Class: Mspire::Mzml::Scan

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

Instance Attribute Summary collapse

Attributes included from CV::Paramable

#cv_params, #ref_param_groups, #user_params

Class Method Summary collapse

Instance Method Summary collapse

Methods included from CV::Paramable

#accessionable_params, #describe!, #describe_many!, #fetch, #fetch_by_accession, #param?, #param_by_accession, #params, #params?

Constructor Details

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

Returns a new instance of Scan.



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# File 'lib/mspire/mzml/scan.rb', line 23

def initialize(opts={params: []}, &block)
  super(opts)
  block.call(self) if block
end

Instance Attribute Details

#from_external_source_file ⇒ Object

a boolean indicating the spectrum is from an external source file



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

def from_external_source_file
  @from_external_source_file
end

#instrument_configuration ⇒ Object

an InstrumentConfiguration object



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

def instrument_configuration
  @instrument_configuration
end

#scan_windows ⇒ Object

ScanWindow objects



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

def scan_windows
  @scan_windows
end

#spectrum ⇒ Object

(optional) the Mspire::Mzml::Spectrum object from which the precursor is derived. (the sourceFileRef is derived from this spectrum object if from_external_source_file == true)



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

def spectrum
  @spectrum
end

Class Method Details

.from_xml(xml) ⇒ Object

takes a nokogiri node def self.from_xml(xml) end



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# File 'lib/mspire/mzml/scan.rb', line 32

def self.from_xml(xml)
  scan = self.new
  [:cvParam, :userParam].each {|v| scan.describe! xml.xpath("./#{v}") }
  scan.scan_windows = xml.xpath('./scanWindowList/scanWindow').map do |scan_window_n|
    Mspire::Mzml::ScanWindow.from_xml(scan_window_n)
  end
  scan
end

Instance Method Details

#to_xml(builder) ⇒ Object 



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# File 'lib/mspire/mzml/scan.rb', line 41

def to_xml(builder)
  atts = {}
  if @from_external_source_file
    atts[:sourceFileRef] = @spectrum.source_file.id
    atts[:externalSpectrumRef] = @spectrum.id
  else
    atts[:spectrumRef] = @spectrum.id if @spectrum
  end
  atts[:instrumentConfigurationRef] = @instrument_configuration.id if @instrument_configuration
  builder.scan(atts) do |prec_n|
    super(prec_n) # description
    ScanWindow.list_xml(@scan_windows, prec_n) if @scan_windows
  end
end