Class: Mspire::Mzml::InstrumentConfiguration

Inherits:
Object
  • Object
show all
Extended by:
List
Includes:
Paramable
Defined in:
lib/mspire/mzml/instrument_configuration.rb

Instance Attribute Summary (collapse)

Attributes included from Paramable

#cv_params, #ref_param_groups, #user_params

Class Method Summary (collapse)

Instance Method Summary (collapse)

Methods included from List

list_xml, list_xml_element

Methods included from Paramable

#accessionable_params, #describe!, #describe_from_xml!, #describe_many!, #describe_self_from_xml!, #each_accessionable_param, #each_param, #fetch, #fetch_by_accession, #param?, #param_by_accession, #params, #params?, #reject!, #replace!, #replace_many!

Constructor Details

- (InstrumentConfiguration) initialize(id, components = []) {|_self| ... }

Returns a new instance of InstrumentConfiguration

Yields:

  • (_self)

Yield Parameters:



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# File 'lib/mspire/mzml/instrument_configuration.rb', line 20

def initialize(id, components=[])
  @id, @components = id, components
  params_init
  yield(self) if block_given?
end

Instance Attribute Details

- (Object) components

a list of Source, Analyzer, Detector objects (optional)



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# File 'lib/mspire/mzml/instrument_configuration.rb', line 15

def components
  @components
end

- (Object) id

(required) the id that this guy can be referenced from



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# File 'lib/mspire/mzml/instrument_configuration.rb', line 12

def id
  @id
end

- (Object) software

a single software object associated with the instrument (optional)



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# File 'lib/mspire/mzml/instrument_configuration.rb', line 18

def software
  @software
end

Class Method Details

+ (Object) from_xml(xml, link)



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# File 'lib/mspire/mzml/instrument_configuration.rb', line 35

def self.from_xml(xml, link)
  obj = self.new(xml[:id])
  next_n = obj.describe_from_xml!(xml, link[:ref_hash])
  if next_n && (next_n.name == 'componentList')
    obj.components = next_n.children.map do |component_n|
      if component_n.is_a?(Nokogiri::XML::Text)
        # TODO: this is a fix for when there is an empty component list but
        # Nokogiri returns a text node.  Really this needs to be fixed
        # in our xml writer!
        nil
      else
        Mspire::Mzml.const_get(component_n.name.capitalize).new.describe_self_from_xml!(component_n, link[:ref_hash])
      end
    end.compact
    next_n = next_n.next
  end
  if next_n && next_n.name == 'softwareRef'
    obj.software = link[:software_hash][next_n[:ref]]
  end
  obj
end

Instance Method Details

- (Object) to_xml(builder)



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# File 'lib/mspire/mzml/instrument_configuration.rb', line 26

def to_xml(builder)
  builder.instrumentConfiguration(id: @id) do |inst_conf_n|
    super(builder)
    Mspire::Mzml::Component.list_xml(components, inst_conf_n)
    inst_conf_n.softwareRef(ref: @software.id) if @software
  end
  builder
end