Module: Mspire::Mzml::DataArrayContainerLike

Includes:
CV::Paramable
Included in:
Chromatogram, Spectrum
Defined in:
lib/mspire/mzml/data_array_container_like.rb

Instance Attribute Summary collapse

Attributes included from CV::Paramable

#cv_params, #ref_param_groups, #user_params

Instance Method Summary collapse

Methods included from CV::Paramable

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

Instance Attribute Details

#data_arrays ⇒ Object

(optional) an array of Mspire::Mzml::DataArray



27
28
29
 
# File 'lib/mspire/mzml/data_array_container_like.rb', line 27

def data_arrays
  @data_arrays
end

#data_processing ⇒ Object

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



20
21
22
 
# File 'lib/mspire/mzml/data_array_container_like.rb', line 20

def data_processing
  @data_processing
end

#id ⇒ Object

(required) the spectrum id matching this general pattern: S+=S+( S+=S+)*)



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

def id
  @id
end

#index ⇒ Object

(required [at xml write time]) the index in the spectrum list



17
18
19
 
# File 'lib/mspire/mzml/data_array_container_like.rb', line 17

def index
  @index
end

Instance Method Details

#default_array_length ⇒ Object 



29
30
31
32
33
34
35
36
37
38
39
 
# File 'lib/mspire/mzml/data_array_container_like.rb', line 29

def default_array_length
  if @data_arrays
    if @data_arrays.first
      @data_arrays.first.size
    else
      0
    end
  else
    0
  end
end

#to_xml(builder, opts = {}, &block) ⇒ Object

see SpectrumList for generating the entire list the opt key :sub_elements can be used to pass in subelements whose to_xml methods will be called.



44
45
46
47
48
49
50
51
52
53
54
55
56
 
# File 'lib/mspire/mzml/data_array_container_like.rb', line 44

def to_xml(builder, opts={}, &block)
  atts = {id: @id, index: @index, defaultArrayLength: default_array_length}
  atts[:dataProcessingRef] = @data_processing.id if @data_processing
  atts.merge!(opts)
  raise "#{self.class} object must have index at xml writing time!" unless atts[:index] 

  builder.spectrum(atts) do |sp_n|
    super(sp_n) # params
    block.call(sp_n) if block
    Mspire::Mzml::DataArray.list_xml(@data_arrays, sp_n) if @data_arrays
  end
  builder
end