Class: Ms::Ident::Pepxml::SearchSummary

Inherits:
Object
  • Object
show all
Includes:
Merge
Defined in:
lib/ms/ident/pepxml/search_summary.rb

Constant Summary collapse

DEFAULT_SEARCH_ID = 
'1'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Merge

#merge!

Constructor Details

#initialize(hash = {}, &block) ⇒ SearchSummary

initializes modifications to an empty array



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 58

def initialize(hash={}, &block)
  @modifications = []
  @search_id = DEFAULT_SEARCH_ID
  merge!(hash, &block)
end

Instance Attribute Details

#base_name ⇒ Object

Returns the value of attribute base_name.



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 26

def base_name
  @base_name
end

#enzymatic_search_constraint ⇒ Object

An EnzymaticSearchConstraint object (at the moment this is merely a hash with a few required keys



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 47

def enzymatic_search_constraint
  @enzymatic_search_constraint
end

#fragment_mass_type ⇒ Object

required: ‘average’ or ‘monoisotopic’



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 44

def fragment_mass_type
  @fragment_mass_type
end

#modifications ⇒ Object

an array of Ms::Ident::Pepxml::Modification objects



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 34

def modifications
  @modifications
end

#out_data ⇒ Object

required in v18-19, optional in later versions



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 30

def out_data
  @out_data
end

#out_data_type ⇒ Object

required in v18-19, optional in later versions



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 28

def out_data_type
  @out_data_type
end

#parameters ⇒ Object

the other search paramaters as a hash



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 38

def parameters
  @parameters
end

#precursor_mass_type ⇒ Object

required: ‘average’ or ‘monoisotopic’



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 42

def precursor_mass_type
  @precursor_mass_type
end

#search_database ⇒ Object

A SearchDatabase object (responds to :local_path and :type)



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

def search_database
  @search_database
end

#search_engine ⇒ Object

the search engine used, SEQUEST, Mascot, Comet, etc.



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

def search_engine
  @search_engine
end

#search_id ⇒ Object

by default, “1”



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

def search_id
  @search_id
end

Class Method Details

.from_pepxml_node(node) ⇒ Object 



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 81

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

Instance Method Details

#block_arg ⇒ Object 



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 49

def block_arg
  [@search_database = Ms::Ident::Pepxml::SearchDatabase.new,
    @enzymatic_search_constraint = Ms::Ident::Pepxml::EnzymaticSearchConstraint.new,
    @modifications,
    @parameters = Ms::Ident::Pepxml::Parameters.new,
  ]
end

#from_pepxml_node(node) ⇒ Object

Raises:

  • (NotImplementedError) 


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# File 'lib/ms/ident/pepxml/search_summary.rb', line 85

def from_pepxml_node(node)
  raise NotImplementedError, "not implemented just yet (just use the raw xml node)"
end

#to_xml(builder = nil) ⇒ Object 



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# File 'lib/ms/ident/pepxml/search_summary.rb', line 64

def to_xml(builder=nil)
  # TODO: out_data and out_data_type are optional in later pepxml versions...
  # should work that in...
  attrs = [:base_name, :search_engine, :precursor_mass_type, :fragment_mass_type, :out_data_type, :out_data, :search_id]
  hash = Hash[ attrs.map {|at| v=send(at) ; [at, v] if v }.compact ]
  xmlb = builder || Nokogiri::XML::Builder.new
  builder.search_summary(hash) do |xmlb|
    search_database.to_xml(xmlb)
    xmlb.enzymatic_search_constraint(enzymatic_search_constraint) if enzymatic_search_constraint
    modifications.each do |mod|
      mod.to_xml(xmlb)
    end
    parameters.to_xml(xmlb) if parameters
  end
  builder || xmlb.doc.root.to_xml 
end