class Ms::Ident::Pepxml::MsmsRunSummary
Attributes
base_name[RW]
The name of the pep xml file without any extension
ms_detector[RW]
ms_ionization[RW]
ms_manufacturer[RW]
The name of the mass spec manufacturer
ms_mass_analyzer[RW]
ms_model[RW]
pepxml_version[RW]
raw_data[RW]
raw_data_type[RW]
sample_enzyme[RW]
A SampleEnzyme object (responds to: name, cut, no_cut, sense)
search_summary[RW]
A SearchSummary object
spectrum_queries[RW]
An array of spectrum_queries
Public Class Methods
from_pepxml_node(node)
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# File lib/ms/ident/pepxml/msms_run_summary.rb, line 66 def self.from_pepxml_node(node) self.new.from_pepxml_node(node) end
new(hash={}, &block)
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takes a hash of name, value pairs if block given, yields a SampleEnzyme object, a SearchSummary and an array for SpectrumQueries
# File lib/ms/ident/pepxml/msms_run_summary.rb, line 42 def initialize(hash={}, &block) @spectrum_queries = [] merge!(hash, &block) block.call(block_arg) if block end
Public Instance Methods
block_arg()
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# File lib/ms/ident/pepxml/msms_run_summary.rb, line 33 def block_arg [@sample_enzyme = Ms::Ident::Pepxml::SampleEnzyme.new, @search_summary = Ms::Ident::Pepxml::SearchSummary.new, @spectrum_queries ] end
from_pepxml_node(node)
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peps correspond to search_results
# File lib/ms/ident/pepxml/msms_run_summary.rb, line 71 def from_pepxml_node(node) @base_name = node['base_name'] @ms_manufacturer = node['msManufacturer'] @ms_model = node['msModel'] @ms_manufacturer = node['msIonization'] @ms_mass_analyzer = node['msMassAnalyzer'] @ms_detector = node['msDetector'] @raw_data_type = node['raw_data_type'] @raw_data = node['raw_data'] self end
to_xml(builder=nil)
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optionally takes an xml builder object and returns the builder, or the xml string if no builder was given sets the index attribute of each spectrum query if it is not already set
# File lib/ms/ident/pepxml/msms_run_summary.rb, line 51 def to_xml(builder=nil) xmlb = builder || Nokogiri::XML::Builder.new hash = {:base_name => base_name, :msManufacturer => ms_manufacturer, :msModel => ms_model, :msIonization => ms_ionization, :msMassAnalyzer => ms_mass_analyzer, :msDetector => ms_detector, :raw_data_type => raw_data_type, :raw_data => raw_data} hash.each {|k,v| hash.delete(k) unless v } xmlb.msms_run_summary(hash) do |xmlb| sample_enzyme.to_xml(xmlb) if sample_enzyme search_summary.to_xml(xmlb) if search_summary spectrum_queries.each_with_index do |sq,i| sq.index = i+1 unless sq.index sq.to_xml(xmlb) end end builder || xmlb.doc.root.to_xml end