of may in the JLS text. This says that a compiler may reject this as invalid, or it may not. That is not a good situation if you are trying to build your Java code to be portable at the source code level. Thus, even if multiple classes in one source file works on your development platform, it is bad practice to do this.
My understanding is that this "permission to reject" is a design decision that is intended in part to make it easier to implement Java on a wider range of platforms. If (conversely) the JLS required all compilers to support source files containing multiple classes, there would be conceptual issues implementing Java on a platform which wasn't file-system based.
In practice, seasoned Java developers don't miss being able to do this at all. Modularization and information hiding are better done using an appropriate combination of packages, class access modifiers and inner or nested classes.

Why is java not removing this restriction now in the age of IDEs? This will not break any existing code (or will it?).
Now all code is uniform. When you see a source file you know what to expect. it is same for every project. If java were to remove this convention you have to relearn code structure for every project you work on, where as now you learn it once and apply it everywhere. We should not be trusting IDE's for everything.

Not really an answer to the question but a data point none the less.
I grepped the headers of my personal C++ utilty library (you can get it yourself from here) and almost all of the header files that actually do declare classes (some just declare free functions) declare more than one class. I like to think of myself as a pretty good C++ designer (though the library is a bit of a bodge in places - I'm its only user), so I suggest that for C++ at least, multiple classes in the same file are normal and even good practice.

It allows for simpler heuristics for going from Foobar.class to Foobar.java.
If Foobar could be in any Java file you have a mapping problem, which may eventually mean you have to do a full scan of all java files to locate the definition of the class.
Personally I have found this to be one of the strange rules that combined result in that Java applications can grow very large and still be sturdy.

Well, actually it is an optional restriction according to Java Language Specification (Section 7.6, Page No. 209) but followed by Oracle Java compiler as a mandatory restriction. According to Java Language Specification,
When packages are stored in a file system (§7.2.1), the host system
may choose to enforce the restriction that it is a compile-time error
if a type is not found in a file under a name composed of the type
name plus an extension (such as .java or .jav) if either of the
following is true:
The type is referred to by code in other compilation units of the package in which the type is declared.
The type is declared public (and therefore is potentially accessible from code in other packages).
This restriction implies that there must be at most one such type per
compilation unit. This restriction makes it easy for a Java compiler
to find a named class within a package.
In practice, many programmers choose to put each class or interface
type in its own compilation unit, whether or not it is public or is
referred to by code in other compilation units.
For example, the source code for a public type wet.sprocket.Toad would
be found in a file Toad.java in the directory wet/sprocket , and the
corresponding object code would be found in the file Toad.class in the
same directory.
To get more clear picture let's imagine there are two public classes public class A and public class B in a same source file and A class have reference to the not yet compiled class B. And we are compiling (compiling-linking-loading) class A now while linking to class B compiler will be forced to examine each *.java files within the current package because class B don’t have it’s specific B.java file. So In above case, it is a little bit time consuming for the compiler to find which class lies under which source file and in which class the main method lies.
So the reason behind keeping one public class per source file is to actually make compilation process faster because it enables a more efficient lookup of the source and compiled files during linking (import statements). The idea is if you know the name of a class, you know where it should be found for each classpath entry and no indexing will be required.
And also as soon as we execute our application JVM by default looks for the public class (since no restrictions and can be accessible from anywhere) and also looks for public static void main(String args[]) in that public class. Public class acts as the initial class from where the JVM instance for the Java application (program) is begun. So when we provide more than one public class in a program the compiler itself stops you by throwing an error. This is because later we can’t confuse the JVM as to which class to be its initial class because only one public class with the public static void main(String args[]) is the initial class for JVM.
You can read more on Why Single Java Source File Can Not Have More Than One public class

What is the purpose of defining a package in a Java file? [closed]

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I am a newbie and just learned that if I define say
package my.first.group.here;
...
then the Java files that are in this package will be placed under my/first/group/here directory.
What is the main purpose of putting some Java files in a package? Also, if I choose to adopt this, how should I group them?
Thank you
EDIT: For anyone who might have the same question again, I just found this tutorial on packages from Sun.

Let's start with the definition of a "Java package", as described in the Wikipedia article:
A Java package is a mechanism for
organizing Java classes into
namespaces similar to the modules of
Modula. Java packages can be stored in
compressed files called JAR files,
allowing classes to download faster as
a group rather than one at a time.
Programmers also typically use
packages to organize classes belonging
to the same category or providing
similar functionality.
So based on that, packages in Java are simply a mechanism used to organize classes and prevent class name collisions. You can name them anything you wish, but Sun has published some naming conventions that you should use when naming packages:
Packages
The prefix of a unique package name is
always written in all-lowercase ASCII
letters and should be one of the
top-level domain names, currently com,
edu, gov, mil, net, org, or one of the
English two-letter codes identifying
countries as specified in ISO Standard
3166, 1981.
Subsequent components of the package
name vary according to an
organization's own internal naming
conventions. Such conventions might
specify that certain directory name
components be division, department,
project, machine, or login names.
Examples:
com.sun.eng
com.apple.quicktime.v2
edu.cmu.cs.bovik.cheese

I a large application, you are bound to have two files named exactly the same (java.util.Date and java.sql.Date), especially when you start bringing in third party jars. So basically, you can use packages to ensure uniqueness.
Most importantly, in my opinion, packaging breaks down projects into meaningful segments. So my SQL package has sql-related code, and my logger package handles logging.

