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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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<head>
<title>Sequence Feature Settings Dialog Box</title>
</head>
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="351" height="350">
+<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 colour and whether
+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 used
-for a feature in the associated alignment by clicking on its colour box.</em></strong></p>
+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> 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>
-Right click on a feature type to order the alignment by either the
-feature's score, or the number of features of that type. The 'Order by
-Score' and 'Order by Density' buttons will order the alignnment based on
-the average score or total number of currently active features and
-groups on each sequence. (Experimental - added in jalview 2.4.1)</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>
+<em>Feature sorting and graduated feature colouring was introduced
+in jalview 2.5</em></p>
+
<p><strong>Transparency and Feature Ordering</strong></p>
<p>It is important to realise that sequence features are often not
distinct and often overlap (for example, a metal binding site feature
git://source.jalview.org / jalview.git / blobdiff