class Bio::KEGG::KGML::Entry

Bio::KEGG:Entry contains an entry element in the KGML.

Attributes

category[RW]

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)

category=[RW]

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)

components[RW]

component elements included in this entry (Array containing Integer objects, or nil)

entry_id[RW]

ID of this entry in this pathway map (Integer or nil). ('id' attribute in 'entry' element)

entry_id=[RW]

ID of this entry in this pathway map (Integer or nil). ('id' attribute in 'entry' element)

graphics[RW]

graphics elements included in this entry (Array containing Graphics objects, or nil)

id[RW]

ID of this entry in this pathway map (Integer or nil). ('id' attribute in 'entry' element)

name[RW]

KEGG-style ID string of this entry (String or nil)

pathway[RW]

(Deprecated?) ('map' attribute in 'entry' element)

reaction[RW]

KEGG-style ID string of this reaction (String or nil)

type[RW]

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

bgcolor() click to toggle source

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
360 def bgcolor
361   _graphics_attr(:bgcolor)
362 end
bgcolor=(val) click to toggle source

Deprecated. Same as self.graphics.bgcolor= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
367 def bgcolor=(val)
368   _graphics_set_attr(:bgcolor=, val)
369 end
fgcolor() click to toggle source

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
345 def fgcolor
346   _graphics_attr(:fgcolor)
347 end
fgcolor=(val) click to toggle source

Deprecated. Same as self.graphics.fgcolor= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
352 def fgcolor=(val)
353   _graphics_set_attr(:fgcolor=, val)
354 end
height() click to toggle source

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
330 def height
331   _graphics_attr(:height)
332 end
height=(val) click to toggle source

Deprecated. Same as self.graphics.height= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
337 def height=(val)
338   _graphics_set_attr(:height=, val)
339 end
label() click to toggle source

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
248 def label
249   _graphics_attr(:name)
250 end
label=(val) click to toggle source

Deprecated. Same as self.graphics.name= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
255 def label=(val)
256   _graphics_set_attr(:name=, val)
257 end
names() click to toggle source

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
382 def names
383   @name.split(/\s+/)
384 end
shape() click to toggle source

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
270 def shape
271   _graphics_attr(:type)
272 end
shape=(val) click to toggle source

Deprecated. Same as self.graphics.type= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
277 def shape=(val)
278   _graphics_set_attr(:type=, val)
279 end
width() click to toggle source

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
315 def width
316   _graphics_attr(:width)
317 end
width=(val) click to toggle source

Deprecated. Same as self.graphics.width= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
322 def width=(val)
323   _graphics_set_attr(:width=, val)
324 end
x() click to toggle source

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
285 def x
286   _graphics_attr(:x)
287 end
x=(val) click to toggle source

Deprecated. Same as self.graphics.x= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
292 def x=(val)
293   _graphics_set_attr(:x=, val)
294 end
y() click to toggle source

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
300 def y
301   _graphics_attr(:y)
302 end
y=(val) click to toggle source

Deprecated. Same as self.graphics.y= (additional nil checks may be needed).

    # File lib/bio/db/kegg/kgml.rb
307 def y=(val)
308   _graphics_set_attr(:y=, val)
309 end