The idea behind the MASK command is to build up a set of character positions that will subsequently be boxed, shaded, set in a particular font, etc. For example, lets say we want to box the most frequently occuring character at each position in an alignment.
tells ALSCRIPT to prepare a mask.
mask FRE ALL
specifies that the most frequently occuring character at each position in the alignment will be masked. This command can be restricted to a region of the alignment using: mask FRE sx sy ex ey, where sx etc define the region in the same way as for font_region and other commands.
mask BOX ALL
Tells ALSCRIPT to create the boxing lines that will separate the masked characters from non-masked characters - this command may also be restricted to a region of the alignment.
The mask can be reset for re-use using the command:
Two further commands define which characters can be used when calculating the mask. This allows gap-characters, or other amino acids to be excluded from the calculation to avoid unwanted boxing.
mask LEGAL "AVLI"
defines the AVL and I as the only characters that will be used when calculating the mask.
mask ILLEGAL ".-_"
defines .- and _ as characters that will not be used when calculating the mask. NOTE: the blank character " " cannot be defined in this way. To avoid boxing " " characters substitute blanks for something else (using SUB_CHARS), calculate the mask, then substitute back.