Method: Bio::Graphics::Panel#initialize

Defined in:
lib/bio/graphics/panel.rb

#initialize(length, opts = {}) ⇒ Panel

Create a new Bio::Graphics::Panel object

g = Bio::Graphics::Panel.new(456)

The height of the image is calculated automatically depending on how many tracks and features it contains. The width of the image defaults to 800 pt but can be set manually by using the width argument to the opts hash:

g = Bio::Graphics::Panel.new(456, :width => 1200)

See also: Bio::Graphics::Panel::Track, Bio::Graphics::Panel::Track::Feature

Arguments:

  • length

    length of the thing you want to visualize, e.g for

    visualizing a sequence that is 3.24 kb long, use 324. (required)

  • :width

    width of the resulting image in pixels. (default: 800)

  • :clickable

    whether the picture should have clickable glyphs or not

    (default: false) If set to true, a html file will be created with the map.

  • :display_start

    start coordinate to be displayed (default: 1)

  • :display_stop

    stop coordinate to be displayed (default: length of sequence)

  • :vertical

    Boolean: false = horizontal (= default)

  • :format

    File format of the picture. Can be :png, :svg, :pdf or :ps

    (default: :png)

Returns

Bio::Graphics::Panel object



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# File 'lib/bio/graphics/panel.rb', line 110

def initialize(length, opts = {})
  @length = length
  opts = {
    :width => DEFAULT_PANEL_WIDTH,
    :display_range => Range.new(0,@length),
    :vertical => false,
    :clickable => false,
    :format => :png
  }.merge(opts)
  
  @width = opts[:width].to_i

  @display_range = opts[:display_range]
  @display_start = [0, @display_range.lend].max
  @display_stop = [@length,@display_range.rend].min
  if @display_stop <= @display_start
    raise "[ERROR] Start coordinate to be displayed has to be smaller than stop coordinate."
  end
  @display_range = Range.new(@display_start,@display_stop)
  
  @vertical = opts[:vertical]
  @clickable = opts[:clickable]
  
  @format = opts[:format]
  if ! [:png, :svg, :pdf, :ps].include?(@format)
    raise "[ERROR] Format has to be one of :png, :svg, :pdf or :ps."
  end
  
  @tracks = Array.new
  @number_of_feature_rows = 0
  @image_map = ImageMap.new

  @rescale_factor = (@display_stop - @display_start).to_f / @width
  
  # To prevent that we do the whole drawing thing multiple times
  @final_panel_destination = nil
end