<p>
Select <strong>View→Feature Settings...</strong> in an alignment
window to open the feature settings dialog box, which allows
- precise control the visibility and appearance of sequence features for
+ precise control of the visibility and appearance of sequence features for
an alignment view.
</p>
<div align="center">
<p>The top section of the dialog box lists all the sequence feature
groups, along with a tickbox for each that controls whether its
features are displayed. When many groups are present, their names may
- be truncated, but the full name be shown in a tooltip when the mouse
+ be truncated, but the full name is shown in a tooltip when the mouse
hovers over their checkbox.</p>
<p><em>Feature colour schemes and filters</em>
<p>
columns by feature</strong></a>
</p>
<p>
- Double-clicking a <strong>feature type</strong> in the <strong>Feature
- Settings</strong> dialog allows you to select columns in the alignment that
- contain (or do not contain) features of that type that are currently visible (e.g. not filtered out or excluded due to an applied colour scheme threshold). If a region of the
- alignment is currently selected, then only features in the current
- selection will be searched. The following keys affect the way in which
- selections are made:
-
- <ul>
+ Double-clicking a <strong>feature type</strong> in the <strong>Feature
+ Settings</strong> dialog allows you to select columns in the
+ alignment that contain (or do not contain) features of that type that
+ are currently visible (e.g. not filtered out or otherwise excluded due
+ to an applied colour scheme threshold). If a region of the alignment
+ is currently selected, then only features in the current selection
+ will be searched. The following keys affect the way in which
+ selections are made:<ul>
<li>Hold down <strong>Alt</strong> to select columns not
containing features of a particular type.
</li>
</p>
<p>
<strong><a name="sortbyfeature">Ordering alignment by
- features</a></strong></p><p>The 'Seq Sort by Score' and 'Seq Sort by
- Density' buttons will sort the alignment based on the average score
- or total number of currently active features and groups on each
- sequence. To order the alignment using a specific feature type, use
- the <em>sort by ..</em> entries in the pop-up menu for that type.<br>
+ features</a></strong>
+ </p>
+ <p>
+ The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort
+ the alignment based on the average score or total number of
+ currently active features and groups on each sequence. A dialog box
+ is shown if there are no features to use for sorting sequences. To
+ order the alignment using a specific feature type, use the
+ <em>sort by ..</em> entries in the pop-up menu for that type.<br> <br>When
+ a selected region exists, only features lying within the columns
+ containing the selected region will be considered, but all sequences
+ (including those not selected) will be reordered.
<em>Feature sorting and graduated feature colouring were
introduced in Jalview 2.5</em>
</p>