bio-svgenes 0.3.0 → 0.3.1

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@@ -1,16 +1,25 @@
1
1
  module Bio
2
2
  class Graphics
3
-
3
+ #The Primitive class is used to hold information about Glyphs.
4
+ #They contain a Glyph type and then a Hash of parameters pertinent for that Glyph
4
5
  class Primitive
5
6
  attr_reader :primitive
6
-
7
+ #Creates a new Primitive and initialises the Hash keys into instance variables
8
+ #
9
+ #+args+
10
+ #* primitive = the Primitive type
11
+ #* args = a hash of parameters needed to initialise the given Glyph type
7
12
  def initialize(primitive,args)
8
13
  @primitive = primitive
9
14
  args.each_key do |k|
10
15
  self.instance_variable_set("@#{k}", args[k])
11
16
  end
12
17
  end
13
-
18
+
19
+ #Updates a Primitive and initialises any new parameters into instance variables
20
+ #
21
+ #+args+
22
+ #* args = a hash of new parameters for the given Glyph type
14
23
  def update(args)
15
24
  args.each_key do |k|
16
25
  self.instance_variable_set("@#{k}", args[k])
@@ -1,8 +1,19 @@
1
1
  module Bio
2
2
  class Graphics
3
-
3
+ #The SVGEE class is used to create the text that will go into the final SVG file.
4
+ #It takes information from the supplied Glyph objects, parses them and creates the SVG text
5
+ #necessary to display the given glyphs.
4
6
  class SVGEE
5
7
  attr_reader :primitives, :defs, :supported_primitives
8
+ #Creates a new SVGEE object which will contain all the necessary objects to display all the features on a page
9
+ #
10
+ #+args+
11
+ #* width = the amount of the page width the svg should take up (100%)
12
+ #* height = the amount of the page height the svg should take up (100%)
13
+ #* style = the svg style information
14
+ #* primitives = an array of glyphs
15
+ #* defs = the gradients that will be used in the SVG
16
+ #* \supported_primitives = a list of permitted Glyphs
6
17
  def initialize(args)
7
18
  opts = {:width => '100%', :height => '100%'}.merge!(args)
8
19
  @width = opts[:width]
@@ -12,11 +23,11 @@ class SVGEE
12
23
  @defs = []
13
24
  @supported_primitives = [:circle, :rectangle, :ellipse, :line, :polyline, :text]
14
25
  end
15
-
26
+ #Produces the opening text for an svg file
16
27
  def open_tag
17
28
  %{<svg xmlns="http://www.w3.org/2000/svg" version="1.1" width="#{@width}" height="#{@height}" style="#{@style}" xmlns:xlink="http://www.w3.org/1999/xlink">}
18
29
  end
19
-
30
+ #Produces the closing text for an svg file
20
31
  def close_tag
21
32
  %{</svg>}
22
33
  end
@@ -81,13 +92,15 @@ class SVGEE
81
92
  end
82
93
 
83
94
  public
84
- def add_primitive(primitive_object) #adds a primitive object to the SVG
95
+ #Adds a Primitive object to the SVGEE object and makes the svg text for that Primitive
96
+ def add_primitive(primitive_object)
85
97
  args = {}
86
98
  primitive_object.instance_variables.each{|v| args[v.to_s.gsub(/@/,"").to_sym] = primitive_object.instance_variable_get(v) }
87
99
  primitive_string = args.delete(:primitive)
88
100
  make_tag(primitive_string, args)
89
101
  end
90
-
102
+ #Takes the gradient information from a Glyph, which must be of type 'radial' or 'linear' and creates the svg text for that gradient
103
+ #* +a+ = a gradient (a gradient type, a colour and the parameters for a given type)
91
104
  def gradient(a)
92
105
  definition_string = case a[:type]
93
106
  when :radial
@@ -100,7 +113,7 @@ class SVGEE
100
113
  end
101
114
  add_def definition_string + (a[:type] == :linear ? '</linearGradient>' : '</radialGradient>')
102
115
  end
103
-
116
+ #Produces the svg text to display all the features on a Page
104
117
  def draw
105
118
  head = self.open_tag
106
119
  defstring = ""
@@ -1,9 +1,11 @@
1
1
  module Bio
2
2
  class Graphics
3
+ #The Track class holds and organises the features, ordering them into different rows if they overlap
3
4
 
4
5
  class Track
5
6
  attr_reader :glyph, :name, :label, :args, :track_height, :scale, :max_y, :min_width
6
7
  attr_accessor :features, :feature_rows, :name, :number_rows, :feature_height
8
+ #Creates a new Track
7
9
  def initialize(args)
8
10
  @args = {:glyph => :generic,
9
11
  :name => "feature_track",
@@ -25,14 +27,15 @@ class Track
25
27
 
