bio-svgenes 0.3.1 → 0.3.2

data/doc/rdoc-style.css

@@ -0,0 +1,208 @@
+
+body {
+    font-family: Verdana,Arial,Helvetica,sans-serif;
+    font-size:   90%;
+    margin: 0;
+    margin-left: 40px;
+    padding: 0;
+    background: white;
+}
+
+h1,h2,h3,h4 { margin: 0; color: #efefef; background: transparent; }
+h1 { font-size: 150%; }
+h2,h3,h4 { margin-top: 1em; }
+
+a { background: #eef; color: #039; text-decoration: none; }
+a:hover { background: #039; color: #eef; }
+
+/* Override the base stylesheet's Anchor inside a table cell */
+td > a {
+  background: transparent;
+  color: #039;
+  text-decoration: none;
+}
+
+/* and inside a section title */
+.section-title > a {
+  background: transparent;
+  color: #eee;
+  text-decoration: none;
+}
+
+/* === Structural elements =================================== */
+
+div#index {
+    margin: 0;
+    margin-left: -40px;
+    padding: 0;
+    font-size: 90%;
+}
+
+
+div#index a {
+    margin-left: 0.7em;
+}
+
+div#index .section-bar {
+   margin-left: 0px;
+   padding-left: 0.7em;
+   background: #ccc;
+   font-size: small;
+}
+
+
+div#classHeader, div#fileHeader {
+    width: auto;
+    color: white;
+    padding: 0.5em 1.5em 0.5em 1.5em;
+    margin: 0;
+    margin-left: -40px;
+    border-bottom: 3px solid #006;
+}
+
+div#classHeader a, div#fileHeader a {
+    background: inherit;
+    color: white;
+}
+
+div#classHeader td, div#fileHeader td {
+    background: inherit;
+    color: white;
+}
+
+
+div#fileHeader {
+    background: #057;
+}
+
+div#classHeader {
+    background: #048;
+}
+
+
+.class-name-in-header {
+  font-size:  180%;
+  font-weight: bold;
+}
+
+
+div#bodyContent {
+    padding: 0 1.5em 0 1.5em;
+}
+
+div#description {
+    padding: 0.5em 1.5em;
+    background: #efefef;
+    border: 1px dotted #999;
+}
+
+div#description h1,h2,h3,h4,h5,h6 {
+    color: #125;;
+    background: transparent;
+}
+
+div#validator-badges {
+    text-align: center;
+}
+div#validator-badges img { border: 0; }
+
+div#copyright {
+    color: #333;
+    background: #efefef;
+    font: 0.75em sans-serif;
+    margin-top: 5em;
+    margin-bottom: 0;
+    padding: 0.5em 2em;
+}
+
+
+/* === Classes =================================== */
+
+table.header-table {
+    color: white;
+    font-size: small;
+}
+
+.type-note {
+    font-size: small;
+    color: #DEDEDE;
+}
+
+.xxsection-bar {
+    background: #eee;
+    color: #333;
+    padding: 3px;
+}
+
+.section-bar {
+   color: #333;
+   border-bottom: 1px solid #999;
+    margin-left: -20px;
+}
+
+
+.section-title {
+    background: #79a;
+    color: #eee;
+    padding: 3px;
+    margin-top: 2em;
+    margin-left: -30px;
+    border: 1px solid #999;
+}
+
+.top-aligned-row {  vertical-align: top }
+.bottom-aligned-row { vertical-align: bottom }
+
+/* --- Context section classes ----------------------- */
+
+.context-row { }
+.context-item-name { font-family: monospace; font-weight: bold; color: black; }
+.context-item-value { font-size: small; color: #448; }
+.context-item-desc { color: #333; padding-left: 2em; }
+
+/* --- Method classes -------------------------- */
+.method-detail {
+    background: #efefef;
+    padding: 0;
+    margin-top: 0.5em;
+    margin-bottom: 1em;
+    border: 1px dotted #ccc;
+}
+.method-heading {
+  color: black;
+  background: #ccc;
+  border-bottom: 1px solid #666;
+  padding: 0.2em 0.5em 0 0.5em;
+}
+.method-signature { color: black; background: inherit; }
+.method-name { font-weight: bold; }
+.method-args { font-style: italic; }
+.method-description { padding: 0 0.5em 0 0.5em; }
+
+/* --- Source code sections -------------------- */
+
+a.source-toggle { font-size: 90%; }
+div.method-source-code {
+    background: #262626;
+    color: #ffdead;
+    margin: 1em;
+    padding: 0.5em;
+    border: 1px dashed #999;
+    overflow: hidden;
+}
+
+div.method-source-code pre { color: #ffdead; overflow: hidden; }
+
+/* --- Ruby keyword styles --------------------- */
+
+.standalone-code { background: #221111; color: #ffdead; overflow: hidden; }
+
+.ruby-constant  { color: #7fffd4; background: transparent; }
+.ruby-keyword { color: #00ffff; background: transparent; }
+.ruby-ivar    { color: #eedd82; background: transparent; }
+.ruby-operator  { color: #00ffee; background: transparent; }
+.ruby-identifier { color: #ffdead; background: transparent; }
+.ruby-node    { color: #ffa07a; background: transparent; }
+.ruby-comment { color: #b22222; font-weight: bold; background: transparent; }
+.ruby-regexp  { color: #ffa07a; background: transparent; }
+.ruby-value   { color: #7fffd4; background: transparent; }

