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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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-<head>Opening URLs from Jalview
-</head>
-<body>
- <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.</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
- 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 "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>.</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 (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.
- </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 for any link templates whose name begins with the database 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>).
- <br /> <em>For example: to create a link for viewing MACiE records
- from PDB Entries, create a new custom link entry with the name
- "PDB in MACiE", and link URL template:
- <pre>https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/index.pl?query_pdb=1&pdb=$DBACCESSION$</pre>
- <br />The sequence ID popup menu for seuqences with a PDB entry
- will now show 'PDB in MACiE|1xyz..' links in the <strong>links</strong>
- submenu.
- </em>
- </p>
- <p>
- <strong><a name="warning">Warning dialog about updating
- your configured URL links</a></strong><br /> In the desktop
- prior to Jalview 2.10.1, the only way to configure custom links for
- a particular database cross-reference for a sequence was to give it
- a name that
- <em>exactly</em> matched the database source, and a regular
- expression for filtering out any spurious matches generated when the
- custom linked was tested against the Sequence's ID string. Since the
- introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$
- will not be used for database cross-reference accession strings, and
- if you have custom links configured, Jalview will raise a warning
- message so let you know that you may need to update your links to
- use $DB_ACCESSION$.
- </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>
- </ul>
- <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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