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Which strategy to use? Object Clone or a simple Map

I need help with something. my code is of the following template.
Assume customObject has multiple property1, property2, ..property100.
List<CustomObject> customObjectList = /*<method call to external API that returns the said list >*/
if(customObjectList != null && customObjectList.size() > 0){
//*** point A ***<clone the Object>
resultList = <some method that process the above list>(customObjectList)
if(resultList.size() > 0){
for(Iterator<Map.Entry<CustomObject, ExternalResponse>> itr = resultList.entrySet().iterator(); itr.hasNext();) {
//code that modifies the properties in the CustomObjects
//*** point B ***resetAProperty(<Object clone>)
}
}
}
At point B, I need the one unmodified specific property of original object to use in the method. I have two strategies for this:
Clone the object at point A, and use the cloned copy to get the
property as shown in above code. At point A, Use a for loop and a
Map to form an associate array of object names, property original
values and traverse them to get the property initial value at point
B

Avoid Cloning because it always requires Deep Cloning
.clone() especially on a List will almost always end in tears because you would have to deep clone all the objects in the list, all their referenced objects, and so on.
Deep Cloning means you have to make a binary copy of every last object in the Object graph. Just copying a reference will give you a shallow copy and you will see any changes that are made to the referenced object. Just miss one property and you will have a hell of a time finding that bug.
Solution
What you should do is make all your CustomObject instances Immutable and then you don't need to worry about versioning, they can never change, mutation would involve creating a new instance that is also Immutable and a complete different object. Then you never had to worry about versions.
Of course all the instance variables that point to other objects will need to be Immutable as well. This is the same problem as the deep clone but taking from another angle. A much more manageable angle.

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>.

Java get an element from an array, edit it, then store it in another array, without altering the first array

I have encountered a problem in one of my Java projects, which causes bugs.
The problem sounds as following:
I have two arrays. Let's name them firstArray and secondArray. Object in this case is a seperate class created by me. It works, the array can be filled with objects of that type.
Object[] firstArray= new Object[];
Object[] secondArray = new Object[];
Now, when I get an element out of the first array, edit it and then copy it in the second array, the object from the first array gets altered too.
tempObj = firstArray[3];
tempObj.modifySomething();
secondArray[3] = tempObj;
Whenever I do this, the (in this case) 3rd element(actually 4th) of the first array gets the modifications. I don't want this. I want the first Array to remain intact, unmodified, and the objects I have extracted from the first array and then modified should be stored in the second so that the second array is actually the first array after some code has been run.
P.S. Even if I get the element from the first array with Array.get(Array, index) and then modify it, the element still gets modified in the first array.
Hopefully you understood what I wanted to say, and if so, please lend me a hand :)
Thank you!

You're going to have to create a new object.
The problem is the modifySomething call. When you do that, it alters the object on which it's called. So if you've only got one object (even by two names), you can't call modifySomething or they will both change.
When you say secondArray[3] = firstArray[3], you aren't creating a new object: you're just assigning a reference. Going through an intermediate temporary reference doesn't change that.
You'll need code that looks like this:
Object tempObj = firstArray[3].clone();
tempObj.modifySomething();
secondArray[3] = tempObj;
The clone() method must return a new object divorced from the original but having identical properties.

When you retrieve an element from your array, you have a reference to it. So if you modify it, the modification are shered through all the object's references.
In order to leave it intact, you should use some method like Object.clone() or create a new Object and use its constructor to initialize its fields.

The object extracted from the first array needs to be cloned to create a new instance that is seperate. Otherwise the modification will affect the object in the first array as it is the same object.

When you retrieve an element from your array, you get a reference to it. So if you modify it, the modification are shared through all the object's references.
In order to leave it intact, you should use some method like Object.clone() or create a new method which take in input your retrieved object and return a new one alike.

In Java, when you do this secondArray[3] = tempObj;, you actually put the reference to the array, not the real object
So firstArray[3] and secondArray[3] point to the same real object
What you need to do is to create a new object that is identical to your original object, and put the reference of the new object to your secondArray
It might worth to point out that default clone() function only does a shallow copy, so if you have mutable objects in your object's fields, it might cause some problems. Take a look at this article about how to do a deep copy

java list cannot add class then alter original class without altering the copy from the list

So i mostly program in C++, and java is very similar to c++.
I have created a list command as such
List<Item> stuff =new ArrayList<Item>();
where Item is a custom class that basically stores data.
I get information from a text file and store it to Item.
Then i use stuff.add to get the item class to stuff.
Afterwards i use a command to erase all data from the item class and see that it has also deleted all the data from the list.
Basically I want to know if there is a way to add a copy of the class and not the address of the class itself.
Edit:
so i found that reinitializing the item class also solved my problem thanks though.

You want to clone the item before adding it to the list. The list just has a reference to the original item that you created. As such, when you mutate your item, the item in the list is also affected (it's the same object).
If you want to "disconnect" the item that you put into your list, then you can clone it first. Your item class will need to implement Cloneable and override the clone() method. If you have only primitives in Item, then you can simply do:
public Object clone()
{
return super.clone();
}
If you have other objects in Item, then the default clone operation will only make a shallow copy, and you will need to make your clone method more extensive so that it makes deep copies. From the Javadoc for Object.clone():
By convention, the object returned by this method should be independent of this object (which is being cloned). To achieve this independence, it may be necessary to modify one or more fields of the object returned by super.clone before returning it. Typically, this means copying any mutable objects that comprise the internal "deep structure" of the object being cloned and replacing the references to these objects with references to the copies. If a class contains only primitive fields or references to immutable objects, then it is usually the case that no fields in the object returned by super.clone need to be modified.

In Java, objects references act like pointers in C++. There is no notion of "copy constructor". You have noticed this when you've added something to a list and then change the item after adding it to a list.
Generally in Java you will use new to create a new Item every time you add a new one to the list. So something like:
while (...) {
Item i = new Item(...);
stuff.add(i);
}
rather than
Item i = new Item();
while (...) {
i.foo = ...;
stuff.add(i);
}
The second example above will add the same object to the list multiple times.

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.