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#_sys_ind_basename Ms::Sequest::Params
#_uniq_peps_by_sequence_charge Bioworks
#aa_mod_to_tot_mass Ms::Sequest::Pepxml::Modifications
#aa_mods Ms::Sequest::Pepxml::Modifications
#accession Bioworks::Prot
#base_name Ms::Sequest::Sqt
#base_name Ms::Sequest::Srf
#bioworks Bioworks::Prot
#character Bioworks::XMLParser
#combined Ms::Sequest::Srf::Header
commandline Ms::Sequest::Srf::Sqt
commandline Ms::Sequest::Srf::Search
commandline Ms::Sequest::Srf::Pepxml
#consensus_score Bioworks::Prot
#coverage Bioworks::Prot
#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
#endElement Bioworks::XMLParser
#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
extract_file_info Bioworks::Pep
#file= Bioworks::Pep
#filter_by_precursor_mass_tolerance! Ms::Sequest::Srf
#filtered_by_precursor_mass_tolerance Ms::Sequest::Srf
#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::Header
#from_io Ms::Sequest::Srf::DtaGen
from_io Ms::Sequest::Srf::Out
from_io Ms::Sequest::Srf::Header
from_io Ms::Sequest::Srf::Out::Peptide
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 Bioworks::Pep
#get Bioworks::Prot
#get_prots_from_xml_stream Bioworks
#get_regex_val Bioworks
get_sequest_params_and_finish_pos Ms::Sequest::Srf
#global_filename Bioworks
#grab_params Ms::Sequest::Params
#group_scan Ms::Sequest::Srf::DtaGen
#header Ms::Sequest::Srf
#header Ms::Sequest::Sqt
#hi_prob_best Bioworks
#index Ms::Sequest::Srf
#initialize Ms::Sequest::Params
#initialize Ms::Sequest::Srf
#initialize Bioworks
#initialize Ms::Sequest::Srf::Out::Protein
#initialize Ms::Sequest::Sqt::Locus
#initialize Bioworks::Prot
#initialize Ms::Sequest::Pepxml::Modifications
#initialize Ms::Sequest::Sqt
#initialize Ms::Sequest::SqtGroup
#initialize Bioworks::XMLParser
#initialize Ms::Sequest::SrfGroup
#inspect Bioworks::Pep
#inspect Ms::Sequest::Srf::Out::Protein
#inspect Ms::Sequest::Srf::Out
#inspect Ms::Sequest::Srf::Dta
#inspect Ms::Sequest::Srf::Out::Peptide
#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
#mh Bioworks::Pep
#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
#modifications Bioworks
#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
#num_proteins Bioworks
#opts Ms::Sequest::Params
#origfilename Bioworks
#origfilepath Bioworks
#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
#parse_xml Bioworks
#parse_xml_by_xmlparser Bioworks
#peps Bioworks::Prot
#peps Bioworks
#peptide_hit_counts Bioworks::Prot
#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
#pi Bioworks::Prot
#ppm Bioworks::Pep
#precursor_mass_type Ms::Sequest::Params
#probability Ms::Sequest::Sqt::Match::Percolator
#probability Bioworks::Pep
#protein_class Ms::Sequest::Srf
#protein_class Ms::Sequest::Sqt
#protein_probability Bioworks::Prot
#proteins Ms::Sequest::Sqt::Match
#proteins Bioworks
#prots Bioworks::XMLParser
#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 Bioworks::Prot
#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::SrfGroup
#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_from_hash_given_text Bioworks::Pep
#set_from_xml_hash Bioworks::Prot
#set_from_xml_hash_xmlparser Bioworks::Prot
#set_from_xml_stream Bioworks::Prot
#set_from_xml_stream Bioworks::Pep
#set_hashes Ms::Sequest::Pepxml::Modifications
#set_modifications Ms::Sequest::Pepxml::Modifications
#sf Bioworks::Prot
#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
#startElement Bioworks::XMLParser
#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_excel Bioworks
#to_mgf Ms::Sequest::Srf::Search
#to_pepxml Ms::Sequest::Srf::Pepxml
#to_pepxml Bioworks
#to_sqt Bioworks
#to_sqt Ms::Sequest::Srf::Sqt
#to_srg Ms::Sequest::SrfGroup
#to_xml Ms::Ident::Pepxml::SearchHit::Sequest
#unified_score Bioworks::Prot
update_deltacns_from_xcorr Ms::Sequest::Srf::Out::Peptide
#update_peptide_hit_counts Bioworks
#version Bioworks
#version Ms::Sequest::Params
#version Ms::Sequest::Srf::Header
#version Ms::Sequest::Srf
#weight Bioworks::Prot
#write_dta_file Ms::Sequest::Srf::Dta
#xcorr Ms::Ident::Pepxml::SearchHit::Sequest