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, line 360
def bgcolor
  _graphics_attr(:bgcolor)
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, line 367
def bgcolor=(val)
  _graphics_set_attr(:bgcolor=, val)
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, line 345
def fgcolor
  _graphics_attr(:fgcolor)
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, line 352
def fgcolor=(val)
  _graphics_set_attr(:fgcolor=, val)
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, line 330
def height
  _graphics_attr(:height)
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, line 337
def height=(val)
  _graphics_set_attr(:height=, val)
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, line 248
def label
  _graphics_attr(:name)
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, line 255
def label=(val)
  _graphics_set_attr(:name=, val)
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, line 382
def names
  @name.split(/\s+/)
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, line 270
def shape
  _graphics_attr(:type)
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, line 277
def shape=(val)
  _graphics_set_attr(:type=, val)
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, line 315
def width
  _graphics_attr(:width)
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, line 322
def width=(val)
  _graphics_set_attr(:width=, val)
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, line 285
def x
  _graphics_attr(:x)
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, line 292
def x=(val)
  _graphics_set_attr(:x=, val)
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, line 300
def y
  _graphics_attr(:y)
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, line 307
def y=(val)
  _graphics_set_attr(:y=, val)
end