+
+
+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. +
+The command +
+mask SETUP +
+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: +
+mask RESET +
+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. +
+