Table of Contents - ms-ident-0.1.1 Documentation
Pages
Classes and Modules
- Merge
- Ms
- Ms::Ident
- Ms::Ident::Peptide
- Ms::Ident::Peptide::Db
- Ms::Ident::Peptide::Db::IO
- Ms::Ident::PeptideHit
- Ms::Ident::PeptideHit::Qvalue
- Ms::Ident::Pepxml
- Ms::Ident::Pepxml::AminoacidModification
- Ms::Ident::Pepxml::EnzymaticSearchConstraint
- Ms::Ident::Pepxml::Ms
- Ms::Ident::Pepxml::Ms::Ident
- Ms::Ident::Pepxml::Ms::Ident::Pepxml
- Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms
- Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident
- Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident::Pepxml
- Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident::Pepxml::SearchHit
- Ms::Ident::Pepxml::MsmsPipelineAnalysis
- Ms::Ident::Pepxml::MsmsRunSummary
- Ms::Ident::Pepxml::Parameters
- Ms::Ident::Pepxml::SampleEnzyme
- Ms::Ident::Pepxml::SearchDatabase
- Ms::Ident::Pepxml::SearchHit
- Ms::Ident::Pepxml::SearchHit::ModificationInfo
- Ms::Ident::Pepxml::SearchResult
- Ms::Ident::Pepxml::SearchSummary
- Ms::Ident::Pepxml::SpectrumQuery
- Ms::Ident::Pepxml::TerminalModification
- Ms::Ident::Protein
- Ms::Ident::ProteinGroup
- Ms::Ident::ProteinHit
- Ms::Ident::Search
- Ms::Ident::SearchGroup
- Numeric
- Proph
- Proph::PepSummary
- Proph::PepSummary::Pep
- Proph::PepSummary::Prot
- Proph::Prot
- Proph::Prot::Pep
- Proph::ProtGroup
- Proph::ProtSummary
- Proph::ProtSummary::Parser
- Sequest
- Sequest::PepXML
- Sequest::PepXML::MSMSRunSummary
- Sequest::PepXML::SearchHit
- SpecID
- SpecID::Pep
- SpecID::Prot
Methods
- ::calc_precursor_neutral_mass — Ms::Ident::Pepxml::SpectrumQuery
- ::cmdline — Ms::Ident::Peptide::Db
- ::expand_peptides — Ms::Ident::Peptide::Db
- ::filetype — Ms::Ident
- ::from_file — Ms::Ident::PeptideHit::Qvalue
- ::from_pepxml_node — Ms::Ident::Pepxml::MsmsRunSummary
- ::from_pepxml_node — Ms::Ident::Pepxml::SampleEnzyme
- ::from_pepxml_node — Ms::Ident::Pepxml::SearchSummary
- ::from_pepxml_node — Ms::Ident::Pepxml::SpectrumQuery
- ::from_phq — Ms::Ident::PeptideHit::Qvalue
- ::members — Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident::Pepxml::SearchHit
- ::members — Ms::Ident::Pepxml::SpectrumQuery
- ::new — Ms::Ident::Peptide::Db
- ::new — Ms::Ident::Peptide::Db::IO
- ::new — Ms::Ident::Pepxml
- ::new — Ms::Ident::Pepxml::AminoacidModification
- ::new — Ms::Ident::Pepxml::TerminalModification
- ::new — Ms::Ident::Pepxml::MsmsPipelineAnalysis
- ::new — Ms::Ident::Pepxml::MsmsRunSummary
- ::new — Proph::PepSummary
- ::new — Proph::ProtSummary
- ::new — Proph::ProtSummary::Parser
- ::new — Proph::ProtGroup
- ::new — Ms::Ident::Pepxml::SampleEnzyme
- ::new — Ms::Ident::Pepxml::SearchDatabase
- ::new — Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident::Pepxml::SearchHit
- ::new — Ms::Ident::Pepxml::SearchResult
- ::new — Ms::Ident::Pepxml::SearchSummary
- ::new — Ms::Ident::Pepxml::SpectrumQuery
- ::new — Ms::Ident::Protein
- ::new — Ms::Ident::ProteinHit
- ::new — Ms::Ident::Search
- ::new — Ms::Ident::SearchGroup
- ::open — Ms::Ident::Peptide::Db::IO
- ::peptide_centric_db — Ms::Ident::Peptide::Db
