-DAS Settings
-Jalview can retrieve and visualize features from many DAS - sources at once. The DAS sources are discovered and selected via the DAS settings panel.
-
-
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. +