The trick with problem sets so sparsely filled with noteworthy information is skipping as many processing steps as possible without marring the final results by skipping something important. I have made some modifications to GFS and am testing those now: If MSMSFit goes through all of the y-ions and finds less than 12% match then [...] Read More

I’m curious if a job on one DTA/PKL file with N spectra will run faster than a job that processes the exact same data broken into N different files. I just wrote a quick java app to take OutputFile2.dta which has 112 spectra and split it into 112 different dta files. At the moment I [...] 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

The above is, generally, what a run of GFS looks like. The tail end is typically longer as Shark often stops before program execution terminates naturally. The tail corresponds to HMM_Score, unless -seqtagscore is enabled, in which case it’s a lot of findLongestCommonSubstring. Zoom in a bit: Read More

Regarding Wednesday’s post, I am finding it difficult to believe that an int array is outperforming a char array in some cases. Especially when the code for the int array requires a few extra lines. Am beginning today with a quick sanity check–am cleaning the target with the char array code and running the test [...] Read More