Class: Mspire::Mzml::Run

Inherits:
Object
  • Object
show all
Includes:
CV::Paramable
Defined in:
lib/mspire/mzml/run.rb

Instance Attribute Summary collapse

Attributes included from CV::Paramable

#params

Instance Method Summary collapse

Methods included from CV::Paramable

#describe!, #describe_many!, #find_param_by_accession, #find_param_value_by_accession, #param_exists_by_accession?

Constructor Details

#initialize(id, default_instrument_configuration, opts = {params: []}, &block) ⇒ Run

yields self if given a block



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# File 'lib/mspire/mzml/run.rb', line 30

def initialize(id, default_instrument_configuration, opts={params: []}, &block)
  @id = id
  @default_instrument_configuration = default_instrument_configuration
  describe_many!(opts[:params])
  block.call(self) if block
end

Instance Attribute Details

#chromatogram_list ⇒ Object

takes a ChromatogramList object (a special array of chromatograms)



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# File 'lib/mspire/mzml/run.rb', line 27

def chromatogram_list
  @chromatogram_list
end

#default_instrument_configuration ⇒ Object

required



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# File 'lib/mspire/mzml/run.rb', line 9

def default_instrument_configuration
  @default_instrument_configuration
end

#default_source_file ⇒ Object

optional



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

def default_source_file
  @default_source_file
end

#id ⇒ Object

required



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

def id
  @id
end

#sample ⇒ Object

optional



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

def sample
  @sample
end

#spectrum_list ⇒ Object

a SpectrumList object (a special array of spectra)



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# File 'lib/mspire/mzml/run.rb', line 24

def spectrum_list
  @spectrum_list
end

#start_time_stamp ⇒ Object

optional



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# File 'lib/mspire/mzml/run.rb', line 21

def start_time_stamp
  @start_time_stamp
end

Instance Method Details

#to_xml(builder) ⇒ Object 



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# File 'lib/mspire/mzml/run.rb', line 37

def to_xml(builder)
  atts = { id: @id,
    defaultInstrumentConfigurationRef: @default_instrument_configuration.id
  }
  atts[:defaultSourceFileRef] = @default_source_file.id if @default_source_file
  atts[:sampleRef] = @sample.id if @sample
  atts[:startTimeStamp] = @start_time_stamp if @start_time_stamp
  
  builder.run(atts) do |run_n|
    super(run_n)
    spectrum_list.to_xml(run_n) if spectrum_list
    chromatogram_list.to_xml(run_n) if chromatogram_list
  end
  builder
end