2 <TITLE> STEP 2 COMMANDS</TITLE>
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10 <H3><A NAME=SECTION00016140000000000000> STEP 2 COMMANDS</A></H3>
12 All these are optional formatting commands.
14 IMPORTANT PLEASE READ THIS NOTE:
16 For those commands that accept region definitions (e.g. SURROUND_CHARS) it
17 is easiest to think of the region being defined in terms of X and Y
18 coordinates, where X is the sequence residue coordinate and Y is the
19 sequence number coordinate. Thus 3 7 means the 3rd residue in sequence 7.
20 3 7 12 42 means the rectangular box bounded by residue 3 of sequence 7 and
21 residue 12 of sequence 42.
23 SURROUND_CHARS <string> ALL
25 Draw lines round, but not between the characters that are in the string.
30 will draw lines round all G and P characters in the alignment, but not
31 between adjacent G and P characters.
33 SURROUND_CHARS <string> <int> <int> <int> <int>
35 Similar command, but the surrounding is restricted to the region defined by
40 SURROUND_CHARS ILVW 3 12 7 32
42 would surround ILVW characters that occur in the region defined
43 from residue positions 3-7 of sequences 12 to 32.
45 SHADE_CHARS <string> ALL <float>
47 Shade all characters in the <string> by the grey value given by <float>.
50 SHADE_CHARS GP ALL 0.5
52 would shade all G and P characters in the alignment by the grey value 0.5.
54 SHADE_CHARS <string> <int> <int> <int> <int> <float>
56 restricts the shading to the region defined by the four integers. Thus
58 SHADE_CHARS ILVW 3 12 7 32 0.7
60 would shade I L V and W characters from residues 3-7 of sequences 12-32
61 inclusive with a grey value of 0.7.
63 FONT_CHARS <string> ALL <int>
69 would use font 7 to write out all G and P characters. Font 7 MUST have been
70 defined using the DEFINE_FONTcommands above.
72 FONT_CHARS <string> <int> <int> <int> <int> <int>
74 Similar to previous command, but restricts the effect to the region defined
75 by the first four integers. The font must have been defined by the
80 FONT_CHARS ILVW 3 45 9 70 7
82 Would set the font to 7 for I L V and W characters for residues 3-9 of
83 sequences 45-70 inclusive. The font must have been defined by the
86 FONT_REGION <int> <int> <int> <int> <int>
88 Define the font to use throughout the region specified by the first four
93 FONT_REGION 3 12 20 40 10
95 Use font 10 for residues from residues 3-20 of sequences 12-40. The font
96 must have been defined using the DEFINE_FONTcommand.
98 FONT_RESIDUE <int> <int> <int>
100 Set the font for use with a single residue position - most useful when used
101 with the TEXT command.
107 Use font 2 for residue 3 of sequence 7. Font 2 must have been defined using
108 the DEFINE_FONT command.
110 LINE <string> <int> <int> <int>
112 There are four commands of this type for drawing horizontal or vertical lines
115 LINE LEFT <int> <int> <int>
117 Draw a line to the left of the character positions indicated.
123 Draw a vertical line starting at residue 3 of sequence 12 and ending at
124 residue 3 of sequence 24.
128 Draw a horizontal line above the character positions from residue 3 of
129 sequence 12 to residue 24 of sequence 12.
131 Similar commands are:
133 LINE BOTTOM <int> <int> <int> Draw a line at bottom of character position.
135 LINE RIGHT <int> <int> <int> Draw a line at right of character position.
137 BOX_REGION <int> <int> <int> <int>
139 Draw a box around the region indicated by the four integers.
145 Would box from residue 2 of sequence 5 to residue 30 of sequence 7.
147 SHADE_REGION <int> <int> <int> <int> <float>
149 Shade the region indicated by the integers with the grey value shown by the
153 SHADE_REGION 30 40 35 46 0.2
155 Would shade from residue 30-35 of sequences 40-46 with a grey value of 0.2.
157 SHADE_RES <int> <int> <float>
159 Shade just one amino acid with the grey value.
165 Shades residue 3 of sequence 7. (Note: this can also be achieved with the
167 SHADE_REGION command, but requires 2 extra numbers)
169 TEXT <int> <int> <qstring>
171 Place the text string at the location indicated.
175 TEXT 30 70 "Active Site His"
177 would put the text Active Site His starting at position 30 of sequence
178 70. (Use FONT_RESIDUE or FONT_REGION commands to set the font of the
179 text). Text added with the TEXT command will not be split across page
180 breaks, so you may in some circumstances need to fiddle a little with
181 the location/pointsize for the text to get the desired result.
183 ID_FONT ALL <int>
185 Set the font for all identifier codes to the font number shown by <int>.
190 Would set all the identifier codes to font 3.
192 ID_FONT <int> <int>
194 Set the font for a specific identifier to font number.
199 Use font 4 for the identifer of sequence 12, default font for all other
202 SUB_CHARS ALL <char> <char>
204 Substitute the characters indicated.
210 would change all occurences of + to * in the alignment.
212 SUB_CHARS <int> <int> <int> <int> <char> <char>
214 restrict the substitution to the region shown.
220 would substitute * for %from residue 1-7 of sequences 1-8.
221 NOTE: To substitute for or with the space character use the word SPACE.
222 e.g. to change all space characters to -.
224 SUB_CHARS ALL SPACE -
226 SUB_ID <int> <qstring>
228 Replace the numbered identifier by the string.
231 SUB_ID 34 "Predicted Secondary Structure"
233 would replace whatever the identifier of sequence 34 was, by the text shown.
234 This is useful when used in conjunction with the ADD_SEQ command shown under
237 INVERSE_CHARS <string> ALL/Range (similar syntax to FONT_CHARS but no
240 Print the selected characters in white. This clearly will only work
241 if you first use the SHADE_CHARScommand to shade the characters with
242 something other than white.
244 CCOL_CHARS <string> ALL <int>
246 Colour all characters in the <string> by the colour defined by <int>.
252 would colour all G and P characters in the alignment by the colour 12.
253 This colour MUST have been defined by the DEFINE_COLOUR command.
255 CCOL_CHARS <string> <int> <int> <int> <int> <int>
257 restricts the colouring to the region defined by the four integers. Thus
259 CCOL_CHARS ILVW 3 12 7 32 7
261 would colour I L V and W characters from residues 3-7 of sequences 12-32
262 inclusive with the colour 7.
264 SCOL_CHARS: This has identical syntax to SCOL_CHARS, but colours the
265 background of the character, rather than the letter itself.
267 COLOUR_REGION <int> <int> <int> <int> <int>
269 COLOR_REGIONColour the region indicated by the integers with the colour number given
274 COLOUR_REGION 30 40 35 46 2
276 Would colour from residue 30-35 of sequences 40-46 with the colour 2.
278 COLOUR_RES <int> <int> <int>
280 Colour just one amino acid with the defined colour.
286 Colours residue 3 of sequence 7. (Note: this can also be achieved with the
287 COLOUR_REGION command, but requires 2 extra numbers)
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