require "matr/version"

module Matr
  def self.default_opt opts, key, default
    opts.has_key?(key) ? opts[key] : default
  end

  def self.main opts

    infile               = opts[:infile]
    mode                 = self.default_opt opts, :mode, "ava"
    self_score           = self.default_opt opts, :self_score, 100
    ensure_self_scores   = self.default_opt opts, :ensure_self_scores, true
    no_header = self.default_opt opts, :no_header, false

    if opts[:na_replace_given]
      missing_score = opts[:na_replace]
    else
      missing_score = "na"
    end

    output_style = self.default_opt opts, :output_style, "wide"

    unless File.exist? infile
      raise StandardError, "FATAL -- infile '#{infile}' does not exist"
    end

    unless output_style == "wide" || output_style == "long"
      raise StandardError, "FATAL -- output style must be either wide or long"
    end

    graph    = Hash.new { |ht, k| ht[k] = Hash.new }
    all_keys = Set.new
    header   = nil

    File.open(infile, "rt").each_line.with_index do |line, idx|
      line.chomp!

      if idx.zero? && !no_header
        header = line
      else
        source, target, score = line.split "\t"

        all_keys << source << target

        # If you have duplicates with different scores, that's an error: a
        # => b = 10 and a => b = 20
        if graph[source].has_key?(target) && graph[source][target] != score
          raise StandardError, "FATAL -- source--target (#{source}--#{target}) was repeated with a different score.  Old score was #{graph[source][target]}, and the new score was #{score}."
        end

        graph[source][target] = score

        if mode == "ava_symmetric"
          # Since you might have a files that specifies a => b = 10, and b
          # => a = 10, that would be okay.  But if you have a => b = 10, and
          # b => a = 5, then that would be an error.
          if graph[target].has_key?(source) && graph[target][source] != score
            raise StandardError, "FATAL -- target--source (#{target}--#{source}) is specified seperately from source--target (#{source}--#{target}), BUT their scores do not match.  This means your matrix is NOT symmetric.  Did you really mean to pass the --ensure-symmetry flag?"
          end

          graph[target][source] = score
        end
      end
    end

    all_keys = all_keys.to_a.sort

    # Zip through and add any self scores that weren't added.
    all_keys.each do |source|
      all_keys.each do |target|
        # With ensure_self_scores, we overwrite the self score even if it was already given.  Otherwise, only if it was NOT given.
        if source == target && (ensure_self_scores || !graph[source][target])
          graph[source][target] = self_score
        end
      end
    end

    if output_style == "long"
      puts header unless no_header

      all_keys.each do |source|
        all_keys.each do |target|
          puts [source, target, graph[source][target] || missing_score].join "\t"
        end
      end
    else
      puts ["", all_keys].join "\t"

      all_keys.each do |source|
        row = all_keys.map do |target|
          graph[source][target] || missing_score
        end

        puts [source, row].join "\t"
      end
    end
  end
end