In addition to the namespacing mentioned in other answers, you can limit access to methods and fields based on the scope declared on that member.
Members with the public scope are freely accessible, to limit access you normally define them as private (i.e. hidden outside the class).
You can also use the protected scope to limit access to the type and its children.
There is also the default scope (a member with no qualifier has the default scope) which allows child types and types in the same package access to the member. This can be an effective way of sharing fields and methods without making them too widely available, and can help with testing.
For example the method below would be visible to all other members of the same package.
public class Foo {
int doSomething() {
return 1;
}
}
To test the method you could define another type in the same package (but probably a different source location), that type would be able to access the method.
public class FooTest {
#Test
int testDoSomething() {
Foo foo = new Foo();
assertEquals(1, foo.doSomething());
}
}

It allows the program to be composed from multiple different programs/components/libraries, so that their class names will not conflict and the components are easier to organize. See http://java.sun.com/docs/books/tutorial/java/package/index.html
In Java it's customary to name packages as reverse domain names. For example, if your company's domain is "initech.com" and you are making a program called "Gizmo", the package names are typically prefixed "com.initech.gizmo", with subpackages for different components of the program.

Packages are important for giving flexibility of classes separation. They can be used for:
separating projects
separating modules
separating application layers (business, web, dao)
further finer grained code separation
For example
com.mycompany.thisproject.thismodule.web
Could indicate the web layer of some module.

Ultimately, there are 3 core reasons we want to use packages in Java.
1) Easier Maintenance
Organizing classes into packages follows the separation of concerns principle by encapsulation and allows for better cohesion in the overall system design. Moving further, packaging-by-feature allows teams of developers to find relevant classes and interfaces for making changes, supporting vertical-slicing techniques for scaled approaches used in agile methodology. For more information, see blog post: Package your classes by Feature and not by Layers and Coding: Packaging by vertical slice.
2) Provide Package security
Packages allow external access to only public access modifiers on methods in contained classes. Using the protected or no modifier will only be accessible to classes within the same package. For more information, see post:
Which Java access modifier allows a member to be accessed only by the subclasses in other package?
3) Avoid similar naming
Similar to the namespaces of .NET, class names are contained within the scope of their containing package. This means that two mutually exclusive packages can contain classes with the same name. This is because the packages themselves have different names and therefore, the fully qualified names are different. For more information, see tutorial [Naming a Package: The Java Tutorials][3].

From the Wikipedia page on the topic:
"A Java package is a mechanism for organizing Java classes into namespaces similar to the modules of Modula. Java packages can be stored in compressed files called JAR files, allowing classes to download faster as a group rather than one at a time. Programmers also typically use packages to organize classes belonging to the same category or providing similar functionality."

also, if i choose to adopt this, how
should i group them?
This depends largely on the design pattern(s) you will employ in your project. For the most part (particularly, if you're quite new) you'll want to group them by functionality or some other logical similarity.

Other people have provided very Java-specific answers which are fine, but here's an analogy: why do you organize files into directories on your hard drive? Why not just have a flat file system with everything in one directory?
The answer, of course, is that packages provide organization. The part of the program that interfaces with the database is different than the part of the program that displays a UI to the user, so they'll be in different packages.
Like directories, it also provides a way to solve name conflicts. You can have a temp.txt in a couple different directories in the same way that you could have two classes that appear in different packages. This becomes important (1) when you start combining code with other people out there on the internet or (2) even realize how Java's classloading works.

Another important thing about packages is the protected member for access control.
Protected is somewhere between public (everyone can access) and private (only class internal can access). Things marked as protected can be accessed from within the same package or from subclasses. This means that for limited access you don't have to put everything in the same class.

Java is very exact in its implementation. It doesn't really leave room for fudging.
If everyone were to use the same package, they would have to find some "World Wide" way to ensure that no two class names ever collided.
This lets every single class ever written fit into its own "Place" that you don't have to look at if you don't want to.
You may have different "Point" objects defined in 4 different places on your system, but your class will only use the one you expect (because you import that one).
The way they ensure that everyone has their own space is to use your reverse domain, so mine is "tv.kress.bill". I own that domain--Actually I share it with my brother "tv.kress.doug" and even though we share the same domain, we can't have a collision.
If a hundred divisions in your company each develop in Java, they can do so without collision and knowing exactly how to divide it.
Systems that don't do this kind of division seem really flaky to me now. I might use them to hack together a script for something personal, but I'd feel uncomfortable developing anything big without some strict packaging going on.