<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).
- </p>
- <p>
<strong><a name="sortbyfeature">Ordering alignment by
- features</a></strong><br> The 'Seq Sort by Score' and 'Seq Sort by
+ features</a></strong></p><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
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>
git://source.jalview.org / jalview.git / blobdiff