X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fdassettings.html;h=a86d37f55426b443dbd0c29126ccb3280d4ae885;hb=1f46c912a14d05f673e19b272fec4e6094874fa5;hp=7ccbbdae06a30c64f3700e19e88ec115cf40f52c;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git
diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html
index 7ccbbda..a86d37f 100644
--- a/help/html/features/dassettings.html
+++ b/help/html/features/dassettings.html
@@ -1,54 +1,75 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
DAS Settings
-Jalview can retrieve sequences and features from many DAS sources. The DAS sources that -it uses are discovered and selected via the DAS settings panel, -opened either from the View→Feature -Settings dialog box from the alignment window's menu bar, or the Tools→Preferences dialog box -opened from the Desktop menu bar.
--
The available sources are listed in the table using each source's -Nickname as its identifier. Clicking on a source's entry in the table -reveals more information about that service in the panel to the right. -Select the tickbox in the "Use Source" column for a source to -add it to the set Jalview queries for alignment and sequence features.
-You can filter the visible DAS sources by authority, type and -"label". You should read the DAS documentation to understand -more about these values. -
Updating the list of sources
-When the DAS Settings panel is first opened, and when the 'Refresh -source' buton is pressed, a list of DAS sources is retrieved from the -DAS registry URL (set by default to the DAS registration server at -http://das.sanger.ac.uk/registry/das1/sources/).
-Adding your own DAS Sources
-You can add your own DAS source to the list by clicking the -"Add Local Source" button. Enter the URL and nickname of your -additional service. It should be noted that Jalview 2.1 will not query -additional sources for more information, but this will be implemented in -future editions. -
+
+ DAS Settings +
++ Jalview can retrieve sequences and features from many DAS sources. The DAS sources that it uses are discovered and + selected via the DAS settings panel, opened either from the + View→Feature Settings + dialog box from the alignment window's menu bar, or the Tools→Preferences dialog box opened from the Desktop menu + bar. +
++ +
The available sources are listed in the table using each + source's Nickname as its identifier. Clicking on a source's entry in + the table reveals more information about that service in the panel + to the right. Select the tickbox in the "Use Source" + column for a source to add it to the set Jalview queries for + alignment and sequence features.
+You can filter the visible DAS sources by authority, type and + "label". You should read the DAS documentation to + understand more about these values. +
+ Updating the list of sources +
+
+ When the DAS Settings panel is first opened, and when the 'Refresh
+ source' buton is pressed, a list of DAS sources is retrieved from
+ the DAS registry URL. Note that the registry hosted at
+ http://www.dasregistry.org/das/ was retired at the start of 2015. An
+ alternative service is currently hosted at
+ http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this
+ service, ensure your .jalview_properties file includes the following
+ line:
DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+
+ Adding your own DAS Sources +
+You can add your own DAS source to the list by clicking the + "Add Local Source" button. Enter the URL and nickname of + your additional service. It should be noted that Jalview 2.1 will + not query additional sources for more information, but this will be + implemented in future editions. +