26
28
  end
27
29
 
28
-
30
+ #Adds a new MiniFeature to the the @features array
29
31
  def add(feature)
30
32
  @features << feature
31
33
  end
32
-
34
+
35
+ #Calculates how many rows are needed per track for overlapping features
36
+ #and which row each feature should be in
37
+
33
38
  def get_rows
34
- #works out how many rows are needed per track for overlapping features
35
- #and which row each feature should be in
36
39
  current_row = 1
37
40
  @feature_rows = Array.new(@features.length,1)
38
41
  @features.each_with_index do |f1, i|
@@ -45,7 +48,13 @@ class Track
45
48
  @number_rows = @feature_rows.max
46
49
  end
47
50
  end
48
-
51
+
52
+ #Calculates if two MiniFeature objects overlap by examining their start and end positions.
53
+ #If two features overlap then then will be placed on separate rows of the track
54
+ #
55
+ #+args+
56
+ #* f1 - a MiniFeature object
57
+ #* f2 - a MiniFeature object
49
58
  def overlaps(f1, f2)
50
59
  (f1.start >= f2.start and f1.start <= f2.end) or (f1.end >= f2.start and f1.end <= f2.end)
51
60
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-svgenes
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.3.0
4
+ version: 0.3.1
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2013-03-04 00:00:00.000000000 Z
12
+ date: 2013-03-05 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: shoulda
@@ -32,7 +32,7 @@ dependencies:
32
32
  requirement: !ruby/object:Gem::Requirement
33
33
  none: false
34
34
  requirements:
35
- - - ~>
35
+ - - ! '>='
36
36
  - !ruby/object:Gem::Version
37
37
  version: 1.0.0
38
38
  type: :development
@@ -40,7 +40,7 @@ dependencies:
40
40
  version_requirements: !ruby/object:Gem::Requirement
41
41
  none: false
42
42
  requirements:
43
- - - ~>
43
+ - - ! '>='
44
44
  - !ruby/object:Gem::Version
45
45
  version: 1.0.0
46
46
  - !ruby/object:Gem::Dependency
@@ -91,6 +91,22 @@ dependencies:
91
91
  - - ! '>='
92
92
  - !ruby/object:Gem::Version
93
93
  version: 1.4.2
94
+ - !ruby/object:Gem::Dependency
95
+ name: json
96
+ requirement: !ruby/object:Gem::Requirement
97
+ none: false
98
+ requirements:
99
+ - - ! '>='
100
+ - !ruby/object:Gem::Version
101
+ version: '1.7'
102
+ type: :development
103
+ prerelease: false
104
+ version_requirements: !ruby/object:Gem::Requirement
105
+ none: false
106
+ requirements:
107
+ - - ! '>='
108
+ - !ruby/object:Gem::Version
109
+ version: '1.7'
94
110
  description: This bio-gem facilitates the creation of pretty, publication quality
95
111
  SVG images from feature data.
96
112
  email: maclean.daniel@gmail.com
@@ -100,7 +116,6 @@ extra_rdoc_files:
100
116
  - LICENSE.txt
101
117
  - README.rdoc
102
118
  files:
103
- - .DS_Store
104
119
  - .document
105
120
  - Gemfile
106
121
  - Gemfile.lock
@@ -109,9 +124,7 @@ files:
109
124
  - Rakefile
110
125
  - VERSION
111
126
  - bio-svgenes.gemspec
112
- - doc/.DS_Store
113
127
  - doc/Bio.html
114
- - doc/Bio/.DS_Store
115
128
  - doc/Bio/Graphics.html
116
129
  - doc/Bio/Graphics/Glyph.html
117
130
  - doc/Bio/Graphics/MiniFeature.html
@@ -155,12 +168,9 @@ files:
155
168
  - doc/js/searcher.js
156
169
  - doc/rdoc.css
157
170
  - doc/table_of_contents.html
158
- - examples/.DS_Store
159
171
  - examples/annotate_snps.rb
160
172
  - examples/data.txt
161
173
  - examples/draw_from_json.rb
162
- - examples/drawn_from_json.svg
163
- - examples/drawn_from_json2.svg
164
174
  - examples/eg2.rb
165
175
  - examples/example.rb
166
176
  - examples/example.svg
@@ -169,19 +179,15 @@ files:
169
179
  - examples/get_coverage_in_windows.rb
170
180
  - examples/make_example.rb
171
181
  - examples/transcripts.gff
172
- - lib/.DS_Store
173
182
  - lib/bio-svgenes.rb
174
- - lib/bio/.DS_Store
175
183
  - lib/bio/graphics/glyph.rb
176
184
  - lib/bio/graphics/mini_feature.rb
177
185
  - lib/bio/graphics/page.rb
178
186
  - lib/bio/graphics/primitive.rb
179
187
  - lib/bio/graphics/svgee.rb
180
188
  - lib/bio/graphics/track.rb
181
- - test/gene.gff
182
189
  - test/helper.rb
183
190
  - test/json_config.json
184
- - test/test_bio-svgenes.rb
185
191
  - test/test_glyph.rb
186
192
  - test/test_mini_feature.rb
187
193
  - test/test_page.rb
@@ -204,7 +210,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
204
210
  version: '0'
205
211
  segments:
206
212
  - 0
207
- hash: 424523065025967701
213
+ hash: 1136117613783362089
208
214
  required_rubygems_version: !ruby/object:Gem::Requirement
209
215
  none: false
210
216
  requirements:
data/.DS_Store DELETED
Binary file
Binary file
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@@ -1,269 +0,0 @@
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