bio-svgenes 0.4.0 → 0.4.1

data/VERSION

@@ -1 +1 @@
-0.4.0
+0.4.1

data/bio-svgenes.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-svgenes"
-  s.version = "0.4.0"
+  s.version = "0.4.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]
-  s.date = "2014-01-03"
+  s.date = "2014-01-06"
   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/lib/bio/graphics/page.rb

@@ -231,16 +231,23 @@ module Bio
           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
+              compute_boundaries(feat)[1]
             }.max
-            @scale_stop = highest if highest > @scale_stop
-            @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
+            if highest > @scale_stop
+              @scale_stop = highest
+              @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
+            end
           end
         end while (@nt_per_px_x - old_nt_per_px_x).abs > 1
       end
 
+      def compute_boundaries(feature)
+        feat_end = feature.end
+        feat_end += (8 * @nt_per_px_x * feature.id.to_s.length).to_i if feature.id and @nt_per_px_x
+        [feature.start, feat_end]
+      end
+
+
       #Adds scale bar to the list of objects to be rendered in the final
       def draw_scale
         Glyph.scale(:start => @scale_start,
@@ -322,7 +329,7 @@ module Bio
           if track.label
             draw_label(:text => track.name, :y => @track_top += 30, :x => 3)
           end
-          track.get_rows ##work out how many rows and which features belong in each row...
+          track.get_rows(self) ##work out how many rows and which features belong in each row...
           track.features.each_with_index do |f, index|
             x = to_px(f.start - @scale_start) #bottom left of feature
             all_sub_blocks = []

data/lib/bio/graphics/track.rb

@@ -118,31 +118,47 @@ class Track
 
   #Calculates how many rows are needed per track for overlapping features
   #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)
+  def get_rows(page=nil)
+    @feature_rows = Array.new(@features.length, -1)
+    rows = Hash.new { |h,k| h[k] = [] }
     @features.each_with_index  do |f1, i|
-      @features.each_with_index do |f2, j|
-        next if i == j or j <= i
-        if overlaps(f1,f2)
-          @feature_rows[i] += 1
+      current_row = 1
+      begin
+        found = true
+        rows[current_row].each_with_index do |f2, j|
+          if overlaps(f1, f2, page)
+            found = false
+            current_row += 1
+            break
+          end
         end
-      end
-      @number_rows = @feature_rows.max
+      end until found
+      @feature_rows[i] = current_row
+      rows[current_row] << f1
     end
+    @number_rows = @feature_rows.max
   end
 
   #Calculates whether two Bio::Graphics::MiniFeature objects overlap by examining their start and end positions.
+  #If the page where they are placed is given, then the function also considers the features' labels.
   #
   #+args+
   #* 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)
+  #* page - the optional Bio::Graphics::Page object where the features are placed
+  def overlaps(f1, f2, page=nil)
+    if not page
+      b1 = [f1.start, f1.end]
+      b2 = [f2.start, f2.end]
+    else
+      b1 = page.compute_boundaries(f1)
+      b2 = page.compute_boundaries(f2)
+    end
+    (b2[0] <= b1[1]) and (b1[0] <= b2[1])
   end
   
 end
 
 
 end
-end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-svgenes
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-03 00:00:00.000000000 Z
+date: 2014-01-06 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: -4059527771038564991
+      hash: -1702096108071708551
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: