-<p><strong>Sequence Feature Settings Dialog Box</strong></p>
-<p>Select <strong>View→Feature Settings...</strong> menu entry
-in an alignment window to open the feature settings dialog box, which
-allows you to precisely control the presence and appearance of sequence
-features for the current alignment.</p>
-<center><img src="featureSettings.gif" width="400" height="452">
-<br>
-Sequence Feature Settings for the Jalview Application</img></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. The table in the middle lists all the features in the
-currently selected groups, along with their display style and whether
-they are currently being displayed (only the ticked features and groups
-are displayed). <strong><em>You can change the colour or
-shading style used for a feature in the associated alignment by clicking
-on its colour box.</em></strong></p>
- <p>
- <a name="selectbyfeature"><strong><em>Selecting
- alignment columns by feature</em></strong></a><br> <strong>Double-clicking
- a 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. 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>
- <li>Hold down <strong>Shift</strong> to add columns to the
- current selection.
- </li>
- <li>Press <strong>Command/Windows key</strong> to toggle column
- selection state (XOR)
- </li>
- </ul>
- Options are also provided in the feature's pop-up menu (see below).
- <br />
- <em>Select columns by feature was added in Jalview 2.8.1</em>
- </p>
- <p><strong><em>Feature settings pop-up menu</em></strong><br>
-<strong>Right-click</strong> on a feature to open a pop-up menu that
-allows you to sort the alignment or current selection using that feature
-type (see below), or toggle the type of colouring used for the feature.
-Features may be highlighted with either a single colour or a <a
- href="featureschemes.html">feature colourscheme</a> based on either the
-scores associated with that feature or from the feature's description
-(e.g. to distinguish different names associated with a DOMAIN feature).</p>
-<p><strong>Ordering alignment by features</strong><br>
-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>
-<em>Feature sorting and graduated feature colouring were introduced
-in Jalview 2.5</em></p>
+ <p>
+ <strong>Sequence Feature Settings Dialog Box</strong>
+ </p>
+ <p>
+ Select <strong>View→Feature Settings...</strong> menu entry in
+ an alignment window to open the feature settings dialog box, which
+ allows you to precisely control the presence and appearance of
+ sequence features for the current alignment.
+ </p>
+ <center>
+ <img src="featureSettings.gif" width="400" height="452"> <br>
+ Sequence Feature Settings for the Jalview Application</img>
+ </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. The table in the middle lists all the
+ features in the currently selected groups, along with their display
+ style and whether they are currently being displayed (only the
+ ticked features and groups are displayed). <strong><em>You
+ can change the colour or shading style used for a feature in the
+ associated alignment by clicking on its colour box.</em></strong>
+ </p>
+ <p>
+ <a name="selectbyfeature"><strong><em>Selecting
+ alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+ a 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. 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>
+ <li>Hold down <strong>Shift</strong> to add columns to the
+ current selection.
+ </li>
+ <li>Press <strong>Command/Windows key</strong> to toggle column
+ selection state (XOR)
+ </li>
+ </ul>
+ Options are also provided in the feature's pop-up menu (see below).
+ <br />
+ <em>Select columns by feature was added in Jalview 2.8.1</em>
+ </p>
+ <p>
+ <strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
+ on a feature to open a pop-up menu that allows you to
+ <ul>
+ <li>Hide, show and select columns containing that feature</li>
+ <li>Sort the alignment or current selection using that feature
+ type (see below)</li>
+ <li>Toggle the type of colouring used for the feature</li>
+ </ul>
+ <p>
+ Features may be highlighted with either a single colour or a <a
+ href="featureschemes.html">feature colourscheme</a> based on
+ either the scores associated with that feature or from the feature's
+ description (e.g. to distinguish different names associated with a
+ DOMAIN feature).
+ </p>
+ <p>
+ <strong><a name="sortbyfeature">Ordering alignment by
+ features</a></strong><br> 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>
+ <em>Feature sorting and graduated feature colouring were
+ introduced in Jalview 2.5</em>
+ </p>