Gap4 contains a separate menu for configuring the global behaviour of
options. However currently not all configurable parameters are
available to be adjusted from within this menu. The main configuration
of Gap4 comes from the .gaprc file which specifies all the
default and startup values to the dialogues.
Additionally, we describe here the window for configuring
colours. This window is common to several locations within Gap4
including the Contig Comparator and the Restriction Enzyme Map.