Class: Bio::KEGG::KGML::Entry

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/kegg/kgml.rb

Overview

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

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Instance Attribute Details

- (Object) components

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



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# File 'lib/bio/db/kegg/kgml.rb', line 377

def components
  @components
end

- (Object) graphics

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



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# File 'lib/bio/db/kegg/kgml.rb', line 373

def graphics
  @graphics
end

- (Object) id Also known as: entry_id

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



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# File 'lib/bio/db/kegg/kgml.rb', line 188

def id
  @id
end

URL pointing information about this entry (String or nil)



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# File 'lib/bio/db/kegg/kgml.rb', line 213

def link
  @link
end

- (Object) name

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



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# File 'lib/bio/db/kegg/kgml.rb', line 194

def name
  @name
end

- (Object) pathway

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



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# File 'lib/bio/db/kegg/kgml.rb', line 219

def pathway
  @pathway
end

- (Object) reaction

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



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# File 'lib/bio/db/kegg/kgml.rb', line 216

def reaction
  @reaction
end

- (Object) type Also known as: category

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)



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# File 'lib/bio/db/kegg/kgml.rb', line 207

def type
  @type
end

Instance Method Details

- (Object) bgcolor

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

background color (String or nil) ('graphics' element)



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# File 'lib/bio/db/kegg/kgml.rb', line 360

def bgcolor
  _graphics_attr(:bgcolor)
end

- (Object) bgcolor=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 367

def bgcolor=(val)
  _graphics_set_attr(:bgcolor=, val)
end

- (Object) fgcolor

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

foreground color (String or nil) ('graphics' element)



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# File 'lib/bio/db/kegg/kgml.rb', line 345

def fgcolor
  _graphics_attr(:fgcolor)
end

- (Object) fgcolor=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 352

def fgcolor=(val)
  _graphics_set_attr(:fgcolor=, val)
end

- (Object) height

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

height (Integer or nil) ('graphics' element)



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# File 'lib/bio/db/kegg/kgml.rb', line 330

def height
  _graphics_attr(:height)
end

- (Object) height=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 337

def height=(val)
  _graphics_set_attr(:height=, val)
end

- (Object) label

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)



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# File 'lib/bio/db/kegg/kgml.rb', line 248

def label
  _graphics_attr(:name)
end

- (Object) label=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 255

def label=(val)
  _graphics_set_attr(:name=, val)
end

- (Object) names

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



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# File 'lib/bio/db/kegg/kgml.rb', line 382

def names
  @name.split(/\s+/)
end

- (Object) shape

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)



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# File 'lib/bio/db/kegg/kgml.rb', line 270

def shape
  _graphics_attr(:type)
end

- (Object) shape=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 277

def shape=(val)
  _graphics_set_attr(:type=, val)
end

- (Object) width

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

width (Integer or nil) ('graphics' element)



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# File 'lib/bio/db/kegg/kgml.rb', line 315

def width
  _graphics_attr(:width)
end

- (Object) width=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 322

def width=(val)
  _graphics_set_attr(:width=, val)
end

- (Object) x

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

X axis position (Integer or nil) ('graphics' element)



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# File 'lib/bio/db/kegg/kgml.rb', line 285

def x
  _graphics_attr(:x)
end

- (Object) x=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 292

def x=(val)
  _graphics_set_attr(:x=, val)
end

- (Object) y

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

Y axis position (Integer or nil) ('graphics' element)



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# File 'lib/bio/db/kegg/kgml.rb', line 300

def y
  _graphics_attr(:y)
end

- (Object) y=(val)

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



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# File 'lib/bio/db/kegg/kgml.rb', line 307

def y=(val)
  _graphics_set_attr(:y=, val)
end