bio-svgenes 0.1.1 → 0.1.2

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bio-svgenes.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-svgenes"
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]
-  s.date = "2012-11-21"
+  s.date = "2012-11-22"
   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 = [

data/lib/bio/graphics/glyph.rb

@@ -1,3 +1,5 @@
+module Bio
+  class Graphics
 class Glyph
   attr_reader :glyphs
   #holds a load of definitions for glyphs .. a glyph is an array of primitives... 
@@ -12,7 +14,7 @@ class Glyph
       :x_round => 1, 
       :y_round => 1, 
       :style => "fill-opacity:0.4;"}.merge!(args)
-    [Primitive.new(:rectangle, args)]
+    [Bio::Graphics::Primitive.new(:rectangle, args)]
   end 
   
   def self.directed(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
@@ -29,7 +31,7 @@ class Glyph
       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]}"      
       end
-    [Primitive.new(:polygon, args)]
+    [Bio::Graphics::Primitive.new(:polygon, args)]
   end
   
   def self.transcript(args)
@@ -65,7 +67,7 @@ class Glyph
                                     :style => args[:utr_style] )
         ##draw the other(s!) 
         args[:utrs].each do |utr|
-          composite <<  Primitive.new(:rectangle, {
+          composite <<  Bio::Graphics::Primitive.new(:rectangle, {
                                                     :x => utr.first, 
                                                     :width => utr.last, 
                                                     :y => args[:y], 
@@ -90,7 +92,7 @@ class Glyph
       end
       #draw any remaining exons
       args[:exons].each do |exon|
-          composite <<  Primitive.new(:rectangle, {
+          composite <<  Bio::Graphics::Primitive.new(:rectangle, {
                                                     :x => exon[0], 
                                                     :width => exon[1], 
                                                     :y => args[:y], 
@@ -103,7 +105,7 @@ class Glyph
       if args[:gap_marker] == "angled" and not args[:block_gaps].empty?
         args[:block_gaps].each do |gap|
           points = "#{gap.first},#{args[:y] + (args[:height]/2) } #{gap.first + (gap.last/2)},#{args[:y]} #{gap.first + gap.last},#{args[:y] + (args[:height]/2)}"
-          composite << Primitive.new(:polyline, {
+          composite << Bio::Graphics::Primitive.new(:polyline, {
                                                  :points => points, 
                                                  :stroke => args[:line_color], 
                                                  :stroke_width => args[:line_width], 
@@ -112,7 +114,7 @@ class Glyph
         end
       else
         #add line
-        composite << Primitive.new(:line, {
+        composite << Bio::Graphics::Primitive.new(:line, {
                                             :x1 => args[:x], 
                                             :x2 => "#{args[:x] + args[:width]}", 
                                             :y1 => args[:y] + (args[:height]/2), 
@@ -135,7 +137,7 @@ class Glyph
     interval_width =  full_dist / args[:number_of_intervals] 
 
 
-    a = [Primitive.new(:line, 
+    a = [Bio::Graphics::Primitive.new(:line, 
                                :stroke => 'black', 
                                :stroke_width => 1, 
                                :x1 => 1, :x2 => args[:page_width] * 1.1, 
@@ -146,7 +148,7 @@ class Glyph
     px_per_nt = full_dist / args[:page_width]
     marks.each do |mark|
       x = (mark.to_f - first_mark )/ px_per_nt
-      a << Primitive.new(:rectangle, 
+      a << Bio::Graphics::Primitive.new(:rectangle, 
                          :x => x, 
                          :y => 20, 
                          :stroke => 'black', 
@@ -154,7 +156,7 @@ class Glyph
                          :width => 1, 
                          :height => 5 )
                          
-      a << Primitive.new(:text, 
+      a << Bio::Graphics::Primitive.new(:text, 
                          :x => x, 
                          :y => 40, :fill => 'black', 
                          :text => mark, 
@@ -164,7 +166,7 @@ class Glyph
   end
   
   def self.label(args)
-    [Primitive.new(:text, 
+    [Bio::Graphics::Primitive.new(:text, 
                    :text => args[:text], 
                    :x => args[:x], 
                    :y => args[:y], 
@@ -239,3 +241,5 @@ class Glyph
   
   
 end
+end
+end

data/lib/bio/graphics/mini_feature.rb

@@ -1,3 +1,5 @@
+module Bio
+  class Graphics
 class MiniFeature
   attr_accessor :start, :end, :strand, :exons, :utrs, :block_gaps, :segment_height, :id
   def initialize(args)
@@ -11,3 +13,6 @@ class MiniFeature
     @segment_height = args[:segment_height]
   end
 end
+
+end
+end

data/lib/bio/graphics/page.rb

@@ -1,3 +1,5 @@
+module Bio
+  class Graphics
 class Page
   
   def initialize(args)
@@ -263,3 +265,5 @@ class Page
     File.open(file, 'w').write(get_markup)
   end
 end
+end
+end

data/lib/bio/graphics/primitive.rb

@@ -1,3 +1,6 @@
+module Bio
+  class Graphics
+
 class Primitive
   attr_reader :primitive
   
@@ -14,4 +17,7 @@ class Primitive
     end
   end
   
+end
+
+end
 end

data/lib/bio/graphics/svgee.rb

@@ -1,3 +1,6 @@
+module Bio
+  class Graphics
+
 class SVGEE
   attr_reader :primitives, :defs, :supported_primitives
   def initialize(args)
@@ -33,7 +36,7 @@ class SVGEE
     else
       add self.send("#{primitive}_tag", args)
     end
-    return Primitive.new(primitive, args)
+    return Bio::Graphics::Primitive.new(primitive, args)
   end
   
   def link_and_tag(primitive, args)
@@ -109,6 +112,8 @@ class SVGEE
   
 end
 
+end
+end
 =begin How to use SVGEE
 s = SVGEE.new
 s.gradient(:radial => "grad1", :cx => 50, :cy => 50, :r => 50, :fx => 50, :fy => 50, :stops => [ {:offset => 0, :color => 'rgb(255,255,255)', :opacity => 0},  {:offset => 100, :color => 'rgb(0,0,255)', :opacity => 1},] )

data/lib/bio/graphics/track.rb

@@ -1,3 +1,6 @@
+module Bio
+  class Graphics
+
 class Track
   attr_reader :glyph, :name, :label, :args, :track_height, :scale, :max_y
   attr_accessor :features, :feature_rows, :name, :number_rows, :feature_height
@@ -47,3 +50,7 @@ class Track
   end
   
 end
+
+
+end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-svgenes
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-21 00:00:00.000000000 Z
+date: 2012-11-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &70210599098300 !ruby/object:Gem::Requirement
+  requirement: &70140177159960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70210599098300
+  version_requirements: *70140177159960
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70210599097720 !ruby/object:Gem::Requirement
+  requirement: &70140177159360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *70210599097720
+  version_requirements: *70140177159360
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70210599113460 !ruby/object:Gem::Requirement
+  requirement: &70140177175080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70210599113460
+  version_requirements: *70140177175080
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &70210599112780 !ruby/object:Gem::Requirement
+  requirement: &70140177174420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70210599112780
+  version_requirements: *70140177174420
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70210599112100 !ruby/object:Gem::Requirement
+  requirement: &70140177173780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,7 +65,7 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *70210599112100
+  version_requirements: *70140177173780
 description: This bio-gem facilitates the creation of pretty, publication quality
   SVG images from feature data.
 email: maclean.daniel@gmail.com
@@ -122,7 +122,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2824846248775866676
+      hash: 90867079773197497
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: