class Geniact::Graphics::MiniFeature

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.

Attributes

block_gaps[RW]
end[RW]
exons[RW]
fill_color[RW]
id[RW]
params[RW]
segment_height[RW]
start[RW]
strand[RW]
utrs[RW]

Public Class Methods

new(args) click to toggle source

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.#

# File lib/geniact/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]
  @link_val = args[:link_val]
  @fill_color = args[:fill_color]
  @params = args[:params]
end