-
Opening URLs from Jalview
-Both the applet and the desktop application are able to open URLs as
-'popups' in your web browser.
-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 Configuring URL Links
-
URL links are defined in the "Connections" tab of the Jalview desktop preferences, or
-specified as applet
-parameters.
-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.
-In the preferences dialog box, click new to add a new
-link, and edit to modify an existing link, or delete
-to remove it.
-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.
-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.
eg.
-UniRef100 =
-http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
-Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
-
-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 (since Jalview 2.4).
Regular Expression Substitution
-A url may contain a string of the form $SEQUENCE_ID=/regular
-expression/=$. 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:
-
+ Opening URLs from Jalview
Both the applet
+ and the desktop application are able to open URLs as 'popups' in
+ your web browser.
Double-clicking on the ID of a sequence + will open whichever URL is selected for 'popups' in the "Links" tab of the Jalview desktop + preferences. + This is by default the EMBL-EBI site, but you can easily configure your own sequence URL links. +
++ 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 Links submenu. +
+
+ Configuring URL Links
URL
+ links are defined in the "Links" tab of the Jalview desktop
+ preferences, or specified as applet
+ parameters.
+ Default Link Settings
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.
+
+ Adding additional links
You can configure your own
+ links via the Jalview Preferences
+ dialog. Jalview also provides persistent URLs for many common
+ bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
+ the identifiers.org website, and the names and URLs are not
+ user editable.
+
+ Creating your own URL link
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 Link submenu.
+ Link URL templates must contain at least one token.
+
UniRef100 = + http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100+
+ Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
+ 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 (since Jalview 2.10.1).
+
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:
+ https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/index.pl?query_pdb=1&pdb=$DBACCESSION$
+
The sequence ID popup menu for seuqences with a PDB entry
+ will now show 'PDB in MACiE|1xyz..' links in the links
+ submenu.
+
+
+ Warning dialog about updating
+ your configured URL links
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
+ exactly 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 $DB_ACCESSION$.
+
+ Regular Expression Substitution
A url may
+ contain a string of the form $SEQUENCE_ID=/regular
+ expression/=$ or $DB_ACCESSION=/regular expression/=$. 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:
+
+