bio-graphics 1.2 → 1.4

data/lib/bio/graphics/glyphs/box.rb

@@ -0,0 +1,21 @@
+# 
+# = bio/graphics/glyphs/box - box glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Box < Bio::Graphics::Glyph::Common
+    def draw
+      @feature_context.move_to(self.left_pixel, 0)
+      @feature_context.line_to(self.right_pixel, 0)
+      @feature_context.line_to(self.right_pixel, Bio::Graphics::FEATURE_HEIGHT)
+      @feature_context.line_to(self.left_pixel, Bio::Graphics::FEATURE_HEIGHT)
+      @feature_context.close_path
+      @feature_context.stroke
+
+    end
+  end
+end

data/lib/bio/graphics/glyphs/common.rb

@@ -0,0 +1,149 @@
+# 
+# = bio/graphics/glyphs/common - common methods for all glyphs
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Common
+    def initialize(subfeature, feature_context)
+      @subfeature, @feature_context = subfeature, feature_context
+    end
+    attr_accessor :subfeature, :feature_context
+
+    def left_pixel
+      if self.class == Bio::Graphics::Glyph::Triangle
+        return @subfeature.pixel_range_collection[0].lend - Bio::Graphics::FEATURE_ARROW_LENGTH
+      elsif self.class == Bio::Graphics::Glyph::Dot
+        return @subfeature.pixel_range_collection[0].lend - @radius
+      else
+        return @subfeature.pixel_range_collection.sort_by{|pr| pr.lend}[0].lend
+      end
+    end
+    
+    def right_pixel
+      if self.class == Bio::Graphics::Glyph::Triangle
+        return @subfeature.pixel_range_collection[0].rend + Bio::Graphics::FEATURE_ARROW_LENGTH
+      elsif self.class == Bio::Graphics::Glyph::Dot
+        return @subfeature.pixel_range_collection[0].rend + @radius
+      else
+        return @subfeature.pixel_range_collection.sort_by{|pr| pr.lend}[-1].rend
+      end
+    end
+    
+    private
+
+    # Method to draw each of the squared spliced rectangles for
+    # spliced and directed_spliced
+    # ---
+    # *Arguments*:
+    # * _track_drawing_::
+    # * _pixel_ranges_:: 
+    # * _top_pixel_of_feature_:: 
+    # * _gap_starts_:: 
+    # * _gap_stops_:: 
+    def draw_spliced(feature_context, pixel_ranges, gap_starts, gap_stops)
+      # draw the parts
+      pixel_ranges.each do |range|
+        feature_context.rectangle(range.lend, 0, range.rend - range.lend, Bio::Graphics::FEATURE_HEIGHT).fill
+        gap_starts.push(range.rend)
+        gap_stops.push(range.lend)
+      end
+
+      # And then draw the connections in the gaps
+      # Start with removing the very first start and the very last stop.
+      gap_starts.sort!.pop
+      gap_stops.sort!.shift
+
+      gap_starts.length.times do |gap_number|
+        connector(feature_context,gap_starts[gap_number].to_f,gap_stops[gap_number].to_f)
+      end
+
+      if @subfeature.hidden_subfeatures_at_stop
+        from = @subfeature.pixel_range_collection.sort_by{|pr| pr.lend}[-1].rend
+        to = @subfeature.feature.track.panel.width
+        feature_context.move_to(from, Bio::Graphics::FEATURE_ARROW_LENGTH)
+        feature_context.line_to(to, Bio::Graphics::FEATURE_ARROW_LENGTH)
+        feature_context.stroke
+      end
+
+      if @subfeature.hidden_subfeatures_at_start
+        from = 1
+        to = @subfeature.pixel_range_collection.sort_by{|pr| pr.lend}[0].lend
+        feature_context.move_to(from, Bio::Graphics::FEATURE_ARROW_LENGTH)
+        feature_context.line_to(to, Bio::Graphics::FEATURE_ARROW_LENGTH)
+        feature_context.stroke
+      end
+    end
+
+    # Method to draw the arrows of directed glyphs. Not to be used
+    # directly, but called by Feature#draw.
+    def arrow(feature_context,direction,x,y,size)
+      case direction
+      when :right
+        feature_context.move_to(x,y)
+        feature_context.rel_line_to(size,size)
+        feature_context.rel_line_to(-size,size)
+        feature_context.close_path.fill
+      when :left
+        feature_context.move_to(x,y)
+        feature_context.rel_line_to(-size,size)
+        feature_context.rel_line_to(size,size)
+        feature_context.close_path.fill
+      when :north
+        feature_context.move_to(x-size,y+size)
+        feature_context.rel_line_to(size,-size)
+        feature_context.rel_line_to(size,size)
+        feature_context.close_path.fill
+      when :south
+        feature_context.move_to(x-size,y-size)
+        feature_context.rel_line_to(size,size)
+        feature_context.rel_line_to(size,-size)
+        feature_context.close_path.fill
+      end
+    end
+
+    # Method to draw the arrows of directed glyphs. Not to be used
+    # directly, but called by Feature#draw.
+    def open_arrow(feature_context,direction,x,y,size)
+      case direction
+      when :right
+        feature_context.move_to(x,y)
+        feature_context.rel_line_to(size,size)
+        feature_context.rel_line_to(-size,size)
+        feature_context.stroke
+      when :left
+        feature_context.move_to(x,y)
+        feature_context.rel_line_to(-size,size)
+        feature_context.rel_line_to(size,size)
+        feature_context.stroke
+      when :north
+        feature_context.move_to(x-size,y+size)
+        feature_context.rel_line_to(size,-size)
+        feature_context.rel_line_to(size,size)
+        feature_context.stroke
+      when :south
+        feature_context.move_to(x-size,y-size)
+        feature_context.rel_line_to(size,size)
+        feature_context.rel_line_to(size,-size)
+        feature_context.stroke
+      end
+    end
+    
+    # Method to draw the connections (introns) of spliced glyphs. Not to
+    # be used directly, but called by Feature#draw.
+    def connector(feature_context,from,to)
+      line_width = feature_context.line_width
+      feature_context.set_line_width(0.5)
+      middle = from + ((to - from)/2)
+      feature_context.move_to(from, 2)
+      feature_context.line_to(middle, 7)
+      feature_context.line_to(to, 2)
+      feature_context.stroke
+      feature_context.set_line_width(line_width)
+    end                    
+
+  end
+end

