Class: Mspire::Ident::Pepxml::MsmsPipelineAnalysis

Inherits:

Object

• Object
• Mspire::Ident::Pepxml::MsmsPipelineAnalysis

show all

Includes:

Merge

Defined in:

lib/mspire/ident/pepxml/msms_pipeline_analysis.rb

Constant Summary

XMLNS =

"http://regis-web.systemsbiology.net/pepXML"

XMLNS_XSI =

"http://www.w3.org/2001/XMLSchema-instance"

XSI_SCHEMA_LOCATION_BASE =

(this doesn't actually exist), also, the space is supposed to be there

"http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v"

PEPXML_VERSION =

the only additions concerning a writer are from v18 are to the 'spectrum': retention_time_sec and activationMethodType

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Instance Attribute Summary (collapse)

• - (Object) date

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

• - (Object) msms_run_summary

  Returns the value of attribute msms_run_summary.

• - (Object) pepxml_version

  an Integer.

• - (Object) summary_xml

  self referential path to the outputfile.

• - (Object) xmlns

  include SpecIDXML Version 1.2.3 attr_writer :date attr_writer :xmlns, :xmlns_xsi, :xsi_schemaLocation attr_accessor :summary_xml.

• - (Object) xmlns_xsi

  Returns the value of attribute xmlns_xsi.

• - (Object) xsi_schema_location

  returns the location based on the pepxml version number.

Instance Method Summary (collapse)

• - (Object) block_arg
• - (MsmsPipelineAnalysis) initialize(hash = {}, &block) constructor

  if block given, yields a new msms_run_summary to return value of block.

• - (Object) to_xml(builder)

  uses the filename as summary_xml (if it is nil) attribute and builds a complete, valid xml document, writing it to the filename.

Methods included from Merge

#merge!

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 39

def initialize(hash={}, &block)
  @xmlns = XMLNS
  @xmlns_xsi = XMLNS_XSI
  @xsi_schema_location = xsi_schema_location
  @pepxml_version = PEPXML_VERSION
  merge!(hash, &block)
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 53

def date
  return @date if @date
  tarr = Time.now.to_a 
  tarr[3..5].reverse.join('-') + "T#{tarr[0..2].reverse.join(':')}"
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 31

def msms_run_summary
  @msms_run_summary
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 28

def pepxml_version
  @pepxml_version
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 30

def summary_xml
  @summary_xml
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 24

def xmlns
  @xmlns
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 25

def xmlns_xsi
  @xmlns_xsi
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 48

def xsi_schema_location
  @xsi_schema_location
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 34

def block_arg 
  @msms_run_summary = Mspire::Ident::Pepxml::MsmsRunSummary.new
end

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# File 'lib/mspire/ident/pepxml/msms_pipeline_analysis.rb', line 61

def to_xml(builder)
  xmlb = builder || Nokogiri::XML::Builder.new
  xmlb.msms_pipeline_analysis(:date => date, :xmlns => xmlns, 'xsi:schemaLocation'.to_sym => xsi_schema_location, :summary_xml => summary_xml) do |xmlb|
    msms_run_summary.to_xml(xmlb) if msms_run_summary
  end
  builder || xmlb.doc.root.to_xml
end