# File lib/bio/db/aaindex.rb, line 217
217:     def initialize(entry)
218:       super(entry)
219:     end

     # File lib/bio/db/aaindex.rb, line 242
242:     def [](aa1 = nil, aa2 = nil)
243:       matrix[cols.index(aa1), rows.index(aa2)]
244:     end

     # File lib/bio/db/aaindex.rb, line 232
232:     def cols
233:       if @data['cols']
234:         @data['cols']
235:       else 
236:         label_data
237:         @cols
238:       end
239:     end

     # File lib/bio/db/aaindex.rb, line 247
247:     def matrix(aa1 = nil, aa2 = nil)
248:       return self[aa1, aa2] if aa1 and aa2
249: 
250:       if @data['matrix'] 
251:         @data['matrix'] 
252:       else
253:         ma = []
254:         label_data.each_line do |line|
255:           ma << line.strip.split(/\s+/).map {|x| x.to_f }
256:         end
257:         @data['matrix'] = Matrix[*ma]
258:       end
259:     end

     # File lib/bio/db/aaindex.rb, line 262
262:     def old_matrix # for AAindex <= ver 5.0
263:       return @data['matrix'] if @data['matrix']
264: 
265:       @aa = {} 
266:       # used to determine row/column of the aa
267:       attr_reader :aa
268:       alias_method :aa, :rows
269:       alias_method :aa, :cols
270: 
271:       field = field_fetch('I')
272: 
273:       case field
274:       when / (ARNDCQEGHILKMFPSTWYV)\s+(.*)/ # 20x19/2 matrix
275:         aalist = $1
276:         values = $2.split(/\s+/)
277: 
278:         0.upto(aalist.length - 1) do |i|
279:           @aa[aalist[i].chr] = i
280:         end
281: 
282:         ma = Array.new
283:         20.times do
284:           ma.push(Array.new(20)) # 2D array of 20x(20)
285:         end
286: 
287:         for i in 0 .. 19 do
288:           for j in i .. 19 do
289:             ma[i][j] = values[i + j*(j+1)/2].to_f
290:             ma[j][i] = ma[i][j]
291:           end
292:         end
293:         @data['matrix'] = Matrix[*ma]
294:       when / -ARNDCQEGHILKMFPSTWYV / # 21x20/2 matrix (with gap)
295:         raise NotImplementedError
296:       when / ACDEFGHIKLMNPQRSTVWYJ- / # 21x21 matrix (with gap)
297:         raise NotImplementedError
298:       end
299:     end

     # File lib/bio/db/aaindex.rb, line 222
222:     def rows
223:       if @data['rows']
224:         @data['rows']
225:       else 
226:         label_data
227:         @rows
228:       end
229:     end