Class: ScbiGo::GoTerm

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_go/go_term.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(go_term, gene_ontology) ⇒ GoTerm

Returns a new instance of GoTerm.



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# File 'lib/scbi_go/go_term.rb', line 5

def initialize(go_term, gene_ontology)

	@term_type=go_term.name
	@gene_ontology=gene_ontology
	@id=go_term['id']
	@name=go_term['name']
	@def=go_term['def']
	@namespace=go_term['namespace']

   #to save is_a relation as strings, cannot save objects directly because they may be not loaded yet.
   @is_a_str=[]
   # tmp var to save a cache with is_a relation as objects
	@is_a=nil
	if go_term['is_a'].is_a?(Array)
		@is_a_str=go_term['is_a']
	elsif !go_term['is_a'].nil?
		@is_a_str=[go_term['is_a']]
	end

	@subset=go_term['subset']
	@comment=go_term['comment']
	@consider=go_term['consider']
	@synonym=go_term['synonym']
 @children = []
end

Instance Attribute Details

#comment ⇒ Object

Returns the value of attribute comment.



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# File 'lib/scbi_go/go_term.rb', line 3

def comment
  @comment
end

#consider ⇒ Object

Returns the value of attribute consider.



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# File 'lib/scbi_go/go_term.rb', line 3

def consider
  @consider
end

#def ⇒ Object

Returns the value of attribute def.



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# File 'lib/scbi_go/go_term.rb', line 3

def def
  @def
end

#id ⇒ Object

Returns the value of attribute id.



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# File 'lib/scbi_go/go_term.rb', line 3

def id
  @id
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/scbi_go/go_term.rb', line 3

def name
  @name
end

#namespace ⇒ Object

Returns the value of attribute namespace.



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# File 'lib/scbi_go/go_term.rb', line 3

def namespace
  @namespace
end

#subset ⇒ Object

Returns the value of attribute subset.



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# File 'lib/scbi_go/go_term.rb', line 3

def subset
  @subset
end

#synonym ⇒ Object

Returns the value of attribute synonym.



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# File 'lib/scbi_go/go_term.rb', line 3

def synonym
  @synonym
end

Instance Method Details

#add_child(child) ⇒ Object

add another node ad child



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# File 'lib/scbi_go/go_term.rb', line 42

def add_child(child)
	@children << child
end

#all_branches_to_top ⇒ Object

recursive function to get all branches from myself to top of the ontology



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# File 'lib/scbi_go/go_term.rb', line 86

def all_branches_to_top

  res=[]
  if parents.count == 0
    res = [[self]]
  else
    parents.each do |parent|
        parent_b = parent.all_branches_to_top
        parent_b.each do |pb|
          res << pb.unshift(self)
        end
    end
  end

  return res

end

#ancestors ⇒ Object

get list of ancestors for a node



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# File 'lib/scbi_go/go_term.rb', line 73

def ancestors 
	res=parents
	parents.each {|c| res += c.ancestors}
	return res.uniq
end

#base_term? ⇒ Boolean

base terms have no parents

Returns:

  • (Boolean) 


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# File 'lib/scbi_go/go_term.rb', line 32

def base_term?
  return @is_a_str.count==0
end

#children ⇒ Object 



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# File 'lib/scbi_go/go_term.rb', line 54

def children
  @children
end

#descendants ⇒ Object

get list of descendants for a node



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# File 'lib/scbi_go/go_term.rb', line 60

def descendants
	res=children
	children.each {|c| res += c.descendants}
	return res.uniq
end

#inspect ⇒ Object 



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# File 'lib/scbi_go/go_term.rb', line 46

def inspect
	"#{@term_type}:#{@id}, #{@name}, is_a: #{@is_a}"
end

#is_a ⇒ Object 



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# File 'lib/scbi_go/go_term.rb', line 36

def is_a
  convert_is_a_to_terms! if @is_a.nil?
  @is_a
end

#parents ⇒ Object 



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# File 'lib/scbi_go/go_term.rb', line 50

def parents
  is_a
end

#self_and_ancestors ⇒ Object

include myself in ancestors



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# File 'lib/scbi_go/go_term.rb', line 80

def self_and_ancestors
	res = [self] + self.ancestors
	return res.uniq
end

#self_and_descendants ⇒ Object

include myself in descendants



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# File 'lib/scbi_go/go_term.rb', line 67

def self_and_descendants
  res = [self] + self.descendants
  return res.uniq
end