compareInternalFrags calculates the masses of all possible internal fragments given a sequence. This should not happen inside of compareInternalFrags but rather outside and be passed to compareInternalFrags so that this calculation is not done over and over unnecessarily.

This is in HMMScoreClass.

compareInternalFrags is called by getIonTypes. getIonTypes is called once in the two different maximumScore methods. I should create a new method which calculates the internal frag weights (eschewing creativity this would be called calculateInternalFragWeights). This new method should be called from the maximumScore and the results passed to getIonTypes which, in turn, passes to compareInternalFrags.