3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
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11 * of the License, or (at your option) any later version.
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14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <p><strong>Alignment Window Format Menu</strong></p>
25 <li><strong>Font...</strong><br>
26 <em>Opens the "Choose Font" dialog box, in order to change the font
27 of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster
28 alignment rendering. </em></em></li>
30 </strong><em>When ticked, the alignment display is "<a
31 href="../features/wrap.html">wrapped</a>" to the width of the alignment
32 window. This is useful if your alignment has only a few sequences to view
33 its full width at once.<br>
34 Additional options for display of sequence numbering and scales are also visible
35 in wrapped layout mode:</em>
37 <li><strong>Scale Left</strong><br>
38 <em>Show the sequence position for the first aligned residue in each row
39 in the left column of the alignment.</em></li>
40 <li><strong>Scale Right</strong><br>
41 <em>Show the sequence position for the last aligned residue in each row
42 in the right-most column of the alignment.</em></li>
43 <li><strong>Scale Above</strong><br>
44 <em>Show the alignment column position scale.</em></li>
46 <li><strong>Show Sequence Limits<br>
47 </strong><em>If this box is selected the sequence name will have the start
48 and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
49 <li><strong>Right Align Sequence ID<br>
50 </strong> <em>If this box is selected then the sequence names displayed in
51 the sequence label area will be aligned against the left-hand edge of the
52 alignment display, rather than the left-hand edge of the alignment window.</em></li>
53 <li><strong>Show Hidden Markers<br>
54 </strong><em>When this box is selected, positions in the alignment where rows
55 and columns are hidden will be marked by blue arrows.</em></li>
56 <li><strong>Boxes</strong><em><br>
57 If this is selected the background of a residue will be coloured using the
58 selected background colour. Useful if used in conjunction with "Colour
59 Text." </em></li>
61 </strong><em>If this is selected the residues will be displayed using the
62 standard 1 character amino acid alphabet.</em></li>
63 <li><strong>Colour Text<br>
64 </strong><em>If this is selected the residues will be coloured according to
65 the background colour associated with that residue. The colour is slightly
66 darker than background so the amino acid symbol remains visible. </em></li>
67 <li><strong>Show Gaps<br>
68 </strong><em>When this is selected, gap characters will be displayed as "."
69 or "-". If unselected, then gap characters will appear as blank
71 You may set the default gap character in <a
72 href="../features/preferences.html">preferences</a>.</em></li>
73 <li><strong>Centre Column Labels<br>
74 </strong><em>When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
76 <li><strong>Show Unconserved<br>
77 </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.