bio-svgenes 0.3.1 → 0.3.2

data/lib/bio/graphics/mini_feature.rb

@@ -1,30 +1,37 @@
 module Bio
   class Graphics
+    
     ##
-    #The MiniFeature class represents any feature (e.g. a gene, transcript, exon, start codon, etc) on a track.
-    #
+    #A Bio::Graphics::MiniFeature object represents a single genomic feature (e.g. a gene, transcript, exon, start codon, etc), it is a lightweight object that 
+    #holds the minimum information needed to do the render.
 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
+  #== args
+  #* :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 for the feature such as the gene name or transcript ID
+  #* :segment_height = the height of the current feature
   #
-  #==Example usage
+  #== 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
+  ## 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 created and added to Bio::Graphics::Track objects which will take responsibility for positioning and syling them.#
   def initialize(args)
     @start = args[:start]
     @end = args[:end]

data/lib/bio/graphics/page.rb

@@ -2,31 +2,17 @@ module Bio
   class Graphics
 
     ##
-    #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
+    #The Bio::Graphics::Page class represents the page of the final rendered SVG and is the top level container into which Bio::Graphics::Tracks are added.
+    #It will contain a scale
+    #and all the tracks along with their features. The scale is calculated 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)
-      #
+      #== args
+      #* :height = the minimum height of the rendered page
+      #* :width = the minimum width of the rendered page
+      #* :background_color = the background color of the page (default none), can be any SVG colour eg rgb(256,0,0) or #FF0000
       def initialize(args)
         @height = args[:height]
         @width = args[:width]
@@ -47,9 +33,9 @@ module Bio
         #  @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
 
+      #Takes a custom-written json file and uses it to generate an SVG document based on the information in that page.
+      #* :json a JSON file describing the parameters and files needed to build an SVG document
       def self.from_json(args)
         require 'rubygems'
         require 'json'
@@ -120,8 +106,8 @@ module Bio
       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
+      #* 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 = []
@@ -132,9 +118,91 @@ module Bio
         a
       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
+      #adds a new Bio::Graphics::Track object to the current Bio::Graphics::Page object
+      #
+      #==args
+      #
+      #* :glyph = one of Bio::Graphics::Glyphs#glyphs currently 
+      # [: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 Bio::Graphics::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 Bio::Graphics::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 Bio::Graphics::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
+      #=== returns
+      # a new Bio::Graphics::Track object
       def add_track(args)
         #sort out the colour/gradient options
         [:fill_color, :exon_fill_color, :utr_fill_color].each do |colour_tag|
@@ -161,12 +229,13 @@ module Bio
         end
       end
 
-      #Adds the  Bio::Graphics::Primitive objects to the SVGEE object
+      #Adds scale bar to the list of objects to be rendered in the final
       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)
@@ -174,48 +243,41 @@ module Bio
                     :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
-      #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
-      #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
 
-      #Takes a Bio::Graphics::Track object and sorts out the input information into a user friendly format.
+      #Takes a Bio::Graphics::Track object and does the work to draw features
       #
       #It examines the the type of track and calculates the required parameters
       #* +args+ - an Array of Bio::Graphics::Track object
@@ -311,15 +373,12 @@ module Bio
                                #@svg.update_width(@width + 200)
 
       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
+      #Calculates the pixel value for a given number
       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
+      #generates the SVG text
       def get_markup
         get_limits
         draw_scale
@@ -328,13 +387,12 @@ module Bio
         end
         @svg.draw
       end
-      #Prints out the svg text
+      #Prints the svg text to STDOUT
       def draw
         puts get_markup
       end
 
-      #Writes the svg text to a file
-      #* +file+ - the file to which the svg text should be written
+      #Writes the SVG text to a file
       def write(file)
         File.open(file, 'w').write(get_markup)
       end

data/lib/bio/graphics/primitive.rb

@@ -1,14 +1,17 @@
 module Bio
   class Graphics
-#The Primitive class is used to hold information about Glyphs.
-#They contain a Glyph type and then a Hash of parameters pertinent for that Glyph
+
+#The Bio::Graphics::Primitive class is used to describe simple shapes. It is basically a simple data container that
+#has lots of dynamically set instance variables including a name. The Bio::Graphics::Primitive object is later translated
+#to an SVG string by the Bio::Graphics::SVGEE class. 
 class Primitive
   attr_reader :primitive
-  #Creates a new Primitive and initialises the Hash keys into instance variables
+  
+  #Creates a new Primitive and initialises instance variables dynamically from the args hash 
   #
-  #+args+
-  #* primitive = the Primitive type
-  #* args = a hash of parameters needed to initialise the given Glyph type
+  #== args+
+  #* :primitive = the Primitive type
+  #* args = a hash of parameters needed to describe the attributes of the primitive type
   def initialize(primitive,args)
     @primitive = primitive
     args.each_key do |k|
@@ -16,10 +19,10 @@ class Primitive
     end 
   end
 
