need to work on getting this method (if that is what it is called) to work. Right now we are having to convert from DTA to PKL. NOTE: reference readPKL — it works with all newline characters. Read More

How many copies of the cleanPeakForHighMass method do we need in this code? Read More

in calcScoresForMSMS the loop which goes through the masses surrounds the loop which goes through the sequence. if we put the sequence loop on the outside this will confer some advantages: translateNucleotideSequence won’t have to be called over and over. the code which produces a probable MSMS spectrum for a given sequence could be called [...] Read More

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 [...] Read More