- ::peptide_hits_to_protein_groups — Ms::Ident::ProteinGroup
- ::prepare_sequence — Ms::Ident::Peptide
- ::remove_non_amino_acids — Ms::Ident::Peptide
- ::sequence_to_aaseq — Ms::Ident::Peptide
- ::simple_search_hits — Ms::Ident::Pepxml
- ::split_sequence — Ms::Ident::Peptide
- ::to_file — Ms::Ident::PeptideHit::Qvalue
- ::to_phq — Ms::Ident::PeptideHit::Qvalue
- #[] — Ms::Ident::Peptide::Db
- #[] — Ms::Ident::Peptide::Db::IO
- #_parse_for_prot_groups — Proph::ProtSummary::Parser
- #aaseq — Proph::Prot::Pep
- #add_stylesheet — Ms::Ident::Pepxml
- #block_arg — Ms::Ident::Pepxml::MsmsPipelineAnalysis
- #block_arg — Ms::Ident::Pepxml::MsmsRunSummary
- #block_arg — Ms::Ident::Pepxml::SearchSummary
- #date — Ms::Ident::Pepxml::MsmsPipelineAnalysis
- #each — Ms::Ident::Peptide::Db::IO
- #extension — Ms::Ident::SearchGroup
- #first_entry — Proph::PepSummary::Prot
- #first_entry — Proph::Prot
- #from_file — Ms::Ident::SearchGroup
- #from_filenames — Ms::Ident::SearchGroup
- #from_pepxml_node — Ms::Ident::Pepxml::MsmsRunSummary
- #from_pepxml_node — Proph::PepSummary::Pep
- #from_pepxml_node — Ms::Ident::Pepxml::SampleEnzyme
- #from_pepxml_node — Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident::Pepxml::SearchHit
- #from_pepxml_node — Ms::Ident::Pepxml::SearchSummary
- #from_pepxml_node — Ms::Ident::Pepxml::SpectrumQuery
- #gene_id — Ms::Ident::ProteinHit
- #get_version — Proph::PepSummary
- #get_version — Proph::ProtSummary
- #hi_prob_best — Proph::PepSummary
- #hi_prob_best — Proph::ProtSummary
- #keys — Ms::Ident::Peptide::Db::IO
- #length — Ms::Ident::Peptide::Db::IO
- #members — Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident::Pepxml::SearchHit
- #members — Ms::Ident::Pepxml::SpectrumQuery
- #merge! — Ms::Ident::Search
- #merge! — Merge
- #name — Proph::Prot
- #num_missed_cleavages — Ms::Ident::Pepxml::SampleEnzyme
- #num_tol_term — Ms::Ident::Pepxml::SampleEnzyme
- #old_bracket — Ms::Ident::Peptide::Db
- #parse_file — Proph::ProtSummary::Parser
- #pepxml_version — Ms::Ident::Pepxml
- #probability — Proph::Prot::Pep
- #reference — Proph::PepSummary::Prot
- #reference — Proph::Prot
- #search_class — Ms::Ident::SearchGroup
- #search_hit_class — Proph::PepSummary
- #set_size_of_residues! — Ms::Ident::Pepxml::SearchDatabase
- #set_trypsin — Ms::Ident::Pepxml::SampleEnzyme
- #size — Ms::Ident::Peptide::Db::IO
- #spectrum_queries — Ms::Ident::Pepxml
- #to_paths — Ms::Ident::SearchGroup
- #to_plus_minus_string — Numeric
- #to_xml — Ms::Ident::Pepxml
- #to_xml — Ms::Ident::Pepxml::AminoacidModification
- #to_xml — Ms::Ident::Pepxml::TerminalModification
- #to_xml — Ms::Ident::Pepxml::MsmsPipelineAnalysis
- #to_xml — Ms::Ident::Pepxml::MsmsRunSummary
- #to_xml — Ms::Ident::Pepxml::Parameters
- #to_xml — Ms::Ident::Pepxml::SampleEnzyme
- #to_xml — Ms::Ident::Pepxml::SearchDatabase
- #to_xml — Ms::Ident::Pepxml::Ms::Ident::Pepxml::Ms::Ident::Pepxml::SearchHit
- #to_xml — Ms::Ident::Pepxml::SearchResult
- #to_xml — Ms::Ident::Pepxml::SearchSummary
- #to_xml — Ms::Ident::Pepxml::SpectrumQuery
- #unique_prots — Proph::ProtSummary
- #values — Ms::Ident::Peptide::Db::IO