class Bio::KEGG::KGML::Entry
Bio::KEGG:Entry contains an entry element in the KGML.
Attributes
type of this entry (String or nil). Normally one of the following:
-
“ortholog”
-
“enzyme”
-
“reaction”
-
“gene”
-
“group”
-
“compound”
-
“map”
See www.genome.jp/kegg/xml/docs/ for details. ('type' attribute in 'entry' element)
type of this entry (String or nil). Normally one of the following:
-
“ortholog”
-
“enzyme”
-
“reaction”
-
“gene”
-
“group”
-
“compound”
-
“map”
See www.genome.jp/kegg/xml/docs/ for details. ('type' attribute in 'entry' element)
component elements included in this entry (Array containing Integer objects, or nil)
ID of this entry in this pathway map (Integer or nil). ('id' attribute in 'entry' element)
ID of this entry in this pathway map (Integer or nil). ('id' attribute in 'entry' element)
graphics elements included in this entry (Array containing Graphics objects, or nil)
ID of this entry in this pathway map (Integer or nil). ('id' attribute in 'entry' element)
URL pointing information about this entry (String or nil)
KEGG-style ID string of this entry (String or nil)
(Deprecated?) ('map' attribute in 'entry' element)
KEGG-style ID string of this reaction (String or nil)
type of this entry (String or nil). Normally one of the following:
-
“ortholog”
-
“enzyme”
-
“reaction”
-
“gene”
-
“group”
-
“compound”
-
“map”
See www.genome.jp/kegg/xml/docs/ for details. ('type' attribute in 'entry' element)
Public Instance Methods
Deprecated. Same as self.graphics.bgcolor (additional nil checks may be needed).
background color (String or nil) ('graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 360 def bgcolor _graphics_attr(:bgcolor) end
Deprecated. Same as self.graphics.bgcolor= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 367 def bgcolor=(val) _graphics_set_attr(:bgcolor=, val) end
Deprecated. Same as self.graphics.fgcolor (additional nil checks may be needed).
foreground color (String or nil) ('graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 345 def fgcolor _graphics_attr(:fgcolor) end
Deprecated. Same as self.graphics.fgcolor= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 352 def fgcolor=(val) _graphics_set_attr(:fgcolor=, val) end
Deprecated. Same as self.graphics.height (additional nil checks may be needed).
height (Integer or nil) ('graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 330 def height _graphics_attr(:height) end
Deprecated. Same as self.graphics.height= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 337 def height=(val) _graphics_set_attr(:height=, val) end
Deprecated. Same as self.graphics.name (additional nil checks may be needed).
label of the 'graphics' element (String or nil) ('name' attribute in 'graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 248 def label _graphics_attr(:name) end
Deprecated. Same as self.graphics.name= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 255 def label=(val) _graphics_set_attr(:name=, val) end
the “name” attribute may contain multiple names separated with space characters. This method returns the names as an array. (Array containing String objects)
# File lib/bio/db/kegg/kgml.rb, line 382 def names @name.split(/\s+/) end
Deprecated. Same as self.graphics.type (additional nil checks may be needed).
shape of the 'graphics' element (String or nil) Normally one of the following:
-
“rectangle”
-
“circle”
-
“roundrectangle”
-
“line”
If not specified, “rectangle” is the default value. ('type' attribute in 'graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 270 def shape _graphics_attr(:type) end
Deprecated. Same as self.graphics.type= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 277 def shape=(val) _graphics_set_attr(:type=, val) end
Deprecated. Same as self.graphics.width (additional nil checks may be needed).
width (Integer or nil) ('graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 315 def width _graphics_attr(:width) end
Deprecated. Same as self.graphics.width= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 322 def width=(val) _graphics_set_attr(:width=, val) end
Deprecated. Same as self.graphics.x (additional nil checks may be needed).
X axis position (Integer or nil) ('graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 285 def x _graphics_attr(:x) end
Deprecated. Same as self.graphics.x= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 292 def x=(val) _graphics_set_attr(:x=, val) end
Deprecated. Same as self.graphics.y (additional nil checks may be needed).
Y axis position (Integer or nil) ('graphics' element)
# File lib/bio/db/kegg/kgml.rb, line 300 def y _graphics_attr(:y) end
Deprecated. Same as self.graphics.y= (additional nil checks may be needed).
# File lib/bio/db/kegg/kgml.rb, line 307 def y=(val) _graphics_set_attr(:y=, val) end
Private Instance Methods
(private) get an attribute value in the graphics object
# File lib/bio/db/kegg/kgml.rb, line 222 def _graphics_attr(attr) if self.graphics then g = self.graphics[-1] g ? g.__send__(attr) : nil else nil end end
(private) get an attribute value in the graphics object
# File lib/bio/db/kegg/kgml.rb, line 233 def _graphics_set_attr(attr, val) self.graphics ||= [] unless g = self.graphics[-1] then g = Graphics.new self.graphics.push(g) end g.__send__(attr, val) end