-  #Updates a Primitive and initialises any new parameters into instance variables
+  #Updates a Primitive and sets the provided values as instance variables
   #
-  #+args+
-  #* args = a hash of new parameters for the given Glyph type
+  #== args
+  #* args = a hash of new parameters for the given primitive type
   def update(args)
     args.each_key do |k|
       self.instance_variable_set("@#{k}", args[k])

data/lib/bio/graphics/svgee.rb

@@ -1,19 +1,15 @@
 module Bio
   class Graphics
- #The SVGEE class is used to create the text that will go into the final SVG file.
- #It takes information from the supplied Glyph objects, parses them and creates the SVG text
-  #necessary to display the given glyphs.
+    
+ #The Bio::Graphics::SVGEE class takes argument information in a hash and creates SVG Markup tags, which it will draw
 class SVGEE
   attr_reader :primitives, :defs, :supported_primitives
-  #Creates a new SVGEE object which will contain all the necessary objects to display all the features on a page
+  #Creates a new Bio::Graphics::SVGEE object which will contain all the necessary objects to display all the features on a page
   #
-  #+args+
-  #* width = the amount of the page width the svg should take up (100%)
-  #* height = the amount of the page height the svg should take up (100%)
-  #* style = the svg style information
-  #* primitives = an array of glyphs
-  #* defs =  the gradients that will be used in the SVG
-  #* \supported_primitives = a list of permitted Glyphs
+  #== args
+  #* :width = the width of the SVG page (100%)
+  #* :height = the amount of the page height the svg should take up (100%)
+  #* :style = the svg style information
   def initialize(args)
     opts = {:width => '100%', :height => '100%'}.merge!(args)
     @width = opts[:width]
@@ -23,10 +19,12 @@ class SVGEE
     @defs = []
     @supported_primitives = [:circle, :rectangle, :ellipse, :line, :polyline, :text]
   end
+  
   #Produces the opening text for an svg file
   def open_tag
     %{<svg xmlns="http://www.w3.org/2000/svg" version="1.1" width="#{@width}" height="#{@height}" style="#{@style}" xmlns:xlink="http://www.w3.org/1999/xlink">}
   end
+  
   #Produces the closing text for an svg file
   def close_tag
     %{</svg>}

data/lib/bio/graphics/track.rb

@@ -1,11 +1,95 @@
 module Bio
   class Graphics
-  #The Track class holds and organises the features, ordering them into different rows if they overlap
-
+    
+  #The Bio::Graphics::Track object acts as a container for Bio::Graphics::MiniFeature objects. The Bio::Graphics::Track takes style information on instantiation.
+  #Style information is applied to each feature in the track by the track
 class Track
   attr_reader :glyph, :name, :label, :args, :track_height, :scale, :max_y, :min_width
   attr_accessor :features, :feature_rows, :name, :number_rows, :feature_height
-  #Creates a new Track
+  
+  #Creates a new Bio::Graphics::Track
+  #
+  #==args
+  #
+  #* :glyph = one of Bio::Graphics::Glyphs#glyphs currently 
+  # [: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 Bio::Graphics::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 Bio::Graphics::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 Bio::Graphics::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
   def initialize(args)
     @args = {:glyph => :generic, 
              :name => "feature_track", 
@@ -27,14 +111,13 @@ class Track
 
   end
   
-  #Adds a new MiniFeature to the the @features array
+  #Adds a new Bio::Graphics::MiniFeature object to the current Bio::Graphics::Track
   def add(feature)
     @features << feature
   end
 
   #Calculates how many rows are needed per track for overlapping features
-  #and which row each feature should be in
-
+  #and which row each feature should be in. Usually only called by the enclosing Bio::Graphics::Page object.
   def get_rows
     current_row = 1
     @feature_rows = Array.new(@features.length,1)
@@ -49,12 +132,11 @@ class Track
     end
   end
 
-  #Calculates if two MiniFeature objects overlap by examining their start and end positions.
-  #If two features overlap then then will be placed on separate rows of the track
+  #Calculates whether two Bio::Graphics::MiniFeature objects overlap by examining their start and end positions.
   #
   #+args+
-  #* f1 - a MiniFeature object
-  #* f2 - a MiniFeature object
+  #* f1 - a Bio::Graphics::MiniFeature object
+  #* f2 - a Bio::Graphics::MiniFeature object
   def overlaps(f1, f2)
     (f1.start >= f2.start and f1.start <= f2.end) or (f1.end >= f2.start and f1.end <= f2.end)
   end