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Is modyfying the referenced object affecting the original object from which the new object was created?

I have a problem with understanding one thing.
I have:
List<Map> resultList = new ArrayList<Map>();
Then this resultList is filled with some data
resultList.addAll(somemethod(something, something, else));
Later in the method I have this kind of code:
Map timeSpan = someMethod(resultList, date);
timeSpan.put(KEY_ART, VALUE_ART);
timeSpan.put(KEY_TIMESPAN, true);
So I have a question now. If Map timeSpan is a map referenced to an element of List<Map> resultList, is using the put() method on the timeSpan map affecting the element in resultList?
I am asking this question cause a collegue told me that this is working this way - modifying an element in timeSpan is also modyfying this element in resultList. She is far more experienced, and I don't just want to believe her but I want to understand why it is working this way.

You have to remember that resultList is a reference to an object. You can copy this reference around and use it in many way, in many places but there is only one object. This means when you alter the object, there is only one view of this object.

Java objects are always instantiated as a reference to a memory space. If you create a second object from the first object, both will point to the same memory space:
Map a = new HashMap();
Map B=b = a;
Here, we first create an instance A which points to a HashMap which is created somewhere in memory. Next, we create an instance of Map b and have it reference to the same memory space as Map a. Now, when we change map b, these changes will also be made to Map a, since they point to the same memory construct.
In you case, you have a List this in itself is a memory construct. Each item in the list references a seperate Map. These are each also created somewhere in memory. The moment you retreive a Map from the list, you retreive the reference to the memory space where the actual map is located. After that, it works exactly as the example.

addAll() will copy all the elements to the current list from the Collection/List you passed as an argument to this method. In your case, as each element is a reference to Map object, after copying, you have 2 references pointing to same Map object, so changes done using any one reference are visible through the other one.

The short answer is yes, put() for timeSpan is affecting resultList, because when a method returns a Map, which is got from the List, it returns a reference to the heap where map elements are located.

Copying an object and changing it (in Java)

I'm having an odd problem that I haven't encountered before with copying objects in Java.
So, I've written a class in my code called "State". This contains a few ints, a 2d array, a string and such...
So, for an instance of State called S, I want to make a copy of it called X (I do this simply by writing State X = S; ). Then I want to make changes to X, do some evaluations based on those changes and then just throw away X and keep using S. However, the problem I'm getting is that S seems to be getting the changes that I make to X.
This seems odd to me, since I feel quite certain that I've done things like this before but never had this problem.
Any thoughts?
(Thanks in advance)

I want to make a copy of it called X (I do this simply by writing State X = S; ).
That does not make a copy of the object.
Variables (of non-primitive types) in Java are references - they are not the objects themselves. By doing
State X = S;
you are not copying an object, you are just copying the reference - the result is that you now have two variables that are referring to the same object. If you modify the object through one reference, you'll see the changes also through the other reference.
One way to copy objects is by using the clone() method. For this to work, the class of the object that you are trying to copy must implement interface Cloneable. Another (and probably better) way is to create a copy constructor, and use it to copy the object:
public class State {
public State(State other) {
// initialize this object by copying content from other
}
}
// Make a copy
State X = new State(S);

Your code is not creating a copy of the object. What you are doing there is creating a new reference and pointing it to the same object.
Search for "how to clone an object in Java". Read up on the Cloneable interface.

Why local non-final variable affects the referenced field? Java

I have following code in my program:
...
private void generateStack() {
List<AdvertisementsModel> adsForModel = Storage.getAdsForId(model.getId());
...
adsForModel.clear();
...
Storage is static class with static fields and methods. generateStack method is in another class and in instance object. Why does adsForModel.clear(); affects the list in Storage class if asdForModel reference is not final?

Storage.getAdsForId(...) returns a copy of the reference to the same List object. So calls via this reference effect the same list. When you call Storage.getAdsForId there is no new List created - just a new reference to the same list.
Therefore it's good practise to either return explicitly ImmutableList or making a defensive copy of the list in Storage.getAdsForId(...) and returning the copy.
Be aware that you need to make a deep copy when AdvertisementsModel is mutable or you'll run into the same problem on a different level. (Otherwise you may have a list copy now but both lists still containing references to the same AdvertisementsModel objects and changing them still effect the list contents inside Storage.)