data/examples/example.rb

@@ -1,24 +1,28 @@
 #!/usr/bin/env ruby
 #
-#  untitled
+#  example.rb
 #
 #  Created by Dan MacLean (TSL) on 2012-09-28.
 #  Copyright (c)  . All rights reserved.
 ###################################################
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+##A very straightforward example that creates all the features and tracks explicitly.
+
 
 require 'bio-svgenes'
 
+##create the page
 p = Bio::Graphics::Page.new(:width => 800, 
              :height => 200, 
-             :number_of_intervals => 10)
-             
+             :number_of_intervals => 10
+             )
              
+##add a generic glyph track             
 generic_track = p.add_track(:glyph => :generic, 
                             :name => 'generic_features', 
                             :label => true  )
-                            
+
+##and some features                            
 feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '+', :id => "MyFeature")
 generic_track.add(feature1) 
 feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
@@ -33,7 +37,7 @@ feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
 generic_track.add(feature2)
 
 
-
+##another generic track
 generic_track = p.add_track(:glyph => :generic, :name => 'more_generic_features', :label => true, :fill_color => 'green' )
 
 feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
@@ -43,7 +47,7 @@ generic_track.add(feature1)
 feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
 generic_track.add(feature1)
 
-
+##another generic 
 generic_track = p.add_track(:glyph => :generic, 
                             :name => 'yet_more_generic_features', 
                             :label => true, 

data/examples/{make_example.rb → example2.rb}

@@ -1,18 +1,8 @@
 #!/usr/bin/env ruby
-#
-#  untitled
-#
-#  Created by Dan MacLean (TSL) on 2013-01-18.
-#  Copyright (c)  . All rights reserved.
-###################################################
+#an example that loads data and renders different features from a gff
+#will select any features in ['gene', 'mRNA','cDNA_match', 'microarray_probe', 'insertion','deletion','substitution','transposable_element_insertion_site'] and
+#render these
 
-##to do:
-## background colour
-## single nt features : minimum size on circles, squares, triangles, diamonds, span (t bar)
-## label sizes
-## label positions 
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'bio-svgenes'
 
 
@@ -129,10 +119,9 @@ end
 
 
 all_features = Bio::Graphics::Page.parse_gff( ARGV[0] )
-puts all_features.length
-#all_features.collect {|f| f.feature }.uniq.each do | feature_type |
+
 ['gene', 'mRNA','cDNA_match', 'microarray_probe', 'insertion','deletion','substitution','transposable_element_insertion_site'].each do |feature_type|
-#['gene', 'mRNA','cDNA_match', 'microarray_probe','transposable_element_insertion_site'].each do |feature_type|
+
   puts "rendering #{feature_type}"
     case feature_type
     when 'gene'

data/lib/bio/graphics/glyph.rb

@@ -1,40 +1,62 @@
 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.
-    #
 
+  #A glyph is a particular shape that represents a genomic feature. Bio::Graphics::Glyph objects represent glyphs. Bio::Graphics::Glyphs are created internally according to
+  #specification from the Bio::Graphics::Track and not instantiated directly by the user.
+  #Internally, these are constructed as an array of Bio::Graphics::Primitive objects, which are collections of simple shapes, combined appropriately to make a glyph
 class Glyph
 
   #The different type of Glyphs are:
-  #* generic
-  #* circle
-  #* directed
-  #* \down_triangle
-  #* \up_triangle
-  #* span
-  #* transcript
-  #* scale
-  #* label
-  #* histogram
+  #* :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... 
+  #only glyphs defined here will be allowed 
   @glyphs = [:generic, :directed, :transcript, :scale, :label, :histogram, :circle, :down_triangle, :up_triangle, :span]
-  #Creates a generic glyph, which is a rectangle
+  
+  #A generic glyph is a block of colour that displays no specific directional information attached.
   #
-  #+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 = the height of the Glyph (default = 10)
+  #* :fill_color = the fill colour 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
+  # [: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
+  #        }, ]
+  # }  #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :x_round = x-axis radius of the ellipse used to round off the corners of the rectangle (default = 1)
+  #* :y_round = y-axis radius of the ellipse used to round off the corners of the rectangle (default = 1)
+  #* :style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
+  #* :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #* :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #
+  #=== returns
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects
+  def self.generic(args)
     args = { 
       :height => 10, 
       :fill_color => 'red', 
@@ -46,17 +68,38 @@ attr_reader :glyphs
     [Bio::Graphics::Primitive.new(:rectangle, args)]
   end
 
