Class: Bio::Graphics::Track

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

Overview

The Bio::Graphics::Track class describes the container for features of the same type. See Bio::Graphics documentation for explanation of interplay between different classes.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(panel, name, opts = {}) ⇒ Track

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

– This is necessary because the track needs to know the rescale_factor and width of the picture, both of which are defined within the panel. ++

Arguments:

  • panel (required)

    Bio::Graphics::Panel object that this track

    belongs to

  • name (required)

    Name of the track to be displayed (e.g. ‘genes’)

  • :label

    Boolean: should the label for each feature be drawn or not

    Default = true

  • :glyph

    Glyph to use for drawing the features. Options are:

    :generic, :directed_generic, :box, directed_box, :spliced, :directed_spliced, :dot, :triangle, :line and :line_with_handles. Default = :generic

  • colour

    Colour to be used to draw the features within the track (in

    RGB) Default = [0,0,1] (i.e. blue)

Returns

Bio::Graphics::Track object



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

def initialize(panel, name, opts = {})
  @panel = panel
  @name = name
  opts = {
    :label => true,
    :glyph => :generic,
    :colour => [0,0,1]
  }.merge(opts)
  
  @show_label = opts[:label]
  @glyph = opts[:glyph]
  @colour = opts[:colour]

  # As far as I know, I can't do this in the glyph file for transcript, so we
  # have to do it here instead.
  if @glyph == :transcript
    @glyph = { 'utr5' => :box, 'utr3' => :directed_box, 'cds' => :spliced }
  end
  
  @features = Array.new
  @number_of_feature_rows = 0
  @vertical_offset = 0
  @grid = Hash.new
end

Instance Attribute Details

#colour ⇒ Object

Returns the value of attribute colour.



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# File 'lib/bio/graphics/track.rb', line 61

def colour
  @colour
end

#features ⇒ Object

Returns the value of attribute features.



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# File 'lib/bio/graphics/track.rb', line 61

def features
  @features
end

#glyph ⇒ Object

Returns the value of attribute glyph.



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# File 'lib/bio/graphics/track.rb', line 61

def glyph
  @glyph
end

#grid ⇒ Object

Returns the value of attribute grid.



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# File 'lib/bio/graphics/track.rb', line 61

def grid
  @grid
end

#height ⇒ Object

Returns the value of attribute height.



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# File 'lib/bio/graphics/track.rb', line 61

def height
  @height
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/bio/graphics/track.rb', line 61

def name
  @name
end

#number_of_feature_rows ⇒ Object

Returns the value of attribute number_of_feature_rows.



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# File 'lib/bio/graphics/track.rb', line 61

def number_of_feature_rows
  @number_of_feature_rows
end

#panel ⇒ Object

Returns the value of attribute panel.



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# File 'lib/bio/graphics/track.rb', line 61

def panel
  @panel
end

#show_label ⇒ Object

Returns the value of attribute show_label.



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# File 'lib/bio/graphics/track.rb', line 61

def show_label
  @show_label
end

#vertical_offset ⇒ Object

Returns the value of attribute vertical_offset.



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# File 'lib/bio/graphics/track.rb', line 61

def vertical_offset
  @vertical_offset
end

Instance Method Details

#add_feature(feature_object, opts = {}) ⇒ Object

Takes a Bio::Feature and adds it as a Bio::Graphics::Feature to this track. A track contains features of the same type, e.g. (for sequence annotation:) genes, polymorphisms, ESTs, etc.

est_track.add_feature(Bio::Feature.new('EST1','50..60'))
est_track.add_feature(Bio::Feature.new('EST2','52..73'))
est_track.add_feature(Bio::Feature.new('EST3','41..69'))
gene_track.add_feature(Bio::Feature.new('gene2','39..73'))

For spliced features:

est_track.add_feature('EST4','join(34..53,153..191)')

Or on the complement strand:

est_track.add_feature('EST5','complement(join(34..53,153..191))')

See the documentation in Bio::Locations for a full description of how locations can be defined.

Features are only added if they are at least partly in the displayed region. If a feature is completely outside of the region, it’s not added. If it should be only partly visible, it is added completely.

Arguments:

  • feature object (required)

    A Bio::Feature object

  • label

    Label for the feature. Default = ‘anonymous’

  • link

    URL to link to for this glyph. Default = nil

  • glyph

    Glyph for the feature. Default = glyph of the track

  • colour

    Colour for the feature. Default = colour of the track

Returns

Bio::Graphics::Feature object that was created or nil



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# File 'lib/bio/graphics/track.rb', line 93

def add_feature(feature_object, opts = {})
  # Calculate the ultimate start and stop of the feature: the start
  # of the first subfeature (e.g. exon) and the stop of the last one.
  # The only reason we want to know these positions, is because we want
  # to determine if the feature falls within the view of the image or
  # not (see below).
  start = feature_object.locations.collect{|l| l.from}.min.to_i
  stop = feature_object.locations.collect{|l| l.to}.max.to_i

  # If the feature wouldn't show because it's not in the region we're
  # looking at, don't bother storing the stuff. I think this makes huge
  # speed and memory differences if you've got a chromosome with
  # thousands of features.
  if stop <= self.panel.display_start or start >= self.panel.display_stop
    return nil
  else #elsif start >= panel.display_start and stop <= panel.display_stop
    @features.push(Bio::Graphics::Feature.new(self, feature_object, opts))
    return @features[-1]
  end

  return self
end

#draw(panel_destination) ⇒ Object

Adds the track to a cairo drawing. This method should not be used directly by the user, but is called by Bio::Graphics::Panel.draw

Arguments:

  • panel__drawing (required)

    the panel cairo object

Returns

FIXME: I don’t know



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# File 'lib/bio/graphics/track.rb', line 123

def draw(panel_destination)
  track_context = Cairo::Context.new(panel_destination)

  # Draw thin line above title
  track_context.set_source_rgb(0.75,0.75,0.75)
  track_context.move_to(0, self.vertical_offset)
  track_context.line_to(self.panel.width, self.vertical_offset)
  track_context.stroke

  # Draw track title
  track_context.set_source_rgb(0,0,0)
  track_context.select_font_face(*(Bio::Graphics::FONT))
  track_context.set_font_size(Bio::Graphics::TRACK_HEADER_HEIGHT)
  track_context.move_to(0,Bio::Graphics::TRACK_HEADER_HEIGHT + self.vertical_offset + 10)
  track_context.show_text(self.name)

  # Draw the features
  @features.sort_by{|f| f.start}.each do |feature|
    # Don't even bother if the feature is not in the view
    if feature.stop <= self.panel.display_start or feature.start >= self.panel.display_stop
      next
    else
      feature.draw(panel_destination)
    end
  end

  @number_of_feature_rows = ( @grid.keys.length == 0 ) ? 1 : @grid.keys.max + 1

  return panel_destination
end