Module: Mspire::CV::Paramable

Included in:
Mzml::Activation, Mzml::Component, Mzml::Contact, Mzml::DataArray, Mzml::DataArrayContainerLike, Mzml::FileContent, Mzml::InstrumentConfiguration, Mzml::IsolationWindow, Mzml::ProcessingMethod, Mzml::ReferenceableParamGroup, Mzml::Run, Mzml::Sample, Mzml::Scan, Mzml::ScanList, Mzml::ScanSettings, Mzml::ScanWindow, Mzml::SelectedIon, Mzml::Software, Mzml::SourceFile
Defined in:
lib/mspire/cv/paramable.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#cv_params ⇒ Object

Returns the value of attribute cv_params.



11
12
13
 
# File 'lib/mspire/cv/paramable.rb', line 11

def cv_params
  @cv_params
end

#ref_param_groups ⇒ Object

Returns the value of attribute ref_param_groups.



13
14
15
 
# File 'lib/mspire/cv/paramable.rb', line 13

def ref_param_groups
  @ref_param_groups
end

#user_params ⇒ Object

Returns the value of attribute user_params.



12
13
14
 
# File 'lib/mspire/cv/paramable.rb', line 12

def user_params
  @user_params
end

Instance Method Details

#accessionable_params ⇒ Object 



26
27
28
 
# File 'lib/mspire/cv/paramable.rb', line 26

def accessionable_params
  cv_params + ref_param_groups.flat_map(&:params)
end

#describe!(*args) ⇒ Object

Expects arguments describing a single CV::Param or Mapire::UserParam. Will also accept an Nokogiri::XML::Node or Nokogiri::XML::NodeSet

obj.describe! 'MS:1000130'  # a positive scan
obj.describe! CV::Param['MS:1000130']  # same behavior

# base peak intensity, units=number of counts
obj.describe! "MS:1000505", 1524.5865478515625, 'MS:1000131'

# given an XML::NodeSet
obj.describe! xml_node.xpath('.//cvParam')

# given an XML
obj.describe! xml_node.xpath('.//cvParam').first

returns self



102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
 
# File 'lib/mspire/cv/paramable.rb', line 102

def describe!(*args)
  return self if args.first.nil?
  case (arg=args.first)
  when String
    @cv_params << Mspire::CV::Param[ *args ]
  when Mspire::Mzml::ReferenceableParamGroup
    @ref_param_groups << arg
  when Nokogiri::XML::Node  # a nokogiri node in particular
    param = 
      case arg.name
      when 'cvParam'
        Mspire::CV::Param[ arg[:accession], arg[:value] ]
      when 'userParam'
        Mspire::UserParam.new(arg[:name], arg[:value], arg[:type])
      end
    if (unit_acc = arg[:unitAccession])
      param.unit = ::CV::Param.new(arg[:unitCvRef], unit_acc, arg[:unitName])
    end
    @cv_params << param
  when Nokogiri::XML::NodeSet
    arg.each {|node| describe!(node) }
  else
    if arg.is_a?(Mspire::UserParam)
      @user_params << arg
    else
      (@cv_params << arg) if arg
    end
  end
  self
end

#describe_many!(array) ⇒ Object

takes an array of values, each of which is fed into describe!



76
77
78
79
80
81
82
83
84
 
# File 'lib/mspire/cv/paramable.rb', line 76

def describe_many!(array)
  array.each do |arg|
    if arg.is_a?(Array)
      describe!(*arg)
    else
      describe!(arg)
    end
  end
end

#fetch(name) ⇒ Object

returns the value if the param exists by that name. Returns true if the param exists but has no value. returns false if no param



40
41
42
43
44
45
46
47
 
# File 'lib/mspire/cv/paramable.rb', line 40

def fetch(name)
  param = params.find {|param| param.name == name}
  if param
    param.value || true
  else
    false
  end
end

#fetch_by_accession(acc) ⇒ Object Also known as: fetch_by_acc 



49
50
51
52
53
54
55
56
 
# File 'lib/mspire/cv/paramable.rb', line 49

def fetch_by_accession(acc)
  param = accessionable_params.find {|v| v.accession == acc }
  if param
    param.value || true
  else
    false
  end
end

#initialize(opts = {params: []}) ⇒ Object 



63
64
65
66
67
68
 
# File 'lib/mspire/cv/paramable.rb', line 63

def initialize(opts={params: []})
  @cv_params = []
  @user_params = []
  @ref_param_groups = []
  describe_many!(opts[:params])
end

#param?(name) ⇒ Boolean

Returns:

  • (Boolean) 


59
60
61
 
# File 'lib/mspire/cv/paramable.rb', line 59

def param?(name)
  params.any? {|param| param.name == name }
end

#param_by_accession(acc) ⇒ Object Also known as: param_by_acc 



70
71
72
 
# File 'lib/mspire/cv/paramable.rb', line 70

def param_by_accession(acc)
  accessionable_params.find {|v| v.accession == acc }
end

#params ⇒ Object 



15
16
17
 
# File 'lib/mspire/cv/paramable.rb', line 15

def params
  cv_params + ref_param_groups.flat_map(&:params) + user_params 
end

#params? ⇒ Boolean

Returns:

  • (Boolean) 


19
20
21
22
23
24
 
# File 'lib/mspire/cv/paramable.rb', line 19

def params?
  total_num_params = cv_params.size + 
    ref_param_groups.reduce(0) {|sum,group| sum + 
      group.params.size } + user_params.size
  total_num_params > 0
end

#to_xml(xml) ⇒ Object

iterates over @params and calls .to_xml on each object.



134
135
136
137
138
139
140
141
 
# File 'lib/mspire/cv/paramable.rb', line 134

def to_xml(xml)
  [:ref_param_groups, :cv_params, :user_params].each do |kind|
    self.send(kind).each do |obj|
      obj.to_xml(xml)
    end
  end
  xml
end