-  #Creates a circular Glyph
+  #A circular glyph centered on the start of the feature it represents
   #
-  #+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
-
+  #== args
+  #* :radius = the radius of the circle  (default = 10)
+  #* :fill_color = the fill colour 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
+  # [: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
+  #        }, ]
+  # }  #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;"
+  #* :x = base x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #* :y = base y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #
+  #=== returns
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects
   def self.circle(args) 
     args = { 
       :radius => 10, 
@@ -70,18 +113,41 @@ attr_reader :glyphs
     [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
+  #A polygon glyph with a point on the end that represents the features strand and direction
+  #== args
+  #* :width = the width of the feature in px
+  #* :fill_color = the fill colour 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
+  # [: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
+  #        }, ]
+  # }
+  #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;"
+  #* :strand = the strand on which the feature is located. May be '+' or '-'
+  #* :points = the x and y axis coordinates that make up the corners of the polygon, calculated and added by the Bio::Graphics::Page object
+  #* :x = base x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #* :y = base y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #The points of the polygon are calculated form the +:x+ and +:y+ co-ordinates
+  #
+  #=== returns
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects 
   def self.directed(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
     args = {
       
@@ -99,17 +165,38 @@ attr_reader :glyphs
       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
-
+  
+  #A downward-pointing triangle glyph
+  #== args
+  #* :height = the height of the Glyph (default = 10)
+  #* :fill_color = the fill colour 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
+  # [: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
+  #        }, ]
+  # } #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
+  #* :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #* :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #
+  #=== returns
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects
   def self.down_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
     args = {
       
@@ -122,17 +209,39 @@ attr_reader :glyphs
       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
-
+  
+  #An upward-pointing triangle glyph
+  #== args
+  #* :height = the height of the Glyph (default = 10)
+  #* :fill_color = the fill colour 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
+  # [: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
+  #        }, ]
+  # }
+  #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
+  #* :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #* :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #
+  #=== returns
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects
   def self.up_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
     args = {
       :height => 10, 
@@ -143,16 +252,40 @@ attr_reader :glyphs
       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
+  
+  #A line (span) glyph
   #
   #+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
+  #* :height = the height of the Glyph (default = 10)
+  #* :fill_color = the fill colour 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
+  # [: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
+  #        }, ]
+  # }
+  #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :stroke_width = The width of the outline stroke (default = 1)
+  #* :style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
+  #* :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #* :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #
+  #=== returns
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects
   def self.span(args)
     args = {
       :height => 10,
@@ -167,26 +300,69 @@ attr_reader :glyphs
     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
+  
+  #Creates a transcript glyph, which is a composite glyph containing generic glyphs for the exons/utrs and a directed glyph
+  #at the end. The glyphs are joined by lines.
   #
-  #+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
+  #== args
+  #* :height = the height of the Glyph (default = 10)
+  #* :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;" 
+  #* :block_gaps = gaps between the rendered blocks - calculated internally by Bio::Graphics::Page object
+  #* :gap_marker = style of the line between blocks - either angled or straight
+  #* :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #* :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object
+  #
+  #+returns+
+  #
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects
   def self.transcript(args)
       args = {
       :height => 10, 
@@ -279,18 +455,18 @@ attr_reader :glyphs
       end
       composite
   end
-  #Creates the scale across the top of the SVG page
+  
+  #Glyph for the scale across the top of the rendered 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
+  #== args
+  #* :start = the start of the scale, usually added by the Bio::Graphics::Page object
+  #* :stop = the end of the scale, usually added by the Bio::Graphics::Page object
+  #* :number_of_intervals = the number of tick-marks the scale will marked with
+  #* :page_width = the minimum width of the page, usually updated by the Bio::Graphics::Page object
   #
   #+returns+
   #
-  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Primitive objects (of type 'line', 'rectangle' and 'text')
-
+  #* An Array[http://www.ruby-doc.org/core-2.0/Array.html] of Bio::Graphic::Primitive objects (of type 'line', 'rectangle' and 'text')
   def self.scale(args)
     first_mark = args[:start]
     last_mark = args[:stop] 
@@ -327,15 +503,15 @@ attr_reader :glyphs
     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
-
+  #* :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], 
@@ -344,26 +520,17 @@ attr_reader :glyphs
                    :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
+  #Sets the the type (linear or radial) and colours for a pre-defined gradient
   #
-  #+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
-
+  #== args
+  #* gradient = a pre-defined gradient type, one of 
+  # [: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