<p>
<strong>Sequence Feature Settings Dialog Box</strong>
</p>
+ <p>
+ Select <strong>View→Feature Settings...</strong> in an alignment
+ window to open the feature settings dialog box, which allows
+ precise control of the visibility and appearance of sequence features for
+ an alignment view.
+ </p>
+ <div align="center">
+ <img src="featureSettings.png" width="400"> <br/>
+ Sequence Feature Settings for the Jalview Application (version 2.11)
+ </div>
+ <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. When many groups are present, their names may
+ be truncated, but the full name is shown in a tooltip when the mouse
+ hovers over their checkbox.</p>
+ <p><em>Feature colour schemes and filters</em>
+ <p>
+ The table in the middle lists all the feature types in the currently
+ selected groups, along with their display style, any configured
+ filters, and a tickbox indicating whether the type is enabled for
+ display.</p><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).The colour used for a feature can
+ be changed by clicking on its <strong><em>colour box</em></strong>. To configure the shading
+ style or filter for a feature, click its <strong><em>configuration</em></strong> box.
+ </p>
+ <p>
+ <em>Feature settings pop-up menu</em><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 according to count or score for that feature
+ type (see below)</li>
+ </ul>
+
+ <p>
+ <strong>Transparency and Feature Ordering</strong>
+ </p>
+ <p>Sequence features represent a variety of different types of
+ positional annotation, 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>
+ Use the <strong><em>Optimise order</em></strong> button to adjust the
+ feature render ordering to place features that on average cover shorter regions
+ of sequence above features annotating longer regions.
+ </p>
+ <p><a name="transparency"></a>
+ The <strong><em>transparency slider</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>
- 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.
+ <strong><em>You can save all features, with their
+ current colours and visibility in a Jalview format file. </em></strong>
</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>
+ <a name="selectbyfeature"><strong>Selecting alignment
+ columns by feature</strong></a>
</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>
+ Double-clicking a <strong>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 that
+ are currently visible (e.g. not filtered out or otherwise excluded due
+ to an applied colour scheme threshold). 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>
<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).
+ <strong><a name="sortbyfeature">Ordering alignment by
+ features</a></strong>
</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>
+ 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. A dialog box
+ is shown if there are no features to use for sorting sequences. 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> <br>When
+ a selected region exists, only features lying within the columns
+ containing the selected region will be considered, but all sequences
+ (including those not selected) will be reordered.
<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><a name="transparency"></a>
- 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>
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