From: Jim Procter Date: Tue, 16 May 2017 13:30:04 +0000 (+0100) Subject: JAL-2316 tweaking docs and links in help X-Git-Tag: Release_2_10_2~3^2~83^2~5 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e7bdaf79ac2aa5ea995c80c559c9cb170f35f4ba;p=jalview.git JAL-2316 tweaking docs and links in help --- diff --git a/help/helpTOC.xml b/help/helpTOC.xml index db47351..52eaf85 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -135,7 +135,7 @@ - + diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index da5d7dd..56469e5 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -57,12 +57,12 @@ Adding additional links
You can configure your own links via the Jalview Preferences dialog. Jalview also provides persistent URLs for many common - bioinformatics databases. These links are downloaded by Jalview from + 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 + 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. @@ -73,10 +73,18 @@ 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 diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index c5859ea..0734271 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -30,6 +30,8 @@ Full details about Jalview 2.10.2 are in the Release Notes, but the highlights are below.