Class: Ms::Mascot::Formats::Xml

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/mascot/formats/xml.rb

Defined Under Namespace

Modules: Utils

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(xml) ⇒ Xml

Returns a new instance of Xml.



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# File 'lib/ms/mascot/formats/xml.rb', line 30

def initialize(xml)
  xml = xml.read if xml.respond_to?(:read)
  xml = xml.sub(%q{xmlns="http://www.matrixscience.com/xmlns/schema/mascot_search_results_2"}, "")
  @doc = Nokogiri::XML(xml)
end

Instance Attribute Details

#doc ⇒ Object (readonly)

Returns the value of attribute doc.



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# File 'lib/ms/mascot/formats/xml.rb', line 28

def doc
  @doc
end

Instance Method Details

#format_parameters ⇒ Object 



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# File 'lib/ms/mascot/formats/xml.rb', line 48

def format_parameters
  doc.xpath("/mascot_search_results/format_parameters")
end

#header ⇒ Object 



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# File 'lib/ms/mascot/formats/xml.rb', line 36

def header
  doc.at("/mascot_search_results/header")
end

#hits ⇒ Object 



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# File 'lib/ms/mascot/formats/xml.rb', line 52

def hits
  doc.xpath("/mascot_search_results/hits/hit")
end

#modifications ⇒ Object 



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# File 'lib/ms/mascot/formats/xml.rb', line 40

def modifications
  doc.xpath("/mascot_search_results/variable_mods/modification")
end

#peptides(protein) ⇒ Object 



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# File 'lib/ms/mascot/formats/xml.rb', line 60

def peptides(protein)
  protein.xpath("peptide")
end

#proteins(hit) ⇒ Object 



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# File 'lib/ms/mascot/formats/xml.rb', line 56

def proteins(hit)
  hit.xpath("protein")
end

#search_parameters ⇒ Object 



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# File 'lib/ms/mascot/formats/xml.rb', line 44

def search_parameters
  doc.xpath("/mascot_search_results/search_parameters")
end