function comparison_matrix(seq)
  matrix = {}
  for i=1,#seq do
    matrix[i] = {}
    for j=1,#seq do
      if seq[i] == seq[j] then
        matrix[i][j] = 1
      else
        matrix[i][j] = 0
      end
    end
  end
  return matrix
end

function split_char(seq)
  t = {}
  seq:gsub(".",function(c) table.insert(t,c) end)
  return t
end

function repr_matrix(matrix)
  repr = ""
  for i=1,#matrix do
    for j=1,#matrix do
      repr = repr .. matrix[i][j] .. " "
    end
    repr = repr .. "\n"
  end
  return repr
end
function comparison_matrix_tabular(matrix, seq1, seq2)
  seq2 = seq2 or seq1
  n=#seq1
  m=#seq2
  repr = [[\begin{tabular}{]] .. string.rep("c", n+1) .. "} \n"
  repr = repr .. "  "
  for i=1,n do
    repr = repr .. "& " .. seq1[i] .. " "
  end
  repr = repr .. "\\\\ \n "
  for j=1,m do
    repr = repr .. seq2[j] .. " "
    for i=1,n do
      repr = repr .. "& " .. matrix[i][j] .. " "
    end
    repr = repr .. " \\\\ \n "
  end
  repr = repr .. [[\end{tabular}]]
  return repr
end

function main()
  seq = split_char("ACGUUACGUUGUU")

  matrix = comparison_matrix(seq)

  print(comparison_matrix_tabular(matrix, seq))
end

function repr_comparison_matrix(seq)
  seq = split_char(seq)
  matrix = comparison_matrix(seq)
  return comparison_matrix_tabular(matrix, seq)
end

main()

return { comparison_matrix=comparison_matrix, comparison_matrix_tabular, repr_comparison_matrix=repr_comparison_matrix }