bio-svgenes 0.3.0 → 0.3.1

data/Gemfile

@@ -7,8 +7,9 @@ source "http://rubygems.org"
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "shoulda", ">= 0"
-  gem "bundler", "~> 1.0.0"
+  gem "bundler", ">= 1.0.0"
   gem "jeweler", "~> 1.6.4"
   gem "rcov", ">= 0"
   gem "bio", ">= 1.4.2"
+  gem "json", ">=1.7"
 end

data/Gemfile.lock

@@ -7,6 +7,7 @@ GEM
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
+    json (1.7.7)
     rake (0.9.2.2)
     rcov (0.9.11)
     shoulda (2.11.3)
@@ -16,7 +17,8 @@ PLATFORMS
 
 DEPENDENCIES
   bio (>= 1.4.2)
-  bundler (~> 1.0.0)
+  bundler (>= 1.0.0)
   jeweler (~> 1.6.4)
+  json (>= 1.7)
   rcov
   shoulda

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

data/bio-svgenes.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-svgenes"
-  s.version = "0.3.0"
+  s.version = "0.3.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]
-  s.date = "2013-03-04"
+  s.date = "2013-03-05"
   s.description = "This bio-gem facilitates the creation of pretty, publication quality SVG images from feature data."
   s.email = "maclean.daniel@gmail.com"
   s.extra_rdoc_files = [
@@ -17,7 +17,6 @@ Gem::Specification.new do |s|
     "README.rdoc"
   ]
   s.files = [
-    ".DS_Store",
     ".document",
     "Gemfile",
     "Gemfile.lock",
@@ -26,9 +25,7 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "bio-svgenes.gemspec",
-    "doc/.DS_Store",
     "doc/Bio.html",
-    "doc/Bio/.DS_Store",
     "doc/Bio/Graphics.html",
     "doc/Bio/Graphics/Glyph.html",
     "doc/Bio/Graphics/MiniFeature.html",
@@ -72,12 +69,9 @@ Gem::Specification.new do |s|
     "doc/js/searcher.js",
     "doc/rdoc.css",
     "doc/table_of_contents.html",
-    "examples/.DS_Store",
     "examples/annotate_snps.rb",
     "examples/data.txt",
     "examples/draw_from_json.rb",
-    "examples/drawn_from_json.svg",
-    "examples/drawn_from_json2.svg",
     "examples/eg2.rb",
     "examples/example.rb",
     "examples/example.svg",
@@ -86,19 +80,15 @@ Gem::Specification.new do |s|
     "examples/get_coverage_in_windows.rb",
     "examples/make_example.rb",
     "examples/transcripts.gff",
-    "lib/.DS_Store",
     "lib/bio-svgenes.rb",
-    "lib/bio/.DS_Store",
     "lib/bio/graphics/glyph.rb",
     "lib/bio/graphics/mini_feature.rb",
     "lib/bio/graphics/page.rb",
     "lib/bio/graphics/primitive.rb",
     "lib/bio/graphics/svgee.rb",
     "lib/bio/graphics/track.rb",
-    "test/gene.gff",
     "test/helper.rb",
     "test/json_config.json",
-    "test/test_bio-svgenes.rb",
     "test/test_glyph.rb",
     "test/test_mini_feature.rb",
     "test/test_page.rb",
@@ -118,23 +108,26 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<bundler>, [">= 1.0.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
       s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_development_dependency(%q<json>, [">= 1.7"])
     else
       s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<bundler>, [">= 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
       s.add_dependency(%q<rcov>, [">= 0"])
       s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<json>, [">= 1.7"])
     end
   else
     s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<bundler>, [">= 1.0.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
     s.add_dependency(%q<rcov>, [">= 0"])
     s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<json>, [">= 1.7"])
   end
 end
 

