bio-svgenes 0.3.3 → 0.4.0

data/VERSION

@@ -1 +1 @@
-0.3.3
+0.4.0

data/bio-svgenes.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-svgenes"
-  s.version = "0.3.3"
+  s.version = "0.4.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]
-  s.date = "2013-06-06"
+  s.date = "2014-01-03"
   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

@@ -431,9 +431,8 @@ attr_reader :glyphs
                                                     :stroke_width => args[:exon_stroke_width], 
                                                     :style => args[:exon_style]} )
       end
-      if args[:exons].length > 1
-        if args[:gap_marker] == "angled" and not args[:block_gaps].empty? 
-          $stderr.puts args[:exons].length
+      if not args[:block_gaps].empty?
+        if args[:gap_marker] == "angled"
           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, {

data/lib/bio/graphics/mini_feature.rb

@@ -5,7 +5,7 @@ module Bio
     #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
+  attr_accessor :start, :end, :strand, :exons, :utrs, :block_gaps, :segment_height, :id, :params
   #Creates a new MiniFeature
   #
   #== args
@@ -41,8 +41,9 @@ class MiniFeature
     @block_gaps = []
     @id = args[:id]
     @segment_height = args[:segment_height]
+    @params = args[:params]
   end
 end
 
 end
-end
+end

data/lib/bio/graphics/page.rb

@@ -227,6 +227,18 @@ module Bio
           @scale_stop = highest if highest > @scale_stop
           @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
         end
+        begin
+          old_nt_per_px_x = @nt_per_px_x
+          @tracks.each do |track|
+            highest = track.features.map { |feat|
+              feat_end = feat.end
+              feat_end += (8 * @nt_per_px_x * feat.id.to_s.length).to_i if feat.id
+              feat_end
+            }.max
+            @scale_stop = highest if highest > @scale_stop
+            @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
+          end
+        end while (@nt_per_px_x - old_nt_per_px_x).abs > 1
       end
 
       #Adds scale bar to the list of objects to be rendered in the final
@@ -358,7 +370,8 @@ module Bio
                                               :exons => f.exons,
                                               :utrs => f.utrs,
                                               :block_gaps => f.block_gaps,
-                                              :height => track.feature_height
+                                              :height => track.feature_height,
+                                              :params => f.params
             }.merge!(track.args))
 
             if f.id
@@ -398,4 +411,4 @@ module Bio
       end
     end
   end
-end
+end

data/lib/bio/graphics/svgee.rb

@@ -81,7 +81,10 @@ class SVGEE
   end
   
   def common_attributes(a={})
-    %{stroke="#{a[:stroke]}" stroke-width="#{a[:stroke_width]}" style="#{a[:style]}"}
+    param_str = ""
+    a[:params].each{|k,v| param_str << %{ #{k}="#{v}"}} if a[:params]
+
+    %{stroke="#{a[:stroke]}" stroke-width="#{a[:stroke_width]}" style="#{a[:style]}"} + param_str
   end
   
   def method_missing(primitive, args={}) #only used to dynamically select the primitive type.. 
@@ -142,4 +145,4 @@ prim.update(:x_center => 200)
 s.add_primitive(prim)  #add one of the returned, updated Primitive objects 
 
 s.draw
-=end
+=end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-svgenes
 version: !ruby/object:Gem::Version
-  version: 0.3.3
+  version: 0.4.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-06 00:00:00.000000000 Z
+date: 2014-01-03 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: -2909691261569895312
+      hash: -4059527771038564991
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: