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REWROTE the whole backend. The code is a little more manageable and also there is better error handling.
Added the ability to separate rows of data pertaining to the same peptide but for different charges. SRM heuristically determines which charge mass ratios should be grouped together using standard deviations times a tolerance multiplier–which can be modified from the GUI. This logic will always run because it doesn't make sense to mix together different mass charge ratios.
Removed the need to specify a heavy water file. The program can determine the body water file from the body enrichment row in the input spreadsheet.