Class: Sequest::PepXML::Parameters

Inherits:
Object
  • Object
show all
Includes:
SpecIDXML
Defined in:
lib/ms/sequest/pepxml.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(obj = nil) ⇒ Parameters

Returns a new instance of Parameters.



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# File 'lib/ms/sequest/pepxml.rb', line 851

def initialize(obj=nil)
  @params = obj
end

Instance Attribute Details

#params ⇒ Object

Returns the value of attribute params.



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# File 'lib/ms/sequest/pepxml.rb', line 849

def params
  @params
end

Instance Method Details

#to_pepxml ⇒ Object

(used to be called pepxml_parameters) Returns xml in the form <parameter name=“#method_name” value=“#method_value”/> for list of symbols



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# File 'lib/ms/sequest/pepxml.rb', line 857

def to_pepxml
  keys_as_symbols = @params.opts.sort.map do |k,v| k.to_s end
  params_xml(@params, *keys_as_symbols)
  # (:peptide_mass_tol, :peptide_mass_units, :fragment_ion_tol, :ion_series, :max_num_differential_AA_per_mod, :nucleotide_reading_frame, :num_output_lines, :remove_precursor_peak, :ion_cutoff_percentage, :match_peak_count, :match_peak_allowed_error, :match_peak_tolerance, :protein_mass_filter, :sequence_header_filter)
end