Class: Bio::Graphics::Panel::Track::Feature

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

Overview

The Bio::Graphics::Track::Feature class describes features to be placed on the graph. See Bio::Graphics documentation for explanation of interplay between different classes.

The position of the Feature is a Bio::Locations object to make it possible to transparently work with simple and spliced features.

Defined Under Namespace

Classes: PixelRange

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(track, name, location = Bio::Locations.new('1..' + track.panel.length.to_s), link = nil) ⇒ Feature

!!Not to be used directly. Use Bio::Graphics::Panel::Track.add_feature instead!! A feature can not exist except within the confines of a Bio::Graphics::Panel::Track object.

– This is necessary because the feature needs to know the colour and glyph, both of which are defined within the panel. ++

Arguments:

  • panel (required)

    Bio::Graphics::Panel::Track object that this

    feature belongs to

  • name (required)

    Name of the feature

  • location

    Bio::Locations object. Default = whole panel, forward strand

  • link

    URL for clickable images

Returns

Bio::Graphics::Track::Feature object



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# File 'lib/bio/graphics/feature.rb', line 37

def initialize(track, name, location = Bio::Locations.new('1..' + track.panel.length.to_s), link = nil)
  @track = track
  @name = name
  @location = location
  @start = location.collect{|l| l.from}.min.to_i
  @stop = location.collect{|l| l.to}.max.to_i
  @strand = location[0].strand.to_i
  @link = link
  @pixel_range_collection = Array.new
  @chopped_at_start = false
  @chopped_at_stop = false
  @hidden_subfeatures_at_start = false
  @hidden_subfeatures_at_stop = false

  # Get all pixel ranges for the subfeatures
  location.each do |l|
    #   xxxxxx  [          ]
    if l.to < track.panel.display_start
      @hidden_subfeatures_at_start = true
      next
    #           [          ]   xxxxx
    elsif l.from > track.panel.display_stop
      @hidden_subfeatures_at_stop = true
      next
    #      xxxx[xxx       ]
    elsif l.from < track.panel.display_start and l.to > track.panel.display_start
      start_pixel = 1
      stop_pixel = ( l.to - track.panel.display_start ).to_f / track.panel.rescale_factor
      @chopped_at_start = true
    #          [      xxxx]xxxx
    elsif l.from < track.panel.display_stop and l.to > track.panel.display_stop
      start_pixel = ( l.from - track.panel.display_start ).to_f / track.panel.rescale_factor
      stop_pixel = track.panel.width
      @chopped_at_stop = true
    #      xxxx[xxxxxxxxxx]xxxx
    elsif l.from < track.panel.display_start and l.to > track.panel.display_stop
      start_pixel = 1
      stop_pixel = track.panel.width
      @chopped_at_start = true
      @chopped_at_stop = true
    #          [   xxxxx  ]
    else
      start_pixel = ( l.from - track.panel.display_start ).to_f / track.panel.rescale_factor
      stop_pixel = ( l.to - track.panel.display_start ).to_f / track.panel.rescale_factor
    end
    
    @pixel_range_collection.push(PixelRange.new(start_pixel, stop_pixel))
    
  end
end

Instance Attribute Details

#chopped_at_start ⇒ Object

Is the first subfeature incomplete?



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# File 'lib/bio/graphics/feature.rb', line 115

def chopped_at_start
  @chopped_at_start
end

#chopped_at_stop ⇒ Object

Is the last subfeature incomplete?



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# File 'lib/bio/graphics/feature.rb', line 118

def chopped_at_stop
  @chopped_at_stop
end

#hidden_subfeatures_at_start ⇒ Object

Are there subfeatures out of view at the left side of the picture?



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# File 'lib/bio/graphics/feature.rb', line 121

def hidden_subfeatures_at_start
  @hidden_subfeatures_at_start
end

#hidden_subfeatures_at_stop ⇒ Object

Are there subfeatures out of view at the right side of the picture?



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# File 'lib/bio/graphics/feature.rb', line 124

def hidden_subfeatures_at_stop
  @hidden_subfeatures_at_stop
end

#link ⇒ Object

The URL to be followed when the glyph for this feature is clicked



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# File 'lib/bio/graphics/feature.rb', line 107

def link
  @link
end

#location ⇒ Object

The location of the feature (which is a Bio::Locations object)



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# File 'lib/bio/graphics/feature.rb', line 95

def location
  @location
end

#name ⇒ Object

The name of the feature



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# File 'lib/bio/graphics/feature.rb', line 92

def name
  @name
end

#pixel_range_collection ⇒ Object

The array keeping the pixel ranges for the sub-features. Unspliced features will just have one element, while spliced features will have more than one.



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# File 'lib/bio/graphics/feature.rb', line 112

def pixel_range_collection
  @pixel_range_collection
end

#start ⇒ Object

The start position of the feature (in bp)



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# File 'lib/bio/graphics/feature.rb', line 98

def start
  @start
end

#stop ⇒ Object

The stop position of the feature (in bp)



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# File 'lib/bio/graphics/feature.rb', line 101

def stop
  @stop
end

#strand ⇒ Object

The strand of the feature



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# File 'lib/bio/graphics/feature.rb', line 104

def strand
  @strand
end

#track ⇒ Object

The track that this feature belongs to



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# File 'lib/bio/graphics/feature.rb', line 89

def track
  @track
end