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.
sequence alignments and EPS files.
</li>
<li>The <a href="#editing"><strong>"Editing"</strong>
- Preferences</a> tab contains settings affecting the export of
- sequence alignments and EPS files.
+ Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+ </li>
+ <li>The <a href="#hmmer"><strong>"HMMER"</strong>
+ Preferences</a> tab allows you to configure locally installed HMMER tools.
</li>
<li>The <a href="dassettings.html"><strong>"DAS
Settings"</strong> Preferences</a> tab allows you to select which DAS
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>e"Editinge" Preferences tab</strong></a>
+ <a name="editing"><strong>"Editing" Preferences tab</strong></a>
</p>
<p>There are currently three options available which can be
selected / deselected.</p>
<em>Sort with New Tree</em> - When selected, any trees calculated or
loaded onto the alignment will automatically sort the alignment.
</p>
- <p> </p>
- <p> </p>
+ <p>
+ <a name="hmmer"><strong>"HMMER" Preferences tab</strong></a>
+ </p>
+ <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+ then you should specify on this screen the location of the installation (the path to the folder
+ containing binary executable programs). Double-click in the input field to open a file browser.</p>
+ <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+ enabled in the Alignment window.</p>
</body>
</html>