bio-graphics 1.0 → 1.2

data/samples/arkdb_features.rb

@@ -2,18 +2,18 @@ require File.dirname(__FILE__) + '/../lib/bio-graphics'
 
 #Initialize graphic for a nucleotide sequence of 4173015 bp, zooming in on the
 #region 11111..3333333
-my_panel = Bio::Graphics::Panel.new(4173015, 800, false, 11111, 3333333)
+my_panel = Bio::Graphics::Panel.new(4173015, 800, true, 11111, 3333333)
 #my_panel = Bio::Graphics::Panel.new(4173015, 800, false, 1, 4173015)
 
 #Create and configure tracks
-scaffold_track = my_panel.add_track('scaffold')
-marker_track = my_panel.add_track('marker')
-clone_track = my_panel.add_track('clone')
+scaffold_track = my_panel.add_track('scaffold', false)
+marker_track = my_panel.add_track('marker', true)
+clone_track = my_panel.add_track('clone', false)
 
-scaffold_track.feature_colour = [1,0,0]
-marker_track.feature_colour = [0,1,0]
-marker_track.feature_glyph = 'triangle'
-clone_track.feature_colour = [0,0,1]
+scaffold_track.colour = [1,0,0]
+marker_track.colour = [0,1,0]
+marker_track.glyph = :triangle
+clone_track.colour = [0,0,1]
 
 # Add data to tracks
 File.open('data.txt').each do |line|

data/samples/glyph_showcase.rb

@@ -1,17 +1,21 @@
 require '../lib/bio-graphics'
 
-my_panel = Bio::Graphics::Panel.new(500, 1000, true)
+my_panel = Bio::Graphics::Panel.new(500, 1000, false)
 
-generic_track = my_panel.add_track('generic')
-directed_track = my_panel.add_track('directed',[0,1,0],'directed_generic')
-triangle_track = my_panel.add_track('triangle',[1,0,0],'triangle')
-spliced_track = my_panel.add_track('spliced',[1,0,0],'spliced')
-directed_spliced_track = my_panel.add_track('directed_spliced',[1,0,1],'directed_spliced')
+generic_track = my_panel.add_track('generic', false)
+line_track = my_panel.add_track('line', false, [0,0,1], :line)
+directed_track = my_panel.add_track('directed', false, [0,1,0], :directed_generic)
+triangle_track = my_panel.add_track('triangle', false, [1,0,0], :triangle)
+spliced_track = my_panel.add_track('spliced', false, [1,0,0], :spliced)
+directed_spliced_track = my_panel.add_track('directed_spliced', false, [1,0,1], :directed_spliced)
 
 generic_track.add_feature('clone1','250..375', 'http://www.newsforge.com')
 generic_track.add_feature('clone2','54..124', 'http://www.thearkdb.org')
 generic_track.add_feature('clone3','100..449', 'http://www.google.com')
 
+line_track.add_feature('primer1','complement(200..320)')
+line_track.add_feature('primer2','355..480', 'http://www.zdnet.co.uk')
+
 directed_track.add_feature('marker1','50..60', 'http://www.google.com')
 directed_track.add_feature('marker2','complement(80..120)', 'http://www.sourceforge.net')
 

data/test/unit/test_creation.rb

@@ -0,0 +1,51 @@
+require 'test/unit'
+require File.dirname(__FILE__) + '/../../lib/bio-graphics'
+
+class TestPanel < Test::Unit::TestCase
+  def test_panel_creation
+    panel = Bio::Graphics::Panel.new(1000, 500, false, 0, 1000)
+    assert_equal(1000, panel.length)
+    assert_equal(500, panel.width)
+    assert_equal(false, panel.clickable)
+    assert_equal(0, panel.display_start)
+    assert_equal(1000, panel.display_stop)
+    assert_equal(1000/500, panel.rescale_factor)
+    assert_equal(0, panel.tracks.length)
+  end
+  
+  def test_panel_creation_out_of_boundaries
+    panel = Bio::Graphics::Panel.new(1000, 500, false, -7, 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)
+  end
+
+  def test_track_creation
+    track = @panel.add_track('test_track', [1,0,0], 'generic')
+    assert_equal('test_track', track.name)
+    assert_equal([1,0,0], track.feature_colour)
+    assert_equal('generic', track.feature_glyph)
+    assert_equal(1, @panel.tracks.length)
+    assert_equal(0, track.features.length)
+  end
+end
+
+class TestFeature < Test::Unit::TestCase
+  def setup
+    @panel = Bio::Graphics::Panel.new(1000, 500, false, 0, 1000)
+    @track = @panel.add_track('test_track', [1,0,0], 'generic')
+  end
+  
+  def test_feature_creation
+    feature = @track.add_feature('test_feature', '123..456')
+    assert_equal('test_feature', feature.name)
+    assert_equal(123, feature.location[0].from)
+    assert_equal(456, feature.location[-1].to)
+  end
+end

metadata

@@ -3,8 +3,8 @@ rubygems_version: 0.9.0
 specification_version: 1
 name: bio-graphics
 version: !ruby/object:Gem::Version 
-  version: "1.0"
-date: 2007-10-01 00:00:00 +01:00
+  version: "1.2"
+date: 2007-10-18 00:00:00 +01:00
 summary: Library for visualizing genomic regions
 require_paths: 
 - lib
@@ -40,6 +40,7 @@ files:
 - doc/images/terms.svg
 - doc/images/terms.png
 - doc/images/glyph_showcase.png
+- doc/images/example_labels.png
 - doc/images/example.png
 - doc/classes/Bio
 - doc/classes/ImageMap.html
@@ -62,7 +63,12 @@ files:
 - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src
 - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html
 - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html
+- doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html
 - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html
+- doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html
+- doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000015.html
+- doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html
+- doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html
 - doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html
 - doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html
 - doc/classes/Bio/Graphics/Panel/Track.src/M000013.html
@@ -72,9 +78,13 @@ files:
 - doc/classes/Bio/Graphics/Panel/Track.src/M000010.html
 - doc/classes/Bio/Graphics/Panel/Track.src/M000008.html
 - doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html
+- doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html
 - doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html
+- doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html
+- doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html
 - doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html
 - doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html
+- doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html
 - doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html
 - doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html
 - doc/classes/Bio/Graphics/Panel.src/M000007.html
@@ -109,9 +119,11 @@ files:
 - samples/data.txt
 - samples/glyph_showcase.rb
 - test/unit
+- test/unit/test_creation.rb
 - images/terms.svg
 - images/terms.png
 - images/glyph_showcase.png
+- images/example_labels.png
 - images/example.png
 test_files: []