Class: Bio::Graphics::Feature

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

Overview

The Bio::Graphics::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.

The Bio::Graphics::Feature class inherits from Bio::Feature.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(track, feature_object, opts = {}) ⇒ Feature

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

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

Arguments:

  • track (required)

    Bio::Graphics::Track object that this

    feature belongs to

  • feature object (required)

    A Bio::Feature object (see bioruby)

  • :label

    Label of the feature. Default = ‘anonymous’

  • :link

    URL for clickable images. Default = nil

  • :glyph

    Glyph to use. Default = glyph of the track

  • :colour

    Colour. Default = colour of the track

Returns

Bio::Graphics::Feature object



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# File 'lib/bio/graphics/feature.rb', line 39

def initialize(track, feature_object, opts = {})
  @track = track
  @feature_object = feature_object
  opts = {
    :label => 'anonymous',
    :link => nil,
    :glyph => @track.glyph,
    :colour => @track.colour
  }.merge(opts)
  
  @label = opts[:label]
  @link = opts[:link]
  @glyph = opts[:glyph]
  @colour = opts[:colour]
  
  @locations = @feature_object.locations

  @start = @locations.collect{|l| l.from}.min.to_i
  @stop = @locations.collect{|l| l.to}.max.to_i

  # Create Bio::Graphics SubFeatures
  # The drawing is handled by subfeatures. If there are no defined, the
  # subfeatures array will just hold one element: the @feature_object of
  # self.
  @subfeatures = Array.new
  if ! @feature_object.subfeatures.empty?
    @feature_object.subfeatures.each do |subfeature|
      @subfeatures.push(Bio::Graphics::SubFeature.new(self, subfeature, :glyph => @glyph, :colour => @colour))
    end
  else
    @subfeatures.push(Bio::Graphics::SubFeature.new(self, @feature_object, :glyph => @glyph, :colour => @colour))
  end

  @left_pixel_of_subfeatures = Array.new
  @right_pixel_of_subfeatures = Array.new
end

Instance Attribute Details

#colour ⇒ Object

The colour to use to draw this (sub)feature



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

def colour
  @colour
end

#feature_object ⇒ Object

The bioruby Bio::Feature object



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# File 'lib/bio/graphics/feature.rb', line 77

def feature_object
  @feature_object
end

#glyph ⇒ Object

The glyph to use to draw this (sub)feature



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

def glyph
  @glyph
end

#label ⇒ Object Also known as: name

The label of the feature



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# File 'lib/bio/graphics/feature.rb', line 88

def label
  @label
end

#left_pixel_of_feature ⇒ Object

Returns the value of attribute left_pixel_of_feature.



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

def left_pixel_of_feature
  @left_pixel_of_feature
end

#left_pixel_of_subfeatures ⇒ Object

Returns the value of attribute left_pixel_of_subfeatures.



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# File 'lib/bio/graphics/feature.rb', line 102

def left_pixel_of_subfeatures
  @left_pixel_of_subfeatures
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 92

def link
  @link
end

#locations ⇒ Object

Returns the value of attribute locations.



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# File 'lib/bio/graphics/feature.rb', line 79

def locations
  @locations
end

#right_pixel_of_subfeatures ⇒ Object

Returns the value of attribute right_pixel_of_subfeatures.



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# File 'lib/bio/graphics/feature.rb', line 102

def right_pixel_of_subfeatures
  @right_pixel_of_subfeatures
end

#start ⇒ Object

Returns the value of attribute start.



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# File 'lib/bio/graphics/feature.rb', line 100

def start
  @start
end

#stop ⇒ Object

Returns the value of attribute stop.



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# File 'lib/bio/graphics/feature.rb', line 100

def stop
  @stop
end

#subfeatures ⇒ Object

The Bio::Graphics SubFeatures



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# File 'lib/bio/graphics/feature.rb', line 82

def subfeatures
  @subfeatures
end

#top_pixel_of_feature ⇒ Object

Returns the value of attribute top_pixel_of_feature.