data/lib/bio/graphics/glyphs/directed_box.rb

@@ -0,0 +1,28 @@
+# 
+# = bio/graphics/glyphs/directed_box - directed_box glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::DirectedBox < Bio::Graphics::Glyph::Common
+    def draw
+      if @subfeature.strand == -1 # Reverse strand
+        @feature_context.move_to(self.left_pixel + Bio::Graphics::FEATURE_ARROW_LENGTH, 0)
+        @feature_context.line_to(self.right_pixel, 0)
+        @feature_context.line_to(self.right_pixel, Bio::Graphics::FEATURE_HEIGHT)
+        @feature_context.line_to(self.left_pixel + Bio::Graphics::FEATURE_ARROW_LENGTH, Bio::Graphics::FEATURE_HEIGHT)
+        @feature_context.stroke
+        open_arrow(@feature_context,:left,self.left_pixel+Bio::Graphics::FEATURE_ARROW_LENGTH,0,Bio::Graphics::FEATURE_ARROW_LENGTH)
+      else #default is forward strand
+        @feature_context.move_to(self.right_pixel - Bio::Graphics::FEATURE_ARROW_LENGTH, 0)
+        @feature_context.line_to(self.left_pixel, 0)
+        @feature_context.line_to(self.left_pixel, Bio::Graphics::FEATURE_HEIGHT)
+        @feature_context.line_to(self.right_pixel - Bio::Graphics::FEATURE_ARROW_LENGTH, Bio::Graphics::FEATURE_HEIGHT)
+        open_arrow(@feature_context, :right, self.right_pixel - Bio::Graphics::FEATURE_ARROW_LENGTH, 0, Bio::Graphics::FEATURE_ARROW_LENGTH)
+      end
+    end
+  end
+end

data/lib/bio/graphics/glyphs/directed_generic.rb

@@ -0,0 +1,23 @@
+# 
+# = bio/graphics/glyphs/directed_generic - directed_generic glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::DirectedGeneric < Bio::Graphics::Glyph::Common
+    def draw
+      if @subfeature.strand == -1 # Reverse strand
+        @feature_context.rectangle(self.left_pixel+Bio::Graphics::FEATURE_ARROW_LENGTH, 0, self.right_pixel - self.left_pixel - Bio::Graphics::FEATURE_ARROW_LENGTH, Bio::Graphics::FEATURE_HEIGHT).fill
+        arrow(@feature_context,:left,self.left_pixel+Bio::Graphics::FEATURE_ARROW_LENGTH,0,Bio::Graphics::FEATURE_ARROW_LENGTH)
+        @feature_context.close_path.fill
+      else #default is forward strand
+        @feature_context.rectangle(self.left_pixel, 0, self.right_pixel- self.left_pixel - Bio::Graphics::FEATURE_ARROW_LENGTH, Bio::Graphics::FEATURE_HEIGHT).fill
+        arrow(@feature_context,:right,self.right_pixel-Bio::Graphics::FEATURE_ARROW_LENGTH,0,Bio::Graphics::FEATURE_ARROW_LENGTH)
+        @feature_context.close_path.fill
+      end
+    end
+  end
+end

data/lib/bio/graphics/glyphs/directed_spliced.rb

@@ -0,0 +1,39 @@
+# 
+# = bio/graphics/glyphs/directed_spliced - directed_spliced glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::DirectedSpliced < Bio::Graphics::Glyph::Common
+    def draw
+      gap_starts = Array.new
+      gap_stops = Array.new
+
+      #   Start with the one with the arrow
+      pixel_ranges = @subfeature.pixel_range_collection.sort_by{|pr| pr.lend}
+      range_with_arrow = nil
+      if @subfeature.strand == -1 # reverse strand => box with arrow is first one
+        range_with_arrow = pixel_ranges.shift
+        @feature_context.rectangle((range_with_arrow.lend)+Bio::Graphics::FEATURE_ARROW_LENGTH, 0, range_with_arrow.rend - range_with_arrow.lend - Bio::Graphics::FEATURE_ARROW_LENGTH, Bio::Graphics::FEATURE_HEIGHT).fill
+        arrow(@feature_context,:left,range_with_arrow.lend+Bio::Graphics::FEATURE_ARROW_LENGTH, 0,Bio::Graphics::FEATURE_ARROW_LENGTH)
+        @feature_context.close_path.fill
+      else # forward strand => box with arrow is last one
+        range_with_arrow = pixel_ranges.pop
+        @feature_context.rectangle(range_with_arrow.lend, 0, range_with_arrow.rend - range_with_arrow.lend - Bio::Graphics::FEATURE_ARROW_LENGTH, Bio::Graphics::FEATURE_HEIGHT).fill
+        arrow(@feature_context,:right,range_with_arrow.rend-Bio::Graphics::FEATURE_ARROW_LENGTH, 0,Bio::Graphics::FEATURE_ARROW_LENGTH)
+        @feature_context.close_path.fill
+      end
+      gap_starts.push(range_with_arrow.rend)
+      gap_stops.push(range_with_arrow.lend)
+
+      #   And then add the others
+      draw_spliced(@feature_context, pixel_ranges, gap_starts, gap_stops)
+
+    end
+  end
+end
+
+

data/lib/bio/graphics/glyphs/dot.rb

@@ -0,0 +1,21 @@
+# 
+# = bio/graphics/glyphs/dot - dot glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Dot < Bio::Graphics::Glyph::Common
+    attr_accessor :radius
+    
+    def draw
+      raise "Start and stop are not the same (necessary if you want triangle glyphs)" if @subfeature.start != @subfeature.stop
+      
+      @radius = Bio::Graphics::FEATURE_HEIGHT/2
+      @feature_context.circle(self.left_pixel + @radius, @radius, @radius).fill
+      @feature_context.close_path.stroke
+    end
+  end
+end

data/lib/bio/graphics/glyphs/generic.rb

@@ -0,0 +1,15 @@
+# 
+# = bio/graphics/glyphs/generic - generic glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Generic < Bio::Graphics::Glyph::Common
+    def draw
+      @feature_context.rectangle(self.left_pixel, 0, (self.right_pixel - self.left_pixel), Bio::Graphics::FEATURE_HEIGHT).fill
+    end
+  end
+end

data/lib/bio/graphics/glyphs/line.rb

@@ -0,0 +1,17 @@
+# 
+# = bio/graphics/glyphs/line - line glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Line < Bio::Graphics::Glyph::Common
+    def draw
+      @feature_context.move_to(self.left_pixel,Bio::Graphics::FEATURE_ARROW_LENGTH)               
+      @feature_context.line_to(self.right_pixel,Bio::Graphics::FEATURE_ARROW_LENGTH)
+      @feature_context.stroke
+    end
+  end
+end

