+
+
+mask SETUP +#Prepares for masking +
+mask LEGAL <qstring> +#defines characters to include in ID or FRE calcs - optional. +
+mask ILLEGAL <qstring> +#defines characters to exclude in ID or FRE calcs - optional. +
+mask ID ALL N +#Calculates a mask that flags the character that occurs at least N +times at a position. The word ALL can be substituted by four numbers +that define a region of the alignment. +
+mask FRE ALL +#calculates a mask that flags the most frequently occuring amino acid +at each position. ALL may be replaced by four numbers defining a region +of the alignment. +
+Multiple mask FRE or mask ID commands may be applied, using different +LEGAL and ILLEGAL character definitions. In this way more complex +effects can be built up. +
+The mask command also allows characters that are identical to one +sequence to be masked. +
+mask AGREE ALL N +
+will mask all positions that are identical to the Nth sequence. Thus, +for sequences that are very similar to a newly sequenced sequence, all +characters identical to the new sequence can be boxed or shaded, or set +in a different font or colour etc... +
+mask NOT ALL +
+allows the mask to be inverted. Thus, all positions that are NOT in the +mask now form the mask. So, having done a mask AGREE, a mask NOT will +allow the positions that are not identical to the selected sequence to +be highlighted or substituted. +
+mask SUB ALL <char> +
+substitutes all characters in the mask with the character <char>. +
+mask REGION ALL +applies a mask to all residues in the defined region. +
+The following effects can now be applied to the masked characters: +
+mask BOX ALL +#boxes the masked residues - ie surrounds them by lines. +
+mask SHADE ALL <grey> +#shades the masked residues by grey value. +
+mask FONT ALL <fontnum> +#Uses font fontnum to output the masked residues. +
+mask INVERSE ALL +#Inverts the masked characters - ie outputs them in white. +
+mask CCOL ALL <colnum> +#outputs the masked characters in the defined colour. +
+mask SCOL ALL <colnum> +#outputs the backgrounds of the masked characters in the defined +colour. +
+In all commands, the word ALL can be replaced by four numbers defining +the region to which the command is applied. +
+mask RESET +#resets the entire mask for re-use +
+
+