Method List
Search:
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_prot_num_and_first_prot_by_pep Sequest::PepXML
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#_sys_ind_basename Ms::Sequest::Params
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#_uniq_peps_by_sequence_charge Bioworks
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#aa_mods Sequest::PepXML::Modifications
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#aaseq Sequest::PepXML::SearchHit
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#aaseq= Sequest::PepXML::SearchHit
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#accession Bioworks::Prot
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#aminoacid Sequest::PepXML::AAModification
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#avg_parent Sequest::PepXML
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#base_name Ms::Sequest::Srf
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#base_name Ms::Sequest::Sqt
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#base_name Sequest::PepXML
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#base_name Sequest::PepXML::MSMSRunSummary
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#base_name Sequest::PepXML::SearchSummary
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base_name_noext Sequest::PepXML
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#binary Sequest::PepXML::AAModification
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#bioworks Bioworks::Prot
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calc_precursor_neutral_mass Sequest::PepXML::SpectrumQuery
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#character Bioworks::XMLParser
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#combined Ms::Sequest::Srf::Header
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commandline Ms::Sequest::Srf::Sqt
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commandline Ms::Sequest::Srf::Search
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#consensus_score Bioworks::Prot
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#coverage Bioworks::Prot
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#create_static_mods Sequest::PepXML::Modifications
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#database Ms::Sequest::Params
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#database_path= Ms::Sequest::Params
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#date Sequest::PepXML
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#date Sequest::PepXML::MSMSPipelineAnalysis
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#db_filename Ms::Sequest::Srf::Header
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db_info Ms::Sequest::Sqt
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db_md5sum Ms::Sequest::Sqt
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db_seq_length_and_locus_count Ms::Sequest::Sqt
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#description Sequest::PepXML::TerminalModification
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#doctype Sequest::PepXML
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#dta_files Ms::Sequest::Srf
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#dta_gen Ms::Sequest::Srf::Header
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#dta_log_filename Ms::Sequest::Srf::Header
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#dta_start_byte Ms::Sequest::Srf
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#endElement Bioworks::XMLParser
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#end_mass Ms::Sequest::Srf::DTAGen
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#end_scan Ms::Sequest::Srf::DTAGen
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#enzyme Ms::Sequest::Srf::Header
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#enzyme Ms::Sequest::Params
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#enzyme_specificity Ms::Sequest::Params
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#extension Ms::Sequest::SqtGroup
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extract_file_info Bioworks::Pep
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#file= Bioworks::Pep
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#filter_by_precursor_mass_tolerance! Ms::Sequest::Srf
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#filtered_by_precursor_mass_tolerance Ms::Sequest::Srf
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#first_entry Ms::Sequest::Sqt::Locus
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#fragment_ion_tol Ms::Sequest::Params
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#fragment_mass_type Ms::Sequest::Params
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#fragment_mass_type Sequest::PepXML
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#from_file Ms::Sequest::Sqt
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#from_file Ms::Sequest::Srf
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#from_handle Ms::Sequest::Sqt::Header
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#from_io Ms::Sequest::Srf::Out::Pep
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#from_io Ms::Sequest::Srf::DTA
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#from_io Ms::Sequest::Srf::Header
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#from_io Ms::Sequest::Srf::Out
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#from_io Ms::Sequest::Srf::DTAGen
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#from_line Ms::Sequest::Sqt::Locus
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#from_line Ms::Sequest::Sqt::Match
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#from_line Ms::Sequest::Sqt::Spectrum
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#from_lines Ms::Sequest::Sqt::Header
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#from_pepxml_node Sequest::PepXML::MSMSRunSummary
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#from_pepxml_node Sequest::PepXML::SearchSummary
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#from_pepxml_node Sequest::PepXML::SpectrumQuery
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#from_pepxml_node Sequest::PepXML::SearchHit::ModificationInfo
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from_pepxml_node Sequest::PepXML::SearchHit::ModificationInfo
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from_pepxml_node Sequest::PepXML::SpectrumQuery
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from_pepxml_node Sequest::PepXML::SearchSummary
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#from_pepxml_node Sequest::PepXML::SearchHit
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from_pepxml_node Sequest::PepXML::MSMSRunSummary
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#get Bioworks::Pep
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#get Bioworks::Prot
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#get_prots_from_xml_stream Bioworks
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#get_regex_val Bioworks
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get_sequest_params_and_finish_pos Ms::Sequest::Srf
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#global_filename Bioworks
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#grab_params Ms::Sequest::Params
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#group_scan Ms::Sequest::Srf::DTAGen
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#h_plus Sequest::PepXML
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#header Sequest::PepXML
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#header Ms::Sequest::Srf
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#header Ms::Sequest::Sqt
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#hi_prob_best Bioworks
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#index Ms::Sequest::Srf
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#initialize Sequest::PepXML::AAModification
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#initialize Bioworks::Prot
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#initialize Sequest::PepXML::SearchSummary
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#initialize Ms::Sequest::Srf
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#initialize Sequest::PepXML::SearchResult
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#initialize Bioworks
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#initialize Sequest::PepXML::Parameters