data/lib/bio/graphics/glyphs/line_with_handles.rb

@@ -0,0 +1,25 @@
+# 
+# = bio/graphics/glyphs/line_with_handles - line_with_handles glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::LineWithHandles < Bio::Graphics::Glyph::Common
+    def draw
+      @feature_context.move_to(self.left_pixel,Bio::Graphics::FEATURE_ARROW_LENGTH)               
+      @feature_context.line_to(self.right_pixel,Bio::Graphics::FEATURE_ARROW_LENGTH)
+      @feature_context.stroke
+
+      @feature_context.set_source_rgb([0,0,0])
+      arrow(@feature_context,:right,self.left_pixel,0,Bio::Graphics::FEATURE_ARROW_LENGTH)
+      @feature_context.close_path.stroke              
+      arrow(@feature_context,:left,self.right_pixel,0,Bio::Graphics::FEATURE_ARROW_LENGTH)
+      @feature_context.close_path.stroke
+
+      @feature_context.set_source_rgb(@subfeature.colour)
+    end
+  end
+end

data/lib/bio/graphics/glyphs/spliced.rb

@@ -0,0 +1,16 @@
+# 
+# = bio/graphics/glyphs/splices - spliced glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Spliced < Bio::Graphics::Glyph::Common
+    def draw
+      pixel_ranges = @subfeature.pixel_range_collection.sort_by{|pr| pr.lend}
+      draw_spliced(@feature_context, pixel_ranges, [], [])
+    end
+  end
+end

data/lib/bio/graphics/glyphs/transcript.rb

@@ -0,0 +1,12 @@
+# 
+# = bio/graphics/glyphs/transcript - transcript glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Transcript < Bio::Graphics::Glyph::Common
+  end
+end

data/lib/bio/graphics/glyphs/triangle.rb

@@ -0,0 +1,18 @@
+# 
+# = bio/graphics/glyphs/triangle - triangle glyph
+#
+# Copyright::   Copyright (C) 2007, 2008
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::Triangle < Bio::Graphics::Glyph::Common
+    def draw
+      raise "Start and stop are not the same (necessary if you want triangle glyphs)" if @subfeature.start != @subfeature.stop
+      
+      arrow(@feature_context,:north, self.left_pixel + Bio::Graphics::FEATURE_ARROW_LENGTH, 0, Bio::Graphics::FEATURE_ARROW_LENGTH)
+      @feature_context.close_path.stroke
+    end
+  end
+end

data/lib/bio/graphics/image_map.rb

@@ -3,25 +3,44 @@
 #
 # Copyright::   Copyright (C) 2007
 #               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+#               Charles Comstock <dgtized@gmail.com>
 # License::     Ruby's
-class ImageMap
+class Bio::Graphics::ImageMap
   def initialize
     @elements = Array.new
   end
   attr_accessor :elements
 
+  def add_element(left,top,right,bottom,url = nil)
+    @elements.push(Element.new(left,top,right,bottom,url))
+  end
+  
   def to_s
     output = Array.new
     output.push('<map name="image_map" border="1">')
     @elements.each do |e|
-      output.push(e.to_s)
+      area = e.to_s
+      if area != ''
+        output.push(e.to_s)
+      end
     end
     output.push('</map>')
     return output.join("\n")
   end
 
 
-  class ImageMapElement
+  # Switch horizontal to vertical orientation
+  def flip_orientation(width)
+    @elements.each do |element|
+      left, top, right, bottom = element.left, element.top, element.right, element.bottom
+      element.left = top
+      element.top = width - right
+      element.right = bottom
+      element.bottom = width - left
+    end
+  end
+  
+  class Element
     def initialize(left, top, right, bottom, url = nil)
       @left, @top, @right, @bottom = left, top, right, bottom
       @url = ( url.nil? ) ? '' : url
@@ -29,7 +48,9 @@ class ImageMap
     attr_accessor :left, :top, :right, :bottom, :url
 
     def to_s
-      unless @url == ''
+      if @url == ''
+        return ''
+      else
         return '<area shape="rect" coords="' + @left.to_s + ' ' + @top.to_s + ' ' + @right.to_s + ' ' + @bottom.to_s + '" href="' + @url + '"/>'
       end
     end