Class: SimpleBioC::Passage

Inherits:
Object
  • Object
show all
Includes:
LocationAdjuster
Defined in:
lib/simple_bioc/passage.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from LocationAdjuster

#adjust_annotation_offsets, choose_offset_candidate, find_all_locations

Constructor Details

#initialize(parent) ⇒ Passage

Returns a new instance of Passage.



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# File 'lib/simple_bioc/passage.rb', line 9

def initialize(parent)
  @infons = {}
  @sentences = []
  @annotations = []
  @relations = []
  @document = parent
end

Instance Attribute Details

#annotations ⇒ Object

Returns the value of attribute annotations.



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# File 'lib/simple_bioc/passage.rb', line 6

def annotations
  @annotations
end

#document ⇒ Object (readonly)

Returns the value of attribute document.



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# File 'lib/simple_bioc/passage.rb', line 7

def document
  @document
end

#infons ⇒ Object

Returns the value of attribute infons.



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# File 'lib/simple_bioc/passage.rb', line 6

def infons
  @infons
end

#offset ⇒ Object

Returns the value of attribute offset.



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# File 'lib/simple_bioc/passage.rb', line 6

def offset
  @offset
end

#relations ⇒ Object

Returns the value of attribute relations.



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# File 'lib/simple_bioc/passage.rb', line 6

def relations
  @relations
end

#sentences ⇒ Object

Returns the value of attribute sentences.



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# File 'lib/simple_bioc/passage.rb', line 6

def sentences
  @sentences
end

#text ⇒ Object

Returns the value of attribute text.



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# File 'lib/simple_bioc/passage.rb', line 6

def text
  @text
end

Instance Method Details

#each_relation ⇒ Object 



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# File 'lib/simple_bioc/passage.rb', line 30

def each_relation
  relations.each{|r| yield r}
  sentences.each{|s| s.each_relation{|r| yield r}}
end

#find_node(id) ⇒ Object 



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# File 'lib/simple_bioc/passage.rb', line 21

def find_node(id)
  (relations+annotations).each{|n| return n if n.id == id}
  sentences.each do |s|
    ret = s.find_node(id)
    return ret unless ret.nil?
  end
  nil
end

#to_s ⇒ Object 



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# File 'lib/simple_bioc/passage.rb', line 17

def to_s
  "Passage @#{offset}: #{text}"  
end