Class: Bio::Graphics::MiniFeature

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/graphics/mini_feature.rb

Overview

A Bio::Graphics::MiniFeature object represents a single genomic feature (e.g. a gene, transcript, exon, start codon, etc), it is a lightweight object that holds the minimum information needed to do the render.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(args) ⇒ MiniFeature

Creates a new MiniFeature

args

  • :start = the start position of the feature

  • :end = the end position of the feature

  • :strand = the strand of the feature

  • :exons = an array of exon positions

  • :utrs = an array of utrs positions

  • :block_gaps = an array of regions with nothing to be drawn, e.g. introns

  • :id = the name for the feature such as the gene name or transcript ID

  • :segment_height = the height of the current feature

Example usage

mini1 = Bio::Graphics::MiniFeature.new(

:start=>3631, 
:end=>5899, 
:strand=>'+',
:exons=>[4000, 4500, 4700, 5000], 
:utrs=>[3631, 3650], 
:segment_height=>5, 
:id=>"AT1G01010"
 )

MiniFeatures and Tracks

MiniFeatures are created and added to Bio::Graphics::Track objects which will take responsibility for positioning and syling them.#



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# File 'lib/bio/graphics/mini_feature.rb', line 35

def initialize(args)
  @start = args[:start]
  @end = args[:end]
  @strand = args[:strand]
  @exons = args[:exons] || []
  @utrs = args[:utrs] || [] #start, ennd, strand, arg[:exons], arg[:utrs]
  @block_gaps = []
  @id = args[:id]
  @segment_height = args[:segment_height]
  @params = args[:params]
end

Instance Attribute Details

#block_gaps ⇒ Object

Returns the value of attribute block_gaps.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def block_gaps
  @block_gaps
end

#end ⇒ Object

Returns the value of attribute end.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def end
  @end
end

#exons ⇒ Object

Returns the value of attribute exons.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def exons
  @exons
end

#id ⇒ Object

Returns the value of attribute id.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def id
  @id
end

#params ⇒ Object

Returns the value of attribute params.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def params
  @params
end

#segment_height ⇒ Object

Returns the value of attribute segment_height.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def segment_height
  @segment_height
end

#start ⇒ Object

Returns the value of attribute start.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def start
  @start
end

#strand ⇒ Object

Returns the value of attribute strand.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def strand
  @strand
end

#utrs ⇒ Object

Returns the value of attribute utrs.



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# File 'lib/bio/graphics/mini_feature.rb', line 8

def utrs
  @utrs
end