Class: String

Inherits:
Object show all
Defined in:
lib/bio/shell/plugin/seq.rb

Direct Known Subclasses

Bio::FANTOM::MaXML::Annotation::DataSrc, Bio::Sequence::AA, Bio::Sequence::Generic, Bio::Sequence::NA

Instance Method Summary (collapse)

Instance Method Details

- (Object) fill(fill_column = 80, indent = 0, separater = ' ', prefix = '', first_line_only = true)

folding with conscious about word boundaries with prefix string



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# File 'lib/bio/shell/plugin/seq.rb', line 208

def fill(fill_column = 80, indent = 0, separater = ' ', prefix = '', first_line_only = true)

  # size : allowed length of the actual text
  unless (size = fill_column - indent) > 0
    warn "Error: indent > fill_column (indent is set to 0)"
    size = fill_column
    indent = 0
  end

  n = pos = 0
  ary = []
  while n < self.length
    pos = self[n, size].rindex(separater)

    if self[n, size].length < size    # last line of the folded str
      pos = nil
    end

    if pos
      ary << self[n, pos+separater.length]
      n += pos + separater.length
    else                              # line too long or the last line
      ary << self[n, size]
      n += size
    end
  end
  str = ary.join("\n")

  str[0,0] = prefix + ' ' * (indent - prefix.length)
  if first_line_only
    head = ' ' * indent
  else
    head = prefix + ' ' * (indent - prefix.length)
  end
  str.gsub!("\n", "\n#{head}")

  return str.chomp
end

- (Object) fold(fill_column = 72, indent = 0)

folding both line end justified



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# File 'lib/bio/shell/plugin/seq.rb', line 190

def fold(fill_column = 72, indent = 0)
  str = ''

  # size : allowed length of the actual text
  unless (size = fill_column - indent) > 0
    warn "Error: indent > fill_column (indent is set to 0)"
    size = fill_column
    indent = 0
  end

  0.step(self.length - 1, size) do |n|
    str << ' ' * indent + self[n, size] + "\n"
  end

  return str
end

- (Object) skip(window_size, step_size = 1) {|[self[from, window_size], from + 1, to]| ... }

Yields:

  • ([self[from, window_size], from + 1, to])


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# File 'lib/bio/shell/plugin/seq.rb', line 171

def skip(window_size, step_size = 1)
  i = 0
  0.step(self.length - window_size, step_size) do |i|
    yield [self[i, window_size], i + 1, i + window_size]
  end
  from = i + step_size
  to  = [self.length, i + step_size + window_size].min
  yield [self[from, window_size], from + 1, to] if from + 1 <= to
end

- (Object) step(window_size) {|self[i + window_size .. -1]| ... }

Yields:

  • (self[i + window_size .. -1])


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# File 'lib/bio/shell/plugin/seq.rb', line 163

def step(window_size)
  i = 0
  0.step(self.length - window_size, window_size) do |i|
    yield self[i, window_size]
  end
  yield self[i + window_size .. -1] if i + window_size < self.length
end

- (Object) to_aaseq



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# File 'lib/bio/shell/plugin/seq.rb', line 185

def to_aaseq
  Bio::Sequence::AA.new(self)
end

- (Object) to_naseq



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# File 'lib/bio/shell/plugin/seq.rb', line 181

def to_naseq
  Bio::Sequence::NA.new(self)
end