-
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
+ 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. @@ -41,56 +41,50 @@
Configuring URL Links
URL
- links are defined in the "Connections" tab of the Jalview desktop
+ links are defined in the "Links" tab of the Jalview desktop
preferences, or specified as applet
parameters.
- By default, the list of available links in the preferences dialog box
- contains the item "EMBL-EBI Search".
- This link is initially configured so that it is the URL which opens on double-clicking on a sequence ID. It is also a
- menu item in the "Link" menu. When clicked, this link will show a web page in your default
- browser with the selected sequence id as part of the URL.
-
- Also by default, the list of available links in the preferences dialog box contains persistent URLs for many common
- bioinformatics databases. These links are downloaded by Jalview from
- the identifiers.org website, and the names and URLs are not user editable.
-
- The list of links can be sorted 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.
-
- In the preferences dialog box, the links which appear in the "Link" menu
- can be configured by selecting or deselecting links in the "In Menu"
- column. The names of selected links will be displayed
- as menu items under the "Link" menu when you right
- click on a sequence id.
- 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).
- Additionally you can click new to add a - new link, and edit to modify an existing link, or delete - 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. +
+ 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/$SEQUENCE_ID$
- 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 $DB_ACCESSION$ string will be replaced with
+ 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
@@ -110,33 +104,29 @@
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
+ 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:
+
-
-
Many Thanks to Bernd Brandt of the Free University of
- Amsterdam for testing this new regular-expression expansion
- feature!
-
-