class Ms::Ident::Pepxml::SearchSummary
Constants
- DEFAULT_SEARCH_ID
Attributes
base_name[RW]
enzymatic_search_constraint[RW]
An EnzymaticSearchConstraint object (at the moment this is merely a hash with a few required keys
fragment_mass_type[RW]
required: ‘average’ or ‘monoisotopic’
modifications[RW]
an array of Ms::Ident::Pepxml::Modification objects
out_data[RW]
required in v18-19, optional in later versions
out_data_type[RW]
required in v18-19, optional in later versions
parameters[RW]
the other search paramaters as a hash
precursor_mass_type[RW]
required: ‘average’ or ‘monoisotopic’
search_database[RW]
A SearchDatabase object (responds to :local_path and :type)
search_engine[RW]
the search engine used, SEQUEST, Mascot, Comet, etc.
search_id[RW]
by default, “1”
Public Class Methods
from_pepxml_node(node)
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# File lib/ms/ident/pepxml/search_summary.rb, line 81 def self.from_pepxml_node(node) self.new.from_pepxml_node(node) end
new(hash={}, &block)
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initializes modifications to an empty array
# File lib/ms/ident/pepxml/search_summary.rb, line 58 def initialize(hash={}, &block) @modifications = [] @search_id = DEFAULT_SEARCH_ID merge!(hash, &block) end
Public Instance Methods
block_arg()
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# File lib/ms/ident/pepxml/search_summary.rb, line 49 def block_arg [@search_database = Ms::Ident::Pepxml::SearchDatabase.new, @enzymatic_search_constraint = Ms::Ident::Pepxml::EnzymaticSearchConstraint.new, @modifications, @parameters = Ms::Ident::Pepxml::Parameters.new, ] end
from_pepxml_node(node)
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# File lib/ms/ident/pepxml/search_summary.rb, line 85 def from_pepxml_node(node) raise NotImplementedError, "not implemented just yet (just use the raw xml node)" end
to_xml(builder=nil)
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# File lib/ms/ident/pepxml/search_summary.rb, line 64 def to_xml(builder=nil) # TODO: out_data and out_data_type are optional in later pepxml versions... # should work that in... attrs = [:base_name, :search_engine, :precursor_mass_type, :fragment_mass_type, :out_data_type, :out_data, :search_id] hash = Hash[ attrs.map {|at| v=send(at) ; [at, v] if v }.compact ] xmlb = builder || Nokogiri::XML::Builder.new builder.search_summary(hash) do |xmlb| search_database.to_xml(xmlb) xmlb.enzymatic_search_constraint(enzymatic_search_constraint) if enzymatic_search_constraint modifications.each do |mod| mod.to_xml(xmlb) end parameters.to_xml(xmlb) if parameters end builder || xmlb.doc.root.to_xml end