class Mspire::Ident::Pepxml::SpectrumQuery
search_specification is a search constraint applied specifically to this query (a String)
Constants
- DEFAULT_MEMBERS
- Optional
- Required
Attributes
members[W]
Public Class Methods
calc_precursor_neutral_mass(m_plus_h, deltamass, h_plus=Mspire::Mass::H_PLUS)
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# File lib/mspire/ident/pepxml/spectrum_query.rb, line 80 def self.calc_precursor_neutral_mass(m_plus_h, deltamass, h_plus=Mspire::Mass::H_PLUS) m_plus_h - h_plus + deltamass end
from_pepxml_node(node)
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# File lib/mspire/ident/pepxml/spectrum_query.rb, line 66 def self.from_pepxml_node(node) self.new.from_pepxml_node(node) end
members()
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# File lib/mspire/ident/pepxml/spectrum_query.rb, line 18 def members @members || DEFAULT_MEMBERS end
new(*args, &block)
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takes either a hash or an ordered list of values to set yeilds an empty search_results array if given a block
# File lib/mspire/ident/pepxml/spectrum_query.rb, line 30 def initialize(*args, &block) @search_results = [] if args.first.is_a?(Hash) merge!(args.first) else self.class.members.zip(args) do |k,v| send("#{k}=", v) end end block.call(@search_results) if block end
Public Instance Methods
from_pepxml_node(node)
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# File lib/mspire/ident/pepxml/spectrum_query.rb, line 70 def from_pepxml_node(node) @spectrum = node['spectrum'] @start_scan = node['start_scan'].to_i @end_scan = node['end_scan'].to_i @precursor_neutral_mass = node['precursor_neutral_mass'].to_f @index = node['index'].to_i @assumed_charge = node['assumed_charge'].to_i self end
members()
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# File lib/mspire/ident/pepxml/spectrum_query.rb, line 42 def members self.class.members end
to_xml(builder=nil)
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FOR PEPXML:
# File lib/mspire/ident/pepxml/spectrum_query.rb, line 49 def to_xml(builder=nil) xmlb = builder || Nokogiri::XML::Builder.new # all through search_specification attrs = members[0, 8].map {|at| v=send(at) ; [at, v] if v }.compact attrs_hash = Hash[attrs] case pepxml_version when 18 attrs_hash.delete(:retention_time_sec) end xmlb.spectrum_query(attrs_hash) do |xmlb| search_results.each do |search_result| search_result.to_xml(xmlb) end end builder || xmlb.doc.root.to_xml end