data/lib/bio/graphics/glyph.rb

@@ -1,10 +1,39 @@
 module Bio
   class Graphics
+    #A Glyph is an array of Primitive objects, holding information about the type of Glyph being created.
+    #Each different type of Glyph has different arguments, pertaining to how the Glyph will be drawn and the parameters provided to SVGEE.
+    #
+
 class Glyph
-  attr_reader :glyphs
+
+  #The different type of Glyphs are:
+  #* generic
+  #* circle
+  #* directed
+  #* \down_triangle
+  #* \up_triangle
+  #* span
+  #* transcript
+  #* scale
+  #* label
+  #* histogram
+
+attr_reader :glyphs
   #holds a load of definitions for glyphs .. a glyph is an array of primitives... 
   @glyphs = [:generic, :directed, :transcript, :scale, :label, :histogram, :circle, :down_triangle, :up_triangle, :span]
-  
+  #Creates a generic glyph, which is a rectangle
+  #
+  #+args+
+  #* height = the height of the Glyph (10)
+  #* fill_color = the fill colour of the Glyph ('red')
+  #* stroke = the outline colour of the Glyph ("black")
+  #* stroke_width = The width of the outline stroke (1)
+  #* x_round = x-axis radius of the ellipse used to round off the corners of the rectangle (1)
+  #* y_round = y-axis radius of the ellipse used to round off the corners of the rectangle (1)
+  #* style = the opacity of the fill color ("fill-opacity:0.4;")
+  #* x = the co-ordinates of the Glyph for the x-axis
+  #* y = the co-ordinates of the Glyph for the y-axis
+
   def self.generic(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height, 
     args = { 
       :height => 10, 
@@ -15,8 +44,19 @@ class Glyph
       :y_round => 1, 
       :style => "fill-opacity:0.4;"}.merge!(args)
     [Bio::Graphics::Primitive.new(:rectangle, args)]
-  end 
-  
+  end
+
+  #Creates a circular Glyph
+  #
+  #+args+
+  #* radius = the radius of the circle  (10)
+  #* fill_color = the fill colour of the Glyph ('red')
+  #* stroke = the outline colour of the Glyph ("black")
+  #* stroke_width = The width of the outline stroke (1)
+  #* style = the opacity of the fill color
+  #* x = x-axis centre of the circle
+  #* y = y-axis centre of the circle
+
   def self.circle(args) 
     args = { 
       :radius => 10, 
@@ -30,7 +70,18 @@ class Glyph
     [Bio::Graphics::Primitive.new(:circle, args)]
   end 
   
-  
+  #Creates a polygon Glyph to indicate the direction in which the Glyph is pointing
+  #+args+
+  #* width = the width of the feature
+  #* fill_color = the fill colour of the Glyph ('red')
+  #* stroke = the outline colour of the Glyph ("black")
+  #* stroke_width = The width of the outline stroke (1)
+  #* style = the opacity of the fill color
+  #* strand = the strand on which the Glyph is located. May be '+' or '-'
+  #* points = the x and y axis points used to calculate the shape of the polygon
+  #* x = the co-ordinates of the Glyph for the x-axis
+  #* y = the co-ordinates of the Glyph for the y-axis
+  #The points of the polygon are calculated form the +x+ and +y+ co-ordinates
   def self.directed(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
     args = {
       
@@ -43,11 +94,22 @@ class Glyph
       if args[:strand] == '-'
         args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + args[:height] } #{args[:x]},#{args[:y] + (args[:height])} #{args[:x] - (args[:height] * 0.2)},#{args[:y] + (args[:height]/2)}"
       else
-        args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + (args[:height]/2) } #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y] + args[:height]} #{args[:x]},#{args[:y] + args[:height]}"      
+        args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + (args[:height]/2) } #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y] + args[:height]} #{args[:x]},#{args[:y] + args[:height]}"
+
       end
     [Bio::Graphics::Primitive.new(:polygon, args)]
   end
-  
+  #Creates a polygon Glyph for a downward-pointing triangle
+  #+args+
+  #* height = the height of the Glyph (10)
+  #* fill_color = the fill colour of the Glyph ('red')
+  #* stroke = the outline colour of the Glyph ("black")
+  #* stroke_width = The width of the outline stroke (1)
+  #* style = the opacity of the fill color ("fill-opacity:0.4;")
+  #* x = the co-ordinates of the Glyph for the x-axis
+  #* y = the co-ordinates of the Glyph for the y-axis
+  #The points of the triangle are calculated form the +x+ and +y+ co-ordinates
+
   def self.down_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
     args = {
       
