3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 <head>Opening URLs from Jalview
27 <strong>Opening URLs from Jalview</strong><br> Both the applet
28 and the desktop application are able to open URLs as 'popups' in
29 your web browser. <br> Double-clicking on the ID of a sequence
30 will open the first URL that can be generated from its sequence ID.
31 This is by default the EMBL-EBI site, but you can easily configure your own <a
32 href="#urllinks">sequence URL links</a>.
35 Other links for a sequence either derived from any other configured
36 URL links, or imported from the sequence's annotation, are accessed
37 by right clicking to open the sequence pop-up menu, and selecting
38 from the <em>Links</em> submenu.
41 <strong><a name="urllinks">Configuring URL Links</a></strong> <br>URL
42 links are defined in the "Connections" tab of the <a
43 href="../features/preferences.html">Jalview desktop
44 preferences</a>, or specified as <a
45 href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
46 parameters</a>. <br> By default the item "EMBL-EBI Search" is added
47 to this link menu. This link will show a web page in your default
48 browser with the selected sequence id as part of the URL.<br>
49 In the preferences dialog box, click <strong>new</strong> to add a
50 new link, and <strong>edit</strong> to modify an existing link, or <strong>delete</strong>
51 to remove it.<br> You can name the link, this will be displayed
52 on a new menu item under the "Link" menu when you right
53 click on a sequence id. <br> The URL string must contain a
54 token that can be replaced with a sequence ID or DB accession ID. The simplest token is
55 "$SEQUENCE_ID$", which will be replaced by the chosen
56 sequence id when you click on it.
60 http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br>
61 Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br> <br>
62 Links will also be made for any database cross references associated
63 with the sequence where the database name exactly matches a URL link
64 name. In this case, the $DB_ACCESSION$ string will be replaced with
65 the accession string for the database cross-reference, rather than
66 the sequence ID for the sequence (<em>since Jalview 2.10.1</em>).
69 <strong><a name="warning">Warning dialog about updating
70 your configured URL links</a></strong><br /> In the desktop
71 prior to Jalview 2.10.1, the only way to configure custom links for
72 a particular database cross-reference for a sequence was to give it
74 <em>exactly</em> matched the database source, and a regular
75 expression for filtering out any spurious matches generated when the
76 custom linked was tested against the Sequence's ID string. Since the
77 introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$
78 will not be used for database cross-reference accession strings, and
79 if you have custom links configured, Jalview will raise a warning
80 message so let you know that you may need to update your links to
84 <strong>Regular Expression Substitution</strong><br> A url may
85 contain a string of the form $SEQUENCE_ID=/<em>regular
86 expression</em>/=$ or $DB_ACCESSION=/<em>regular expression</em>/=$.
87 In this case, the regular expression will be
88 applied to the full sequence ID or DB accession ID string and the resulting match will
89 be inserted into the URL. Groups of parentheses can be used to
90 specify which regions of the regular expression will be used to
93 <li>Each top level parenthesis will yield a URL containing the
94 text matched within that parenthesis.</li>
95 <li>Regions matching sub-parentheses within a top-level
96 parenthesis will be concatenated to form the text inserted into
97 the URL for the top-level parenthesis.</li>
100 <li>The regular expressions supported by Jalview are those
101 provided by the <a href="http://www.javaregex.com">Stevesoft
102 javaregex package</a>.
104 <li>Some characters must be escaped when specifying them as
105 a match within a regular expression.</li>
106 </ul> <br> Many Thanks to Bernd Brandt of the Free University of
107 Amsterdam for testing this new regular-expression expansion