Java is pass by value (of the reference). So, if Storage.getAdsForId(model.getId()) returns a reference which is staticly stored within Storage then calling clear() on it in the instance will affect the same List within Storage as well. You could do this instead:
return new ArrayList<AdvertisementsModel>(Storage.getAdsForId(model.getId()));
to return a copy of the list instead which would avoid affecting the list within Storage. Of course, modifying an element of this list will still affect the same element present within the list in Storage. To avoid that, you'd have to deep copy each element in the list.

getAdsForId should return a copy of the list, otherwise it will return a reference and calling clear on the list will empty the original one.

If it is final, is the original list not affected? I have doubts about that... It's the same list instance. For this, I'd use either
new ArrayList<AdvertisementsModel>(Storage.getAdsForId(model.getId()));
which creates a new list instance and if possible, modified the Storage class to return an UnmofifiableList of the original list:
return Collections.unmodifiableList(adsForIdList);
I'd prefer this, as this solution does not create a new List instance with each call, it is the responsibility of the receiving code to decide if that needs to be created or not. However, in multithreaded environments, if the original list might be modified, this might result in ConcurrentModificationExceptions - so in that case it is wiser to create a "defensive copy" of the list in the getter itself. Be sure to keep in mind, that then the modifications to the copy will not affect the original list...

Deep copy of an object Java

I am trying to clone an object of MyGraph and I want it to be a deep copy so the arraylists inside the object are also cloned. Right now I have:
public static MyGraph deepCopy(MyGraph G){
MyGraph Copy = (MyGraph) G.clone();
Copy.VertexG = (ArrayList<Integer>) G.VertexG.clone();
Copy.EdgeG = (ArrayList<String>) G.EdgeG.clone();
return Copy;
}
This returns an error when it tries to clone the arraylist. I am not sure if this is the right way to add the arraylists to the object.

The clone operation in ArrayList returns a shallow copy of the object, and will not be suitable for your purposes. The manual workaround is to:
Create a target array list of the same size as the source list
Iterate the source list and create a clone of each of it's items, into the target list
Obviously, this will only work if the array list contains items that implement clone, and in addition that the items clone operation actually returns a deep copy. In other words, its not guaranteed. Actually, implementing deep clone functionality for Java objects is not at all easy, refer to extensive discussions in Java: recommended solution for deep cloning/copying an instance and other SO threads to get a feel for the options available. In addition to the answers provided there, here are some other options:
Serialization
If all (the required) objects in your hierarchy can be serialized then you can use this simple code to do a deep clone:
public MyGraph deepCopy() {
try {
final ByteArrayOutputStream baos = new ByteArrayOutputStream(256);
final ObjectOutputStream oos = new ObjectOutputStream(baos);
oos.writeObject(this);
oos.close();
final ObjectInputStream ois = new ObjectInputStream(
new ByteArrayInputStream(baos.toByteArray()));
final MyGraph clone = (QuicksortTest) ois.readObject();
return clone;
} catch (final Exception e) {
throw new RuntimeException("Cloning failed");
}
}
Note that some deep-clone libraries combine standard Java serialization with reflection hacks and/or byte code instrumentation in order to make the entire object hierarchy fully serializable. You may, or may not, need that.
Copy tools
For example, Dozer, provide fast deep-copy functionality. Orika can also achieve the same, albeit with more configuration:
public MyGraph deepCopy() {
final DozerBeanMapper mapper = new DozerBeanMapper();
final QuicksortTest clone = mapper.map(this, MyGraph.class);
return clone;
}
The only downside of course, being the additional dependencies you need to pull into your project.
On a total tangent, your deepCopy method should not be static. Also, you should seriously considering encapsulating the state of your object by making it private and implementing getters/setters.

Every class you call clone() on has to implement the Cloneable interface. From your comments, i understand your MyGraph class does not implement the Cloneable interface. In that case, Object.clone() throws the CloneNotSupportedException.