@@ -56,10 +118,21 @@ class Glyph
       :stroke => "black", 
       :stroke_width => 1, 
       :style => "fill-opacity:0.4;"}.merge!(args)
+
       args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{ args[:x] + (args[:width]/2) },#{(args[:y] + args[:height]) }"
     [Bio::Graphics::Primitive.new(:polygon, args)]
   end
-  
+  #Creates a polygon Glyph for an upward-pointing triangle
+  #+args+
+  #* height = the height of the Glyph (10)
+  #* fill_color = the fill colour of the Glyph ('red')
+  #* stroke = the outline colour of the Glyph ("black")
+  #* stroke_width = The width of the outline stroke (1)
+  #* style = the opacity of the fill color ("fill-opacity:0.4;")
+  #* x = the co-ordinates of the Glyph for the x-axis
+  #* y = the co-ordinates of the Glyph for the y-axis
+  #The points of the triangle are calculated form the +x+ and +y+ co-ordinates
+
   def self.up_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
     args = {
       :height => 10, 
@@ -70,7 +143,16 @@ class Glyph
       args[:points] = "#{args[:x]},#{args[:y] + args[:height]} #{args[:x] + args[:width]},#{args[:y] + args[:height]} #{ args[:x] + (args[:width]/2) },#{args[:y] }"
     [Bio::Graphics::Primitive.new(:polygon, args)]
   end
-  
+  #Creates a span glyph, which is a line
+  #
+  #+args+
+  #* height = the height of the Glyph (10)
+  #* fill_color = the fill colour of the Glyph ('red')
+  #* stroke = the outline colour of the Glyph ("black")
+  #* stroke_width = The width of the outline stroke (1)
+  #* style = the opacity of the fill color ("fill-opacity:0.4;")
+  #* x = the co-ordinates of the Glyph for the x-axis
+  #* y = the co-ordinates of the Glyph for the y-axis
   def self.span(args)
     args = {
       :height => 10,
@@ -85,7 +167,26 @@ class Glyph
     args[:y2] = args[:y]
     [Bio::Graphics::Primitive.new(:line, args)]
   end
-  
+  #Creates a transcript glyph, which is a number of different types of Glyph, depending on the features
+  #within the transcript
+  #
+  #+args+
+  #* height = the height of the Glyph (10)
+  #* utr_fill_color = the fill colour of the Glyph ('black')
+  #* utr_stroke = the outline colour of the Glyph ("black")
+  #* utr_stroke_width = The width of the outline stroke (1)
+  #* exon_fill_color = the fill colour of the Glyph ('red')
+  #* exon_stroke = the outline colour of the Glyph ("black")
+  #* exon_stroke_width = The width of the outline stroke (1)
+  #* line_color = the colour for any line Glyphs
+  #* line_width = the width for any line Glyphs
+  #* exon_style = the opacity of the fill color for exons ("fill-opacity:0.4;")
+  #* utr_style = the opacity of the fill color for utrs
+  #* line_style = the opacity of the fill color for lines
+  #* block_gaps = ****I'm not sure what these are****
+  #* gap_marker = ****I'm not sure what these are****
+  #* x = the co-ordinates of the Glyph for the x-axis
+  #* y = the co-ordinates of the Glyph for the y-axis
   def self.transcript(args)
       args = {
       :height => 10, 
@@ -178,10 +279,19 @@ class Glyph
       end
       composite
   end
-  
+  #Creates the scale across the top of the SVG page
+  #
+  #+args+
+  #* start = the start of the scale
+  #* stop = the end of the scale
+  #* \number_of_intervals = the number of tick-marks on the scale to show the current position
+  #* page_width = the width of the page
+  #
+  #+returns+
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Primitive objects (of type 'line', 'rectangle' and 'text')
+
   def self.scale(args)
-    
-    
     first_mark = args[:start]
     last_mark = args[:stop] 
     #(num.to_f / @nt_per_px_x.to_f)
@@ -217,7 +327,15 @@ class Glyph
     end
     return a
   end
-  
+  #Creates a label Glyph to write text
+  #
+  #+args+
+  #* text = the text to write
+  #* fill = the colour of the text ("black")
+  #* style = the style of writing ("font-family:monospace;")
+  #* x = the co-ordinates of the Glyph for the x-axis
+  #* y = the co-ordinates of the Glyph for the y-axis
+
   def self.label(args)
     [Bio::Graphics::Primitive.new(:text, 
                    :text => args[:text], 
@@ -226,11 +344,26 @@ class Glyph
                    :fill => "black", 
                    :style => "font-family:monospace;")]
   end
-  
+  #The list of pre-defined gradients
   def self.gradients #needs to know which of its gradients are predefined
     [:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
   end
-  
+
+  #Sets the the type (linear or radial) and colour of gradient for a pre-defined gradient
+  #along with the pertinent parameters for that type
+  #
+  #+args+
+  #* gradient = a pre-defined gradient
+  #The types of gradient are:
+  #* red_white_h
+  #* green_white_h
+  #* blue_white_h
+  #* yellow_white_h
+  #* red_white_radial
+  #* green_white_radial
+  #* blue_white_radial
+  #* yellow_white_radial
+
   def self.gradient(gradient)
     type, color = case gradient
     when :red_white_h

data/lib/bio/graphics/mini_feature.rb

@@ -1,7 +1,30 @@
 module Bio
   class Graphics
+    ##
+    #The MiniFeature class represents any feature (e.g. a gene, transcript, exon, start codon, etc) on a track.
+    #
 class MiniFeature
   attr_accessor :start, :end, :strand, :exons, :utrs, :block_gaps, :segment_height, :id
+  #Creates a new MiniFeature
+  #
+  #_Arguments_
+  #* start = the start position of the feature
+  #* end = the end position of the feature
+  #* strand  = the strand of the feature
+  #* exons = an array of exon positions
+  #* utrs = an array of utrs positions
+  #* \block_gaps = an array of regions with nothing to be drawn, e.g. introns
+  #* id = the name of the feature such as the gene name or transcript ID
+  #* \segment_height = the height of the current feature
+  #
+  #==Example usage
+  #
+  ##@mini1 = Bio::Graphics::MiniFeature.new(:start=>3631, :end=>5899, :strand=>'+',
+  # :exons=>[4000, 4500, 4700, 5000], :utrs=>[3631, 3650], :segment_height=>5, :id=>"AT1G01010")
+  #
+  #===MiniFeatures and Tracks
+  #MiniFeatures are added to Track objects, with overlapping MiniFeatures being placed onto separate rows
+  #
   def initialize(args)
     @start = args[:start]
     @end = args[:end]

