Class Bio::KEGG::KGML::Entry
In: lib/bio/db/kegg/kgml.rb
Parent: Object

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

Methods

bgcolor   bgcolor=   fgcolor   fgcolor=   height   height=   label   label=   names   shape   shape=   width   width=   x   x=   y   y=  

External Aliases

id -> entry_id
id= -> entry_id=
type -> category
type= -> category=

Attributes

components  [RW]  component elements included in this entry (Array containing Integer objects, or nil)
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)
link  [RW]  URL pointing information about this entry (String or nil)
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

Deprecated. Same as self.graphics[-1].bgcolor (additional nil checks may be needed).

background color (String or nil) (‘graphics’ element)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 360
360:     def bgcolor
361:       _graphics_attr(:bgcolor)
362:     end

Deprecated. Same as self.graphics[-1].bgcolor= (additional nil checks may be needed).

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 367
367:     def bgcolor=(val)
368:       _graphics_set_attr(:bgcolor=, val)
369:     end

Deprecated. Same as self.graphics[-1].fgcolor (additional nil checks may be needed).

foreground color (String or nil) (‘graphics’ element)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 345
345:     def fgcolor
346:       _graphics_attr(:fgcolor)
347:     end

Deprecated. Same as self.graphics[-1].fgcolor= (additional nil checks may be needed).

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 352
352:     def fgcolor=(val)
353:       _graphics_set_attr(:fgcolor=, val)
354:     end

Deprecated. Same as self.graphics[-1].height (additional nil checks may be needed).

height (Integer or nil) (‘graphics’ element)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 330
330:     def height
331:       _graphics_attr(:height)
332:     end

Deprecated. Same as self.graphics[-1].height= (additional nil checks may be needed).

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 337
337:     def height=(val)
338:       _graphics_set_attr(:height=, val)
339:     end

Deprecated. Same as self.graphics[-1].name (additional nil checks may be needed).

label of the ‘graphics’ element (String or nil) (‘name’ attribute in ‘graphics’ element)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 248
248:     def label
249:       _graphics_attr(:name)
250:     end

Deprecated. Same as self.graphics[-1].name= (additional nil checks may be needed).

[Source]

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

the "name" attribute may contain multiple names separated with space characters. This method returns the names as an array. (Array containing String objects)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 382
382:     def names
383:       @name.split(/\s+/)
384:     end

Deprecated. Same as self.graphics[-1].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)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 270
270:     def shape
271:       _graphics_attr(:type)
272:     end

Deprecated. Same as self.graphics[-1].type= (additional nil checks may be needed).

[Source]

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

Deprecated. Same as self.graphics[-1].width (additional nil checks may be needed).

width (Integer or nil) (‘graphics’ element)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 315
315:     def width
316:       _graphics_attr(:width)
317:     end

Deprecated. Same as self.graphics[-1].width= (additional nil checks may be needed).

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 322
322:     def width=(val)
323:       _graphics_set_attr(:width=, val)
324:     end

Deprecated. Same as self.graphics[-1].x (additional nil checks may be needed).

X axis position (Integer or nil) (‘graphics’ element)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 285
285:     def x
286:       _graphics_attr(:x)
287:     end

Deprecated. Same as self.graphics[-1].x= (additional nil checks may be needed).

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 292
292:     def x=(val)
293:       _graphics_set_attr(:x=, val)
294:     end

Deprecated. Same as self.graphics[-1].y (additional nil checks may be needed).

Y axis position (Integer or nil) (‘graphics’ element)

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 300
300:     def y
301:       _graphics_attr(:y)
302:     end

Deprecated. Same as self.graphics[-1].y= (additional nil checks may be needed).

[Source]

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

[Validate]