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#<=> Reverser
#add_sequences_to_segments TopPred::Parser
#avg_overlap TransmembraneIndex
#calculate_background_frequency Ms::ErrorRate::Sbv
default_index TopPred
default_index Phobius
expand_peptides Ms::Ident
#file_to_index TopPred::Parser
#file_to_index Phobius::Parser
filetype TopPred::Parser
filetype TransmembraneIndex
#frequency_indicator_opposite Ms::ErrorRate::Sbv
generate_hashes Ms::ErrorRate::Sbv::ProteinBased
generate_hashes Ms::ErrorRate::Sbv
generate_hashes Ms::ErrorRate::Sbv::PeptideBased
#get_root_node_from_io TopPred::Parser_XML::AXML
#get_root_node_from_io TopPred::Parser_XML::LibXML
#group_by Array
#indicator_by_aaseq Ms::ErrorRate::Sbv
#indicators_signify_true_hit Ms::ErrorRate::Sbv
#initialize Ms::ErrorRate::Sbv
#initialize TopPred::Index
#initialize Phobius::Index
#initialize Reverser
mixed_target_decoy Ms::ErrorRate::Qvalue
new Phobius::Parser
new TopPred::Parser_XML
new TransmembraneIndex
new TopPred::Parser
#num_certain_index TransmembraneIndex
#num_overlapping_chars TransmembraneIndex
#num_transmem_aa TransmembraneIndex
#obj Reverser
#parse TopPred::Parser_XML
peptide_centric_db Ms::Ident
precision Ms::ErrorRate::Decoy
#prediction_to_array Phobius::ParserShort
qvalues Ms::ErrorRate::Qvalue::Mascot
qvalues Ms::ErrorRate::Qvalue::Mascot::Percolator
#reference_to_key TopPred::Index
#reference_to_key Phobius::Index
#reference_to_key TransmembraneIndex
#rev Object
#size_to_freq Ms::ErrorRate::Sbv
#sort_by_attributes Enumerable
tab_txt Ms::ErrorRate::Qvalue::Mascot::Percolator
target_decoy_qvalues Ms::ErrorRate::Qvalue
#to_index TopPred::Parser_XML::DOM
#to_index TopPred::Parser_Text
#to_index Phobius::ParserShort
#to_yaml Ms::ErrorRate::Qvalue::Mascot::MascotPeptideHit
#update_precision Ms::ErrorRate::Sbv