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

#cv_params, #ref_param_groups, #user_params

Attributes included from SpectrumLike

#centroided, #data_arrays, #scans

Class Method Summary collapse

Instance Method Summary collapse

Methods included from DataArrayContainerLike

#data_array_xml_atts, #default_array_length

Methods included from CV::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!

Methods included from SpectrumLike

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

Methods included from Enumerable

#index_by, #uniq_by

Constructor Details

#initialize(id) {|_self| ... } ⇒ Spectrum

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

This would generate a spectrum of ms_level 2 :

spec = Mspire::Mzml::Spectrum.new("scan=1").describe!('MS:1000511')

Yields:

  • (_self)

Yield Parameters:



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# File 'lib/mspire/mzml/spectrum.rb', line 167

def initialize(id)
  @id = id
  params_initialize
  yield(self) if block_given?
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 67

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 71

def products
  @products
end

#scan_list ⇒ Object

(optional) a ScanList object



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

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 50

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 56

def spot_id
  @spot_id
end

Class Method Details

.from_arrays(id, arrays) ⇒ Object

sets the data_arrays from the given array objects. Sets the type of the first array to be an m/z array, and the second to be an intensity array.



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# File 'lib/mspire/mzml/spectrum.rb', line 176

def self.from_arrays(id, arrays)
  spec = self.new(id)
  arrays.zip(['MS:1000514','MS:1000515']).each do |ar, acc|
    dar = DataArray.new(ar).describe!(acc)
  end
  spec
end

.from_xml(xml, link) ⇒ Object

takes a Nokogiri node and sets relevant properties

link is a hash that should contain the following keys and associated objects (some are required by downstream objects, like Scan):

:ref_hash                         id -> ReferenceableParamGroup
:spectrum_list                    SpectrumList object
:data_processing_hash             id -> DataProcessing object
:default_data_processing          DataProcessing object
:instrument_configuration_hash    id -> InstrumentConfiguration object
:default_instrument_configuration InstrumentConfiguration object
:source_file_hash                 id -> SourceFile object



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# File 'lib/mspire/mzml/spectrum.rb', line 124

def self.from_xml(xml, link)
  obj = self.new(xml[:id])
  obj.spot_id = xml[:spotID]

  obj.data_processing = link[:data_processing_hash][xml[:dataProcessingRef]] || link[:spectrum_default_data_processing]

  if source_file_ref=xml[:sourceFileRef]
    obj.source_file = link[:source_file_hash][source_file_ref]
  end

  xml_n = obj.describe_from_xml!(xml, link[:ref_hash])
  return obj unless xml_n

  loop do
    case xml_n.name
    when 'scanList'
      obj.scan_list = Mspire::Mzml::ScanList.from_xml(xml_n, link)
    when 'precursorList'
      obj.precursors = xml_n.children.map do |prec_n|
        Mspire::Mzml::Precursor.from_xml(prec_n, link)
      end
    when 'productList'
      obj.products = xml_n.children.map do |product_n|
        Mspire::Mzml::Product.from_xml(product_n, link)
      end
    when 'binaryDataArrayList'
      obj.data_arrays = Mspire::Mzml::DataArray.data_arrays_from_xml(xml_n, link)
    end
    break unless xml_n = xml_n.next
  end
  unless obj.data_arrays
    obj.data_arrays = Mspire::Mzml::DataArray.empty_data_arrays
  end

  obj
end

Instance Method Details

#centroided? ⇒ Boolean

Returns:

  • (Boolean) 


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

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

#ms_level ⇒ Object

returns the ms_level as an Integer



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

def ms_level
  fetch_by_acc('MS:1000511')
end

#params_initialize ⇒ Object 



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# File 'lib/mspire/mzml/spectrum.rb', line 47

alias_method :params_initialize, :initialize

#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 104

def precursor_charge
  precursors.andand.first.andand.selected_ions.andand.first.andand.fetch_by_acc('MS:1000041')
end

#precursor_mz ⇒ Object 



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# File 'lib/mspire/mzml/spectrum.rb', line 108

def precursor_mz
  precursors.andand.first.andand.selected_ions.andand.first.andand.fetch_by_acc('MS:1000744')
end

#profile? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mspire/mzml/spectrum.rb', line 99

def profile?
  fetch_by_acc('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 75

def retention_time
  rt_param = scan_list.first.param_by_acc('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, default_ids) ⇒ Object

see SpectrumList for generating the entire list



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# File 'lib/mspire/mzml/spectrum.rb', line 185

def to_xml(builder, default_ids)
  io = builder.target!

  atts = data_array_xml_atts
  if @data_processing && default_ids[:spectrum_data_processing] != @data_processing.id 
    atts[:dataProcessingRef] = @data_processing.id 
  end
  atts[:sourceFileRef] = @source_file.id if @source_file
  atts[:spotID] = @spot_id if @spot_id

  builder.spectrum(atts) do |sp_n|
    super(sp_n)
    @scan_list.list_xml( sp_n, default_ids ) if @scan_list
    Mspire::Mzml::Precursor.list_xml(@precursors, sp_n) if @precursors
    Mspire::Mzml::Product.list_xml(@products, sp_n) if @products
    Mspire::Mzml::DataArray.list_xml(@data_arrays, sp_n) if @data_arrays
  end
  builder
end