Develop Reference

In java, do I always need a Main class?

I know that I'll need a main method, but can that main method be in a different class other than the Main class?

Not all Java applications require a main method.
Java can also be used to create web applications, for instance, which don't require main methods to run.
The answer to your question depends on what exactly you mean. Do you mean a class with the name 'Main'? Then, no, there is no requirement for this at all.
The only requirement that Java has, is that the signature of the method is correct. the main method must:
be public
be main
be static
have returntype void
accept an array of Strings as (only) parameter
It's easier to add it in the public class in a file, but not mandatory. The name of the class it is in, is entirely up to you, though many will choose a name like 'Main' or 'Open', simply to more easily find it.
If you want to be able to run your application, by simple double-clicking the .jar file, you'll need to point to the class that contains the main method (to use: your application might contain a lot of main classes, used for internal testing, but only one can be used to start the actual application) in the manifest file: Manifest files
Prior to Java 7, it was possible to run a desktop application without a main method, by (ab)using an instantiation block, but this was removed as of Java 7, because this is not what the instantiation block was intended for.

It's not necessary to define yout main method in a main class. You can place your main method wherever you want, as long the syntax i correct :
public static void main (String[] args){
//...
}

You absolutely don't.
The method itself can be placed whereever you want it to be, there is no limitation.
However, I personally would recommend putting it in a class which at least contains something like "Main", because when others look at your code, and they are not using an IDE which supports jumping to the main method, people usually have an easier time finding your starting point.
However, that is just for sake of readability, and as I said, jumping to main is/should be usually a widespread supported feature

Yes, the Main method is required to run a function although a java class can be without the Main method. Though, it won't run...

How can i use redefineClasses() method in javaagents

I have been using premain() with addTransformer(). Since, it gives javassist.ClassNotFound exceptions for certain classes when i run the agent with a server, i thought to try the agentMain() with redefineClasses(). I went through many links, but so far i am unable to find a piece of code that gives me clear idea on how to set up a simple java agent using these two methods. Some help would be really appreciated.
Can we use redefineClasses() with premain()? (When we use redefineClasses() do we still need the transform method?)
I am trying to instrument set of methods of set of classes, where i know the fully qualified name of those classes as com.test.Foo. I wanted to instrument them without going through the entire set of classes loaded onto JVM. I have been reading those documents back and forth, but still i am unable to get a clear idea on how to use that redefineClasses method?

You can call redefineClasses from anywhere, also from a premain method which is nothing but an extension to a normal Java program run by the same JVM process previous to a main method.
A trivial example for running a redefinition is:
instrumentation.redefineClasses(new ClassDefinition(Foo.class, new byte[] {...}));
This way, Foo is set to be represented by the byte array that must contain a valid class file for Foo where all signatures of fields and methods are the same as by the loaded Foo.class. You can use a tool like ASM for instrumenting the class.
If you really only want to instrument Foo, then this might just be the way to go instead of using a ClassFileTransformer.

A better way to call static methods in user-submitted code?

I have a large data set. I am creating a system which allows users to submit java source files, which will then be applied to the data set. To be more specific, each submitted java source file must contain a static method with a specific name, let's say toBeInvoked(). toBeInvoked will take a row of the data set as an array parameter. I want to call the toBeInvoked method of each submitted source file on each row in the data set. I also need to implement security measures (so toBeInvoked() can't do I/O, can't call exit, etc.).
Currently, my implementation is this: I have a list of the names of the java source files. For each file, I create an instance of the custom secure ClassLoader which I coded, which compiles the source file and returns the compiled class. I use reflection to extract the static method toBeInvoked() (e.g. method = c.getMethod("toBeInvoked", double[].class)). Then, I iterate over the rows of the data set, and invoke the method on each row.
There are at least two problems with my approach:
it appears to be painfully slow (I've heard reflection tends to be slow)
the code is more complicated than I would like
Is there a better way to accomplish what I am trying to do?

There is no significantly better approach given the constraints that you have set yourself.
For what it is worth, what makes this "painfully slow" is compiling the source files to class files and loading them. That is many orders of magnitude slower than the use of reflection to call the methods.
(Use of a common interface rather than static methods is not going to make a measurable difference to speed, and the reduction in complexity is relatively small.)
If you really want to simplify this and speed it up, change your architecture so that the code is provided as a JAR file containing all of the compiled classes.

Assuming your #toBeInvoked() could be defined in an interface rather than being static (it should be!), you could just load the class and cast it to the interface:
Class<? extends YourInterface> c = Class.forName("name", true, classLoader).asSubclass(YourInterface.class);
YourInterface i = c.newInstance();
Afterwards invoke #toBeInvoked() directly.
Also have a look into java.util.ServiceLoader, which could be helpful for finding the right class to load in case you have more than one source file.

Personally, I would use an interface. This will allow you to have multiple instance with their own state (useful for multi-threading) but more importantly you can use an interface, first to define which methods must be implemented but also to call the methods.
Reflection is slow but this is only relative to other options such as a direct method call. If you are scanning a large data set, the fact you have to pulling data from main memory is likely to be much more expensive.

