+ <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>