bio-svgenes 0.2.3 → 0.3.0

data/test/test_track.rb

@@ -0,0 +1,53 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+require 'rubygems'
+require 'helper'
+require 'bio-svgenes'
+require 'pp'
+
+
+class TestTrack < Test::Unit::TestCase
+  def setup
+
+    @track = Bio::Graphics::Track.new(:glyph => :generic,
+                                       :name => 'generic_features',
+                                       :label => true, :feature_height => 12)
+    @feature1 = Bio::Graphics::MiniFeature.new(:start => 100, :end => 200, :strand => '+', :id => "MyFeature1")
+    @feature2 = Bio::Graphics::MiniFeature.new(:start => 190, :end => 250, :strand => '+', :id => "MyFeature2")
+    @feature3 = Bio::Graphics::MiniFeature.new(:start => 300, :end => 350, :strand => '+', :id => "MyFeature3")
+
+  end
+
+
+  def test_track_class
+    assert_equal(Bio::Graphics::Track, @track.class)
+
+    assert_equal(:generic, @track.glyph)
+    assert_equal('generic_features', @track.name)
+    assert_equal(true, @track.label)
+    assert_equal(nil, @track.track_height)
+
+  end
+
+  def test_overlaps
+    assert(@track.overlaps(@feature1, @feature2))
+    assert_equal(false, @track.overlaps(@feature2, @feature3))
+  end
+
+  def test_get_rows_and_add
+    @track.add(@feature1)
+    assert_not_equal(2, @track.features.length)
+    assert_equal(1, @track.features.length)
+    @track.add(@feature2)
+    assert_equal(2, @track.features.length)
+    @track.add(@feature3)
+    assert_equal(3, @track.features.length)
+
+    #hasn't been called yet, so should be nil
+    assert_nil(@track.number_rows)
+    #call method - @feature1 and @feature2 overlap, but @feature3 doesn't so there should be two rows
+    @track.get_rows
+    assert_equal(2, @track.number_rows)
+
+  end
+end

data/test/test_transcripts.gff

@@ -0,0 +1,4 @@
+##gff-version	3
+##sequence-region	ctg123	1	1497228	
+ctg123	.	mRNA	900	9200	.	+	.	ID=mRNA00001;Name=EDEN.1
+ctg123	.	utr	900	1000	.	+	.	ID=utr00001;Parent=mRNA00001

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-svgenes
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-30 00:00:00.000000000 Z
+date: 2013-03-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &70232196114400 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70232196114400
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70232196113480 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +37,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *70232196113480
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70232196112820 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +53,15 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70232196112820
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &70232196111740 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +69,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70232196111740
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70232196111080 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,7 +85,12 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *70232196111080
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
 description: This bio-gem facilitates the creation of pretty, publication quality
   SVG images from feature data.
 email: maclean.daniel@gmail.com
@@ -84,6 +109,52 @@ files:
 - Rakefile
 - VERSION
 - bio-svgenes.gemspec
+- doc/.DS_Store
+- doc/Bio.html
+- doc/Bio/.DS_Store
+- doc/Bio/Graphics.html
+- doc/Bio/Graphics/Glyph.html
+- doc/Bio/Graphics/MiniFeature.html
+- doc/Bio/Graphics/Page.html
+- doc/Bio/Graphics/Primitive.html
+- doc/Bio/Graphics/SVGEE.html
+- doc/Bio/Graphics/Track.html
+- doc/LICENSE_txt.html
+- doc/created.rid
+- doc/images/add.png
+- doc/images/arrow_up.png
+- doc/images/brick.png
+- doc/images/brick_link.png
+- doc/images/bug.png
+- doc/images/bullet_black.png
+- doc/images/bullet_toggle_minus.png
+- doc/images/bullet_toggle_plus.png
+- doc/images/date.png
+- doc/images/delete.png
+- doc/images/find.png
+- doc/images/loadingAnimation.gif
+- doc/images/macFFBgHack.png
+- doc/images/package.png
+- doc/images/page_green.png
+- doc/images/page_white_text.png
+- doc/images/page_white_width.png
+- doc/images/plugin.png
+- doc/images/ruby.png
+- doc/images/tag_blue.png
+- doc/images/tag_green.png
+- doc/images/transparent.png
+- doc/images/wrench.png
+- doc/images/wrench_orange.png
+- doc/images/zoom.png
+- doc/index.html
+- doc/js/darkfish.js
+- doc/js/jquery.js
+- doc/js/navigation.js
+- doc/js/search.js
+- doc/js/search_index.js
+- doc/js/searcher.js
+- doc/rdoc.css
+- doc/table_of_contents.html
 - examples/.DS_Store
 - examples/annotate_snps.rb
 - examples/data.txt
@@ -107,8 +178,17 @@ files:
 - lib/bio/graphics/primitive.rb
 - lib/bio/graphics/svgee.rb
 - lib/bio/graphics/track.rb
+- test/gene.gff
 - test/helper.rb
+- test/json_config.json
 - test/test_bio-svgenes.rb
+- test/test_glyph.rb
+- test/test_mini_feature.rb
+- test/test_page.rb
+- test/test_primitive.rb
+- test/test_svgee.rb
+- test/test_track.rb
+- test/test_transcripts.gff
 homepage: http://github.com/danmaclean/bioruby-svgenes
 licenses:
 - MIT
@@ -124,7 +204,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1694400785006489552
+      hash: 424523065025967701
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -133,7 +213,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: Create pretty SVG-format images of features, gene models and data tracks