Class: Mspire::Mzml::Spectrum

Inherits:
Object
  • Object
show all
Includes:
DataArrayContainerLike, SpectrumLike
Defined in:
lib/mspire/mzml/spectrum.rb

Overview

MAY supply a child term of MS:1000465 (scan polarity) only once

  e.g.: MS:1000129 (negative scan)
  e.g.: MS:1000130 (positive scan)
MUST supply a *child* term of MS:1000559 (spectrum type) only once
  e.g.: MS:1000322 (charge inversion mass spectrum)
  e.g.: MS:1000325 (constant neutral gain spectrum)
  e.g.: MS:1000326 (constant neutral loss spectrum)
  e.g.: MS:1000328 (e/2 mass spectrum)
  e.g.: MS:1000341 (precursor ion spectrum)
  e.g.: MS:1000581 (CRM spectrum)
  e.g.: MS:1000582 (SIM spectrum)
  e.g.: MS:1000583 (SRM spectrum)
  e.g.: MS:1000789 (enhanced multiply charged spectrum)
  e.g.: MS:1000790 (time-delayed fragmentation spectrum)
  et al.
MUST supply term MS:1000525 (spectrum representation) or any of its children only once
  e.g.: MS:1000127 (centroid spectrum)
  e.g.: MS:1000128 (profile spectrum)
MAY supply a *child* term of MS:1000499 (spectrum attribute) one or more times
  e.g.: MS:1000285 (total ion current)
  e.g.: MS:1000497 (zoom scan)
  e.g.: MS:1000504 (base peak m/z)
  e.g.: MS:1000505 (base peak intensity)
  e.g.: MS:1000511 (ms level)
  e.g.: MS:1000527 (highest observed m/z)
  e.g.: MS:1000528 (lowest observed m/z)
  e.g.: MS:1000618 (highest observed wavelength)
  e.g.: MS:1000619 (lowest observed wavelength)
  e.g.: MS:1000796 (spectrum title)
  et al.

Instance Attribute Summary collapse

Attributes included from DataArrayContainerLike

#data_arrays, #data_processing, #id, #index

Attributes included from CV::Paramable

#params

Attributes included from SpectrumLike

#centroided, #data_arrays, #scans

Class Method Summary collapse

Instance Method Summary collapse

Methods included from DataArrayContainerLike

#default_array_length

Methods included from CV::Paramable

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

Methods included from SpectrumLike

#==, #[], #find_all_nearest, #find_all_nearest_index, #find_nearest, #find_nearest_index, #intensities, #intensities=, #merge, #mzs, #mzs=, #mzs_and_intensities, #normalize, #points, #size, #sort!, #tic

Constructor Details

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

the most common param to pass in would be ms level: ‘MS:1000511’

This would generate a spectrum of ms_level=2 :

Mspire::Mzml::Spectrum.new(0, "scan=1", 'MS:1000511')



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# File 'lib/mspire/mzml/spectrum.rb', line 145

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

Instance Attribute Details

#precursors ⇒ Object

(optional) List and descriptions of precursor isolations to the spectrum currently being described, ordered.



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# File 'lib/mspire/mzml/spectrum.rb', line 63

def precursors
  @precursors
end

#products ⇒ Object

(optional) List and descriptions of product isolations to the spectrum currently being described, ordered.



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# File 'lib/mspire/mzml/spectrum.rb', line 67

def products
  @products
end

#scan_list ⇒ Object

(optional) a ScanList object



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# File 'lib/mspire/mzml/spectrum.rb', line 59

def scan_list
  @scan_list
end

#source_file ⇒ Object

(optional) an Mspire::Mzml::SourceFile object



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# File 'lib/mspire/mzml/spectrum.rb', line 48

def source_file
  @source_file
end

#spot_id ⇒ Object

(optional) The identifier for the spot from which this spectrum was derived, if a MALDI or similar run.



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# File 'lib/mspire/mzml/spectrum.rb', line 52

def spot_id
  @spot_id
end

Class Method Details

.from_xml(xml) ⇒ Object

takes a Nokogiri node and sets relevant properties



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# File 'lib/mspire/mzml/spectrum.rb', line 109

def self.from_xml(xml)
  spec = Mspire::Mzml::Spectrum.new(xml[:id])

  spec.spot_id = xml[:spotID]

  [:cvParam, :userParam].each {|v| spec.describe! xml.xpath("./#{v}") }

  scan_list = Mspire::Mzml::ScanList.new
  xml.xpath('./scanList/scan').each do |scan_n|
    scan_list << Mspire::Mzml::Scan.from_xml(scan_n)
  end
  spec.scan_list = scan_list

  spec.precursors = xml.xpath('./precursorList/precursor').map do |prec_n|
    Mspire::Mzml::Precursor.from_xml(prec_n)
  end

  data_arrays = xml.xpath('./binaryDataArrayList/binaryDataArray').map do |binary_data_array_n|
    accessions = binary_data_array_n.xpath('./cvParam').map {|node| node['accession'] }
    base64 = binary_data_array_n.xpath('./binary').text
    Mspire::Mzml::DataArray.from_binary(base64, accessions)
  end

  # if there is no spectrum, we will still return a spectrum object, it
  # just has no mzs or intensities
  data_arrays = [Mspire::Mzml::DataArray.new, Mspire::Mzml::DataArray.new] if data_arrays.size == 0
  spec.data_arrays = data_arrays
  spec
end

Instance Method Details

#centroided? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mspire/mzml/spectrum.rb', line 91

def centroided?
  param_exists_by_accession?('MS:1000127')
end

#ms_level ⇒ Object

returns the ms_level as an Integer



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# File 'lib/mspire/mzml/spectrum.rb', line 87

def ms_level
  find_param_value_by_accession('MS:1000511', :to_i)
end

#precursor_charge ⇒ Object

returns the charge state of the first precursor as an integer



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# File 'lib/mspire/mzml/spectrum.rb', line 100

def precursor_charge
  precursors.andand.first.andand.selected_ions.andand.first.andand.find_param_value_by_accession('MS:1000041', :to_i)
end

#precursor_mz ⇒ Object 



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# File 'lib/mspire/mzml/spectrum.rb', line 104

def precursor_mz
  precursors.andand.first.andand.selected_ions.andand.first.andand.find_param_value_by_accession('MS:1000744', :to_f)
end

#profile? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mspire/mzml/spectrum.rb', line 95

def profile?
  param_exists_by_accession?('MS:1000128')
end

#retention_time ⇒ Object

returns the retention time of the first scan object in the scan list *in seconds*!



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# File 'lib/mspire/mzml/spectrum.rb', line 71

def retention_time
  rt_param = scan_list.first.find_param_by_accession('MS:1000016')
  if rt_param
    multiplier = 
      case rt_param.unit.accession
      when 'UO:0000010' ; 1  # second
      when 'UO:0000031' ; 60 # minute
      when 'UO:0000032' ; 3600 # hour
      when 'UO:0000028' ; 0.001 # millisecond
      else raise 'unsupported units'
      end
    rt_param.value.to_f * multiplier
  end
end

#to_xml(builder) ⇒ Object

see SpectrumList for generating the entire list



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# File 'lib/mspire/mzml/spectrum.rb', line 153

def to_xml(builder)
  atts = {}
  atts[:sourceFileRef] = @source_file.id if @source_file
  atts[:spotID] = @spot_id if @spot_id
  super(builder, atts) do |node|
    @scan_list.list_xml( node ) if @scan_list
    Mspire::Mzml::Precursor.list_xml(@precursors, node) if @precursors
    Mspire::Mzml::Product.list_xml(@products, node) if @products
  end
end