Class: Bio::Genscan::Report::Gene

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/genscan/report.rb

Overview

Container class of predicted gene structures.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(gn) ⇒ Gene

Bio::Genescan::Report::Gene.new(gene_number)



197
198
199
200
201
202
203
204
 
# File 'lib/bio/appl/genscan/report.rb', line 197

def initialize(gn)
  @number = gn.to_i
  @aaseq = Bio::FastaFormat.new("")
  @naseq = Bio::FastaFormat.new("")
  @promoter = nil
  @exons    = []
  @polyA    = nil
end

Instance Attribute Details

#aaseq ⇒ Object (readonly)

Returns Bio::FastaFormat object.



210
211
212
 
# File 'lib/bio/appl/genscan/report.rb', line 210

def aaseq
  @aaseq
end

#exons ⇒ Object (readonly)

Returns Array of Bio::Genscan::Report::Exon.



216
217
218
 
# File 'lib/bio/appl/genscan/report.rb', line 216

def exons
  @exons
end

#naseq ⇒ Object (readonly)

Returns Bio::FastaFormat object.



213
214
215
 
# File 'lib/bio/appl/genscan/report.rb', line 213

def naseq
  @naseq
end

#number ⇒ Object (readonly)

Returns “Gn”, gene number field.



207
208
209
 
# File 'lib/bio/appl/genscan/report.rb', line 207

def number
  @number
end

#polyA ⇒ Object (readonly)

Returns Bio::Genscan::Report::Exon object.



222
223
224
 
# File 'lib/bio/appl/genscan/report.rb', line 222

def polyA
  @polyA
end

#promoter ⇒ Object (readonly)

Returns Bio::Genscan::Report::Exon object.



219
220
221
 
# File 'lib/bio/appl/genscan/report.rb', line 219

def promoter
  @promoter
end

Instance Method Details

#set_aaseq(seq) ⇒ Object

Bio::Genescan::Report::Gene#seq_aaseq



226
227
228
 
# File 'lib/bio/appl/genscan/report.rb', line 226

def set_aaseq(seq)
  @aaseq = seq
end

#set_naseq(seq) ⇒ Object

Bio::Genescan::Report::Gene#seq_naseq



232
233
234
 
# File 'lib/bio/appl/genscan/report.rb', line 232

def set_naseq(seq)
  @naseq = seq
end

#set_polyA(segment) ⇒ Object

Bio::Genescan::Report::Gene#seq_polyA



244
245
246
 
# File 'lib/bio/appl/genscan/report.rb', line 244

def set_polyA(segment)
  @polyA = segment
end

#set_promoter(segment) ⇒ Object

Bio::Genescan::Report::Gene#seq_promoter



238
239
240
 
# File 'lib/bio/appl/genscan/report.rb', line 238

def set_promoter(segment)
  @promoter = segment
end