Module: Bio::BioAlignment::MaskSerialMutations

Includes:
MarkRows
Defined in:
lib/bio-alignment/edit/mask_serial_mutations.rb

Instance Method Summary collapse

Methods included from MarkRows

#mark_row_elements, #mark_rows

Instance Method Details

#mark_serial_mutations(min_serial = 5) ⇒ Object

edit copied alignment and mark elements if they are a continuous of unique mutations in the alignment. The default is at least 5 mutations in a row.



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# File 'lib/bio-alignment/edit/mask_serial_mutations.rb', line 12

def mark_serial_mutations min_serial=5
  mark_row_elements { |row,rownum| 
    # if an element is unique, mask it
    row.each_with_index do |e,colnum|
      e.state = ElementMaskedState.new
      column = columns[colnum]
      e.state.mask! if column.count{|e2| !e2.gap? and e2 == e } == 1
      # print e,',',e.state,';'
    end
    # now make sure there are at least 5 in a row, otherwise
    # start unmasking. First group all elements
    group = []
    row.each_with_index do |e,colnum|
      next if e.gap?
      if e.state.masked?
        group << e
      else
        if group.length <= min_serial
          # the group is too small
          group.each do | e2 |
            e2.state.unmask!
          end
        end
        group = []
      end
    end
    row  # return changed sequence
  }
end