Class: Sequest::PepXML::SearchSummary

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

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(prms = nil, modifications_string = '', args = nil) ⇒ SearchSummary

if given a sequest params object, then will set the following attributes: args is a hash of parameters modifications_string -> See Modifications



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# File 'lib/ms/sequest/pepxml.rb', line 810

def initialize(prms=nil, modifications_string='', args=nil)
  @search_id = "1"
  if prms
    @params = prms
    @modifications = Sequest::PepXML::Modifications.new(prms, modifications_string)
  end
  if args ; set_from_hash(args) end
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(symbol, *args) ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 819

def method_missing(symbol, *args)
  if @params ; @params.send(symbol, *args) end
end

Instance Attribute Details

#base_name ⇒ Object

Returns the value of attribute base_name.



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# File 'lib/ms/sequest/pepxml.rb', line 799

def base_name
  @base_name
end

#modifications ⇒ Object

Returns the value of attribute modifications.



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# File 'lib/ms/sequest/pepxml.rb', line 804

def modifications
  @modifications
end

#out_data ⇒ Object

Returns the value of attribute out_data.



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# File 'lib/ms/sequest/pepxml.rb', line 801

def out_data
  @out_data
end

#out_data_type ⇒ Object

Returns the value of attribute out_data_type.



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# File 'lib/ms/sequest/pepxml.rb', line 800

def out_data_type
  @out_data_type
end

#params ⇒ Object

Returns the value of attribute params.



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# File 'lib/ms/sequest/pepxml.rb', line 798

def params
  @params
end

#search_database ⇒ Object

A SearchDatabase object (responds to :local_path and :type)



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# File 'lib/ms/sequest/pepxml.rb', line 806

def search_database
  @search_database
end

#search_id ⇒ Object

by default, “1”



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# File 'lib/ms/sequest/pepxml.rb', line 803

def search_id
  @search_id
end

Class Method Details

.from_pepxml_node(node) ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 836

def self.from_pepxml_node(node)
  self.new.from_pepxml_node(node)
end

Instance Method Details

#from_pepxml_node(node) ⇒ Object

Raises:

  • (NotImplementedError) 


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# File 'lib/ms/sequest/pepxml.rb', line 840

def from_pepxml_node(node)
  raise NotImplementedError, "right now we just have the xml node at your disposal"
end

#to_pepxml ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 823

def to_pepxml
  element_xml(:search_summary, [:base_name, :search_engine, :precursor_mass_type, :fragment_mass_type, :out_data_type, :out_data, :search_id]) do
    search_database.to_pepxml +
      if @params.enzyme =~ /^No_Enzyme/
        ''
      else
        short_element_xml(:enzymatic_search_constraint, [:enzyme, :max_num_internal_cleavages, :min_number_termini])
      end +
      @modifications.to_pepxml +
      Sequest::PepXML::Parameters.new(@params).to_pepxml
  end
end