- <p>
- By default, the list of available links in the preferences dialog box
- contains the item "EMBL-EBI Search",
- which is set as the URL which opens on double-clicking on a sequence ID, and as a
- menu item in the Links menu. This link will show a web page in your default
- browser with the selected sequence id as part of the URL.
- <br>
- Also by default, the list of available links contains persistent URLs for many common
- bioinformatics databases. These links are downloaded by Jalview from
- the <em>identifiers.org</em> website, and the names and URLs are not user editable.
- <br>
- The list of links is sortable, by clicking on the headers of the table. The list
- can be filtered using the free text search box below the table, or the
- "Custom Only" button, which displays only user-defined links.
- </p>
- <p>
- In the preferences dialog box, the links which appear in the Links menu
- can be configured by selecting or deselecting links in the "In Menu"
- column. The names of selected links will be displayed
- on new menu items under the "Link" menu when you right
- click on a sequence id.<br>
- You can configure which link is used when double-clicking on a sequence
- by selecting or deselecting links in the "On Click" column. Exactly one
- link must be configured for double-clicking. Since the link uses the sequence id
- to construct the URL to open, the selected link must contain the
- "$SEQUENCE_ID$" token (see below for details of the "$SEQUENCE_ID$"
- and other tokens).</p>
- <p>
- Additionally you can click <strong>new</strong> to add a
- new link, and <strong>edit</strong> to modify an existing link, or <strong>delete</strong>
- to remove it. Only URLs entered by the user (or the default EMBL-EBI link) may
- be edited or deleted. When adding or editing a link, the URL string must contain a
- token that can be replaced with a sequence ID or DB accession ID. The simplest token is
- "$SEQUENCE_ID$", which will be replaced by the chosen
- sequence id when you click on it.
+ <p>
+ <em>Default Link Settings</em><br /> The "EMBL-EBI Search"
+ link is the default link shown in the "Link" submenu, and
+ opened when double-clicking on a sequence ID. When clicked, this
+ link will show a web page in your default browser with the selected
+ sequence ID as part of the URL.
+ </p>
+ <p>
+ <em>Adding additional links</em><br /> You can configure your own
+ links via the Jalview <a href="../features/preferences.html#links"><strong>Preferences</strong></a>
+ dialog. Jalview also provides 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.
+ </p>
+ <p>
+ <em>Creating your own URL link</em> <br/>URL links are specified as a
+ template containing special tokens that Jalview will replace with
+ the Sequence ID or Database Accession of the sequence when you
+ double click on its ID or open it's <strong>Link</strong> submenu.
+ Link URL templates must contain at least one token.