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#_sys_ind_basename MS::Sequest::Params
#aa_mod_to_tot_mass MS::Sequest::Pepxml::Modifications
#aa_mods MS::Sequest::Pepxml::Modifications
#base_name MS::Sequest::Srf
#base_name MS::Sequest::Sqt
#combined MS::Sequest::Srf::Header
commandline MS::Sequest::Srf::Sqt
commandline MS::Sequest::Srf::Pepxml
commandline MS::Sequest::Srf::Search
#create_static_mods MS::Sequest::Pepxml::Modifications
#database MS::Sequest::Params
#database_path= MS::Sequest::Params
#db_filename MS::Sequest::Srf::Header
db_info MS::Sequest::Sqt
db_md5sum MS::Sequest::Sqt
db_seq_length_and_locus_count MS::Sequest::Sqt
#deltacn MS::Ident::Pepxml::SearchHit::Sequest
#deltacnstar MS::Ident::Pepxml::SearchHit::Sequest
#dta_files MS::Sequest::Srf
#dta_gen MS::Sequest::Srf::Header
#dta_log_filename MS::Sequest::Srf::Header
#dta_start_byte MS::Sequest::Srf
#end_mass MS::Sequest::Srf::DtaGen
#end_scan MS::Sequest::Srf::DtaGen
#enzyme MS::Sequest::Params
#enzyme MS::Sequest::Srf::Header
#enzyme_specificity MS::Sequest::Params
#extension MS::Sequest::SqtGroup
#filter_by_precursor_mass_tolerance! MS::Sequest::Srf
#filtered_by_precursor_mass_tolerance MS::Sequest::Srf
#first_entry MS::Sequest::Srf::Out::Protein
#first_entry MS::Sequest::Sqt::Locus
#fragment_ion_tol MS::Sequest::Params
#fragment_mass_type MS::Sequest::Params
#from_file MS::Sequest::Sqt
#from_file MS::Sequest::Srf
#from_handle MS::Sequest::Sqt::Header
#from_io MS::Sequest::Srf::DtaGen
from_io MS::Sequest::Srf::DtaGen
#from_io MS::Sequest::Srf::Header
from_io MS::Sequest::Srf::Header
from_io MS::Sequest::Srf::Out::Peptide
from_io MS::Sequest::Srf::Out
from_io MS::Sequest::Srf::Dta
from_line MS::Sequest::Sqt::Locus
#from_line MS::Sequest::Sqt::Match
#from_line MS::Sequest::Sqt::Spectrum
#from_lines MS::Sequest::Sqt::Header
get_sequest_params_and_finish_pos MS::Sequest::Srf
#grab_params MS::Sequest::Params
#group_scan MS::Sequest::Srf::DtaGen
#header MS::Sequest::Srf
#header MS::Sequest::Sqt
#id MS::Sequest::Sqt::Locus
#index MS::Sequest::Srf
#initialize MS::Sequest::Sqt::Locus
#initialize MS::Sequest::Sqt
#initialize MS::Sequest::SqtGroup
#initialize MS::Sequest::Pepxml::Modifications
#initialize MS::Sequest::Srf
#initialize MS::Sequest::Params
#inspect MS::Sequest::Srf::Out::Peptide
#inspect MS::Sequest::Srf::Out
#inspect MS::Sequest::Srf::Dta
#ion_series MS::Sequest::Srf::Header
#mass_index MS::Sequest::Params
#max_num_differential_AA_per_mod MS::Sequest::Params
#max_num_internal_cleavages MS::Sequest::Params
#method_missing MS::Sequest::Params
#min_group_count MS::Sequest::Srf::DtaGen
#min_ion_threshold MS::Sequest::Srf::DtaGen
#min_number_termini MS::Sequest::Params
#mod_symbols_hash MS::Sequest::Pepxml::Modifications
#model MS::Sequest::Srf::Header
#modification_info MS::Sequest::Pepxml::Modifications
#modifications MS::Sequest::Srf::Header
#modifications MS::Sequest::Pepxml::Modifications
#mods MS::Sequest::Params
#negative_q_value MS::Sequest::Sqt::Match::Percolator
#negative_q_value= MS::Sequest::Sqt::Match::Percolator
#num_dta_files MS::Sequest::Srf::Header
#num_dta_files MS::Sequest::Srf::DtaGen
#opts MS::Sequest::Params
#out_files MS::Sequest::Srf
#params MS::Sequest::Srf
#params MS::Sequest::Pepxml::Modifications
#params_filename MS::Sequest::Srf::Header
#parse_file MS::Sequest::Params
#parse_io MS::Sequest::Params
#peptide_mass_tol MS::Sequest::Params
#percolator_results MS::Sequest::Sqt
#percolator_score MS::Sequest::Sqt::Match::Percolator
#percolator_score= MS::Sequest::Sqt::Match::Percolator
#precursor_mass_type MS::Sequest::Params
#probability MS::Sequest::Sqt::Match::Percolator
#protein_class MS::Sequest::Srf
#protein_class MS::Sequest::Sqt
#proteins MS::Sequest::Sqt::Match
#q_value MS::Sequest::Sqt::Match::Percolator
#raw_filename MS::Sequest::Srf::Header
#read_dta_and_out_interleaved MS::Sequest::Srf
#read_dta_files MS::Sequest::Srf
read_extra_references MS::Sequest::Srf::Out::Peptide
#read_out_files MS::Sequest::Srf
#read_scan_index MS::Sequest::Srf
#reference MS::Sequest::Sqt::Locus
#resident_dir MS::Sequest::Srf
#round MS::Sequest::Srf::Dta
#sample_enzyme MS::Sequest::Params
#sample_enzyme_hash MS::Sequest::Params
#search_class MS::Sequest::SqtGroup
#sequence MS::Sequest::Params
#sequest_log_filename MS::Sequest::Srf::Header
set_deltacn MS::Sequest::Sqt::Spectrum
set_deltacn_from_deltacn_orig MS::Sequest::Srf::Out::Peptide
#set_hashes MS::Sequest::Pepxml::Modifications
#set_modifications MS::Sequest::Pepxml::Modifications
#spectra MS::Sequest::Sqt
spectra_from_handle MS::Sequest::Sqt::Spectrum
split_ions MS::Ident::Pepxml::SearchHit::Sequest
#sprank MS::Ident::Pepxml::SearchHit::Sequest
#spscore MS::Ident::Pepxml::SearchHit::Sequest
#start_mass MS::Sequest::Srf::DtaGen
#start_scan MS::Sequest::Srf::DtaGen
#start_time MS::Sequest::Srf::DtaGen
#static_mods MS::Sequest::Params
#term_mods MS::Sequest::Pepxml::Modifications
#to_dta MS::Sequest::Srf::Search
#to_dta_file_data MS::Sequest::Srf::Dta
#to_mgf MS::Sequest::Srf::Search
#to_pepxml MS::Sequest::Srf::Pepxml
#to_sqt MS::Sequest::Srf::Sqt
#to_xml MS::Ident::Pepxml::SearchHit::Sequest
update_deltacns_from_xcorr MS::Sequest::Srf::Out::Peptide
#version MS::Sequest::Params
#version MS::Sequest::Srf::Header
#version MS::Sequest::Srf
#write_dta_file MS::Sequest::Srf::Dta
#xcorr MS::Ident::Pepxml::SearchHit::Sequest