MutableState has non-mutable initializations resulting in errors on deepCopy calls

[EdwardRaff]

The initialization of these lists uses the emptyList collection that is hard-coded to be an always empty list, and so will throw an error if anything is added to these lists.

byteseek/src/main/java/net/byteseek/automata/MutableState.java

Lines 94 to 98 in 2600c05

	public MutableState(final boolean isFinal) {
	this.isFinal = isFinal;
	this.transitions = Collections.emptyList();
	this.associations = Collections.emptyList(); // = new ArrayList<T>(0);
	}

In most of the code base this results in several isEmpty() checks to create a new ArrayList as necessary to add to it.

However, this does not occur in the deepCopy method, resulting in an error when I attempt to build a rather large regex (it has 10000 matchers, not yet at a minimum viable example, but I think this bug is pretty easy/clear fix).

byteseek/src/main/java/net/byteseek/automata/MutableState.java

Lines 418 to 431 in 2600c05

	public MutableState<T> deepCopy(Map<DeepCopy, DeepCopy> oldToNewObjects) {
	@SuppressWarnings("unchecked")
	// if there is a copy of this in the map, it will be of the same type.
	MutableState<T> stateCopy = (MutableState<T>) oldToNewObjects.get(this);
	if (stateCopy == null) {
	stateCopy = new MutableState<T>(this.isFinal);
	oldToNewObjects.put(this, stateCopy);
	for (Transition<T> transition : transitions) {
	final Transition<T> transitionCopy = transition.deepCopy(oldToNewObjects);
	stateCopy.transitions.add(transitionCopy);
	}
	}
	return stateCopy;
	}

This is blocking me from being able to create a new TrieMultiSequenceMatcher

[nishihatapalmer]

Hi Edward, thanks for the bug report. It is indeed a bug in the deepCopy implementation. The fix should be to use the normal addTransition() method of the stateCopy, instead of trying to add them directly to the collection.

public MutableState<T> deepCopy(Map<DeepCopy, DeepCopy> oldToNewObjects) {
		@SuppressWarnings("unchecked")
		// if there is a copy of this in the map, it will be of the same type.
		MutableState<T> stateCopy = (MutableState<T>) oldToNewObjects.get(this);
		if (stateCopy == null) {
			stateCopy = new MutableState<T>(this.isFinal);
			oldToNewObjects.put(this, stateCopy);
			for (Transition<T> transition : transitions) {
				final Transition<T> transitionCopy = transition.deepCopy(oldToNewObjects);
				stateCopy.addTransition(transitionCopy);
			}
		}
		return stateCopy;
	}

[nishihatapalmer]

To set expectations here, I am unlikely to issue a bug fix for the current version of byteseek. I have been working on byteseek 3 for some years now, and that will be the next release I make. Hopefully this year, but I have some important other priorities taking up my time at the moment.

To further set expectations, all of the multi-string matching and searching in byteseek 3 is being placed in an "incubator" status. This means that it is largely untested code, whereas the rest of byteseek will be fully tested. I am not getting rid of it, but being honest, I do not know how much time I will have to develop this aspect of byteseek going forward. I guess if there is actual interest in this aspect, that might motivate me!