data/lib/bio/graphics/page.rb

@@ -1,290 +1,343 @@
 module Bio
   class Graphics
-class Page
-  
-  def initialize(args)
-    @height = args[:height]
-    @width = args[:width]
-    args[:style] = "background-color:#{args[:background_color]};" if args[:background_color]
-    @svg = SVGEE.new(args)
-    @scale_start = 1.0/0.0
-    @scale_stop = -1.0/0.0
-    @tracks = [] #array of track objects with loads of features in it...
-    @nt_per_percent = 1;
-    @num_intervals = args[:number_of_intervals] 
-    @track_top = 30  
-    
-    def @svg.update_height(height)
-      @height = height 
-    end
-    
-    #def @svg.update_width(width)
-    #  @width = width
-    #end
-  end
-  
-  def self.from_json(args)
-    require 'rubygems'
-    require 'json'
-    data = JSON.parse(File.open(args[:json], 'r').read)
-    p = Page.new(:width => data["Page"]["width"], 
-                 :height => data["Page"]["height"], 
-                 :number_of_intervals => data["Page"]["intervals"])         
-    data["Tracks"].each do |track|
-      #prep the track args
-      track_args = track.dup
-      track_args.delete("file")
-      track_args.delete("file_type")
-      track_args = track_args.inject({}){|memo,(k,v)| memo[k.to_sym] = v; memo}
-      ##convert any of the pre-made gradient strings in the keys to symbol
-      track_args.each_key do |k|
-        next unless track_args[k].respond_to?(:to_sym)
-        track_args[k] = track_args[k].to_sym if Glyph.gradients.include?(track_args[k].to_sym)
+
+    ##
+    #The Page class represents the top level container on which svg objects are written. It will contain a scale
+    #and all the tracks along with their features. The scale will start at the genomic co-ordinates of the start
+    #of the first feature and stop at the end of the last feature)
+    #
+
+
+    class Page
+      #Creates a new Page object.
+      #
+      #A new Page contains the following arguments:
+      #* height = the height of the page
+      #* width = the width of the page
+      #* style = includes the a background colour
+      #* svg = a new SVGEE object
+      #* scale_start = the scale-start of the page (1.0/0.0)
+      #* scale_stop = the scale-stop of the page (-1.0/0.0)
+      #* tracks = an array of track objects with loads of features in it...
+      #* nt_per_percent = the number of nucleotides that are represented by 1% of the page (1);
+      #* num_intervals = the number of intervals
+      #* track_top = the position of the top of the first track (30)
+      #
+      #A new page maybe set up as follows:
+      # @page = Bio::Graphics::Page.new(:width => 800,
+      # :height => 110, :number_of_intervals => 10)
+      #
+      def initialize(args)
+        @height = args[:height]
+        @width = args[:width]
+        args[:style] = "background-color:#{args[:background_color]};" if args[:background_color]
+        @svg = SVGEE.new(args)
+        @scale_start = 1.0/0.0
+        @scale_stop = -1.0/0.0
+        @tracks = [] #array of track objects with loads of features in it...
+        @nt_per_percent = 1;
+        @num_intervals = args[:number_of_intervals]
+        @track_top = 30
+
+        def @svg.update_height(height)
+          @height = height
+        end
+
+        #def @svg.update_width(width)
+        #  @width = width
+        #end
       end
+      #Takes a custom-written json file and writes an svg page to file which will contain the given features described within the json file.
+      #* +args+ - a custom-written json file describing the parameters and resources needed for a new page
 
