<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head>
<title>Sequence Feature Settings Dialog Box</title>
</head>
<body>
-<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="351" height="350"> <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 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>
-<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 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 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 dragging it up and down the list with the
- mouse</strong></em>.</p>
-<p>The <strong><em>Optimise order</em></strong> button (currently only available in the application) will re-order the feature render ordering based on the average length of each feature type.</p>
-<p>
- The <strong><em>transparency slider setting</em></strong> (currently only available
- in the application version) controls the visibility of features
- rendered below other features. Reducing the transparency will mean
- that features at the top of the list can obscure features lower
- down, and increasing it allows the user to 'see through' the upper
- layers of a set of features.</p>
-<p><strong><em>You can save all features, with their current colours and visibility
- in a Jalview format file. </em></strong>
-</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>
+
+ <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 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 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 dragging it up and down the list with
+ the mouse (not applet)</strong></em>.
+ </p>
+ <p>
+ The <strong><em>Optimise order</em></strong> button (currently only
+ available in the application) will re-order the feature render
+ ordering based on the average length of each feature type.
+ </p>
+ <p>
+ The <strong><em>transparency slider setting</em></strong> controls
+ the visibility of features rendered below other features. Reducing
+ the transparency will mean that features at the top of the list can
+ obscure features lower down, and increasing it allows the user to
+ 'see through' the upper layers of a set of features.
+ </p>
+ <p>
+ <strong><em>You can save all features, with their
+ current colours and visibility in a Jalview format file. </em></strong>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff