converted Bio::Graphics::Panel.new to use hash arguments for changing

default options


git-svn-id: svn+ssh://rubyforge.org/var/svn/bio-graphics@32 a2f46d20-7dc0-45cf-9d05-bfa4e4ff58eb

trunk/lib/bio/graphics/panel.rb

@@ -73,9 +73,9 @@ class Bio::Graphics::Panel
     #
     # The height of the image is calculated automatically depending on how many
     # tracks and features it contains. The width of the image defaults to 800 pt
-    # but can be set manually by using a second argument:
+    # but can be set manually by using the width argument to the opts hash:
     #
-    #   g = Bio::Graphics::Panel.new(456, 1200)
+    #   g = Bio::Graphics::Panel.new(456, :width => 1200)
     #
     #
     # See also: Bio::Graphics::Panel::Track,
@@ -84,25 +84,26 @@ class Bio::Graphics::Panel
     # *Arguments*:
     # * _length_ :: length of the thing you want to visualize, e.g for
     #   visualizing a sequence that is 3.24 kb long, use 324.
-    # * _width_ :: width of the resulting image in pt. This should be a string
-    #   and not an integer. Default = '800' (Notice the quotes...).
-    # * _clickable_ :: whether the picture should have clickable glyphs or not
+    # * _:width_ :: width of the resulting image in pixels. (default: 800)
+    # * _:clickable_ :: whether the picture should have clickable glyphs or not
     #   (default: false) If set to true, a html file will be created with
     #   the map.
-    # * _display_start_ :: start coordinate to be displayed (default: 1)
-    # * _display_stop_ :: stop coordinate to be displayed (default: length of sequence)
-    # * _verticle_ :: Boolean: false = horizontal (= default)
+    # * _:display_start_ :: start coordinate to be displayed (default: 1)
+    # * _:display_stop_ :: stop coordinate to be displayed (default: length of sequence)
+    # * _:verticle_ :: Boolean: false = horizontal (= default)
     # *Returns*:: Bio::Graphics::Panel object
-    def initialize(length, width = DEFAULT_PANEL_WIDTH, clickable = false, display_start = nil, display_stop = nil, verticle = false)
+    def initialize(length, opts = {})
       @length = length.to_i
-      @width = width.to_i
-      @verticle = verticle
+      @width = (opts[:width] || DEFAULT_PANEL_WIDTH).to_i
+      @display_start = [0,opts[:display_start] || 0].max
+      @display_stop = [@length,opts[:display_stop] || @length].min
+      @verticle = opts[:verticle] || false
+      @clickable = opts[:clickable] || false
+
       @tracks = Array.new
       @number_of_feature_rows = 0
-      @clickable = clickable
-      @image_map = ( clickable ) ? ImageMap.new : nil
-      @display_start = ( display_start.nil? or display_start < 0 ) ? 0 : display_start
-      @display_stop = ( display_stop.nil? or display_stop > @length ) ? @length : display_stop
+      @image_map = ( @clickable ) ? ImageMap.new : nil
+
       if @display_stop <= @display_start
         raise "[ERROR] Start coordinate to be displayed has to be smaller than stop coordinate."
       end

trunk/samples/arkdb_features.rb

@@ -2,7 +2,10 @@
 
 #Initialize graphic for a nucleotide sequence of 4173015 bp, zooming in on the
 #region 11111..3333333
-my_panel = Bio::Graphics::Panel.new(4173015, 600, true, 11111, 3333333, true)
+my_panel = Bio::Graphics::Panel.new(4173015, :width => 600, :clickable => true,
+                                    :display_start => 11111,
+                                    :display_stop => 3333333,
+                                    :verticle => true)
 #my_panel = Bio::Graphics::Panel.new(4173015, 800, false, 1, 4173015)
 
 #Create and configure tracks

trunk/samples/glyph_showcase.rb

@@ -1,6 +1,6 @@
 require '../lib/bio-graphics'
 
-my_panel = Bio::Graphics::Panel.new(500, 1000, true)
+my_panel = Bio::Graphics::Panel.new(500, :width => 1000, :clickable => true)
 
 generic_track = my_panel.add_track('generic', false)
 line_track = my_panel.add_track('line', false, :line, [0,0,1])

trunk/samples/protein_domains.rb

@@ -1,6 +1,6 @@
 # Data from http://pfam.sanger.ac.uk/protein?id=Q8C6V9_MOUSE
 require '../lib/bio-graphics'
-my_panel = Bio::Graphics::Panel.new(700, 600)
+my_panel = Bio::Graphics::Panel.new(700, :width => 600)
 
 track = my_panel.add_track('Q8C6V9_MOUSE')
 track.glyph = :generic
@@ -16,4 +16,4 @@
 track.add_feature(cimr_2, 'CIMR', nil, track.glyph, [0,1,0])
 track.add_feature(cimr_3, 'CIMR', nil, track.glyph, [0,1,0])
 