-      svg_track = p.add_track(track_args)
-      features = [] ##set up the features... 
-      
-      case track["file_type"] ##deal with the gff and data files
-      when "gff"
-        groups = {}
-        parentless_features = []
-        Page.parse_gff(track["file"]).each do |gff| #gets features in a list and links their children to them as members of the array at the key
-          parent_id = gff.attributes.select { |a| a.first == 'Parent'}
-          if parent_id.empty?
-            parentless_features << gff
-          else
-            if groups[parent_id.first.last].nil?
-              groups[parent_id.first.last] = []
-              groups[parent_id.first.last] << gff
-            else
-              groups[parent_id.first.last] << gff
-            end
+      def self.from_json(args)
+        require 'rubygems'
+        require 'json'
+        data = JSON.parse(File.open(args[:json], 'r').read)
+        p = Page.new(:width => data["Page"]["width"],
+                     :height => data["Page"]["height"],
+                     :number_of_intervals => data["Page"]["intervals"])
+        data["Tracks"].each do |track|
+          #prep the track args
+          track_args = track.dup
+          track_args.delete("file")
+          track_args.delete("file_type")
+          track_args = track_args.inject({}) { |memo, (k, v)| memo[k.to_sym] = v; memo }
+          ##convert any of the pre-made gradient strings in the keys to symbol
+          track_args.each_key do |k|
+            next unless track_args[k].respond_to?(:to_sym)
+            track_args[k] = track_args[k].to_sym if Glyph.gradients.include?(track_args[k].to_sym)
           end
-        end
-          #now flick through the parentless features and add any exons / UTRs
-          parentless_features.each do |plf|
-            require 'pp'
-            pp parentless_features
-            gff_id = plf.attributes.select {|a| a.first == 'ID'}
-            gff_id = gff_id.first.last
-            exons = []
-            utrs = []
-            children = groups[gff_id] || children = []
-            children.each do |child|
-              if child.feature == 'exon' or child.feature == 'CDS'
-                exons += [child.start,child.end]
-              elsif child.feature =~ /utr/i
-                utrs += [child.start,child.end]
+
+          svg_track = p.add_track(track_args)
+          features = [] ##set up the features...
+
+          case track["file_type"] ##deal with the gff and data files
+            when "gff"
+              groups = {}
+              parentless_features = []
+              Page.parse_gff(track["file"]).each do |gff| #gets features in a list and links their children to them as members of the array at the key
+                parent_id = gff.attributes.select { |a| a.first == 'Parent' }
+                if parent_id.empty?
+                  parentless_features << gff
+                else
+                  if groups[parent_id.first.last].nil?
+                    groups[parent_id.first.last] = []
+                    groups[parent_id.first.last] << gff
+                  else
+                    groups[parent_id.first.last] << gff
+                  end
+                end
               end
-            end
-            features << MiniFeature.new(:start => plf.start, :end => plf.end, :exons => exons, :utrs => utrs, :strand => plf.strand, :id => gff_id)
-          end #parentless features end
-      when "data"
-        ##each line is a data feature
-        File.open(track["file"], "r").each do |line|
-          start,stop,value = line.split(/\t/)
-          features << MiniFeature.new(:start => start.to_i, :end => stop.to_i, :segment_height => value.to_f)
+              #now flick through the parentless features and add any exons / UTRs
+              parentless_features.each do |plf|
+                require 'pp'
+                #pp parentless_features
+                gff_id = plf.attributes.select { |a| a.first == 'ID' }
+                gff_id = gff_id.first.last
+                exons = []
+                utrs = []
+                children = groups[gff_id] || children = []
+                children.each do |child|
+                  if child.feature == 'exon' or child.feature == 'CDS'
+                    exons += [child.start, child.end]
+                  elsif child.feature =~ /utr/i
+                    utrs += [child.start, child.end]
+                  end
+                end
+                features << MiniFeature.new(:start => plf.start, :end => plf.end, :exons => exons, :utrs => utrs, :strand => plf.strand, :id => gff_id)
+              end #parentless features end
+            when "data"
+              ##each line is a data feature
+              File.open(track["file"], "r").each do |line|
+                start, stop, value = line.split(/\t/)
+                features << MiniFeature.new(:start => start.to_i, :end => stop.to_i, :segment_height => value.to_f)
+              end
+          end #data end
+          features.each { |f| svg_track.add(f) }
+        end #track end
+        p.write(args[:outfile])
+      end
+
+      #Parses a GFF file into an Array of Bio::GFF::GFF3::Record[http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html] objects
+      #* +gff_file+ - a GFF-formatted file
+      #* +returns+ - an Array of Bio::GFF::GFF3::Record[http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html] objects
+      def self.parse_gff(gff_file)
+        require 'bio'
+        a = []
+        File.open(gff_file).each do |line|
+          next if line =~ /^#/
+          a << Bio::GFF::GFF3::Record.new(line)
         end
-      end #data end
-      features.each {|f| svg_track.add(f) }
-    end #track end
-    p.write(args[:outfile])
-  end
-  
-  def self.parse_gff(gff_file)
-    require 'bio'
-    a = []
-    File.open( gff_file ).each do |line|
-      next if line =~ /^#/
-     a << Bio::GFF::GFF3::Record.new(line)
-    end
-    a
-  end
-  
-  def add_track(args)
-    #sort out the colour/gradient options
-    [:fill_color, :exon_fill_color, :utr_fill_color].each do |colour_tag|
-      if Glyph.gradients.include?(args[colour_tag])
-        @svg.gradient(Glyph.gradient(args[colour_tag]) )
-        args[colour_tag] = "url(##{args[colour_tag]})"
-      elsif 
-        args[colour_tag].instance_of?(Hash)
-        @svg.gradient(args[colour_tag])
-        args[colour_tag] = "url(##{args[colour_tag][:id]})"
+        a
       end
-    end
-    @tracks << Track.new(args)
-    return @tracks.last
-  end
-  
-  def get_limits
-    @tracks.each do |track|
-      lowest = track.features.sort {|x,y| x.start <=> y.start}.first.start
-      highest = track.features.sort {|x,y| y.end <=> x.end}.first.end
-      @scale_start = lowest if lowest < @scale_start 
-      @scale_stop = highest if highest > @scale_stop
-      @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
-    end
-  end
-  
-  def draw_scale
-    Glyph.scale(:start => @scale_start, 
-                :stop => @scale_stop, 
-                :number_of_intervals => @num_intervals, :page_width => @width).each {|g| @svg.add_primitive(g)}
-  end
-  
-  def draw_label(args)
-    Glyph.label(:text => args[:text], 
-                :x => args[:x], 
-                :y => args[:y] ).each {|g| @svg.add_primitive(g)}
-  end
-  
-  def draw_generic(args) #remember presentation info comes from track@args when the track is defined
-    Glyph.generic(args).each {|g| @svg.add_primitive(g) }
-  end
-  
-  def draw_directed(args)
-      Glyph.directed(args).each {|g| @svg.add_primitive(g) }
-  end
-  
-  def draw_circle(args)
-      Glyph.circle(args).each {|g| @svg.add_primitive(g) }
-  end
-  
-  def draw_transcript(args)
-    Glyph.transcript(args).each {|g| @svg.add_primitive(g) }
-  end
-  
-  def draw_histogram(args)
-    Glyph.generic(args).each {|g| @svg.add_primitive(g) }
-  end
-  
-  def draw_up_triangle(args)
-    Glyph.up_triangle(args).each {|g| @svg.add_primitive(g) }
-  end
 