Trying to do deep copy with cloning is complicated as you need to ensure that all classes implement Cloneable interface and they have clone() definition.
Better way would be to do it through Copy Constructor or Serialization. Here is my blog on which i have discussed it in detail. hope it helps :)

A fundamental conceptual problem with cloning in Java [arguably the fundamental problem] is it's possible for a field of a type like List<String> to represent at least five very different things:
The only extant reference to a mutable list, which is used to encapsulate the mutable state thereof, but which--being the only extant reference--would not encapsulate its identity (the list could be replaced with a different list holding the same items, without altering the program's semantics). A correct clone of the object that contains this field would hold a reference to a different list holding the same items.
A reference to a mutable list which, while it would allow itself to be mutated, will never be exposed to anything that would actually mutate it. This reference may be shared with other code only if that other code will refrain from mutating the list or exposing it to code that might do so. A correct clone of the object that contains this field could hold a reference to either the original list or a different list holding the same items.
A reference to an immutable list. This reference may be shared freely with other code without regard for how that code might expose it. As above, the correct clone of the object containing this field could hold a reference to either the original list or a copy.
A reference to a mutable list which is owned by some other object, which is held for purpose of binding this to those aspects of the other object's state which are encapsulated in the list. A correct clone of the object holding the field must hold a reference to that same list, and not a copy thereof.
A reference to a mutable list which this object owns, but to which other objects also have a reference for purpose of either observing this object's state, or feeding information to this object. The object holding this field cannot be correctly cloned in isolation, though it might be possible to clone a group of inter-connected objects and give the new set of objects a set of interconnections which was isomorphic to those in the original group.
The concrete type of the object to which the field holds a reference may distinguish between some of the above cases, but it cannot distinguish among all of them. In particular, the first and fourth scenarios require different behavior on the part of the cloning method, despite the fact that in both scenarios the reference might likely pointing to an ArrayList<string>.

How do I copy an arraylist from one class to another in Java?

I understand that in order to copy an arraylist and have two lists independent of one another you must use a deep copy (copying the objects from one list to another not just the references), however is there a way this can be done cross-class?
For example; I am calling Class2 from Class1. In Class2 objects are added to an ArrayList of custom objects upon an event. I would like to be able to transfer this ArrayList to Class1 but whenever I try I get a NullPointer.
Any clues??

This is highly indicative of a design flaw.
See if you can't accomplish the same goal by wrapping your list in a class, sharing the class and using it to control access to the list.
The only case where this wouldn't just outright work is if your two classes must modify the list independently.
If this is a requirement, then I would probably hand a different instance of the wrapper class to each modifying class (with a reference to the same source list), then have a way for newly added data to be tagged with an ID referring to the original class--that way when you query, the wrapper would only return untagged items (items that were part of the original shared list) and items tagged with it's own ID.
Either that or the wrapper class could contain a second list and when queried, return the combined results of the original and second lists.
I've almost never wanted a deep copy. It happens, but it's quite rare.
If you post more info, maybe we can be more specific in helping with the redesign.
ALSO: (Edit)
Chances are that the copied array list isn't your problem--it's probably that it wasn't TRULY a deep copy. For a deep copy, it means you implement a copy method (I believe they are supposed to be called .clone(), I never use this stuff--as I said, it's bad juju) for each object in the array list, then you call your copy method on each one to get the new copy in your next list.
Furthermore, any objects referenced by your copied object should probably be cloned as well. "Deep" means all the way down the tree.
I'm guessing you're failing somewhere in the process.
I'd really like to hear why you feel you need a copy instead of a reference.

My suggestion is for you to create a getArray() method and call it from the other class. This method should create a copy of the ArrayList because you should not "transfer" variables within classes; always with get() method so OO paradigm stays intact.
Do something like this:
Class 1
public ArrayList<Object> getArray() {
ArrayList<Object> aux = new ArrayList<Object>();
for(Object x : list) //object is the string, int, etc...
aux.add(x.clone()) //assuming the Object has a clone method!
return aux;
}
On Class 2, just call this method. Then just look at the test from the other answer about the null exception, should work.
Hope it helps.