# File lib/bio/shell/plugin/seq.rb, line 208
208:   def fill(fill_column = 80, indent = 0, separater = ' ', prefix = '', first_line_only = true)
209: 
210:     # size : allowed length of the actual text
211:     unless (size = fill_column - indent) > 0
212:       warn "Error: indent > fill_column (indent is set to 0)"
213:       size = fill_column
214:       indent = 0
215:     end
216: 
217:     n = pos = 0
218:     ary = []
219:     while n < self.length
220:       pos = self[n, size].rindex(separater)
221: 
222:       if self[n, size].length < size    # last line of the folded str
223:         pos = nil
224:       end
225: 
226:       if pos
227:         ary << self[n, pos+separater.length]
228:         n += pos + separater.length
229:       else                              # line too long or the last line
230:         ary << self[n, size]
231:         n += size
232:       end
233:     end
234:     str = ary.join("\n")
235: 
236:     str[0,0] = prefix + ' ' * (indent - prefix.length)
237:     if first_line_only
238:       head = ' ' * indent
239:     else
240:       head = prefix + ' ' * (indent - prefix.length)
241:     end
242:     str.gsub!("\n", "\n#{head}")
243: 
244:     return str.chomp
245:   end

     # File lib/bio/shell/plugin/seq.rb, line 190
190:   def fold(fill_column = 72, indent = 0)
191:     str = ''
192: 
193:     # size : allowed length of the actual text
194:     unless (size = fill_column - indent) > 0
195:       warn "Error: indent > fill_column (indent is set to 0)"
196:       size = fill_column
197:       indent = 0
198:     end
199: 
200:     0.step(self.length - 1, size) do |n|
201:       str << ' ' * indent + self[n, size] + "\n"
202:     end
203: 
204:     return str
205:   end

     # File lib/bio/shell/plugin/seq.rb, line 171
171:   def skip(window_size, step_size = 1)
172:     i = 0
173:     0.step(self.length - window_size, step_size) do |i|
174:       yield [self[i, window_size], i + 1, i + window_size]
175:     end
176:     from = i + step_size
177:     to  = [self.length, i + step_size + window_size].min
178:     yield [self[from, window_size], from + 1, to] if from + 1 <= to
179:   end

     # File lib/bio/shell/plugin/seq.rb, line 163
163:   def step(window_size)
164:     i = 0
165:     0.step(self.length - window_size, window_size) do |i|
166:       yield self[i, window_size]
167:     end
168:     yield self[i + window_size .. -1] if i + window_size < self.length
169:   end

     # File lib/bio/shell/plugin/seq.rb, line 185
185:   def to_aaseq
186:     Bio::Sequence::AA.new(self)
187:   end

     # File lib/bio/shell/plugin/seq.rb, line 181
181:   def to_naseq
182:     Bio::Sequence::NA.new(self)
183:   end