class Bio::TRANSFAC::MATRIX

Public Class Methods

new(entry) click to toggle source

Calls superclass method Bio::TRANSFAC::new

   # File lib/bio/db/transfac.rb
90 def initialize(entry)
91   super(entry)
92 end

Public Instance Methods

ba() click to toggle source

BA Statistical basis

    # File lib/bio/db/transfac.rb
132 def ba
133   field_fetch('BA')
134 end

bf() click to toggle source

BF List of linked factor entries

    # File lib/bio/db/transfac.rb
105 def bf
106   field_fetch('bf')
107 end

de() click to toggle source

DE Short factor description

    # File lib/bio/db/transfac.rb
100 def de
101   field_fetch('DE')
102 end

ma() click to toggle source

    # File lib/bio/db/transfac.rb
110 def ma
111   ma_dat = {}
112   ma_ary = []
113   key = ''
114   @orig.each do |k, v|
115     if k =~ /^0*(\d+)/
116       key = $1.to_i
117       ma_dat[key] = fetch(k) unless ma_dat[key]
118     end
119   end
120   ma_dat.keys.sort.each_with_index do |k, i|
121     ma_dat[k].slice!(-1, 1)
122     ma_dat[k].slice!(-1, 1)
123     ma_ary[i] = ma_dat[k].split(/\s+/)
124     ma_ary[i].each_with_index do |x, j|
125       ma_ary[i][j] = x.to_i
126     end
127   end
128   Matrix[*ma_ary]
129 end

na() click to toggle source

NA Name of the binding factor

   # File lib/bio/db/transfac.rb
95 def na
96   field_fetch('NA')
97 end