X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Furllinks.html;h=0a4c650ba89fe9ef054492206985615ba47566a9;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=ef77c7ef3ef6aef58f544a75a386498026e00c7f;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index ef77c7e..0a4c650 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -1,90 +1,99 @@ -
-Opening URLs from Jalview + --> +Opening URLs from Jalview --
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 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 "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 the first URL that can be generated from its sequence ID.
+ This is often the SRS 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 "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:
+