Class: Sequest::PepXML::MSMSRunSummary

Inherits:
Object
  • Object
show all
Includes:
SpecID, SpecIDXML
Defined in:
lib/ms/sequest/pepxml.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash = nil) ⇒ MSMSRunSummary

takes a hash of name, value pairs if block given, spectrum_queries (should be array of spectrum queries) is set to the return value of the block



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# File 'lib/ms/sequest/pepxml.rb', line 121

def initialize(hash=nil)
  @spectrum_queries = []
  if hash
    instance_var_set_from_hash(hash)
  end
  if block_given? ; @spectrum_queries = yield end
end

Instance Attribute Details

#base_nameObject

the version of TPP you are using (determines xml output) The name of the pep xml file (without extension) (but this is a long filename!!!)



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# File 'lib/ms/sequest/pepxml.rb', line 100

def base_name
  @base_name
end

#ms_detectorObject

Returns the value of attribute ms_detector.



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# File 'lib/ms/sequest/pepxml.rb', line 105

def ms_detector
  @ms_detector
end

#ms_ionizationObject

Returns the value of attribute ms_ionization.



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# File 'lib/ms/sequest/pepxml.rb', line 108

def ms_ionization
  @ms_ionization
end

#ms_manufacturerObject

The name of the mass spec manufacturer



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# File 'lib/ms/sequest/pepxml.rb', line 102

def ms_manufacturer
  @ms_manufacturer
end

#ms_mass_analyzerObject

Returns the value of attribute ms_mass_analyzer.



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# File 'lib/ms/sequest/pepxml.rb', line 104

def ms_mass_analyzer
  @ms_mass_analyzer
end

#ms_modelObject

Returns the value of attribute ms_model.



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# File 'lib/ms/sequest/pepxml.rb', line 103

def ms_model
  @ms_model
end

#pepxml_versionObject

Returns the value of attribute pepxml_version.



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# File 'lib/ms/sequest/pepxml.rb', line 109

def pepxml_version
  @pepxml_version
end

#raw_dataObject

Returns the value of attribute raw_data.



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# File 'lib/ms/sequest/pepxml.rb', line 107

def raw_data
  @raw_data
end

#raw_data_typeObject

Returns the value of attribute raw_data_type.



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# File 'lib/ms/sequest/pepxml.rb', line 106

def raw_data_type
  @raw_data_type
end

#sample_enzymeObject

A SampleEnzyme object (responds to: name, cut, no_cut, sense)



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# File 'lib/ms/sequest/pepxml.rb', line 112

def sample_enzyme
  @sample_enzyme
end

#search_summaryObject

A SearchSummary object



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# File 'lib/ms/sequest/pepxml.rb', line 114

def search_summary
  @search_summary
end

#spectrum_queriesObject

An array of spectrum_queries



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# File 'lib/ms/sequest/pepxml.rb', line 116

def spectrum_queries
  @spectrum_queries
end

Class Method Details

.from_pepxml_node(node) ⇒ Object



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# File 'lib/ms/sequest/pepxml.rb', line 144

def self.from_pepxml_node(node)
  self.new.from_pepxml_node(node)
end

Instance Method Details

#from_pepxml_node(node) ⇒ Object

peps correspond to search_results



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# File 'lib/ms/sequest/pepxml.rb', line 149

def from_pepxml_node(node)
  @base_name = node['base_name']
  @ms_manufacturer = node['msManufacturer']
  @ms_model = node['msModel']
  @ms_manufacturer = node['msIonization']
  @ms_mass_analyzer = node['msMassAnalyzer']
  @ms_detector = node['msDetector']
  @raw_data_type = node['raw_data_type']
  @raw_data = node['raw_data']
  self
end

#search_hit_classObject



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# File 'lib/ms/sequest/pepxml.rb', line 140

def search_hit_class
  Sequest::PepXML::SearchHit
end

#to_pepxmlObject



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# File 'lib/ms/sequest/pepxml.rb', line 129

def to_pepxml
  case Sequest::PepXML.pepxml_version
  when 18
    element_xml_and_att_string(:msms_run_summary, "base_name=\"#{base_name}\" msManufacturer=\"#{ms_manufacturer}\" msModel=\"#{ms_model}\" msIonization=\"#{ms_ionization}\" msMassAnalyzer=\"#{ms_mass_analyzer}\" msDetector=\"#{ms_detector}\" raw_data_type=\"#{raw_data_type}\" raw_data=\"#{raw_data}\"") do
      sample_enzyme.to_pepxml +
        search_summary.to_pepxml +
        spectrum_queries.map {|sq| sq.to_pepxml }.join
    end
  end
end