X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=9b8d66c44ca3ab4c6dcd65b4cdfa2ab7ee54086e;hb=bb49a7496f16118471764acae958b416e08c152c;hp=a0449ad5dc06023b4e6f4cb831fc8e75266affb3;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index a0449ad..9b8d66c 100755
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -1,46 +1,53 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Web Service Menu
Web Service Menu
This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:
-
- - Fetch DB References
This
- will use any of the database services that Jalview is aware of
- (e.g. DAS sequence servers and the WSDBFetch service provided by
- the EBI) to verify the sequence and retrieve all database cross
- references and PDB ids associated with all or just the selected
- sequences in the alignment.
'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.
- - Envision2 Services
Submits one or
- more sequences, sequence IDs or database references to analysis
- workflows provided by the EnVision2 web
- application. This allows Jalview users to easily access the EnCore
- network of databases and analysis services developed by members of
- ENFIN.
-
- Selecting items from the following submenus will start a
+
+
+ - Fetch DB References
This
+ submenu contains options for accessing any of the database services
+ that Jalview is aware of (e.g. DAS sequence servers and the
+ WSDBFetch service provided by the EBI) to verify sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+
+ - 'Retrieve full Sequence' - when checked, Jalview will
+ retrieve the full sequence for any accessions associated with
+ sequences in the alignment.
Note: This
+ could cause out of memory errors when working with genomic
+ sequence records !
Added in Jalview 2.8.1
+
+ - 'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<
+
Other submenus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+
+
+
+ Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or
elsewhere. You need a continuous network connection in order to use
these services through Jalview.
@@ -78,10 +85,10 @@
Analysis
- - Sequence Harmony Multi-Relief
Performs
+ - Multi-Harmony
Performs
functional residue analysis on a protein family alignment with
sub-families defined on it. See the SHMR client entry for more
+ href="../webServices/shmr.html">Multi-Harmony service entry for more
information.