Class: Bioroebe::SVG::Track

Inherits:
Object
  • Object
show all
Defined in:
lib/bioroebe/svg/track.rb

Overview

Bioroebe::SVG::Track

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(args) ⇒ Track

#

initialize

Creates a new Bioroebe::SVG::Track.

Arguments:

:glyph = one of Bioroebe::SVG::Glyphs#glyphs, currently being

[:generic,   :directed, :transcript, :scale, :label,
 :histogram, :circle, :down_triangle, :up_triangle,
 :span]

:stroke_color = the outline colour of the glyphs in the track

(default = "black"), can be any SVG colour eg rgb(256,0,0)
or #FF0000.

:fill_color = the fill colour of the glyphs in the track (default = ‘red’), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bioroebe::SVG::Glyph#gradients

[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ] or a custom definition of a gradient: {:type => :radial, 

:id => :custom, 
:cx => 5, 
:cy => 5, 
:r => 50, 
:fx => 50, 
:fy => 50, 
:stops => [ {
      :offset => 0, 
      :color => 'rgb(255,255,255)', 
      :opacity => 0
      },  {
      :offset => 100, 
      :color => 'rgb(0,127,200)', 
      :opacity => 1
      }, ]

}

:track_height = minimum height for the track, will be modified automatically if more space is needed e.g for overlapping features (default = auto), :name = a displayed name for the track (default = ‘feature_track’) :label = display the name given to the track (default = true), :stroke_width = width in pixels of the outline of the glyphs (default=1) :x_round = x radius of the ellipse used to round off the corners of rectangles (default = 1) :y_round = y radius of the ellipse used to round off the corners of rectangles (default = 1) :utr_fill_color = the fill colour of the utr part of the glyph (default = ‘black’), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bioroebe::SVG::Glyph#gradients

:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial

or a custom definition of a gradient {:type => :radial, :id => :custom, :cx => 5, :cy => 5, :r => 50, :fx => 50, :fy => 50, 

:stops => [ {
     :offset => 0, 
     :color => 'rgb(255,255,255)', 
     :opacity => 0
     },  {
     :offset => 100, 
     :color => 'rgb(0,127,200)', 
     :opacity => 1
     }, ]

}

  • :utr_stroke = the outline colour of the utr part of the glyph

(default = “black”), can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :utr_stroke_width = The width of the outline stroke for the utr part of the glyph (default = 1)

  • :exon_fill_color = the fill colour of the utr part of the glyph (default = ‘red’), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bioroebe::SVG::Glyph#gradients or a custom definition of a gradient

:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial

or a custom definition of a gradient {:type => :radial, :id => :custom, :cx => 5, :cy => 5, :r => 50, :fx => 50, :fy => 50, 

:stops => [ {
     :offset => 0, 
     :color => 'rgb(255,255,255)', 
     :opacity => 0
     },  {
     :offset => 100, 
     :color => 'rgb(0,127,200)', 
     :opacity => 1
     }, ]

:exon_stroke = the outline colour of the exon part of the glyph 

default = "black") can be any SVG colour eg rgb(256,0,0) or #FF0000

:exon_stroke_width = The width of the outline stroke for the exon part of the glyph (default = 1) :line_color = the colour for the line part that joins the blocks (default = ‘black’) can be any SVG colour eg rgb(256,0,0) or #FF0000 :line_width = the width ffor the line part that joins the blocks (default = 1) :exon_style = an arbitrary SVG compliant style string eg “fill-opacity:0.4;” :utr_style = an arbitrary SVG compliant style string eg “fill-opacity:0.4;” :line_style = an arbitrary SVG compliant style string eg “fill-opacity:0.4;” :gap_marker = style of the line between blocks - either angled or straight

#


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# File 'lib/bioroebe/svg/track.rb', line 131

def initialize(args)
  @args = {
    :glyph => :generic, 
    :name  => 'feature_track', 
    :label => true, 
    :feature_height => 10,
    :track_height => nil
  }.merge!(args) # Append in the arguments.
  @glyph = @args[:glyph]
  @name = @args[:name]
  @label = @args[:label]
  @track_height = @args[:track_height]
  # ======================================================================= #
  # === @features
  # ======================================================================= #
  @features = []
  # ======================================================================= #
  # === @feature_rows
  # ======================================================================= #
  @feature_rows = []
  # ======================================================================= #
  # === @scale
  # ======================================================================= #
  @scale = @args[:scale]
  # ======================================================================= #
  # === @feature_height
  # ======================================================================= #
  @feature_height = @args[:feature_height]
  @max_y = args[:max_y]
  @min_width = args[:min_width]
  reset
end

Instance Attribute Details

#args ⇒ Object (readonly)

Returns the value of attribute args.



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# File 'lib/bioroebe/svg/track.rb', line 20

def args
  @args
end

#feature_height ⇒ Object

Returns the value of attribute feature_height.



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# File 'lib/bioroebe/svg/track.rb', line 27

def feature_height
  @feature_height
end

#feature_rows ⇒ Object

Returns the value of attribute feature_rows.



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# File 'lib/bioroebe/svg/track.rb', line 24

def feature_rows
  @feature_rows
end

#features ⇒ Object

Returns the value of attribute features.



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# File 'lib/bioroebe/svg/track.rb', line 23

def features
  @features
end

#glyph ⇒ Object (readonly)

Returns the value of attribute glyph.



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# File 'lib/bioroebe/svg/track.rb', line 21

def glyph
  @glyph
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/bioroebe/svg/track.rb', line 25

def name
  @name
end

#number_rows ⇒ Object

Returns the value of attribute number_rows.



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# File 'lib/bioroebe/svg/track.rb', line 26

def number_rows
  @number_rows
end

Instance Method Details

#add(feature) ⇒ Object

#

add

Adds a new Bioroebe::SVG::MiniFeature object to the current Bioroebe::SVG::Track.

#


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# File 'lib/bioroebe/svg/track.rb', line 201

def add(feature)
  @features << feature
end

#get_rows(page = nil) ⇒ Object

#

get_rows

Calculates how many rows are needed per track for overlapping features and which row each feature should be in. Usually only called by the enclosing Bioroebe::SVG::Page object.

#


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# File 'lib/bioroebe/svg/track.rb', line 219

def get_rows(
    page = nil
  )
  @feature_rows = Array.new(@features.length, -1)
  rows = Hash.new { |h, key| h[key] = [] }
  @features.each_with_index { |f1, i|
    current_row = 1
    begin
      found = true
      rows[current_row].each_with_index { |f2, j|
        if overlaps(f1, f2, page)
          found = false
          current_row += 1
          break
        end
      }
    end until found
    @feature_rows[i] = current_row
    rows[current_row] << f1
  }
  @number_rows = @feature_rows.max
end

#label? ⇒ Boolean Also known as: label

#

label?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/svg/track.rb', line 191

def label?
  @label
end

#max_y? ⇒ Boolean Also known as: max_y

#

max_y?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/svg/track.rb', line 177

def max_y?
  @max_y
end

#min_width? ⇒ Boolean Also known as: min_width

#

min_width?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/svg/track.rb', line 275

def min_width?
  @min_width
end

#overlaps(f1, f2, page = nil) ⇒ Object

#

overlaps

Calculates whether two Bioroebe::SVG::MiniFeature objects overlap by examining their start and end positions.

If the page where they are placed is given, then the function also considers the features’ labels.

Arguments:

f1 - a Bioroebe::SVG::MiniFeature object
f2 - a Bioroebe::SVG::MiniFeature object
page - the optional Bioroebe::SVG::Page object where the features
are placed
#


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# File 'lib/bioroebe/svg/track.rb', line 259

def overlaps(
    f1, f2, page = nil
  )
  if !page
    b1 = [f1.start, f1.end]
    b2 = [f2.start, f2.end]
  else
    b1 = page.compute_boundaries(f1)
    b2 = page.compute_boundaries(f2)
  end
  (b2[0] <= b1[1]) and (b1[0] <= b2[1])
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/svg/track.rb', line 167

def reset
  # ======================================================================= #
  # === @number_of_rows
  # ======================================================================= #
  @number_of_rows = 1
end

#scale? ⇒ Boolean Also known as: scale

#

scale?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/svg/track.rb', line 184

def scale?
  @scale
end

#track_height? ⇒ Boolean Also known as: track_height

#

track_height?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/svg/track.rb', line 208

def track_height?
  @track_height
end