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