-  def draw_down_triangle(args)
-    Glyph.down_triangle(args).each {|g| @svg.add_primitive(g) }
-  end
+      #Calculates the colour or gradient for the supplied Bio::Graphics::Track objects and adds them to the Track array for the current Page
+      #* +args+ - an Array of Bio::Graphics::Track objects
+      #* +returns+ - the last element of the Track array
+      def add_track(args)
+        #sort out the colour/gradient options
+        [:fill_color, :exon_fill_color, :utr_fill_color].each do |colour_tag|
+          if Glyph.gradients.include?(args[colour_tag])
+            @svg.gradient(Glyph.gradient(args[colour_tag]))
+            args[colour_tag] = "url(##{args[colour_tag]})"
+          elsif args[colour_tag].instance_of?(Hash)
+            @svg.gradient(args[colour_tag])
+            args[colour_tag] = "url(##{args[colour_tag][:id]})"
+          end
+        end
+        @tracks << Track.new(args)
+        return @tracks.last
+      end
 
-  def draw_span(args)
-    Glyph.span(args).each {|g| @svg.add_primitive(g) }
-  end
-  
-  def draw_features(track) #sort out the input information into a user friendly format..
-    if [:histogram, "histogram"].include?(track.glyph) #do different stuff for data tracks...
+      #Calculates the Page scale-start and scale-stop position and the nucleotides per pixel for the current Page
+      def get_limits
+        @tracks.each do |track|
+          lowest = track.features.sort { |x, y| x.start <=> y.start }.first.start
+          highest = track.features.sort { |x, y| y.end <=> x.end }.first.end
+          @scale_start = lowest if lowest < @scale_start
+          @scale_stop = highest if highest > @scale_stop
+          @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
+        end
+      end
 
