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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
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<head>
<title>Sequence Feature Settings Dialog Box</title>
</head>
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>
- <strong><em>Selecting alignment columns by feature</em></strong><br>
- <strong>Double-click</strong> a feature to add all the columns where
- that feature is found to the current column selection. <strong>Shift+Double-click</strong>
- will add all the columns where that feature is <strong>not</strong>
- found. You can also find these options 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>
+ <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
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>
+<em>Feature sorting and graduated feature colouring were 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
may be attached to one position along a stretch of sequence marked with
a secondary structure feature).</p>
<p>The ordering of the sequence features in the dialog box list is
-the order used by jalview for rendering sequence features. A feature at
+the order used by Jalview for rendering sequence features. A feature at
the bottom of the list is rendered <em>below</em> a feature higher up in
the list.<br>
<em><strong>You can change the order of a feature by