bio-svgenes 0.3.2 → 0.3.3

data/VERSION

@@ -1 +1 @@
-0.3.2
+0.3.3

data/bio-svgenes.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-svgenes"
-  s.version = "0.3.2"
+  s.version = "0.3.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]
-  s.date = "2013-04-10"
+  s.date = "2013-06-06"
   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/examples/example.rb

@@ -8,7 +8,7 @@
 
 ##A very straightforward example that creates all the features and tracks explicitly.
 
-
+require 'rubygems'
 require 'bio-svgenes'
 
 ##create the page
@@ -242,6 +242,13 @@ feature3 = Bio::Graphics::MiniFeature.new(:start => 923,
                            :utrs => [923,1000,2000,2345])
 transcript_track.add(feature3)
 
+feature3 = Bio::Graphics::MiniFeature.new(:start => 923, 
+                           :end => 2345, 
+                           :strand => '-', 
+                           :exons => [1000,1200])
+transcript_track.add(feature3)
+
+
 feature1 = Bio::Graphics::MiniFeature.new(:start => 467, 
                            :end => 15000, 
                            :exons => [1500,2500, 3000,7000, 9000,12000], 

data/lib/bio/graphics/glyph.rb

@@ -431,27 +431,30 @@ attr_reader :glyphs
                                                     :stroke_width => args[:exon_stroke_width], 
                                                     :style => args[:exon_style]} )
       end
-      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 << Bio::Graphics::Primitive.new(:polyline, {
-                                                 :points => points, 
-                                                 :stroke => args[:line_color], 
-                                                 :stroke_width => args[:line_width], 
-                                                 :fill => "none", 
-                                                 :line_style => args[:line_style]})
-        end
-      else
+      if args[:exons].length > 1
+        if args[:gap_marker] == "angled" and not args[:block_gaps].empty? 
+          $stderr.puts args[:exons].length
+          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 << Bio::Graphics::Primitive.new(:polyline, {
+                                                  :points => points, 
+                                                  :stroke => args[:line_color], 
+                                                  :stroke_width => args[:line_width], 
+                                                  :fill => "none", 
+                                                  :line_style => args[:line_style]})
+          end
+        else
         #add line
-        composite << Bio::Graphics::Primitive.new(:line, {
-                                            :x1 => args[:x], 
-                                            :x2 => "#{args[:x] + args[:width]}", 
-                                            :y1 => args[:y] + (args[:height]/2), 
-                                            :y2 => args[:y] + (args[:height]/2), 
-                                            :stroke => args[:line_color], 
-                                            :stroke_width => args[:line_width], 
-                                            :line_style => args[:line_style]})
+          composite << Bio::Graphics::Primitive.new(:line, {
+                                              :x1 => args[:x], 
+                                              :x2 => "#{args[:x] + args[:width]}", 
+                                              :y1 => args[:y] + (args[:height]/2), 
+                                              :y2 => args[:y] + (args[:height]/2), 
+                                              :stroke => args[:line_color], 
+                                              :stroke_width => args[:line_width], 
+                                              :line_style => args[:line_style]})
 
+        end
       end
       composite
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-svgenes
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 0.3.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-10 00:00:00.000000000 Z
+date: 2013-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -333,7 +333,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2365228172068893639
+      hash: -2909691261569895312
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: