class IGV

# File lib/igv.rb, line 14
def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
  @host = host
  @port = port
  @history = []
  connect
  set_snapshot_dir(snapshot_dir)
end

# File lib/igv.rb, line 74
def clear
  send 'clear'
end

# File lib/igv.rb, line 70
def collapse(_track = '')
  send "collapse #{track}"
end

# File lib/igv.rb, line 25
def connect
  @socket&.close
  @socket = Socket.new(Socket::AF_INET, Socket::SOCK_STREAM)
  addr = Socket.sockaddr_in(port, host)
  @socket.connect(addr)
end

# File lib/igv.rb, line 78
def exit
  send 'exit'
end

# File lib/igv.rb, line 66
def expand(_track = '')
  send "expand #{track}"
end

# File lib/igv.rb, line 37
def genome(name_or_path)
  path = File.expand_path(name_or_path)
  if File.exist?(path)
    send "genome #{path}"
  else
    send "genome #{name_or_path}"
  end
end

# File lib/igv.rb, line 32
def go(position)
  send "goto #{position}"
end

# File lib/igv.rb, line 46
def load(path_or_url)
  if URI.parse(path_or_url).scheme
    send "load #{path_or_url}"
  else
    send "load #{File.expand_path(path_or_url)}"
  end
end

# File lib/igv.rb, line 54
def region(contig, start, end_)
  send ['region', contig, start, end_].join(' ')
end

# File lib/igv.rb, line 99
def save(file_path = nil)
  if file_path
    # igv assumes the path is just a single filename, but
    # we can set the snapshot dir. then just use the filename.
    dir_path = File.dirname(file_path)
    set_snapshot_dir(File.expand_path(dir_path)) if dir_path != '.'
    send "snapshot #{File.basename(file_path)}"
  else
    send 'snapshot'
  end
end

# File lib/igv.rb, line 83
def send(cmd)
  @history << cmd
  @socket.puts(cmd.encode(Encoding::UTF_8))
  @socket.gets&.chomp("\n")
end

# File lib/igv.rb, line 89
def snapshot_dir=(snapshot_dir)
  snapshot_dir = File.expand_path(snapshot_dir)
  return if snapshot_dir == @snaphot_dir

  FileUtils.mkdir_p(snapshot_dir)
  send "snapshotDirectory #{snapshot_dir}"
  @snapshot_dir = snapshot_dir
end

# File lib/igv.rb, line 58
def sort(option = 'base')
  unless %w[base position strand quality sample readGroup].include? option
    raise 'options is one of: base, position, strand, quality, sample, and readGroup.'
  end

  send "sort #{option}"
end