I would suggest following steps for your problem.
To check if the method contains any unwanted code, you need to have a check script which can do these checks at upload time.
Create an Interface having a method toBeInvoked() (not a static method).
All the classes which are uploaded must implement this interface and add the logic inside this method.
you can have your custom class loader scan a particular folder for new classes being added and load them accordingly.
When a file is uploaded and successfully validated, you can compile and copy the class file to the folder which class loader scans.
You processor class can lookup for new files and then call toBeInvoked() method on loaded class when required.
Hope this help. (Note that i have used a similar mechanism to load dynamically workflow step classes in Workflow Engine tool which was developed).

Do I have any method to override System Properties in Java?

I am getting a practical issue and the issue can be dascribed as follows.
We are developing a component (Say a plugin) to do some task when an event is triggered within an external CMS using the API provided by them. They have provided some jar libraries, So what we are doing is implementing an Interface provided by them. Then an internal method is called when an event is triggered. (The CMS is creating only one instance of class when the first event triggers, then it just executes the method with each event trigger)
The function can be summarized as follows,
import com.external.ProvidedInterface;
public class MonitorProgram implements ProvidedInterface{
public void process(){
//This method is called when an event is triggered in CMS
}
}
Within our class we are using "javax.net.ssl.HttpsURLConnection" (JAVA 1.5). But HttpsURLConnection migrated to javax.net.ssl from com.sun.net.ssl for 1.4. But it seems the CMS I am referring to (We dont know their implementation actually) uses something like this
System.setProperty("java.protocol.handler.pkgs","com.sun.net.ssl.internal.www.protocol");
leading to a ClassCastException in our code.
I think my question is clear. In our case we cant set VM parameters,
-Djava.protocol.handler.pkgs=
Also we cant set it back using,
System.setProperty("")
because the VM instance is same for CMS and our program.
What can I do for get this problem resolved? And idea or experiences?

This is not clear for me.
Do you want to overwrite a system property?
You can do this.
Overwrite the System.property before calling the external library method and when the method returns you can set the old System.property back
final String propertyName = "Property";
String oldProperty = System.getProperty(propertyName);
System.setProperty(propertyName,"NEW_VALUE");
monitorProgram.process();
System.setProperty(propertyName,oldProperty);
Or do you want to prevent, that the called process overwrites the system.property?
And why you can not set the system property by hand?

I don't think you are going to have much success getting two pieces of code to use different properties.
In your own code however, you can define your own URLStreamHandlerFactory. Doing this will allow you to create a javax.net.ssl.HttpsURLConnection from a URL. While protocol handlers aren't the easiest thing to figure out, I think you can get them to do the job.
See http://java.sun.com/developer/onlineTraining/protocolhandlers/

Find the offending class in the stack trace
Use jad or a similar tool to decompile it.
Fix the name of the property
Compile the resulting file and either replace the .class file in the CMS's jar or put it into a place which is earlier in the classpath.
Use ant to automate this process (well, the compile and build of the JAR; not the decompiling)
When it works, make sure you save everything (original file, changed file, build file) somewhere so you can easily do it again.
While this may sound like a ridiculous or dangerous way to fix the issue, it will work. Especially since your CMS provider doesn't seem to develop his product actively.

Modify a string in Java bytecode (jar)

I want to modify a connection string that's hard-coded in a Java application (jar without source).
I presume it's possible to decompile the jar, then change the source and recompile to a new jar, but is there a quicker way to do this?
EDIT:
It's a standalone application, not a jar I'm loading from my own code
I doubt it will have been obfuscated: niche scientific application, author AWOL.
A solution that entails modifying the string "in memory" while the app is running would also suffice, but not ideal

In your application that uses that jar, you could use reflection to set the connection String. (Reflection can be used even with private setters).
Obviously, if the setter is public, you could just call it without reflection.

I think decompilation is probably the quickest way, provided the code hasn't been obfuscated such that a decompilation/compilation round-trip is not possible. You're going to have to decompile the code anyway to find the connection string, so you're half-way there already.
More importantly, you can take advantage of this method to pull the connection string out into a properties file, and hence (hopefully) only perform the decompilation once!

Since Jars are often not compressed, there's a small chance that the address will be visible as plain text in the Jar. You could try editing the Jar with an editor that's not afraid of binary data (I use vim) and just search for and change the text, provided the old address and the new use the same number of characters. That's primitive but very simple.
If it doesn't work, you'll need one of the other approaches.
Of course you'll want to keep a backup copy of the jar in case this approach fails.

Since jar files are simply ZIP-Files with a certain structure, you can use a zip tool (WinZip etc.) to extract the class files; then you use a hex editor to modfiy the class files (should not be too difficult if the new connection string has the same length like the old one); after that, you zip it back into the jar file.
Of course this should only be your last-ditch attempt when all the other possibilities described above don't work.

I assume you already thought of this, but maybe you could simply use inheritance, if the compiled method in the .jar file looks something like this:
public String getConnectionString(){...
then just extend the class, override the method to return your new string and use your class instead. Obviously this only works if the super class is not final, the method is not final, and it's public or protected (if you can use the same package name).