Class: Mspire::Mzml::Precursor
- Inherits:
-
Object
- Object
- Mspire::Mzml::Precursor
- Extended by:
- List
- Defined in:
- lib/mspire/mzml/precursor.rb
Overview
The method of precursor ion selection and activation
Instance Attribute Summary collapse
-
#activation ⇒ Object
(required) The type and energy level used for activation.
-
#from_external_source_file ⇒ Object
a boolean indicating the spectrum is from an external source file.
-
#isolation_window ⇒ Object
(optional).
-
#selected_ions ⇒ Object
(optional) An array of ions that were selected.
-
#spectrum ⇒ Object
(optional) the Mspire::Mzml::Spectrum object from which the precursor is derived.
Class Method Summary collapse
Instance Method Summary collapse
-
#initialize(spectrum_derived_from = nil) ⇒ Precursor
constructor
A new instance of Precursor.
- #to_xml(builder) ⇒ Object
Methods included from List
Constructor Details
#initialize(spectrum_derived_from = nil) ⇒ Precursor
Returns a new instance of Precursor.
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# File 'lib/mspire/mzml/precursor.rb', line 26 def initialize(spectrum_derived_from=nil) @spectrum=spectrum_derived_from end |
Instance Attribute Details
#activation ⇒ Object
(required) The type and energy level used for activation.
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# File 'lib/mspire/mzml/precursor.rb', line 21 def activation @activation end |
#from_external_source_file ⇒ Object
a boolean indicating the spectrum is from an external source file
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# File 'lib/mspire/mzml/precursor.rb', line 24 def from_external_source_file @from_external_source_file end |
#isolation_window ⇒ Object
(optional)
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# File 'lib/mspire/mzml/precursor.rb', line 15 def isolation_window @isolation_window end |
#selected_ions ⇒ Object
(optional) An array of ions that were selected.
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# File 'lib/mspire/mzml/precursor.rb', line 18 def selected_ions @selected_ions end |
#spectrum ⇒ Object
(optional) the Mspire::Mzml::Spectrum object from which the precursor is derived
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# File 'lib/mspire/mzml/precursor.rb', line 12 def spectrum @spectrum end |
Class Method Details
.from_xml(xml) ⇒ Object
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# File 'lib/mspire/mzml/precursor.rb', line 30 def self.from_xml(xml) obj = self.new %w(isolationWindow activation).each do |el| sub_node = xml.xpath("./#{el}").first el[0] = el[0].capitalize Mspire::Mzml.const_get(el).from_xml(sub_node) if sub_node end obj.selected_ions = xml.xpath('./selectedIonList/selectedIon').map do |si_n| Mspire::Mzml::SelectedIon.from_xml(si_n) end obj end |
Instance Method Details
#to_xml(builder) ⇒ Object
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# File 'lib/mspire/mzml/precursor.rb', line 43 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 builder.precursor(atts) do |prec_n| @isolation_window.to_xml(prec_n) if @isolation_window Mspire::Mzml::SelectedIon.list_xml(@selected_ions, prec_n) if @selected_ions @activation.to_xml(prec_n) if @activation end end |