-      y = @track_top + (track.track_height)
-      max = track.max_y ? track.max_y : track.features.sort {|a,b| a.segment_height <=> b.segment_height}.last.segment_height
-      min = 0
-      if track.label
-        draw_label(:text => track.name, :y => @track_top += 30, :x => 3 )
+      #Adds the  Bio::Graphics::Primitive objects to the SVGEE object
+      def draw_scale
+        Glyph.scale(:start => @scale_start,
+                    :stop => @scale_stop,
+                    :number_of_intervals => @num_intervals, :page_width => @width).each { |g| @svg.add_primitive(g) }
+      end
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive object
+      def draw_label(args)
+        Glyph.label(:text => args[:text],
+                    :x => args[:x],
+                    :y => args[:y]).each { |g| @svg.add_primitive(g) }
+      end
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_generic(args) #remember presentation info comes from track@args when the track is defined
+        Glyph.generic(args).each { |g| @svg.add_primitive(g) }
+      end
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_directed(args)
+        Glyph.directed(args).each { |g| @svg.add_primitive(g) }
+      end
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_circle(args)
+        Glyph.circle(args).each { |g| @svg.add_primitive(g) }
       end
-      draw_label(:text => max, :x => to_px(@scale_stop - @scale_start ) + 5, :y => @track_top + 5)
-      draw_label(:text => min, :x => to_px(@scale_stop - @scale_start ) + 5, :y => @track_top + track.track_height + 5)
-      data_interval = max - min
-      data_per_px = track.track_height.to_f / data_interval.to_f
-      track.features.each do |f|
-        x = to_px(f.start - @scale_start)
-        width = to_px( (f.end - @scale_start) - (f.start - @scale_start) )
-        height = f.segment_height.to_f * data_per_px
-        y = @track_top + track.track_height - height + 5
-        #$stderr.puts f.segment_height, data_per_px, data_interval, max, min, "------"
-        self.send("draw_#{track.glyph}", {:x => x, 
-          :y => y, 
-          :width => width, 
-          :height => height  }.merge!(track.args) )
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_transcript(args)
+        Glyph.transcript(args).each { |g| @svg.add_primitive(g) }
       end
-      @track_top += (track.track_height) + 20
-    else ##following stuff for the features
-      if track.label
-        draw_label(:text => track.name, :y => @track_top += 30, :x => 3 )
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_histogram(args)
+        Glyph.generic(args).each { |g| @svg.add_primitive(g) }
+      end
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_up_triangle(args)
+        Glyph.up_triangle(args).each { |g| @svg.add_primitive(g) }
+      end
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_down_triangle(args)
+        Glyph.down_triangle(args).each { |g| @svg.add_primitive(g) }
+      end
+      #Adds the Bio::Graphics::Primitive objects to the SVGEE object
+      #* +args+ - an Array of Bio::Graphics::Primitive objects of the stated type
+      def draw_span(args)
+        Glyph.span(args).each { |g| @svg.add_primitive(g) }
       end
-      track.get_rows ##work out how many rows and which features belong in each row...
-      track.features.each_with_index do |f,index|       
-        x = to_px(f.start - @scale_start) #bottom left of feature
-        all_sub_blocks = []
 
-        #convert the exon and utr start stops to px start stops and px widths 
-        exons = []
-        if f.exons
-          f.exons.each_slice(2).each do |exon|
-            all_sub_blocks << exon
-            next if exon.nil?
-            exons << [to_px(exon[0] - @scale_start), to_px( (exon[1] - @scale_start) - (exon[0] - @scale_start)  )  ]
-          end
-        end
-        f.exons = exons
+      #Takes a Bio::Graphics::Track object and sorts out the input information into a user friendly format.
+      #
+      #It examines the the type of track and calculates the required parameters
+      #* +args+ - an Array of Bio::Graphics::Track object
+      def draw_features(track)
+        if [:histogram, "histogram"].include?(track.glyph) #do different stuff for data tracks...
 
-        utrs = []
-        if f.utrs
-          f.utrs.each_slice(2).each do |utr|
-            all_sub_blocks << utr
-            next if utr.nil?
-            utrs << [to_px(utr[0] - @scale_start), to_px( (utr[1] - @scale_start) - (utr[0] - @scale_start)  )  ]
+          y = @track_top + (track.track_height)
+          max = track.max_y ? track.max_y : track.features.sort { |a, b| a.segment_height <=> b.segment_height }.last.segment_height
+          min = 0
+          if track.label
+            draw_label(:text => track.name, :y => @track_top += 30, :x => 3)
           end
-        end
-        f.utrs = utrs
+          draw_label(:text => max, :x => to_px(@scale_stop - @scale_start) + 5, :y => @track_top + 5)
+          draw_label(:text => min, :x => to_px(@scale_stop - @scale_start) + 5, :y => @track_top + track.track_height + 5)
+          data_interval = max - min
+          data_per_px = track.track_height.to_f / data_interval.to_f
+          track.features.each do |f|
+            x = to_px(f.start - @scale_start)
+            width = to_px((f.end - @scale_start) - (f.start - @scale_start))
+            height = f.segment_height.to_f * data_per_px
+            y = @track_top + track.track_height - height + 5
+            #$stderr.puts f.segment_height, data_per_px, data_interval, max, min, "------"
+            self.send("draw_#{track.glyph}", {:x => x,
+                                              :y => y,
+                                              :width => width,
+                                              :height => height}.merge!(track.args))
+          end
+          @track_top += (track.track_height) + 20
+        else ##following stuff for the features
+          if track.label
+            draw_label(:text => track.name, :y => @track_top += 30, :x => 3)
+          end
+          track.get_rows ##work out how many rows and which features belong in each row...
+          track.features.each_with_index do |f, index|
+            x = to_px(f.start - @scale_start) #bottom left of feature
+            all_sub_blocks = []
+
+            #convert the exon and utr start stops to px start stops and px widths
+            exons = []
+            if f.exons
+              f.exons.each_slice(2).each do |exon|
+                all_sub_blocks << exon
+                next if exon.nil?
+                exons << [to_px(exon[0] - @scale_start), to_px((exon[1] - @scale_start) - (exon[0] - @scale_start))]
+              end
+            end
+            f.exons = exons
+
+            utrs = []
+            if f.utrs
+              f.utrs.each_slice(2).each do |utr|
+                all_sub_blocks << utr
+                next if utr.nil?
+                utrs << [to_px(utr[0] - @scale_start), to_px((utr[1] - @scale_start) - (utr[0] - @scale_start))]
+              end
+            end
+            f.utrs = utrs
+
+            #if there are any intron like gaps.. get where they would be
+            if not all_sub_blocks.empty?
+              all_sub_blocks = all_sub_blocks.sort { |a, b| a.first <=> b.first }
+              all_sub_blocks.each_index do |i|
+                next if i + 1 == all_sub_blocks.length or all_sub_blocks[i].last >= all_sub_blocks[i + 1].first #skip if there is no gap
+                f.block_gaps << [to_px(all_sub_blocks[i].last - @scale_start), to_px((all_sub_blocks[i + 1].first - @scale_start) - (all_sub_blocks[i].last - @scale_start))]
+              end
+            end
 
