Class: Sequest::PepXML::MSMSPipelineAnalysis

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash = nil) ⇒ MSMSPipelineAnalysis

if block given, sets msms_run_summary to block



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# File 'lib/ms/sequest/pepxml.rb', line 40

def initialize(hash=nil)
  @xmlns = nil
  @xmlns_xsi = nil
  @xsi_schema_location = nil
  if hash
    self.set_from_hash(hash)
  end
  if block_given?
    @msms_run_summary = yield
  end
end

Instance Attribute Details

#date ⇒ Object

if no date string given, then it will set to Time.now



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# File 'lib/ms/sequest/pepxml.rb', line 53

def date
  if @date ; @date 
  else
    case Sequest::PepXML.pepxml_version
    when 18 ;  tarr = Time.now.to_a ; tarr[3..5].reverse.join('-') + "T#{tarr[0..2].reverse.join(':')}"
    end
  end
end

#msms_run_summary ⇒ Object

Returns the value of attribute msms_run_summary.



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# File 'lib/ms/sequest/pepxml.rb', line 37

def msms_run_summary
  @msms_run_summary
end

#pepxml_version ⇒ Object

Returns the value of attribute pepxml_version.



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# File 'lib/ms/sequest/pepxml.rb', line 36

def pepxml_version
  @pepxml_version
end

#summary_xml ⇒ Object

Returns the value of attribute summary_xml.



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# File 'lib/ms/sequest/pepxml.rb', line 33

def summary_xml
  @summary_xml
end

#xmlns ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 62

def xmlns
  if @xmlns ; @xmlns
  else ; "http://regis-web.systemsbiology.net/pepXML"
  end
end

#xmlns_xsi ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 68

def xmlns_xsi
  if @xmlns_xsi ; @xmlns_xsi
  else ; "http://www.w3.org/2001/XMLSchema-instance"
  end
end

#xsi_schema_location ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 74

def xsi_schema_location
  if @xsi_schema_location ; @xsi_schema_location 
  else ; "http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd"
  end
end

#xsi_schemaLocation=(value) ⇒ Object (writeonly)

Sets the attribute xsi_schemaLocation

Parameters:

  • value —

    the value to set the attribute xsi_schemaLocation to.



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# File 'lib/ms/sequest/pepxml.rb', line 32

def xsi_schemaLocation=(value)
  @xsi_schemaLocation = value
end

Instance Method Details

#to_pepxml ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 80

def to_pepxml
  case Sequest::PepXML.pepxml_version
  when 18
    element_xml_and_att_string(:msms_pipeline_analysis, "date=\"#{date}\" xmlns=\"#{xmlns}\" xmlns:xsi=\"#{xmlns_xsi}\" xsi:schemaLocation=\"#{xsi_schema_location}\" summary_xml=\"#{summary_xml}\"") do
      @msms_run_summary.to_pepxml
    end
  else
    abort "Don't know how to deal with version: #{Sequest::PepXML.pepxml_version}"
  end
end