Preferences</a> tab allows you to configure default colourschemes
for a new alignment window.
</li>
+ <li>The <a href="#overview"><strong>"Overview"</strong>
+ Preferences</a> tab configures defaults for the overview window.
+ </li>
<li>The <a href="#structure"><strong>"Structure"</strong>
Preferences</a> tab allows you to configure options for obtaining
and displaying structure information.
<p>
<em>Show Annotations</em> - If this is selected the new window will
display an annotation panel below the sequences. This annotation
- panel may have several rows describing the whole alignment. The 3
- standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
- for the alignment may be shown or hidden by default using the
- checkboxes below.
+ panel may have several rows describing the whole alignment. The 4
+ standard annotations <em>Conservation</em>, <em>Quality</em>,
+ <em>Occupancy</em> and <em>Consensus</em> for the alignment may
+ be shown or hidden by default using the checkboxes adjacent and
+ below.
</p>
<p>
<em>Show group: Conservation and Consensus</em> controls the display
by Annotation...</a> is selected from the alignment window's colours
menu.
</p>
+ <p>
+ <a name="overview"><strong>"Overview"
+ Preferences tab</strong>
+ </p>
+ <p>
+ <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
+ Jalview's overview shows gaps as white, and sequences with no
+ colourscheme applied as grey.
+ </p>
+ <p>
+ <em>Show Hidden regions when opening overview</em> - default setting
+ for inclusion of hidden regions.
+ </p>
+ <p>
+ <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
+ configures the default colour for gaps in the overview.
+ </p>
+ <p>
+ <em>Hidden Colour</em> - colour used to highlight regions in the
+ overview that are hidden in the alignment.
+ </p>
+ <p>
+ <em>Gap Colour</em> - The default colour scheme for a new alignment
+ window. If the chosen option is "User Defined" then the
+ last User Defined Colour loaded or saved via the User Defined
+ Colours panel will be loaded.
+ </p>
<p>
<a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
The <em>Custom only</em> button limits the entries in the table to
just those you have configured yourself <em>via</em> the <em>Edit
Links</em> buttons. Press <em>Show all</em> to clear any filters.
- <p>
+ </p>
+ <p>The links table is prepoulated with persistent URLs for many common
+ bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
+ the <em>identifiers.org</em> website, and the names and URLs are not
+ user editable.
<a href="../webServices/urllinks.html#urllinks">Read more about configuring
URL links.</a>
</p>
and PDB file association (if available). The Jalview id/start-end
option is ignored if Modeller output is selected.
<p>
- <a name="editing"><strong>Editing Preferences tab</strong></a>
+ <a name="editing"><strong>e"Editinge" Preferences tab</strong></a>
</p>
<p>There are currently three options available which can be
selected / deselected.</p>