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

def top_pixel_of_feature
  @top_pixel_of_feature
end

#track ⇒ Object

The track that this feature belongs to



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# File 'lib/bio/graphics/feature.rb', line 85

def track
  @track
end

#vertical_offset ⇒ Object

Returns the value of attribute vertical_offset.



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

def vertical_offset
  @vertical_offset
end

Instance Method Details

#draw(panel_destination) ⇒ Object

Adds the feature to the track cairo context. This method should not be used directly by the user, but is called by Bio::Graphics::Track.draw

Arguments:

  • track_drawing (required)

    the track cairo object

Returns

FIXME: I don’t know



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# File 'lib/bio/graphics/feature.rb', line 113

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

  # Move the feature drawing down based on track it's in and the number
  # of times is has to be bumped
  row = self.find_row

  @vertical_offset = self.track.vertical_offset + Bio::Graphics::TRACK_HEADER_HEIGHT + Bio::Graphics::FEATURE_V_DISTANCE
  @vertical_offset += (Bio::Graphics::FEATURE_HEIGHT+Bio::Graphics::FEATURE_V_DISTANCE)*row
  
  feature_context.translate(0, @vertical_offset)

  # Let the subfeatures do the drawing.
  @subfeatures.each do |subfeature|
    subfeature.draw(feature_context)
  end

  @left_pixel_of_feature = @left_pixel_of_subfeatures.min
  @right_pixel_of_feature = @right_pixel_of_subfeatures.max
  
  # Add the label for the feature
  if @track.show_label
    pango_layout = feature_context.create_pango_layout
    pango_layout.text = @label
    fdesc = Pango::FontDescription.new('Sans Serif')
    fdesc.set_size(8 * Pango::SCALE)
    pango_layout.font_description = fdesc

    text_range = @start.floor..(@start.floor + pango_layout.pixel_size[0]*@track.panel.rescale_factor)
    if @track.grid[row+1].nil?
      @track.grid[row+1] = Array.new
    end
    @track.grid[row].push(text_range)
    @track.grid[row+1].push(text_range)
    feature_context.move_to(@left_pixel_of_feature, Bio::Graphics::TRACK_HEADER_HEIGHT)
    feature_context.set_source_rgb(0,0,0)
    feature_context.show_pango_layout(pango_layout)
    feature_context.set_source_rgb(@colour)
  end


  # And add the region to the image map
  # Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!
  @track.panel.image_map.add_element(@left_pixel_of_feature,
                                     @vertical_offset,
                                     @right_pixel_of_feature,
                                     @vertical_offset + Bio::Graphics::FEATURE_HEIGHT,
                                     @link
                                     )
end

#find_row ⇒ Object

Calculates the row within the track where this feature should be drawn. This method should not be used directly by the user, but is called by Bio::Graphics::Feature.draw

Arguments

none

Returns

row number



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# File 'lib/bio/graphics/feature.rb', line 171

def find_row
  row_found = false

  # We've got to find out what row to draw the feature on. If two 
  # features overlap, one of them has to be 'bumped' down. So we'll
  # first try to draw a new feature at the top of the track. If
  # it however would overlap with another one, we'll bump it down
  # to the next row.
  feature_range = (@start.floor - 1..@stop.ceil + 1)
  row = 1
  row_available = true
  until row_found
    if ! @track.grid[row].nil?
      @track.grid[row].each do |covered|
        if feature_range.include?(covered.first) or covered.include?(feature_range.first)
          row_available = false
        end
      end
      if ! @track.grid[row+1].nil? #Still have to check if there is no label there.
        @track.grid[row+1].each do |covered|
          if feature_range.include?(covered.first) or covered.include?(feature_range.first)
            row_available = false
          end
        end
      end
    end

    if ! row_available
      row += 1
      row_available = true
    else # We've found the place where to draw the feature.
      if @track.grid[row].nil?
        @track.grid[row] = Array.new
      end
      @track.grid[row].push(feature_range)
      row_found = true
    end
  end
  return row
end