3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <p><strong>Alignment Window Format Menu</strong></p>
22 <li><strong>Font...</strong><br>
23 <em>Opens the "Choose Font" dialog box, in order to change the font
24 of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster
25 alignment rendering. </em></em></li>
27 </strong><em>When ticked, the alignment display is "<a
28 href="../features/wrap.html">wrapped</a>" to the width of the alignment
29 window. This is useful if your alignment has only a few sequences to view
30 its full width at once.<br>
31 Additional options for display of sequence numbering and scales are also visible
32 in wrapped layout mode:</em>
34 <li><strong>Scale Left</strong><br>
35 <em>Show the sequence position for the first aligned residue in each row
36 in the left column of the alignment.</em></li>
37 <li><strong>Scale Right</strong><br>
38 <em>Show the sequence position for the last aligned residue in each row
39 in the right-most column of the alignment.</em></li>
40 <li><strong>Scale Above</strong><br>
41 <em>Show the alignment column position scale.</em></li>
43 <li><strong>Show Sequence Limits<br>
44 </strong><em>If this box is selected the sequence name will have the start
45 and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
46 <li><strong>Right Align Sequence ID<br>
47 </strong> <em>If this box is selected then the sequence names displayed in
48 the sequence label area will be aligned against the left-hand edge of the
49 alignment display, rather than the left-hand edge of the alignment window.</em></li>
50 <li><strong>Show Hidden Markers<br>
51 </strong><em>When this box is selected, positions in the alignment where rows
52 and columns are hidden will be marked by blue arrows.</em></li>
53 <li><strong>Boxes</strong><em><br>
54 If this is selected the background of a residue will be coloured using the
55 selected background colour. Useful if used in conjunction with "Colour
56 Text." </em></li>
58 </strong><em>If this is selected the residues will be displayed using the
59 standard 1 character amino acid alphabet.</em></li>
60 <li><strong>Colour Text<br>
61 </strong><em>If this is selected the residues will be coloured according to
62 the background colour associated with that residue. The colour is slightly
63 darker than background so the amino acid symbol remains visible. </em></li>
64 <li><strong>Show Gaps<br>
65 </strong><em>When this is selected, gap characters will be displayed as "."
66 or "-". If unselected, then gap characters will appear as blank
68 You may set the default gap character in <a
69 href="../features/preferences.html">preferences</a>.</em></li>
70 <li><strong>Centre Column Labels<br>
71 </strong><em>When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
73 <li><strong>Show Unconserved<br>
74 </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.