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#initialize Ms::Sequest::Sqt
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#initialize Ms::Sequest::Params
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#initialize Ms::Sequest::SrfGroup
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#initialize Ms::Sequest::Srf::Out::Prot
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#initialize Sequest::PepXML::Modifications
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#initialize Sequest::PepXML::SearchHit
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#initialize Sequest::PepXML::SearchDatabase
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#initialize Sequest::PepXML
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#initialize Sequest::PepXML::MSMSPipelineAnalysis
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#initialize Bioworks::XMLParser
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#initialize Sequest::PepXML::MSMSRunSummary
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#initialize Sequest::PepXML::TerminalModification
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#initialize Ms::Sequest::SqtGroup
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#inspect Ms::Sequest::Srf::Out::Prot
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#inspect Bioworks::Pep
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#inspect Ms::Sequest::Srf::Out
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#inspect Ms::Sequest::Srf::Out::Pep
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#inspect Ms::Sequest::Srf::DTA
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#inspect Sequest::PepXML::SearchHit
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#ion_series Ms::Sequest::Srf::Header
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#local_path Sequest::PepXML::SearchDatabase
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make_base_name Sequest::PepXML
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#mass Sequest::PepXML::AAModification
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#mass Sequest::PepXML::TerminalModification
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#mass_index Ms::Sequest::Params
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#massdiff Sequest::PepXML::AAModification
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#massdiff Sequest::PepXML::TerminalModification
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#masses_by_diff_mod_hash Sequest::PepXML::Modifications
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#max_num_differential_AA_per_mod Ms::Sequest::Params
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#max_num_internal_cleavages Ms::Sequest::Params
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#method_missing Ms::Sequest::Params
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#method_missing Sequest::PepXML::SearchSummary
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#mh Bioworks::Pep
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#min_group_count Ms::Sequest::Srf::DTAGen
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#min_ion_threshold Ms::Sequest::Srf::DTAGen
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#min_number_termini Ms::Sequest::Params
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#mod_symbols_hash Sequest::PepXML::Modifications
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#model Ms::Sequest::Srf::Header
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#modification_info Sequest::PepXML::Modifications
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#modifications Sequest::PepXML::SearchSummary
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#modifications Ms::Sequest::Srf::Header
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#modifications Bioworks
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#mods Ms::Sequest::Params
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#ms_detector Sequest::PepXML::MSMSRunSummary
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#ms_ionization Sequest::PepXML::MSMSRunSummary
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#ms_manufacturer Sequest::PepXML::MSMSRunSummary
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#ms_mass_analyzer Sequest::PepXML::MSMSRunSummary
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#ms_model Sequest::PepXML::MSMSRunSummary
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#msms_pipeline_analysis Sequest::PepXML
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#msms_run_summary Sequest::PepXML::MSMSPipelineAnalysis
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#negative_q_value Ms::Sequest::Sqt::Match::Percolator
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#negative_q_value= Ms::Sequest::Sqt::Match::Percolator
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new_from_srf Sequest::PepXML
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#num_dta_files Ms::Sequest::Srf::DTAGen
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#num_dta_files Ms::Sequest::Srf::Header
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#num_prots Bioworks
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#opts Ms::Sequest::Params
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#origfilename Bioworks
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#origfilepath Bioworks
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#out_data Sequest::PepXML::SearchSummary
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#out_data_type Sequest::PepXML::SearchSummary
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#out_files Ms::Sequest::Srf
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#params Sequest::PepXML::Parameters
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#params Sequest::PepXML::SearchSummary
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#params Ms::Sequest::Srf
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#params Sequest::PepXML::Modifications
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#params_filename Ms::Sequest::Srf::Header
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#parse_file Ms::Sequest::Params
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#parse_io Ms::Sequest::Params
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#parse_xml Bioworks
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#parse_xml_by_xmlparser Bioworks
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#peps Bioworks::Prot
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#peps Bioworks
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#peptide_hit_counts Bioworks::Prot
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#peptide_mass_tol Ms::Sequest::Params
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#peptide_terminus Sequest::PepXML::AAModification
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#pepxml_version Sequest::PepXML
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pepxml_version Sequest::PepXML
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#pepxml_version Sequest::PepXML::MSMSRunSummary
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#pepxml_version Sequest::PepXML::MSMSPipelineAnalysis
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#percolator_results Ms::Sequest::Sqt
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#percolator_score Ms::Sequest::Sqt::Match::Percolator
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#percolator_score= Ms::Sequest::Sqt::Match::Percolator
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#pi Bioworks::Prot
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#ppm Bioworks::Pep
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#precursor_mass_type Sequest::PepXML
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#precursor_mass_type Ms::Sequest::Params
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#probability Bioworks::Pep
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#probability Ms::Sequest::Sqt::Match::Percolator
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#protein_class Ms::Sequest::Srf
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#protein_class Ms::Sequest::Sqt
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#protein_probability Bioworks::Prot
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#protein_terminus Sequest::PepXML::TerminalModification
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#prots Bioworks::XMLParser