-        #if there are any intron like gaps.. get where they would be
-        if not all_sub_blocks.empty? 
-          all_sub_blocks = all_sub_blocks.sort {|a,b| a.first <=> b.first}
-          all_sub_blocks.each_index do |i|
-            next if i + 1 == all_sub_blocks.length or all_sub_blocks[i].last >= all_sub_blocks[i + 1].first  #skip if there is no gap
-            f.block_gaps << [to_px(all_sub_blocks[i].last  - @scale_start) , to_px( (all_sub_blocks[i + 1].first - @scale_start) - (all_sub_blocks[i].last - @scale_start) ) ]
+            width = to_px((f.end - @scale_start) - (f.start - @scale_start))
+            if track.min_width and width < track.min_width
+              width = track.min_width
+            end
+            y = @track_top + (track.feature_rows[index] * 2 * track.feature_height)
+
+            self.send("draw_#{track.glyph}", {:x => x,
+                                              :y => y,
+                                              :width => width,
+                                              :strand => f.strand,
+                                              :exons => f.exons,
+                                              :utrs => f.utrs,
+                                              :block_gaps => f.block_gaps,
+                                              :height => track.feature_height
+            }.merge!(track.args))
+
+            if f.id
+              draw_label(:y => y, :x => x + width +2, :text => f.id)
+            end
           end
+          @track_top += (track.feature_height * track.number_rows * 2) + 20
         end
 
-        width = to_px( (f.end - @scale_start) - (f.start - @scale_start) )
-        if track.min_width and width < track.min_width
-          width = track.min_width
-        end
-        y = @track_top + (track.feature_rows[index] * 2 * track.feature_height)
+        @height = @track_top + 100 #fudge...
+        @svg.update_height(@height)
+                               #@svg.update_width(@width + 200)
 
-        self.send("draw_#{track.glyph}", {:x => x, 
-          :y => y, 
-          :width => width, 
-          :strand => f.strand, 
-          :exons => f.exons, 
-          :utrs => f.utrs, 
-          :block_gaps => f.block_gaps, 
-          :height => track.feature_height
-           }.merge!(track.args) )
-          
-        if f.id
-          draw_label(:y => y, :x => x + width +2, :text => f.id)
+      end
+      #Provides the number of pixels required for a given number of nucleotides, e.g the length of a certain exon
+      #* +num+ - the number of nucleotides
+      #* +returns+ -  the required number of pixels to draw the object
+      def to_px(num)
+        (num.to_f / @nt_per_px_x.to_f)
+      end
+
+      #Pulls together all track information to create svg text which will draw all the features on the page to scale
+      #Uses the methods +get_limits+ and +draw_scale+ and then +draw_feature+ for each track on the page
+      def get_markup
+        get_limits
+        draw_scale
+        @tracks.each do |track|
+          draw_features(track)
         end
+        @svg.draw
+      end
+      #Prints out the svg text
+      def draw
+        puts get_markup
       end
-      @track_top += (track.feature_height * track.number_rows * 2) + 20
-    end
-    
-    @height = @track_top + 100 #fudge...
-    @svg.update_height(@height)
-    #@svg.update_width(@width + 200)
 
-  end  
-  
-  def to_px(num)
-    (num.to_f / @nt_per_px_x.to_f)
-  end
-  
-  def get_markup
-    get_limits
-    draw_scale
-    @tracks.each do |track|
-      draw_features(track)
+      #Writes the svg text to a file
+      #* +file+ - the file to which the svg text should be written
+      def write(file)
+        File.open(file, 'w').write(get_markup)
+      end
     end
-    @svg.draw
-  end
-  
-  def draw
-    puts get_markup
-  end
-  
-  def write(file)
-    File.open(file, 'w').write(get_markup)
   end
-end
-end
 end