Class: Mspire::Mzml::Chromatogram

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

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

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!

Constructor Details

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

Returns a new instance of Chromatogram.

Yields:

  • (_self)

Yield Parameters:



16
17
18
19
20
 
# File 'lib/mspire/mzml/chromatogram.rb', line 16

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

Instance Attribute Details

#precursor ⇒ Object

(optional) precursor isolations to the chromatogram currently being described



11
12
13
 
# File 'lib/mspire/mzml/chromatogram.rb', line 11

def precursor
  @precursor
end

#product ⇒ Object

(optional) Description of product isolation to the chromatogram



14
15
16
 
# File 'lib/mspire/mzml/chromatogram.rb', line 14

def product
  @product
end

Class Method Details

.from_xml(xml, link) ⇒ Object 



22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
 
# File 'lib/mspire/mzml/chromatogram.rb', line 22

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

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

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

  loop do
    case xml_n.name
    when 'precursor'
      obj.precursor = Mspire::Mzml::Precursor.from_xml(xml_n, link)
    when 'product'
      obj.product = Mspire::Mzml::Product.from_xml(xml_n, link)
    when 'binaryDataArrayList'
      obj.data_arrays = Mspire::Mzml::DataArray.data_arrays_from_xml(xml_n, link)
      break
    end
    break unless xml_n = xml_n.next
  end
  obj
end

Instance Method Details

#intensities ⇒ Object 



48
49
50
 
# File 'lib/mspire/mzml/chromatogram.rb', line 48

def intensities
  data_arrays[1]
end

#params_initialize ⇒ Object 



7
 
# File 'lib/mspire/mzml/chromatogram.rb', line 7

alias_method :params_initialize, :initialize

#times ⇒ Object 



44
45
46
 
# File 'lib/mspire/mzml/chromatogram.rb', line 44

def times
  data_arrays[0]
end

#to_xml(builder, default_ids) ⇒ Object

see ChromatogramList for generating the entire list



53
54
55
56
57
58
59
60
61
62
63
64
65
 
# File 'lib/mspire/mzml/chromatogram.rb', line 53

def to_xml(builder, default_ids)
  atts = data_array_xml_atts
  if @data_processing && default_ids[:chromatogram_data_processing] != @data_processing.id 
    atts[:dataProcessingRef] = @data_processing.id 
  end

  builder.chromatogram(atts) do |chrom_n|
    super(chrom_n)
    @precursor.to_xml(chrom_n) if @precursor
    @product.to_xml(chrom_n) if @product
    Mspire::Mzml::DataArray.list_xml(@data_arrays, chrom_n) if @data_arrays
  end
end