<html>
-<head>
-Opening URLs from Jalview
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * 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 first URL that can
-be generated from its sequence ID. This is often the SRS 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>. <br>
-By default the item "SRS" 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. 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 $SEQUENCE_ID$ string will be replaced with the
-accession string for the database cross-reference, rather than the
-sequence ID for the sequence (<em>since Jalview 2.4</em>).</p>
-<p><strong>Regular Expression Substitution</strong><br>
-A url may contain a string of the form $SEQUENCE_ID=/<em>regular
-expression</em>/=$. In this case, the regular expression will be applied to
-the full sequence 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="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>
+ <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.
+ This is often the SRS 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>. <br> By default the item "SRS"
+ 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. 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 $SEQUENCE_ID$ string will be replaced with
+ the accession string for the database cross-reference, rather than
+ the sequence ID for the sequence (<em>since Jalview 2.4</em>).
+ </p>
+ <p>
+ <strong>Regular Expression Substitution</strong><br> A url may
+ contain a string of the form $SEQUENCE_ID=/<em>regular
+ expression</em>/=$. In this case, the regular expression will be
+ applied to the full sequence 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="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>
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+</html>
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