Removing from front of ArrayList

[niemasd]

I'm not sure how time-consuming this step is, so not sure if it is negligible:

https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/blob/master/src/clusterPicking/ClusterPicker.java#L456

But you are storing the things you want to process in an ArrayList, but you're iteratively removing from the front of the ArrayList, which is O(n) each time (where n is the number of elements in the ArrayList). You should use a Queue (which is implemented as a LinkedList) for O(1) removal from the front, given that you don't care about random access of elements