3 <title>Alignment Window Menus</title>
7 <p><strong>Alignment Window View Menu</strong></p>
9 <li><strong>New View (Control T)</strong><em><br>
10 Creates a new view from the current alignment view. </em></li>
11 <li><strong>Expand Views (X)</strong><em><br>
12 Display each view associated with the alignment in its own alignment window,
13 allowing several views to be displayed simultaneously. </em></li>
14 <li><strong>Gather Views (G)</strong><em><br>
15 Each view associated with the alignment will be displayed within its own tab
16 on the current alignment window. </em></li>
17 <li><strong>Show→(all Columns / Sequences)</strong><em><br>
18 All hidden Columns / Sequences will be revealed. </em></li>
19 <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
20 Hides the currently selected Columns / Sequences</em></li>
21 <li><strong>Show Annotations<br>
22 </strong><em>If this is selected the "Annotation Panel" will be
23 displayed below the alignment. The default setting is to display the conservation
24 calculation, quality calculation and consensus values as bar charts. </em></li>
25 <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
27 <strong>Apply to all groups<br></strong>
28 When ticked, any settings will be applied to all autocalculated annotation.
31 <strong>Show Consensus Histogram<br></strong>
32 Enable or disable the display of the histogram above the consensus sequence.
35 <strong>Show Consensus Profile<br></strong>
36 Enable or disable the display of the sequence logo above the consensus sequence.
39 <strong>Group Conservation<br></strong>
40 When ticked, display a conservation row for all groups (only available for protein alignments).
43 <strong>Apply to all groups<br></strong>
44 When ticked, display a consensus row for all groups.
48 <li><strong>Automatic Scrolling<br>
49 </strong><em>When selected, the view will automatically scroll to display the
50 highlighted sequence position corresponding to the position under the mouse
51 pointer in a linked alignment or structure view.</em>
53 <li><strong>Show Sequence Features</strong><br>
54 <em>Show or hide sequence features on this alignment.</em></li>
55 <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
56 Opens the Sequence Feature Settings dialog box to control the colour and display
57 of sequence features on the alignment, and configure and retrieve features
58 from DAS annotation servers.</em></li>
59 <li><strong>Sequence ID Tooltip</strong><em> (application only)
60 <br>This submenu's options allow the inclusion or exclusion of
61 non-positional sequence features or database cross references
62 from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
63 <li><strong>Alignment Properties...<br>
64 </strong><em>Displays some simple statistics computed for the
65 current alignment view and any named properties defined on the
66 whole alignment.</em></li>
67 <li><strong><a href="../features/overview.html">Overview Window</a><br>
68 </strong><em>A scaled version of the alignment will be displayed in a small
69 window. A red box will indicate the currently visible area of the alignment.
70 Move the visible region using the mouse. </em></li>