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#prots Bioworks
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#prots Ms::Sequest::Sqt::Match
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#q_value Ms::Sequest::Sqt::Match::Percolator
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#raw_data Sequest::PepXML::MSMSRunSummary
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#raw_data_type Sequest::PepXML::MSMSRunSummary
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#raw_filename Ms::Sequest::Srf::Header
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#read_dta_and_out_interleaved Ms::Sequest::Srf
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#read_dta_files Ms::Sequest::Srf
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read_extra_references Ms::Sequest::Srf::Out::Pep
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#read_out_files Ms::Sequest::Srf
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#read_scan_index Ms::Sequest::Srf
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#reference Bioworks::Prot
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#reference Ms::Sequest::Sqt::Locus
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#round Ms::Sequest::Srf::DTA
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#sample_enzyme Sequest::PepXML::MSMSRunSummary
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#search_class Ms::Sequest::SrfGroup
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#search_class Ms::Sequest::SqtGroup
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#search_database Sequest::PepXML::SearchSummary
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#search_hit_class Sequest::PepXML::MSMSRunSummary
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#search_hits Sequest::PepXML::SearchResult
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#search_id Sequest::PepXML::SearchSummary
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#search_score_xml Sequest::PepXML::SearchHit
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#search_scores_xml Sequest::PepXML::SearchHit
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#search_summary Sequest::PepXML::MSMSRunSummary
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#seq_type Sequest::PepXML::SearchDatabase
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#sequence Ms::Sequest::Params
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#sequest_log_filename Ms::Sequest::Srf::Header
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set_deltacn Ms::Sequest::Sqt::Spectrum
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set_deltacn_from_deltacn_orig Ms::Sequest::Srf::Out::Pep
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set_from_bioworks Sequest::PepXML
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set_from_bioworks_xml Sequest::PepXML
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#set_from_hash_given_text Bioworks::Pep
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#set_from_xml_hash Bioworks::Prot
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#set_from_xml_hash_xmlparser Bioworks::Prot
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#set_from_xml_stream Bioworks::Prot
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#set_from_xml_stream Bioworks::Pep
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#set_hashes Sequest::PepXML::Modifications
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#set_modifications Sequest::PepXML::Modifications
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#set_mono_or_avg Sequest::PepXML
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#sf Bioworks::Prot
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#spectra Ms::Sequest::Sqt
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spectra_from_handle Ms::Sequest::Sqt::Spectrum
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#spectrum_queries Sequest::PepXML
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#spectrum_queries Sequest::PepXML::MSMSRunSummary
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split_ions Sequest::PepXML::SearchHit
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#startElement Bioworks::XMLParser
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#start_mass Ms::Sequest::Srf::DTAGen
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#start_scan Ms::Sequest::Srf::DTAGen
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#start_time Ms::Sequest::Srf::DTAGen
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#static_mods Ms::Sequest::Params
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#style_sheet Sequest::PepXML
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#summary_xml Sequest::PepXML
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#summary_xml Sequest::PepXML::MSMSPipelineAnalysis
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#symbol Sequest::PepXML::TerminalModification
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#symbol Sequest::PepXML::AAModification
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#term_mods Sequest::PepXML::Modifications
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#terminus Sequest::PepXML::TerminalModification
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#to_dta Ms::Sequest::Srf::Search
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#to_dta_file_data Ms::Sequest::Srf::DTA
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#to_excel Bioworks
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#to_mgf Ms::Sequest::Srf::Search
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#to_pepxml Sequest::PepXML
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#to_pepxml Sequest::PepXML::SearchResult
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#to_pepxml Sequest::PepXML::SearchSummary
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#to_pepxml Sequest::PepXML::MSMSRunSummary
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#to_pepxml Sequest::PepXML::MSMSPipelineAnalysis
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#to_pepxml Sequest::PepXML::SearchHit
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#to_pepxml Sequest::PepXML::SearchHit::ModificationInfo
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#to_pepxml Bioworks
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#to_pepxml Sequest::PepXML::SearchDatabase
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#to_pepxml Sequest::PepXML::SpectrumQuery
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#to_pepxml Sequest::PepXML::TerminalModification
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#to_pepxml Sequest::PepXML::AAModification
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#to_pepxml Sequest::PepXML::Modifications
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#to_pepxml Sequest::PepXML::Parameters
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#to_plus_minus_string Numeric
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#to_sqt Bioworks
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#to_sqt Ms::Sequest::Srf::Sqt
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#to_srg Ms::Sequest::SrfGroup
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#unified_score Bioworks::Prot
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update_deltacns_from_xcorr Ms::Sequest::Srf::Out::Pep
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#update_peptide_hit_counts Bioworks
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#variable Sequest::PepXML::TerminalModification
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#variable Sequest::PepXML::AAModification
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#version Ms::Sequest::Params
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#version Ms::Sequest::Srf::Header
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#version Ms::Sequest::Srf
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#version Bioworks
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#weight Bioworks::Prot
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#write_dta_file Ms::Sequest::Srf::DTA
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#xml_version Sequest::PepXML
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#xmlns Sequest::PepXML::MSMSPipelineAnalysis
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#xmlns_xsi Sequest::PepXML::MSMSPipelineAnalysis
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#xsi_schema_location Sequest::PepXML::MSMSPipelineAnalysis