-my_panel.draw('protein_domains.png')
+my_panel.draw('protein_domains.png')

trunk/samples/subfeatures.rb

@@ -1,5 +1,5 @@
 require '../lib/bio-graphics'
-my_panel = Bio::Graphics::Panel.new(700, 600)
+my_panel = Bio::Graphics::Panel.new(700, :width => 600)
 
 track = my_panel.add_track('transcripts')
 track.glyph = :directed_spliced

trunk/test/unit/test_creation.rb

@@ -3,7 +3,8 @@
 
 class TestPanel < Test::Unit::TestCase
   def test_panel_creation
-    panel = Bio::Graphics::Panel.new(1000, 500, false, 0, 1000)
+    panel = Bio::Graphics::Panel.new(1000, :width => 500, :clickable => false,
+                                     :display_start => 0, :display_stop => 1000)
     assert_equal(1000, panel.length)
     assert_equal(500, panel.width)
     assert_equal(false, panel.clickable)
@@ -14,16 +15,18 @@ def test_panel_creation
   end
 
   def test_panel_creation_out_of_boundaries
-    panel = Bio::Graphics::Panel.new(1000, 500, false, -7, 5000)
+    panel = Bio::Graphics::Panel.new(1000, :width => 500, :clickable => false,
+                                     :display_start => -7, :display_stop => 5000)
     assert_same(0, panel.display_start)
     assert_same(1000, panel.display_stop)
   end
 
 end
 
 class TestTrack < Test::Unit::TestCase
-	def setup
-    @panel = Bio::Graphics::Panel.new(1000, 500, false, 0, 1000)
+  def setup
+    @panel = Bio::Graphics::Panel.new(1000, :width => 500, :clickable => false,
+                                      :display_start => 0, :display_stop => 1000)
   end
 
   def test_track_creation
@@ -38,7 +41,7 @@ def test_track_creation
 
 class TestFeature < Test::Unit::TestCase
   def setup
-    @panel = Bio::Graphics::Panel.new(1000, 500, false, 0, 1000)
+    @panel = Bio::Graphics::Panel.new(1000, :width => 500)
     @track = @panel.add_track('test_track', false, :generic, [1,0,0])
   end
 

trunk/test/unit/test_draw.rb

@@ -3,7 +3,7 @@
 
 class TestPanel < Test::Unit::TestCase
   def test_draw_showcase
-    my_panel = Bio::Graphics::Panel.new(500, 1000, false)
+    my_panel = Bio::Graphics::Panel.new(500, :width => 1000)
 
     generic_track = my_panel.add_track('generic', false)
     line_track = my_panel.add_track('line', false, :line, [0,0,1])
@@ -30,7 +30,6 @@ def test_draw_showcase
     dot_track.add_feature(Bio::Feature.new('marker', '57'), 'thing3')
     dot_track.add_feature(Bio::Feature.new('marker', '114'), 'thing2','http://digg.com')
 
-
     spliced_track.add_feature(Bio::Feature.new('gene','join(34..52,109..183)'), 'gene1','http://news.bbc.co.uk')
     spliced_track.add_feature(Bio::Feature.new('gene','complement(join(170..231,264..299,350..360,409..445))'), 'gene2')
     spliced_track.add_feature(Bio::Feature.new('gene','join(134..152,209..283)'), 'gene3')
@@ -43,11 +42,10 @@ def test_draw_showcase
     my_panel.draw(output_file)
     system("display " + output_file + "& sleep 2 && kill $!")
     File.delete(output_file)
-
   end
 
   def test_arkdb_features
-    my_panel = Bio::Graphics::Panel.new(4173015, 600, false, 1, 4173015, true)
+    my_panel = Bio::Graphics::Panel.new(4173015, :width => 600, :verticle => true)
 
     #Create and configure tracks
     scaffold_track = my_panel.add_track('scaffold', false)
@@ -82,12 +80,11 @@ def test_arkdb_features
     my_panel.draw(output_file)
 
     system("display " + output_file + "& sleep 2 && kill $!")
-    File.delete(output_file)
-
+    File.delete(output_file)    
   end
 
   def test_subfeatures
-    my_panel = Bio::Graphics::Panel.new(500, 600, false, 1, 500, false)
+    my_panel = Bio::Graphics::Panel.new(500, :width => 600)
 
     track = my_panel.add_track('mrna')
 
@@ -109,12 +106,11 @@ def test_subfeatures
     my_panel.draw(output_file)
 
     system("display " + output_file + "& sleep 2 && kill $!")
-    File.delete(output_file)
-
+    File.delete(output_file)    
   end
 
   def test_feature_specific_colouring
-    my_panel = Bio::Graphics::Panel.new(375, 600, false, 1, 375, false)
+    my_panel = Bio::Graphics::Panel.new(375, :width => 600)
 
     track = my_panel.add_track('mrna')
 
@@ -131,8 +127,6 @@ def test_feature_specific_colouring
     my_panel.draw(output_file)
 
     system("display " + output_file + "& sleep 2 && kill $!")
-    File.delete(output_file)
-
-  end
-
+    File.delete(output_file)    
+  end  
 end