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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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+ * of the License, or (at your option) any later version.
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* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>Opening URLs from Jalview
+</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 URL designated for 'popups' in the "Connections" tab of the <a
+ href="../features/preferences.html">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
+ 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
+ preferences</a>, or specified as <a
+ href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
+ parameters</a>.</p>
+ <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>
+ <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>
+ 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
+ the accession string for the database cross-reference, rather than
+ the sequence ID for the sequence (<em>since Jalview 2.10.1</em>).
+ </p>
+ <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
+ 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>
+</body>
+</html>