X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Furllinks.html;h=3dac542404fb162c199a31c1420166dbc64a16c0;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=e4fdac7b2b31267c360b58f11fb9434384458a25;hpb=3d54cb06f65ea70832b8795fdefc466f26154ac5;p=jalview.git diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index e4fdac7..3dac542 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -1,72 +1,100 @@ - -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 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: -

Each top level parenthesis will yield a URL containing the - text matched within that parenthesis.
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.

Please Note: -
-
The regular expressions supported by Jalview are those - provided by the Stevesoft javaregex - package.
-
Some characters must be escaped when specifying them as a - match within a regular expression.
-
-
- Many Thanks to Bernd Brandt of the Free University of Amsterdam for - testing this new regular-expression expansion feature!

-
-
+
+
+ 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: +
+
Each top level parenthesis will yield a URL containing the + text matched within that parenthesis.
+
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.
+ Please Note: +
+
The regular expressions supported by Jalview are those + provided by the Stevesoft + javaregex package. +
+
Some characters must be escaped when specifying them as + a match within a regular expression.
+

Many Thanks to Bernd Brandt of the Free University of + Amsterdam for testing this new regular-expression expansion + feature! + + +
+
+
- \ No newline at end of file +