3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 <title>Alignment Window Menus</title>
24 <p><strong>Alignment Window View Menu</strong></p>
26 <li><strong>New View (Control T)</strong><em><br>
27 Creates a new view from the current alignment view. </em></li>
28 <li><strong>Expand Views (X)</strong><em><br>
29 Display each view associated with the alignment in its own alignment window,
30 allowing several views to be displayed simultaneously. </em></li>
31 <li><strong>Gather Views (G)</strong><em><br>
32 Each view associated with the alignment will be displayed within its own tab
33 on the current alignment window. </em></li>
34 <li><strong>Show→(all Columns / Sequences / Sequences and Columns</strong> )</strong><em><br>
35 All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
36 <li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region)</strong><em><br>
37 Hides the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
38 <li><strong>Show Annotations<br>
39 </strong><em>If this is selected the "Annotation Panel" will be
40 displayed below the alignment. The default setting is to display the conservation
41 calculation, quality calculation and consensus values as bar charts. </em></li>
42 <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
44 <strong>Apply to all groups<br></strong>
45 When ticked, any modification to the current settings will be applied to all autocalculated annotation.
48 <strong>Show Consensus Histogram<br></strong>
49 Enable or disable the display of the histogram above the consensus sequence.
52 <strong>Show Consensus Logo<br></strong>
53 Enable or disable the display of the sequence logo above the consensus sequence.
55 <li><strong>Normalise Consensus Logo<br>
56 </strong><em>When enabled, scales all logo stacks to the same height,
57 making it easier to compare symbol diversity in highly variable
61 <strong>Group Conservation<br></strong>
62 When ticked, display a conservation row for all groups (only available for protein alignments).
65 <strong>Apply to all groups<br></strong>
66 When ticked, display a consensus row for all groups.
70 <li><strong>Automatic Scrolling<br>
71 </strong><em>When selected, the view will automatically scroll to display the
72 highlighted sequence position corresponding to the position under the mouse
73 pointer in a linked alignment or structure view.</em>
75 <li><strong>Show Sequence Features</strong><br>
76 <em>Show or hide sequence features on this alignment.</em></li>
77 <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
78 Opens the Sequence Feature Settings dialog box to control the colour and display
79 of sequence features on the alignment, and configure and retrieve features
80 from DAS annotation servers.</em></li>
81 <li><strong>Sequence ID Tooltip</strong><em> (application only)
82 <br>This submenu's options allow the inclusion or exclusion of
83 non-positional sequence features or database cross references
84 from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
85 <li><strong>Alignment Properties...<br>
86 </strong><em>Displays some simple statistics computed for the
87 current alignment view and any named properties defined on the
88 whole alignment.</em></li>
89 <li><strong><a href="../features/overview.html">Overview Window</a><br>
90 </strong><em>A scaled version of the alignment will be displayed in a small
91 window. A red box will indicate the currently visible area of the alignment.
92 Move the visible region using the mouse. </em></li>