/common/base/   Amino acids, ptms, residues and etc 
/common/util/   String utilities, file utilities, and etc
/common/xml/    Functions for handling xml files   
/console/       Main functions for topfd, toppic, topmg, and topmerge
/filter/        Protein sequence filtering methods
/gui/           GUI for topfd, toppic, topmg, and topmerge
/merge/         Merging proteoform identifications from several samples
/ms/            Mass spectra, envelops, LC-MS maps, and features
/prsm/          Proteoform spectrum matches and related functions
/search/        Various database search algorithms
/seq/           Fasta sequences and proteoforms
/spec/          Peak and spectrum classes
/stat/local/    Charaterization and localization of mass shifts
/stat/mcmc/     An Markov chain Monte Carlo method for E-value estimation
/stat/tdgf/     A generation function method for E-value estimation
/suffix/        Suffix tree used in the manuscript Deng et al, Bioinformatics 31, 532-538
/topdia/        Code for TopDIA
/topfd/         Code for TopFD
/visual/        Functions for visualization of proteoform spectrum matches
