</head>
<body>
<p>
- <p>
<strong>Opening URLs from Jalview</strong><br> Both the applet
and the desktop application are able to open URLs as 'popups' in
- your web browser. <br> Double-clicking on the ID of a sequence
- will open the first URL that can be generated from its sequence ID.
+ your web browser.</p>
+ <p> Double-clicking on the ID of a sequence
+ will open whichever URL is selected for 'popups' in the <strong>"Links"</strong> tab of the <a
+ href="../features/preferences.html#links">Jalview desktop
+ preferences</a>.
This is by default the EMBL-EBI site, but you can easily configure your own <a
href="#urllinks">sequence URL links</a>.
</p>
<p>
- Other links for a sequence either derived from any other configured
+ Other links for a sequence, either derived from any other configured
URL links, or imported from the sequence's annotation, are accessed
by right clicking to open the sequence pop-up menu, and selecting
from the <em>Links</em> submenu.
</p>
<p>
<strong><a name="urllinks">Configuring URL Links</a></strong> <br>URL
- links are defined in the "Connections" tab of the <a
- href="../features/preferences.html">Jalview desktop
+ links are defined in the "Links" tab of the <a
+ href="../features/preferences.html#links">Jalview desktop
preferences</a>, or specified as <a
href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
- parameters</a>. <br> By default the item "EMBL-EBI Search" is added
- to this link menu. This link will show a web page in your default
- browser with the selected sequence id as part of the URL.<br>
- In the preferences dialog box, 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.<br> You can name the link, this will be displayed
- on a new menu item under the "Link" menu when you right
- click on a sequence id. <br> 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.
+ parameters</a>.</p>
+ <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. These links are downloaded by Jalview from
+ the <em>identifiers.org</em> website, and the names and URLs are not
+ user editable.
</p>
<p>
- eg.<br> UniRef100 =
- http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br>
- Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br> <br>
+ <em>Creating your own URL link</em> 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.
+ </p>
+ <em>eg.</em><pre> UniRef100 =
+ http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br/>
+ Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br> </pre>
+ <p>
Links will also be made for any database cross references associated
with the sequence where the database name exactly matches a URL link
name. In this case, the $DB_ACCESSION$ string will be replaced with
<p>
<strong>Regular Expression Substitution</strong><br> A url may
contain a string of the form $SEQUENCE_ID=/<em>regular
- expression</em>/=$ or $DB_ACCESSION=/<em>regular expression</em>/=$.
- In this case, the regular expression will be
- applied to the full sequence ID or DB accession ID string and the resulting match will
+ expression</em>/=$ or $DB_ACCESSION=/<em>regular expression</em>/=$. In
+ this case, the regular expression will be applied to the full
+ sequence ID or DB accession ID string and the resulting match will
be inserted into the URL. Groups of parentheses can be used to
specify which regions of the regular expression will be used to
generate the URL:
+
<ul>
<li>Each top level parenthesis will yield a URL containing the
text matched within that parenthesis.</li>
<li>Regions matching sub-parentheses within a top-level
parenthesis will be concatenated to form the text inserted into
the URL for the top-level parenthesis.</li>
- <em>Please Note:
- <ul>
- <li>The regular expressions supported by Jalview are those
- provided by the <a href="http://www.javaregex.com">Stevesoft
- javaregex package</a>.
- </li>
- <li>Some characters must be escaped when specifying them as
- a match within a regular expression.</li>
- </ul> <br> Many Thanks to Bernd Brandt of the Free University of
- Amsterdam for testing this new regular-expression expansion
- feature!
- </em>
- <em>
</ul>
- </p>
- </p>
+ <em>Please Note:</em>
+ <ul>
+ <li>The regular expressions supported by Jalview are those
+ provided by the <a href="http://www.javaregex.com">Stevesoft
+ javaregex package</a>.
+ </li>
+ <li>Some characters must be escaped when specifying them as a
+ match within a regular expression.</li>
+ </ul> <br> Many Thanks to Bernd Brandt of the Free University of
+ Amsterdam for testing the regular-expression expansion feature!
</body>
</html>
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