Class Bio::TRANSFAC::MATRIX
In: lib/bio/db/transfac.rb
Parent: TRANSFAC

Methods

ba   bf   de   ma   na   new  

Public Class methods

[Source]

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

Public Instance methods

BA Statistical basis

[Source]

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

BF List of linked factor entries

[Source]

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

DE Short factor description

[Source]

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

[Source]

     # File lib/bio/db/transfac.rb, line 110
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:         rep_nt = 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 Name of the binding factor

[Source]

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

[Validate]