2 <TITLE> Summary of mask commands</TITLE>
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10 <H2><A NAME=SECTION00013100000000000000> Summary of mask commands</A></H2>
15 mask LEGAL <qstring>
16 #defines characters to include in ID or FRE calcs - optional.
18 mask ILLEGAL <qstring>
19 #defines characters to exclude in ID or FRE calcs - optional.
22 #Calculates a mask that flags the character that occurs at least N
23 times at a position. The word ALL can be substituted by four numbers
24 that define a region of the alignment.
27 #calculates a mask that flags the most frequently occuring amino acid
28 at each position. ALL may be replaced by four numbers defining a region
31 Multiple mask FRE or mask ID commands may be applied, using different
32 LEGAL and ILLEGAL character definitions. In this way more complex
33 effects can be built up.
35 The mask command also allows characters that are identical to one
36 sequence to be masked.
40 will mask all positions that are identical to the Nth sequence. Thus,
41 for sequences that are very similar to a newly sequenced sequence, all
42 characters identical to the new sequence can be boxed or shaded, or set
43 in a different font or colour etc...
47 allows the mask to be inverted. Thus, all positions that are NOT in the
48 mask now form the mask. So, having done a mask AGREE, a mask NOT will
49 allow the positions that are not identical to the selected sequence to
50 be highlighted or substituted.
52 mask SUB ALL <char>
54 substitutes all characters in the mask with the character <char>.
57 applies a mask to all residues in the defined region.
59 The following effects can now be applied to the masked characters:
62 #boxes the masked residues - ie surrounds them by lines.
64 mask SHADE ALL <grey>
65 #shades the masked residues by grey value.
67 mask FONT ALL <fontnum>
68 #Uses font fontnum to output the masked residues.
71 #Inverts the masked characters - ie outputs them in white.
73 mask CCOL ALL <colnum>
74 #outputs the masked characters in the defined colour.
76 mask SCOL ALL <colnum>
77 #outputs the backgrounds of the masked characters in the defined
80 In all commands, the word ALL can be replaced by four numbers defining
81 the region to which the command is applied.
84 #resets the entire mask for re-use
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