Class: Mspire::Mzml::Run

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

#initialize(id, default_instrument_configuration) ⇒ Run

yields self if given a block



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# File 'lib/mspire/mzml/run.rb', line 33

def initialize(id, default_instrument_configuration)
  @id = id
  @default_instrument_configuration = default_instrument_configuration
  params_init
  if block_given?
    yield self
  end
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 30

def chromatogram_list
  @chromatogram_list
end

#default_instrument_configuration ⇒ Object

required



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

def default_instrument_configuration
  @default_instrument_configuration
end

#default_source_file ⇒ Object

optional



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

def default_source_file
  @default_source_file
end

#id ⇒ Object

required



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

def id
  @id
end

#sample ⇒ Object

optional



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

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 27

def spectrum_list
  @spectrum_list
end

#start_time_stamp ⇒ Object

optional



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

def start_time_stamp
  @start_time_stamp
end

Class Method Details

.from_xml(io, xml, link) ⇒ Object

expects link to have the following keys:

:ref_hash
:instrument_config_hash
:source_file_hash
:sample_hash
:data_processing_hash
:spectrum_default_data_processing
:chromatogram_default_data_processing
:index_list



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# File 'lib/mspire/mzml/run.rb', line 70

def self.from_xml(io, xml, link)

  # expects that the DataProcessing objects to link to have *already* been
  # parsed (parse the defaultDataProcessingRef's after grabbing the
  # index, then grab the DataProcessing object associated with that id).
  
  obj = self.new(xml[:id], 
    link[:instrument_configuration_hash][xml[:defaultInstrumentConfigurationRef]]
  )
  obj.start_time_stamp = xml[:startTimeStamp]

  link[:default_instrument_configuration] = obj.default_instrument_configuration

  # two optional object refs
  if def_source_ref=xml[:defaultSourceFileRef]
    obj.default_source_file = link[:source_file_hash][def_source_ref]
  end
  if sample_ref=xml[:sampleRef]
    obj.sample = link[:sample_hash][sample_ref]
  end

  obj.describe_from_xml!(xml, link[:ref_hash])

  index_list = link[:index_list]
  [:spectrum, :chromatogram].each do |list_type|
    next unless (byte_index = index_list[list_type])

    io_index = IOIndex.new(io, byte_index, link)

    list_obj = Mspire::Mzml.const_get(list_type.to_s.capitalize + "List")
      .new(link["#{list_type}_default_data_processing".to_sym], 
           io_index, 
           Hash[byte_index.ids.each_with_index.map.to_a]
          )

    obj.send(list_type.to_s + "_list=", list_obj)
  end
  obj
end

Instance Method Details

#to_xml(builder) ⇒ Object 



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# File 'lib/mspire/mzml/run.rb', line 42

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

  default_ids = { instrument_configuration: @default_instrument_configuration.id }
  
  builder.run(atts) do |run_n|
    super(run_n)
    spectrum_list.to_xml(run_n, default_ids) if spectrum_list
    chromatogram_list.to_xml(run_n, default_ids) if chromatogram_list
  end
  builder
end